[med-svn] [rockhopper] 01/02: New upstream version 2.0.3+dfsg
Andreas Tille
tille at debian.org
Fri Feb 9 15:59:46 UTC 2018
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository rockhopper.
commit 86d16169fd3c12959dea36518b31a34d6a3decc3
Author: Andreas Tille <tille at debian.org>
Date: Fri Feb 9 16:03:03 2018 +0100
New upstream version 2.0.3+dfsg
---
Alignment.java | 662 +++
Assembler.java | 1195 ++++
Condition.java | 185 +
DeNovoIndex.java | 568 ++
DeNovoTranscript.java | 451 ++
DeNovoTranscripts.java | 452 ++
Dictionary.java | 430 ++
EDU/oswego/cs/dl/util/concurrent/Barrier.class | Bin 0 -> 175 bytes
.../cs/dl/util/concurrent/BoundedBuffer.class | Bin 0 -> 2747 bytes
.../cs/dl/util/concurrent/BoundedChannel.class | Bin 0 -> 215 bytes
.../cs/dl/util/concurrent/BoundedLinkedQueue.class | Bin 0 -> 3529 bytes
.../dl/util/concurrent/BoundedPriorityQueue.class | Bin 0 -> 1402 bytes
.../util/concurrent/BrokenBarrierException.class | Bin 0 -> 427 bytes
EDU/oswego/cs/dl/util/concurrent/Callable.class | Bin 0 -> 216 bytes
EDU/oswego/cs/dl/util/concurrent/Channel.class | Bin 0 -> 485 bytes
.../dl/util/concurrent/ClockDaemon$RunLoop.class | Bin 0 -> 870 bytes
.../dl/util/concurrent/ClockDaemon$TaskNode.class | Bin 0 -> 1044 bytes
EDU/oswego/cs/dl/util/concurrent/ClockDaemon.class | Bin 0 -> 2925 bytes
.../dl/util/concurrent/ConcurrentHashMap$1.class | Bin 0 -> 258 bytes
.../util/concurrent/ConcurrentHashMap$Entry.class | Bin 0 -> 1545 bytes
.../concurrent/ConcurrentHashMap$EntrySet.class | Bin 0 -> 1608 bytes
.../ConcurrentHashMap$HashIterator.class | Bin 0 -> 2132 bytes
.../concurrent/ConcurrentHashMap$KeyIterator.class | Bin 0 -> 712 bytes
.../util/concurrent/ConcurrentHashMap$KeySet.class | Bin 0 -> 1292 bytes
.../concurrent/ConcurrentHashMap$Segment.class | Bin 0 -> 511 bytes
.../ConcurrentHashMap$ValueIterator.class | Bin 0 -> 718 bytes
.../util/concurrent/ConcurrentHashMap$Values.class | Bin 0 -> 1190 bytes
.../cs/dl/util/concurrent/ConcurrentHashMap.class | Bin 0 -> 8365 bytes
.../concurrent/ConcurrentReaderHashMap$1.class | Bin 0 -> 276 bytes
.../ConcurrentReaderHashMap$BarrierLock.class | Bin 0 -> 400 bytes
.../concurrent/ConcurrentReaderHashMap$Entry.class | Bin 0 -> 1575 bytes
.../ConcurrentReaderHashMap$EntrySet.class | Bin 0 -> 1626 bytes
.../ConcurrentReaderHashMap$HashIterator.class | Bin 0 -> 2013 bytes
.../ConcurrentReaderHashMap$KeyIterator.class | Bin 0 -> 748 bytes
.../ConcurrentReaderHashMap$KeySet.class | Bin 0 -> 1346 bytes
.../ConcurrentReaderHashMap$ValueIterator.class | Bin 0 -> 754 bytes
.../ConcurrentReaderHashMap$Values.class | Bin 0 -> 1244 bytes
.../util/concurrent/ConcurrentReaderHashMap.class | Bin 0 -> 8732 bytes
EDU/oswego/cs/dl/util/concurrent/CondVar.class | Bin 0 -> 1490 bytes
.../CopyOnWriteArrayList$COWIterator.class | Bin 0 -> 1297 bytes
...teArrayList$COWSubList$COWSubListIterator.class | Bin 0 -> 1791 bytes
.../CopyOnWriteArrayList$COWSubList.class | Bin 0 -> 2830 bytes
.../dl/util/concurrent/CopyOnWriteArrayList.class | Bin 0 -> 7881 bytes
.../dl/util/concurrent/CopyOnWriteArraySet.class | Bin 0 -> 1648 bytes
EDU/oswego/cs/dl/util/concurrent/CountDown.class | Bin 0 -> 1159 bytes
.../cs/dl/util/concurrent/CyclicBarrier.class | Bin 0 -> 2158 bytes
.../util/concurrent/DefaultChannelCapacity.class | Bin 0 -> 745 bytes
.../cs/dl/util/concurrent/DirectExecutor.class | Bin 0 -> 543 bytes
EDU/oswego/cs/dl/util/concurrent/Executor.class | Bin 0 -> 233 bytes
.../concurrent/FIFOReadWriteLock$ReaderSync.class | Bin 0 -> 885 bytes
.../concurrent/FIFOReadWriteLock$WriterSync.class | Bin 0 -> 888 bytes
.../cs/dl/util/concurrent/FIFOReadWriteLock.class | Bin 0 -> 2133 bytes
.../concurrent/FIFOSemaphore$FIFOWaitQueue.class | Bin 0 -> 1072 bytes
.../cs/dl/util/concurrent/FIFOSemaphore.class | Bin 0 -> 558 bytes
EDU/oswego/cs/dl/util/concurrent/FJTask$Par.class | Bin 0 -> 647 bytes
EDU/oswego/cs/dl/util/concurrent/FJTask$Par2.class | Bin 0 -> 568 bytes
EDU/oswego/cs/dl/util/concurrent/FJTask$Seq.class | Bin 0 -> 711 bytes
EDU/oswego/cs/dl/util/concurrent/FJTask$Seq2.class | Bin 0 -> 620 bytes
EDU/oswego/cs/dl/util/concurrent/FJTask$Wrap.class | Bin 0 -> 456 bytes
EDU/oswego/cs/dl/util/concurrent/FJTask.class | Bin 0 -> 2468 bytes
.../concurrent/FJTaskRunner$VolatileTaskRef.class | Bin 0 -> 826 bytes
.../cs/dl/util/concurrent/FJTaskRunner.class | Bin 0 -> 6247 bytes
.../FJTaskRunnerGroup$InvokableFJTask.class | Bin 0 -> 1024 bytes
.../cs/dl/util/concurrent/FJTaskRunnerGroup.class | Bin 0 -> 4985 bytes
.../cs/dl/util/concurrent/FutureResult$1.class | Bin 0 -> 931 bytes
.../cs/dl/util/concurrent/FutureResult.class | Bin 0 -> 1925 bytes
EDU/oswego/cs/dl/util/concurrent/Heap.class | Bin 0 -> 1821 bytes
EDU/oswego/cs/dl/util/concurrent/Latch.class | Bin 0 -> 980 bytes
EDU/oswego/cs/dl/util/concurrent/LayeredSync.class | Bin 0 -> 1030 bytes
EDU/oswego/cs/dl/util/concurrent/LinkedNode.class | Bin 0 -> 541 bytes
EDU/oswego/cs/dl/util/concurrent/LinkedQueue.class | Bin 0 -> 2308 bytes
.../cs/dl/util/concurrent/LockedExecutor.class | Bin 0 -> 743 bytes
EDU/oswego/cs/dl/util/concurrent/Mutex.class | Bin 0 -> 1069 bytes
EDU/oswego/cs/dl/util/concurrent/NullSync.class | Bin 0 -> 585 bytes
.../concurrent/ObservableSync$SyncObserver.class | Bin 0 -> 318 bytes
.../cs/dl/util/concurrent/ObservableSync.class | Bin 0 -> 1609 bytes
.../PooledExecutor$AbortWhenBlocked.class | Bin 0 -> 802 bytes
.../PooledExecutor$BlockedExecutionHandler.class | Bin 0 -> 385 bytes
.../PooledExecutor$DiscardOldestWhenBlocked.class | Bin 0 -> 1067 bytes
.../PooledExecutor$DiscardWhenBlocked.class | Bin 0 -> 711 bytes
.../concurrent/PooledExecutor$RunWhenBlocked.class | Bin 0 -> 753 bytes
.../PooledExecutor$WaitWhenBlocked.class | Bin 0 -> 1030 bytes
.../dl/util/concurrent/PooledExecutor$Worker.class | Bin 0 -> 985 bytes
.../cs/dl/util/concurrent/PooledExecutor.class | Bin 0 -> 6780 bytes
.../PrioritySemaphore$PriorityWaitQueue.class | Bin 0 -> 1390 bytes
.../cs/dl/util/concurrent/PrioritySemaphore.class | Bin 0 -> 578 bytes
.../concurrent/PropertyChangeMulticaster.class | Bin 0 -> 4074 bytes
EDU/oswego/cs/dl/util/concurrent/Puttable.class | Bin 0 -> 278 bytes
.../cs/dl/util/concurrent/QueuedExecutor$1.class | Bin 0 -> 342 bytes
.../util/concurrent/QueuedExecutor$RunLoop.class | Bin 0 -> 1032 bytes
.../cs/dl/util/concurrent/QueuedExecutor.class | Bin 0 -> 2327 bytes
.../QueuedSemaphore$WaitQueue$WaitNode.class | Bin 0 -> 1538 bytes
.../concurrent/QueuedSemaphore$WaitQueue.class | Bin 0 -> 624 bytes
.../cs/dl/util/concurrent/QueuedSemaphore.class | Bin 0 -> 2011 bytes
.../cs/dl/util/concurrent/ReadWriteLock.class | Bin 0 -> 223 bytes
.../concurrent/ReaderPreferenceReadWriteLock.class | Bin 0 -> 429 bytes
.../cs/dl/util/concurrent/ReentrantLock.class | Bin 0 -> 1679 bytes
.../ReentrantWriterPreferenceReadWriteLock.class | Bin 0 -> 2487 bytes
.../concurrent/Rendezvous$RendezvousFunction.class | Bin 0 -> 308 bytes
.../cs/dl/util/concurrent/Rendezvous$Rotator.class | Bin 0 -> 563 bytes
EDU/oswego/cs/dl/util/concurrent/Rendezvous.class | Bin 0 -> 3231 bytes
EDU/oswego/cs/dl/util/concurrent/Semaphore.class | Bin 0 -> 1347 bytes
.../concurrent/SemaphoreControlledChannel.class | Bin 0 -> 2436 bytes
EDU/oswego/cs/dl/util/concurrent/Slot.class | Bin 0 -> 889 bytes
EDU/oswego/cs/dl/util/concurrent/Sync.class | Bin 0 -> 536 bytes
.../SyncCollection$SyncCollectionIterator.class | Bin 0 -> 1467 bytes
.../cs/dl/util/concurrent/SyncCollection.class | Bin 0 -> 4100 bytes
.../SyncList$SyncCollectionListIterator.class | Bin 0 -> 2233 bytes
EDU/oswego/cs/dl/util/concurrent/SyncList.class | Bin 0 -> 3806 bytes
EDU/oswego/cs/dl/util/concurrent/SyncMap.class | Bin 0 -> 4367 bytes
EDU/oswego/cs/dl/util/concurrent/SyncSet.class | Bin 0 -> 1306 bytes
.../cs/dl/util/concurrent/SyncSortedMap.class | Bin 0 -> 2040 bytes
.../cs/dl/util/concurrent/SyncSortedSet.class | Bin 0 -> 2110 bytes
.../dl/util/concurrent/SynchronizedBoolean.class | Bin 0 -> 2250 bytes
.../cs/dl/util/concurrent/SynchronizedByte.class | Bin 0 -> 2898 bytes
.../cs/dl/util/concurrent/SynchronizedChar.class | Bin 0 -> 2190 bytes
.../cs/dl/util/concurrent/SynchronizedDouble.class | Bin 0 -> 2284 bytes
.../cs/dl/util/concurrent/SynchronizedFloat.class | Bin 0 -> 2245 bytes
.../cs/dl/util/concurrent/SynchronizedInt.class | Bin 0 -> 2826 bytes
.../cs/dl/util/concurrent/SynchronizedLong.class | Bin 0 -> 2945 bytes
.../cs/dl/util/concurrent/SynchronizedRef.class | Bin 0 -> 1272 bytes
.../cs/dl/util/concurrent/SynchronizedShort.class | Bin 0 -> 2914 bytes
.../dl/util/concurrent/SynchronizedVariable.class | Bin 0 -> 796 bytes
.../util/concurrent/SynchronousChannel$Queue.class | Bin 0 -> 784 bytes
.../cs/dl/util/concurrent/SynchronousChannel.class | Bin 0 -> 3599 bytes
EDU/oswego/cs/dl/util/concurrent/Takable.class | Bin 0 -> 274 bytes
.../cs/dl/util/concurrent/ThreadFactory.class | Bin 0 -> 203 bytes
.../ThreadFactoryUser$DefaultThreadFactory.class | Bin 0 -> 586 bytes
.../cs/dl/util/concurrent/ThreadFactoryUser.class | Bin 0 -> 775 bytes
.../cs/dl/util/concurrent/ThreadedExecutor.class | Bin 0 -> 775 bytes
.../cs/dl/util/concurrent/TimedCallable.class | Bin 0 -> 1173 bytes
.../cs/dl/util/concurrent/TimeoutException.class | Bin 0 -> 422 bytes
EDU/oswego/cs/dl/util/concurrent/TimeoutSync.class | Bin 0 -> 813 bytes
.../concurrent/VetoableChangeMulticaster.class | Bin 0 -> 4330 bytes
.../cs/dl/util/concurrent/WaitFreeQueue$Node.class | Bin 0 -> 674 bytes
.../cs/dl/util/concurrent/WaitFreeQueue.class | Bin 0 -> 2026 bytes
.../cs/dl/util/concurrent/WaitableBoolean.class | Bin 0 -> 1885 bytes
.../cs/dl/util/concurrent/WaitableByte.class | Bin 0 -> 2847 bytes
.../cs/dl/util/concurrent/WaitableChar.class | Bin 0 -> 2155 bytes
.../cs/dl/util/concurrent/WaitableDouble.class | Bin 0 -> 2198 bytes
.../cs/dl/util/concurrent/WaitableFloat.class | Bin 0 -> 2164 bytes
EDU/oswego/cs/dl/util/concurrent/WaitableInt.class | Bin 0 -> 2840 bytes
.../cs/dl/util/concurrent/WaitableLong.class | Bin 0 -> 2897 bytes
EDU/oswego/cs/dl/util/concurrent/WaitableRef.class | Bin 0 -> 1547 bytes
.../cs/dl/util/concurrent/WaitableShort.class | Bin 0 -> 2850 bytes
.../concurrent/WaiterPreferenceSemaphore.class | Bin 0 -> 1382 bytes
.../WriterPreferenceReadWriteLock$ReaderLock.class | Bin 0 -> 2137 bytes
.../WriterPreferenceReadWriteLock$Signaller.class | Bin 0 -> 597 bytes
.../WriterPreferenceReadWriteLock$WriterLock.class | Bin 0 -> 2162 bytes
.../concurrent/WriterPreferenceReadWriteLock.class | Bin 0 -> 2494 bytes
.../cs/dl/util/concurrent/misc/AClongRNG.class | Bin 0 -> 1063 bytes
.../cs/dl/util/concurrent/misc/AllSynchRNG.class | Bin 0 -> 539 bytes
.../cs/dl/util/concurrent/misc/CVBuffer.class | Bin 0 -> 2499 bytes
.../cs/dl/util/concurrent/misc/ChanRNG.class | Bin 0 -> 1539 bytes
.../cs/dl/util/concurrent/misc/DelegatedRNG.class | Bin 0 -> 980 bytes
.../util/concurrent/misc/DirectExecutorRNG.class | Bin 0 -> 583 bytes
.../cs/dl/util/concurrent/misc/ExecutorRNG.class | Bin 0 -> 2421 bytes
.../cs/dl/util/concurrent/misc/FIFORWlockRNG.class | Bin 0 -> 403 bytes
.../cs/dl/util/concurrent/misc/FIFOSlot.class | Bin 0 -> 1663 bytes
.../cs/dl/util/concurrent/misc/FifoRNG.class | Bin 0 -> 399 bytes
.../util/concurrent/misc/ForcedStartRunnable.class | Bin 0 -> 695 bytes
.../misc/ForcedStartThreadedExecutor.class | Bin 0 -> 671 bytes
.../cs/dl/util/concurrent/misc/Fraction.class | Bin 0 -> 3083 bytes
.../cs/dl/util/concurrent/misc/GetFunction.class | Bin 0 -> 606 bytes
.../cs/dl/util/concurrent/misc/LockedSemRNG.class | Bin 0 -> 697 bytes
.../cs/dl/util/concurrent/misc/MutexRNG.class | Bin 0 -> 384 bytes
.../cs/dl/util/concurrent/misc/NextFunction.class | Bin 0 -> 608 bytes
.../cs/dl/util/concurrent/misc/NoSynchRNG.class | Bin 0 -> 567 bytes
.../cs/dl/util/concurrent/misc/PCTestLoop$1.class | Bin 0 -> 2368 bytes
.../cs/dl/util/concurrent/misc/PCTestLoop.class | Bin 0 -> 1115 bytes
.../cs/dl/util/concurrent/misc/PipedChannel.class | Bin 0 -> 2035 bytes
.../util/concurrent/misc/PooledExecutorRNG.class | Bin 0 -> 722 bytes
.../dl/util/concurrent/misc/PrioritySemRNG.class | Bin 0 -> 410 bytes
.../dl/util/concurrent/misc/PublicSynchRNG.class | Bin 0 -> 490 bytes
.../util/concurrent/misc/QueuedExecutorRNG.class | Bin 0 -> 981 bytes
EDU/oswego/cs/dl/util/concurrent/misc/RNG.class | Bin 0 -> 3953 bytes
.../cs/dl/util/concurrent/misc/RWLockRNG.class | Bin 0 -> 1699 bytes
.../util/concurrent/misc/ReaderPrefRWlockRNG.class | Bin 0 -> 425 bytes
.../util/concurrent/misc/ReentrantRWlockRNG.class | Bin 0 -> 1157 bytes
.../cs/dl/util/concurrent/misc/RlockRNG.class | Bin 0 -> 392 bytes
.../cs/dl/util/concurrent/misc/SDelegatedRNG.class | Bin 0 -> 737 bytes
EDU/oswego/cs/dl/util/concurrent/misc/SemRNG.class | Bin 0 -> 394 bytes
.../cs/dl/util/concurrent/misc/SwingWorker$1.class | Bin 0 -> 530 bytes
.../cs/dl/util/concurrent/misc/SwingWorker$2.class | Bin 0 -> 691 bytes
.../cs/dl/util/concurrent/misc/SwingWorker$3.class | Bin 0 -> 589 bytes
.../cs/dl/util/concurrent/misc/SwingWorker.class | Bin 0 -> 3259 bytes
.../dl/util/concurrent/misc/SyncDelegatedRNG.class | Bin 0 -> 1441 bytes
.../cs/dl/util/concurrent/misc/SynchLongRNG.class | Bin 0 -> 725 bytes
.../concurrent/misc/SynchronizationTimer$1.class | Bin 0 -> 439 bytes
.../concurrent/misc/SynchronizationTimer$10.class | Bin 0 -> 901 bytes
.../concurrent/misc/SynchronizationTimer$11.class | Bin 0 -> 1071 bytes
.../concurrent/misc/SynchronizationTimer$12.class | Bin 0 -> 1075 bytes
.../concurrent/misc/SynchronizationTimer$13.class | Bin 0 -> 1075 bytes
.../concurrent/misc/SynchronizationTimer$14.class | Bin 0 -> 1254 bytes
.../concurrent/misc/SynchronizationTimer$15.class | Bin 0 -> 1128 bytes
.../concurrent/misc/SynchronizationTimer$16.class | Bin 0 -> 1054 bytes
.../concurrent/misc/SynchronizationTimer$17.class | Bin 0 -> 1053 bytes
.../concurrent/misc/SynchronizationTimer$18.class | Bin 0 -> 1047 bytes
.../concurrent/misc/SynchronizationTimer$19.class | Bin 0 -> 1031 bytes
.../concurrent/misc/SynchronizationTimer$2.class | Bin 0 -> 947 bytes
.../concurrent/misc/SynchronizationTimer$20.class | Bin 0 -> 927 bytes
.../concurrent/misc/SynchronizationTimer$21.class | Bin 0 -> 1039 bytes
.../concurrent/misc/SynchronizationTimer$22.class | Bin 0 -> 1305 bytes
.../concurrent/misc/SynchronizationTimer$23.class | Bin 0 -> 1083 bytes
.../concurrent/misc/SynchronizationTimer$24.class | Bin 0 -> 1031 bytes
.../concurrent/misc/SynchronizationTimer$25.class | Bin 0 -> 1100 bytes
.../concurrent/misc/SynchronizationTimer$3.class | Bin 0 -> 938 bytes
.../concurrent/misc/SynchronizationTimer$4.class | Bin 0 -> 863 bytes
.../concurrent/misc/SynchronizationTimer$5.class | Bin 0 -> 1206 bytes
.../concurrent/misc/SynchronizationTimer$6.class | Bin 0 -> 1437 bytes
.../concurrent/misc/SynchronizationTimer$7.class | Bin 0 -> 693 bytes
.../concurrent/misc/SynchronizationTimer$8.class | Bin 0 -> 700 bytes
.../concurrent/misc/SynchronizationTimer$9.class | Bin 0 -> 700 bytes
.../misc/SynchronizationTimer$BarrierTimer.class | Bin 0 -> 686 bytes
.../misc/SynchronizationTimer$OneTest.class | Bin 0 -> 6923 bytes
.../misc/SynchronizationTimer$PrintStart.class | Bin 0 -> 826 bytes
.../misc/SynchronizationTimer$TestSeries.class | Bin 0 -> 2538 bytes
.../misc/SynchronizationTimer$TestedClass.class | Bin 0 -> 7327 bytes
.../misc/SynchronizationTimer$ThreadInfo.class | Bin 0 -> 911 bytes
.../concurrent/misc/SynchronizationTimer.class | Bin 0 -> 18792 bytes
.../cs/dl/util/concurrent/misc/TestLoop$1.class | Bin 0 -> 2435 bytes
.../cs/dl/util/concurrent/misc/TestLoop.class | Bin 0 -> 2023 bytes
.../util/concurrent/misc/ThreadedExecutorRNG.class | Bin 0 -> 987 bytes
.../dl/util/concurrent/misc/Threads$MyThread.class | Bin 0 -> 677 bytes
.../cs/dl/util/concurrent/misc/Threads.class | Bin 0 -> 1208 bytes
.../cs/dl/util/concurrent/misc/UpdateCommand.class | Bin 0 -> 764 bytes
.../cs/dl/util/concurrent/misc/WpRWlockRNG.class | Bin 0 -> 413 bytes
.../cs/dl/util/concurrent/misc/WpSemRNG.class | Bin 0 -> 412 bytes
ExperimentsGUI.java | 525 ++
FileOps.java | 765 +++
Gene.java | 787 +++
Genome.java | 420 ++
Hit.java | 132 +
IGV_Ops.java | 88 +
Index.java | 324 ++
Jama/CholeskyDecomposition.class | Bin 0 -> 1726 bytes
Jama/EigenvalueDecomposition.class | Bin 0 -> 10473 bytes
Jama/LUDecomposition.class | Bin 0 -> 2747 bytes
Jama/Matrix.class | Bin 0 -> 11405 bytes
Jama/QRDecomposition.class | Bin 0 -> 2545 bytes
Jama/SingularValueDecomposition.class | Bin 0 -> 5949 bytes
Jama/examples/MagicSquareExample.class | Bin 0 -> 3547 bytes
Jama/test/TestMatrix.class | Bin 0 -> 19740 bytes
Jama/util/Maths.class | Bin 0 -> 414 bytes
LICENSE.sun | 10 +
LICENSE.txt | 27 +
Lowess.java | 293 +
Matrix.java | 310 ++
Misc.java | 179 +
NCBI.java | 283 +
NegativeBinomial.java | 138 +
Operons.java | 575 ++
ParametersGUI.java | 674 +++
Peregrine.java | 1379 +++++
ProgressGUI.java | 122 +
Replicate.java | 330 ++
Replicon.java | 298 +
Rockhopper.java | 916 ++++
RockhopperGUI.java | 993 ++++
SamOps.java | 987 ++++
SmoothDistribution.java | 197 +
Table.java | 219 +
Transcripts.java | 1005 ++++
biz/source_code/base64Coder/Base64Coder.class | Bin 0 -> 4588 bytes
com/jidesoft/comparator/AlphanumComparator.class | Bin 0 -> 1776 bytes
com/jidesoft/comparator/BooleanComparator.class | Bin 0 -> 1317 bytes
com/jidesoft/comparator/CalendarComparator.class | Bin 0 -> 1357 bytes
.../comparator/CharSequenceComparator.class | Bin 0 -> 2227 bytes
com/jidesoft/comparator/ComparableComparator.class | Bin 0 -> 1718 bytes
com/jidesoft/comparator/ComparatorContext.class | Bin 0 -> 495 bytes
com/jidesoft/comparator/DateComparator.class | Bin 0 -> 1351 bytes
com/jidesoft/comparator/DefaultComparator.class | Bin 0 -> 728 bytes
.../comparator/FastComparableComparator.class | Bin 0 -> 1431 bytes
com/jidesoft/comparator/NumberComparator.class | Bin 0 -> 1876 bytes
.../comparator/ObjectComparatorManager.class | Bin 0 -> 5845 bytes
.../comparator/PrioritizedObjectComparator.class | Bin 0 -> 717 bytes
com/jidesoft/comparator/package-info.class | Bin 0 -> 129 bytes
com/jidesoft/converter/AbstractContext.class | Bin 0 -> 978 bytes
com/jidesoft/converter/ArrayConverter.class | Bin 0 -> 2375 bytes
com/jidesoft/converter/BigDecimalConverter.class | Bin 0 -> 1034 bytes
com/jidesoft/converter/BooleanConverter.class | Bin 0 -> 1528 bytes
com/jidesoft/converter/ByteConverter.class | Bin 0 -> 765 bytes
com/jidesoft/converter/CacheMap$Cache.class | Bin 0 -> 720 bytes
com/jidesoft/converter/CacheMap.class | Bin 0 -> 5004 bytes
com/jidesoft/converter/CalendarConverter.class | Bin 0 -> 770 bytes
com/jidesoft/converter/ColorConverter.class | Bin 0 -> 624 bytes
com/jidesoft/converter/ConverterContext.class | Bin 0 -> 1379 bytes
.../converter/ConverterContextSupport.class | Bin 0 -> 411 bytes
com/jidesoft/converter/CurrencyConverter.class | Bin 0 -> 557 bytes
com/jidesoft/converter/DateConverter.class | Bin 0 -> 3349 bytes
com/jidesoft/converter/DefaultArrayConverter.class | Bin 0 -> 2679 bytes
.../converter/DefaultObjectConverter.class | Bin 0 -> 1196 bytes
com/jidesoft/converter/DimensionConverter.class | Bin 0 -> 1342 bytes
com/jidesoft/converter/DoubleConverter.class | Bin 0 -> 686 bytes
com/jidesoft/converter/EnumConverter.class | Bin 0 -> 3553 bytes
com/jidesoft/converter/FileConverter.class | Bin 0 -> 874 bytes
com/jidesoft/converter/FloatConverter.class | Bin 0 -> 682 bytes
com/jidesoft/converter/FontConverter.class | Bin 0 -> 2064 bytes
com/jidesoft/converter/FontNameConverter.class | Bin 0 -> 1269 bytes
com/jidesoft/converter/HexColorConverter.class | Bin 0 -> 1919 bytes
com/jidesoft/converter/InsetsConverter.class | Bin 0 -> 1513 bytes
com/jidesoft/converter/IntegerConverter.class | Bin 0 -> 773 bytes
com/jidesoft/converter/LongConverter.class | Bin 0 -> 765 bytes
com/jidesoft/converter/MonthConverter.class | Bin 0 -> 1903 bytes
com/jidesoft/converter/MonthNameConverter.class | Bin 0 -> 2496 bytes
.../converter/MultilineStringConverter.class | Bin 0 -> 1303 bytes
com/jidesoft/converter/MultipleEnumConverter.class | Bin 0 -> 2640 bytes
.../converter/NaturalNumberConverter.class | Bin 0 -> 1011 bytes
com/jidesoft/converter/NumberConverter.class | Bin 0 -> 2419 bytes
com/jidesoft/converter/NumberFormatConverter.class | Bin 0 -> 511 bytes
com/jidesoft/converter/ObjectConverter.class | Bin 0 -> 478 bytes
.../converter/ObjectConverterManager.class | Bin 0 -> 8921 bytes
com/jidesoft/converter/PasswordConverter.class | Bin 0 -> 1211 bytes
com/jidesoft/converter/PercentConverter.class | Bin 0 -> 883 bytes
com/jidesoft/converter/PointConverter.class | Bin 0 -> 1325 bytes
com/jidesoft/converter/QuarterNameConverter.class | Bin 0 -> 2138 bytes
com/jidesoft/converter/RectangleConverter.class | Bin 0 -> 1454 bytes
com/jidesoft/converter/RegistrationEvent.class | Bin 0 -> 1664 bytes
com/jidesoft/converter/RegistrationListener.class | Bin 0 -> 204 bytes
com/jidesoft/converter/Resource.class | Bin 0 -> 626 bytes
com/jidesoft/converter/RgbColorConverter.class | Bin 0 -> 1863 bytes
com/jidesoft/converter/ShortConverter.class | Bin 0 -> 769 bytes
com/jidesoft/converter/StringArrayConverter.class | Bin 0 -> 1459 bytes
com/jidesoft/converter/StringConverter.class | Bin 0 -> 485 bytes
com/jidesoft/converter/XmlUtils.class | Bin 0 -> 2654 bytes
com/jidesoft/converter/YearNameConverter.class | Bin 0 -> 1129 bytes
com/jidesoft/converter/converter.properties | 19 +
com/jidesoft/converter/package-info.class | Bin 0 -> 128 bytes
com/jidesoft/dialog/AbstractDialogPage$1.class | Bin 0 -> 640 bytes
com/jidesoft/dialog/AbstractDialogPage.class | Bin 0 -> 4242 bytes
com/jidesoft/dialog/AbstractPage.class | Bin 0 -> 3676 bytes
com/jidesoft/dialog/BannerPanel$1.class | Bin 0 -> 620 bytes
com/jidesoft/dialog/BannerPanel$2.class | Bin 0 -> 644 bytes
com/jidesoft/dialog/BannerPanel$3.class | Bin 0 -> 2086 bytes
com/jidesoft/dialog/BannerPanel.class | Bin 0 -> 7303 bytes
com/jidesoft/dialog/ButtonEvent.class | Bin 0 -> 2176 bytes
com/jidesoft/dialog/ButtonListener.class | Bin 0 -> 183 bytes
com/jidesoft/dialog/ButtonNames.class | Bin 0 -> 843 bytes
com/jidesoft/dialog/ButtonPanel$1.class | Bin 0 -> 614 bytes
com/jidesoft/dialog/ButtonPanel.class | Bin 0 -> 6025 bytes
com/jidesoft/dialog/ButtonPanelLayout.class | Bin 0 -> 10534 bytes
com/jidesoft/dialog/ButtonResources.class | Bin 0 -> 625 bytes
.../dialog/DialogPageListCellRenderer.class | Bin 0 -> 505 bytes
.../dialog/DialogPageTreeCellRenderer.class | Bin 0 -> 4604 bytes
com/jidesoft/dialog/JideOptionPane$1.class | Bin 0 -> 709 bytes
com/jidesoft/dialog/JideOptionPane$2.class | Bin 0 -> 665 bytes
com/jidesoft/dialog/JideOptionPane$3.class | Bin 0 -> 1091 bytes
com/jidesoft/dialog/JideOptionPane.class | Bin 0 -> 7739 bytes
com/jidesoft/dialog/Laziness.class | Bin 0 -> 111 bytes
com/jidesoft/dialog/MultiplePageDialog$1.class | Bin 0 -> 749 bytes
com/jidesoft/dialog/MultiplePageDialog$10$1.class | Bin 0 -> 952 bytes
com/jidesoft/dialog/MultiplePageDialog$10.class | Bin 0 -> 1599 bytes
com/jidesoft/dialog/MultiplePageDialog$11.class | Bin 0 -> 1191 bytes
com/jidesoft/dialog/MultiplePageDialog$12.class | Bin 0 -> 1218 bytes
com/jidesoft/dialog/MultiplePageDialog$13.class | Bin 0 -> 1668 bytes
com/jidesoft/dialog/MultiplePageDialog$14.class | Bin 0 -> 1393 bytes
com/jidesoft/dialog/MultiplePageDialog$15.class | Bin 0 -> 1294 bytes
com/jidesoft/dialog/MultiplePageDialog$16.class | Bin 0 -> 1154 bytes
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com/jidesoft/dialog/MultiplePageDialog$5.class | Bin 0 -> 1360 bytes
com/jidesoft/dialog/MultiplePageDialog$6.class | Bin 0 -> 1433 bytes
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com/jidesoft/dialog/MultiplePageDialog$8.class | Bin 0 -> 1570 bytes
com/jidesoft/dialog/MultiplePageDialog$9.class | Bin 0 -> 3158 bytes
com/jidesoft/dialog/MultiplePageDialog.class | Bin 0 -> 15716 bytes
com/jidesoft/dialog/MultiplePageDialogPane$1.class | Bin 0 -> 856 bytes
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com/jidesoft/dialog/MultiplePageDialogPane$2.class | Bin 0 -> 925 bytes
com/jidesoft/dialog/MultiplePageDialogPane$3.class | Bin 0 -> 1380 bytes
com/jidesoft/dialog/MultiplePageDialogPane$4.class | Bin 0 -> 1457 bytes
com/jidesoft/dialog/MultiplePageDialogPane$5.class | Bin 0 -> 1366 bytes
com/jidesoft/dialog/MultiplePageDialogPane$6.class | Bin 0 -> 1590 bytes
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com/jidesoft/dialog/MultiplePageDialogPane$8.class | Bin 0 -> 1620 bytes
com/jidesoft/dialog/MultiplePageDialogPane$9.class | Bin 0 -> 1206 bytes
com/jidesoft/dialog/MultiplePageDialogPane.class | Bin 0 -> 14880 bytes
com/jidesoft/dialog/MutableTreeNodeEx.class | Bin 0 -> 664 bytes
com/jidesoft/dialog/PageEvent.class | Bin 0 -> 946 bytes
com/jidesoft/dialog/PageList.class | Bin 0 -> 2258 bytes
com/jidesoft/dialog/PageListener.class | Bin 0 -> 177 bytes
com/jidesoft/dialog/ScrollableButtonPanel.class | Bin 0 -> 1159 bytes
com/jidesoft/dialog/StandardDialog$1.class | Bin 0 -> 599 bytes
com/jidesoft/dialog/StandardDialog$2.class | Bin 0 -> 708 bytes
com/jidesoft/dialog/StandardDialog$3.class | Bin 0 -> 708 bytes
.../StandardDialog$DefaultStandardDialogPane.class | Bin 0 -> 733 bytes
...og$StandardDialogPropertyChangeListener$1.class | Bin 0 -> 1219 bytes
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com/jidesoft/dialog/StandardDialog.class | Bin 0 -> 5084 bytes
com/jidesoft/dialog/StandardDialogPane$1.class | Bin 0 -> 962 bytes
com/jidesoft/dialog/StandardDialogPane.class | Bin 0 -> 2871 bytes
.../dialog/TreeIconsFactory$CellRenderer.class | Bin 0 -> 458 bytes
com/jidesoft/dialog/TreeIconsFactory.class | Bin 0 -> 576 bytes
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com/jidesoft/dialog/icons/blank-16.gif | Bin 0 -> 100 bytes
com/jidesoft/dialog/icons/selected-b16.gif | Bin 0 -> 860 bytes
com/jidesoft/dialog/icons/selected-c16.gif | Bin 0 -> 138 bytes
com/jidesoft/dialog/package-info.class | Bin 0 -> 125 bytes
com/jidesoft/grouper/AbstractObjectGrouper.class | Bin 0 -> 394 bytes
com/jidesoft/grouper/DefaultObjectGrouper.class | Bin 0 -> 622 bytes
com/jidesoft/grouper/GroupResources.class | Bin 0 -> 624 bytes
com/jidesoft/grouper/GrouperContext.class | Bin 0 -> 419 bytes
com/jidesoft/grouper/ObjectGrouper.class | Bin 0 -> 427 bytes
com/jidesoft/grouper/ObjectGrouperManager.class | Bin 0 -> 4289 bytes
.../grouper/date/DateDayOfMonthGrouper.class | Bin 0 -> 1392 bytes
.../grouper/date/DateDayOfWeekGrouper.class | Bin 0 -> 1425 bytes
.../grouper/date/DateDayOfWeekInMonthGrouper.class | Bin 0 -> 1406 bytes
.../grouper/date/DateDayOfYearGrouper.class | Bin 0 -> 922 bytes
com/jidesoft/grouper/date/DateGrouper.class | Bin 0 -> 1161 bytes
com/jidesoft/grouper/date/DateMonthGrouper.class | Bin 0 -> 1569 bytes
com/jidesoft/grouper/date/DateQuarterGrouper.class | Bin 0 -> 1433 bytes
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com/jidesoft/grouper/date/DateYearGrouper.class | Bin 0 -> 1104 bytes
com/jidesoft/grouper/date/package-info.class | Bin 0 -> 131 bytes
com/jidesoft/grouper/group.properties | 12 +
com/jidesoft/grouper/package-info.class | Bin 0 -> 126 bytes
com/jidesoft/hints/AbstractIntelliHints$1.class | Bin 0 -> 769 bytes
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com/jidesoft/hints/AbstractIntelliHints$8$1.class | Bin 0 -> 916 bytes
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.../AbstractIntelliHints$LazyDelegateAction.class | Bin 0 -> 2129 bytes
com/jidesoft/hints/AbstractIntelliHints.class | Bin 0 -> 7850 bytes
.../hints/AbstractListIntelliHints$1.class | Bin 0 -> 798 bytes
com/jidesoft/hints/AbstractListIntelliHints.class | Bin 0 -> 2602 bytes
com/jidesoft/hints/FileIntelliHints$1.class | Bin 0 -> 1152 bytes
.../FileIntelliHints$PrefixListCellRenderer.class | Bin 0 -> 843 bytes
com/jidesoft/hints/FileIntelliHints.class | Bin 0 -> 2625 bytes
com/jidesoft/hints/IntelliHints.class | Bin 0 -> 387 bytes
com/jidesoft/hints/ListDataIntelliHints$1.class | Bin 0 -> 694 bytes
com/jidesoft/hints/ListDataIntelliHints.class | Bin 0 -> 2194 bytes
com/jidesoft/hints/package-info.class | Bin 0 -> 124 bytes
com/jidesoft/icons/ColorFilter.class | Bin 0 -> 1535 bytes
com/jidesoft/icons/IconSet$Direction.class | Bin 0 -> 873 bytes
com/jidesoft/icons/IconSet$Edit.class | Bin 0 -> 605 bytes
com/jidesoft/icons/IconSet$File.class | Bin 0 -> 857 bytes
com/jidesoft/icons/IconSet$FindReplace.class | Bin 0 -> 555 bytes
com/jidesoft/icons/IconSet$Hardware.class | Bin 0 -> 1191 bytes
com/jidesoft/icons/IconSet$Help.class | Bin 0 -> 387 bytes
com/jidesoft/icons/IconSet$MediaControl.class | Bin 0 -> 992 bytes
com/jidesoft/icons/IconSet$Movement.class | Bin 0 -> 729 bytes
com/jidesoft/icons/IconSet$Overlay.class | Bin 0 -> 964 bytes
com/jidesoft/icons/IconSet$Software.class | Bin 0 -> 1174 bytes
com/jidesoft/icons/IconSet$Text.class | Bin 0 -> 780 bytes
com/jidesoft/icons/IconSet$View.class | Bin 0 -> 1278 bytes
com/jidesoft/icons/IconSet.class | Bin 0 -> 1357 bytes
com/jidesoft/icons/IconSetManager.class | Bin 0 -> 2852 bytes
com/jidesoft/icons/IconsFactory$1.class | Bin 0 -> 497 bytes
com/jidesoft/icons/IconsFactory.class | Bin 0 -> 12934 bytes
com/jidesoft/icons/JideIconsFactory$Arrow.class | Bin 0 -> 529 bytes
com/jidesoft/icons/JideIconsFactory$Cursor.class | Bin 0 -> 1261 bytes
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com/jidesoft/icons/JideIconsFactory$FileType.class | Bin 0 -> 420 bytes
com/jidesoft/icons/JideIconsFactory$View.class | Bin 0 -> 369 bytes
.../icons/JideIconsFactory$WindowMenu.class | Bin 0 -> 447 bytes
com/jidesoft/icons/JideIconsFactory.class | Bin 0 -> 1608 bytes
com/jidesoft/icons/MaskFilter.class | Bin 0 -> 1477 bytes
com/jidesoft/icons/MenuCheckIcon.class | Bin 0 -> 905 bytes
com/jidesoft/icons/NetworkIconSet$Ecommerce.class | Bin 0 -> 705 bytes
com/jidesoft/icons/NetworkIconSet$Email.class | Bin 0 -> 1376 bytes
com/jidesoft/icons/NetworkIconSet$Interface.class | Bin 0 -> 759 bytes
com/jidesoft/icons/NetworkIconSet$Internet.class | Bin 0 -> 1286 bytes
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com/jidesoft/icons/jide/cursor_delete.gif | Bin 0 -> 150 bytes
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com/jidesoft/icons/jide/cursor_move_east.gif | Bin 0 -> 111 bytes
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com/jidesoft/icons/jide/cursor_west.gif | Bin 0 -> 97 bytes
com/jidesoft/icons/jide/direction_dot.gif | Bin 0 -> 91 bytes
com/jidesoft/icons/jide/direction_down.gif | Bin 0 -> 96 bytes
com/jidesoft/icons/jide/direction_left.gif | Bin 0 -> 98 bytes
com/jidesoft/icons/jide/direction_right.gif | Bin 0 -> 98 bytes
com/jidesoft/icons/jide/direction_up.gif | Bin 0 -> 96 bytes
com/jidesoft/icons/jide/dockableframe_1.gif | Bin 0 -> 337 bytes
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com/jidesoft/icons/jide/dockableframe_8.gif | Bin 0 -> 348 bytes
com/jidesoft/icons/jide/dockableframe_9.gif | Bin 0 -> 345 bytes
com/jidesoft/icons/jide/dockableframe_blank.gif | Bin 0 -> 218 bytes
com/jidesoft/icons/jide/file_html.png | Bin 0 -> 307 bytes
com/jidesoft/icons/jide/file_java.png | Bin 0 -> 581 bytes
com/jidesoft/icons/jide/file_text.png | Bin 0 -> 265 bytes
com/jidesoft/icons/jide/jide32.png | Bin 0 -> 5163 bytes
com/jidesoft/icons/jide/jide50.png | Bin 0 -> 7239 bytes
com/jidesoft/icons/jide/jide_logo.png | Bin 0 -> 9501 bytes
com/jidesoft/icons/jide/jide_logo_small.png | Bin 0 -> 7709 bytes
com/jidesoft/icons/jide/jide_logo_small_2.png | Bin 0 -> 7670 bytes
com/jidesoft/icons/jide/menu_checkbox_eclipse.gif | Bin 0 -> 116 bytes
com/jidesoft/icons/jide/menu_checkbox_vsnet.gif | Bin 0 -> 851 bytes
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com/jidesoft/icons/jide/menu_radiobutton_vsnet.gif | Bin 0 -> 845 bytes
com/jidesoft/icons/jide/save.png | Bin 0 -> 488 bytes
com/jidesoft/icons/jide/view_design.gif | Bin 0 -> 864 bytes
com/jidesoft/icons/jide/view_html.gif | Bin 0 -> 865 bytes
.../jide/windows_new_horizontal_tab_group.png | Bin 0 -> 110 bytes
.../icons/jide/windows_new_vertical_tab_group.png | Bin 0 -> 122 bytes
com/jidesoft/icons/package-info.class | Bin 0 -> 124 bytes
.../list/StyledListCellRenderer$UIResource.class | Bin 0 -> 269 bytes
com/jidesoft/list/StyledListCellRenderer.class | Bin 0 -> 3042 bytes
.../plaf/CachedLookAndFeel$CustomUIDefaults.class | Bin 0 -> 1104 bytes
com/jidesoft/plaf/CachedLookAndFeel.class | Bin 0 -> 2560 bytes
.../plaf/ExtWindowsDesktopProperty$1.class | Bin 0 -> 537 bytes
.../plaf/ExtWindowsDesktopProperty$WeakPCL.class | Bin 0 -> 834 bytes
com/jidesoft/plaf/ExtWindowsDesktopProperty.class | Bin 0 -> 3249 bytes
com/jidesoft/plaf/FolderChooserUI.class | Bin 0 -> 85 bytes
com/jidesoft/plaf/GripperUI.class | Bin 0 -> 154 bytes
com/jidesoft/plaf/HeaderBoxUI.class | Bin 0 -> 153 bytes
com/jidesoft/plaf/JideButtonUI.class | Bin 0 -> 154 bytes
com/jidesoft/plaf/JideTabbedPaneUI.class | Bin 0 -> 394 bytes
com/jidesoft/plaf/LookAndFeelExtension.class | Bin 0 -> 129 bytes
com/jidesoft/plaf/LookAndFeelFactory$1.class | Bin 0 -> 687 bytes
.../plaf/LookAndFeelFactory$GTKCustomizer$1.class | Bin 0 -> 805 bytes
.../plaf/LookAndFeelFactory$GTKCustomizer.class | Bin 0 -> 952 bytes
.../plaf/LookAndFeelFactory$GTKInitializer.class | Bin 0 -> 785 bytes
.../LookAndFeelFactory$MotifCustomizer$1.class | Bin 0 -> 815 bytes
.../plaf/LookAndFeelFactory$MotifCustomizer.class | Bin 0 -> 884 bytes
.../LookAndFeelFactory$NimbusCustomizer$1.class | Bin 0 -> 820 bytes
.../plaf/LookAndFeelFactory$NimbusCustomizer.class | Bin 0 -> 964 bytes
.../LookAndFeelFactory$NimbusInitializer.class | Bin 0 -> 2397 bytes
.../LookAndFeelFactory$SyntheticaCustomizer.class | Bin 0 -> 12521 bytes
.../LookAndFeelFactory$SyntheticaInitializer.class | Bin 0 -> 1416 bytes
.../LookAndFeelFactory$UIDefaultsCustomizer.class | Bin 0 -> 255 bytes
.../LookAndFeelFactory$UIDefaultsInitializer.class | Bin 0 -> 258 bytes
com/jidesoft/plaf/LookAndFeelFactory.class | Bin 0 -> 16169 bytes
com/jidesoft/plaf/PopupUI.class | Bin 0 -> 198 bytes
com/jidesoft/plaf/SidePaneUI.class | Bin 0 -> 336 bytes
com/jidesoft/plaf/UIDefaultsLookup.class | Bin 0 -> 5732 bytes
com/jidesoft/plaf/WindowsDesktopProperty$1.class | Bin 0 -> 525 bytes
.../plaf/WindowsDesktopProperty$WeakPCL.class | Bin 0 -> 828 bytes
com/jidesoft/plaf/WindowsDesktopProperty.class | Bin 0 -> 3472 bytes
com/jidesoft/plaf/XPUtils.class | Bin 0 -> 1831 bytes
com/jidesoft/plaf/aqua/AquaGripperUI.class | Bin 0 -> 875 bytes
com/jidesoft/plaf/aqua/AquaJidePopupMenuUI.class | Bin 0 -> 485 bytes
com/jidesoft/plaf/aqua/AquaJideSplitButtonUI.class | Bin 0 -> 344 bytes
.../AquaJideTabbedPaneUI$AquaTabCloseButton.class | Bin 0 -> 3391 bytes
com/jidesoft/plaf/aqua/AquaJideTabbedPaneUI.class | Bin 0 -> 2964 bytes
com/jidesoft/plaf/aqua/AquaJideUtils$1.class | Bin 0 -> 445 bytes
com/jidesoft/plaf/aqua/AquaJideUtils$2.class | Bin 0 -> 511 bytes
com/jidesoft/plaf/aqua/AquaJideUtils.class | Bin 0 -> 20715 bytes
com/jidesoft/plaf/aqua/AquaPainter.class | Bin 0 -> 3507 bytes
com/jidesoft/plaf/aqua/AquaPreferences.class | Bin 0 -> 2705 bytes
.../AquaRangeSliderUI$RangeTrackListener.class | Bin 0 -> 4387 bytes
com/jidesoft/plaf/aqua/AquaRangeSliderUI.class | Bin 0 -> 8118 bytes
com/jidesoft/plaf/aqua/BinaryPListParser$1.class | Bin 0 -> 202 bytes
.../plaf/aqua/BinaryPListParser$BPLArray.class | Bin 0 -> 1209 bytes
.../plaf/aqua/BinaryPListParser$BPLDict.class | Bin 0 -> 1503 bytes
com/jidesoft/plaf/aqua/BinaryPListParser.class | Bin 0 -> 7522 bytes
com/jidesoft/plaf/aqua/XMLElement.class | Bin 0 -> 12424 bytes
com/jidesoft/plaf/aqua/XMLParseException.class | Bin 0 -> 875 bytes
com/jidesoft/plaf/aqua/icons/pressed.gif | Bin 0 -> 289 bytes
com/jidesoft/plaf/aqua/icons/rollover.gif | Bin 0 -> 287 bytes
com/jidesoft/plaf/aqua/icons/selected.gif | Bin 0 -> 185 bytes
com/jidesoft/plaf/aqua/package-info.class | Bin 0 -> 128 bytes
com/jidesoft/plaf/basic/BasicCheckBoxListUI.class | Bin 0 -> 886 bytes
.../plaf/basic/BasicFileSystemTree$1.class | Bin 0 -> 807 bytes
.../BasicFileSystemTree$FolderTreeListener.class | Bin 0 -> 1435 bytes
com/jidesoft/plaf/basic/BasicFileSystemTree.class | Bin 0 -> 2177 bytes
.../basic/BasicFileSystemTreeCellRenderer.class | Bin 0 -> 869 bytes
.../plaf/basic/BasicFileSystemTreeModel.class | Bin 0 -> 1491 bytes
.../plaf/basic/BasicFileSystemTreeNode.class | Bin 0 -> 3530 bytes
.../BasicFolderChooserIconsFactory$ToolBar.class | Bin 0 -> 600 bytes
.../basic/BasicFolderChooserIconsFactory.class | Bin 0 -> 602 bytes
.../plaf/basic/BasicFolderChooserUI$1.class | Bin 0 -> 645 bytes
.../plaf/basic/BasicFolderChooserUI$2.class | Bin 0 -> 951 bytes
.../plaf/basic/BasicFolderChooserUI$3$1.class | Bin 0 -> 941 bytes
.../plaf/basic/BasicFolderChooserUI$3.class | Bin 0 -> 6208 bytes
.../plaf/basic/BasicFolderChooserUI$4.class | Bin 0 -> 842 bytes
.../plaf/basic/BasicFolderChooserUI$5.class | Bin 0 -> 756 bytes
...sicFolderChooserUI$ApproveSelectionAction.class | Bin 0 -> 824 bytes
...serUI$FolderChooserPropertyChangeListener.class | Bin 0 -> 2933 bytes
...rChooserUI$FolderChooserSelectionListener.class | Bin 0 -> 2039 bytes
...lderChooserUI$NavigationTextFieldListener.class | Bin 0 -> 1738 bytes
com/jidesoft/plaf/basic/BasicFolderChooserUI.class | Bin 0 -> 10707 bytes
.../BasicGripperUI$GripperMouseListener.class | Bin 0 -> 793 bytes
com/jidesoft/plaf/basic/BasicGripperUI.class | Bin 0 -> 3418 bytes
...asicHeaderBoxUI$RolloverMouseInputAdapter.class | Bin 0 -> 1680 bytes
com/jidesoft/plaf/basic/BasicHeaderBoxUI.class | Bin 0 -> 2897 bytes
.../basic/BasicJideButtonListener$Actions.class | Bin 0 -> 1108 bytes
.../plaf/basic/BasicJideButtonListener.class | Bin 0 -> 4132 bytes
com/jidesoft/plaf/basic/BasicJideButtonUI.class | Bin 0 -> 13802 bytes
.../plaf/basic/BasicJideComboBoxButton$1.class | Bin 0 -> 599 bytes
.../plaf/basic/BasicJideComboBoxButton.class | Bin 0 -> 3446 bytes
...sicJideComboBoxUI$BasicJideComboBoxBorder.class | Bin 0 -> 1372 bytes
...BasicJideComboBoxUI$BasicJideComboBoxIcon.class | Bin 0 -> 813 bytes
.../BasicJideComboBoxUI$RolloverListener$1.class | Bin 0 -> 1183 bytes
.../BasicJideComboBoxUI$RolloverListener.class | Bin 0 -> 1452 bytes
com/jidesoft/plaf/basic/BasicJideComboBoxUI.class | Bin 0 -> 4722 bytes
com/jidesoft/plaf/basic/BasicJideLabelUI.class | Bin 0 -> 3885 bytes
.../plaf/basic/BasicJideOptionPaneUI$1.class | Bin 0 -> 1301 bytes
.../plaf/basic/BasicJideOptionPaneUI$2.class | Bin 0 -> 2193 bytes
.../plaf/basic/BasicJideOptionPaneUI$3.class | Bin 0 -> 1020 bytes
.../plaf/basic/BasicJideOptionPaneUI$4.class | Bin 0 -> 707 bytes
.../BasicJideOptionPaneUI$ButtonFactory.class | Bin 0 -> 784 bytes
.../plaf/basic/BasicJideOptionPaneUI.class | Bin 0 -> 14347 bytes
.../plaf/basic/BasicJidePopupMenuUI$1.class | Bin 0 -> 1670 bytes
com/jidesoft/plaf/basic/BasicJidePopupMenuUI.class | Bin 0 -> 2089 bytes
.../plaf/basic/BasicJidePopupUI$PopupLayout.class | Bin 0 -> 2603 bytes
...icJidePopupUI$PopupPropertyChangeListener.class | Bin 0 -> 923 bytes
com/jidesoft/plaf/basic/BasicJidePopupUI.class | Bin 0 -> 6804 bytes
.../plaf/basic/BasicJideSplitButtonUI$1.class | Bin 0 -> 776 bytes
.../basic/BasicJideSplitButtonUI$Actions.class | Bin 0 -> 1360 bytes
.../BasicJideSplitButtonUI$MouseInputHandler.class | Bin 0 -> 4419 bytes
.../plaf/basic/BasicJideSplitButtonUI.class | Bin 0 -> 18357 bytes
.../plaf/basic/BasicJideTabbedPaneUI$1.class | Bin 0 -> 1133 bytes
.../plaf/basic/BasicJideTabbedPaneUI$2.class | Bin 0 -> 1523 bytes
.../plaf/basic/BasicJideTabbedPaneUI$3.class | Bin 0 -> 866 bytes
.../plaf/basic/BasicJideTabbedPaneUI$4.class | Bin 0 -> 885 bytes
.../plaf/basic/BasicJideTabbedPaneUI$5.class | Bin 0 -> 1101 bytes
.../basic/BasicJideTabbedPaneUI$AbstractTab.class | Bin 0 -> 436 bytes
.../BasicJideTabbedPaneUI$ActivateTabAction.class | Bin 0 -> 831 bytes
.../BasicJideTabbedPaneUI$CloseTabAction.class | Bin 0 -> 3002 bytes
.../BasicJideTabbedPaneUI$ComponentHandler.class | Bin 0 -> 1922 bytes
.../BasicJideTabbedPaneUI$ContainerHandler.class | Bin 0 -> 2607 bytes
...BasicJideTabbedPaneUI$DefaultMouseHandler.class | Bin 0 -> 1088 bytes
...ideTabbedPaneUI$DefaultMouseMotionHandler.class | Bin 0 -> 917 bytes
.../basic/BasicJideTabbedPaneUI$DownAction.class | Bin 0 -> 794 bytes
.../BasicJideTabbedPaneUI$DragOverTimer.class | Bin 0 -> 1307 bytes
.../basic/BasicJideTabbedPaneUI$DropListener.class | Bin 0 -> 1722 bytes
.../basic/BasicJideTabbedPaneUI$LeftAction.class | Bin 0 -> 795 bytes
.../BasicJideTabbedPaneUI$MouseHandler$1.class | Bin 0 -> 1246 bytes
.../basic/BasicJideTabbedPaneUI$MouseHandler.class | Bin 0 -> 2790 bytes
.../BasicJideTabbedPaneUI$MouseMotionHandler.class | Bin 0 -> 434 bytes
.../BasicJideTabbedPaneUI$MouseWheelHandler.class | Bin 0 -> 1415 bytes
.../basic/BasicJideTabbedPaneUI$NextAction.class | Bin 0 -> 795 bytes
.../BasicJideTabbedPaneUI$PageDownAction.class | Bin 0 -> 862 bytes
.../basic/BasicJideTabbedPaneUI$PageUpAction.class | Bin 0 -> 859 bytes
.../BasicJideTabbedPaneUI$PreviousAction.class | Bin 0 -> 803 bytes
...sicJideTabbedPaneUI$PropertyChangeHandler.class | Bin 0 -> 4767 bytes
.../BasicJideTabbedPaneUI$RequestFocusAction.class | Bin 0 -> 779 bytes
...TabbedPaneUI$RequestFocusForVisibleAction.class | Bin 0 -> 841 bytes
.../basic/BasicJideTabbedPaneUI$RightAction.class | Bin 0 -> 796 bytes
...asicJideTabbedPaneUI$RolloverMouseHandler.class | Bin 0 -> 1065 bytes
...deTabbedPaneUI$RolloverMouseMotionHandler.class | Bin 0 -> 951 bytes
...JideTabbedPaneUI$ScrollTabsBackwardAction.class | Bin 0 -> 1651 bytes
...cJideTabbedPaneUI$ScrollTabsForwardAction.class | Bin 0 -> 1647 bytes
...asicJideTabbedPaneUI$ScrollTabsListAction.class | Bin 0 -> 1828 bytes
.../BasicJideTabbedPaneUI$ScrollableTabPanel.class | Bin 0 -> 3220 bytes
...icJideTabbedPaneUI$ScrollableTabSupport$1.class | Bin 0 -> 1137 bytes
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com/jidesoft/popup/JidePopup.class | Bin 0 -> 27891 bytes
com/jidesoft/popup/JidePopupFactory.class | Bin 0 -> 1003 bytes
com/jidesoft/popup/package-info.class | Bin 0 -> 124 bytes
com/jidesoft/range/AbstractNumericRange.class | Bin 0 -> 254 bytes
com/jidesoft/range/AbstractRange.class | Bin 0 -> 1261 bytes
com/jidesoft/range/AggregatedRange.class | Bin 0 -> 2778 bytes
com/jidesoft/range/Category.class | Bin 0 -> 2495 bytes
com/jidesoft/range/CategoryRange.class | Bin 0 -> 4903 bytes
com/jidesoft/range/CombinedNumericRange.class | Bin 0 -> 2901 bytes
com/jidesoft/range/IntegerRange.class | Bin 0 -> 2624 bytes
com/jidesoft/range/NumericRange.class | Bin 0 -> 2503 bytes
com/jidesoft/range/Positionable.class | Bin 0 -> 234 bytes
com/jidesoft/range/Range.class | Bin 0 -> 647 bytes
com/jidesoft/range/TimeRange.class | Bin 0 -> 3740 bytes
com/jidesoft/range/package-info.class | Bin 0 -> 124 bytes
com/jidesoft/spinner/DateSpinner.class | Bin 0 -> 2918 bytes
com/jidesoft/spinner/PointFormatter.class | Bin 0 -> 1890 bytes
.../spinner/PointSpinner$PointEditor$1.class | Bin 0 -> 1312 bytes
.../spinner/PointSpinner$PointEditor.class | Bin 0 -> 1780 bytes
com/jidesoft/spinner/PointSpinner.class | Bin 0 -> 1571 bytes
com/jidesoft/spinner/SpinnerPointModel.class | Bin 0 -> 1096 bytes
com/jidesoft/spinner/SpinnerWheelSupport$1.class | Bin 0 -> 1129 bytes
com/jidesoft/spinner/SpinnerWheelSupport.class | Bin 0 -> 971 bytes
com/jidesoft/spinner/package-info.class | Bin 0 -> 126 bytes
com/jidesoft/swing/Alignable.class | Bin 0 -> 318 bytes
com/jidesoft/swing/AlignmentSupport.class | Bin 0 -> 228 bytes
com/jidesoft/swing/Animator.class | Bin 0 -> 2185 bytes
com/jidesoft/swing/AnimatorListener.class | Bin 0 -> 247 bytes
...owKeyNavigationSupport$NavigationAction$1.class | Bin 0 -> 1928 bytes
...rrowKeyNavigationSupport$NavigationAction.class | Bin 0 -> 3096 bytes
com/jidesoft/swing/ArrowKeyNavigationSupport.class | Bin 0 -> 2127 bytes
com/jidesoft/swing/AutoCompletion$1.class | Bin 0 -> 1235 bytes
com/jidesoft/swing/AutoCompletion$2.class | Bin 0 -> 1117 bytes
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com/jidesoft/swing/AutoCompletion.class | Bin 0 -> 7476 bytes
com/jidesoft/swing/AutoCompletionComboBox.class | Bin 0 -> 1101 bytes
com/jidesoft/swing/AutoRepeatButtonUtils.class | Bin 0 -> 2374 bytes
com/jidesoft/swing/AutoResizingTextArea$1.class | Bin 0 -> 200 bytes
...ResizingTextArea$ResizingDocumentListener.class | Bin 0 -> 930 bytes
com/jidesoft/swing/AutoResizingTextArea.class | Bin 0 -> 2724 bytes
.../swing/AutoScroll$AutoScrollActionHandler.class | Bin 0 -> 564 bytes
com/jidesoft/swing/AutoScroll.class | Bin 0 -> 3376 bytes
com/jidesoft/swing/ButtonStyle.class | Bin 0 -> 676 bytes
com/jidesoft/swing/Calculator$BackspaceIcon.class | Bin 0 -> 1019 bytes
.../swing/Calculator$CalculatorLayoutManager.class | Bin 0 -> 1901 bytes
.../swing/Calculator$ToggleNegativeIcon.class | Bin 0 -> 1031 bytes
com/jidesoft/swing/Calculator.class | Bin 0 -> 11768 bytes
com/jidesoft/swing/CheckBoxList$Handler.class | Bin 0 -> 4020 bytes
com/jidesoft/swing/CheckBoxList.class | Bin 0 -> 7435 bytes
.../CheckBoxListCellRenderer$UIResource.class | Bin 0 -> 275 bytes
com/jidesoft/swing/CheckBoxListCellRenderer.class | Bin 0 -> 4463 bytes
.../swing/CheckBoxListSelectionModel.class | Bin 0 -> 904 bytes
.../swing/CheckBoxListWithSelectable$Handler.class | Bin 0 -> 2711 bytes
.../swing/CheckBoxListWithSelectable.class | Bin 0 -> 6205 bytes
com/jidesoft/swing/CheckBoxTree$1.class | Bin 0 -> 1046 bytes
com/jidesoft/swing/CheckBoxTree$2.class | Bin 0 -> 1016 bytes
com/jidesoft/swing/CheckBoxTree$Handler.class | Bin 0 -> 3995 bytes
com/jidesoft/swing/CheckBoxTree.class | Bin 0 -> 5618 bytes
com/jidesoft/swing/CheckBoxTreeCellRenderer.class | Bin 0 -> 4002 bytes
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com/jidesoft/swing/ClickThroughLabel.class | Bin 0 -> 1703 bytes
com/jidesoft/swing/ClickThroughStyledLabel.class | Bin 0 -> 1721 bytes
com/jidesoft/swing/ComboBoxSearchable$1.class | Bin 0 -> 598 bytes
com/jidesoft/swing/ComboBoxSearchable.class | Bin 0 -> 3967 bytes
com/jidesoft/swing/ComponentStateSupport.class | Bin 0 -> 261 bytes
com/jidesoft/swing/ContentContainer.class | Bin 0 -> 1342 bytes
com/jidesoft/swing/Contour$Outline.class | Bin 0 -> 694 bytes
com/jidesoft/swing/Contour.class | Bin 0 -> 7865 bytes
com/jidesoft/swing/CornerScroller$1.class | Bin 0 -> 659 bytes
.../swing/CornerScroller$ScrollerIcon.class | Bin 0 -> 1561 bytes
com/jidesoft/swing/CornerScroller.class | Bin 0 -> 1202 bytes
com/jidesoft/swing/DefaultOverlayable.class | Bin 0 -> 5787 bytes
com/jidesoft/swing/DefaultSelectable.class | Bin 0 -> 1032 bytes
com/jidesoft/swing/DefaultSplitButtonModel.class | Bin 0 -> 1169 bytes
com/jidesoft/swing/DelayUndoManager$1.class | Bin 0 -> 569 bytes
com/jidesoft/swing/DelayUndoManager.class | Bin 0 -> 2545 bytes
.../DelegateAction$PassthroughDelegateAction.class | Bin 0 -> 456 bytes
com/jidesoft/swing/DelegateAction.class | Bin 0 -> 3704 bytes
.../swing/DelegateMouseInputListener.class | Bin 0 -> 838 bytes
com/jidesoft/swing/DelegateMouseListener.class | Bin 0 -> 673 bytes
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com/jidesoft/swing/DragableHandle.class | Bin 0 -> 85 bytes
com/jidesoft/swing/FastGradientPainter.class | Bin 0 -> 2589 bytes
com/jidesoft/swing/Flashable$1.class | Bin 0 -> 893 bytes
com/jidesoft/swing/Flashable$2.class | Bin 0 -> 641 bytes
com/jidesoft/swing/Flashable$FlashTimer.class | Bin 0 -> 529 bytes
com/jidesoft/swing/Flashable.class | Bin 0 -> 2540 bytes
com/jidesoft/swing/FolderChooser.class | Bin 0 -> 3621 bytes
com/jidesoft/swing/FontUtils$FontAttribute.class | Bin 0 -> 726 bytes
com/jidesoft/swing/FontUtils.class | Bin 0 -> 1013 bytes
com/jidesoft/swing/GradientCache.class | Bin 0 -> 2602 bytes
com/jidesoft/swing/GradientCacheEntry.class | Bin 0 -> 773 bytes
com/jidesoft/swing/GradientInfo.class | Bin 0 -> 1185 bytes
com/jidesoft/swing/Gripper.class | Bin 0 -> 2322 bytes
com/jidesoft/swing/HeaderBox.class | Bin 0 -> 887 bytes
com/jidesoft/swing/HeavyweightWrapper$1.class | Bin 0 -> 712 bytes
com/jidesoft/swing/HeavyweightWrapper.class | Bin 0 -> 2963 bytes
com/jidesoft/swing/IContour.class | Bin 0 -> 1119 bytes
com/jidesoft/swing/InfiniteProgressPanel.class | Bin 0 -> 3613 bytes
...llRendererPane$AccessibleCellRendererPane.class | Bin 0 -> 688 bytes
com/jidesoft/swing/JCellRendererPane.class | Bin 0 -> 2390 bytes
com/jidesoft/swing/JToolTipFactory.class | Bin 0 -> 1317 bytes
com/jidesoft/swing/JideBorderLayout.class | Bin 0 -> 5262 bytes
com/jidesoft/swing/JideBoxLayout.class | Bin 0 -> 9153 bytes
com/jidesoft/swing/JideButton.class | Bin 0 -> 4796 bytes
com/jidesoft/swing/JideComboBox.class | Bin 0 -> 945 bytes
com/jidesoft/swing/JideCursors.class | Bin 0 -> 4287 bytes
com/jidesoft/swing/JideLabel.class | Bin 0 -> 1752 bytes
com/jidesoft/swing/JideMenu$1.class | Bin 0 -> 1117 bytes
com/jidesoft/swing/JideMenu$HideTimer.class | Bin 0 -> 707 bytes
com/jidesoft/swing/JideMenu$MenuCreator.class | Bin 0 -> 280 bytes
.../swing/JideMenu$PopupMenuCustomizer.class | Bin 0 -> 235 bytes
.../swing/JideMenu$PopupMenuOriginCalculator.class | Bin 0 -> 276 bytes
com/jidesoft/swing/JideMenu.class | Bin 0 -> 6846 bytes
com/jidesoft/swing/JidePopupMenu$1.class | Bin 0 -> 186 bytes
...ePopupMenu$ToolTipSwitchPopupMenuListener.class | Bin 0 -> 1158 bytes
com/jidesoft/swing/JidePopupMenu.class | Bin 0 -> 3451 bytes
com/jidesoft/swing/JideScrollPane.class | Bin 0 -> 7110 bytes
com/jidesoft/swing/JideScrollPaneConstants.class | Bin 0 -> 576 bytes
.../swing/JideScrollPaneLayout$UIResource.class | Bin 0 -> 331 bytes
com/jidesoft/swing/JideScrollPaneLayout.class | Bin 0 -> 11456 bytes
com/jidesoft/swing/JideSplitButton.class | Bin 0 -> 6123 bytes
com/jidesoft/swing/JideSplitPane$1.class | Bin 0 -> 809 bytes
.../JideSplitPane$AccessibleJideSplitPane.class | Bin 0 -> 1145 bytes
.../swing/JideSplitPane$JideSplitPaneContour.class | Bin 0 -> 474 bytes
...SplitPane$JideSplitPaneHeavyweightWrapper.class | Bin 0 -> 453 bytes
com/jidesoft/swing/JideSplitPane.class | Bin 0 -> 14416 bytes
com/jidesoft/swing/JideSplitPaneDivider$1.class | Bin 0 -> 1458 bytes
com/jidesoft/swing/JideSplitPaneDivider$2.class | Bin 0 -> 1480 bytes
.../JideSplitPaneDivider$DragController.class | Bin 0 -> 2863 bytes
.../swing/JideSplitPaneDivider$MouseHandler.class | Bin 0 -> 1904 bytes
...ideSplitPaneDivider$OneTouchActionHandler.class | Bin 0 -> 1452 bytes
...deSplitPaneDivider$VerticalDragController.class | Bin 0 -> 2306 bytes
com/jidesoft/swing/JideSplitPaneDivider.class | Bin 0 -> 8881 bytes
com/jidesoft/swing/JideSplitPaneLayout.class | Bin 0 -> 4644 bytes
com/jidesoft/swing/JideSwingUtilities$1.class | Bin 0 -> 800 bytes
com/jidesoft/swing/JideSwingUtilities$10.class | Bin 0 -> 570 bytes
com/jidesoft/swing/JideSwingUtilities$11.class | Bin 0 -> 590 bytes
com/jidesoft/swing/JideSwingUtilities$12.class | Bin 0 -> 590 bytes
com/jidesoft/swing/JideSwingUtilities$13.class | Bin 0 -> 1656 bytes
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com/jidesoft/swing/JideSwingUtilities$19.class | Bin 0 -> 644 bytes
com/jidesoft/swing/JideSwingUtilities$2.class | Bin 0 -> 783 bytes
com/jidesoft/swing/JideSwingUtilities$20.class | Bin 0 -> 602 bytes
com/jidesoft/swing/JideSwingUtilities$3.class | Bin 0 -> 657 bytes
com/jidesoft/swing/JideSwingUtilities$4.class | Bin 0 -> 877 bytes
com/jidesoft/swing/JideSwingUtilities$5.class | Bin 0 -> 695 bytes
com/jidesoft/swing/JideSwingUtilities$6$1.class | Bin 0 -> 916 bytes
com/jidesoft/swing/JideSwingUtilities$6$2.class | Bin 0 -> 926 bytes
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com/jidesoft/swing/JideSwingUtilities$7.class | Bin 0 -> 959 bytes
com/jidesoft/swing/JideSwingUtilities$8.class | Bin 0 -> 959 bytes
com/jidesoft/swing/JideSwingUtilities$9.class | Bin 0 -> 921 bytes
.../JideSwingUtilities$ConditionHandler.class | Bin 0 -> 320 bytes
.../swing/JideSwingUtilities$GetHandler.class | Bin 0 -> 295 bytes
.../JideSwingUtilities$GetPropertyAction.class | Bin 0 -> 657 bytes
.../swing/JideSwingUtilities$Handler.class | Bin 0 -> 291 bytes
.../JideSwingUtilities$TraceDebugBorder.class | Bin 0 -> 896 bytes
...ies$viewportSynchronizationChangeListener.class | Bin 0 -> 2187 bytes
com/jidesoft/swing/JideSwingUtilities.class | Bin 0 -> 45765 bytes
com/jidesoft/swing/JideTabbedPane$1.class | Bin 0 -> 892 bytes
.../swing/JideTabbedPane$ColorProvider.class | Bin 0 -> 292 bytes
.../JideTabbedPane$GradientColorProvider.class | Bin 0 -> 331 bytes
...TabbedPane$IgnoreableSingleSelectionModel.class | Bin 0 -> 614 bytes
.../swing/JideTabbedPane$NoFocusButton.class | Bin 0 -> 4900 bytes
.../JideTabbedPane$OneNoteColorProvider.class | Bin 0 -> 758 bytes
.../JideTabbedPane$PageLastFocusTracker$1.class | Bin 0 -> 872 bytes
.../JideTabbedPane$PageLastFocusTracker.class | Bin 0 -> 1177 bytes
.../swing/JideTabbedPane$TabListCellRenderer.class | Bin 0 -> 1143 bytes
com/jidesoft/swing/JideTabbedPane.class | Bin 0 -> 22145 bytes
com/jidesoft/swing/JideTitledBorder.class | Bin 0 -> 6955 bytes
com/jidesoft/swing/JideToggleButton$1.class | Bin 0 -> 1075 bytes
.../JideToggleButton$AccessibleJToggleButton.class | Bin 0 -> 1465 bytes
.../swing/JideToggleButton$ToggleButtonModel.class | Bin 0 -> 1511 bytes
com/jidesoft/swing/JideToggleButton.class | Bin 0 -> 3020 bytes
...ToggleSplitButton$AccessibleJToggleButton.class | Bin 0 -> 1490 bytes
...eToggleSplitButton$ToggleSplitButtonModel.class | Bin 0 -> 1594 bytes
com/jidesoft/swing/JideToggleSplitButton.class | Bin 0 -> 1619 bytes
com/jidesoft/swing/LabeledTextField$1.class | Bin 0 -> 597 bytes
com/jidesoft/swing/LabeledTextField$2.class | Bin 0 -> 586 bytes
com/jidesoft/swing/LabeledTextField$3.class | Bin 0 -> 876 bytes
com/jidesoft/swing/LabeledTextField$4.class | Bin 0 -> 950 bytes
.../LabeledTextField$PopupMenuCustomizer.class | Bin 0 -> 288 bytes
com/jidesoft/swing/LabeledTextField.class | Bin 0 -> 7935 bytes
com/jidesoft/swing/LegacyTristateCheckBox$1.class | Bin 0 -> 974 bytes
com/jidesoft/swing/LegacyTristateCheckBox$2.class | Bin 0 -> 1041 bytes
.../swing/LegacyTristateCheckBox$State.class | Bin 0 -> 395 bytes
.../LegacyTristateCheckBox$TristateDecorator.class | Bin 0 -> 3226 bytes
com/jidesoft/swing/LegacyTristateCheckBox.class | Bin 0 -> 3463 bytes
com/jidesoft/swing/ListSearchable.class | Bin 0 -> 3031 bytes
com/jidesoft/swing/MarqueePane$1.class | Bin 0 -> 1870 bytes
com/jidesoft/swing/MarqueePane.class | Bin 0 -> 2633 bytes
com/jidesoft/swing/MeterProgressBar.class | Bin 0 -> 1424 bytes
com/jidesoft/swing/MouseInputListeners.class | Bin 0 -> 1114 bytes
com/jidesoft/swing/MultilineLabel$1.class | Bin 0 -> 527 bytes
com/jidesoft/swing/MultilineLabel.class | Bin 0 -> 1565 bytes
com/jidesoft/swing/MultilineToggleButton.class | Bin 0 -> 1734 bytes
com/jidesoft/swing/NullButton.class | Bin 0 -> 831 bytes
com/jidesoft/swing/NullCheckBox.class | Bin 0 -> 1070 bytes
com/jidesoft/swing/NullJideButton.class | Bin 0 -> 845 bytes
com/jidesoft/swing/NullLabel.class | Bin 0 -> 903 bytes
com/jidesoft/swing/NullPanel.class | Bin 0 -> 735 bytes
com/jidesoft/swing/NullRadioButton.class | Bin 0 -> 1076 bytes
com/jidesoft/swing/NullTristateCheckBox.class | Bin 0 -> 715 bytes
com/jidesoft/swing/OverlayCheckBox.class | Bin 0 -> 838 bytes
com/jidesoft/swing/OverlayComboBox.class | Bin 0 -> 585 bytes
com/jidesoft/swing/OverlayPasswordField.class | Bin 0 -> 619 bytes
com/jidesoft/swing/OverlayRadioButton.class | Bin 0 -> 844 bytes
com/jidesoft/swing/OverlayTextArea.class | Bin 0 -> 691 bytes
com/jidesoft/swing/OverlayTextField.class | Bin 0 -> 611 bytes
com/jidesoft/swing/Overlayable.class | Bin 0 -> 699 bytes
com/jidesoft/swing/OverlayableIconsFactory.class | Bin 0 -> 799 bytes
com/jidesoft/swing/OverlayableUtils.class | Bin 0 -> 1447 bytes
com/jidesoft/swing/PaintPanel.class | Bin 0 -> 2172 bytes
com/jidesoft/swing/PartialEtchedBorder.class | Bin 0 -> 2075 bytes
com/jidesoft/swing/PartialGradientLineBorder.class | Bin 0 -> 1848 bytes
com/jidesoft/swing/PartialLineBorder.class | Bin 0 -> 2072 bytes
com/jidesoft/swing/PartialSide.class | Bin 0 -> 309 bytes
com/jidesoft/swing/PopupWindow$1.class | Bin 0 -> 653 bytes
com/jidesoft/swing/PopupWindow$2.class | Bin 0 -> 596 bytes
com/jidesoft/swing/PopupWindow$3.class | Bin 0 -> 587 bytes
com/jidesoft/swing/PopupWindow$4.class | Bin 0 -> 674 bytes
com/jidesoft/swing/PopupWindow$5.class | Bin 0 -> 571 bytes
com/jidesoft/swing/PopupWindow$6.class | Bin 0 -> 483 bytes
com/jidesoft/swing/PopupWindow.class | Bin 0 -> 6388 bytes
com/jidesoft/swing/Prioritized.class | Bin 0 -> 110 bytes
com/jidesoft/swing/RangeSlider.class | Bin 0 -> 2720 bytes
com/jidesoft/swing/Resizable$ResizeCorner.class | Bin 0 -> 1595 bytes
com/jidesoft/swing/Resizable.class | Bin 0 -> 3137 bytes
com/jidesoft/swing/ResizableDialog$1$1.class | Bin 0 -> 1203 bytes
com/jidesoft/swing/ResizableDialog$1.class | Bin 0 -> 2208 bytes
com/jidesoft/swing/ResizableDialog$2.class | Bin 0 -> 732 bytes
com/jidesoft/swing/ResizableDialog.class | Bin 0 -> 2588 bytes
com/jidesoft/swing/ResizableFrame$1$1.class | Bin 0 -> 1197 bytes
com/jidesoft/swing/ResizableFrame$1.class | Bin 0 -> 2202 bytes
com/jidesoft/swing/ResizableFrame$2.class | Bin 0 -> 695 bytes
com/jidesoft/swing/ResizableFrame.class | Bin 0 -> 1735 bytes
.../swing/ResizableMouseInputAdapter.class | Bin 0 -> 8016 bytes
com/jidesoft/swing/ResizablePanel.class | Bin 0 -> 1069 bytes
com/jidesoft/swing/ResizableSupport.class | Bin 0 -> 250 bytes
com/jidesoft/swing/ResizableWindow$1$1.class | Bin 0 -> 1164 bytes
com/jidesoft/swing/ResizableWindow$1.class | Bin 0 -> 2208 bytes
com/jidesoft/swing/ResizableWindow$2.class | Bin 0 -> 732 bytes
com/jidesoft/swing/ResizableWindow.class | Bin 0 -> 1829 bytes
com/jidesoft/swing/Resource.class | Bin 0 -> 614 bytes
com/jidesoft/swing/ScrollPaneOverview$1.class | Bin 0 -> 1534 bytes
com/jidesoft/swing/ScrollPaneOverview.class | Bin 0 -> 5695 bytes
com/jidesoft/swing/Searchable$1$1.class | Bin 0 -> 720 bytes
com/jidesoft/swing/Searchable$1.class | Bin 0 -> 1161 bytes
com/jidesoft/swing/Searchable$2.class | Bin 0 -> 1042 bytes
com/jidesoft/swing/Searchable$3.class | Bin 0 -> 807 bytes
com/jidesoft/swing/Searchable$4.class | Bin 0 -> 724 bytes
com/jidesoft/swing/Searchable$5.class | Bin 0 -> 863 bytes
.../swing/Searchable$DefaultSearchPopup$1$1.class | Bin 0 -> 583 bytes
.../swing/Searchable$DefaultSearchPopup$1.class | Bin 0 -> 2383 bytes
.../swing/Searchable$DefaultSearchPopup.class | Bin 0 -> 4333 bytes
com/jidesoft/swing/Searchable$SearchField.class | Bin 0 -> 1364 bytes
com/jidesoft/swing/Searchable$SearchPopup.class | Bin 0 -> 1815 bytes
com/jidesoft/swing/Searchable.class | Bin 0 -> 16452 bytes
com/jidesoft/swing/SearchableBar$1.class | Bin 0 -> 928 bytes
com/jidesoft/swing/SearchableBar$10.class | Bin 0 -> 825 bytes
com/jidesoft/swing/SearchableBar$11.class | Bin 0 -> 863 bytes
com/jidesoft/swing/SearchableBar$12.class | Bin 0 -> 895 bytes
com/jidesoft/swing/SearchableBar$2.class | Bin 0 -> 752 bytes
com/jidesoft/swing/SearchableBar$3.class | Bin 0 -> 1611 bytes
com/jidesoft/swing/SearchableBar$4.class | Bin 0 -> 1609 bytes
com/jidesoft/swing/SearchableBar$5.class | Bin 0 -> 591 bytes
com/jidesoft/swing/SearchableBar$6.class | Bin 0 -> 618 bytes
com/jidesoft/swing/SearchableBar$7.class | Bin 0 -> 635 bytes
com/jidesoft/swing/SearchableBar$8$1.class | Bin 0 -> 657 bytes
com/jidesoft/swing/SearchableBar$8.class | Bin 0 -> 1265 bytes
com/jidesoft/swing/SearchableBar$9.class | Bin 0 -> 603 bytes
com/jidesoft/swing/SearchableBar$Installer.class | Bin 0 -> 264 bytes
com/jidesoft/swing/SearchableBar.class | Bin 0 -> 13230 bytes
.../swing/SearchableBarIconsFactory$Buttons.class | Bin 0 -> 1134 bytes
com/jidesoft/swing/SearchableBarIconsFactory.class | Bin 0 -> 582 bytes
com/jidesoft/swing/SearchableProvider.class | Bin 0 -> 222 bytes
com/jidesoft/swing/SearchableUtils.class | Bin 0 -> 1231 bytes
com/jidesoft/swing/SelectAllUtils$1$1.class | Bin 0 -> 1197 bytes
com/jidesoft/swing/SelectAllUtils$1.class | Bin 0 -> 1211 bytes
com/jidesoft/swing/SelectAllUtils$2.class | Bin 0 -> 995 bytes
com/jidesoft/swing/SelectAllUtils$3.class | Bin 0 -> 747 bytes
com/jidesoft/swing/SelectAllUtils.class | Bin 0 -> 1390 bytes
com/jidesoft/swing/Selectable.class | Bin 0 -> 209 bytes
com/jidesoft/swing/SelectionModelGroup.class | Bin 0 -> 1733 bytes
com/jidesoft/swing/ShadowFactory.class | Bin 0 -> 4528 bytes
.../swing/SidePane$AccessibleSidePane.class | Bin 0 -> 806 bytes
com/jidesoft/swing/SidePane.class | Bin 0 -> 3177 bytes
com/jidesoft/swing/SidePaneGroup.class | Bin 0 -> 3016 bytes
com/jidesoft/swing/SidePaneItem.class | Bin 0 -> 2133 bytes
.../swing/SimpleScrollPane$ScrollButton.class | Bin 0 -> 2493 bytes
com/jidesoft/swing/SimpleScrollPane.class | Bin 0 -> 7194 bytes
.../swing/SimpleScrollPaneLayout$UIResource.class | Bin 0 -> 271 bytes
com/jidesoft/swing/SimpleScrollPaneLayout.class | Bin 0 -> 5962 bytes
com/jidesoft/swing/SoftHashMap$1.class | Bin 0 -> 1148 bytes
com/jidesoft/swing/SoftHashMap.class | Bin 0 -> 2377 bytes
com/jidesoft/swing/SplitButtonGroup.class | Bin 0 -> 1210 bytes
com/jidesoft/swing/SplitButtonModel.class | Bin 0 -> 294 bytes
com/jidesoft/swing/Sticky$1.class | Bin 0 -> 172 bytes
.../swing/Sticky$StrickyMouseMotionListener.class | Bin 0 -> 1184 bytes
com/jidesoft/swing/Sticky.class | Bin 0 -> 2814 bytes
com/jidesoft/swing/StringConverter.class | Bin 0 -> 145 bytes
com/jidesoft/swing/StyleRange.class | Bin 0 -> 3449 bytes
com/jidesoft/swing/StyledLabel.class | Bin 0 -> 2847 bytes
com/jidesoft/swing/StyledLabelBuilder$1.class | Bin 0 -> 196 bytes
.../StyledLabelBuilder$ParsedStyleResult.class | Bin 0 -> 669 bytes
com/jidesoft/swing/StyledLabelBuilder.class | Bin 0 -> 10362 bytes
com/jidesoft/swing/TabColorProvider.class | Bin 0 -> 162 bytes
com/jidesoft/swing/TabEditingEvent.class | Bin 0 -> 740 bytes
com/jidesoft/swing/TabEditingListener.class | Bin 0 -> 238 bytes
com/jidesoft/swing/TabEditingValidator.class | Bin 0 -> 218 bytes
com/jidesoft/swing/TableSearchable.class | Bin 0 -> 4641 bytes
com/jidesoft/swing/TextComponentSearchable$1.class | Bin 0 -> 558 bytes
com/jidesoft/swing/TextComponentSearchable$2.class | Bin 0 -> 906 bytes
.../TextComponentSearchable$HighlighCache.class | Bin 0 -> 1084 bytes
com/jidesoft/swing/TextComponentSearchable.class | Bin 0 -> 8044 bytes
com/jidesoft/swing/TitledSeparator.class | Bin 0 -> 4549 bytes
com/jidesoft/swing/TopLevelMenuContainer.class | Bin 0 -> 118 bytes
com/jidesoft/swing/TreeSearchable.class | Bin 0 -> 3946 bytes
com/jidesoft/swing/TristateButtonModel.class | Bin 0 -> 1736 bytes
com/jidesoft/swing/TristateCheckBox.class | Bin 0 -> 2159 bytes
com/jidesoft/swing/TristateCheckBoxIcon.class | Bin 0 -> 3957 bytes
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com/jidesoft/swing/event/SearchableEvent.class | Bin 0 -> 2131 bytes
com/jidesoft/swing/event/SearchableListener.class | Bin 0 -> 205 bytes
com/jidesoft/swing/event/SidePaneEvent.class | Bin 0 -> 733 bytes
com/jidesoft/swing/event/SidePaneListener.class | Bin 0 -> 232 bytes
com/jidesoft/swing/event/package-info.class | Bin 0 -> 130 bytes
com/jidesoft/swing/icons/close.png | Bin 0 -> 3439 bytes
com/jidesoft/swing/icons/closeR.png | Bin 0 -> 3371 bytes
com/jidesoft/swing/icons/error.png | Bin 0 -> 3343 bytes
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com/jidesoft/swing/icons/next.png | Bin 0 -> 3619 bytes
com/jidesoft/swing/icons/nextD.png | Bin 0 -> 3568 bytes
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com/jidesoft/swing/icons/overlay_attention.png | Bin 0 -> 3243 bytes
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com/jidesoft/swing/icons/overlay_error.png | Bin 0 -> 3262 bytes
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com/jidesoft/swing/package-info.class | Bin 0 -> 124 bytes
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com/jidesoft/utils/AbstractWildcardSupport.class | Bin 0 -> 973 bytes
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com/jidesoft/utils/BasicTransferable.class | Bin 0 -> 3343 bytes
com/jidesoft/utils/BigDecimalMathUtils.class | Bin 0 -> 3777 bytes
com/jidesoft/utils/CachedArrayList.class | Bin 0 -> 3328 bytes
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com/jidesoft/utils/ColorUtils.class | Bin 0 -> 2202 bytes
com/jidesoft/utils/DateUtils.class | Bin 0 -> 3115 bytes
com/jidesoft/utils/DefaultWildcardSupport.class | Bin 0 -> 415 bytes
com/jidesoft/utils/FontFilesResource.class | Bin 0 -> 614 bytes
com/jidesoft/utils/HtmlUtils.class | Bin 0 -> 997 bytes
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com/jidesoft/utils/JideFocusTracker.class | Bin 0 -> 2032 bytes
com/jidesoft/utils/LoggerUtils$1.class | Bin 0 -> 952 bytes
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com/jidesoft/utils/MathUtils.class | Bin 0 -> 1352 bytes
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com/jidesoft/utils/PersistenceUtilsCallback.class | Bin 0 -> 256 bytes
com/jidesoft/utils/PortingUtils$1.class | Bin 0 -> 1752 bytes
com/jidesoft/utils/PortingUtils.class | Bin 0 -> 7682 bytes
com/jidesoft/utils/ProductNames.class | Bin 0 -> 2382 bytes
com/jidesoft/utils/ReflectionUtils.class | Bin 0 -> 3090 bytes
com/jidesoft/utils/ResourceProvider.class | Bin 0 -> 156 bytes
com/jidesoft/utils/SecurityUtils$FontStruct.class | Bin 0 -> 296 bytes
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com/jidesoft/utils/SortedList$1.class | Bin 0 -> 634 bytes
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com/jidesoft/utils/StringUtils.class | Bin 0 -> 1136 bytes
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com/jidesoft/utils/SwingWorker$StateValue.class | Bin 0 -> 996 bytes
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com/jidesoft/utils/SwingWorker.class | Bin 0 -> 5335 bytes
com/jidesoft/utils/SystemInfo$JavaVersion.class | Bin 0 -> 2163 bytes
com/jidesoft/utils/SystemInfo.class | Bin 0 -> 4679 bytes
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com/jidesoft/utils/TimeUtils.class | Bin 0 -> 3262 bytes
com/jidesoft/utils/TypeUtils.class | Bin 0 -> 1933 bytes
com/jidesoft/utils/WildcardSupport.class | Bin 0 -> 251 bytes
com/jidesoft/utils/package-info.class | Bin 0 -> 124 bytes
com/jidesoft/validation/RowValidationObject.class | Bin 0 -> 865 bytes
com/jidesoft/validation/RowValidationResult.class | Bin 0 -> 1034 bytes
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com/jidesoft/validation/ValidationResult$1.class | Bin 0 -> 352 bytes
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com/jidesoft/validation/Validator.class | Bin 0 -> 226 bytes
com/jidesoft/validation/package-info.class | Bin 0 -> 129 bytes
com/keypoint/PngEncoder.class | Bin 0 -> 8583 bytes
com/mysql/jdbc/AssertionFailedException.class | Bin 0 -> 914 bytes
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com/mysql/jdbc/ByteArrayBuffer.class | Bin 0 -> 9324 bytes
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com/mysql/jdbc/ChannelBuffer.class | Bin 0 -> 10125 bytes
com/mysql/jdbc/CharsetMapping.class | Bin 0 -> 9828 bytes
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com/mysql/jdbc/Connection$1.class | Bin 0 -> 1135 bytes
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com/mysql/jdbc/Connection$UltraDevWorkAround.class | Bin 0 -> 20387 bytes
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com/mysql/jdbc/DocsConnectionPropsHelper.class | Bin 0 -> 718 bytes
com/mysql/jdbc/Driver.class | Bin 0 -> 692 bytes
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com/mysql/jdbc/EscapeProcessorResult.class | Bin 0 -> 462 bytes
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com/mysql/jdbc/LicenseConfiguration.class | Bin 0 -> 502 bytes
com/mysql/jdbc/LocalizedErrorMessages.properties | 404 ++
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com/mysql/jdbc/PacketTooBigException.class | Bin 0 -> 930 bytes
com/mysql/jdbc/PreparedStatement$BatchParams.class | Bin 0 -> 1224 bytes
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com/mysql/jdbc/PreparedStatement$ParseInfo.class | Bin 0 -> 4216 bytes
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com/mysql/jdbc/ReplicationConnection.class | Bin 0 -> 7637 bytes
com/mysql/jdbc/ReplicationDriver.class | Bin 0 -> 731 bytes
com/mysql/jdbc/ResultSet.class | Bin 0 -> 80385 bytes
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com/mysql/jdbc/SQLError.class | Bin 0 -> 13736 bytes
com/mysql/jdbc/Security.class | Bin 0 -> 4076 bytes
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com/mysql/jdbc/SingleByteCharsetConverter.class | Bin 0 -> 3607 bytes
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com/mysql/jdbc/StringUtils.class | Bin 0 -> 17334 bytes
com/mysql/jdbc/TimeUtil.class | Bin 0 -> 33179 bytes
com/mysql/jdbc/UpdatableResultSet.class | Bin 0 -> 25496 bytes
com/mysql/jdbc/Util$RandStructcture.class | Bin 0 -> 565 bytes
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com/mysql/jdbc/VersionedStringProperty.class | Bin 0 -> 2174 bytes
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com/mysql/jdbc/configs/3-0-Compat.properties | 16 +
com/mysql/jdbc/configs/clusterBase.properties | 4 +
com/mysql/jdbc/configs/fullDebug.properties | 6 +
com/mysql/jdbc/configs/maxPerformance.properties | 25 +
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com/mysql/jdbc/jdbc2/optional/WrapperBase.class | Bin 0 -> 897 bytes
com/mysql/jdbc/log/CommonsLogger.class | Bin 0 -> 2725 bytes
com/mysql/jdbc/log/Jdk14Logger.class | Bin 0 -> 4520 bytes
com/mysql/jdbc/log/Log.class | Bin 0 -> 489 bytes
com/mysql/jdbc/log/Log4JLogger.class | Bin 0 -> 2752 bytes
com/mysql/jdbc/log/LogFactory.class | Bin 0 -> 3090 bytes
com/mysql/jdbc/log/LogUtils.class | Bin 0 -> 3161 bytes
com/mysql/jdbc/log/NullLogger.class | Bin 0 -> 1908 bytes
com/mysql/jdbc/log/StandardLogger.class | Bin 0 -> 4161 bytes
com/mysql/jdbc/profiler/ProfileEventSink.class | Bin 0 -> 1835 bytes
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com/mysql/jdbc/util/BaseBugReport.class | Bin 0 -> 2200 bytes
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com/mysql/jdbc/util/LRUCache.class | Bin 0 -> 636 bytes
com/mysql/jdbc/util/PropertiesDocGenerator.class | Bin 0 -> 721 bytes
com/mysql/jdbc/util/ReadAheadInputStream.class | Bin 0 -> 4549 bytes
com/mysql/jdbc/util/ResultSetUtil.class | Bin 0 -> 1718 bytes
com/mysql/jdbc/util/ServerController.class | Bin 0 -> 4914 bytes
com/mysql/jdbc/util/TimezoneDump.class | Bin 0 -> 1825 bytes
com/mysql/jdbc/util/VersionFSHierarchyMaker.class | Bin 0 -> 3699 bytes
copyright.txt | 18 +
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.../datastrutures/IntervalTree$FwdIterator.class | Bin 0 -> 2570 bytes
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edu/mit/broad/prodinfo/genomicplot/Feature.class | Bin 0 -> 196 bytes
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edu/mit/broad/prodinfo/sequence/WindowSlider.class | Bin 0 -> 2017 bytes
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jargs/gnu/CmdLineParser$OptionException.class | Bin 0 -> 453 bytes
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javax/xml/XMLConstants.class | Bin 0 -> 990 bytes
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javax/xml/datatype/DatatypeConstants$Field.class | Bin 0 -> 636 bytes
javax/xml/datatype/DatatypeConstants.class | Bin 0 -> 2170 bytes
javax/xml/datatype/DatatypeFactory.class | Bin 0 -> 3984 bytes
javax/xml/datatype/Duration.class | Bin 0 -> 4426 bytes
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javax/xml/datatype/FactoryFinder.class | Bin 0 -> 4870 bytes
javax/xml/datatype/SecuritySupport$1.class | Bin 0 -> 467 bytes
javax/xml/datatype/SecuritySupport$2.class | Bin 0 -> 474 bytes
javax/xml/datatype/SecuritySupport$3.class | Bin 0 -> 485 bytes
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javax/xml/datatype/SecuritySupport.class | Bin 0 -> 1585 bytes
javax/xml/datatype/XMLGregorianCalendar.class | Bin 0 -> 2223 bytes
javax/xml/namespace/NamespaceContext.class | Bin 0 -> 240 bytes
javax/xml/namespace/QName$1.class | Bin 0 -> 428 bytes
javax/xml/namespace/QName.class | Bin 0 -> 2827 bytes
javax/xml/parsers/DocumentBuilder.class | Bin 0 -> 2488 bytes
javax/xml/parsers/DocumentBuilderFactory.class | Bin 0 -> 3115 bytes
javax/xml/parsers/FactoryConfigurationError.class | Bin 0 -> 652 bytes
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javax/xml/parsers/FactoryFinder.class | Bin 0 -> 4334 bytes
javax/xml/parsers/FilePathToURI.class | Bin 0 -> 1657 bytes
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javax/xml/parsers/SAXParser.class | Bin 0 -> 3896 bytes
javax/xml/parsers/SAXParserFactory.class | Bin 0 -> 2406 bytes
javax/xml/parsers/SecuritySupport$1.class | Bin 0 -> 466 bytes
javax/xml/parsers/SecuritySupport$2.class | Bin 0 -> 473 bytes
javax/xml/parsers/SecuritySupport$3.class | Bin 0 -> 484 bytes
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javax/xml/transform/OutputKeys.class | Bin 0 -> 666 bytes
javax/xml/transform/Result.class | Bin 0 -> 392 bytes
javax/xml/transform/SecuritySupport$1.class | Bin 0 -> 468 bytes
javax/xml/transform/SecuritySupport$2.class | Bin 0 -> 475 bytes
javax/xml/transform/SecuritySupport$3.class | Bin 0 -> 486 bytes
javax/xml/transform/SecuritySupport$4.class | Bin 0 -> 636 bytes
javax/xml/transform/SecuritySupport$5.class | Bin 0 -> 508 bytes
javax/xml/transform/SecuritySupport.class | Bin 0 -> 1591 bytes
javax/xml/transform/Source.class | Bin 0 -> 169 bytes
javax/xml/transform/SourceLocator.class | Bin 0 -> 208 bytes
javax/xml/transform/Templates.class | Bin 0 -> 283 bytes
javax/xml/transform/Transformer.class | Bin 0 -> 1723 bytes
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javax/xml/transform/URIResolver.class | Bin 0 -> 239 bytes
javax/xml/transform/dom/DOMLocator.class | Bin 0 -> 179 bytes
javax/xml/transform/dom/DOMResult.class | Bin 0 -> 1736 bytes
javax/xml/transform/dom/DOMSource.class | Bin 0 -> 781 bytes
javax/xml/transform/sax/SAXResult.class | Bin 0 -> 971 bytes
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javax/xml/transform/stream/FilePathToURI.class | Bin 0 -> 1666 bytes
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javax/xml/transform/stream/StreamSource.class | Bin 0 -> 1547 bytes
javax/xml/validation/Schema.class | Bin 0 -> 276 bytes
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javax/xml/validation/SchemaFactoryFinder$2.class | Bin 0 -> 736 bytes
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javax/xml/validation/SchemaFactoryLoader.class | Bin 0 -> 235 bytes
javax/xml/validation/SecuritySupport$1.class | Bin 0 -> 469 bytes
javax/xml/validation/SecuritySupport$2.class | Bin 0 -> 476 bytes
javax/xml/validation/SecuritySupport$3.class | Bin 0 -> 487 bytes
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javax/xml/validation/SecuritySupport$8.class | Bin 0 -> 509 bytes
javax/xml/validation/SecuritySupport.class | Bin 0 -> 2265 bytes
javax/xml/validation/TypeInfoProvider.class | Bin 0 -> 320 bytes
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org/apache/batik/css/dom/CSSOMSVGColor.class | Bin 0 -> 8358 bytes
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org/apache/batik/css/engine/CSSContext.class | Bin 0 -> 851 bytes
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org/apache/batik/css/engine/FontFaceRule.class | Bin 0 -> 1446 bytes
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org/apache/batik/dom/svg/SVGOMAElement.class | Bin 0 -> 2686 bytes
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org/apache/batik/dom/svg/SVGOMAnimatedNumber.class | Bin 0 -> 3725 bytes
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org/apache/batik/dom/svg/SVGOMAnimatedPoints.class | Bin 0 -> 4068 bytes
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org/apache/batik/dom/svg/SVGOMAnimatedString.class | Bin 0 -> 2597 bytes
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org/apache/batik/dom/svg/SVGOMCircleElement.class | Bin 0 -> 2336 bytes
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org/apache/batik/dom/svg/SVGOMEllipseElement.class | Bin 0 -> 2478 bytes
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org/apache/batik/dom/svg/SVGOMFEBlendElement.class | Bin 0 -> 2855 bytes
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org/apache/batik/dom/svg/SVGOMMPathElement.class | Bin 0 -> 2739 bytes
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org/apache/batik/dom/svg/SVGPathSegConstants.class | Bin 0 -> 1565 bytes
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org/apache/batik/dom/svg/SVGPathSupport.class | Bin 0 -> 1335 bytes
.../batik/dom/svg/SVGPointShapeElement.class | Bin 0 -> 2154 bytes
org/apache/batik/dom/svg/SVGSVGContext.class | Bin 0 -> 697 bytes
.../batik/dom/svg/SVGStylableElement$1.class | Bin 0 -> 1954 bytes
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.../batik/dom/svg/SVGStylableElement$3.class | Bin 0 -> 1988 bytes
...GStylableElement$OverrideStyleDeclaration.class | Bin 0 -> 2027 bytes
...leElement$PresentationAttributeColorValue.class | Bin 0 -> 3069 bytes
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.../svg/SVGStylableElement$StyleDeclaration.class | Bin 0 -> 3824 bytes
org/apache/batik/dom/svg/SVGStylableElement.class | Bin 0 -> 8604 bytes
.../svg/SVGStyleSheetProcessingInstruction.class | Bin 0 -> 3023 bytes
org/apache/batik/dom/svg/SVGTestsSupport.class | Bin 0 -> 1128 bytes
org/apache/batik/dom/svg/SVGTextContent.class | Bin 0 -> 502 bytes
.../batik/dom/svg/SVGTextContentSupport$1.class | Bin 0 -> 2000 bytes
.../batik/dom/svg/SVGTextContentSupport$2.class | Bin 0 -> 1221 bytes
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.../svg/SVGTextContentSupport$SVGTextPoint.class | Bin 0 -> 1038 bytes
.../batik/dom/svg/SVGTextContentSupport.class | Bin 0 -> 3950 bytes
.../dom/svg/SVGURIReferenceGraphicsElement.class | Bin 0 -> 1860 bytes
.../SVGURIReferenceTextPositioningElement.class | Bin 0 -> 1929 bytes
.../batik/dom/svg/SVGZoomAndPanSupport.class | Bin 0 -> 1363 bytes
org/apache/batik/dom/svg/TraitAccess.class | Bin 0 -> 128 bytes
org/apache/batik/dom/svg/TraitInformation.class | Bin 0 -> 1076 bytes
.../batik/dom/svg/resources/Messages.properties | 99 +
.../dom/svg/resources/UserAgentStyleSheet.css | 6 +
.../batik/dom/svg/resources/dtdids.properties | 68 +
.../batik/dom/svg/resources/svg-animation.mod | 278 +
.../dom/svg/resources/svg-animevents-attrib.mod | 49 +
.../batik/dom/svg/resources/svg-basic-clip.mod | 101 +
.../batik/dom/svg/resources/svg-basic-filter.mod | 554 ++
.../batik/dom/svg/resources/svg-basic-font.mod | 328 ++
.../svg/resources/svg-basic-graphics-attrib.mod | 43 +
.../dom/svg/resources/svg-basic-structure.mod | 309 ++
.../batik/dom/svg/resources/svg-basic-text.mod | 194 +
org/apache/batik/dom/svg/resources/svg-clip.mod | 101 +
.../batik/dom/svg/resources/svg-conditional.mod | 133 +
.../dom/svg/resources/svg-container-attrib.mod | 37 +
.../batik/dom/svg/resources/svg-core-attrib.mod | 50 +
org/apache/batik/dom/svg/resources/svg-cursor.mod | 78 +
.../batik/dom/svg/resources/svg-datatypes.mod | 87 +
.../dom/svg/resources/svg-docevents-attrib.mod | 59 +
.../batik/dom/svg/resources/svg-extensibility.mod | 115 +
.../dom/svg/resources/svg-extresources-attrib.mod | 34 +
org/apache/batik/dom/svg/resources/svg-filter.mod | 807 +++
org/apache/batik/dom/svg/resources/svg-font.mod | 378 ++
.../batik/dom/svg/resources/svg-framework.mod | 51 +
.../batik/dom/svg/resources/svg-gradient.mod | 150 +
.../dom/svg/resources/svg-graphevents-attrib.mod | 80 +
.../dom/svg/resources/svg-graphics-attrib.mod | 69 +
.../batik/dom/svg/resources/svg-hyperlink.mod | 123 +
org/apache/batik/dom/svg/resources/svg-image.mod | 93 +
org/apache/batik/dom/svg/resources/svg-marker.mod | 135 +
org/apache/batik/dom/svg/resources/svg-mask.mod | 133 +
.../batik/dom/svg/resources/svg-opacity-attrib.mod | 44 +
.../batik/dom/svg/resources/svg-paint-attrib.mod | 113 +
org/apache/batik/dom/svg/resources/svg-pattern.mod | 127 +
org/apache/batik/dom/svg/resources/svg-profile.mod | 73 +
org/apache/batik/dom/svg/resources/svg-qname.mod | 257 +
org/apache/batik/dom/svg/resources/svg-script.mod | 63 +
org/apache/batik/dom/svg/resources/svg-shape.mod | 319 ++
.../batik/dom/svg/resources/svg-structure.mod | 341 ++
org/apache/batik/dom/svg/resources/svg-style.mod | 81 +
org/apache/batik/dom/svg/resources/svg-text.mod | 428 ++
org/apache/batik/dom/svg/resources/svg-view.mod | 64 +
.../dom/svg/resources/svg-viewport-attrib.mod | 42 +
.../batik/dom/svg/resources/svg-xlink-attrib.mod | 80 +
org/apache/batik/dom/svg/resources/svg10.dtd | 1539 ++++++
.../batik/dom/svg/resources/svg11-attribs.mod | 186 +
.../dom/svg/resources/svg11-basic-attribs.mod | 174 +
.../batik/dom/svg/resources/svg11-basic-flat.dtd | 5329 ++++++++++++++++++
.../batik/dom/svg/resources/svg11-basic-model.mod | 191 +
org/apache/batik/dom/svg/resources/svg11-basic.dtd | 317 ++
org/apache/batik/dom/svg/resources/svg11-flat.dtd | 5788 ++++++++++++++++++++
org/apache/batik/dom/svg/resources/svg11-model.mod | 197 +
.../batik/dom/svg/resources/svg11-tiny-attribs.mod | 62 +
.../batik/dom/svg/resources/svg11-tiny-flat.dtd | 3449 ++++++++++++
.../batik/dom/svg/resources/svg11-tiny-model.mod | 139 +
org/apache/batik/dom/svg/resources/svg11-tiny.dtd | 245 +
org/apache/batik/dom/svg/resources/svg11.dtd | 333 ++
org/apache/batik/dom/svg/resources/svg12-flat.dtd | 5788 ++++++++++++++++++++
org/apache/batik/dom/svg12/BindableElement.class | Bin 0 -> 1871 bytes
org/apache/batik/dom/svg12/Global.class | Bin 0 -> 120 bytes
.../batik/dom/svg12/SVG12DOMImplementation$1.class | Bin 0 -> 862 bytes
.../batik/dom/svg12/SVG12DOMImplementation$2.class | Bin 0 -> 867 bytes
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...lementation$FlowRegionBreakElementFactory.class | Bin 0 -> 1078 bytes
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...mentation$FlowRegionExcludeElementFactory.class | Bin 0 -> 1086 bytes
...2DOMImplementation$FlowRootElementFactory.class | Bin 0 -> 1050 bytes
...2DOMImplementation$FlowSpanElementFactory.class | Bin 0 -> 1050 bytes
...12DOMImplementation$HandlerElementFactory.class | Bin 0 -> 1046 bytes
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...OMImplementation$SolidColorElementFactory.class | Bin 0 -> 1058 bytes
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...MImplementation$SubImageRefElementFactory.class | Bin 0 -> 1058 bytes
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...mplementation$XBLDefinitionElementFactory.class | Bin 0 -> 1063 bytes
...lementation$XBLHandlerGroupElementFactory.class | Bin 0 -> 1071 bytes
...DOMImplementation$XBLImportElementFactory.class | Bin 0 -> 1047 bytes
...mplementation$XBLShadowTreeElementFactory.class | Bin 0 -> 1063 bytes
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...G12DOMImplementation$XBLXBLElementFactory.class | Bin 0 -> 1035 bytes
.../batik/dom/svg12/SVG12DOMImplementation.class | Bin 0 -> 9942 bytes
org/apache/batik/dom/svg12/SVG12OMDocument.class | Bin 0 -> 3600 bytes
org/apache/batik/dom/svg12/SVGGlobal.class | Bin 0 -> 268 bytes
.../batik/dom/svg12/SVGOMFlowDivElement.class | Bin 0 -> 869 bytes
.../batik/dom/svg12/SVGOMFlowLineElement.class | Bin 0 -> 832 bytes
.../batik/dom/svg12/SVGOMFlowParaElement.class | Bin 0 -> 832 bytes
.../dom/svg12/SVGOMFlowRegionBreakElement.class | Bin 0 -> 860 bytes
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.../dom/svg12/SVGOMFlowRegionExcludeElement.class | Bin 0 -> 859 bytes
.../batik/dom/svg12/SVGOMFlowRootElement.class | Bin 0 -> 823 bytes
.../batik/dom/svg12/SVGOMFlowSpanElement.class | Bin 0 -> 832 bytes
.../batik/dom/svg12/SVGOMHandlerElement.class | Bin 0 -> 813 bytes
.../batik/dom/svg12/SVGOMMultiImageElement.class | Bin 0 -> 831 bytes
.../batik/dom/svg12/SVGOMSolidColorElement.class | Bin 0 -> 831 bytes
.../batik/dom/svg12/SVGOMSubImageElement.class | Bin 0 -> 823 bytes
.../batik/dom/svg12/SVGOMSubImageRefElement.class | Bin 0 -> 835 bytes
org/apache/batik/dom/svg12/SVGOMWheelEvent.class | Bin 0 -> 1105 bytes
org/apache/batik/dom/svg12/XBLEventSupport.class | Bin 0 -> 9685 bytes
.../batik/dom/svg12/XBLOMContentElement.class | Bin 0 -> 815 bytes
.../batik/dom/svg12/XBLOMDefinitionElement.class | Bin 0 -> 1686 bytes
org/apache/batik/dom/svg12/XBLOMElement.class | Bin 0 -> 2607 bytes
.../batik/dom/svg12/XBLOMHandlerGroupElement.class | Bin 0 -> 835 bytes
.../batik/dom/svg12/XBLOMImportElement.class | Bin 0 -> 811 bytes
.../batik/dom/svg12/XBLOMShadowTreeElement.class | Bin 0 -> 2095 bytes
.../batik/dom/svg12/XBLOMShadowTreeEvent.class | Bin 0 -> 1305 bytes
.../batik/dom/svg12/XBLOMTemplateElement.class | Bin 0 -> 819 bytes
org/apache/batik/dom/svg12/XBLOMXBLElement.class | Bin 0 -> 799 bytes
.../batik/dom/traversal/DOMNodeIterator.class | Bin 0 -> 3712 bytes
org/apache/batik/dom/traversal/DOMTreeWalker.class | Bin 0 -> 4275 bytes
.../batik/dom/traversal/TraversalSupport.class | Bin 0 -> 2358 bytes
.../dom/util/CSSStyleDeclarationFactory.class | Bin 0 -> 237 bytes
org/apache/batik/dom/util/DOMUtilities.class | Bin 0 -> 12867 bytes
.../batik/dom/util/DOMUtilitiesSupport.class | Bin 0 -> 954 bytes
.../batik/dom/util/DocumentDescriptor$Entry.class | Bin 0 -> 1220 bytes
org/apache/batik/dom/util/DocumentDescriptor.class | Bin 0 -> 2843 bytes
org/apache/batik/dom/util/DocumentFactory.class | Bin 0 -> 791 bytes
org/apache/batik/dom/util/HashTable$Entry.class | Bin 0 -> 716 bytes
org/apache/batik/dom/util/HashTable.class | Bin 0 -> 3337 bytes
.../batik/dom/util/HashTableStack$Link.class | Bin 0 -> 766 bytes
org/apache/batik/dom/util/HashTableStack.class | Bin 0 -> 1555 bytes
org/apache/batik/dom/util/IntTable$Entry.class | Bin 0 -> 694 bytes
org/apache/batik/dom/util/IntTable.class | Bin 0 -> 3548 bytes
org/apache/batik/dom/util/ListNodeList.class | Bin 0 -> 763 bytes
.../dom/util/SAXDocumentFactory$CDataInfo.class | Bin 0 -> 888 bytes
.../dom/util/SAXDocumentFactory$CommentInfo.class | Bin 0 -> 886 bytes
.../dom/util/SAXDocumentFactory$PreInfo.class | Bin 0 -> 308 bytes
...DocumentFactory$ProcessingInstructionInfo.class | Bin 0 -> 1039 bytes
.../dom/util/SAXDocumentFactory$TextInfo.class | Bin 0 -> 872 bytes
org/apache/batik/dom/util/SAXDocumentFactory.class | Bin 0 -> 14567 bytes
org/apache/batik/dom/util/SAXIOException.class | Bin 0 -> 737 bytes
.../batik/dom/util/TriplyIndexedTable$Entry.class | Bin 0 -> 1198 bytes
org/apache/batik/dom/util/TriplyIndexedTable.class | Bin 0 -> 2432 bytes
org/apache/batik/dom/util/XLinkSupport.class | Bin 0 -> 2729 bytes
org/apache/batik/dom/util/XMLHttpRequest.class | Bin 0 -> 1102 bytes
org/apache/batik/dom/util/XMLSupport.class | Bin 0 -> 2131 bytes
org/apache/batik/dom/xbl/GenericXBLManager.class | Bin 0 -> 2697 bytes
org/apache/batik/dom/xbl/NodeXBL.class | Bin 0 -> 621 bytes
org/apache/batik/dom/xbl/OriginalEvent.class | Bin 0 -> 190 bytes
org/apache/batik/dom/xbl/ShadowTreeEvent.class | Bin 0 -> 473 bytes
org/apache/batik/dom/xbl/XBLManager.class | Bin 0 -> 767 bytes
org/apache/batik/dom/xbl/XBLManagerData.class | Bin 0 -> 231 bytes
.../batik/dom/xbl/XBLShadowTreeElement.class | Bin 0 -> 242 bytes
.../batik/ext/awt/AreaOfInterestHintKey.class | Bin 0 -> 655 bytes
org/apache/batik/ext/awt/AvoidTilingHintKey.class | Bin 0 -> 783 bytes
.../batik/ext/awt/BufferedImageHintKey.class | Bin 0 -> 802 bytes
org/apache/batik/ext/awt/ColorSpaceHintKey.class | Bin 0 -> 1198 bytes
org/apache/batik/ext/awt/LinearGradientPaint.class | Bin 0 -> 4581 bytes
.../batik/ext/awt/LinearGradientPaintContext.class | Bin 0 -> 8521 bytes
.../awt/MultipleGradientPaint$ColorSpaceEnum.class | Bin 0 -> 468 bytes
.../MultipleGradientPaint$CycleMethodEnum.class | Bin 0 -> 471 bytes
.../batik/ext/awt/MultipleGradientPaint.class | Bin 0 -> 3350 bytes
.../ext/awt/MultipleGradientPaintContext.class | Bin 0 -> 18021 bytes
org/apache/batik/ext/awt/RadialGradientPaint.class | Bin 0 -> 4993 bytes
.../batik/ext/awt/RadialGradientPaintContext.class | Bin 0 -> 9100 bytes
.../batik/ext/awt/RenderingHintsKeyExt.class | Bin 0 -> 2148 bytes
org/apache/batik/ext/awt/TranscodingHintKey.class | Bin 0 -> 648 bytes
.../batik/ext/awt/color/ICCColorSpaceExt.class | Bin 0 -> 2135 bytes
.../batik/ext/awt/color/NamedProfileCache.class | Bin 0 -> 1582 bytes
org/apache/batik/ext/awt/font/TextPathLayout.class | Bin 0 -> 3095 bytes
.../batik/ext/awt/g2d/AbstractGraphics2D.class | Bin 0 -> 12662 bytes
.../batik/ext/awt/g2d/DefaultGraphics2D.class | Bin 0 -> 3488 bytes
org/apache/batik/ext/awt/g2d/GraphicContext.class | Bin 0 -> 9105 bytes
.../ext/awt/g2d/TransformStackElement$1.class | Bin 0 -> 670 bytes
.../ext/awt/g2d/TransformStackElement$2.class | Bin 0 -> 708 bytes
.../ext/awt/g2d/TransformStackElement$3.class | Bin 0 -> 670 bytes
.../ext/awt/g2d/TransformStackElement$4.class | Bin 0 -> 670 bytes
.../ext/awt/g2d/TransformStackElement$5.class | Bin 0 -> 693 bytes
.../batik/ext/awt/g2d/TransformStackElement.class | Bin 0 -> 3485 bytes
org/apache/batik/ext/awt/g2d/TransformType.class | Bin 0 -> 1802 bytes
.../batik/ext/awt/geom/AbstractSegment.class | Bin 0 -> 4772 bytes
org/apache/batik/ext/awt/geom/Cubic.class | Bin 0 -> 8565 bytes
.../ext/awt/geom/ExtendedGeneralPath$EPI.class | Bin 0 -> 2430 bytes
.../batik/ext/awt/geom/ExtendedGeneralPath.class | Bin 0 -> 10744 bytes
.../batik/ext/awt/geom/ExtendedPathIterator.class | Bin 0 -> 570 bytes
org/apache/batik/ext/awt/geom/ExtendedShape.class | Bin 0 -> 250 bytes
org/apache/batik/ext/awt/geom/Linear.class | Bin 0 -> 5512 bytes
.../ext/awt/geom/PathLength$PathSegment.class | Bin 0 -> 1413 bytes
.../PathLength$SingleSegmentPathIterator.class | Bin 0 -> 1537 bytes
org/apache/batik/ext/awt/geom/PathLength.class | Bin 0 -> 5757 bytes
org/apache/batik/ext/awt/geom/Polygon2D.class | Bin 0 -> 6173 bytes
org/apache/batik/ext/awt/geom/Polyline2D.class | Bin 0 -> 5757 bytes
org/apache/batik/ext/awt/geom/Quadradic.class | Bin 0 -> 7250 bytes
.../ext/awt/geom/RectListManager$RLMIterator.class | Bin 0 -> 2875 bytes
.../awt/geom/RectListManager$RectXComparator.class | Bin 0 -> 735 bytes
.../batik/ext/awt/geom/RectListManager.class | Bin 0 -> 13590 bytes
.../batik/ext/awt/geom/Segment$SplitResults.class | Bin 0 -> 833 bytes
org/apache/batik/ext/awt/geom/Segment.class | Bin 0 -> 981 bytes
.../ext/awt/geom/SegmentList$SplitResults.class | Bin 0 -> 938 bytes
org/apache/batik/ext/awt/geom/SegmentList.class | Bin 0 -> 4267 bytes
.../batik/ext/awt/geom/ShapeExtender$EPIWrap.class | Bin 0 -> 1229 bytes
org/apache/batik/ext/awt/geom/ShapeExtender.class | Bin 0 -> 2192 bytes
org/apache/batik/ext/awt/image/ARGBChannel.class | Bin 0 -> 1418 bytes
org/apache/batik/ext/awt/image/AbstractLight.class | Bin 0 -> 1887 bytes
.../ext/awt/image/ComponentTransferFunction.class | Bin 0 -> 503 bytes
org/apache/batik/ext/awt/image/CompositeRule.class | Bin 0 -> 3040 bytes
.../image/ConcreteComponentTransferFunction.class | Bin 0 -> 2360 bytes
.../batik/ext/awt/image/DiscreteTransfer.class | Bin 0 -> 880 bytes
org/apache/batik/ext/awt/image/DistantLight.class | Bin 0 -> 1646 bytes
org/apache/batik/ext/awt/image/GammaTransfer.class | Bin 0 -> 989 bytes
org/apache/batik/ext/awt/image/GraphicsUtil.class | Bin 0 -> 26435 bytes
.../batik/ext/awt/image/IdentityTransfer.class | Bin 0 -> 629 bytes
org/apache/batik/ext/awt/image/Light.class | Bin 0 -> 328 bytes
.../batik/ext/awt/image/LinearTransfer.class | Bin 0 -> 888 bytes
org/apache/batik/ext/awt/image/PadMode.class | Bin 0 -> 1088 bytes
org/apache/batik/ext/awt/image/PointLight.class | Bin 0 -> 1292 bytes
.../SVGComposite$AlphaPreCompositeContext.class | Bin 0 -> 1560 bytes
...mposite$AlphaPreCompositeContext_INT_PACK.class | Bin 0 -> 2481 bytes
.../image/SVGComposite$ArithCompositeContext.class | Bin 0 -> 2154 bytes
...GComposite$ArithCompositeContext_INT_PACK.class | Bin 0 -> 2054 bytes
...posite$ArithCompositeContext_INT_PACK_LUT.class | Bin 0 -> 1933 bytes
.../image/SVGComposite$AtopCompositeContext.class | Bin 0 -> 1735 bytes
...VGComposite$AtopCompositeContext_INT_PACK.class | Bin 0 -> 1490 bytes
.../SVGComposite$DarkenCompositeContext.class | Bin 0 -> 1991 bytes
...Composite$DarkenCompositeContext_INT_PACK.class | Bin 0 -> 1871 bytes
.../image/SVGComposite$InCompositeContext.class | Bin 0 -> 1679 bytes
.../SVGComposite$InCompositeContext_INT_PACK.class | Bin 0 -> 1397 bytes
.../SVGComposite$LightenCompositeContext.class | Bin 0 -> 1994 bytes
...omposite$LightenCompositeContext_INT_PACK.class | Bin 0 -> 1874 bytes
.../SVGComposite$MultiplyCompositeContext.class | Bin 0 -> 1838 bytes
...mposite$MultiplyCompositeContext_INT_PACK.class | Bin 0 -> 1745 bytes
.../image/SVGComposite$OutCompositeContext.class | Bin 0 -> 1686 bytes
...SVGComposite$OutCompositeContext_INT_PACK.class | Bin 0 -> 1404 bytes
.../image/SVGComposite$OverCompositeContext.class | Bin 0 -> 1729 bytes
...VGComposite$OverCompositeContext_INT_PACK.class | Bin 0 -> 1469 bytes
...omposite$OverCompositeContext_INT_PACK_NA.class | Bin 0 -> 1457 bytes
...osite$OverCompositeContext_INT_PACK_UNPRE.class | Bin 0 -> 2506 bytes
.../SVGComposite$OverCompositeContext_NA.class | Bin 0 -> 1739 bytes
.../SVGComposite$ScreenCompositeContext.class | Bin 0 -> 1826 bytes
...Composite$ScreenCompositeContext_INT_PACK.class | Bin 0 -> 1658 bytes
.../image/SVGComposite$XorCompositeContext.class | Bin 0 -> 1775 bytes
...SVGComposite$XorCompositeContext_INT_PACK.class | Bin 0 -> 1509 bytes
org/apache/batik/ext/awt/image/SVGComposite.class | Bin 0 -> 6458 bytes
org/apache/batik/ext/awt/image/SpotLight.class | Bin 0 -> 3037 bytes
org/apache/batik/ext/awt/image/TableTransfer.class | Bin 0 -> 972 bytes
.../batik/ext/awt/image/TransferFunction.class | Bin 0 -> 176 bytes
org/apache/batik/ext/awt/image/URLImageCache.class | Bin 0 -> 1640 bytes
.../AbstractColorInterpolationRable.class | Bin 0 -> 2246 bytes
.../ext/awt/image/renderable/AbstractRable.class | Bin 0 -> 7008 bytes
.../ext/awt/image/renderable/AffineRable.class | Bin 0 -> 465 bytes
.../ext/awt/image/renderable/AffineRable8Bit.class | Bin 0 -> 3786 bytes
.../batik/ext/awt/image/renderable/ClipRable.class | Bin 0 -> 512 bytes
.../ext/awt/image/renderable/ClipRable8Bit.class | Bin 0 -> 5314 bytes
.../awt/image/renderable/ColorMatrixRable.class | Bin 0 -> 610 bytes
.../image/renderable/ColorMatrixRable8Bit.class | Bin 0 -> 3912 bytes
.../image/renderable/ComponentTransferRable.class | Bin 0 -> 729 bytes
.../renderable/ComponentTransferRable8Bit.class | Bin 0 -> 5559 bytes
.../ext/awt/image/renderable/CompositeRable.class | Bin 0 -> 425 bytes
.../awt/image/renderable/CompositeRable8Bit.class | Bin 0 -> 5154 bytes
.../awt/image/renderable/ConvolveMatrixRable.class | Bin 0 -> 892 bytes
.../image/renderable/ConvolveMatrixRable8Bit.class | Bin 0 -> 12009 bytes
.../ext/awt/image/renderable/DeferRable.class | Bin 0 -> 4077 bytes
.../image/renderable/DiffuseLightingRable.class | Bin 0 -> 796 bytes
.../renderable/DiffuseLightingRable8Bit.class | Bin 0 -> 6690 bytes
.../image/renderable/DisplacementMapRable.class | Bin 0 -> 702 bytes
.../renderable/DisplacementMapRable8Bit.class | Bin 0 -> 5915 bytes
.../batik/ext/awt/image/renderable/Filter.class | Bin 0 -> 371 bytes
.../awt/image/renderable/FilterAlphaRable.class | Bin 0 -> 2900 bytes
.../awt/image/renderable/FilterAsAlphaRable.class | Bin 0 -> 2916 bytes
.../awt/image/renderable/FilterChainRable.class | Bin 0 -> 616 bytes
.../image/renderable/FilterChainRable8Bit.class | Bin 0 -> 4167 bytes
.../renderable/FilterColorInterpolation.class | Bin 0 -> 364 bytes
.../ext/awt/image/renderable/FilterResRable.class | Bin 0 -> 495 bytes
.../awt/image/renderable/FilterResRable8Bit.class | Bin 0 -> 8189 bytes
.../ext/awt/image/renderable/FloodRable.class | Bin 0 -> 405 bytes
.../ext/awt/image/renderable/FloodRable8Bit.class | Bin 0 -> 3167 bytes
.../awt/image/renderable/GaussianBlurRable.class | Bin 0 -> 503 bytes
.../image/renderable/GaussianBlurRable8Bit.class | Bin 0 -> 7570 bytes
.../ext/awt/image/renderable/MorphologyRable.class | Bin 0 -> 518 bytes
.../awt/image/renderable/MorphologyRable8Bit.class | Bin 0 -> 7009 bytes
.../ext/awt/image/renderable/OffsetRable.class | Bin 0 -> 449 bytes
.../batik/ext/awt/image/renderable/PadRable.class | Bin 0 -> 586 bytes
.../ext/awt/image/renderable/PadRable8Bit.class | Bin 0 -> 5675 bytes
.../ext/awt/image/renderable/PaintRable.class | Bin 0 -> 191 bytes
.../ext/awt/image/renderable/ProfileRable.class | Bin 0 -> 2279 bytes
.../batik/ext/awt/image/renderable/RedRable.class | Bin 0 -> 3255 bytes
.../image/renderable/SpecularLightingRable.class | Bin 0 -> 858 bytes
.../renderable/SpecularLightingRable8Bit.class | Bin 0 -> 6935 bytes
.../batik/ext/awt/image/renderable/TileRable.class | Bin 0 -> 585 bytes
.../ext/awt/image/renderable/TileRable8Bit.class | Bin 0 -> 10610 bytes
.../ext/awt/image/renderable/TurbulenceRable.class | Bin 0 -> 681 bytes
.../awt/image/renderable/TurbulenceRable8Bit.class | Bin 0 -> 4453 bytes
.../batik/ext/awt/image/rendered/AbstractRed.class | Bin 0 -> 11570 bytes
.../ext/awt/image/rendered/AbstractTiledRed.class | Bin 0 -> 11090 bytes
.../batik/ext/awt/image/rendered/AffineRed.class | Bin 0 -> 7485 bytes
.../ext/awt/image/rendered/Any2LsRGBRed.class | Bin 0 -> 6781 bytes
.../batik/ext/awt/image/rendered/Any2LumRed.class | Bin 0 -> 5444 bytes
.../batik/ext/awt/image/rendered/Any2sRGBRed.class | Bin 0 -> 7152 bytes
.../image/rendered/BufferedImageCachableRed.class | Bin 0 -> 3230 bytes
.../batik/ext/awt/image/rendered/BumpMap.class | Bin 0 -> 7191 bytes
.../batik/ext/awt/image/rendered/CachableRed.class | Bin 0 -> 321 bytes
.../ext/awt/image/rendered/ColorMatrixRed.class | Bin 0 -> 5326 bytes
.../image/rendered/ComponentTransferRed$1.class | Bin 0 -> 800 bytes
.../awt/image/rendered/ComponentTransferRed.class | Bin 0 -> 2606 bytes
.../ext/awt/image/rendered/CompositeRed.class | Bin 0 -> 8524 bytes
.../awt/image/rendered/DiffuseLightingRed.class | Bin 0 -> 4107 bytes
.../rendered/DisplacementMapRed$TileOffsets.class | Bin 0 -> 899 bytes
.../awt/image/rendered/DisplacementMapRed.class | Bin 0 -> 13188 bytes
.../ext/awt/image/rendered/FilterAlphaRed.class | Bin 0 -> 2287 bytes
.../ext/awt/image/rendered/FilterAsAlphaRed.class | Bin 0 -> 3951 bytes
.../batik/ext/awt/image/rendered/FloodRed.class | Bin 0 -> 3460 bytes
.../batik/ext/awt/image/rendered/FormatRed.class | Bin 0 -> 5727 bytes
.../awt/image/rendered/GaussianBlurRed8Bit.class | Bin 0 -> 10584 bytes
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.../categoryexplorer/CategoryNodeEditor$7.class | Bin 0 -> 1129 bytes
.../categoryexplorer/CategoryNodeEditor$8.class | Bin 0 -> 909 bytes
.../categoryexplorer/CategoryNodeEditor.class | Bin 0 -> 8075 bytes
.../CategoryNodeEditorRenderer.class | Bin 0 -> 1064 bytes
.../categoryexplorer/CategoryNodeRenderer.class | Bin 0 -> 3584 bytes
.../lf5/viewer/categoryexplorer/CategoryPath.class | Bin 0 -> 2593 bytes
.../viewer/categoryexplorer/TreeModelAdapter.class | Bin 0 -> 836 bytes
.../viewer/configure/ConfigurationManager.class | Bin 0 -> 14343 bytes
.../lf5/viewer/configure/MRUFileManager.class | Bin 0 -> 4908 bytes
.../lf5/viewer/images/channelexplorer_new.gif | Bin 0 -> 778 bytes
.../viewer/images/channelexplorer_satellite.gif | Bin 0 -> 256 bytes
.../log4j/lf5/viewer/images/lf5_small_icon.gif | Bin 0 -> 1249 bytes
org/apache/log4j/net/DefaultEvaluator.class | Bin 0 -> 803 bytes
org/apache/log4j/net/JMSAppender.class | Bin 0 -> 7738 bytes
org/apache/log4j/net/JMSSink.class | Bin 0 -> 5498 bytes
org/apache/log4j/net/SMTPAppender$1.class | Bin 0 -> 858 bytes
org/apache/log4j/net/SMTPAppender.class | Bin 0 -> 11250 bytes
org/apache/log4j/net/SimpleSocketServer.class | Bin 0 -> 3544 bytes
.../log4j/net/SocketAppender$Connector.class | Bin 0 -> 2317 bytes
org/apache/log4j/net/SocketAppender.class | Bin 0 -> 5836 bytes
.../net/SocketHubAppender$ServerMonitor.class | Bin 0 -> 3410 bytes
org/apache/log4j/net/SocketHubAppender.class | Bin 0 -> 3466 bytes
org/apache/log4j/net/SocketNode.class | Bin 0 -> 4164 bytes
org/apache/log4j/net/SocketServer.class | Bin 0 -> 5793 bytes
org/apache/log4j/net/SyslogAppender.class | Bin 0 -> 8931 bytes
.../log4j/net/TelnetAppender$SocketHandler.class | Bin 0 -> 3102 bytes
org/apache/log4j/net/TelnetAppender.class | Bin 0 -> 2089 bytes
org/apache/log4j/nt/NTEventLogAppender.class | Bin 0 -> 3390 bytes
org/apache/log4j/or/DefaultRenderer.class | Bin 0 -> 548 bytes
org/apache/log4j/or/ObjectRenderer.class | Bin 0 -> 189 bytes
org/apache/log4j/or/RendererMap.class | Bin 0 -> 3842 bytes
org/apache/log4j/or/ThreadGroupRenderer.class | Bin 0 -> 1518 bytes
org/apache/log4j/or/jms/MessageRenderer.class | Bin 0 -> 2102 bytes
org/apache/log4j/or/sax/AttributesRenderer.class | Bin 0 -> 1139 bytes
org/apache/log4j/spi/AppenderAttachable.class | Bin 0 -> 465 bytes
org/apache/log4j/spi/Configurator.class | Bin 0 -> 320 bytes
.../log4j/spi/DefaultRepositorySelector.class | Bin 0 -> 657 bytes
org/apache/log4j/spi/ErrorCode.class | Bin 0 -> 414 bytes
org/apache/log4j/spi/ErrorHandler.class | Bin 0 -> 485 bytes
org/apache/log4j/spi/Filter.class | Bin 0 -> 839 bytes
org/apache/log4j/spi/HierarchyEventListener.class | Bin 0 -> 263 bytes
org/apache/log4j/spi/LocationInfo.class | Bin 0 -> 3755 bytes
org/apache/log4j/spi/LoggerFactory.class | Bin 0 -> 208 bytes
org/apache/log4j/spi/LoggerRepository.class | Bin 0 -> 914 bytes
org/apache/log4j/spi/LoggingEvent.class | Bin 0 -> 9127 bytes
org/apache/log4j/spi/NOPLogger.class | Bin 0 -> 4987 bytes
org/apache/log4j/spi/NOPLoggerRepository.class | Bin 0 -> 2526 bytes
org/apache/log4j/spi/NullWriter.class | Bin 0 -> 577 bytes
org/apache/log4j/spi/OptionHandler.class | Bin 0 -> 160 bytes
org/apache/log4j/spi/RendererSupport.class | Bin 0 -> 276 bytes
org/apache/log4j/spi/RepositorySelector.class | Bin 0 -> 212 bytes
org/apache/log4j/spi/RootCategory.class | Bin 0 -> 1000 bytes
org/apache/log4j/spi/RootLogger.class | Bin 0 -> 885 bytes
org/apache/log4j/spi/ThrowableInformation.class | Bin 0 -> 1998 bytes
.../log4j/spi/TriggeringEventEvaluator.class | Bin 0 -> 219 bytes
org/apache/log4j/spi/VectorWriter.class | Bin 0 -> 2027 bytes
org/apache/log4j/varia/DenyAllFilter.class | Bin 0 -> 777 bytes
.../log4j/varia/ExternallyRolledFileAppender.class | Bin 0 -> 1142 bytes
org/apache/log4j/varia/FallbackErrorHandler.class | Bin 0 -> 2839 bytes
org/apache/log4j/varia/HUP.class | Bin 0 -> 1586 bytes
org/apache/log4j/varia/HUPNode.class | Bin 0 -> 1920 bytes
org/apache/log4j/varia/LevelMatchFilter.class | Bin 0 -> 1480 bytes
org/apache/log4j/varia/LevelRangeFilter.class | Bin 0 -> 1470 bytes
org/apache/log4j/varia/NullAppender.class | Bin 0 -> 1000 bytes
.../varia/ReloadingPropertyConfigurator.class | Bin 0 -> 765 bytes
org/apache/log4j/varia/Roller.class | Bin 0 -> 3583 bytes
org/apache/log4j/varia/StringMatchFilter.class | Bin 0 -> 1866 bytes
org/apache/log4j/xml/DOMConfigurator$1.class | Bin 0 -> 1355 bytes
org/apache/log4j/xml/DOMConfigurator$2.class | Bin 0 -> 1315 bytes
org/apache/log4j/xml/DOMConfigurator$3.class | Bin 0 -> 1544 bytes
org/apache/log4j/xml/DOMConfigurator$4.class | Bin 0 -> 1518 bytes
org/apache/log4j/xml/DOMConfigurator$5.class | Bin 0 -> 1340 bytes
.../log4j/xml/DOMConfigurator$ParseAction.class | Bin 0 -> 389 bytes
org/apache/log4j/xml/DOMConfigurator.class | Bin 0 -> 22754 bytes
org/apache/log4j/xml/Log4jEntityResolver.class | Bin 0 -> 1536 bytes
org/apache/log4j/xml/SAXErrorHandler.class | Bin 0 -> 1523 bytes
.../log4j/xml/UnrecognizedElementHandler.class | Bin 0 -> 286 bytes
org/apache/log4j/xml/XMLLayout.class | Bin 0 -> 4109 bytes
org/apache/log4j/xml/XMLWatchdog.class | Bin 0 -> 745 bytes
org/apache/log4j/xml/log4j.dtd | 227 +
org/apache/tomcat/util/Ascii.class | Bin 0 -> 2196 bytes
org/apache/tomcat/util/HttpDate.class | Bin 0 -> 3533 bytes
org/apache/xmlcommons/Version.class | Bin 0 -> 713 bytes
org/broad/igv/DirectoryManager.class | Bin 0 -> 10595 bytes
org/broad/igv/Globals.class | Bin 0 -> 5326 bytes
org/broad/igv/IGVPreferences.class | Bin 0 -> 6103 bytes
org/broad/igv/PreferenceManager$1.class | Bin 0 -> 1161 bytes
org/broad/igv/PreferenceManager.class | Bin 0 -> 26891 bytes
org/broad/igv/batch/BatchRunner.class | Bin 0 -> 3250 bytes
org/broad/igv/batch/CommandExecutor.class | Bin 0 -> 18933 bytes
org/broad/igv/batch/CommandListener.class | Bin 0 -> 9091 bytes
org/broad/igv/batch/Exec.class | Bin 0 -> 1461 bytes
org/broad/igv/batch/TestClient.class | Bin 0 -> 6476 bytes
org/broad/igv/bbfile/BBFileHeader.class | Bin 0 -> 6263 bytes
org/broad/igv/bbfile/BBFileReader.class | Bin 0 -> 8512 bytes
org/broad/igv/bbfile/BBTotalSummaryBlock.class | Bin 0 -> 3620 bytes
org/broad/igv/bbfile/BBZoomLevelFormat.class | Bin 0 -> 3487 bytes
org/broad/igv/bbfile/BBZoomLevelHeader.class | Bin 0 -> 3562 bytes
org/broad/igv/bbfile/BBZoomLevels.class | Bin 0 -> 4279 bytes
org/broad/igv/bbfile/BPTree.class | Bin 0 -> 11208 bytes
org/broad/igv/bbfile/BPTreeChildNode.class | Bin 0 -> 3461 bytes
org/broad/igv/bbfile/BPTreeChildNodeItem.class | Bin 0 -> 2227 bytes
org/broad/igv/bbfile/BPTreeHeader.class | Bin 0 -> 3892 bytes
org/broad/igv/bbfile/BPTreeLeafNode.class | Bin 0 -> 3306 bytes
org/broad/igv/bbfile/BPTreeLeafNodeItem.class | Bin 0 -> 2081 bytes
org/broad/igv/bbfile/BPTreeNode.class | Bin 0 -> 518 bytes
org/broad/igv/bbfile/BPTreeNodeItem.class | Bin 0 -> 302 bytes
org/broad/igv/bbfile/BedFeature.class | Bin 0 -> 2244 bytes
org/broad/igv/bbfile/BigBedDataBlock.class | Bin 0 -> 5397 bytes
org/broad/igv/bbfile/BigBedIterator.class | Bin 0 -> 4377 bytes
org/broad/igv/bbfile/BigWigDataBlock.class | Bin 0 -> 3842 bytes
org/broad/igv/bbfile/BigWigIterator.class | Bin 0 -> 6022 bytes
org/broad/igv/bbfile/BigWigSection.class | Bin 0 -> 5800 bytes
.../bbfile/BigWigSectionHeader$WigItemType.class | Bin 0 -> 1351 bytes
org/broad/igv/bbfile/BigWigSectionHeader.class | Bin 0 -> 4430 bytes
org/broad/igv/bbfile/RPChromosomeRegion.class | Bin 0 -> 3581 bytes
org/broad/igv/bbfile/RPTree.class | Bin 0 -> 10175 bytes
org/broad/igv/bbfile/RPTreeChildNodeItem.class | Bin 0 -> 2148 bytes
org/broad/igv/bbfile/RPTreeHeader.class | Bin 0 -> 4866 bytes
org/broad/igv/bbfile/RPTreeLeafNodeItem.class | Bin 0 -> 1840 bytes
org/broad/igv/bbfile/RPTreeNode.class | Bin 0 -> 2065 bytes
org/broad/igv/bbfile/RPTreeNodeItem.class | Bin 0 -> 1693 bytes
org/broad/igv/bbfile/RPTreeNodeProxy.class | Bin 0 -> 623 bytes
org/broad/igv/bbfile/WigItem.class | Bin 0 -> 1811 bytes
org/broad/igv/bbfile/ZoomDataBlock.class | Bin 0 -> 5885 bytes
org/broad/igv/bbfile/ZoomDataRecord.class | Bin 0 -> 3061 bytes
.../bbfile/ZoomLevelIterator$EmptyIterator.class | Bin 0 -> 586 bytes
org/broad/igv/bbfile/ZoomLevelIterator.class | Bin 0 -> 6029 bytes
org/broad/igv/bigwig/BigWigDataSource$1.class | Bin 0 -> 800 bytes
.../bigwig/BigWigDataSource$RawDataInterval.class | Bin 0 -> 979 bytes
.../bigwig/BigWigDataSource$WrappedIterator.class | Bin 0 -> 1752 bytes
org/broad/igv/bigwig/BigWigDataSource.class | Bin 0 -> 14491 bytes
org/broad/igv/cbio/AttributeFilter.class | Bin 0 -> 3631 bytes
org/broad/igv/cbio/AttributeFilter.jfd | 306 ++
org/broad/igv/cbio/FilterGeneNetworkUI$1.class | Bin 0 -> 792 bytes
org/broad/igv/cbio/FilterGeneNetworkUI$10.class | Bin 0 -> 876 bytes
org/broad/igv/cbio/FilterGeneNetworkUI$11.class | Bin 0 -> 876 bytes
org/broad/igv/cbio/FilterGeneNetworkUI$2.class | Bin 0 -> 3193 bytes
org/broad/igv/cbio/FilterGeneNetworkUI$3.class | Bin 0 -> 880 bytes
org/broad/igv/cbio/FilterGeneNetworkUI$4.class | Bin 0 -> 899 bytes
org/broad/igv/cbio/FilterGeneNetworkUI$5.class | Bin 0 -> 787 bytes
org/broad/igv/cbio/FilterGeneNetworkUI$6.class | Bin 0 -> 1178 bytes
org/broad/igv/cbio/FilterGeneNetworkUI$7.class | Bin 0 -> 882 bytes
org/broad/igv/cbio/FilterGeneNetworkUI$8.class | Bin 0 -> 873 bytes
org/broad/igv/cbio/FilterGeneNetworkUI$9.class | Bin 0 -> 874 bytes
.../cbio/FilterGeneNetworkUI$GraphListModel.class | Bin 0 -> 3717 bytes
.../cbio/FilterGeneNetworkUI$RefreshListener.class | Bin 0 -> 1354 bytes
org/broad/igv/cbio/FilterGeneNetworkUI.class | Bin 0 -> 19883 bytes
org/broad/igv/cbio/FilterGeneNetworkUI.jfd | 911 +++
org/broad/igv/cbio/GeneNetwork$1.class | Bin 0 -> 1443 bytes
org/broad/igv/cbio/GeneNetwork$2.class | Bin 0 -> 1116 bytes
.../GeneNetwork$ByteArrayOutputStreamChild.class | Bin 0 -> 665 bytes
org/broad/igv/cbio/GeneNetwork$ScoreData.class | Bin 0 -> 975 bytes
org/broad/igv/cbio/GeneNetwork.class | Bin 0 -> 23251 bytes
org/broad/igv/cbio/resources/post_stub.html | 39 +
org/broad/igv/charts/Axis$Orientation.class | Bin 0 -> 1116 bytes
org/broad/igv/charts/Axis.class | Bin 0 -> 2656 bytes
org/broad/igv/charts/AxisPanel.class | Bin 0 -> 3741 bytes
org/broad/igv/charts/ChartLayout.class | Bin 0 -> 5628 bytes
org/broad/igv/charts/ChartPanel$LegendIcon.class | Bin 0 -> 1274 bytes
.../igv/charts/ChartPanel$LegendPanel$1.class | Bin 0 -> 1544 bytes
.../igv/charts/ChartPanel$LegendPanel$2.class | Bin 0 -> 1629 bytes
org/broad/igv/charts/ChartPanel$LegendPanel.class | Bin 0 -> 4529 bytes
org/broad/igv/charts/ChartPanel$PlotPanel$1.class | Bin 0 -> 3796 bytes
org/broad/igv/charts/ChartPanel$PlotPanel.class | Bin 0 -> 1618 bytes
org/broad/igv/charts/ChartPanel.class | Bin 0 -> 3102 bytes
org/broad/igv/charts/ScatterPlot.class | Bin 0 -> 9746 bytes
org/broad/igv/charts/ScatterPlotData.class | Bin 0 -> 5514 bytes
org/broad/igv/charts/ScatterPlotDemo$1.class | Bin 0 -> 789 bytes
org/broad/igv/charts/ScatterPlotDemo.class | Bin 0 -> 3670 bytes
org/broad/igv/charts/ScatterPlotFrame$1.class | Bin 0 -> 864 bytes
org/broad/igv/charts/ScatterPlotFrame$2.class | Bin 0 -> 864 bytes
org/broad/igv/charts/ScatterPlotFrame$3.class | Bin 0 -> 864 bytes
org/broad/igv/charts/ScatterPlotFrame$4.class | Bin 0 -> 864 bytes
org/broad/igv/charts/ScatterPlotFrame.class | Bin 0 -> 10298 bytes
org/broad/igv/charts/ScatterPlotFrame.jfd | 359 ++
org/broad/igv/charts/ScatterPlotUtils$1.class | Bin 0 -> 770 bytes
.../igv/charts/ScatterPlotUtils$SampleData.class | Bin 0 -> 2100 bytes
org/broad/igv/charts/ScatterPlotUtils.class | Bin 0 -> 10081 bytes
org/broad/igv/charts/SelectionPath.class | Bin 0 -> 1552 bytes
org/broad/igv/charts/XYDataModel.class | Bin 0 -> 3824 bytes
org/broad/igv/charts/XYDataPoint.class | Bin 0 -> 1226 bytes
org/broad/igv/charts/XYSeries.class | Bin 0 -> 1790 bytes
.../igv/das/DASFeatureSource$DasReader$1.class | Bin 0 -> 1494 bytes
org/broad/igv/das/DASFeatureSource$DasReader.class | Bin 0 -> 12847 bytes
.../igv/das/DASFeatureSource$IteratorWrapper.class | Bin 0 -> 1518 bytes
org/broad/igv/das/DASFeatureSource.class | Bin 0 -> 5020 bytes
org/broad/igv/data/AbstractDataParser.class | Bin 0 -> 1736 bytes
org/broad/igv/data/AbstractDataSource.class | Bin 0 -> 8961 bytes
org/broad/igv/data/BasicScore.class | Bin 0 -> 2201 bytes
org/broad/igv/data/Bin.class | Bin 0 -> 157 bytes
org/broad/igv/data/CharArrayList.class | Bin 0 -> 1430 bytes
org/broad/igv/data/ChromosomeData.class | Bin 0 -> 1669 bytes
org/broad/igv/data/ChromosomeSummary.class | Bin 0 -> 870 bytes
.../data/CombinedDataSource$MergedIterator.class | Bin 0 -> 1889 bytes
.../igv/data/CombinedDataSource$ScoreWrapper.class | Bin 0 -> 943 bytes
org/broad/igv/data/CombinedDataSource.class | Bin 0 -> 3977 bytes
org/broad/igv/data/CompositeScore.class | Bin 0 -> 3144 bytes
org/broad/igv/data/CoverageDataSource.class | Bin 0 -> 244 bytes
org/broad/igv/data/DataSource.class | Bin 0 -> 711 bytes
org/broad/igv/data/DataStatistics$1.class | Bin 0 -> 1087 bytes
org/broad/igv/data/DataStatistics.class | Bin 0 -> 2561 bytes
org/broad/igv/data/DataTile.class | Bin 0 -> 1041 bytes
org/broad/igv/data/DataTile2D.class | Bin 0 -> 1032 bytes
.../igv/data/DataUtils$AsciiFileMetrics.class | Bin 0 -> 836 bytes
org/broad/igv/data/DataUtils.class | Bin 0 -> 2384 bytes
org/broad/igv/data/Dataset.class | Bin 0 -> 711 bytes
org/broad/igv/data/DatasetDataSource.class | Bin 0 -> 4373 bytes
org/broad/igv/data/DatasetSizeTest$TestScore.class | Bin 0 -> 1487 bytes
org/broad/igv/data/DatasetSizeTest.class | Bin 0 -> 2401 bytes
org/broad/igv/data/ExpressionProbe.class | Bin 0 -> 2283 bytes
org/broad/igv/data/FeatureBin.class | Bin 0 -> 1878 bytes
org/broad/igv/data/FeatureBinCalculator.class | Bin 0 -> 2352 bytes
org/broad/igv/data/GenomeSummaryData.class | Bin 0 -> 5792 bytes
org/broad/igv/data/IGVDataset.class | Bin 0 -> 6736 bytes
.../data/IGVDatasetParser$WholeGenomeData.class | Bin 0 -> 1441 bytes
org/broad/igv/data/IGVDatasetParser.class | Bin 0 -> 17686 bytes
org/broad/igv/data/LocusScoreUtils$1.class | Bin 0 -> 812 bytes
org/broad/igv/data/LocusScoreUtils.class | Bin 0 -> 3989 bytes
org/broad/igv/data/NamedScore.class | Bin 0 -> 1284 bytes
org/broad/igv/data/ProbeSet.class | Bin 0 -> 2453 bytes
org/broad/igv/data/ProcessingUtils$1.class | Bin 0 -> 1216 bytes
org/broad/igv/data/ProcessingUtils$Interval.class | Bin 0 -> 691 bytes
org/broad/igv/data/ProcessingUtils.class | Bin 0 -> 3268 bytes
org/broad/igv/data/SummaryScore.class | Bin 0 -> 2122 bytes
org/broad/igv/data/SummaryTile.class | Bin 0 -> 1678 bytes
org/broad/igv/data/SummaryTile2D.class | Bin 0 -> 2023 bytes
org/broad/igv/data/WiggleDataset$1.class | Bin 0 -> 919 bytes
org/broad/igv/data/WiggleDataset.class | Bin 0 -> 7192 bytes
org/broad/igv/data/WiggleParser$Type.class | Bin 0 -> 1261 bytes
org/broad/igv/data/WiggleParser.class | Bin 0 -> 10120 bytes
org/broad/igv/data/ZipUtils.class | Bin 0 -> 3334 bytes
.../igv/data/expression/ExpressionDataset.class | Bin 0 -> 5654 bytes
.../data/expression/ExpressionFileParser$1.class | Bin 0 -> 1332 bytes
.../data/expression/ExpressionFileParser$2.class | Bin 0 -> 1231 bytes
.../expression/ExpressionFileParser$FileType.class | Bin 0 -> 1521 bytes
.../ExpressionFileParser$FormatDescriptor.class | Bin 0 -> 1801 bytes
.../data/expression/ExpressionFileParser$Row.class | Bin 0 -> 892 bytes
.../igv/data/expression/ExpressionFileParser.class | Bin 0 -> 18161 bytes
.../igv/data/expression/GeneToLocusHelper.class | Bin 0 -> 6543 bytes
.../igv/data/expression/ProbeToLocusMap$1.class | Bin 0 -> 985 bytes
.../ProbeToLocusMap$MappingUrlCache.class | Bin 0 -> 1845 bytes
.../data/expression/ProbeToLocusMap$Platform.class | Bin 0 -> 1450 bytes
.../igv/data/expression/ProbeToLocusMap.class | Bin 0 -> 9204 bytes
org/broad/igv/data/rnai/RNAIDataSource.class | Bin 0 -> 4828 bytes
org/broad/igv/data/rnai/RNAIGCTDatasetParser.class | Bin 0 -> 9162 bytes
org/broad/igv/data/rnai/RNAIGeneScore.class | Bin 0 -> 4848 bytes
.../igv/data/rnai/RNAIGeneScoreParser$Type.class | Bin 0 -> 1210 bytes
org/broad/igv/data/rnai/RNAIGeneScoreParser.class | Bin 0 -> 5894 bytes
org/broad/igv/data/rnai/RNAIHairpinCache$1.class | Bin 0 -> 247 bytes
...NAIHairpinCache$RNAIHairpinNameComparator.class | Bin 0 -> 1679 bytes
org/broad/igv/data/rnai/RNAIHairpinCache.class | Bin 0 -> 2471 bytes
org/broad/igv/data/rnai/RNAIHairpinParser.class | Bin 0 -> 3968 bytes
org/broad/igv/data/rnai/RNAIHairpinValue.class | Bin 0 -> 1563 bytes
.../data/rnai/resources/RNAi_probe_mapping.txt.gz | Bin 0 -> 159676 bytes
org/broad/igv/data/seg/FreqData$Bin.class | Bin 0 -> 2398 bytes
org/broad/igv/data/seg/FreqData.class | Bin 0 -> 7221 bytes
org/broad/igv/data/seg/SegFileParser.class | Bin 0 -> 277 bytes
org/broad/igv/data/seg/Segment.class | Bin 0 -> 2211 bytes
.../igv/data/seg/SegmentFileParser$Type.class | Bin 0 -> 1231 bytes
org/broad/igv/data/seg/SegmentFileParser.class | Bin 0 -> 6423 bytes
org/broad/igv/data/seg/SegmentedAsciiDataSet.class | Bin 0 -> 7184 bytes
.../SegmentedBinaryDataSet$ChromosomeChunk.class | Bin 0 -> 469 bytes
.../igv/data/seg/SegmentedBinaryDataSet.class | Bin 0 -> 5228 bytes
.../igv/data/seg/SegmentedBinaryLocalReader.class | Bin 0 -> 7295 bytes
org/broad/igv/data/seg/SegmentedBinaryReader.class | Bin 0 -> 422 bytes
.../igv/data/seg/SegmentedBinaryRemoteReader.class | Bin 0 -> 4821 bytes
.../igv/data/seg/SegmentedChromosomeData.class | Bin 0 -> 5222 bytes
org/broad/igv/data/seg/SegmentedDataSet.class | Bin 0 -> 728 bytes
org/broad/igv/data/seg/SegmentedDataSource.class | Bin 0 -> 2662 bytes
org/broad/igv/dev/README | 1 +
.../dev/affective/AffectiveAnnotationParser.class | Bin 0 -> 4631 bytes
.../dev/affective/AffectiveAnnotationTrack.class | Bin 0 -> 5501 bytes
.../igv/dev/affective/AffectiveChromosome.class | Bin 0 -> 1588 bytes
.../igv/dev/affective/AffectiveDataSource.class | Bin 0 -> 5183 bytes
.../igv/dev/affective/AffectiveGenome$1.class | Bin 0 -> 1125 bytes
org/broad/igv/dev/affective/AffectiveGenome.class | Bin 0 -> 6285 bytes
.../igv/dev/affective/AffectiveLogParser$1.class | Bin 0 -> 1175 bytes
.../dev/affective/AffectiveLogParser$Header.class | Bin 0 -> 1765 bytes
.../igv/dev/affective/AffectiveLogParser.class | Bin 0 -> 6425 bytes
org/broad/igv/dev/affective/AffectiveUtils.class | Bin 0 -> 6095 bytes
org/broad/igv/dev/affective/Annotation.class | Bin 0 -> 1336 bytes
.../igv/dev/db/DBManager$ConnectionWrapper.class | Bin 0 -> 8855 bytes
org/broad/igv/dev/db/DBManager.class | Bin 0 -> 4915 bytes
org/broad/igv/dev/db/DBReader.class | Bin 0 -> 1246 bytes
org/broad/igv/dev/db/SampleInfoSQLReader.class | Bin 0 -> 2890 bytes
org/broad/igv/dev/db/SegmentedSQLReader.class | Bin 0 -> 3005 bytes
org/broad/igv/event/StatusChangeEvent.class | Bin 0 -> 620 bytes
org/broad/igv/exceptions/DataLoadException.class | Bin 0 -> 989 bytes
.../igv/exceptions/HttpResponseException.class | Bin 0 -> 1103 bytes
.../LoadResourceFromServerException.class | Bin 0 -> 1437 bytes
org/broad/igv/exceptions/ParserException.class | Bin 0 -> 2339 bytes
.../igv/exceptions/ProbeMappingException.class | Bin 0 -> 994 bytes
org/broad/igv/feature/AbstractFeature.class | Bin 0 -> 6505 bytes
org/broad/igv/feature/AbstractFeatureParser.class | Bin 0 -> 11863 bytes
org/broad/igv/feature/AlternativeSpliceGraph.class | Bin 0 -> 2354 bytes
org/broad/igv/feature/AminoAcid.class | Bin 0 -> 1175 bytes
org/broad/igv/feature/AminoAcidManager.class | Bin 0 -> 6388 bytes
org/broad/igv/feature/AminoAcidSequence.class | Bin 0 -> 1706 bytes
org/broad/igv/feature/BasicFeature$1.class | Bin 0 -> 1130 bytes
org/broad/igv/feature/BasicFeature.class | Bin 0 -> 8260 bytes
org/broad/igv/feature/Chromosome.class | Bin 0 -> 309 bytes
org/broad/igv/feature/ChromosomeImpl.class | Bin 0 -> 1483 bytes
org/broad/igv/feature/Codon.class | Bin 0 -> 3246 bytes
org/broad/igv/feature/CytoBandFileParser.class | Bin 0 -> 3918 bytes
org/broad/igv/feature/Cytoband.class | Bin 0 -> 1994 bytes
.../EmblFeatureTableParser$EmblRecord.class | Bin 0 -> 4878 bytes
org/broad/igv/feature/EmblFeatureTableParser.class | Bin 0 -> 12631 bytes
org/broad/igv/feature/Exon$ExonLocHandler.class | Bin 0 -> 2681 bytes
org/broad/igv/feature/Exon.class | Bin 0 -> 5557 bytes
org/broad/igv/feature/FeatureCodecParser.class | Bin 0 -> 794 bytes
.../igv/feature/FeatureDB$FeatureComparator.class | Bin 0 -> 1748 bytes
org/broad/igv/feature/FeatureDB.class | Bin 0 -> 10507 bytes
org/broad/igv/feature/FeatureFileUtils.class | Bin 0 -> 7051 bytes
org/broad/igv/feature/FeatureParser.class | Bin 0 -> 689 bytes
org/broad/igv/feature/FeatureType.class | Bin 0 -> 1276 bytes
org/broad/igv/feature/FeatureUtils$1.class | Bin 0 -> 795 bytes
org/broad/igv/feature/FeatureUtils$2.class | Bin 0 -> 902 bytes
org/broad/igv/feature/FeatureUtils.class | Bin 0 -> 6927 bytes
org/broad/igv/feature/GFFParser$GFF2Helper.class | Bin 0 -> 3992 bytes
org/broad/igv/feature/GFFParser$GFF3Helper.class | Bin 0 -> 4171 bytes
.../igv/feature/GFFParser$GFF3Transcript.class | Bin 0 -> 5564 bytes
org/broad/igv/feature/GFFParser$Helper.class | Bin 0 -> 795 bytes
org/broad/igv/feature/GFFParser.class | Bin 0 -> 15873 bytes
org/broad/igv/feature/GisticFileParser.class | Bin 0 -> 7105 bytes
org/broad/igv/feature/GisticScore$Type.class | Bin 0 -> 1122 bytes
org/broad/igv/feature/GisticScore.class | Bin 0 -> 2643 bytes
org/broad/igv/feature/IExon.class | Bin 0 -> 221 bytes
org/broad/igv/feature/IGVFeature.class | Bin 0 -> 728 bytes
org/broad/igv/feature/Locus.class | Bin 0 -> 3430 bytes
org/broad/igv/feature/LocusScore.class | Bin 0 -> 309 bytes
.../igv/feature/MaximumContigGenomeException.class | Bin 0 -> 615 bytes
org/broad/igv/feature/Mutation.class | Bin 0 -> 8489 bytes
org/broad/igv/feature/MutationParser.class | Bin 0 -> 7546 bytes
org/broad/igv/feature/NamedFeature.class | Bin 0 -> 201 bytes
org/broad/igv/feature/RegionOfInterest.class | Bin 0 -> 2625 bytes
org/broad/igv/feature/SpliceJunctionFeature.class | Bin 0 -> 4923 bytes
org/broad/igv/feature/Strand.class | Bin 0 -> 1037 bytes
org/broad/igv/feature/dranger/DRangerFeature.class | Bin 0 -> 4856 bytes
org/broad/igv/feature/dranger/DRangerParser.class | Bin 0 -> 7302 bytes
.../igv/feature/dranger/DRangerRenderer.class | Bin 0 -> 2726 bytes
.../igv/feature/genome/ChromosomeCoordinate.class | Bin 0 -> 666 bytes
.../feature/genome/FastaDirectorySequence.class | Bin 0 -> 2467 bytes
.../FastaIndex$FastaSequenceIndexEntry.class | Bin 0 -> 1597 bytes
org/broad/igv/feature/genome/FastaIndex.class | Bin 0 -> 3788 bytes
.../igv/feature/genome/FastaIndexedSequence.class | Bin 0 -> 4009 bytes
org/broad/igv/feature/genome/FastaSequence.class | Bin 0 -> 2642 bytes
org/broad/igv/feature/genome/FastaUtils.class | Bin 0 -> 4675 bytes
org/broad/igv/feature/genome/Genome.class | Bin 0 -> 972 bytes
.../igv/feature/genome/GenomeBuilderDialog$1.class | Bin 0 -> 933 bytes
.../igv/feature/genome/GenomeBuilderDialog$2.class | Bin 0 -> 933 bytes
.../igv/feature/genome/GenomeBuilderDialog.class | Bin 0 -> 6025 bytes
.../igv/feature/genome/GenomeBuilderDialog.jfd | 209 +
.../igv/feature/genome/GenomeBuilderPane$1.class | Bin 0 -> 919 bytes
.../igv/feature/genome/GenomeBuilderPane$2.class | Bin 0 -> 919 bytes
.../igv/feature/genome/GenomeBuilderPane$3.class | Bin 0 -> 919 bytes
.../igv/feature/genome/GenomeBuilderPane$4.class | Bin 0 -> 919 bytes
.../igv/feature/genome/GenomeBuilderPane.class | Bin 0 -> 11381 bytes
org/broad/igv/feature/genome/GenomeBuilderPane.jfd | 800 +++
.../igv/feature/genome/GenomeDescriptor.class | Bin 0 -> 3333 bytes
org/broad/igv/feature/genome/GenomeException.class | Bin 0 -> 572 bytes
.../genome/GenomeImpl$ChromosomeComparator.class | Bin 0 -> 2086 bytes
org/broad/igv/feature/genome/GenomeImpl.class | Bin 0 -> 12395 bytes
org/broad/igv/feature/genome/GenomeImporter.class | Bin 0 -> 9325 bytes
org/broad/igv/feature/genome/GenomeListItem.class | Bin 0 -> 1752 bytes
org/broad/igv/feature/genome/GenomeManager.class | Bin 0 -> 23438 bytes
.../igv/feature/genome/GenomeServerException.class | Bin 0 -> 608 bytes
.../igv/feature/genome/GenomeZipDescriptor.class | Bin 0 -> 3280 bytes
org/broad/igv/feature/genome/IGVSequence.class | Bin 0 -> 4121 bytes
org/broad/igv/feature/genome/Sequence.class | Bin 0 -> 176 bytes
.../genome/SequenceHelper$SequenceTile.class | Bin 0 -> 969 bytes
org/broad/igv/feature/genome/SequenceHelper.class | Bin 0 -> 5890 bytes
.../feature/genome/SequenceServletWrapper.class | Bin 0 -> 3061 bytes
org/broad/igv/feature/genome/ServletSequence.class | Bin 0 -> 760 bytes
.../feature/tribble/CachingFeatureReader$Bin.class | Bin 0 -> 1997 bytes
.../tribble/CachingFeatureReader$BinIterator.class | Bin 0 -> 2346 bytes
.../igv/feature/tribble/CachingFeatureReader.class | Bin 0 -> 7424 bytes
org/broad/igv/feature/tribble/CodecFactory.class | Bin 0 -> 4695 bytes
.../igv/feature/tribble/FeatureFileHeader.class | Bin 0 -> 1648 bytes
.../igv/feature/tribble/GFFCodec$GFF2Helper.class | Bin 0 -> 3448 bytes
.../igv/feature/tribble/GFFCodec$GFF3Helper.class | Bin 0 -> 3281 bytes
.../igv/feature/tribble/GFFCodec$Helper.class | Bin 0 -> 733 bytes
.../igv/feature/tribble/GFFCodec$Version.class | Bin 0 -> 1177 bytes
org/broad/igv/feature/tribble/GFFCodec.class | Bin 0 -> 9319 bytes
org/broad/igv/feature/tribble/IGVBEDCodec.class | Bin 0 -> 10019 bytes
org/broad/igv/feature/tribble/Locus.class | Bin 0 -> 760 bytes
org/broad/igv/feature/tribble/PSLCodec.class | Bin 0 -> 3158 bytes
org/broad/igv/feature/tribble/REPMaskCodec.class | Bin 0 -> 5001 bytes
org/broad/igv/feature/tribble/SAMCodec.class | Bin 0 -> 2256 bytes
org/broad/igv/feature/tribble/UCSCCodec.class | Bin 0 -> 3370 bytes
.../igv/feature/tribble/UCSCGeneTableCodec$1.class | Bin 0 -> 983 bytes
.../feature/tribble/UCSCGeneTableCodec$Type.class | Bin 0 -> 1294 bytes
.../igv/feature/tribble/UCSCGeneTableCodec.class | Bin 0 -> 5788 bytes
org/broad/igv/feature/tribble/VCFFeature.class | Bin 0 -> 4866 bytes
.../igv/feature/tribble/VCFWrapperCodec.class | Bin 0 -> 1971 bytes
org/broad/igv/goby/GobyAlignment$1.class | Bin 0 -> 1121 bytes
org/broad/igv/goby/GobyAlignment.class | Bin 0 -> 19698 bytes
org/broad/igv/goby/GobyAlignmentIterator.class | Bin 0 -> 5456 bytes
org/broad/igv/goby/GobyAlignmentQueryReader.class | Bin 0 -> 5299 bytes
.../igv/goby/GobyCountArchiveDataSource.class | Bin 0 -> 8004 bytes
.../igv/goby/GobyCountArchiveDataSourceTest.class | Bin 0 -> 1774 bytes
org/broad/igv/goby/package.html | 4 +
org/broad/igv/graph/Edge.class | Bin 0 -> 1004 bytes
org/broad/igv/graph/GeneUtils$1.class | Bin 0 -> 1017 bytes
org/broad/igv/graph/GeneUtils.class | Bin 0 -> 4152 bytes
org/broad/igv/graph/Graph$1.class | Bin 0 -> 1046 bytes
org/broad/igv/graph/Graph$NodeGrid.class | Bin 0 -> 1538 bytes
org/broad/igv/graph/Graph.class | Bin 0 -> 4268 bytes
org/broad/igv/graph/GraphPanel2.class | Bin 0 -> 2850 bytes
org/broad/igv/graph/MainWindow.class | Bin 0 -> 1367 bytes
org/broad/igv/graph/Node.class | Bin 0 -> 777 bytes
org/broad/igv/graph/SubGraph.class | Bin 0 -> 1628 bytes
org/broad/igv/gs/GSFileBrowser$1.class | Bin 0 -> 1907 bytes
org/broad/igv/gs/GSFileBrowser$2.class | Bin 0 -> 819 bytes
org/broad/igv/gs/GSFileBrowser$3.class | Bin 0 -> 819 bytes
org/broad/igv/gs/GSFileBrowser$4.class | Bin 0 -> 819 bytes
org/broad/igv/gs/GSFileBrowser$CellRenderer.class | Bin 0 -> 1834 bytes
org/broad/igv/gs/GSFileBrowser$ListModel.class | Bin 0 -> 950 bytes
org/broad/igv/gs/GSFileBrowser$Mode.class | Bin 0 -> 1101 bytes
org/broad/igv/gs/GSFileBrowser.class | Bin 0 -> 11313 bytes
org/broad/igv/gs/GSFileBrowser.jfd | 280 +
org/broad/igv/gs/GSOpenSessionMenuAction$1.class | Bin 0 -> 1104 bytes
org/broad/igv/gs/GSOpenSessionMenuAction.class | Bin 0 -> 3140 bytes
org/broad/igv/gs/GSSaveSessionMenuAction.class | Bin 0 -> 4144 bytes
org/broad/igv/gs/GSUtils.class | Bin 0 -> 6295 bytes
org/broad/igv/gs/atm/ATMUtils.class | Bin 0 -> 6838 bytes
org/broad/igv/gs/atm/FileParameter.class | Bin 0 -> 2368 bytes
org/broad/igv/gs/atm/GSDataFormat.class | Bin 0 -> 619 bytes
org/broad/igv/gs/atm/SubToolDescriptor.class | Bin 0 -> 1816 bytes
org/broad/igv/gs/atm/WebToolDescriptor.class | Bin 0 -> 2217 bytes
org/broad/igv/gs/dm/DMUtils.class | Bin 0 -> 7654 bytes
org/broad/igv/gs/dm/GSDataFormat.class | Bin 0 -> 790 bytes
org/broad/igv/gs/dm/GSDirectoryListing.class | Bin 0 -> 1677 bytes
org/broad/igv/gs/dm/GSFileMetadata.class | Bin 0 -> 1977 bytes
org/broad/igv/gwas/DescriptionCache.class | Bin 0 -> 3845 bytes
org/broad/igv/gwas/GWASData.class | Bin 0 -> 4620 bytes
org/broad/igv/gwas/GWASParser.class | Bin 0 -> 7372 bytes
org/broad/igv/gwas/GWASTrack$1.class | Bin 0 -> 1430 bytes
org/broad/igv/gwas/GWASTrack$2.class | Bin 0 -> 1053 bytes
org/broad/igv/gwas/GWASTrack$3.class | Bin 0 -> 1061 bytes
org/broad/igv/gwas/GWASTrack$4.class | Bin 0 -> 1056 bytes
org/broad/igv/gwas/GWASTrack$5.class | Bin 0 -> 1667 bytes
org/broad/igv/gwas/GWASTrack$6.class | Bin 0 -> 1675 bytes
org/broad/igv/gwas/GWASTrack$7.class | Bin 0 -> 795 bytes
org/broad/igv/gwas/GWASTrack$8.class | Bin 0 -> 795 bytes
org/broad/igv/gwas/GWASTrack.class | Bin 0 -> 22490 bytes
org/broad/igv/hic/ColorRangeDialog$1.class | Bin 0 -> 846 bytes
org/broad/igv/hic/ColorRangeDialog$2.class | Bin 0 -> 846 bytes
org/broad/igv/hic/ColorRangeDialog.class | Bin 0 -> 5211 bytes
org/broad/igv/hic/ColorRangeDialog.jfd | 403 ++
org/broad/igv/hic/ColorScalePanel.class | Bin 0 -> 1307 bytes
org/broad/igv/hic/Context.class | Bin 0 -> 1585 bytes
org/broad/igv/hic/EigenvectorTrack.class | Bin 0 -> 2345 bytes
org/broad/igv/hic/HeatmapPanel$1.class | Bin 0 -> 768 bytes
org/broad/igv/hic/HeatmapPanel$DragMode.class | Bin 0 -> 1174 bytes
.../igv/hic/HeatmapPanel$HeatmapMouseHandler.class | Bin 0 -> 7292 bytes
org/broad/igv/hic/HeatmapPanel$ImageTile.class | Bin 0 -> 587 bytes
org/broad/igv/hic/HeatmapPanel.class | Bin 0 -> 8184 bytes
org/broad/igv/hic/HeatmapRenderer$1.class | Bin 0 -> 884 bytes
org/broad/igv/hic/HeatmapRenderer.class | Bin 0 -> 6786 bytes
org/broad/igv/hic/HiC$1.class | Bin 0 -> 1310 bytes
org/broad/igv/hic/HiC$2.class | Bin 0 -> 1324 bytes
org/broad/igv/hic/HiC$3.class | Bin 0 -> 1159 bytes
org/broad/igv/hic/HiC$4.class | Bin 0 -> 1798 bytes
org/broad/igv/hic/HiC.class | Bin 0 -> 8444 bytes
org/broad/igv/hic/HiCColorScale.class | Bin 0 -> 1588 bytes
org/broad/igv/hic/HiCGlobals.class | Bin 0 -> 703 bytes
org/broad/igv/hic/HiCLayout.class | Bin 0 -> 6921 bytes
org/broad/igv/hic/HiCReferenceFrame.class | Bin 0 -> 656 bytes
org/broad/igv/hic/HiCRenderContext.class | Bin 0 -> 3742 bytes
org/broad/igv/hic/HiCRulerPanel$ClickLink.class | Bin 0 -> 754 bytes
org/broad/igv/hic/HiCRulerPanel$Orientation.class | Bin 0 -> 1167 bytes
org/broad/igv/hic/HiCRulerPanel$TickSpacing.class | Bin 0 -> 1257 bytes
org/broad/igv/hic/HiCRulerPanel.class | Bin 0 -> 6525 bytes
org/broad/igv/hic/IGVUtils$1.class | Bin 0 -> 2199 bytes
org/broad/igv/hic/IGVUtils$SocketHelper.class | Bin 0 -> 690 bytes
org/broad/igv/hic/IGVUtils.class | Bin 0 -> 2099 bytes
org/broad/igv/hic/MainWindow$1.class | Bin 0 -> 2854 bytes
org/broad/igv/hic/MainWindow$10.class | Bin 0 -> 1821 bytes
org/broad/igv/hic/MainWindow$11.class | Bin 0 -> 807 bytes
org/broad/igv/hic/MainWindow$12.class | Bin 0 -> 807 bytes
org/broad/igv/hic/MainWindow$13.class | Bin 0 -> 807 bytes
org/broad/igv/hic/MainWindow$14.class | Bin 0 -> 807 bytes
org/broad/igv/hic/MainWindow$15.class | Bin 0 -> 1195 bytes
org/broad/igv/hic/MainWindow$16.class | Bin 0 -> 816 bytes
org/broad/igv/hic/MainWindow$17.class | Bin 0 -> 1764 bytes
org/broad/igv/hic/MainWindow$18.class | Bin 0 -> 807 bytes
org/broad/igv/hic/MainWindow$19.class | Bin 0 -> 807 bytes
org/broad/igv/hic/MainWindow$2.class | Bin 0 -> 1395 bytes
org/broad/igv/hic/MainWindow$20.class | Bin 0 -> 2822 bytes
org/broad/igv/hic/MainWindow$21.class | Bin 0 -> 807 bytes
org/broad/igv/hic/MainWindow$22.class | Bin 0 -> 807 bytes
org/broad/igv/hic/MainWindow$23.class | Bin 0 -> 737 bytes
org/broad/igv/hic/MainWindow$24.class | Bin 0 -> 1252 bytes
org/broad/igv/hic/MainWindow$25.class | Bin 0 -> 527 bytes
org/broad/igv/hic/MainWindow$3.class | Bin 0 -> 1865 bytes
org/broad/igv/hic/MainWindow$4.class | Bin 0 -> 1867 bytes
org/broad/igv/hic/MainWindow$5.class | Bin 0 -> 1924 bytes
org/broad/igv/hic/MainWindow$6.class | Bin 0 -> 1908 bytes
org/broad/igv/hic/MainWindow$7.class | Bin 0 -> 1901 bytes
org/broad/igv/hic/MainWindow$8.class | Bin 0 -> 1901 bytes
org/broad/igv/hic/MainWindow$9.class | Bin 0 -> 1914 bytes
org/broad/igv/hic/MainWindow$DisplayOption.class | Bin 0 -> 1455 bytes
.../hic/MainWindow$FileDropTargetListener.class | Bin 0 -> 3106 bytes
org/broad/igv/hic/MainWindow.class | Bin 0 -> 29530 bytes
org/broad/igv/hic/ObservedColorScale.class | Bin 0 -> 2358 bytes
org/broad/igv/hic/ThumbnailPanel$1.class | Bin 0 -> 1837 bytes
org/broad/igv/hic/ThumbnailPanel$2.class | Bin 0 -> 1329 bytes
org/broad/igv/hic/ThumbnailPanel$SquareDonut.class | Bin 0 -> 2154 bytes
org/broad/igv/hic/ThumbnailPanel.class | Bin 0 -> 4267 bytes
org/broad/igv/hic/TrackPanel.class | Bin 0 -> 1630 bytes
org/broad/igv/hic/data.uml | 85 +
org/broad/igv/hic/data/Block.class | Bin 0 -> 1759 bytes
org/broad/igv/hic/data/Chromosome.class | Bin 0 -> 804 bytes
org/broad/igv/hic/data/ContactRecord.class | Bin 0 -> 897 bytes
org/broad/igv/hic/data/ContactRecordCodec.class | Bin 0 -> 2729 bytes
org/broad/igv/hic/data/Dataset.class | Bin 0 -> 2257 bytes
org/broad/igv/hic/data/DatasetReader.class | Bin 0 -> 6702 bytes
org/broad/igv/hic/data/DensityFunction.class | Bin 0 -> 1618 bytes
org/broad/igv/hic/data/GM.java.expected.txt | 303 +
org/broad/igv/hic/data/HumanAugust.densities.txt | 303 +
org/broad/igv/hic/data/Matrix.class | Bin 0 -> 1094 bytes
org/broad/igv/hic/data/MatrixZoomData$1.class | Bin 0 -> 239 bytes
.../hic/data/MatrixZoomData$PearsonsMinMax.class | Bin 0 -> 1358 bytes
.../hic/data/MatrixZoomData$PearsonsResetNan.class | Bin 0 -> 1119 bytes
.../hic/data/MatrixZoomData$ScaleParameters.class | Bin 0 -> 663 bytes
org/broad/igv/hic/data/MatrixZoomData.class | Bin 0 -> 15472 bytes
org/broad/igv/hic/data/binary_file_layout.txt | 80 +
org/broad/igv/hic/tools/AlignmentPair.class | Bin 0 -> 797 bytes
org/broad/igv/hic/tools/AlignmentsSorter$1.class | Bin 0 -> 1404 bytes
.../tools/AlignmentsSorter$AlignmentRecord.class | Bin 0 -> 518 bytes
.../igv/hic/tools/AlignmentsSorter$Codec.class | Bin 0 -> 3017 bytes
org/broad/igv/hic/tools/AlignmentsSorter.class | Bin 0 -> 4358 bytes
org/broad/igv/hic/tools/AsciiPairIterator.class | Bin 0 -> 3439 bytes
org/broad/igv/hic/tools/AsciiToBinConverter.class | Bin 0 -> 2695 bytes
org/broad/igv/hic/tools/BAMPairIterator.class | Bin 0 -> 3135 bytes
org/broad/igv/hic/tools/BinPairIterator.class | Bin 0 -> 1844 bytes
org/broad/igv/hic/tools/DensityCalculation.class | Bin 0 -> 7235 bytes
org/broad/igv/hic/tools/DensityUtil.class | Bin 0 -> 6736 bytes
.../igv/hic/tools/HiCTools$CommandLineParser.class | Bin 0 -> 2395 bytes
org/broad/igv/hic/tools/HiCTools.class | Bin 0 -> 11265 bytes
org/broad/igv/hic/tools/PairIterator.class | Bin 0 -> 379 bytes
org/broad/igv/hic/tools/Preprocessor$1.class | Bin 0 -> 1363 bytes
.../tools/Preprocessor$BufferedByteWriter.class | Bin 0 -> 2074 bytes
.../igv/hic/tools/Preprocessor$IndexEntry.class | Bin 0 -> 684 bytes
.../igv/hic/tools/Preprocessor$MatrixPP.class | Bin 0 -> 2960 bytes
.../hic/tools/Preprocessor$MatrixZoomDataPP.class | Bin 0 -> 3589 bytes
org/broad/igv/hic/tools/Preprocessor.class | Bin 0 -> 16510 bytes
org/broad/igv/hic/tools/b37.chrom.sizes | 25 +
org/broad/igv/hic/tools/dMel.chrom.sizes | 7 +
org/broad/igv/hic/tools/hg18.chrom.sizes | 25 +
org/broad/igv/hic/tools/mm9.chrom.sizes | 22 +
org/broad/igv/lists/GeneList$1.class | Bin 0 -> 1361 bytes
org/broad/igv/lists/GeneList.class | Bin 0 -> 3902 bytes
org/broad/igv/lists/GeneListEditDialog$1.class | Bin 0 -> 872 bytes
org/broad/igv/lists/GeneListEditDialog$2.class | Bin 0 -> 872 bytes
org/broad/igv/lists/GeneListEditDialog.class | Bin 0 -> 7463 bytes
org/broad/igv/lists/GeneListEditDialog.jfd | 374 ++
org/broad/igv/lists/GeneListGroup.class | Bin 0 -> 2032 bytes
org/broad/igv/lists/GeneListManager.class | Bin 0 -> 12997 bytes
org/broad/igv/lists/GeneListManagerUI$1.class | Bin 0 -> 1296 bytes
org/broad/igv/lists/GeneListManagerUI$10.class | Bin 0 -> 904 bytes
org/broad/igv/lists/GeneListManagerUI$11.class | Bin 0 -> 835 bytes
org/broad/igv/lists/GeneListManagerUI$12.class | Bin 0 -> 868 bytes
org/broad/igv/lists/GeneListManagerUI$13.class | Bin 0 -> 868 bytes
org/broad/igv/lists/GeneListManagerUI$14.class | Bin 0 -> 868 bytes
org/broad/igv/lists/GeneListManagerUI$15.class | Bin 0 -> 868 bytes
org/broad/igv/lists/GeneListManagerUI$16.class | Bin 0 -> 868 bytes
org/broad/igv/lists/GeneListManagerUI$17.class | Bin 0 -> 868 bytes
org/broad/igv/lists/GeneListManagerUI$18.class | Bin 0 -> 868 bytes
org/broad/igv/lists/GeneListManagerUI$2.class | Bin 0 -> 1394 bytes
org/broad/igv/lists/GeneListManagerUI$3.class | Bin 0 -> 824 bytes
org/broad/igv/lists/GeneListManagerUI$4.class | Bin 0 -> 874 bytes
org/broad/igv/lists/GeneListManagerUI$5.class | Bin 0 -> 902 bytes
org/broad/igv/lists/GeneListManagerUI$6.class | Bin 0 -> 865 bytes
org/broad/igv/lists/GeneListManagerUI$7.class | Bin 0 -> 865 bytes
org/broad/igv/lists/GeneListManagerUI$8.class | Bin 0 -> 865 bytes
org/broad/igv/lists/GeneListManagerUI$9.class | Bin 0 -> 833 bytes
.../lists/GeneListManagerUI$GeneListModel.class | Bin 0 -> 1432 bytes
.../lists/GeneListManagerUI$ListListModel$1.class | Bin 0 -> 1283 bytes
.../lists/GeneListManagerUI$ListListModel.class | Bin 0 -> 3708 bytes
org/broad/igv/lists/GeneListManagerUI.class | Bin 0 -> 17628 bytes
org/broad/igv/lists/GeneListManagerUI.jfd | 912 +++
org/broad/igv/lists/Preloader.class | Bin 0 -> 2473 bytes
org/broad/igv/lists/VariantListEntry.class | Bin 0 -> 1365 bytes
org/broad/igv/lists/VariantListManager.class | Bin 0 -> 3154 bytes
org/broad/igv/lists/VariantListNavigator$1.class | Bin 0 -> 923 bytes
org/broad/igv/lists/VariantListNavigator$2.class | Bin 0 -> 886 bytes
org/broad/igv/lists/VariantListNavigator$3$1.class | Bin 0 -> 2119 bytes
org/broad/igv/lists/VariantListNavigator$3.class | Bin 0 -> 2627 bytes
org/broad/igv/lists/VariantListNavigator.class | Bin 0 -> 6243 bytes
org/broad/igv/lists/VariantListNavigator.jfd | 123 +
org/broad/igv/lists/biocarta_cancer_cp.gmt | 21 +
org/broad/igv/lists/examples.gmt | 10 +
org/broad/igv/lists/kegg_cancer_cp.gmt | 12 +
org/broad/igv/lists/mckd1.gmt | 9 +
org/broad/igv/lists/reactome_cp.gmt | 431 ++
org/broad/igv/maf/MAFConfigurationDialog$1.class | Bin 0 -> 890 bytes
org/broad/igv/maf/MAFConfigurationDialog$2.class | Bin 0 -> 890 bytes
org/broad/igv/maf/MAFConfigurationDialog$3.class | Bin 0 -> 890 bytes
org/broad/igv/maf/MAFConfigurationDialog$4.class | Bin 0 -> 890 bytes
org/broad/igv/maf/MAFConfigurationDialog$5.class | Bin 0 -> 890 bytes
org/broad/igv/maf/MAFConfigurationDialog$6.class | Bin 0 -> 959 bytes
.../igv/maf/MAFConfigurationDialog$Category.class | Bin 0 -> 1270 bytes
...nfigurationDialog$SpeciesSelectionPanel$1.class | Bin 0 -> 1090 bytes
...ConfigurationDialog$SpeciesSelectionPanel.class | Bin 0 -> 4694 bytes
org/broad/igv/maf/MAFConfigurationDialog.class | Bin 0 -> 8953 bytes
org/broad/igv/maf/MAFListReader$1.class | Bin 0 -> 1854 bytes
org/broad/igv/maf/MAFListReader.class | Bin 0 -> 4112 bytes
org/broad/igv/maf/MAFLocalReader.class | Bin 0 -> 3654 bytes
org/broad/igv/maf/MAFManager$1.class | Bin 0 -> 1745 bytes
org/broad/igv/maf/MAFManager.class | Bin 0 -> 7501 bytes
org/broad/igv/maf/MAFReader.class | Bin 0 -> 404 bytes
org/broad/igv/maf/MAFRemoteReader.class | Bin 0 -> 3197 bytes
org/broad/igv/maf/MAFRenderer.class | Bin 0 -> 7114 bytes
org/broad/igv/maf/MAFTile$Gap.class | Bin 0 -> 973 bytes
org/broad/igv/maf/MAFTile$MASequence.class | Bin 0 -> 1075 bytes
org/broad/igv/maf/MAFTile.class | Bin 0 -> 3101 bytes
org/broad/igv/maf/MAFTileCodec.class | Bin 0 -> 2762 bytes
org/broad/igv/maf/MAFTrack$1.class | Bin 0 -> 814 bytes
org/broad/igv/maf/MAFTrack$2.class | Bin 0 -> 720 bytes
org/broad/igv/maf/MAFTrack.class | Bin 0 -> 10023 bytes
org/broad/igv/maf/MAFUtils.class | Bin 0 -> 814 bytes
org/broad/igv/maf/species.properties | 62 +
org/broad/igv/methyl/BBMethylDataSource$Type.class | Bin 0 -> 1170 bytes
.../BBMethylDataSource$WrappedIterator.class | Bin 0 -> 3283 bytes
org/broad/igv/methyl/BBMethylDataSource.class | Bin 0 -> 3114 bytes
org/broad/igv/methyl/CachingMethylSource$Bin.class | Bin 0 -> 1729 bytes
.../methyl/CachingMethylSource$BinIterator.class | Bin 0 -> 2370 bytes
org/broad/igv/methyl/CachingMethylSource.class | Bin 0 -> 6457 bytes
org/broad/igv/methyl/MethylDataSource.class | Bin 0 -> 296 bytes
org/broad/igv/methyl/MethylScore.class | Bin 0 -> 2176 bytes
org/broad/igv/methyl/MethylTrack$1.class | Bin 0 -> 2465 bytes
org/broad/igv/methyl/MethylTrack$Interval.class | Bin 0 -> 1118 bytes
org/broad/igv/methyl/MethylTrack.class | Bin 0 -> 5201 bytes
.../methyl/ZillerDataSource2$RawDataInterval.class | Bin 0 -> 983 bytes
org/broad/igv/methyl/ZillerDataSource2.class | Bin 0 -> 4559 bytes
org/broad/igv/methyl/readme | 1 +
org/broad/igv/peaks/BedToPeaks$PeakRecord.class | Bin 0 -> 609 bytes
org/broad/igv/peaks/BedToPeaks.class | Bin 0 -> 13819 bytes
org/broad/igv/peaks/Peak.class | Bin 0 -> 3340 bytes
org/broad/igv/peaks/PeakCodec.class | Bin 0 -> 2094 bytes
org/broad/igv/peaks/PeakCommandBar$1.class | Bin 0 -> 853 bytes
org/broad/igv/peaks/PeakCommandBar$2.class | Bin 0 -> 853 bytes
org/broad/igv/peaks/PeakCommandBar$3.class | Bin 0 -> 879 bytes
org/broad/igv/peaks/PeakCommandBar$4.class | Bin 0 -> 879 bytes
org/broad/igv/peaks/PeakCommandBar$5.class | Bin 0 -> 879 bytes
org/broad/igv/peaks/PeakCommandBar$6.class | Bin 0 -> 844 bytes
org/broad/igv/peaks/PeakCommandBar$7.class | Bin 0 -> 844 bytes
org/broad/igv/peaks/PeakCommandBar$8.class | Bin 0 -> 844 bytes
org/broad/igv/peaks/PeakCommandBar.class | Bin 0 -> 8394 bytes
org/broad/igv/peaks/PeakCommandBar.jfd | 479 ++
org/broad/igv/peaks/PeakControlDialog$1.class | Bin 0 -> 874 bytes
org/broad/igv/peaks/PeakControlDialog$2.class | Bin 0 -> 874 bytes
org/broad/igv/peaks/PeakControlDialog.class | Bin 0 -> 4963 bytes
org/broad/igv/peaks/PeakControlDialog.jfd | 243 +
org/broad/igv/peaks/PeakParser.class | Bin 0 -> 4741 bytes
org/broad/igv/peaks/PeakRenderer.class | Bin 0 -> 6644 bytes
org/broad/igv/peaks/PeakTimePlotFrame.class | Bin 0 -> 1700 bytes
org/broad/igv/peaks/PeakTimePlotFrame.jfd | 136 +
org/broad/igv/peaks/PeakToolTip.class | Bin 0 -> 302 bytes
org/broad/igv/peaks/PeakTrack$1.class | Bin 0 -> 2119 bytes
org/broad/igv/peaks/PeakTrack$ColorOption.class | Bin 0 -> 1151 bytes
org/broad/igv/peaks/PeakTrack$InViewInterval.class | Bin 0 -> 626 bytes
.../igv/peaks/PeakTrack$WrappedDataSource.class | Bin 0 -> 3802 bytes
org/broad/igv/peaks/PeakTrack.class | Bin 0 -> 17746 bytes
org/broad/igv/peaks/PeakTrackMenu$1.class | Bin 0 -> 944 bytes
org/broad/igv/peaks/PeakTrackMenu$2.class | Bin 0 -> 1227 bytes
org/broad/igv/peaks/PeakTrackMenu$3.class | Bin 0 -> 1226 bytes
org/broad/igv/peaks/PeakTrackMenu$4.class | Bin 0 -> 1097 bytes
org/broad/igv/peaks/PeakTrackMenu$5.class | Bin 0 -> 1103 bytes
org/broad/igv/peaks/PeakTrackMenu.class | Bin 0 -> 8801 bytes
org/broad/igv/peaks/descriptor.txt | 4 +
org/broad/igv/renderer/AbstractColorScale.class | Bin 0 -> 1091 bytes
org/broad/igv/renderer/BarChartRenderer.class | Bin 0 -> 1068 bytes
org/broad/igv/renderer/ColorScale.class | Bin 0 -> 326 bytes
org/broad/igv/renderer/ColorScaleFactory.class | Bin 0 -> 1666 bytes
.../ContinuousColorScale$ColorGradient.class | Bin 0 -> 2766 bytes
org/broad/igv/renderer/ContinuousColorScale.class | Bin 0 -> 7431 bytes
org/broad/igv/renderer/CosmicFeatureRenderer.class | Bin 0 -> 3629 bytes
org/broad/igv/renderer/CytobandRenderer.class | Bin 0 -> 6025 bytes
org/broad/igv/renderer/DataRange$Type.class | Bin 0 -> 1116 bytes
org/broad/igv/renderer/DataRange.class | Bin 0 -> 3533 bytes
org/broad/igv/renderer/DataRenderer.class | Bin 0 -> 3198 bytes
.../igv/renderer/FeatureDensityRenderer.class | Bin 0 -> 2860 bytes
org/broad/igv/renderer/FeatureRenderer.class | Bin 0 -> 996 bytes
org/broad/igv/renderer/GeneTrackRenderer.class | Bin 0 -> 621 bytes
org/broad/igv/renderer/GenotypeRenderer.class | Bin 0 -> 14146 bytes
org/broad/igv/renderer/GisticTrackRenderer.class | Bin 0 -> 4514 bytes
org/broad/igv/renderer/GraphicUtils.class | Bin 0 -> 6338 bytes
org/broad/igv/renderer/HeatmapRenderer.class | Bin 0 -> 4567 bytes
org/broad/igv/renderer/IGVFeatureRenderer.class | Bin 0 -> 18287 bytes
org/broad/igv/renderer/LineplotRenderer.class | Bin 0 -> 4033 bytes
org/broad/igv/renderer/MappedColorScale.class | Bin 0 -> 3542 bytes
org/broad/igv/renderer/MonocolorScale.class | Bin 0 -> 1628 bytes
org/broad/igv/renderer/MutationRenderer.class | Bin 0 -> 3378 bytes
org/broad/igv/renderer/PointsRenderer.class | Bin 0 -> 1050 bytes
org/broad/igv/renderer/RNAiBarChartRenderer.class | Bin 0 -> 3856 bytes
org/broad/igv/renderer/Renderer.class | Bin 0 -> 431 bytes
org/broad/igv/renderer/SequenceArray.class | Bin 0 -> 425 bytes
...SequenceRenderer$TranslatedSequenceDrawer.class | Bin 0 -> 7133 bytes
org/broad/igv/renderer/SequenceRenderer.class | Bin 0 -> 7519 bytes
.../igv/renderer/SpliceJunctionRenderer.class | Bin 0 -> 8085 bytes
org/broad/igv/renderer/TestGraphicUtils$1$1.class | Bin 0 -> 800 bytes
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.../igv/renderer/TestGraphicUtils$TestPanel.class | Bin 0 -> 902 bytes
org/broad/igv/renderer/TestGraphicUtils.class | Bin 0 -> 2426 bytes
org/broad/igv/renderer/XYPlotRenderer.class | Bin 0 -> 9737 bytes
org/broad/igv/repeats/RepeatMaskSplitter.class | Bin 0 -> 5569 bytes
org/broad/igv/sam/AbstractAlignment.class | Bin 0 -> 8598 bytes
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org/broad/igv/sam/AlignmentBlockFS.class | Bin 0 -> 932 bytes
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org/broad/igv/sam/AlignmentCounts.class | Bin 0 -> 870 bytes
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.../AlignmentDataManager$DownsampleOptions.class | Bin 0 -> 1481 bytes
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.../sam/AlignmentInterval$AlignmentIterator.class | Bin 0 -> 2705 bytes
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.../igv/sam/AlignmentPacker$BucketCollection.class | Bin 0 -> 809 bytes
.../AlignmentPacker$DenseBucketCollection.class | Bin 0 -> 2137 bytes
.../AlignmentPacker$SparseBucketCollection.class | Bin 0 -> 3631 bytes
org/broad/igv/sam/AlignmentPacker.class | Bin 0 -> 9071 bytes
org/broad/igv/sam/AlignmentRenderer$1.class | Bin 0 -> 1198 bytes
org/broad/igv/sam/AlignmentRenderer$2.class | Bin 0 -> 1198 bytes
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org/broad/igv/sam/AlignmentRenderer.class | Bin 0 -> 27730 bytes
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org/broad/igv/sam/AlignmentTrack$ColorOption.class | Bin 0 -> 1876 bytes
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org/broad/igv/sam/AlignmentTrack$GroupOption.class | Bin 0 -> 1588 bytes
org/broad/igv/sam/AlignmentTrack$PopupMenu$1.class | Bin 0 -> 1309 bytes
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.../igv/sam/AlignmentTrack$PopupMenu$12.class | Bin 0 -> 1143 bytes
.../igv/sam/AlignmentTrack$PopupMenu$13.class | Bin 0 -> 1134 bytes
.../igv/sam/AlignmentTrack$PopupMenu$14.class | Bin 0 -> 1262 bytes
.../igv/sam/AlignmentTrack$PopupMenu$15.class | Bin 0 -> 1272 bytes
.../igv/sam/AlignmentTrack$PopupMenu$16.class | Bin 0 -> 1126 bytes
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.../igv/sam/AlignmentTrack$PopupMenu$21$1.class | Bin 0 -> 1472 bytes
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.../igv/sam/AlignmentTrack$PopupMenu$22$1.class | Bin 0 -> 3061 bytes
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org/broad/igv/sam/AlignmentTrack$PopupMenu$3.class | Bin 0 -> 1618 bytes
org/broad/igv/sam/AlignmentTrack$PopupMenu$4.class | Bin 0 -> 1454 bytes
org/broad/igv/sam/AlignmentTrack$PopupMenu$5.class | Bin 0 -> 1792 bytes
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org/broad/igv/sam/AlignmentTrack$PopupMenu$8.class | Bin 0 -> 1319 bytes
org/broad/igv/sam/AlignmentTrack$PopupMenu$9.class | Bin 0 -> 1859 bytes
org/broad/igv/sam/AlignmentTrack$PopupMenu.class | Bin 0 -> 17423 bytes
.../igv/sam/AlignmentTrack$RenderOptions.class | Bin 0 -> 7490 bytes
org/broad/igv/sam/AlignmentTrack$SortOption.class | Bin 0 -> 1798 bytes
org/broad/igv/sam/AlignmentTrack.class | Bin 0 -> 28678 bytes
org/broad/igv/sam/AlignmentUtils.class | Bin 0 -> 2011 bytes
org/broad/igv/sam/BaseAlignmentCounts.class | Bin 0 -> 8260 bytes
org/broad/igv/sam/BedRenderer.class | Bin 0 -> 2673 bytes
.../igv/sam/BisulfiteBaseInfo$DisplayStatus.class | Bin 0 -> 1263 bytes
org/broad/igv/sam/BisulfiteBaseInfo.class | Bin 0 -> 5496 bytes
org/broad/igv/sam/BisulfiteBaseInfoNOMeseq.class | Bin 0 -> 2271 bytes
org/broad/igv/sam/BisulfiteCounts$1.class | Bin 0 -> 1077 bytes
org/broad/igv/sam/BisulfiteCounts$Count.class | Bin 0 -> 638 bytes
org/broad/igv/sam/BisulfiteCounts.class | Bin 0 -> 5675 bytes
org/broad/igv/sam/CachingQueryReader$1.class | Bin 0 -> 241 bytes
.../sam/CachingQueryReader$AlignmentSorter.class | Bin 0 -> 1233 bytes
...gQueryReader$AlignmentTile$SamplingBucket.class | Bin 0 -> 2368 bytes
.../igv/sam/CachingQueryReader$AlignmentTile.class | Bin 0 -> 7080 bytes
.../CachingQueryReader$DownsampledInterval.class | Bin 0 -> 1405 bytes
.../igv/sam/CachingQueryReader$TiledIterator.class | Bin 0 -> 2330 bytes
org/broad/igv/sam/CachingQueryReader.class | Bin 0 -> 16164 bytes
org/broad/igv/sam/CoverageTrack$1.class | Bin 0 -> 2558 bytes
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org/broad/igv/sam/CoverageTrack$5.class | Bin 0 -> 1480 bytes
.../igv/sam/CoverageTrack$IntervalRenderer.class | Bin 0 -> 6706 bytes
org/broad/igv/sam/CoverageTrack.class | Bin 0 -> 19024 bytes
org/broad/igv/sam/DenseAlignmentCounts$1.class | Bin 0 -> 1004 bytes
org/broad/igv/sam/DenseAlignmentCounts.class | Bin 0 -> 7501 bytes
org/broad/igv/sam/DotAlignedAlignment.class | Bin 0 -> 5430 bytes
org/broad/igv/sam/EWigTrack.class | Bin 0 -> 7670 bytes
org/broad/igv/sam/EmptyAlignmentIterator.class | Bin 0 -> 1084 bytes
org/broad/igv/sam/FeatureRenderer.class | Bin 0 -> 702 bytes
org/broad/igv/sam/FeatureWrappedAlignment.class | Bin 0 -> 5886 bytes
org/broad/igv/sam/GeraldAlignment.class | Bin 0 -> 3547 bytes
org/broad/igv/sam/PEStats$Orientation.class | Bin 0 -> 1150 bytes
org/broad/igv/sam/PEStats.class | Bin 0 -> 2482 bytes
org/broad/igv/sam/PairedAlignment.class | Bin 0 -> 6510 bytes
org/broad/igv/sam/ReadMate.class | Bin 0 -> 1660 bytes
org/broad/igv/sam/SAMWriter.class | Bin 0 -> 2603 bytes
org/broad/igv/sam/SamAlignment$CigarOperator.class | Bin 0 -> 522 bytes
...mAlignment$FlowOrderAndSignalsBlockHelper.class | Bin 0 -> 2965 bytes
org/broad/igv/sam/SamAlignment.class | Bin 0 -> 20310 bytes
...rseAlignmentCounts$SparsePositionIterator.class | Bin 0 -> 1460 bytes
org/broad/igv/sam/SparseAlignmentCounts.class | Bin 0 -> 9052 bytes
.../igv/sam/SpliceJunctionFinderTrack$1.class | Bin 0 -> 894 bytes
org/broad/igv/sam/SpliceJunctionFinderTrack.class | Bin 0 -> 6931 bytes
org/broad/igv/sam/SpliceJunctionHelper$1.class | Bin 0 -> 1151 bytes
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org/broad/igv/sam/notes.txt | 41 +
org/broad/igv/sam/reader/AlignmentIndexer$1.class | Bin 0 -> 1209 bytes
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org/broad/igv/sam/reader/AlignmentReader.class | Bin 0 -> 685 bytes
.../igv/sam/reader/AlignmentReaderFactory.class | Bin 0 -> 7597 bytes
.../sam/reader/BAMFileReader$EmptyIterator.class | Bin 0 -> 1083 bytes
org/broad/igv/sam/reader/BAMFileReader.class | Bin 0 -> 4754 bytes
org/broad/igv/sam/reader/BAMHttpReader.class | Bin 0 -> 9734 bytes
.../BAMWebserviceReader$RemoteQueryIterator.class | Bin 0 -> 2479 bytes
org/broad/igv/sam/reader/BAMWebserviceReader.class | Bin 0 -> 5250 bytes
org/broad/igv/sam/reader/CGIAlignmentReader.class | Bin 0 -> 7953 bytes
org/broad/igv/sam/reader/DotAlignedCodec.class | Bin 0 -> 3192 bytes
org/broad/igv/sam/reader/DotAlignedIndexer.class | Bin 0 -> 1801 bytes
org/broad/igv/sam/reader/DotAlignedParser.class | Bin 0 -> 3433 bytes
.../sam/reader/FeatureIndex$ChromosomeIndex.class | Bin 0 -> 1921 bytes
.../igv/sam/reader/FeatureIndex$TileDef.class | Bin 0 -> 693 bytes
org/broad/igv/sam/reader/FeatureIndex.class | Bin 0 -> 6514 bytes
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org/broad/igv/sam/reader/GeraldParser.class | Bin 0 -> 7213 bytes
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.../reader/GeraldReader$GeraldQueryIterator.class | Bin 0 -> 3859 bytes
org/broad/igv/sam/reader/GeraldReader.class | Bin 0 -> 4266 bytes
org/broad/igv/sam/reader/IndexLoadException.class | Bin 0 -> 392 bytes
.../igv/sam/reader/IndexNotFoundException.class | Bin 0 -> 795 bytes
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...ader$MergedFileIterator$RecordIterWrapper.class | Bin 0 -> 2256 bytes
.../MergedAlignmentReader$MergedFileIterator.class | Bin 0 -> 4265 bytes
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...rgedFileIterator$AlignmentStartComparator.class | Bin 0 -> 2328 bytes
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...MergedAlignmentReader2$MergedFileIterator.class | Bin 0 -> 3972 bytes
.../igv/sam/reader/MergedAlignmentReader2.class | Bin 0 -> 3282 bytes
org/broad/igv/sam/reader/PSLAlignmentParser.class | Bin 0 -> 1282 bytes
org/broad/igv/sam/reader/ReadGroupFilter.class | Bin 0 -> 2928 bytes
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org/broad/igv/sam/reader/SAMFileGroup.class | Bin 0 -> 1462 bytes
org/broad/igv/sam/reader/SAMQueryIterator.class | Bin 0 -> 2628 bytes
org/broad/igv/sam/reader/SAMReader.class | Bin 0 -> 6587 bytes
org/broad/igv/sam/reader/SAMReaderTest.class | Bin 0 -> 7858 bytes
.../igv/sam/reader/SamIndexCreatorDialog$1.class | Bin 0 -> 925 bytes
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.../SamIndexCreatorDialog$ProgressListener.class | Bin 0 -> 1575 bytes
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org/broad/igv/sam/reader/SamIndexer.class | Bin 0 -> 1773 bytes
org/broad/igv/sam/reader/SamUtils.class | Bin 0 -> 4764 bytes
.../igv/sam/reader/SolexaQualityConverter.class | Bin 0 -> 1297 bytes
.../igv/sam/reader/UnsortedFileException.class | Bin 0 -> 780 bytes
org/broad/igv/sam/reader/WrappedIterator.class | Bin 0 -> 1421 bytes
org/broad/igv/session/History$Entry.class | Bin 0 -> 906 bytes
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org/broad/igv/session/IGVSessionReader$1.class | Bin 0 -> 3180 bytes
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org/broad/igv/session/IGVSessionReader.class | Bin 0 -> 28758 bytes
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org/broad/igv/session/Session$Locus.class | Bin 0 -> 562 bytes
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org/broad/igv/session/SessionWriter.class | Bin 0 -> 14145 bytes
org/broad/igv/session/UCSCSessionReader$1.class | Bin 0 -> 2003 bytes
org/broad/igv/session/UCSCSessionReader.class | Bin 0 -> 7393 bytes
org/broad/igv/synteny/AbstractMapping.class | Bin 0 -> 2209 bytes
org/broad/igv/synteny/Anchor.class | Bin 0 -> 640 bytes
org/broad/igv/synteny/BlastMapping$Block.class | Bin 0 -> 1303 bytes
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.../igv/synteny/BlastMappingUtils$BasicScore.class | Bin 0 -> 2145 bytes
org/broad/igv/synteny/BlastMappingUtils.class | Bin 0 -> 4910 bytes
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org/broad/igv/synteny/SyntenyUtils$1.class | Bin 0 -> 1030 bytes
org/broad/igv/synteny/SyntenyUtils.class | Bin 0 -> 12531 bytes
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org/broad/igv/tdf/TDFDataset$DataType.class | Bin 0 -> 1310 bytes
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org/broad/igv/tdf/TDFReader$IndexEntry.class | Bin 0 -> 595 bytes
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org/broad/igv/tdf/TDFUtils.class | Bin 0 -> 8366 bytes
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org/broad/igv/tdf/notes.txt | 77 +
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org/broad/igv/tools/sort/GFFSorter.class | Bin 0 -> 1347 bytes
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org/broad/igv/tools/sort/Parser.class | Bin 0 -> 2080 bytes
org/broad/igv/tools/sort/SAMSorter.class | Bin 0 -> 1258 bytes
org/broad/igv/tools/sort/SortableRecord.class | Bin 0 -> 777 bytes
org/broad/igv/tools/sort/SortableRecordCodec.class | Bin 0 -> 3403 bytes
org/broad/igv/tools/sort/SortedTxtSorter.class | Bin 0 -> 871 bytes
org/broad/igv/tools/sort/Sorter$1.class | Bin 0 -> 1958 bytes
org/broad/igv/tools/sort/Sorter.class | Bin 0 -> 7934 bytes
org/broad/igv/tools/sort/VCFSorter.class | Bin 0 -> 1636 bytes
org/broad/igv/tools/ui/CoverageGui$1.class | Bin 0 -> 745 bytes
org/broad/igv/tools/ui/CoverageGui$10.class | Bin 0 -> 3357 bytes
org/broad/igv/tools/ui/CoverageGui$11.class | Bin 0 -> 2782 bytes
org/broad/igv/tools/ui/CoverageGui$2.class | Bin 0 -> 841 bytes
org/broad/igv/tools/ui/CoverageGui$3.class | Bin 0 -> 806 bytes
org/broad/igv/tools/ui/CoverageGui$4.class | Bin 0 -> 841 bytes
org/broad/igv/tools/ui/CoverageGui$5.class | Bin 0 -> 853 bytes
org/broad/igv/tools/ui/CoverageGui$6.class | Bin 0 -> 841 bytes
org/broad/igv/tools/ui/CoverageGui$7.class | Bin 0 -> 841 bytes
org/broad/igv/tools/ui/CoverageGui$8.class | Bin 0 -> 882 bytes
org/broad/igv/tools/ui/CoverageGui$9.class | Bin 0 -> 1121 bytes
org/broad/igv/tools/ui/CoverageGui$Mode.class | Bin 0 -> 1135 bytes
org/broad/igv/tools/ui/CoverageGui.class | Bin 0 -> 16648 bytes
org/broad/igv/tools/ui/CoverageGui.jfd | 1166 ++++
org/broad/igv/tools/ui/IndexGui$1.class | Bin 0 -> 1854 bytes
org/broad/igv/tools/ui/IndexGui$2.class | Bin 0 -> 785 bytes
org/broad/igv/tools/ui/IndexGui$3.class | Bin 0 -> 820 bytes
org/broad/igv/tools/ui/IndexGui$4.class | Bin 0 -> 820 bytes
org/broad/igv/tools/ui/IndexGui.class | Bin 0 -> 7020 bytes
org/broad/igv/tools/ui/IndexGui.jfd | 590 ++
org/broad/igv/track/AbstractTrack$1.class | Bin 0 -> 863 bytes
org/broad/igv/track/AbstractTrack.class | Bin 0 -> 28436 bytes
.../track/AttributeManager$ColumnMetaData.class | Bin 0 -> 2317 bytes
org/broad/igv/track/AttributeManager.class | Bin 0 -> 15491 bytes
org/broad/igv/track/CNFreqTrack.class | Bin 0 -> 5683 bytes
.../track/CombinedFeatureSource$Operation.class | Bin 0 -> 1626 bytes
org/broad/igv/track/CombinedFeatureSource.class | Bin 0 -> 6996 bytes
org/broad/igv/track/DataSourceTrack.class | Bin 0 -> 4731 bytes
org/broad/igv/track/DataTrack$InViewInterval.class | Bin 0 -> 626 bytes
org/broad/igv/track/DataTrack.class | Bin 0 -> 13257 bytes
...eatureCollectionSource$CoverageDataSource.class | Bin 0 -> 6084 bytes
org/broad/igv/track/FeatureCollectionSource.class | Bin 0 -> 8103 bytes
org/broad/igv/track/FeatureDirSource.class | Bin 0 -> 5473 bytes
org/broad/igv/track/FeatureSource.class | Bin 0 -> 604 bytes
org/broad/igv/track/FeatureTrack$1.class | Bin 0 -> 3990 bytes
org/broad/igv/track/FeatureTrack.class | Bin 0 -> 25973 bytes
org/broad/igv/track/FeatureTrackUtils.class | Bin 0 -> 316 bytes
org/broad/igv/track/GisticTrack.class | Bin 0 -> 9410 bytes
org/broad/igv/track/LoadedDataInterval.class | Bin 0 -> 1172 bytes
org/broad/igv/track/MultiFileWrapper.class | Bin 0 -> 2498 bytes
org/broad/igv/track/MutationTrack$1$1.class | Bin 0 -> 818 bytes
org/broad/igv/track/MutationTrack$1.class | Bin 0 -> 2683 bytes
org/broad/igv/track/MutationTrack.class | Bin 0 -> 5552 bytes
org/broad/igv/track/PackedFeatures$1.class | Bin 0 -> 1270 bytes
.../igv/track/PackedFeatures$FeatureRow.class | Bin 0 -> 1466 bytes
org/broad/igv/track/PackedFeatures.class | Bin 0 -> 6820 bytes
.../track/PackedFeaturesSpliceJunctions$1.class | Bin 0 -> 1366 bytes
.../track/PackedFeaturesSpliceJunctions$2.class | Bin 0 -> 1459 bytes
...ns$IteratorSplitterByCharge$PerStrandIter.class | Bin 0 -> 2764 bytes
...sSpliceJunctions$IteratorSplitterByCharge.class | Bin 0 -> 2188 bytes
.../igv/track/PackedFeaturesSpliceJunctions.class | Bin 0 -> 7171 bytes
org/broad/igv/track/RegionScoreType.class | Bin 0 -> 1252 bytes
org/broad/igv/track/RenderContext.class | Bin 0 -> 681 bytes
org/broad/igv/track/RenderContextImpl.class | Bin 0 -> 3541 bytes
org/broad/igv/track/SequenceTrack$1.class | Bin 0 -> 844 bytes
org/broad/igv/track/SequenceTrack$2.class | Bin 0 -> 1223 bytes
org/broad/igv/track/SequenceTrack.class | Bin 0 -> 6706 bytes
org/broad/igv/track/TestUtils.class | Bin 0 -> 1487 bytes
org/broad/igv/track/Track$DisplayMode.class | Bin 0 -> 1171 bytes
org/broad/igv/track/Track.class | Bin 0 -> 3639 bytes
org/broad/igv/track/TrackClickEvent.class | Bin 0 -> 1031 bytes
org/broad/igv/track/TrackGroup$1.class | Bin 0 -> 2145 bytes
org/broad/igv/track/TrackGroup$2.class | Bin 0 -> 1647 bytes
org/broad/igv/track/TrackGroup$3.class | Bin 0 -> 1609 bytes
org/broad/igv/track/TrackGroup.class | Bin 0 -> 9743 bytes
org/broad/igv/track/TrackLoader.class | Bin 0 -> 41603 bytes
org/broad/igv/track/TrackMenuUtils$1.class | Bin 0 -> 1206 bytes
org/broad/igv/track/TrackMenuUtils$10.class | Bin 0 -> 1935 bytes
org/broad/igv/track/TrackMenuUtils$11.class | Bin 0 -> 2680 bytes
org/broad/igv/track/TrackMenuUtils$12.class | Bin 0 -> 1042 bytes
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org/broad/igv/track/TrackMenuUtils$14.class | Bin 0 -> 1542 bytes
org/broad/igv/track/TrackMenuUtils$15.class | Bin 0 -> 1545 bytes
org/broad/igv/track/TrackMenuUtils$16.class | Bin 0 -> 1066 bytes
org/broad/igv/track/TrackMenuUtils$17.class | Bin 0 -> 1066 bytes
org/broad/igv/track/TrackMenuUtils$18.class | Bin 0 -> 1067 bytes
org/broad/igv/track/TrackMenuUtils$19.class | Bin 0 -> 2748 bytes
org/broad/igv/track/TrackMenuUtils$2.class | Bin 0 -> 887 bytes
org/broad/igv/track/TrackMenuUtils$20.class | Bin 0 -> 2337 bytes
org/broad/igv/track/TrackMenuUtils$21.class | Bin 0 -> 1384 bytes
org/broad/igv/track/TrackMenuUtils$22.class | Bin 0 -> 828 bytes
org/broad/igv/track/TrackMenuUtils$23.class | Bin 0 -> 1298 bytes
org/broad/igv/track/TrackMenuUtils$24.class | Bin 0 -> 838 bytes
org/broad/igv/track/TrackMenuUtils$25.class | Bin 0 -> 822 bytes
org/broad/igv/track/TrackMenuUtils$26.class | Bin 0 -> 928 bytes
org/broad/igv/track/TrackMenuUtils$3.class | Bin 0 -> 905 bytes
org/broad/igv/track/TrackMenuUtils$4.class | Bin 0 -> 905 bytes
org/broad/igv/track/TrackMenuUtils$5.class | Bin 0 -> 889 bytes
org/broad/igv/track/TrackMenuUtils$6.class | Bin 0 -> 1045 bytes
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org/broad/igv/track/TrackMenuUtils$8.class | Bin 0 -> 813 bytes
org/broad/igv/track/TrackMenuUtils$9$1.class | Bin 0 -> 852 bytes
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org/broad/igv/track/TrackMenuUtils.class | Bin 0 -> 22593 bytes
.../igv/track/TrackProperties$BaseCoord.class | Bin 0 -> 1230 bytes
org/broad/igv/track/TrackProperties.class | Bin 0 -> 9143 bytes
org/broad/igv/track/TrackReader.class | Bin 0 -> 236 bytes
org/broad/igv/track/TrackSet.class | Bin 0 -> 1141 bytes
org/broad/igv/track/TrackType.class | Bin 0 -> 1928 bytes
org/broad/igv/track/TribbleFeatureSource.class | Bin 0 -> 6755 bytes
org/broad/igv/track/WindowFunction.class | Bin 0 -> 2642 bytes
org/broad/igv/ui/AWTFrameTest$TestPanel.class | Bin 0 -> 768 bytes
org/broad/igv/ui/AWTFrameTest.class | Bin 0 -> 1607 bytes
org/broad/igv/ui/AboutDialog$1.class | Bin 0 -> 807 bytes
org/broad/igv/ui/AboutDialog$2$1.class | Bin 0 -> 740 bytes
org/broad/igv/ui/AboutDialog$2.class | Bin 0 -> 868 bytes
org/broad/igv/ui/AboutDialog.class | Bin 0 -> 3889 bytes
org/broad/igv/ui/AbstractDataPanelTool.class | Bin 0 -> 1621 bytes
org/broad/igv/ui/AttributeCheckList.class | Bin 0 -> 569 bytes
org/broad/igv/ui/AttributeSelectionDialog$1.class | Bin 0 -> 898 bytes
org/broad/igv/ui/AttributeSelectionDialog$2.class | Bin 0 -> 898 bytes
org/broad/igv/ui/AttributeSelectionDialog$3.class | Bin 0 -> 685 bytes
org/broad/igv/ui/AttributeSelectionDialog.class | Bin 0 -> 5146 bytes
org/broad/igv/ui/DataRangeDialog$1.class | Bin 0 -> 835 bytes
org/broad/igv/ui/DataRangeDialog$2.class | Bin 0 -> 835 bytes
org/broad/igv/ui/DataRangeDialog$3$1.class | Bin 0 -> 764 bytes
org/broad/igv/ui/DataRangeDialog$3.class | Bin 0 -> 929 bytes
org/broad/igv/ui/DataRangeDialog.class | Bin 0 -> 6380 bytes
org/broad/igv/ui/DefaultExceptionHandler.class | Bin 0 -> 1348 bytes
org/broad/igv/ui/FontManager.class | Bin 0 -> 2239 bytes
org/broad/igv/ui/GenomeSelectionDialog$1.class | Bin 0 -> 875 bytes
org/broad/igv/ui/GenomeSelectionDialog$2.class | Bin 0 -> 875 bytes
org/broad/igv/ui/GenomeSelectionDialog$3.class | Bin 0 -> 673 bytes
org/broad/igv/ui/GenomeSelectionDialog.class | Bin 0 -> 5604 bytes
org/broad/igv/ui/HeatmapDialog$1.class | Bin 0 -> 730 bytes
org/broad/igv/ui/HeatmapDialog$2.class | Bin 0 -> 730 bytes
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org/broad/igv/ui/HeatmapScaleDialog$1.class | Bin 0 -> 819 bytes
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org/broad/igv/ui/HeatmapScaleDialog$6.class | Bin 0 -> 854 bytes
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org/broad/igv/ui/HeatmapScaleDialog$8.class | Bin 0 -> 854 bytes
org/broad/igv/ui/HeatmapScaleDialog$9.class | Bin 0 -> 854 bytes
.../igv/ui/HeatmapScaleDialog$LegendPanel.class | Bin 0 -> 2595 bytes
org/broad/igv/ui/HeatmapScaleDialog.class | Bin 0 -> 12185 bytes
org/broad/igv/ui/IGV$1.class | Bin 0 -> 1732 bytes
org/broad/igv/ui/IGV$10.class | Bin 0 -> 2926 bytes
org/broad/igv/ui/IGV$11.class | Bin 0 -> 2072 bytes
org/broad/igv/ui/IGV$2.class | Bin 0 -> 483 bytes
org/broad/igv/ui/IGV$3.class | Bin 0 -> 946 bytes
org/broad/igv/ui/IGV$4.class | Bin 0 -> 4402 bytes
org/broad/igv/ui/IGV$5.class | Bin 0 -> 2169 bytes
org/broad/igv/ui/IGV$6.class | Bin 0 -> 1512 bytes
org/broad/igv/ui/IGV$7.class | Bin 0 -> 880 bytes
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org/broad/igv/ui/IGV$9.class | Bin 0 -> 1217 bytes
org/broad/igv/ui/IGV$StartupRunnable$1.class | Bin 0 -> 1373 bytes
org/broad/igv/ui/IGV$StartupRunnable.class | Bin 0 -> 6142 bytes
org/broad/igv/ui/IGV.class | Bin 0 -> 62272 bytes
org/broad/igv/ui/IGVCommandBar$1.class | Bin 0 -> 880 bytes
org/broad/igv/ui/IGVCommandBar$10.class | Bin 0 -> 823 bytes
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org/broad/igv/ui/IGVCommandBar$13.class | Bin 0 -> 1486 bytes
org/broad/igv/ui/IGVCommandBar$14.class | Bin 0 -> 1683 bytes
org/broad/igv/ui/IGVCommandBar$15.class | Bin 0 -> 1671 bytes
org/broad/igv/ui/IGVCommandBar$2.class | Bin 0 -> 881 bytes
org/broad/igv/ui/IGVCommandBar$3.class | Bin 0 -> 712 bytes
org/broad/igv/ui/IGVCommandBar$4.class | Bin 0 -> 877 bytes
org/broad/igv/ui/IGVCommandBar$5.class | Bin 0 -> 821 bytes
org/broad/igv/ui/IGVCommandBar$6.class | Bin 0 -> 821 bytes
org/broad/igv/ui/IGVCommandBar$7.class | Bin 0 -> 821 bytes
org/broad/igv/ui/IGVCommandBar$8.class | Bin 0 -> 1018 bytes
org/broad/igv/ui/IGVCommandBar$9.class | Bin 0 -> 1021 bytes
.../igv/ui/IGVCommandBar$ComboBoxRenderer.class | Bin 0 -> 2026 bytes
.../IGVCommandBar$GenomeBoxActionListener$1.class | Bin 0 -> 4988 bytes
.../ui/IGVCommandBar$GenomeBoxActionListener.class | Bin 0 -> 1069 bytes
org/broad/igv/ui/IGVCommandBar$SearchHints.class | Bin 0 -> 2041 bytes
org/broad/igv/ui/IGVCommandBar.class | Bin 0 -> 23656 bytes
org/broad/igv/ui/IGVContentPane.class | Bin 0 -> 4611 bytes
org/broad/igv/ui/IGVMainFrame.class | Bin 0 -> 458 bytes
org/broad/igv/ui/IGVMenuBar$1.class | Bin 0 -> 1163 bytes
org/broad/igv/ui/IGVMenuBar$10.class | Bin 0 -> 1474 bytes
org/broad/igv/ui/IGVMenuBar$11.class | Bin 0 -> 1010 bytes
org/broad/igv/ui/IGVMenuBar$12.class | Bin 0 -> 1426 bytes
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org/broad/igv/ui/IGVMenuBar$2.class | Bin 0 -> 1165 bytes
org/broad/igv/ui/IGVMenuBar$20.class | Bin 0 -> 1482 bytes
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org/broad/igv/ui/IGVMenuBar$24$1.class | Bin 0 -> 1235 bytes
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org/broad/igv/ui/IGVMenuBar$3.class | Bin 0 -> 1077 bytes
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org/broad/igv/ui/IGVMenuBar$6$1.class | Bin 0 -> 768 bytes
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org/broad/igv/ui/IGVMenuBar$7.class | Bin 0 -> 1068 bytes
org/broad/igv/ui/IGVMenuBar$8.class | Bin 0 -> 1431 bytes
org/broad/igv/ui/IGVMenuBar$9.class | Bin 0 -> 2259 bytes
org/broad/igv/ui/IGVMenuBar.class | Bin 0 -> 16300 bytes
org/broad/igv/ui/InsertSizeSettingsDialog$1.class | Bin 0 -> 896 bytes
org/broad/igv/ui/InsertSizeSettingsDialog$10.class | Bin 0 -> 910 bytes
org/broad/igv/ui/InsertSizeSettingsDialog$11.class | Bin 0 -> 899 bytes
org/broad/igv/ui/InsertSizeSettingsDialog$2.class | Bin 0 -> 896 bytes
org/broad/igv/ui/InsertSizeSettingsDialog$3.class | Bin 0 -> 861 bytes
org/broad/igv/ui/InsertSizeSettingsDialog$4.class | Bin 0 -> 920 bytes
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org/broad/igv/ui/InsertSizeSettingsDialog.class | Bin 0 -> 11570 bytes
org/broad/igv/ui/InsertSizeSettingsDialog.jfd | 620 +++
org/broad/igv/ui/Main$1.class | Bin 0 -> 739 bytes
org/broad/igv/ui/Main$2.class | Bin 0 -> 1037 bytes
org/broad/igv/ui/Main$IGVArgs.class | Bin 0 -> 4113 bytes
org/broad/igv/ui/Main.class | Bin 0 -> 4877 bytes
org/broad/igv/ui/MessageCollection.class | Bin 0 -> 1854 bytes
org/broad/igv/ui/PreferencesEditor$1.class | Bin 0 -> 1302 bytes
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org/broad/igv/ui/PreferencesEditor$86.class | Bin 0 -> 815 bytes
org/broad/igv/ui/PreferencesEditor$87.class | Bin 0 -> 850 bytes
org/broad/igv/ui/PreferencesEditor$88.class | Bin 0 -> 815 bytes
org/broad/igv/ui/PreferencesEditor$89.class | Bin 0 -> 850 bytes
org/broad/igv/ui/PreferencesEditor$9.class | Bin 0 -> 847 bytes
org/broad/igv/ui/PreferencesEditor$90.class | Bin 0 -> 815 bytes
org/broad/igv/ui/PreferencesEditor$91.class | Bin 0 -> 850 bytes
org/broad/igv/ui/PreferencesEditor$92.class | Bin 0 -> 815 bytes
org/broad/igv/ui/PreferencesEditor$93.class | Bin 0 -> 850 bytes
org/broad/igv/ui/PreferencesEditor$94.class | Bin 0 -> 850 bytes
org/broad/igv/ui/PreferencesEditor$95.class | Bin 0 -> 850 bytes
org/broad/igv/ui/PreferencesEditor$96.class | Bin 0 -> 815 bytes
org/broad/igv/ui/PreferencesEditor$97.class | Bin 0 -> 850 bytes
org/broad/igv/ui/PreferencesEditor$98.class | Bin 0 -> 815 bytes
org/broad/igv/ui/PreferencesEditor$99.class | Bin 0 -> 850 bytes
org/broad/igv/ui/PreferencesEditor.class | Bin 0 -> 86029 bytes
org/broad/igv/ui/PreferencesEditor.jfd | 5555 +++++++++++++++++++
org/broad/igv/ui/ReadmeParser.class | Bin 0 -> 3545 bytes
org/broad/igv/ui/ResourceFileBuilder.class | Bin 0 -> 9495 bytes
org/broad/igv/ui/ResourceFileBuilderDialog.class | Bin 0 -> 1262 bytes
org/broad/igv/ui/ResourceTree$1.class | Bin 0 -> 2793 bytes
.../igv/ui/ResourceTree$CancelableOptionPane.class | Bin 0 -> 747 bytes
.../igv/ui/ResourceTree$CheckableResource.class | Bin 0 -> 2553 bytes
org/broad/igv/ui/ResourceTree$DataResource.class | Bin 0 -> 423 bytes
org/broad/igv/ui/ResourceTree$NodeRenderer.class | Bin 0 -> 3389 bytes
.../igv/ui/ResourceTree$ResourceEditor$1.class | Bin 0 -> 1035 bytes
org/broad/igv/ui/ResourceTree$ResourceEditor.class | Bin 0 -> 7230 bytes
.../igv/ui/ResourceTree$SelectableResource.class | Bin 0 -> 357 bytes
.../igv/ui/ResourceTree$TreeExpansionFlag.class | Bin 0 -> 1277 bytes
org/broad/igv/ui/ResourceTree.class | Bin 0 -> 18473 bytes
org/broad/igv/ui/ShutdownThread.class | Bin 0 -> 3444 bytes
org/broad/igv/ui/SimpleFormDialog.jfd | 244 +
org/broad/igv/ui/StatusWindow.class | Bin 0 -> 1347 bytes
org/broad/igv/ui/StatusWindow.jfd | 70 +
org/broad/igv/ui/TestLauncher$1.class | Bin 0 -> 749 bytes
org/broad/igv/ui/TestLauncher.class | Bin 0 -> 584 bytes
org/broad/igv/ui/TooltipTextFrame$1.class | Bin 0 -> 1222 bytes
org/broad/igv/ui/TooltipTextFrame$2.class | Bin 0 -> 1399 bytes
.../ui/TooltipTextFrame$MyTransferHandler$1.class | Bin 0 -> 2119 bytes
.../ui/TooltipTextFrame$MyTransferHandler.class | Bin 0 -> 3304 bytes
.../igv/ui/TooltipTextFrame$MyTransferable.class | Bin 0 -> 1692 bytes
org/broad/igv/ui/TooltipTextFrame.class | Bin 0 -> 5805 bytes
org/broad/igv/ui/TrackConfigurationDialog$1.class | Bin 0 -> 898 bytes
org/broad/igv/ui/TrackConfigurationDialog$2.class | Bin 0 -> 898 bytes
.../igv/ui/TrackConfigurationDialog$3$1.class | Bin 0 -> 818 bytes
org/broad/igv/ui/TrackConfigurationDialog$3.class | Bin 0 -> 959 bytes
org/broad/igv/ui/TrackConfigurationDialog.class | Bin 0 -> 8549 bytes
org/broad/igv/ui/TrackFilter.class | Bin 0 -> 2230 bytes
org/broad/igv/ui/TrackFilterComponent.class | Bin 0 -> 2987 bytes
org/broad/igv/ui/TrackFilterElement.class | Bin 0 -> 1602 bytes
org/broad/igv/ui/TrackFilterPane.class | Bin 0 -> 3174 bytes
org/broad/igv/ui/UIConstants.class | Bin 0 -> 4640 bytes
org/broad/igv/ui/UserDefinedGenomeCheckList.class | Bin 0 -> 801 bytes
org/broad/igv/ui/UserPasswordPane.class | Bin 0 -> 2091 bytes
.../igv/ui/WaitCursorManager$CursorToken.class | Bin 0 -> 419 bytes
org/broad/igv/ui/WaitCursorManager.class | Bin 0 -> 1606 bytes
.../igv/ui/action/ClearGenomeCacheAction$1.class | Bin 0 -> 887 bytes
.../igv/ui/action/ClearGenomeCacheAction.class | Bin 0 -> 2266 bytes
.../igv/ui/action/ClearRegionsMenuAction$1.class | Bin 0 -> 1327 bytes
.../igv/ui/action/ClearRegionsMenuAction.class | Bin 0 -> 1292 bytes
org/broad/igv/ui/action/Command.class | Bin 0 -> 143 bytes
.../igv/ui/action/ExportRegionsMenuAction$1.class | Bin 0 -> 793 bytes
.../igv/ui/action/ExportRegionsMenuAction.class | Bin 0 -> 4358 bytes
.../igv/ui/action/ExportTrackNamesMenuAction.class | Bin 0 -> 4246 bytes
.../igv/ui/action/FilterTracksMenuAction$1.class | Bin 0 -> 1107 bytes
.../igv/ui/action/FilterTracksMenuAction$2.class | Bin 0 -> 1107 bytes
.../igv/ui/action/FilterTracksMenuAction$3.class | Bin 0 -> 1458 bytes
.../igv/ui/action/FilterTracksMenuAction.class | Bin 0 -> 8979 bytes
.../igv/ui/action/FitDataToWindowMenuAction.class | Bin 0 -> 3400 bytes
.../igv/ui/action/GroupTracksMenuAction$1.class | Bin 0 -> 767 bytes
.../igv/ui/action/GroupTracksMenuAction.class | Bin 0 -> 2825 bytes
.../igv/ui/action/ImportRegionsMenuAction$1.class | Bin 0 -> 1085 bytes
.../igv/ui/action/ImportRegionsMenuAction.class | Bin 0 -> 3974 bytes
org/broad/igv/ui/action/LoadFilesMenuAction.class | Bin 0 -> 3821 bytes
.../igv/ui/action/LoadFromDatabaseAction$1.class | Bin 0 -> 2892 bytes
.../igv/ui/action/LoadFromDatabaseAction.class | Bin 0 -> 1340 bytes
org/broad/igv/ui/action/LoadFromGSMenuAction.class | Bin 0 -> 2230 bytes
org/broad/igv/ui/action/LoadFromServerAction.class | Bin 0 -> 9922 bytes
.../igv/ui/action/LoadFromURLMenuAction.class | Bin 0 -> 3419 bytes
org/broad/igv/ui/action/MenuAction.class | Bin 0 -> 1358 bytes
.../ui/action/NavigateRegionsMenuAction$1.class | Bin 0 -> 1216 bytes
.../igv/ui/action/NavigateRegionsMenuAction.class | Bin 0 -> 1289 bytes
org/broad/igv/ui/action/NewSessionMenuAction.class | Bin 0 -> 815 bytes
.../igv/ui/action/OpenSessionMenuAction.class | Bin 0 -> 3033 bytes
.../action/RemoveUserDefinedGenomeMenuAction.class | Bin 0 -> 4183 bytes
.../igv/ui/action/ResetPreferencesAction$1.class | Bin 0 -> 771 bytes
.../igv/ui/action/ResetPreferencesAction.class | Bin 0 -> 1566 bytes
.../igv/ui/action/RunScriptMenuAction$1.class | Bin 0 -> 953 bytes
org/broad/igv/ui/action/RunScriptMenuAction.class | Bin 0 -> 2424 bytes
.../igv/ui/action/SaveSessionMenuAction.class | Bin 0 -> 3642 bytes
org/broad/igv/ui/action/SearchCommand$1.class | Bin 0 -> 1270 bytes
org/broad/igv/ui/action/SearchCommand$2.class | Bin 0 -> 997 bytes
.../igv/ui/action/SearchCommand$ResultType.class | Bin 0 -> 1436 bytes
.../igv/ui/action/SearchCommand$SearchResult.class | Bin 0 -> 2841 bytes
org/broad/igv/ui/action/SearchCommand.class | Bin 0 -> 15851 bytes
.../igv/ui/action/SetTrackHeightMenuAction.class | Bin 0 -> 3992 bytes
.../igv/ui/action/SortTracksMenuAction$1.class | Bin 0 -> 774 bytes
org/broad/igv/ui/action/SortTracksMenuAction.class | Bin 0 -> 2206 bytes
org/broad/igv/ui/color/ColorChooserPanel$1.class | Bin 0 -> 860 bytes
org/broad/igv/ui/color/ColorChooserPanel$2.class | Bin 0 -> 883 bytes
org/broad/igv/ui/color/ColorChooserPanel.class | Bin 0 -> 4979 bytes
org/broad/igv/ui/color/ColorPalette.class | Bin 0 -> 672 bytes
org/broad/igv/ui/color/ColorPanel$1.class | Bin 0 -> 1895 bytes
org/broad/igv/ui/color/ColorPanel$Palette.class | Bin 0 -> 982 bytes
org/broad/igv/ui/color/ColorPanel$Swatch.class | Bin 0 -> 573 bytes
org/broad/igv/ui/color/ColorPanel.class | Bin 0 -> 3979 bytes
org/broad/igv/ui/color/ColorTable.class | Bin 0 -> 177 bytes
org/broad/igv/ui/color/ColorUtilities.class | Bin 0 -> 9667 bytes
org/broad/igv/ui/color/PaletteColorTable.class | Bin 0 -> 4616 bytes
org/broad/igv/ui/color/PaletteToolFrame$1.class | Bin 0 -> 876 bytes
org/broad/igv/ui/color/PaletteToolFrame$2.class | Bin 0 -> 876 bytes
org/broad/igv/ui/color/PaletteToolFrame.class | Bin 0 -> 4994 bytes
org/broad/igv/ui/color/PaletteToolFrame.jfd | 137 +
org/broad/igv/ui/color/resources/colorPalettes.txt | 20 +
.../igv/ui/dnd/AbstractGhostDropManager.class | Bin 0 -> 1387 bytes
org/broad/igv/ui/dnd/GhostDropAdapter.class | Bin 0 -> 1570 bytes
org/broad/igv/ui/dnd/GhostDropEvent.class | Bin 0 -> 2176 bytes
org/broad/igv/ui/dnd/GhostDropListener.class | Bin 0 -> 202 bytes
org/broad/igv/ui/dnd/GhostGlassPane.class | Bin 0 -> 1515 bytes
.../igv/ui/event/AlignmentTrackEvent$Type.class | Bin 0 -> 1264 bytes
org/broad/igv/ui/event/AlignmentTrackEvent.class | Bin 0 -> 781 bytes
.../igv/ui/event/AlignmentTrackEventListener.class | Bin 0 -> 271 bytes
org/broad/igv/ui/event/GlobalKeyDispatcher$1.class | Bin 0 -> 911 bytes
.../igv/ui/event/GlobalKeyDispatcher$10.class | Bin 0 -> 1050 bytes
.../igv/ui/event/GlobalKeyDispatcher$11.class | Bin 0 -> 1409 bytes
org/broad/igv/ui/event/GlobalKeyDispatcher$2.class | Bin 0 -> 911 bytes
org/broad/igv/ui/event/GlobalKeyDispatcher$3.class | Bin 0 -> 881 bytes
org/broad/igv/ui/event/GlobalKeyDispatcher$4.class | Bin 0 -> 881 bytes
org/broad/igv/ui/event/GlobalKeyDispatcher$5.class | Bin 0 -> 881 bytes
org/broad/igv/ui/event/GlobalKeyDispatcher$6.class | Bin 0 -> 881 bytes
org/broad/igv/ui/event/GlobalKeyDispatcher$7.class | Bin 0 -> 1700 bytes
org/broad/igv/ui/event/GlobalKeyDispatcher$8.class | Bin 0 -> 1492 bytes
org/broad/igv/ui/event/GlobalKeyDispatcher$9.class | Bin 0 -> 1045 bytes
org/broad/igv/ui/event/GlobalKeyDispatcher.class | Bin 0 -> 9470 bytes
org/broad/igv/ui/event/TrackGroupEvent.class | Bin 0 -> 384 bytes
.../igv/ui/event/TrackGroupEventListener.class | Bin 0 -> 255 bytes
.../igv/ui/filefilters/AlignmentFileFilter.class | Bin 0 -> 1142 bytes
.../igv/ui/filefilters/CoverageFileFilter.class | Bin 0 -> 1004 bytes
.../igv/ui/legend/ChromosomeColorLegend.class | Bin 0 -> 2119 bytes
org/broad/igv/ui/legend/ColorMapEditor$1.class | Bin 0 -> 1724 bytes
org/broad/igv/ui/legend/ColorMapEditor$2.class | Bin 0 -> 842 bytes
org/broad/igv/ui/legend/ColorMapEditor$3.class | Bin 0 -> 879 bytes
org/broad/igv/ui/legend/ColorMapEditor.class | Bin 0 -> 4913 bytes
.../igv/ui/legend/HeatmapLegendEditor$1.class | Bin 0 -> 903 bytes
.../igv/ui/legend/HeatmapLegendEditor$2.class | Bin 0 -> 903 bytes
.../igv/ui/legend/HeatmapLegendEditor$3.class | Bin 0 -> 903 bytes
.../igv/ui/legend/HeatmapLegendEditor$4.class | Bin 0 -> 903 bytes
org/broad/igv/ui/legend/HeatmapLegendEditor.class | Bin 0 -> 10162 bytes
org/broad/igv/ui/legend/HeatmapLegendEditor.jfd | 367 ++
.../igv/ui/legend/HeatmapLegendPanel$1$1.class | Bin 0 -> 910 bytes
org/broad/igv/ui/legend/HeatmapLegendPanel$1.class | Bin 0 -> 2242 bytes
.../ui/legend/HeatmapLegendPanel$Orientation.class | Bin 0 -> 1249 bytes
org/broad/igv/ui/legend/HeatmapLegendPanel.class | Bin 0 -> 5025 bytes
org/broad/igv/ui/legend/LegendDialog$1.class | Bin 0 -> 854 bytes
org/broad/igv/ui/legend/LegendDialog$2.class | Bin 0 -> 854 bytes
org/broad/igv/ui/legend/LegendDialog$3.class | Bin 0 -> 854 bytes
org/broad/igv/ui/legend/LegendDialog$4.class | Bin 0 -> 854 bytes
org/broad/igv/ui/legend/LegendDialog$5.class | Bin 0 -> 854 bytes
org/broad/igv/ui/legend/LegendDialog$6.class | Bin 0 -> 854 bytes
org/broad/igv/ui/legend/LegendDialog$7.class | Bin 0 -> 854 bytes
org/broad/igv/ui/legend/LegendDialog$8.class | Bin 0 -> 854 bytes
org/broad/igv/ui/legend/LegendDialog$9$1.class | Bin 0 -> 781 bytes
org/broad/igv/ui/legend/LegendDialog$9.class | Bin 0 -> 915 bytes
org/broad/igv/ui/legend/LegendDialog.class | Bin 0 -> 10324 bytes
org/broad/igv/ui/legend/LegendDialog.jfd | 821 +++
org/broad/igv/ui/legend/LegendPanel$1.class | Bin 0 -> 1024 bytes
org/broad/igv/ui/legend/LegendPanel$2.class | Bin 0 -> 722 bytes
org/broad/igv/ui/legend/LegendPanel.class | Bin 0 -> 1756 bytes
org/broad/igv/ui/legend/LohLegendPanel.class | Bin 0 -> 2284 bytes
org/broad/igv/ui/legend/MutationLegendPanel.class | Bin 0 -> 4758 bytes
.../igv/ui/panel/AttributeHeaderPanel$1.class | Bin 0 -> 2557 bytes
org/broad/igv/ui/panel/AttributeHeaderPanel.class | Bin 0 -> 5064 bytes
...AttributePanel$AttributePanelMouseAdapter.class | Bin 0 -> 1974 bytes
org/broad/igv/ui/panel/AttributePanel.class | Bin 0 -> 8248 bytes
org/broad/igv/ui/panel/ClickTaskScheduler.class | Bin 0 -> 888 bytes
org/broad/igv/ui/panel/CytobandPanel$1.class | Bin 0 -> 3478 bytes
org/broad/igv/ui/panel/CytobandPanel.class | Bin 0 -> 5041 bytes
org/broad/igv/ui/panel/DataPanel$1.class | Bin 0 -> 2062 bytes
.../panel/DataPanel$DataPanelMouseAdapter$1.class | Bin 0 -> 2626 bytes
.../ui/panel/DataPanel$DataPanelMouseAdapter.class | Bin 0 -> 4763 bytes
.../igv/ui/panel/DataPanel$PopupTextUpdater.class | Bin 0 -> 1093 bytes
org/broad/igv/ui/panel/DataPanel.class | Bin 0 -> 15769 bytes
org/broad/igv/ui/panel/DataPanelContainer$1.class | Bin 0 -> 1156 bytes
...DataPanelContainer$FileDropTargetListener.class | Bin 0 -> 4578 bytes
org/broad/igv/ui/panel/DataPanelContainer.class | Bin 0 -> 4605 bytes
org/broad/igv/ui/panel/DataPanelLayout.class | Bin 0 -> 4248 bytes
org/broad/igv/ui/panel/DataPanelPainter.class | Bin 0 -> 4188 bytes
.../igv/ui/panel/DragAndDropTransferHandler.class | Bin 0 -> 1051 bytes
org/broad/igv/ui/panel/DragEvent.class | Bin 0 -> 298 bytes
org/broad/igv/ui/panel/DragEventManager.class | Bin 0 -> 1622 bytes
org/broad/igv/ui/panel/DragListener.class | Bin 0 -> 190 bytes
org/broad/igv/ui/panel/FrameManager.class | Bin 0 -> 6939 bytes
.../igv/ui/panel/HeaderDropTargetListener.class | Bin 0 -> 3501 bytes
org/broad/igv/ui/panel/HeaderPanel$1.class | Bin 0 -> 2220 bytes
org/broad/igv/ui/panel/HeaderPanel$2.class | Bin 0 -> 1181 bytes
org/broad/igv/ui/panel/HeaderPanel$3.class | Bin 0 -> 1145 bytes
.../HeaderPanel$HeaderDropTargetListener.class | Bin 0 -> 3611 bytes
org/broad/igv/ui/panel/HeaderPanel.class | Bin 0 -> 8587 bytes
org/broad/igv/ui/panel/HeaderPanelContainer.class | Bin 0 -> 3893 bytes
org/broad/igv/ui/panel/IGVPanel.class | Bin 0 -> 3301 bytes
org/broad/igv/ui/panel/IGVPopupMenu$1.class | Bin 0 -> 1308 bytes
org/broad/igv/ui/panel/IGVPopupMenu.class | Bin 0 -> 1266 bytes
org/broad/igv/ui/panel/MainPanel$1.class | Bin 0 -> 1076 bytes
org/broad/igv/ui/panel/MainPanel$2.class | Bin 0 -> 778 bytes
org/broad/igv/ui/panel/MainPanel$3.class | Bin 0 -> 1367 bytes
org/broad/igv/ui/panel/MainPanel$4.class | Bin 0 -> 1102 bytes
org/broad/igv/ui/panel/MainPanel$SplitPane.class | Bin 0 -> 720 bytes
org/broad/igv/ui/panel/MainPanel.class | Bin 0 -> 16400 bytes
.../MouseableRegion$AttributePanelRegion.class | Bin 0 -> 2089 bytes
.../panel/MouseableRegion$SingleTrackRegion.class | Bin 0 -> 1237 bytes
.../igv/ui/panel/MouseableRegion$TrackCltn.class | Bin 0 -> 392 bytes
org/broad/igv/ui/panel/MouseableRegion.class | Bin 0 -> 2460 bytes
org/broad/igv/ui/panel/NameHeaderPanel.class | Bin 0 -> 618 bytes
org/broad/igv/ui/panel/Paintable.class | Bin 0 -> 194 bytes
org/broad/igv/ui/panel/PanTool.class | Bin 0 -> 3534 bytes
org/broad/igv/ui/panel/ReferenceFrame$Range.class | Bin 0 -> 912 bytes
org/broad/igv/ui/panel/ReferenceFrame.class | Bin 0 -> 12953 bytes
org/broad/igv/ui/panel/RegionMenu$1.class | Bin 0 -> 1405 bytes
org/broad/igv/ui/panel/RegionMenu$2.class | Bin 0 -> 1535 bytes
org/broad/igv/ui/panel/RegionMenu$3.class | Bin 0 -> 1531 bytes
org/broad/igv/ui/panel/RegionMenu$4.class | Bin 0 -> 1537 bytes
org/broad/igv/ui/panel/RegionMenu$5.class | Bin 0 -> 1541 bytes
org/broad/igv/ui/panel/RegionMenu$6.class | Bin 0 -> 1532 bytes
org/broad/igv/ui/panel/RegionMenu$7.class | Bin 0 -> 1489 bytes
org/broad/igv/ui/panel/RegionMenu.class | Bin 0 -> 3372 bytes
.../igv/ui/panel/RegionNavigatorDialog$1.class | Bin 0 -> 887 bytes
.../igv/ui/panel/RegionNavigatorDialog$2.class | Bin 0 -> 1357 bytes
.../igv/ui/panel/RegionNavigatorDialog$3.class | Bin 0 -> 880 bytes
.../RegionNavigatorDialog$AddRegionAction.class | Bin 0 -> 2919 bytes
.../panel/RegionNavigatorDialog$CancelAction.class | Bin 0 -> 1416 bytes
.../RegionNavigatorDialog$RegionRowFilter.class | Bin 0 -> 1072 bytes
...nNavigatorDialog$RegionTableModelListener.class | Bin 0 -> 2031 bytes
...NavigatorDialog$RegionTablePopupHandler$1.class | Bin 0 -> 1893 bytes
...NavigatorDialog$RegionTablePopupHandler$2.class | Bin 0 -> 1738 bytes
...onNavigatorDialog$RegionTablePopupHandler.class | Bin 0 -> 3334 bytes
...igatorDialog$RegionTableSelectionListener.class | Bin 0 -> 2839 bytes
...vigatorDialog$RemoveSelectedRegionsAction.class | Bin 0 -> 2354 bytes
...vigatorDialog$SearchFieldDocumentListener.class | Bin 0 -> 1702 bytes
...orDialog$ShowAllChromosomesCheckboxAction.class | Bin 0 -> 1308 bytes
.../RegionNavigatorDialog$ViewSelectedAction.class | Bin 0 -> 3739 bytes
org/broad/igv/ui/panel/RegionNavigatorDialog.class | Bin 0 -> 16558 bytes
org/broad/igv/ui/panel/RegionNavigatorDialog.jfd | 632 +++
.../igv/ui/panel/RegionOfInterestPanel$1.class | Bin 0 -> 1714 bytes
.../igv/ui/panel/RegionOfInterestPanel$2.class | Bin 0 -> 1726 bytes
.../igv/ui/panel/RegionOfInterestPanel$3$1.class | Bin 0 -> 1528 bytes
.../igv/ui/panel/RegionOfInterestPanel$3.class | Bin 0 -> 1166 bytes
.../igv/ui/panel/RegionOfInterestPanel$4.class | Bin 0 -> 1513 bytes
.../RegionOfInterestPanel$ROIMouseAdapater.class | Bin 0 -> 2569 bytes
org/broad/igv/ui/panel/RegionOfInterestPanel.class | Bin 0 -> 6250 bytes
org/broad/igv/ui/panel/RegionOfInterestTool.class | Bin 0 -> 2882 bytes
org/broad/igv/ui/panel/ReorderPanelsDialog$1.class | Bin 0 -> 897 bytes
org/broad/igv/ui/panel/ReorderPanelsDialog$2.class | Bin 0 -> 897 bytes
.../igv/ui/panel/ReorderPanelsDialog$Wrapper.class | Bin 0 -> 1539 bytes
org/broad/igv/ui/panel/ReorderPanelsDialog.class | Bin 0 -> 5330 bytes
org/broad/igv/ui/panel/ReorderPanelsDialog.jfd | 247 +
org/broad/igv/ui/panel/RulerPanel$1$1.class | Bin 0 -> 1663 bytes
org/broad/igv/ui/panel/RulerPanel$1.class | Bin 0 -> 3995 bytes
org/broad/igv/ui/panel/RulerPanel$2.class | Bin 0 -> 2480 bytes
org/broad/igv/ui/panel/RulerPanel$ClickLink.class | Bin 0 -> 761 bytes
.../igv/ui/panel/RulerPanel$TickSpacing.class | Bin 0 -> 1260 bytes
org/broad/igv/ui/panel/RulerPanel.class | Bin 0 -> 12734 bytes
org/broad/igv/ui/panel/TrackNamePanel$1.class | Bin 0 -> 1015 bytes
org/broad/igv/ui/panel/TrackNamePanel$2.class | Bin 0 -> 1028 bytes
.../igv/ui/panel/TrackNamePanel$DropListener.class | Bin 0 -> 3903 bytes
.../igv/ui/panel/TrackNamePanel$GroupExtent.class | Bin 0 -> 993 bytes
.../TrackNamePanel$NamePanelMouseAdapter$1.class | Bin 0 -> 1332 bytes
.../TrackNamePanel$NamePanelMouseAdapter$2.class | Bin 0 -> 1807 bytes
.../TrackNamePanel$NamePanelMouseAdapter.class | Bin 0 -> 7142 bytes
org/broad/igv/ui/panel/TrackNamePanel.class | Bin 0 -> 13636 bytes
org/broad/igv/ui/panel/TrackPanel$1.class | Bin 0 -> 1837 bytes
org/broad/igv/ui/panel/TrackPanel.class | Bin 0 -> 12816 bytes
org/broad/igv/ui/panel/TrackPanelComponent$1.class | Bin 0 -> 875 bytes
org/broad/igv/ui/panel/TrackPanelComponent$2.class | Bin 0 -> 1124 bytes
org/broad/igv/ui/panel/TrackPanelComponent.class | Bin 0 -> 8356 bytes
.../igv/ui/panel/TrackPanelScrollPane$1.class | Bin 0 -> 1043 bytes
.../igv/ui/panel/TrackPanelScrollPane$2.class | Bin 0 -> 1233 bytes
org/broad/igv/ui/panel/TrackPanelScrollPane.class | Bin 0 -> 3610 bytes
org/broad/igv/ui/panel/ZoomSliderPanel$1$1.class | Bin 0 -> 1457 bytes
org/broad/igv/ui/panel/ZoomSliderPanel$1.class | Bin 0 -> 1951 bytes
org/broad/igv/ui/panel/ZoomSliderPanel.class | Bin 0 -> 5276 bytes
org/broad/igv/ui/panel/flowlayout.txt | 577 ++
org/broad/igv/ui/panel/resources/IGV_64.png | Bin 0 -> 6732 bytes
org/broad/igv/ui/svg/SVGGraphics.class | Bin 0 -> 16010 bytes
org/broad/igv/ui/svg/SVGTest.class | Bin 0 -> 3842 bytes
org/broad/igv/ui/util/ApplicationStatusBar$1.class | Bin 0 -> 1059 bytes
org/broad/igv/ui/util/ApplicationStatusBar$2.class | Bin 0 -> 1060 bytes
.../ApplicationStatusBar$MemoryUpdateTask.class | Bin 0 -> 1559 bytes
org/broad/igv/ui/util/ApplicationStatusBar.class | Bin 0 -> 3617 bytes
org/broad/igv/ui/util/CheckList$1.class | Bin 0 -> 812 bytes
org/broad/igv/ui/util/CheckList$2.class | Bin 0 -> 812 bytes
org/broad/igv/ui/util/CheckList.class | Bin 0 -> 7392 bytes
org/broad/igv/ui/util/CheckListDialog$1.class | Bin 0 -> 863 bytes
org/broad/igv/ui/util/CheckListDialog$2.class | Bin 0 -> 863 bytes
org/broad/igv/ui/util/CheckListDialog$3.class | Bin 0 -> 863 bytes
org/broad/igv/ui/util/CheckListDialog.class | Bin 0 -> 7613 bytes
org/broad/igv/ui/util/CheckListDialog.jfd | 267 +
org/broad/igv/ui/util/ConfirmDialog$1.class | Bin 0 -> 849 bytes
org/broad/igv/ui/util/ConfirmDialog$2.class | Bin 0 -> 849 bytes
org/broad/igv/ui/util/ConfirmDialog.class | Bin 0 -> 5790 bytes
org/broad/igv/ui/util/ConfirmDialog.jfd | 248 +
org/broad/igv/ui/util/DataPanelTool.class | Bin 0 -> 338 bytes
org/broad/igv/ui/util/FileChooser.class | Bin 0 -> 619 bytes
org/broad/igv/ui/util/FileChooserDialog$1.class | Bin 0 -> 1895 bytes
org/broad/igv/ui/util/FileChooserDialog$2.class | Bin 0 -> 879 bytes
org/broad/igv/ui/util/FileChooserDialog$3.class | Bin 0 -> 1269 bytes
org/broad/igv/ui/util/FileChooserDialog$4.class | Bin 0 -> 672 bytes
org/broad/igv/ui/util/FileChooserDialog.class | Bin 0 -> 8384 bytes
org/broad/igv/ui/util/FileDialogUtils$1.class | Bin 0 -> 1057 bytes
org/broad/igv/ui/util/FileDialogUtils.class | Bin 0 -> 5806 bytes
org/broad/igv/ui/util/FilterComponent$1.class | Bin 0 -> 865 bytes
org/broad/igv/ui/util/FilterComponent$2.class | Bin 0 -> 966 bytes
org/broad/igv/ui/util/FilterComponent$3.class | Bin 0 -> 865 bytes
org/broad/igv/ui/util/FilterComponent$4.class | Bin 0 -> 865 bytes
org/broad/igv/ui/util/FilterComponent$5.class | Bin 0 -> 865 bytes
org/broad/igv/ui/util/FilterComponent$6.class | Bin 0 -> 865 bytes
org/broad/igv/ui/util/FilterComponent.class | Bin 0 -> 8889 bytes
org/broad/igv/ui/util/FilterPane.class | Bin 0 -> 6646 bytes
org/broad/igv/ui/util/FontChooser$1.class | Bin 0 -> 835 bytes
org/broad/igv/ui/util/FontChooser$2.class | Bin 0 -> 835 bytes
org/broad/igv/ui/util/FontChooser$3.class | Bin 0 -> 835 bytes
org/broad/igv/ui/util/FontChooser$4.class | Bin 0 -> 872 bytes
org/broad/igv/ui/util/FontChooser$5.class | Bin 0 -> 835 bytes
org/broad/igv/ui/util/FontChooser$6.class | Bin 0 -> 835 bytes
org/broad/igv/ui/util/FontChooser.class | Bin 0 -> 8709 bytes
org/broad/igv/ui/util/FontChooser.jfd | 357 ++
org/broad/igv/ui/util/FontChooser2$1.class | Bin 0 -> 850 bytes
org/broad/igv/ui/util/FontChooser2$2.class | Bin 0 -> 777 bytes
org/broad/igv/ui/util/FontChooser2$3.class | Bin 0 -> 1031 bytes
org/broad/igv/ui/util/FontChooser2$4.class | Bin 0 -> 1588 bytes
org/broad/igv/ui/util/FontChooser2.class | Bin 0 -> 4976 bytes
org/broad/igv/ui/util/HistoryMenu$1.class | Bin 0 -> 914 bytes
org/broad/igv/ui/util/HistoryMenu$2.class | Bin 0 -> 913 bytes
org/broad/igv/ui/util/HistoryMenu$3.class | Bin 0 -> 916 bytes
org/broad/igv/ui/util/HistoryMenu$4$1.class | Bin 0 -> 1309 bytes
org/broad/igv/ui/util/HistoryMenu$4.class | Bin 0 -> 2896 bytes
org/broad/igv/ui/util/HistoryMenu.class | Bin 0 -> 1980 bytes
org/broad/igv/ui/util/IconFactory$IconID.class | Bin 0 -> 2066 bytes
org/broad/igv/ui/util/IconFactory.class | Bin 0 -> 3532 bytes
.../IndefiniteProgressMonitor$CycleTask$1.class | Bin 0 -> 983 bytes
.../util/IndefiniteProgressMonitor$CycleTask.class | Bin 0 -> 1392 bytes
.../igv/ui/util/IndefiniteProgressMonitor.class | Bin 0 -> 1006 bytes
org/broad/igv/ui/util/LinkCheckBox$1.class | Bin 0 -> 844 bytes
org/broad/igv/ui/util/LinkCheckBox$2.class | Bin 0 -> 1030 bytes
org/broad/igv/ui/util/LinkCheckBox.class | Bin 0 -> 5513 bytes
org/broad/igv/ui/util/MagetabSignalDialog$1.class | Bin 0 -> 1040 bytes
org/broad/igv/ui/util/MagetabSignalDialog$2.class | Bin 0 -> 920 bytes
org/broad/igv/ui/util/MagetabSignalDialog$3.class | Bin 0 -> 1137 bytes
org/broad/igv/ui/util/MagetabSignalDialog.class | Bin 0 -> 3121 bytes
org/broad/igv/ui/util/MenuAndToolbarUtils.class | Bin 0 -> 2239 bytes
org/broad/igv/ui/util/MessageUtils$1.class | Bin 0 -> 1300 bytes
org/broad/igv/ui/util/MessageUtils$2.class | Bin 0 -> 1215 bytes
org/broad/igv/ui/util/MessageUtils$3.class | Bin 0 -> 1114 bytes
org/broad/igv/ui/util/MessageUtils$4.class | Bin 0 -> 920 bytes
.../igv/ui/util/MessageUtils$ValueHolder.class | Bin 0 -> 451 bytes
org/broad/igv/ui/util/MessageUtils.class | Bin 0 -> 4891 bytes
org/broad/igv/ui/util/OkCancelDialog$1.class | Bin 0 -> 858 bytes
org/broad/igv/ui/util/OkCancelDialog$2.class | Bin 0 -> 858 bytes
org/broad/igv/ui/util/OkCancelDialog.class | Bin 0 -> 3994 bytes
org/broad/igv/ui/util/Packable.class | Bin 0 -> 149 bytes
org/broad/igv/ui/util/ProgressBar$1.class | Bin 0 -> 983 bytes
.../igv/ui/util/ProgressBar$ProgressDialog.class | Bin 0 -> 656 bytes
org/broad/igv/ui/util/ProgressBar.class | Bin 0 -> 4532 bytes
org/broad/igv/ui/util/ProgressMonitor.class | Bin 0 -> 1634 bytes
org/broad/igv/ui/util/PropertyManager.class | Bin 0 -> 303 bytes
.../ui/util/ReorderableJList$MyDragListener.class | Bin 0 -> 2647 bytes
.../util/ReorderableJList$MyListDropHandler.class | Bin 0 -> 2594 bytes
org/broad/igv/ui/util/ReorderableJList.class | Bin 0 -> 3426 bytes
org/broad/igv/ui/util/SimpleFormDialog$1.class | Bin 0 -> 870 bytes
org/broad/igv/ui/util/SimpleFormDialog$2.class | Bin 0 -> 870 bytes
org/broad/igv/ui/util/SimpleFormDialog.class | Bin 0 -> 7016 bytes
org/broad/igv/ui/util/SnapshotFileChooser$1.class | Bin 0 -> 920 bytes
.../igv/ui/util/SnapshotFileChooser$2$1.class | Bin 0 -> 1019 bytes
org/broad/igv/ui/util/SnapshotFileChooser$2.class | Bin 0 -> 2261 bytes
.../SnapshotFileChooser$SnapshotFileFilter.class | Bin 0 -> 1474 bytes
.../SnapshotFileChooser$SnapshotFileType.class | Bin 0 -> 2204 bytes
org/broad/igv/ui/util/SnapshotFileChooser.class | Bin 0 -> 3919 bytes
org/broad/igv/ui/util/SnapshotUtilities$1.class | Bin 0 -> 622 bytes
org/broad/igv/ui/util/SnapshotUtilities$2.class | Bin 0 -> 1030 bytes
org/broad/igv/ui/util/SnapshotUtilities.class | Bin 0 -> 8065 bytes
org/broad/igv/ui/util/SortDialog$1.class | Bin 0 -> 869 bytes
org/broad/igv/ui/util/SortDialog$2.class | Bin 0 -> 869 bytes
org/broad/igv/ui/util/SortDialog$3.class | Bin 0 -> 664 bytes
org/broad/igv/ui/util/SortDialog.class | Bin 0 -> 6605 bytes
.../igv/ui/util/SwitchingLabelUI$Orientation.class | Bin 0 -> 1223 bytes
org/broad/igv/ui/util/SwitchingLabelUI.class | Bin 0 -> 3979 bytes
org/broad/igv/ui/util/TracingRepaintManager.class | Bin 0 -> 1922 bytes
org/broad/igv/ui/util/UIUtilities.class | Bin 0 -> 3066 bytes
org/broad/igv/ui/util/VerticalLabelUI.class | Bin 0 -> 3417 bytes
org/broad/igv/util/AlphaColorGradient.class | Bin 0 -> 1091 bytes
org/broad/igv/util/ArrayHeapIntSorter.class | Bin 0 -> 1590 bytes
org/broad/igv/util/ArrayHeapObjectSorter.class | Bin 0 -> 2046 bytes
org/broad/igv/util/AsciiEcho.class | Bin 0 -> 696 bytes
org/broad/igv/util/BrowserLauncher.class | Bin 0 -> 3216 bytes
org/broad/igv/util/ByteConverter.class | Bin 0 -> 2364 bytes
org/broad/igv/util/ChromosomeColors.class | Bin 0 -> 3756 bytes
org/broad/igv/util/CompressionUtils.class | Bin 0 -> 4335 bytes
org/broad/igv/util/ConvertPlasmodium.class | Bin 0 -> 1938 bytes
org/broad/igv/util/DumpHttpHeaders.class | Bin 0 -> 2209 bytes
org/broad/igv/util/FileUtils$1.class | Bin 0 -> 1027 bytes
org/broad/igv/util/FileUtils$2.class | Bin 0 -> 1015 bytes
org/broad/igv/util/FileUtils.class | Bin 0 -> 12907 bytes
org/broad/igv/util/Filter.class | Bin 0 -> 1891 bytes
.../igv/util/FilterElement$BooleanOperator.class | Bin 0 -> 1647 bytes
org/broad/igv/util/FilterElement$Operator.class | Bin 0 -> 2427 bytes
org/broad/igv/util/FilterElement.class | Bin 0 -> 4694 bytes
org/broad/igv/util/GapToWigConverter.class | Bin 0 -> 314 bytes
org/broad/igv/util/GenomeUtils.class | Bin 0 -> 3868 bytes
org/broad/igv/util/HttpUtils$1.class | Bin 0 -> 1023 bytes
.../igv/util/HttpUtils$IGVAuthenticator.class | Bin 0 -> 2533 bytes
org/broad/igv/util/HttpUtils$ProxySettings.class | Bin 0 -> 792 bytes
org/broad/igv/util/HttpUtils.class | Bin 0 -> 21379 bytes
org/broad/igv/util/IlluminaUtils.class | Bin 0 -> 3505 bytes
org/broad/igv/util/IntComparator.class | Bin 0 -> 152 bytes
org/broad/igv/util/LRUCache$1.class | Bin 0 -> 994 bytes
org/broad/igv/util/LRUCache.class | Bin 0 -> 3068 bytes
org/broad/igv/util/LoggingUtils.class | Bin 0 -> 909 bytes
org/broad/igv/util/LoginDialog$1.class | Bin 0 -> 817 bytes
org/broad/igv/util/LoginDialog$2.class | Bin 0 -> 817 bytes
org/broad/igv/util/LoginDialog.class | Bin 0 -> 6745 bytes
org/broad/igv/util/LoginDialog.jfd | 390 ++
org/broad/igv/util/LongRunningTask.class | Bin 0 -> 3041 bytes
org/broad/igv/util/MD5Checksum.class | Bin 0 -> 1883 bytes
org/broad/igv/util/MacroSnapshotAction.class | Bin 0 -> 3005 bytes
org/broad/igv/util/NamedRunnable.class | Bin 0 -> 193 bytes
org/broad/igv/util/ObjectCache.class | Bin 0 -> 2986 bytes
org/broad/igv/util/ObserverForObject.class | Bin 0 -> 1244 bytes
org/broad/igv/util/Pair.class | Bin 0 -> 1461 bytes
org/broad/igv/util/ParsingUtils.class | Bin 0 -> 14042 bytes
.../igv/util/ResourceLocator$AttributeType.class | Bin 0 -> 2155 bytes
org/broad/igv/util/ResourceLocator.class | Bin 0 -> 4734 bytes
org/broad/igv/util/RuntimeUtils.class | Bin 0 -> 3402 bytes
org/broad/igv/util/SOLIDUtils.class | Bin 0 -> 940 bytes
org/broad/igv/util/SequenceGC.class | Bin 0 -> 6565 bytes
org/broad/igv/util/StringUtils.class | Bin 0 -> 3736 bytes
org/broad/igv/util/UCSCUtils.class | Bin 0 -> 4020 bytes
org/broad/igv/util/UnzipGenomes.class | Bin 0 -> 2948 bytes
org/broad/igv/util/UserPasswordDialog$1.class | Bin 0 -> 866 bytes
org/broad/igv/util/UserPasswordDialog$2.class | Bin 0 -> 866 bytes
org/broad/igv/util/UserPasswordDialog.class | Bin 0 -> 6166 bytes
org/broad/igv/util/UserPasswordDialog.jfd | 378 ++
org/broad/igv/util/UserPasswordInputImpl.class | Bin 0 -> 1290 bytes
org/broad/igv/util/Utilities$1.class | Bin 0 -> 1726 bytes
org/broad/igv/util/Utilities.class | Bin 0 -> 4402 bytes
.../igv/util/ZipArchiveWrapper$ZipIterator.class | Bin 0 -> 2295 bytes
org/broad/igv/util/ZipArchiveWrapper.class | Bin 0 -> 2117 bytes
.../igv/util/collections/DoubleArrayList.class | Bin 0 -> 2393 bytes
.../igv/util/collections/FloatArrayList.class | Bin 0 -> 2389 bytes
org/broad/igv/util/collections/IntArrayList.class | Bin 0 -> 2535 bytes
.../igv/util/collections/StringArrayList.class | Bin 0 -> 1983 bytes
.../igv/util/converters/DensitiesToBedGraph.class | Bin 0 -> 2704 bytes
.../igv/util/converters/TarjeiToBedgraph.class | Bin 0 -> 4133 bytes
org/broad/igv/util/index/Interval.class | Bin 0 -> 1945 bytes
org/broad/igv/util/index/IntervalTree$Node.class | Bin 0 -> 2270 bytes
org/broad/igv/util/index/IntervalTree.class | Bin 0 -> 8541 bytes
org/broad/igv/util/stats/Distribution.class | Bin 0 -> 1600 bytes
org/broad/igv/util/stats/KMPlotFrame$1.class | Bin 0 -> 853 bytes
org/broad/igv/util/stats/KMPlotFrame$2.class | Bin 0 -> 853 bytes
org/broad/igv/util/stats/KMPlotFrame$3.class | Bin 0 -> 853 bytes
.../igv/util/stats/KMPlotFrame$DataPoint.class | Bin 0 -> 1204 bytes
org/broad/igv/util/stats/KMPlotFrame.class | Bin 0 -> 12080 bytes
org/broad/igv/util/stats/KMPlotFrame.jfd | 330 ++
.../util/stats/KaplanMeierEstimator$Interval.class | Bin 0 -> 1814 bytes
.../igv/util/stats/KaplanMeierEstimator.class | Bin 0 -> 3327 bytes
.../igv/util/stream/IGVSeekableFTPStream.class | Bin 0 -> 3728 bytes
.../igv/util/stream/IGVSeekableStreamFactory.class | Bin 0 -> 1778 bytes
org/broad/igv/util/stream/IGVUrlHelper.class | Bin 0 -> 1931 bytes
.../igv/util/stream/SeekablePicardStream.class | Bin 0 -> 1876 bytes
.../igv/util/stream/SeekableServiceStream.class | Bin 0 -> 3735 bytes
.../SeekableSplitStream$PartDescriptor.class | Bin 0 -> 1188 bytes
.../igv/util/stream/SeekableSplitStream.class | Bin 0 -> 4786 bytes
org/broad/igv/variant/Allele.class | Bin 0 -> 141 bytes
org/broad/igv/variant/Genotype.class | Bin 0 -> 654 bytes
org/broad/igv/variant/Variant.class | Bin 0 -> 1055 bytes
org/broad/igv/variant/VariantMenu$1.class | Bin 0 -> 1105 bytes
org/broad/igv/variant/VariantMenu$10.class | Bin 0 -> 1625 bytes
org/broad/igv/variant/VariantMenu$11.class | Bin 0 -> 1635 bytes
org/broad/igv/variant/VariantMenu$12.class | Bin 0 -> 1258 bytes
org/broad/igv/variant/VariantMenu$13.class | Bin 0 -> 1257 bytes
org/broad/igv/variant/VariantMenu$14.class | Bin 0 -> 1257 bytes
org/broad/igv/variant/VariantMenu$15.class | Bin 0 -> 946 bytes
org/broad/igv/variant/VariantMenu$2.class | Bin 0 -> 1462 bytes
org/broad/igv/variant/VariantMenu$3.class | Bin 0 -> 1029 bytes
org/broad/igv/variant/VariantMenu$4.class | Bin 0 -> 1350 bytes
org/broad/igv/variant/VariantMenu$5.class | Bin 0 -> 1346 bytes
org/broad/igv/variant/VariantMenu$6.class | Bin 0 -> 1365 bytes
org/broad/igv/variant/VariantMenu$7.class | Bin 0 -> 1301 bytes
org/broad/igv/variant/VariantMenu$8.class | Bin 0 -> 1638 bytes
org/broad/igv/variant/VariantMenu$9$1.class | Bin 0 -> 1231 bytes
org/broad/igv/variant/VariantMenu$9.class | Bin 0 -> 1582 bytes
.../igv/variant/VariantMenu$DepthComparator.class | Bin 0 -> 1598 bytes
.../variant/VariantMenu$GenotypeComparator.class | Bin 0 -> 1769 bytes
.../variant/VariantMenu$QualityComparator.class | Bin 0 -> 1414 bytes
org/broad/igv/variant/VariantMenu.class | Bin 0 -> 10405 bytes
org/broad/igv/variant/VariantRenderer$1.class | Bin 0 -> 974 bytes
org/broad/igv/variant/VariantRenderer.class | Bin 0 -> 9443 bytes
org/broad/igv/variant/VariantTrack$1.class | Bin 0 -> 2960 bytes
org/broad/igv/variant/VariantTrack$2.class | Bin 0 -> 866 bytes
.../igv/variant/VariantTrack$BackgroundType.class | Bin 0 -> 1254 bytes
org/broad/igv/variant/VariantTrack$ColorMode.class | Bin 0 -> 1232 bytes
.../igv/variant/VariantTrack$SampleBounds.class | Bin 0 -> 744 bytes
org/broad/igv/variant/VariantTrack.class | Bin 0 -> 34521 bytes
org/broad/igv/variant/util/AutismUtils.class | Bin 0 -> 2219 bytes
org/broad/igv/variant/util/PedigreeUtils.class | Bin 0 -> 1930 bytes
org/broad/igv/variant/util/VCFtoBed.class | Bin 0 -> 3292 bytes
org/broad/igv/variant/vcf/VCFAllele.class | Bin 0 -> 615 bytes
org/broad/igv/variant/vcf/VCFGenotype.class | Bin 0 -> 3063 bytes
.../igv/variant/vcf/VCFVariant$ZygosityCount.class | Bin 0 -> 1274 bytes
org/broad/igv/variant/vcf/VCFVariant.class | Bin 0 -> 7671 bytes
.../utils/codecs/vcf/AbstractVCFCodec$1.class | Bin 0 -> 283 bytes
.../AbstractVCFCodec$LazyVCFGenotypesParser.class | Bin 0 -> 1840 bytes
.../vcf/AbstractVCFCodec$VCFLocFeature.class | Bin 0 -> 1321 bytes
.../sting/utils/codecs/vcf/AbstractVCFCodec.class | Bin 0 -> 23548 bytes
.../sting/utils/codecs/vcf/IndexingVCFWriter.class | Bin 0 -> 4813 bytes
.../utils/codecs/vcf/ManualSortingVCFWriter.class | Bin 0 -> 975 bytes
.../sting/utils/codecs/vcf/SortingVCFWriter.class | Bin 0 -> 1441 bytes
.../utils/codecs/vcf/SortingVCFWriterBase$1.class | Bin 0 -> 295 bytes
.../vcf/SortingVCFWriterBase$VCFRecord.class | Bin 0 -> 679 bytes
...ingVCFWriterBase$VariantContextComparator.class | Bin 0 -> 1796 bytes
.../utils/codecs/vcf/SortingVCFWriterBase.class | Bin 0 -> 4396 bytes
.../sting/utils/codecs/vcf/StandardVCFWriter.class | Bin 0 -> 16976 bytes
.../sting/utils/codecs/vcf/VCF3Codec.class | Bin 0 -> 8530 bytes
.../sting/utils/codecs/vcf/VCF3Parser.class | Bin 0 -> 2599 bytes
.../sting/utils/codecs/vcf/VCF4Parser.class | Bin 0 -> 2856 bytes
.../sting/utils/codecs/vcf/VCFAltHeaderLine.class | Bin 0 -> 1327 bytes
.../sting/utils/codecs/vcf/VCFCodec.class | Bin 0 -> 9406 bytes
.../utils/codecs/vcf/VCFCompoundHeaderLine$1.class | Bin 0 -> 1075 bytes
...ompoundHeaderLine$SupportedHeaderLineType.class | Bin 0 -> 1590 bytes
.../utils/codecs/vcf/VCFCompoundHeaderLine.class | Bin 0 -> 7118 bytes
.../sting/utils/codecs/vcf/VCFConstants.class | Bin 0 -> 3806 bytes
.../utils/codecs/vcf/VCFFilterHeaderLine.class | Bin 0 -> 1339 bytes
.../utils/codecs/vcf/VCFFormatHeaderLine.class | Bin 0 -> 2572 bytes
.../utils/codecs/vcf/VCFHeader$HEADER_FIELDS.class | Bin 0 -> 1596 bytes
.../sting/utils/codecs/vcf/VCFHeader.class | Bin 0 -> 7343 bytes
.../sting/utils/codecs/vcf/VCFHeaderLine.class | Bin 0 -> 3619 bytes
.../utils/codecs/vcf/VCFHeaderLineCount.class | Bin 0 -> 1282 bytes
.../utils/codecs/vcf/VCFHeaderLineTranslator.class | Bin 0 -> 1935 bytes
.../sting/utils/codecs/vcf/VCFHeaderLineType.class | Bin 0 -> 1331 bytes
.../sting/utils/codecs/vcf/VCFHeaderVersion.class | Bin 0 -> 3379 bytes
.../sting/utils/codecs/vcf/VCFInfoHeaderLine.class | Bin 0 -> 2260 bytes
.../sting/utils/codecs/vcf/VCFLineParser.class | Bin 0 -> 365 bytes
.../utils/codecs/vcf/VCFNamedHeaderLine.class | Bin 0 -> 200 bytes
...FSimpleHeaderLine$SupportedHeaderLineType.class | Bin 0 -> 1462 bytes
.../utils/codecs/vcf/VCFSimpleHeaderLine.class | Bin 0 -> 3532 bytes
.../sting/utils/codecs/vcf/VCFUtils$1.class | Bin 0 -> 259 bytes
.../codecs/vcf/VCFUtils$HeaderConflictWarner.class | Bin 0 -> 1647 bytes
.../sting/utils/codecs/vcf/VCFUtils.class | Bin 0 -> 10368 bytes
.../sting/utils/codecs/vcf/VCFWriter.class | Bin 0 -> 326 bytes
.../DynamicClassResolutionException.class | Bin 0 -> 1881 bytes
.../utils/exceptions/ReviewedStingException.class | Bin 0 -> 663 bytes
.../sting/utils/exceptions/StingException.class | Bin 0 -> 609 bytes
.../UserException$BadArgumentValue.class | Bin 0 -> 882 bytes
.../utils/exceptions/UserException$BadInput.class | Bin 0 -> 665 bytes
.../utils/exceptions/UserException$BadTmpDir.class | Bin 0 -> 991 bytes
.../UserException$CannotExecuteQScript.class | Bin 0 -> 989 bytes
.../UserException$CannotExecuteRScript.class | Bin 0 -> 1132 bytes
.../UserException$CommandLineException.class | Bin 0 -> 712 bytes
.../UserException$CouldNotCreateOutputFile.class | Bin 0 -> 1404 bytes
...xception$CouldNotCreateReferenceIndexFile.class | Bin 0 -> 1398 bytes
...dNotCreateReferenceIndexFileBecauseOfLock.class | Bin 0 -> 1065 bytes
.../UserException$CouldNotReadInputFile.class | Bin 0 -> 1661 bytes
.../UserException$DeprecatedArgument.class | Bin 0 -> 890 bytes
.../UserException$ErrorWritingBamFile.class | Bin 0 -> 1049 bytes
...xception$IncompatibleSequenceDictionaries.class | Bin 0 -> 1184 bytes
...LexicographicallySortedSequenceDictionary.class | Bin 0 -> 1466 bytes
.../exceptions/UserException$MalformedBAM.class | Bin 0 -> 1469 bytes
.../exceptions/UserException$MalformedFile.class | Bin 0 -> 1905 bytes
.../UserException$MalformedGenomeLoc.class | Bin 0 -> 965 bytes
.../exceptions/UserException$MalformedVCF.class | Bin 0 -> 1077 bytes
.../UserException$MalformedVCFHeader.class | Bin 0 -> 730 bytes
.../exceptions/UserException$MissingArgument.class | Bin 0 -> 875 bytes
.../exceptions/UserException$MissingWalker.class | Bin 0 -> 766 bytes
.../exceptions/UserException$MissortedBAM.class | Bin 0 -> 2115 bytes
.../exceptions/UserException$MissortedFile.class | Bin 0 -> 963 bytes
.../UserException$ReadMissingReadGroup.class | Bin 0 -> 1164 bytes
.../UserException$TooManyOpenFiles.class | Bin 0 -> 809 bytes
.../UserException$UnknownTribbleType.class | Bin 0 -> 885 bytes
...eption$VariantContextMissingRequiredField.class | Bin 0 -> 1166 bytes
.../sting/utils/exceptions/UserException.class | Bin 0 -> 5115 bytes
.../sting/utils/help/DocumentedGATKFeature.class | Bin 0 -> 690 bytes
.../sting/utils/variantcontext/Allele.class | Bin 0 -> 10188 bytes
.../sting/utils/variantcontext/CommonInfo.class | Bin 0 -> 8093 bytes
.../sting/utils/variantcontext/Genotype$Type.class | Bin 0 -> 1493 bytes
.../sting/utils/variantcontext/Genotype.class | Bin 0 -> 15801 bytes
.../utils/variantcontext/GenotypeLikelihoods.class | Bin 0 -> 5142 bytes
.../utils/variantcontext/GenotypesContext$1.class | Bin 0 -> 1472 bytes
.../GenotypesContext$InOrderIterator.class | Bin 0 -> 2085 bytes
.../utils/variantcontext/GenotypesContext.class | Bin 0 -> 17469 bytes
.../sting/utils/variantcontext/JEXLMap.class | Bin 0 -> 9661 bytes
.../LazyGenotypesContext$LazyData.class | Bin 0 -> 1540 bytes
.../LazyGenotypesContext$LazyParser.class | Bin 0 -> 685 bytes
.../variantcontext/LazyGenotypesContext.class | Bin 0 -> 3231 bytes
.../utils/variantcontext/VariantContext$1.class | Bin 0 -> 1085 bytes
.../utils/variantcontext/VariantContext$Type.class | Bin 0 -> 1537 bytes
.../variantcontext/VariantContext$Validation.class | Bin 0 -> 1428 bytes
.../utils/variantcontext/VariantContext.class | Bin 0 -> 30536 bytes
.../variantcontext/VariantContextBuilder.class | Bin 0 -> 9344 bytes
.../VariantContextUtils$AlleleMapper.class | Bin 0 -> 2923 bytes
.../VariantContextUtils$CompareByPriority.class | Bin 0 -> 2626 bytes
...riantContextUtils$FilteredRecordMergeType.class | Bin 0 -> 1529 bytes
.../VariantContextUtils$GenotypeMergeType.class | Bin 0 -> 1577 bytes
.../VariantContextUtils$JexlVCMatchExp.class | Bin 0 -> 736 bytes
.../utils/variantcontext/VariantContextUtils.class | Bin 0 -> 41919 bytes
.../variantcontext/VariantJEXLContext$1.class | Bin 0 -> 850 bytes
.../variantcontext/VariantJEXLContext$10.class | Bin 0 -> 1022 bytes
.../variantcontext/VariantJEXLContext$11.class | Bin 0 -> 1025 bytes
.../variantcontext/VariantJEXLContext$2.class | Bin 0 -> 961 bytes
.../variantcontext/VariantJEXLContext$3.class | Bin 0 -> 1017 bytes
.../variantcontext/VariantJEXLContext$4.class | Bin 0 -> 1144 bytes
.../variantcontext/VariantJEXLContext$5.class | Bin 0 -> 1034 bytes
.../variantcontext/VariantJEXLContext$6.class | Bin 0 -> 963 bytes
.../variantcontext/VariantJEXLContext$7.class | Bin 0 -> 1020 bytes
.../variantcontext/VariantJEXLContext$8.class | Bin 0 -> 1023 bytes
.../variantcontext/VariantJEXLContext$9.class | Bin 0 -> 1023 bytes
.../VariantJEXLContext$AttributeGetter.class | Bin 0 -> 397 bytes
.../utils/variantcontext/VariantJEXLContext.class | Bin 0 -> 3539 bytes
org/gjt/mm/mysql/Driver.class | Bin 0 -> 336 bytes
org/hamcrest/BaseDescription.class | Bin 0 -> 4784 bytes
org/hamcrest/BaseMatcher.class | Bin 0 -> 821 bytes
org/hamcrest/CoreMatchers.class | Bin 0 -> 4099 bytes
org/hamcrest/Description.class | Bin 0 -> 1027 bytes
org/hamcrest/Factory.class | Bin 0 -> 380 bytes
org/hamcrest/Matcher.class | Bin 0 -> 347 bytes
org/hamcrest/SelfDescribing.class | Bin 0 -> 175 bytes
org/hamcrest/StringDescription.class | Bin 0 -> 1646 bytes
org/hamcrest/core/AllOf.class | Bin 0 -> 2283 bytes
org/hamcrest/core/AnyOf.class | Bin 0 -> 2282 bytes
org/hamcrest/core/DescribedAs.class | Bin 0 -> 2694 bytes
org/hamcrest/core/Is.class | Bin 0 -> 2109 bytes
org/hamcrest/core/IsAnything.class | Bin 0 -> 1784 bytes
org/hamcrest/core/IsEqual.class | Bin 0 -> 2245 bytes
org/hamcrest/core/IsInstanceOf.class | Bin 0 -> 1401 bytes
org/hamcrest/core/IsNot.class | Bin 0 -> 1809 bytes
org/hamcrest/core/IsNull.class | Bin 0 -> 1670 bytes
org/hamcrest/core/IsSame.class | Bin 0 -> 1392 bytes
org/hamcrest/core/package.html | 7 +
org/hamcrest/internal/ArrayIterator.class | Bin 0 -> 1253 bytes
org/hamcrest/internal/SelfDescribingValue.class | Bin 0 -> 973 bytes
.../internal/SelfDescribingValueIterator.class | Bin 0 -> 1328 bytes
org/hamcrest/package.html | 9 +
org/jdesktop/layout/AquaBaseline.class | Bin 0 -> 15029 bytes
.../layout/AquaLayoutStyle$ComponentInsets.class | Bin 0 -> 1621 bytes
org/jdesktop/layout/AquaLayoutStyle.class | Bin 0 -> 14076 bytes
org/jdesktop/layout/Baseline.class | Bin 0 -> 20943 bytes
org/jdesktop/layout/GnomeLayoutStyle.class | Bin 0 -> 1240 bytes
org/jdesktop/layout/GroupLayout$1.class | Bin 0 -> 211 bytes
.../layout/GroupLayout$AutopaddingMatch.class | Bin 0 -> 1277 bytes
.../layout/GroupLayout$AutopaddingSpring.class | Bin 0 -> 5509 bytes
.../layout/GroupLayout$BaselineGroup.class | Bin 0 -> 2445 bytes
.../layout/GroupLayout$ComponentInfo.class | Bin 0 -> 5815 bytes
.../layout/GroupLayout$ComponentSpring.class | Bin 0 -> 4753 bytes
.../GroupLayout$ContainerAutopaddingSpring.class | Bin 0 -> 3541 bytes
org/jdesktop/layout/GroupLayout$GapSpring.class | Bin 0 -> 1151 bytes
org/jdesktop/layout/GroupLayout$Group.class | Bin 0 -> 4449 bytes
.../layout/GroupLayout$PaddingSpring.class | Bin 0 -> 1658 bytes
.../layout/GroupLayout$ParallelGroup.class | Bin 0 -> 4865 bytes
.../layout/GroupLayout$SequentialGroup.class | Bin 0 -> 8858 bytes
org/jdesktop/layout/GroupLayout$Spring.class | Bin 0 -> 2119 bytes
org/jdesktop/layout/GroupLayout$SpringDelta.class | Bin 0 -> 1003 bytes
org/jdesktop/layout/GroupLayout.class | Bin 0 -> 17150 bytes
org/jdesktop/layout/LayoutStyle.class | Bin 0 -> 6736 bytes
org/jdesktop/layout/MetalLayoutStyle.class | Bin 0 -> 3860 bytes
org/jdesktop/layout/SwingLayoutStyle.class | Bin 0 -> 4369 bytes
org/jdesktop/layout/WindowsLayoutStyle.class | Bin 0 -> 3087 bytes
org/jfree/JCommon.class | Bin 0 -> 810 bytes
org/jfree/JCommonInfo.class | Bin 0 -> 2940 bytes
org/jfree/base/AbstractBoot.class | Bin 0 -> 7079 bytes
org/jfree/base/BaseBoot.class | Bin 0 -> 2490 bytes
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org/jfree/base/ClassPathDebugger.class | Bin 0 -> 2899 bytes
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org/jfree/base/log/MemoryUsageMessage.class | Bin 0 -> 859 bytes
org/jfree/base/log/PadMessage.class | Bin 0 -> 894 bytes
org/jfree/base/log/module.properties | 14 +
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org/jfree/base/modules/DefaultModuleInfo.class | Bin 0 -> 2593 bytes
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org/jfree/base/modules/SubSystem.class | Bin 0 -> 326 bytes
org/jfree/chart/ChartColor.class | Bin 0 -> 2221 bytes
org/jfree/chart/ChartFactory.class | Bin 0 -> 32183 bytes
org/jfree/chart/ChartFrame.class | Bin 0 -> 1107 bytes
org/jfree/chart/ChartMouseEvent.class | Bin 0 -> 1082 bytes
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org/jfree/chart/ChartTransferable.class | Bin 0 -> 1882 bytes
org/jfree/chart/ChartUtilities.class | Bin 0 -> 9382 bytes
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org/jfree/chart/DrawableLegendItem.class | Bin 0 -> 2276 bytes
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org/jfree/chart/HashUtilities.class | Bin 0 -> 3298 bytes
org/jfree/chart/JFreeChart.class | Bin 0 -> 24718 bytes
org/jfree/chart/JFreeChartInfo.class | Bin 0 -> 5618 bytes
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org/jfree/chart/LocalizationBundle.properties | 19 +
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org/jfree/chart/LocalizationBundle_ru.properties | 19 +
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org/jfree/chart/MouseWheelHandler.class | Bin 0 -> 2858 bytes
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org/jfree/chart/PolarChartPanel.class | Bin 0 -> 3703 bytes
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org/jfree/chart/StrokeMap.class | Bin 0 -> 3376 bytes
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org/jfree/chart/axis/Axis.class | Bin 0 -> 18202 bytes
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org/jfree/chart/axis/MonthDateFormat.class | Bin 0 -> 5408 bytes
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org/jfree/chart/axis/PeriodAxisLabelInfo.class | Bin 0 -> 6468 bytes
org/jfree/chart/axis/QuarterDateFormat.class | Bin 0 -> 3085 bytes
...egmentedTimeline$BaseTimelineSegmentRange.class | Bin 0 -> 733 bytes
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org/jfree/chart/axis/StandardTickUnitSource.class | Bin 0 -> 1612 bytes
org/jfree/chart/axis/SubCategoryAxis.class | Bin 0 -> 8550 bytes
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org/jfree/chart/block/AbstractBlock.class | Bin 0 -> 8841 bytes
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org/jfree/chart/demo/BarChartDemo1.class | Bin 0 -> 4510 bytes
org/jfree/chart/demo/PieChartDemo1.class | Bin 0 -> 2270 bytes
org/jfree/chart/demo/TimeSeriesChartDemo1.class | Bin 0 -> 4968 bytes
org/jfree/chart/editor/ChartEditor.class | Bin 0 -> 182 bytes
org/jfree/chart/editor/ChartEditorFactory.class | Bin 0 -> 232 bytes
org/jfree/chart/editor/ChartEditorManager.class | Bin 0 -> 1161 bytes
org/jfree/chart/editor/DefaultAxisEditor.class | Bin 0 -> 7748 bytes
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org/jfree/chart/editor/DefaultColorBarEditor.class | Bin 0 -> 4893 bytes
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.../chart/editor/LocalizationBundle.properties | 68 +
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org/jfree/chart/editor/PaletteChooserPanel.class | Bin 0 -> 1385 bytes
org/jfree/chart/editor/PaletteSample.class | Bin 0 -> 2809 bytes
org/jfree/chart/encoders/EncoderUtil.class | Bin 0 -> 2603 bytes
org/jfree/chart/encoders/ImageEncoder.class | Bin 0 -> 429 bytes
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org/jfree/chart/entity/AxisEntity.class | Bin 0 -> 3248 bytes
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.../AbstractCategoryItemLabelGenerator.class | Bin 0 -> 4556 bytes
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org/jfree/chart/labels/PieToolTipGenerator.class | Bin 0 -> 248 bytes
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org/jfree/chart/labels/XYItemLabelGenerator.class | Bin 0 -> 222 bytes
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org/jfree/chart/labels/XYToolTipGenerator.class | Bin 0 -> 220 bytes
org/jfree/chart/labels/XYZToolTipGenerator.class | Bin 0 -> 272 bytes
org/jfree/chart/needle/ArrowNeedle.class | Bin 0 -> 2663 bytes
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org/jfree/chart/needle/WindNeedle.class | Bin 0 -> 1517 bytes
org/jfree/chart/panel/AbstractOverlay.class | Bin 0 -> 2248 bytes
org/jfree/chart/panel/CrosshairOverlay.class | Bin 0 -> 11088 bytes
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org/jfree/chart/plot/CategoryCrosshairState.class | Bin 0 -> 2197 bytes
org/jfree/chart/plot/CategoryMarker.class | Bin 0 -> 2353 bytes
org/jfree/chart/plot/CategoryPlot.class | Bin 0 -> 61849 bytes
org/jfree/chart/plot/ColorPalette.class | Bin 0 -> 5291 bytes
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org/jfree/chart/plot/CombinedDomainXYPlot.class | Bin 0 -> 12357 bytes
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org/jfree/chart/plot/CombinedRangeXYPlot.class | Bin 0 -> 12356 bytes
org/jfree/chart/plot/CompassPlot.class | Bin 0 -> 12899 bytes
org/jfree/chart/plot/ContourPlot.class | Bin 0 -> 26414 bytes
org/jfree/chart/plot/ContourPlotUtilities.class | Bin 0 -> 817 bytes
org/jfree/chart/plot/ContourValuePlot.class | Bin 0 -> 210 bytes
org/jfree/chart/plot/Crosshair.class | Bin 0 -> 8629 bytes
org/jfree/chart/plot/CrosshairState.class | Bin 0 -> 3713 bytes
org/jfree/chart/plot/DatasetRenderingOrder.class | Bin 0 -> 1370 bytes
org/jfree/chart/plot/DefaultDrawingSupplier.class | Bin 0 -> 7267 bytes
org/jfree/chart/plot/DialShape.class | Bin 0 -> 1385 bytes
org/jfree/chart/plot/DrawingSupplier.class | Bin 0 -> 354 bytes
org/jfree/chart/plot/FastScatterPlot.class | Bin 0 -> 15282 bytes
org/jfree/chart/plot/GreyPalette.class | Bin 0 -> 823 bytes
org/jfree/chart/plot/IntervalMarker.class | Bin 0 -> 2926 bytes
org/jfree/chart/plot/JThermometer.class | Bin 0 -> 5657 bytes
org/jfree/chart/plot/LocalizationBundle.properties | 23 +
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org/jfree/chart/plot/Marker.class | Bin 0 -> 8694 bytes
org/jfree/chart/plot/MeterInterval.class | Bin 0 -> 3222 bytes
org/jfree/chart/plot/MeterPlot.class | Bin 0 -> 19830 bytes
org/jfree/chart/plot/MultiplePiePlot.class | Bin 0 -> 12842 bytes
org/jfree/chart/plot/Pannable.class | Bin 0 -> 362 bytes
org/jfree/chart/plot/PieLabelDistributor.class | Bin 0 -> 3108 bytes
org/jfree/chart/plot/PieLabelLinkStyle.class | Bin 0 -> 1430 bytes
org/jfree/chart/plot/PieLabelRecord.class | Bin 0 -> 2782 bytes
org/jfree/chart/plot/PiePlot.class | Bin 0 -> 43058 bytes
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org/jfree/chart/plot/PlotOrientation.class | Bin 0 -> 1382 bytes
org/jfree/chart/plot/PlotRenderingInfo.class | Bin 0 -> 3858 bytes
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org/jfree/chart/plot/PlotUtilities.class | Bin 0 -> 814 bytes
org/jfree/chart/plot/PolarPlot.class | Bin 0 -> 20352 bytes
org/jfree/chart/plot/RainbowPalette.class | Bin 0 -> 6044 bytes
org/jfree/chart/plot/RingPlot.class | Bin 0 -> 10900 bytes
org/jfree/chart/plot/SeriesRenderingOrder.class | Bin 0 -> 1365 bytes
org/jfree/chart/plot/SpiderWebPlot.class | Bin 0 -> 23476 bytes
org/jfree/chart/plot/ThermometerPlot.class | Bin 0 -> 22534 bytes
org/jfree/chart/plot/ValueAxisPlot.class | Bin 0 -> 210 bytes
org/jfree/chart/plot/ValueMarker.class | Bin 0 -> 1505 bytes
org/jfree/chart/plot/WaferMapPlot.class | Bin 0 -> 7487 bytes
org/jfree/chart/plot/XYCrosshairState.class | Bin 0 -> 338 bytes
org/jfree/chart/plot/XYPlot.class | Bin 0 -> 66569 bytes
org/jfree/chart/plot/Zoomable.class | Bin 0 -> 538 bytes
org/jfree/chart/plot/dial/AbstractDialLayer.class | Bin 0 -> 3535 bytes
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org/jfree/chart/plot/dial/DialLayer.class | Bin 0 -> 480 bytes
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org/jfree/chart/plot/dial/DialPlot.class | Bin 0 -> 11481 bytes
org/jfree/chart/plot/dial/DialPointer$Pin.class | Bin 0 -> 4649 bytes
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org/jfree/chart/plot/dial/DialScale.class | Bin 0 -> 221 bytes
org/jfree/chart/plot/dial/DialTextAnnotation.class | Bin 0 -> 5855 bytes
org/jfree/chart/plot/dial/DialValueIndicator.class | Bin 0 -> 10193 bytes
org/jfree/chart/plot/dial/StandardDialFrame.class | Bin 0 -> 5555 bytes
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org/jfree/chart/renderer/AbstractRenderer.class | Bin 0 -> 36557 bytes
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org/jfree/chart/renderer/PolarItemRenderer.class | Bin 0 -> 894 bytes
org/jfree/chart/renderer/RendererState.class | Bin 0 -> 1015 bytes
org/jfree/chart/renderer/RendererUtilities.class | Bin 0 -> 2863 bytes
org/jfree/chart/renderer/WaferMapRenderer.class | Bin 0 -> 6600 bytes
.../category/AbstractCategoryItemRenderer.class | Bin 0 -> 28505 bytes
.../chart/renderer/category/AreaRenderer.class | Bin 0 -> 8016 bytes
org/jfree/chart/renderer/category/BarPainter.class | Bin 0 -> 452 bytes
.../chart/renderer/category/BarRenderer.class | Bin 0 -> 21999 bytes
.../chart/renderer/category/BarRenderer3D.class | Bin 0 -> 15963 bytes
.../renderer/category/BoxAndWhiskerRenderer.class | Bin 0 -> 17333 bytes
.../renderer/category/CategoryItemRenderer.class | Bin 0 -> 7084 bytes
.../category/CategoryItemRendererState.class | Bin 0 -> 2058 bytes
.../category/CategoryStepRenderer$State.class | Bin 0 -> 769 bytes
.../renderer/category/CategoryStepRenderer.class | Bin 0 -> 7513 bytes
.../category/DefaultCategoryItemRenderer.class | Bin 0 -> 504 bytes
.../chart/renderer/category/GanttRenderer.class | Bin 0 -> 11308 bytes
.../renderer/category/GradientBarPainter.class | Bin 0 -> 5789 bytes
.../category/GroupedStackedBarRenderer.class | Bin 0 -> 8183 bytes
.../renderer/category/IntervalBarRenderer.class | Bin 0 -> 5796 bytes
.../renderer/category/LayeredBarRenderer.class | Bin 0 -> 8477 bytes
.../chart/renderer/category/LevelRenderer.class | Bin 0 -> 9151 bytes
.../renderer/category/LineAndShapeRenderer.class | Bin 0 -> 13679 bytes
.../chart/renderer/category/LineRenderer3D.class | Bin 0 -> 11975 bytes
.../category/MinMaxCategoryRenderer$1.class | Bin 0 -> 1788 bytes
.../category/MinMaxCategoryRenderer$2.class | Bin 0 -> 1664 bytes
.../renderer/category/MinMaxCategoryRenderer.class | Bin 0 -> 8724 bytes
.../chart/renderer/category/ScatterRenderer.class | Bin 0 -> 9853 bytes
.../renderer/category/StackedAreaRenderer.class | Bin 0 -> 7904 bytes
.../renderer/category/StackedBarRenderer.class | Bin 0 -> 8011 bytes
.../renderer/category/StackedBarRenderer3D.class | Bin 0 -> 13979 bytes
.../renderer/category/StandardBarPainter.class | Bin 0 -> 3686 bytes
.../renderer/category/StatisticalBarRenderer.class | Bin 0 -> 10261 bytes
.../category/StatisticalLineAndShapeRenderer.class | Bin 0 -> 8587 bytes
.../renderer/category/WaterfallBarRenderer.class | Bin 0 -> 9388 bytes
.../chart/renderer/xy/AbstractXYItemRenderer.class | Bin 0 -> 28259 bytes
.../chart/renderer/xy/CandlestickRenderer.class | Bin 0 -> 12308 bytes
.../chart/renderer/xy/ClusteredXYBarRenderer.class | Bin 0 -> 7158 bytes
.../xy/CyclicXYItemRenderer$OverwriteDataSet.class | Bin 0 -> 2783 bytes
.../chart/renderer/xy/CyclicXYItemRenderer.class | Bin 0 -> 4529 bytes
.../chart/renderer/xy/DefaultXYItemRenderer.class | Bin 0 -> 470 bytes
.../renderer/xy/DeviationRenderer$State.class | Bin 0 -> 807 bytes
.../chart/renderer/xy/DeviationRenderer.class | Bin 0 -> 6863 bytes
.../chart/renderer/xy/GradientXYBarPainter.class | Bin 0 -> 5731 bytes
org/jfree/chart/renderer/xy/HighLowRenderer.class | Bin 0 -> 7664 bytes
.../renderer/xy/SamplingXYLineRenderer$State.class | Bin 0 -> 1278 bytes
.../chart/renderer/xy/SamplingXYLineRenderer.class | Bin 0 -> 7652 bytes
...XYAreaRenderer$StackedXYAreaRendererState.class | Bin 0 -> 1763 bytes
.../chart/renderer/xy/StackedXYAreaRenderer.class | Bin 0 -> 10520 bytes
.../chart/renderer/xy/StackedXYAreaRenderer2.class | Bin 0 -> 8094 bytes
.../chart/renderer/xy/StackedXYBarRenderer.class | Bin 0 -> 9098 bytes
.../chart/renderer/xy/StandardXYBarPainter.class | Bin 0 -> 3628 bytes
.../renderer/xy/StandardXYItemRenderer$State.class | Bin 0 -> 1581 bytes
.../chart/renderer/xy/StandardXYItemRenderer.class | Bin 0 -> 16144 bytes
org/jfree/chart/renderer/xy/VectorRenderer.class | Bin 0 -> 6510 bytes
org/jfree/chart/renderer/xy/WindItemRenderer.class | Bin 0 -> 4445 bytes
.../xy/XYAreaRenderer$XYAreaRendererState.class | Bin 0 -> 845 bytes
org/jfree/chart/renderer/xy/XYAreaRenderer.class | Bin 0 -> 11608 bytes
org/jfree/chart/renderer/xy/XYAreaRenderer2.class | Bin 0 -> 9629 bytes
org/jfree/chart/renderer/xy/XYBarPainter.class | Bin 0 -> 442 bytes
.../xy/XYBarRenderer$XYBarRendererState.class | Bin 0 -> 995 bytes
org/jfree/chart/renderer/xy/XYBarRenderer.class | Bin 0 -> 20002 bytes
org/jfree/chart/renderer/xy/XYBlockRenderer.class | Bin 0 -> 6979 bytes
.../renderer/xy/XYBoxAndWhiskerRenderer.class | Bin 0 -> 13493 bytes
org/jfree/chart/renderer/xy/XYBubbleRenderer.class | Bin 0 -> 7662 bytes
.../chart/renderer/xy/XYDifferenceRenderer.class | Bin 0 -> 19112 bytes
org/jfree/chart/renderer/xy/XYDotRenderer.class | Bin 0 -> 7054 bytes
org/jfree/chart/renderer/xy/XYErrorRenderer.class | Bin 0 -> 6869 bytes
org/jfree/chart/renderer/xy/XYItemRenderer.class | Bin 0 -> 7091 bytes
.../chart/renderer/xy/XYItemRendererState.class | Bin 0 -> 1584 bytes
org/jfree/chart/renderer/xy/XYLine3DRenderer.class | Bin 0 -> 3563 bytes
.../renderer/xy/XYLineAndShapeRenderer$State.class | Bin 0 -> 1257 bytes
.../chart/renderer/xy/XYLineAndShapeRenderer.class | Bin 0 -> 17442 bytes
org/jfree/chart/renderer/xy/XYShapeRenderer.class | Bin 0 -> 9330 bytes
.../xy/XYSplineRenderer$ControlPoint.class | Bin 0 -> 902 bytes
org/jfree/chart/renderer/xy/XYSplineRenderer.class | Bin 0 -> 5552 bytes
.../chart/renderer/xy/XYStepAreaRenderer.class | Bin 0 -> 8260 bytes
org/jfree/chart/renderer/xy/XYStepRenderer.class | Bin 0 -> 6056 bytes
.../chart/renderer/xy/YIntervalRenderer.class | Bin 0 -> 6909 bytes
.../chart/resources/JFreeChartResources.class | Bin 0 -> 897 bytes
org/jfree/chart/servlet/ChartDeleter.class | Bin 0 -> 1660 bytes
org/jfree/chart/servlet/DisplayChart.class | Bin 0 -> 2711 bytes
org/jfree/chart/servlet/ServletUtilities.class | Bin 0 -> 6730 bytes
org/jfree/chart/title/CompositeTitle.class | Bin 0 -> 4126 bytes
org/jfree/chart/title/DateTitle.class | Bin 0 -> 2328 bytes
org/jfree/chart/title/ImageTitle.class | Bin 0 -> 5657 bytes
org/jfree/chart/title/LegendGraphic.class | Bin 0 -> 10216 bytes
.../chart/title/LegendItemBlockContainer.class | Bin 0 -> 3255 bytes
org/jfree/chart/title/LegendTitle.class | Bin 0 -> 12700 bytes
org/jfree/chart/title/PaintScaleLegend.class | Bin 0 -> 12662 bytes
org/jfree/chart/title/ShortTextTitle.class | Bin 0 -> 4496 bytes
org/jfree/chart/title/TextTitle.class | Bin 0 -> 13704 bytes
org/jfree/chart/title/Title.class | Bin 0 -> 6433 bytes
org/jfree/chart/urls/CategoryURLGenerator.class | Bin 0 -> 230 bytes
.../chart/urls/CustomCategoryURLGenerator.class | Bin 0 -> 2379 bytes
org/jfree/chart/urls/CustomPieURLGenerator.class | Bin 0 -> 2889 bytes
org/jfree/chart/urls/CustomXYURLGenerator.class | Bin 0 -> 2390 bytes
org/jfree/chart/urls/PieURLGenerator.class | Bin 0 -> 235 bytes
.../chart/urls/StandardCategoryURLGenerator.class | Bin 0 -> 3055 bytes
org/jfree/chart/urls/StandardPieURLGenerator.class | Bin 0 -> 2530 bytes
org/jfree/chart/urls/StandardXYURLGenerator.class | Bin 0 -> 2286 bytes
org/jfree/chart/urls/StandardXYZURLGenerator.class | Bin 0 -> 697 bytes
org/jfree/chart/urls/TimeSeriesURLGenerator.class | Bin 0 -> 3222 bytes
org/jfree/chart/urls/URLUtilities.class | Bin 0 -> 2072 bytes
org/jfree/chart/urls/XYURLGenerator.class | Bin 0 -> 206 bytes
org/jfree/chart/urls/XYZURLGenerator.class | Bin 0 -> 252 bytes
org/jfree/chart/util/HexNumberFormat.class | Bin 0 -> 1986 bytes
org/jfree/chart/util/LineUtilities.class | Bin 0 -> 1595 bytes
org/jfree/chart/util/LogFormat.class | Bin 0 -> 3027 bytes
org/jfree/chart/util/RelativeDateFormat.class | Bin 0 -> 7080 bytes
org/jfree/chart/util/ResourceBundleWrapper.class | Bin 0 -> 1870 bytes
org/jfree/chart/util/XYCoordinateType.class | Bin 0 -> 1278 bytes
org/jfree/data/ComparableObjectItem.class | Bin 0 -> 1866 bytes
org/jfree/data/ComparableObjectSeries.class | Bin 0 -> 5120 bytes
org/jfree/data/DataUtilities.class | Bin 0 -> 3649 bytes
org/jfree/data/DefaultKeyedValue.class | Bin 0 -> 1983 bytes
org/jfree/data/DefaultKeyedValues.class | Bin 0 -> 6374 bytes
org/jfree/data/DefaultKeyedValues2D.class | Bin 0 -> 6855 bytes
org/jfree/data/DomainInfo.class | Bin 0 -> 237 bytes
org/jfree/data/DomainOrder.class | Bin 0 -> 1402 bytes
org/jfree/data/KeyToGroupMap.class | Bin 0 -> 4704 bytes
org/jfree/data/KeyedObject.class | Bin 0 -> 1502 bytes
org/jfree/data/KeyedObjects.class | Bin 0 -> 4465 bytes
org/jfree/data/KeyedObjects2D.class | Bin 0 -> 6539 bytes
org/jfree/data/KeyedValue.class | Bin 0 -> 188 bytes
org/jfree/data/KeyedValueComparator.class | Bin 0 -> 2276 bytes
org/jfree/data/KeyedValueComparatorType.class | Bin 0 -> 1066 bytes
org/jfree/data/KeyedValues.class | Bin 0 -> 342 bytes
org/jfree/data/KeyedValues2D.class | Bin 0 -> 451 bytes
org/jfree/data/Range.class | Bin 0 -> 3984 bytes
org/jfree/data/RangeInfo.class | Bin 0 -> 232 bytes
org/jfree/data/RangeType.class | Bin 0 -> 1384 bytes
org/jfree/data/UnknownKeyException.class | Bin 0 -> 394 bytes
org/jfree/data/Value.class | Bin 0 -> 148 bytes
org/jfree/data/Values.class | Bin 0 -> 180 bytes
org/jfree/data/Values2D.class | Bin 0 -> 209 bytes
org/jfree/data/category/CategoryDataset.class | Bin 0 -> 209 bytes
org/jfree/data/category/CategoryRangeInfo.class | Bin 0 -> 208 bytes
org/jfree/data/category/CategoryToPieDataset.class | Bin 0 -> 4157 bytes
.../data/category/DefaultCategoryDataset.class | Bin 0 -> 4465 bytes
.../category/DefaultIntervalCategoryDataset.class | Bin 0 -> 9530 bytes
.../data/category/IntervalCategoryDataset.class | Bin 0 -> 352 bytes
.../data/category/SlidingCategoryDataset.class | Bin 0 -> 4204 bytes
org/jfree/data/contour/ContourDataset.class | Bin 0 -> 496 bytes
org/jfree/data/contour/DefaultContourDataset.class | Bin 0 -> 6000 bytes
org/jfree/data/contour/NonGridContourDataset.class | Bin 0 -> 3204 bytes
org/jfree/data/function/Function2D.class | Bin 0 -> 151 bytes
org/jfree/data/function/LineFunction2D.class | Bin 0 -> 555 bytes
.../function/NormalDistributionFunction2D.class | Bin 0 -> 1080 bytes
org/jfree/data/function/PowerFunction2D.class | Bin 0 -> 604 bytes
org/jfree/data/gantt/GanttCategoryDataset.class | Bin 0 -> 594 bytes
.../data/gantt/SlidingGanttCategoryDataset.class | Bin 0 -> 6497 bytes
org/jfree/data/gantt/Task.class | Bin 0 -> 3257 bytes
org/jfree/data/gantt/TaskSeries.class | Bin 0 -> 2474 bytes
org/jfree/data/gantt/TaskSeriesCollection.class | Bin 0 -> 9007 bytes
org/jfree/data/gantt/XYTaskDataset.class | Bin 0 -> 5469 bytes
org/jfree/data/general/AbstractDataset.class | Bin 0 -> 4075 bytes
org/jfree/data/general/AbstractSeriesDataset.class | Bin 0 -> 1174 bytes
org/jfree/data/general/CombinationDataset.class | Bin 0 -> 246 bytes
.../data/general/CombinedDataset$DatasetInfo.class | Bin 0 -> 1064 bytes
org/jfree/data/general/CombinedDataset.class | Bin 0 -> 6709 bytes
org/jfree/data/general/Dataset.class | Bin 0 -> 352 bytes
org/jfree/data/general/DatasetChangeEvent.class | Bin 0 -> 642 bytes
org/jfree/data/general/DatasetChangeListener.class | Bin 0 -> 251 bytes
org/jfree/data/general/DatasetGroup.class | Bin 0 -> 1200 bytes
org/jfree/data/general/DatasetUtilities.class | Bin 0 -> 25512 bytes
org/jfree/data/general/DefaultHeatMapDataset.class | Bin 0 -> 3366 bytes
.../data/general/DefaultKeyedValueDataset.class | Bin 0 -> 2595 bytes
.../data/general/DefaultKeyedValues2DDataset.class | Bin 0 -> 525 bytes
.../data/general/DefaultKeyedValuesDataset.class | Bin 0 -> 483 bytes
org/jfree/data/general/DefaultPieDataset.class | Bin 0 -> 4111 bytes
org/jfree/data/general/DefaultValueDataset.class | Bin 0 -> 1701 bytes
org/jfree/data/general/HeatMapDataset.class | Bin 0 -> 419 bytes
org/jfree/data/general/HeatMapUtilities.class | Bin 0 -> 2577 bytes
org/jfree/data/general/KeyedValueDataset.class | Bin 0 -> 209 bytes
org/jfree/data/general/KeyedValues2DDataset.class | Bin 0 -> 191 bytes
org/jfree/data/general/KeyedValuesDataset.class | Bin 0 -> 181 bytes
org/jfree/data/general/PieDataset.class | Bin 0 -> 196 bytes
org/jfree/data/general/Series.class | Bin 0 -> 4843 bytes
org/jfree/data/general/SeriesChangeEvent.class | Bin 0 -> 482 bytes
org/jfree/data/general/SeriesChangeListener.class | Bin 0 -> 247 bytes
org/jfree/data/general/SeriesDataset.class | Bin 0 -> 296 bytes
org/jfree/data/general/SeriesException.class | Bin 0 -> 482 bytes
org/jfree/data/general/SubSeriesDataset.class | Bin 0 -> 3874 bytes
org/jfree/data/general/ValueDataset.class | Bin 0 -> 194 bytes
org/jfree/data/general/WaferMapDataset.class | Bin 0 -> 3644 bytes
org/jfree/data/io/CSV.class | Bin 0 -> 2874 bytes
org/jfree/data/jdbc/JDBCCategoryDataset.class | Bin 0 -> 4186 bytes
org/jfree/data/jdbc/JDBCPieDataset.class | Bin 0 -> 3618 bytes
org/jfree/data/jdbc/JDBCXYDataset.class | Bin 0 -> 6954 bytes
.../data/resources/DataPackageResources.class | Bin 0 -> 720 bytes
.../data/resources/DataPackageResources_de.class | Bin 0 -> 731 bytes
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.../data/resources/DataPackageResources_fr.class | Bin 0 -> 730 bytes
.../data/resources/DataPackageResources_pl.class | Bin 0 -> 729 bytes
.../data/resources/DataPackageResources_ru.class | Bin 0 -> 729 bytes
.../data/statistics/BoxAndWhiskerCalculator.class | Bin 0 -> 3492 bytes
.../statistics/BoxAndWhiskerCategoryDataset.class | Bin 0 -> 680 bytes
org/jfree/data/statistics/BoxAndWhiskerItem.class | Bin 0 -> 3093 bytes
.../data/statistics/BoxAndWhiskerXYDataset.class | Bin 0 -> 521 bytes
.../DefaultBoxAndWhiskerCategoryDataset.class | Bin 0 -> 9063 bytes
.../statistics/DefaultBoxAndWhiskerXYDataset.class | Bin 0 -> 6081 bytes
.../DefaultMultiValueCategoryDataset.class | Bin 0 -> 5503 bytes
.../DefaultStatisticalCategoryDataset.class | Bin 0 -> 7496 bytes
org/jfree/data/statistics/HistogramBin.class | Bin 0 -> 1650 bytes
org/jfree/data/statistics/HistogramDataset.class | Bin 0 -> 6238 bytes
org/jfree/data/statistics/HistogramType.class | Bin 0 -> 1382 bytes
.../data/statistics/MeanAndStandardDeviation.class | Bin 0 -> 1908 bytes
.../statistics/MultiValueCategoryDataset.class | Bin 0 -> 320 bytes
org/jfree/data/statistics/Regression.class | Bin 0 -> 2792 bytes
org/jfree/data/statistics/SimpleHistogramBin.class | Bin 0 -> 2540 bytes
.../data/statistics/SimpleHistogramDataset.class | Bin 0 -> 5669 bytes
.../statistics/StatisticalCategoryDataset.class | Bin 0 -> 362 bytes
org/jfree/data/statistics/Statistics.class | Bin 0 -> 5608 bytes
org/jfree/data/time/DateRange.class | Bin 0 -> 1890 bytes
org/jfree/data/time/Day.class | Bin 0 -> 5437 bytes
...DynamicTimeSeriesCollection$ValueSequence.class | Bin 0 -> 1183 bytes
.../data/time/DynamicTimeSeriesCollection.class | Bin 0 -> 11261 bytes
org/jfree/data/time/FixedMillisecond.class | Bin 0 -> 2523 bytes
org/jfree/data/time/Hour.class | Bin 0 -> 5670 bytes
org/jfree/data/time/Millisecond.class | Bin 0 -> 5001 bytes
org/jfree/data/time/Minute.class | Bin 0 -> 5793 bytes
org/jfree/data/time/Month.class | Bin 0 -> 5902 bytes
org/jfree/data/time/MovingAverage.class | Bin 0 -> 5474 bytes
org/jfree/data/time/Quarter.class | Bin 0 -> 5685 bytes
org/jfree/data/time/RegularTimePeriod.class | Bin 0 -> 4688 bytes
org/jfree/data/time/Second.class | Bin 0 -> 5659 bytes
org/jfree/data/time/SimpleTimePeriod.class | Bin 0 -> 2116 bytes
org/jfree/data/time/TimePeriod.class | Bin 0 -> 206 bytes
org/jfree/data/time/TimePeriodAnchor.class | Bin 0 -> 1418 bytes
.../data/time/TimePeriodFormatException.class | Bin 0 -> 422 bytes
org/jfree/data/time/TimePeriodValue.class | Bin 0 -> 2340 bytes
org/jfree/data/time/TimePeriodValues.class | Bin 0 -> 7004 bytes
.../data/time/TimePeriodValuesCollection.class | Bin 0 -> 6837 bytes
org/jfree/data/time/TimeSeries.class | Bin 0 -> 14409 bytes
org/jfree/data/time/TimeSeriesCollection.class | Bin 0 -> 8996 bytes
org/jfree/data/time/TimeSeriesDataItem.class | Bin 0 -> 2338 bytes
org/jfree/data/time/TimeSeriesTableModel.class | Bin 0 -> 3641 bytes
org/jfree/data/time/TimeTableXYDataset.class | Bin 0 -> 7241 bytes
org/jfree/data/time/Week.class | Bin 0 -> 6839 bytes
org/jfree/data/time/Year.class | Bin 0 -> 4321 bytes
org/jfree/data/time/ohlc/OHLC.class | Bin 0 -> 1075 bytes
org/jfree/data/time/ohlc/OHLCItem.class | Bin 0 -> 1550 bytes
org/jfree/data/time/ohlc/OHLCSeries.class | Bin 0 -> 1542 bytes
.../data/time/ohlc/OHLCSeriesCollection.class | Bin 0 -> 5411 bytes
org/jfree/data/xml/CategoryDatasetHandler.class | Bin 0 -> 2495 bytes
org/jfree/data/xml/CategorySeriesHandler.class | Bin 0 -> 3105 bytes
org/jfree/data/xml/DatasetReader.class | Bin 0 -> 2588 bytes
org/jfree/data/xml/DatasetTags.class | Bin 0 -> 419 bytes
org/jfree/data/xml/ItemHandler.class | Bin 0 -> 2886 bytes
org/jfree/data/xml/KeyHandler.class | Bin 0 -> 2435 bytes
org/jfree/data/xml/PieDatasetHandler.class | Bin 0 -> 2111 bytes
org/jfree/data/xml/RootHandler.class | Bin 0 -> 1461 bytes
org/jfree/data/xml/ValueHandler.class | Bin 0 -> 2595 bytes
org/jfree/data/xy/AbstractIntervalXYDataset.class | Bin 0 -> 1250 bytes
org/jfree/data/xy/AbstractXYDataset.class | Bin 0 -> 1053 bytes
org/jfree/data/xy/AbstractXYZDataset.class | Bin 0 -> 688 bytes
org/jfree/data/xy/CategoryTableXYDataset.class | Bin 0 -> 4795 bytes
org/jfree/data/xy/DefaultHighLowDataset.class | Bin 0 -> 3858 bytes
org/jfree/data/xy/DefaultIntervalXYDataset.class | Bin 0 -> 5526 bytes
org/jfree/data/xy/DefaultOHLCDataset.class | Bin 0 -> 3718 bytes
org/jfree/data/xy/DefaultTableXYDataset.class | Bin 0 -> 8571 bytes
org/jfree/data/xy/DefaultWindDataset.class | Bin 0 -> 4297 bytes
org/jfree/data/xy/DefaultXYDataset.class | Bin 0 -> 4384 bytes
org/jfree/data/xy/DefaultXYZDataset.class | Bin 0 -> 4785 bytes
org/jfree/data/xy/IntervalXYDataset.class | Bin 0 -> 373 bytes
org/jfree/data/xy/IntervalXYDelegate.class | Bin 0 -> 5146 bytes
org/jfree/data/xy/IntervalXYZDataset.class | Bin 0 -> 340 bytes
org/jfree/data/xy/MatrixSeries.class | Bin 0 -> 2158 bytes
org/jfree/data/xy/MatrixSeriesCollection.class | Bin 0 -> 3832 bytes
org/jfree/data/xy/NormalizedMatrixSeries.class | Bin 0 -> 1424 bytes
org/jfree/data/xy/OHLCDataItem.class | Bin 0 -> 2048 bytes
org/jfree/data/xy/OHLCDataset.class | Bin 0 -> 398 bytes
org/jfree/data/xy/TableXYDataset.class | Bin 0 -> 191 bytes
org/jfree/data/xy/Vector.class | Bin 0 -> 1260 bytes
org/jfree/data/xy/VectorDataItem.class | Bin 0 -> 1307 bytes
org/jfree/data/xy/VectorSeries.class | Bin 0 -> 1790 bytes
org/jfree/data/xy/VectorSeriesCollection.class | Bin 0 -> 4214 bytes
org/jfree/data/xy/VectorXYDataset.class | Bin 0 -> 277 bytes
org/jfree/data/xy/WindDataItem.class | Bin 0 -> 1467 bytes
org/jfree/data/xy/WindDataset.class | Bin 0 -> 231 bytes
org/jfree/data/xy/XIntervalDataItem.class | Bin 0 -> 1243 bytes
org/jfree/data/xy/XIntervalSeries.class | Bin 0 -> 1565 bytes
org/jfree/data/xy/XIntervalSeriesCollection.class | Bin 0 -> 4449 bytes
org/jfree/data/xy/XYBarDataset.class | Bin 0 -> 3859 bytes
org/jfree/data/xy/XYCoordinate.class | Bin 0 -> 1780 bytes
org/jfree/data/xy/XYDataItem.class | Bin 0 -> 2752 bytes
org/jfree/data/xy/XYDataset.class | Bin 0 -> 352 bytes
org/jfree/data/xy/XYDatasetTableModel.class | Bin 0 -> 2199 bytes
org/jfree/data/xy/XYDomainInfo.class | Bin 0 -> 193 bytes
org/jfree/data/xy/XYInterval.class | Bin 0 -> 1216 bytes
org/jfree/data/xy/XYIntervalDataItem.class | Bin 0 -> 1529 bytes
org/jfree/data/xy/XYIntervalSeries.class | Bin 0 -> 1850 bytes
org/jfree/data/xy/XYIntervalSeriesCollection.class | Bin 0 -> 4543 bytes
org/jfree/data/xy/XYRangeInfo.class | Bin 0 -> 212 bytes
org/jfree/data/xy/XYSeries.class | Bin 0 -> 10550 bytes
org/jfree/data/xy/XYSeriesCollection.class | Bin 0 -> 8832 bytes
org/jfree/data/xy/XYZDataset.class | Bin 0 -> 222 bytes
org/jfree/data/xy/XisSymbolic.class | Bin 0 -> 277 bytes
org/jfree/data/xy/YInterval.class | Bin 0 -> 933 bytes
org/jfree/data/xy/YIntervalDataItem.class | Bin 0 -> 1211 bytes
org/jfree/data/xy/YIntervalSeries.class | Bin 0 -> 1565 bytes
org/jfree/data/xy/YIntervalSeriesCollection.class | Bin 0 -> 4165 bytes
org/jfree/data/xy/YWithXInterval.class | Bin 0 -> 948 bytes
org/jfree/data/xy/YisSymbolic.class | Bin 0 -> 277 bytes
org/jfree/date/AnnualDateRule.class | Bin 0 -> 546 bytes
org/jfree/date/DateUtilities.class | Bin 0 -> 924 bytes
org/jfree/date/DayAndMonthRule.class | Bin 0 -> 1391 bytes
org/jfree/date/DayOfWeekInMonthRule.class | Bin 0 -> 1638 bytes
org/jfree/date/EasterSundayRule.class | Bin 0 -> 820 bytes
org/jfree/date/MonthConstants.class | Bin 0 -> 506 bytes
org/jfree/date/RelativeDayOfWeekRule.class | Bin 0 -> 2162 bytes
org/jfree/date/SerialDate.class | Bin 0 -> 9197 bytes
org/jfree/date/SerialDateUtilities.class | Bin 0 -> 3400 bytes
org/jfree/date/SpreadsheetDate.class | Bin 0 -> 4461 bytes
org/jfree/io/FileUtilities.class | Bin 0 -> 1351 bytes
org/jfree/io/IOUtils.class | Bin 0 -> 6581 bytes
org/jfree/io/SerialUtilities.class | Bin 0 -> 10492 bytes
org/jfree/layout/CenterLayout.class | Bin 0 -> 2613 bytes
org/jfree/layout/FormatLayout.class | Bin 0 -> 11332 bytes
org/jfree/layout/LCBLayout.class | Bin 0 -> 3896 bytes
org/jfree/layout/RadialLayout.class | Bin 0 -> 4513 bytes
org/jfree/resources/JCommonResources.class | Bin 0 -> 864 bytes
org/jfree/text/G2TextMeasurer.class | Bin 0 -> 1124 bytes
org/jfree/text/TextBlock.class | Bin 0 -> 5236 bytes
org/jfree/text/TextBlockAnchor.class | Bin 0 -> 2039 bytes
org/jfree/text/TextBox.class | Bin 0 -> 6792 bytes
org/jfree/text/TextFragment.class | Bin 0 -> 5763 bytes
org/jfree/text/TextLine.class | Bin 0 -> 3861 bytes
org/jfree/text/TextMeasurer.class | Bin 0 -> 171 bytes
org/jfree/text/TextUtilities.class | Bin 0 -> 13681 bytes
org/jfree/threads/ReaderWriterLock$1.class | Bin 0 -> 225 bytes
.../ReaderWriterLock$ReaderWriterNode.class | Bin 0 -> 981 bytes
org/jfree/threads/ReaderWriterLock.class | Bin 0 -> 2818 bytes
org/jfree/ui/Align.class | Bin 0 -> 1580 bytes
org/jfree/ui/ApplicationFrame.class | Bin 0 -> 1316 bytes
org/jfree/ui/ArrowPanel.class | Bin 0 -> 2004 bytes
org/jfree/ui/BevelArrowIcon.class | Bin 0 -> 3024 bytes
org/jfree/ui/DateCellRenderer.class | Bin 0 -> 1326 bytes
org/jfree/ui/DateChooserPanel.class | Bin 0 -> 8374 bytes
org/jfree/ui/Drawable.class | Bin 0 -> 179 bytes
org/jfree/ui/DrawablePanel.class | Bin 0 -> 1814 bytes
org/jfree/ui/ExtendedDrawable.class | Bin 0 -> 245 bytes
org/jfree/ui/ExtensionFileFilter.class | Bin 0 -> 941 bytes
org/jfree/ui/FilesystemFilter.class | Bin 0 -> 1886 bytes
org/jfree/ui/FloatDimension.class | Bin 0 -> 2175 bytes
org/jfree/ui/FloatingButtonEnabler.class | Bin 0 -> 1437 bytes
org/jfree/ui/FontChooserDialog.class | Bin 0 -> 1938 bytes
org/jfree/ui/FontChooserPanel.class | Bin 0 -> 4468 bytes
org/jfree/ui/FontDisplayField.class | Bin 0 -> 1553 bytes
org/jfree/ui/GradientPaintTransformType.class | Bin 0 -> 1653 bytes
org/jfree/ui/GradientPaintTransformer.class | Bin 0 -> 231 bytes
org/jfree/ui/HorizontalAlignment.class | Bin 0 -> 1451 bytes
org/jfree/ui/InsetsChooserPanel.class | Bin 0 -> 3496 bytes
org/jfree/ui/InsetsTextField.class | Bin 0 -> 1527 bytes
org/jfree/ui/IntegerDocument.class | Bin 0 -> 1061 bytes
org/jfree/ui/JTextObserver.class | Bin 0 -> 1364 bytes
.../ui/KeyedComboBoxModel$ComboBoxItemPair.class | Bin 0 -> 857 bytes
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8707 files changed, 73424 insertions(+)
diff --git a/Alignment.java b/Alignment.java
new file mode 100644
index 0000000..0fece23
--- /dev/null
+++ b/Alignment.java
@@ -0,0 +1,662 @@
+/*
+ * Copyright 2013 Brian Tjaden
+ *
+ * This file is part of Rockhopper.
+ *
+ * Rockhopper is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * any later version.
+ *
+ * Rockhopper is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * (in the file gpl.txt) along with Rockhopper.
+ * If not, see <http://www.gnu.org/licenses/>.
+ */
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.util.Scanner;
+
+/*************************************************************
+ * An instance of the Alignment class represents an alignment
+ * of a sequence read to a reference (genome) sequence.
+ *************************************************************/
+public class Alignment {
+
+ /*********************************************************
+ ****************** INSTANCE VARIABLES *******************
+ *********************************************************/
+
+ // Parameters
+ private int numErrors;
+ private int threshold;
+
+ private String seq1;
+ private int start1;
+ private int stop1;
+ private String seq2;
+ private int start2;
+ private int stop2;
+ private int[] qualities;
+ private int[][] table;
+ private int[][] errors;
+ private int[][] backtrack; // 1=LEFT, 2=DIAGONAL, 3=ABOVE, -1=DONE
+ private int size;
+ private int optimalScore_post;
+ private int optimalRow_post;
+ private int optimalCol_post;
+ private int optimalError_post;
+ private int optimalScore_pre;
+ private int optimalRow_pre;
+ private int optimalCol_pre;
+ private int optimalError_pre;
+ private StringBuilder formattedAlignment;
+
+
+
+ /*********************************************************
+ ****************** CONSTRUCTORS *************************
+ *********************************************************/
+
+ public Alignment() {
+ this(0, 0);
+ }
+
+ public Alignment(int numErrors, int threshold) {
+ this.size = 120;
+ this.table = new int[size][size];
+ this.errors = new int[size][size];
+ this.numErrors = numErrors;
+ this.threshold = threshold;
+ }
+
+
+
+ /*********************************************************
+ ****************** PUBLIC INSTANCE METHODS **************
+ *********************************************************/
+
+ public void setNumErrors(int numErrors) {
+ this.numErrors = numErrors;
+ }
+
+ public void setThreshold(int threshold) {
+ this.threshold = threshold;
+ }
+
+ public void align(File file1, File file2) {
+ String genome = readSequenceFromFile(file1);
+ String read = readSequenceFromFile(file2);
+ int[] qualityScores = new int[read.length()];
+ for (int i=0; i<qualityScores.length; i++) qualityScores[i] = 40;
+ this.align(genome, -1, 0, read, -1, 0, qualityScores);
+ }
+
+ /**
+ * Align seq1 (genome) and seq2 (read). The exclusive (start1:stop1) and (start2:stop2)
+ * coordinates represent a perfect match seed between the two sequences.
+ */
+ public void align(String seq1, int start1, int stop1, String seq2, int start2, int stop2, int[] qualities) {
+ optimalError_post = 0;
+ optimalError_pre = 0;
+
+ if (seq1.length()-stop1 < seq2.length()-stop2) { // genome is not long enough for read
+ optimalScore_post = -2;
+ optimalScore_pre = -2;
+ return;
+ }
+ if (start1 < start2) { // genome is not long enough for read
+ optimalScore_post = -2;
+ optimalScore_pre = -2;
+ return;
+ }
+
+ this.seq1 = seq1;
+ this.start1 = start1;
+ this.stop1 = stop1;
+ this.seq2 = seq2;
+ this.start2 = start2;
+ this.stop2 = stop2;
+ this.qualities = qualities;
+ if (this.seq2.length() > this.size - this.numErrors) {
+ this.size = this.seq2.length() + this.numErrors;
+ this.table = new int[this.size][this.size];
+ this.errors = new int[this.size][this.size];
+ }
+
+ // Align post-seed
+ this.optimalScore_post = Integer.MAX_VALUE;
+ this.optimalRow_post = -2;
+ this.optimalCol_post = -2;
+ this.optimalError_post = 0;
+ postAlign();
+
+ // Align pre-seed
+ this.optimalScore_pre = Integer.MAX_VALUE;
+ this.optimalRow_pre = -2;
+ this.optimalCol_pre = -2;
+ this.optimalError_pre = 0;
+ preAlign();
+ }
+
+ public int getScore() {
+ if ((optimalScore_pre == -2) || (optimalScore_post == -2)) return -2;
+ return optimalScore_pre + optimalScore_post;
+ }
+
+ public int getErrors() {
+ return optimalError_pre + optimalError_post;
+ }
+
+ /**
+ * Return the starting coordinate in the genome (seq1) of the alignment.
+ */
+ public int getStart() {
+ if (optimalRow_pre >= 0) // There is a region preceding the seed
+ return start1 - optimalRow_pre + 1;
+ else // No region in front of the seed
+ return start1 + 2;
+ }
+
+ /**
+ * Return the stopping coordinate in the genome (seq1) of the alignment.
+ */
+ public int getStop() {
+ if (optimalRow_post >= 0) // There is a region following the seed
+ return stop1 + optimalRow_post + 1;
+ else // No region following the seed
+ return stop1;
+ }
+
+ /**
+ * Returns a String representation of this Alignment.
+ */
+ public String toString() {
+ if ((optimalScore_pre == -2) || (optimalScore_post == -2)) return "No Alignment.";
+ return "\n" + "Errors:\t" + (optimalError_post+optimalError_pre) + "\n" + "Score:\t" + (optimalScore_post+optimalScore_pre);
+ }
+
+
+
+ /*********************************************************
+ ****************** PUBLIC CLASS METHODS *****************
+ *********************************************************/
+
+
+
+ /*********************************************************
+ ****************** PRIVATE INSTANCE METHODS *************
+ *********************************************************/
+
+ /**
+ * Align region after seed.
+ */
+ private void postAlign() {
+
+ // Initialize first row and column in table
+ if ((stop1 >= seq1.length()) || (stop2 >= seq2.length())) {
+ optimalScore_post = 0;
+ optimalError_post = 0;
+ optimalRow_post = -2;
+ return;
+ }
+ table[0][0] = mismatch(stop1, stop2)*qualities[stop2];
+ errors[0][0] = mismatch(stop1, stop2);
+ int j = 0;
+ for (j=1; j<Math.min(numErrors+1, seq2.length()-stop2); j++) { // First row
+ int gapLeft = table[0][j-1] + qualities[stop2+j];
+ int match = j*qualities[stop2+j] + mismatch(stop1, stop2+j)*qualities[stop2+j];
+ if (optimalError_pre + errors[0][j-1]+1 > numErrors) gapLeft = Integer.MAX_VALUE;
+ if (optimalError_pre + j+mismatch(stop1, stop2+j) > numErrors) match = Integer.MAX_VALUE;
+ int minimum = Math.min(gapLeft, match);
+ table[0][j] = minimum;
+ if (match == minimum) {
+ errors[0][j] = j + mismatch(stop1, stop2+j);
+ } else { // Gap left
+ errors[0][j] = errors[0][j-1] + 1;
+ }
+ }
+ for (int i=1; i<Math.min(numErrors+1, seq1.length()-stop1); i++) { // First column
+ int gapAbove = table[i-1][0] + qualities[stop2];
+ int match = i*qualities[stop2] + mismatch(stop1+i, stop2)*qualities[stop2];
+ if (optimalError_pre + errors[i-1][0]+1 > numErrors) gapAbove = Integer.MAX_VALUE;
+ if (optimalError_pre + i+mismatch(stop1+i, stop2) > numErrors) match = Integer.MAX_VALUE;
+ int minimum = Math.min(gapAbove, match);
+ table[i][0] = minimum;
+ if (match == minimum) {
+ errors[i][0] = i + mismatch(stop1+i, stop2);
+ } else { // Gap above
+ errors[i][0] = errors[i-1][0] + 1;
+ }
+ }
+
+ // Check if this is optimal alignment (i.e., final column in table)
+ if (stop2 == seq2.length()-1) { // Only one column in table
+ optimalScore_post = table[0][0];
+ optimalRow_post = 0;
+ optimalCol_post = 0;
+ optimalError_post = errors[0][0];
+ for (int i=1; i<Math.min(numErrors+1, seq1.length()-stop1); i++) {
+ if (table[i][0] < optimalScore_post) {
+ optimalScore_post = table[i][0];
+ optimalRow_post = i;
+ optimalCol_post = 0;
+ optimalError_post = errors[i][0];
+ }
+ }
+ } else if (stop2+j-1 == seq2.length()-1) {
+ optimalScore_post = table[0][j-1];
+ optimalRow_post = 0;
+ optimalCol_post = j-1;
+ optimalError_post = errors[0][j-1];
+ }
+
+ // Populate table
+ for (int i=1; i<Math.min(seq2.length()-stop2+numErrors, seq1.length()-stop1); i++) {
+ for (j=Math.max(i-numErrors, 1); j<Math.min(i+numErrors+1, seq2.length()-stop2); j++) {
+
+ int gapLeft = Integer.MAX_VALUE;
+ int gapAbove = Integer.MAX_VALUE;
+ int gapLeft_errors = Integer.MAX_VALUE;
+ int gapAbove_errors = Integer.MAX_VALUE;
+ if (j == i-numErrors) { // Left table entry is unavailable
+ gapAbove = table[i-1][j] + qualities[stop2+j];
+ gapAbove_errors = errors[i-1][j] + 1;
+ } else if (j == i+numErrors) { // Above table entry is unavailable
+ gapLeft = table[i][j-1] + qualities[stop2+j];
+ gapLeft_errors = errors[i][j-1] + 1;
+ } else { // Both left and above table entries are available
+ gapAbove = table[i-1][j] + qualities[stop2+j];
+ gapLeft = table[i][j-1] + qualities[stop2+j];
+ gapAbove_errors = errors[i-1][j] + 1;
+ gapLeft_errors = errors[i][j-1] + 1;
+ }
+ int match = table[i-1][j-1] + mismatch(stop1+i, stop2+j)*qualities[stop2+j];
+ int match_errors = errors[i-1][j-1] + mismatch(stop1+i, stop2+j);
+ if ((match_errors < gapAbove_errors) || (gapLeft_errors < gapAbove_errors) || (gapAbove_errors + optimalError_pre > numErrors)) gapAbove = Integer.MAX_VALUE;
+ if ((match_errors < gapLeft_errors) || (gapAbove_errors < gapLeft_errors) || (gapLeft_errors + optimalError_pre > numErrors)) gapLeft = Integer.MAX_VALUE;
+ if ((gapAbove_errors < match_errors) || (gapLeft_errors < match_errors) || (match_errors + optimalError_pre > numErrors)) match = Integer.MAX_VALUE;
+ int minimum = min(match, gapAbove, gapLeft);
+
+ // Assign value to table
+ table[i][j] = minimum;
+ if (match == minimum) {
+ errors[i][j] = errors[i-1][j-1] + mismatch(stop1+i, stop2+j);
+ } else if (gapAbove == minimum) {
+ errors[i][j] = errors[i-1][j] + 1;
+ } else if (gapLeft == minimum) {
+ errors[i][j] = errors[i][j-1] + 1;
+ } else {
+ // Impossible case. Do nothing.
+ }
+
+ // Check if this is optimal alignment (i.e., final column in table)
+ if ((stop2 + j == seq2.length()-1) && (table[i][j] < optimalScore_post)) {
+ optimalScore_post = table[i][j];
+ optimalRow_post = i;
+ optimalCol_post = j;
+ optimalError_post = errors[i][j];
+ }
+ }
+ }
+ }
+
+ /**
+ * Align region before seed.
+ */
+ private void preAlign() {
+
+ // Initialize first row and column in table
+ if ((start1 < 0) || (start2 < 0)) {
+ optimalScore_pre = 0;
+ optimalError_pre = 0;
+ optimalRow_pre = -2;
+ return;
+ }
+ table[0][0] = mismatch(start1, start2)*qualities[start2];
+ errors[0][0] = mismatch(start1, start2);
+ int j = 0;
+ for (j=1; j<Math.min(numErrors+1, start2+1); j++) { // First row
+ int gapLeft = table[0][j-1] + qualities[start2-j];
+ int match = j*qualities[start2-j] + mismatch(start1, start2-j)*qualities[start2-j];
+ if (optimalError_post + errors[0][j-1]+1 > numErrors) gapLeft = Integer.MAX_VALUE;
+ if (optimalError_post + j+mismatch(start1, start2-j) > numErrors) match = Integer.MAX_VALUE;
+ int minimum = Math.min(gapLeft, match);
+ table[0][j] = minimum;
+ if (match == minimum) {
+ errors[0][j] = j + mismatch(start1, start2-j);
+ } else { // Gap left
+ errors[0][j] = errors[0][j-1] + 1;
+ }
+ }
+ for (int i=1; i<Math.min(numErrors+1, start1+1); i++) { // First column
+ int gapAbove = table[i-1][0] + qualities[start2];
+ int match = i*qualities[start2] + mismatch(start1-i, start2)*qualities[start2];
+ if (optimalError_post + errors[i-1][0]+1 > numErrors) gapAbove = Integer.MAX_VALUE;
+ if (optimalError_post + i+mismatch(start1-i, start2) > numErrors) match = Integer.MAX_VALUE;
+ int minimum = Math.min(gapAbove, match);
+ table[i][0] = minimum;
+ if (match == minimum) {
+ errors[i][0] = i + mismatch(start1-i, start2);
+ } else { // Gap above
+ errors[i][0] = errors[i-1][0] + 1;
+ }
+ }
+
+ // Check if this is optimal alignment (i.e., final column in table)
+ if (start2 == 0) { // Only one column in table
+ optimalScore_pre = table[0][0];
+ optimalRow_pre = 0;
+ optimalCol_pre = 0;
+ optimalError_pre = errors[0][0];
+ for (int i=1; i<Math.min(numErrors+1, start1+1); i++) {
+ if (table[i][0] < optimalScore_pre) {
+ optimalScore_pre = table[i][0];
+ optimalRow_pre = i;
+ optimalCol_pre = 0;
+ optimalError_pre = errors[i][0];
+ }
+ }
+ } else if (start2-j+1 == 0) {
+ optimalScore_pre = table[0][j-1];
+ optimalRow_pre = 0;
+ optimalCol_pre = j-1;
+ optimalError_pre = errors[0][j-1];
+ }
+
+ // Populate table
+ for (int i=1; i<Math.min(start2+1+numErrors, start1+1); i++) {
+ for (j=Math.max(i-numErrors, 1); j<Math.min(i+numErrors+1, start2+1); j++) {
+
+ int gapLeft = Integer.MAX_VALUE;
+ int gapAbove = Integer.MAX_VALUE;
+ int gapLeft_errors = Integer.MAX_VALUE;
+ int gapAbove_errors = Integer.MAX_VALUE;
+ if (j == i-numErrors) { // Left table entry is unavailable
+ gapAbove = table[i-1][j] + qualities[start2-j];
+ gapAbove_errors = errors[i-1][j] + 1;
+ } else if (j == i+numErrors) { // Above table entry is unavailable
+ gapLeft = table[i][j-1] + qualities[start2-j];
+ gapLeft_errors = errors[i][j-1] + 1;
+ } else { // Both left and above table entries are available
+ gapAbove = table[i-1][j] + qualities[start2-j];
+ gapLeft = table[i][j-1] + qualities[start2-j];
+ gapAbove_errors = errors[i-1][j] + 1;
+ gapLeft_errors = errors[i][j-1] + 1;
+ }
+ int match = table[i-1][j-1] + mismatch(start1-i, start2-j)*qualities[start2-j];
+ int match_errors = errors[i-1][j-1] + mismatch(start1-i, start2-j);
+ if ((match_errors < gapAbove_errors) || (gapLeft_errors < gapAbove_errors) || (gapAbove_errors + optimalError_post > numErrors)) gapAbove = Integer.MAX_VALUE;
+ if ((match_errors < gapLeft_errors) || (gapAbove_errors < gapLeft_errors) || (gapLeft_errors + optimalError_post > numErrors)) gapLeft = Integer.MAX_VALUE;
+ if ((gapAbove_errors < match_errors) || (gapLeft_errors < match_errors) || (match_errors + optimalError_post > numErrors)) match = Integer.MAX_VALUE;
+ int minimum = min(match, gapAbove, gapLeft);
+
+ // Assign value to table
+ table[i][j] = minimum;
+ if (match == minimum) {
+ errors[i][j] = errors[i-1][j-1] + mismatch(start1-i, start2-j);
+ } else if (gapAbove == minimum) {
+ errors[i][j] = errors[i-1][j] + 1;
+ } else if (gapLeft == minimum) {
+ errors[i][j] = errors[i][j-1] + 1;
+ } else {
+ // Impossible case. Do nothing.
+ }
+
+ // Check if this is optimal alignment (i.e., final column in table)
+ if ((start2 - j == 0) && (table[i][j] < optimalScore_pre)) {
+ optimalScore_pre = table[i][j];
+ optimalRow_pre = i;
+ optimalCol_pre = j;
+ optimalError_pre = errors[i][j];
+ }
+ }
+ }
+ }
+
+ /**
+ * Once an alignment score has been computed, the backtracking table is searched to
+ * determine a StringBuilder representation of the alignment.
+ */
+ private void backtrack_post(StringBuilder s1_alignment, StringBuilder alignment, StringBuilder s2_alignment) {
+
+ // Begin backtracking search at optimal alignment score (found in last column in table)
+ int i = optimalRow_post;
+ int j = optimalCol_post; // Last column in table
+
+ // Backtrack through table to beginning of alignment
+ while ((i >= 0) || (j >= 0)) {
+ if (backtrack[i][j] == 2) { // Diagonal
+ s1_alignment.append(seq1.charAt(stop1+i));
+ alignment.append(getMatchMismatchChar(seq1.charAt(stop1+i), seq2.charAt(stop2+j)));
+ s2_alignment.append(seq2.charAt(stop2+j));
+ i--;
+ j--;
+ } else if (backtrack[i][j] == 3) { // Gap above
+ s1_alignment.append(seq1.charAt(stop1+i));
+ alignment.append(' ');
+ s2_alignment.append('-');
+ i--;
+ } else if (backtrack[i][j] == 1) { // Gap left
+ s1_alignment.append('-');
+ alignment.append(' ');
+ s2_alignment.append(seq2.charAt(stop2+j));
+ j--;
+ } else if (backtrack[i][j] == -1) { // DONE
+ s1_alignment.append(seq1.charAt(stop1+i));
+ alignment.append(getMatchMismatchChar(seq1.charAt(stop1+i), seq2.charAt(stop2+j)));
+ s2_alignment.append(seq2.charAt(stop2+j));
+ while (i != 0) { // We're in first column. Alignment begins with gaps.
+ s1_alignment.append(seq1.charAt(stop1+i-1));
+ alignment.append(' ');
+ s2_alignment.append('-');
+ i--;
+ }
+ while (j != 0) { // We're in first row. Alignment begins with gaps.
+ s1_alignment.append('-');
+ alignment.append(' ');
+ s2_alignment.append(seq2.charAt(stop2+j-1));
+ j--;
+ }
+ i--;
+ j--;
+ } else { // Impossible case.
+ Peregrine.output("\nThere was an error when backtracking.\n\n");
+ i = -1;
+ j = -1;
+ }
+ }
+
+ // Add seed region to alignment
+ i = stop1 - 1;
+ j = stop2 - 1;
+ while ((i > start1) && (j > start2)) {
+ s1_alignment.append(seq1.charAt(i));
+ alignment.append(getMatchMismatchChar(seq1.charAt(i), seq2.charAt(j)));
+ s2_alignment.append(seq2.charAt(j));
+ i--;
+ j--;
+ }
+
+ // Reverse the alignment
+ s1_alignment.reverse();
+ alignment.reverse();
+ s2_alignment.reverse();
+ }
+
+ /**
+ * Once an alignment score has been computed, the backtracking table is searched to
+ * determine a StringBuilder representation of the alignment.
+ */
+ private void backtrack_pre(StringBuilder s1_alignment, StringBuilder alignment, StringBuilder s2_alignment) {
+
+ // Begin backtracking search at optimal alignment score (found in last column in table)
+ int i = optimalRow_pre;
+ int j = optimalCol_pre; // Last column in table
+
+ // Backtrack through table to beginning of alignment
+ while ((i >= 0) || (j >= 0)) {
+ if (backtrack[i][j] == 2) { // Diagonal
+ s1_alignment.append(seq1.charAt(start1-i));
+ alignment.append(getMatchMismatchChar(seq1.charAt(start1-i), seq2.charAt(start2-j)));
+ s2_alignment.append(seq2.charAt(start2-j));
+ i--;
+ j--;
+ } else if (backtrack[i][j] == 3) { // Gap above
+ s1_alignment.append(seq1.charAt(start1-i));
+ alignment.append(' ');
+ s2_alignment.append('-');
+ i--;
+ } else if (backtrack[i][j] == 1) { // Gap left
+ s1_alignment.append('-');
+ alignment.append(' ');
+ s2_alignment.append(seq2.charAt(start2-j));
+ j--;
+ } else if (backtrack[i][j] == -1) { // DONE
+ s1_alignment.append(seq1.charAt(start1-i));
+ alignment.append(getMatchMismatchChar(seq1.charAt(start1-i), seq2.charAt(start2-j)));
+ s2_alignment.append(seq2.charAt(start2-j));
+ while (i != 0) { // We're in first column. Alignment begins with gaps.
+ s1_alignment.append(seq1.charAt(start1-i+1));
+ alignment.append(' ');
+ s2_alignment.append('-');
+ i--;
+ }
+ while (j != 0) { // We're in first row. Alignment begins with gaps.
+ s1_alignment.append('-');
+ alignment.append(' ');
+ s2_alignment.append(seq2.charAt(start2-j+1));
+ j--;
+ }
+ i--;
+ j--;
+ } else { // Impossible case.
+ Peregrine.output("\nThere was an error when backtracking.\n\n");
+ i = -1;
+ j = -1;
+ }
+ }
+ }
+
+ /**
+ * Returns 1 if the characters at the specified indices in
+ * the two sequences mismatch.
+ * Returns 0 if the characters at the specified indices in
+ * the two sequence are the same.
+ */
+ private int mismatch(int x, int y) {
+ if (seq1.charAt(x) == seq2.charAt(y)) return 0;
+ return 1;
+ }
+
+ /**
+ * Returns an alignment character if the two specified characters are the same.
+ * Returns a space character otherwise.
+ */
+ private char getMatchMismatchChar(char a, char b) {
+ if (a == b) return '|';
+ else return ' ';
+ }
+
+ /**
+ * Returns a String representation of a 2D integer array.
+ */
+ private String tableToString_post(int[][] a) {
+ StringBuilder sb = new StringBuilder();
+ for (int j=0; j<seq2.length()-stop2; j++)
+ sb.append("\t" + seq2.charAt(stop2 + j));
+ sb.append("\n");
+ for (int i=0; i<seq1.length()-stop1; i++) {
+ sb.append(seq1.charAt(stop1 + i));
+ for (int j=0; j<seq2.length()-stop2; j++) {
+ sb.append("\t" + a[i][j]);
+ }
+ sb.append("\n");
+ }
+ return sb.toString();
+ }
+
+ /**
+ * Returns a String representation of a 2D integer array.
+ */
+ private String tableToString_pre(int[][] a) {
+ StringBuilder sb = new StringBuilder();
+ for (int j=0; j<start2+1; j++)
+ sb.append("\t" + seq2.charAt(start2 - j));
+ sb.append("\n");
+ for (int i=0; i<start1+1; i++) {
+ sb.append(seq1.charAt(start1 - i));
+ for (int j=0; j<start2+1; j++) {
+ sb.append("\t" + a[i][j]);
+ }
+ sb.append("\n");
+ }
+ return sb.toString();
+ }
+
+ /**
+ * Returns the minimum of three integers.
+ */
+ private int min(int a, int b, int c) {
+ return Math.min(a, Math.min(b, c));
+ }
+
+
+
+ /*********************************************************
+ ****************** PRIVATE CLASS METHODS ****************
+ *********************************************************/
+
+ /**
+ * Reads in and returns a genomic sequence from the specified FASTA file.
+ *
+ * @param f a <code>File</code> object referring to a FASTA file containing a genomic sequence
+ * @return the genomic sequence read in from a FASTA file
+ */
+ private static String readSequenceFromFile(File f) {
+ StringBuilder sequence = new StringBuilder();
+ try {
+ Scanner reader = new Scanner(f);
+ String header = reader.nextLine(); // Header line of FASTA file
+ if ((header.length() == 0) || (header.charAt(0) != '>')) {
+ Peregrine.output("Error - first line of file " + f + " is not in FASTA format.\n");
+ return sequence.toString();
+ }
+ while (reader.hasNext()) { // continue until we reach end of file
+ sequence.append(reader.nextLine());
+ }
+ reader.close();
+ } catch (FileNotFoundException e) {
+ Peregrine.output("Error - the file " + f + " could not be found and opened.\n");
+ return sequence.toString();
+ }
+ return sequence.toString();
+ }
+
+
+
+ /*********************************************************
+ ****************** MAIN METHOD **************************
+ *********************************************************/
+
+ public static void main(String [] args) {
+
+ if (args.length < 2) {
+ System.err.println("\nWhen executing this program, please enter the name of two files,");
+ System.err.println("each containing a sequence. The program will align the two sequences.\n");
+ System.err.println("\tjava Alignment file1.txt file2.txt\n");
+ System.exit(0);
+ }
+
+ Alignment a = new Alignment(2, 100);
+ a.align(new File(args[0]), new File(args[1]));
+ System.out.println(a);
+ }
+
+}
+
diff --git a/Assembler.java b/Assembler.java
new file mode 100644
index 0000000..f402a62
--- /dev/null
+++ b/Assembler.java
@@ -0,0 +1,1195 @@
+/*
+ * Copyright 2014 Brian Tjaden
+ *
+ * This file is part of Rockhopper.
+ *
+ * Rockhopper is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * any later version.
+ *
+ * Rockhopper is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * (in the file gpl.txt) along with Rockhopper.
+ * If not, see <http://www.gnu.org/licenses/>.
+ */
+
+import java.util.ArrayList;
+import java.util.Scanner;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.BufferedReader;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.io.InputStreamReader;
+import java.io.FileInputStream;
+import java.util.zip.GZIPInputStream;
+import java.util.concurrent.atomic.AtomicInteger;
+import javax.swing.JTextArea;
+
+public class Assembler {
+
+ /********************************************
+ ********** Instance Variables **********
+ ********************************************/
+
+ private Dictionary kDict;
+ private int PHRED_offset;
+ private BufferedReader reader;
+ private BufferedReader reader2; // Mate-pair file if using paired-end reads
+ private PrintWriter samWriter; // Output reads to SAM file
+ private boolean isCompressedFile; // True if gzip file. False otherwise.
+ private SamOps sam; // Used if reads file is in SAM/BAM format
+ private AtomicInteger nameCount; // Used when outputting SAM file and reads have no name
+ private boolean firstLineDone; // Used when reading in the first line of FASTA files
+ private long totalTime; // Time taken to read in sequencing reads and assemble transcripts
+ private boolean mapFullReadsToTranscriptome; // First pass (false), second pass (true).
+ private DeNovoTranscripts transcripts;
+
+ // Results
+ public AtomicInteger totalReads;
+ private AtomicInteger invalidQualityReads; // Reads containing an invalid quality score
+ private AtomicInteger ambiguousReads; // Reads with ambiguous nucleotides
+ private AtomicInteger lowQualityReads; // Reads with quality scores too low for mapping
+
+
+
+ /*****************************************
+ ********** Class Variables **********
+ *****************************************/
+
+ // Parameters
+ public static JTextArea output; // Output to GUI or, if null, to System.out
+ public static int k = 25; // Size of k-mer
+ private static int readsInputFormat; // 0=FASTQ, 1=QSEQ, 2=FASTA, 3=SAM(single), 4=SAM(paired), 5=BAM(single), 6=BAM(paired)
+ public static ArrayList<String> conditionFiles = new ArrayList<String>();
+ public static boolean singleEndOrientationReverseComplement = false; // RevComp reads
+ public static int numThreads = 1; // Number of threads
+ public static int minReadLength = 35; // Minimum allowed sequencing read length
+ public static boolean stopAfterOneHit = true;
+ public static boolean computeExpression = true; // PARAM: compute differential expression
+ public static int CAPACITY_POWER = 25; // PARAM: capacity of hashtable is ~2^n
+ public static int MIN_READS_MAPPING = 20; // PARAM: Min # of full length reads mapping to do novo transcripts
+ public static int minTranscriptLength; // PARAM: Min transcript length: 2*k
+ public static int minSeedExpression = 50; // PARAM: Min expression to initiate a transcript
+ public static int minExpression = 5; // PARAM: Min number of occurrences to be part of transcript
+ public static boolean unstranded = false; // PARAM: Is RNA-seq data strand specific or ambiguous?
+ public static String pairedEndOrientation = "fr"; // PARAM: ff, fr, rf, rr
+ public static boolean isPairedEnd = false; // Do we have paired-end reads?
+ private static String pairedEndFile; // Name of mate-pair file if using paired-end reads
+ public static int maxPairedEndLength = 500;
+ public static String[] labels;
+ public static int readsFileIndex; // Keep track of current sequencing reads file
+ public static PrintWriter summaryWriter = null; // For outputting summary file
+ private static String summaryFile = "summary.txt";
+ public static String expressionFile = "transcripts.txt";
+ public static boolean outputSAM = false; // Output reads to SAM file
+ public static String output_DIR = "Assembler_Results/"; // PARAM: write output files to this directory
+ public static boolean time = false; // PARAM: output execution time of program
+ public static boolean verbose = false; // PARAM: verbose output
+
+
+
+ /**************************************
+ ********** Constructors **********
+ **************************************/
+
+ public Assembler() {
+
+ totalTime = System.currentTimeMillis();
+ FileOps foo = new FileOps(getCompressedFileName(), conditionFiles);
+ if (foo.isValid()) {
+ output("\n");
+ for (int i=0; i<conditionFiles.size(); i++) {
+ String[] files = conditionFiles.get(i).split(",");
+ for (int j=0; j<files.length; j++) {
+ String[] parse_readFiles = files[j].split("%");
+ if (parse_readFiles.length == 1) { // Using single-end reads (except maybe SAM/BAM)
+ String file1 = parse_readFiles[0];
+ output("Assembling transcripts from reads in file: \t" + removePath(file1) + "\n");
+ Rockhopper.updateProgress();
+ Rockhopper.updateProgress();
+ Assembler.isPairedEnd = false;
+ } else { // Using paired-end reads
+ String file1 = parse_readFiles[0];
+ String file2 = parse_readFiles[1];
+ output("Assembling transcripts from reads in files:\n");
+ output("\t" + removePath(file1) + "\n");
+ output("\t" + removePath(file2) + "\n");
+ Rockhopper.updateProgress();
+ Rockhopper.updateProgress();
+ Assembler.isPairedEnd = true;
+ }
+ }
+ }
+ transcripts = new DeNovoTranscripts(foo.getTranscripts());
+ readsFileIndex = 0;
+ output("\n");
+ for (int i=0; i<conditionFiles.size(); i++) {
+ String[] files = conditionFiles.get(i).split(",");
+ for (int j=0; j<files.length; j++) {
+ String[] parse_readFiles = files[j].split("%");
+ if (parse_readFiles.length == 1) { // Using single-end reads (except maybe SAM/BAM)
+ String file1 = parse_readFiles[0];
+ output("Aligning reads to assembled transcripts using file:\t" + removePath(file1) + "\n");
+ Assembler.isPairedEnd = false;
+ output("\n\tTotal reads in file: \t" + DeNovoTranscripts.numReads[readsFileIndex] + "\n");
+ output("\tPerfectly aligned reads: \t" + DeNovoTranscripts.numMappingReads[readsFileIndex] + "\t" + Math.round((100.0*DeNovoTranscripts.numMappingReads[readsFileIndex])/DeNovoTranscripts.numReads[readsFileIndex]) + "%" + "\n\n");
+ Rockhopper.updateProgress();
+ } else { // Using paired-end reads
+ String file1 = parse_readFiles[0];
+ String file2 = parse_readFiles[1];
+ output("Aligning reads to assembled transcripts using files:\n");
+ output("\t" + removePath(file1) + "\n");
+ output("\t" + removePath(file2) + "\n");
+ Assembler.isPairedEnd = true;
+ output("\n\tTotal reads in files: \t" + DeNovoTranscripts.numReads[readsFileIndex] + "\n");
+ output("\tPerfectly aligned reads: \t" + DeNovoTranscripts.numMappingReads[readsFileIndex] + "\t" + Math.round((100.0*DeNovoTranscripts.numMappingReads[readsFileIndex])/DeNovoTranscripts.numReads[readsFileIndex]) + "%" + "\n\n");
+ Rockhopper.updateProgress();
+ }
+ readsFileIndex++;
+ }
+ }
+ if (outputSAM) output("Rockhopper did not output a SAM file since sequencing read alignments were previously cached. If you want a SAM file to be output, you must first clear the cache." + "\n\n");
+ } else {
+
+ // Create k-mer dictionary and assemble transcripts de novo
+ kDict = new Dictionary(k);
+ totalReads = new AtomicInteger(0);
+ invalidQualityReads = new AtomicInteger(0);
+ ambiguousReads = new AtomicInteger(0);
+ lowQualityReads = new AtomicInteger(0);
+ mapFullReadsToTranscriptome = false;
+ readsFileIndex = 0;
+ output("\n");
+ for (int i=0; i<conditionFiles.size(); i++) {
+ String[] files = conditionFiles.get(i).split(",");
+ for (int j=0; j<files.length; j++) {
+ String[] parse_readFiles = files[j].split("%");
+ if (parse_readFiles.length == 1) { // Using single-end reads (except maybe SAM/BAM)
+ String file1 = parse_readFiles[0];
+ output("Assembling transcripts from reads in file: \t" + removePath(file1) + "\n");
+ Assembler.isPairedEnd = false;
+ Assembler.pairedEndFile = null;
+ readsInputFormat = getReadsInputFileType(file1);
+ this.PHRED_offset = getPhredOffset(file1);
+ if (outputSAM) outputSamHeader(file1);
+ int numThreads_OLD = numThreads;
+ if ((readsInputFormat == 5) || (readsInputFormat == 6)) numThreads = 1;
+ firstLineDone = false;
+ readInSequencingReads(file1); // Read in the sequencing reads
+ numThreads = numThreads_OLD;
+ if (samWriter != null) {
+ samWriter.close();
+ output("Sequencing reads written to SAM file: \t" + output_DIR + getFileNameBase(file1) + ".sam" + "\n");
+ }
+ Rockhopper.updateProgress();
+ Rockhopper.updateProgress();
+ } else { // Using paired-end reads
+ String file1 = parse_readFiles[0];
+ String file2 = parse_readFiles[1];
+ output("Assembling transcripts from reads in files:\n");
+ output("\t" + removePath(file1) + "\n");
+ output("\t" + removePath(file2) + "\n");
+ Assembler.isPairedEnd = true;
+ Assembler.pairedEndFile = file2;
+ readsInputFormat = getReadsInputFileType(file1);
+ this.PHRED_offset = getPhredOffset(file1);
+ if (outputSAM) outputSamHeader(file1);
+ int numThreads_OLD = numThreads;
+ if ((readsInputFormat == 5) || (readsInputFormat == 6)) numThreads = 1;
+ firstLineDone = false;
+ readInSequencingReads(file1); // Read in the sequencing reads
+ numThreads = numThreads_OLD;
+ if (samWriter != null) {
+ samWriter.close();
+ output("Sequencing reads written to SAM file: \t" + output_DIR + getFileNameBase(file1) + ".sam" + "\n");
+ }
+ Rockhopper.updateProgress();
+ Rockhopper.updateProgress();
+ }
+ readsFileIndex++;
+ }
+ }
+ kDict.assembleTranscripts(); // Assemble transcripts for final time
+
+ // Map full length reads to transcripts
+ totalReads = new AtomicInteger(0);
+ invalidQualityReads = new AtomicInteger(0);
+ ambiguousReads = new AtomicInteger(0);
+ lowQualityReads = new AtomicInteger(0);
+ mapFullReadsToTranscriptome = true;
+ kDict.initializeReadMapping(stopAfterOneHit);
+ readsFileIndex = 0;
+ output("\n");
+ for (int i=0; i<conditionFiles.size(); i++) {
+ String[] files = conditionFiles.get(i).split(",");
+ for (int j=0; j<files.length; j++) {
+ String[] parse_readFiles = files[j].split("%");
+ if (parse_readFiles.length == 1) { // Using single-end reads (except maybe SAM/BAM)
+ String file1 = parse_readFiles[0];
+ output("Aligning reads to assembled transcripts using file:\t" + removePath(file1) + "\n");
+ Assembler.isPairedEnd = false;
+ Assembler.pairedEndFile = null;
+ readsInputFormat = getReadsInputFileType(file1);
+ this.PHRED_offset = getPhredOffset(file1);
+ int numThreads_OLD = numThreads;
+ if ((readsInputFormat == 5) || (readsInputFormat == 6)) numThreads = 1;
+ firstLineDone = false;
+ readInSequencingReads(file1); // Read in the sequencing reads
+ numThreads = numThreads_OLD;
+ if (unstranded) kDict.bwtIndex.halveReads(readsFileIndex); // Fix read double counting
+ output("\n\tTotal reads in file: \t" + kDict.bwtIndex.getNumReads(readsFileIndex) + "\n");
+ output("\tPerfectly aligned reads: \t" + kDict.bwtIndex.getNumMappingReads(readsFileIndex) + "\t" + Math.round((100.0*kDict.bwtIndex.getNumMappingReads(readsFileIndex))/kDict.bwtIndex.getNumReads(readsFileIndex)) + "%" + "\n\n");
+ Rockhopper.updateProgress();
+ } else { // Using paired-end reads
+ String file1 = parse_readFiles[0];
+ String file2 = parse_readFiles[1];
+ output("Aligning reads to assembled transcripts using files:\n");
+ output("\t" + removePath(file1) + "\n");
+ output("\t" + removePath(file2) + "\n");
+ Assembler.isPairedEnd = true;
+ Assembler.pairedEndFile = file2;
+ readsInputFormat = getReadsInputFileType(file1);
+ this.PHRED_offset = getPhredOffset(file1);
+ int numThreads_OLD = numThreads;
+ if ((readsInputFormat == 5) || (readsInputFormat == 6)) numThreads = 1;
+ firstLineDone = false;
+ readInSequencingReads(file1); // Read in the sequencing reads
+ numThreads = numThreads_OLD;
+ output("\n\tTotal reads in files: \t" + kDict.bwtIndex.getNumReads(readsFileIndex) + "\n");
+ output("\tPerfectly aligned reads: \t" + kDict.bwtIndex.getNumMappingReads(readsFileIndex) + "\t" + Math.round((100.0*kDict.bwtIndex.getNumMappingReads(readsFileIndex))/kDict.bwtIndex.getNumReads(readsFileIndex)) + "%" + "\n\n");
+ Rockhopper.updateProgress();
+ }
+ readsFileIndex++;
+ }
+ }
+ transcripts = new DeNovoTranscripts(kDict.bwtIndex);
+ if (computeExpression) transcripts.setMinDiffExpressionLevels(kDict.bwtIndex);
+ kDict.bwtIndex = null; // Clear Index and Dictionary
+ kDict = null; // Clear Index and Dictionary
+ System.gc(); // Clear Index and Dictionary
+ if (computeExpression) transcripts.computeDifferentialExpression();
+ FileOps.writeCompressedFile(getCompressedFileName(), conditionFiles, DeNovoTranscripts.numReads, DeNovoTranscripts.numMappingReads, transcripts);
+ }
+
+ // Incorporate results from SAM file
+ if (sam != null) {
+ totalReads.addAndGet(sam.badReads.get());
+ invalidQualityReads.addAndGet(sam.badReads.get());
+ }
+
+ outputToFile(output_DIR + expressionFile, transcripts.toString(labels));
+ totalTime = System.currentTimeMillis() - totalTime;
+ outputResults();
+ summaryWriter.close();
+ Rockhopper.updateProgress();
+ }
+
+
+
+ /*************************************************
+ ********** Public Instance Methods **********
+ *************************************************/
+
+ /**
+ * Read in sequencing reads from file.
+ */
+ public void processReads() {
+ String line = "";;
+ String name = "";
+ String nextName = ""; // Special case (FASTA)
+ String read = "";
+ String quality = "";
+ String quality_fasta = ""; // Special case (FASTA)
+ int[] qualities = new int[0];
+ String[] parse_line = null;
+
+ // Using paired-end reads
+ String line2 = "";;
+ String name2 = "";
+ String nextName2 = ""; // Special case (FASTA)
+ String read2 = "";
+ String quality2 = "";
+ String quality_fasta2 = ""; // Special case (FASTA)
+ int[] qualities2 = new int[0];
+ String[] parse_line2 = null;
+
+ try {
+
+ synchronized(reader) {
+ if ((readsInputFormat == 2) && !firstLineDone) { // Special case (FASTA)
+ line = reader.readLine(); // Special case (FASTA)
+ if (line.startsWith(">")) nextName = line.substring(1);
+ if (isPairedEnd) {
+ line2 = reader2.readLine();
+ if (line2.startsWith(">")) nextName2 = line2.substring(1);
+ }
+ }
+ firstLineDone = true;
+ }
+
+ while (line != null) {
+
+ synchronized(reader) { // Thread safe reading from file
+ if (readsInputFormat < 5) line = reader.readLine(); // Not a BAM file
+ if (line == null) continue;
+ if (readsInputFormat == 0) { // FASTQ file
+ name = line;
+ read = reader.readLine();
+ line = reader.readLine();
+ quality = reader.readLine();
+ } else if (readsInputFormat == 1) { // QSEQ file
+ parse_line = line.split("\t");
+ name = parse_line[0] + ":" + parse_line[2] + ":" + parse_line[3] + ":" + parse_line[4] + ":" + parse_line[5] + ":" + parse_line[6] + ":" + parse_line[7];
+ read = parse_line[8];
+ quality = parse_line[9];
+ } else if (readsInputFormat == 2) { // FASTA file
+ name = nextName;
+ read = "";
+ while ((line != null) && ((line.length() == 0) || (line.charAt(0) != '>'))) {
+ read += line;
+ line = reader.readLine();
+ }
+ if (line == null) nextName = "";
+ else if (line.startsWith(">")) nextName = line.substring(1);
+ else nextName = ""; // Case should never be reached
+ if (quality_fasta.length() != read.length()) quality_fasta = new String(new char[read.length()]).replace('\0', '(');
+ quality = quality_fasta;
+ } else if (readsInputFormat == 3) { // SAM file (single-end)
+ if (SamOps.isHeaderLine(line)) continue;
+ } else if (readsInputFormat == 4) { // SAM file (paired-end)
+ if (SamOps.isHeaderLine(line)) continue;
+ line2 = reader.readLine();
+ } else if (readsInputFormat == 5) { // BAM file (single-end)
+ parse_line = sam.parseAlignmentLine_BAM();
+ if (parse_line == null) {
+ line = null;
+ continue;
+ }
+ if (parse_line == SamOps.emptyStringArray) continue;
+ if (parse_line[0].startsWith("U")) {
+ read = parse_line[9];
+ quality = mapPhred(parse_line[10]);
+ } else if (samWriter != null) {
+ name = parse_line[0].substring(1);
+ while (name.startsWith("@")) name = name.substring(1);
+ int flag = 4;
+ synchronized(samWriter) {
+ samWriter.println(name + "\t" + flag + "\t" + "*" + "\t" + "0" + "\t" + "255" + "\t" + "*" + "\t" + "*" + "\t" + "0" + "\t" + "0" + "\t" + parse_line[9] + "\t" + mapPhred(parse_line[10]));
+ continue;
+ }
+ } else continue;
+ } else if (readsInputFormat == 6) { // BAM file (paired-end)
+ parse_line = sam.parseAlignmentLine_BAM();
+ if (parse_line == null) {
+ line = null;
+ continue;
+ }
+ parse_line2 = sam.parseAlignmentLine_BAM();
+ if (parse_line2 == null) {
+ line = null;
+ continue;
+ }
+ if ((parse_line == SamOps.emptyStringArray) || (parse_line2 == SamOps.emptyStringArray)) continue;
+ if ((parse_line[0].startsWith("U")) || parse_line2[0].startsWith("U")) {
+ read = parse_line[9];
+ quality = mapPhred(parse_line[10]);
+ read2 = parse_line2[9];
+ quality2 = mapPhred(parse_line2[10]);
+ } else if (samWriter != null) {
+ name = parse_line[0].substring(1);
+ while (name.startsWith("@")) name = name.substring(1);
+ name2 = parse_line2[0].substring(1);
+ while (name2.startsWith("@")) name2 = name2.substring(1);
+ int flag = 77; // 01001101
+ int flag2 = 141; // 10001101
+ synchronized(samWriter) {
+ samWriter.println(name + "\t" + flag + "\t" + "*" + "\t" + "0" + "\t" + "255" + "\t" + "*" + "\t" + "*" + "\t" + "0" + "\t" + "0" + "\t" + parse_line[9] + "\t" + mapPhred(parse_line[10]));
+ samWriter.println(name2 + "\t" + flag2 + "\t" + "*" + "\t" + "0" + "\t" + "255" + "\t" + "*" + "\t" + "*" + "\t" + "0" + "\t" + "0" + "\t" + parse_line2[9] + "\t" + mapPhred(parse_line2[10]));
+ continue;
+ }
+ } else continue;
+ }
+
+ if (isPairedEnd) { // Using paired-end reads
+ synchronized(reader2) { // Thread safe reading from file
+ line2 = reader2.readLine();
+ if (line2 == null) {
+ output("Error - the two files of mate-pair reads contain different numbers of sequencing reads.");
+ continue;
+ }
+ if (readsInputFormat == 0) { // FASTQ file
+ name2 = line;
+ read2 = reader2.readLine();
+ line2 = reader2.readLine();
+ quality2 = reader2.readLine();
+ } else if (readsInputFormat == 1) { // QSEQ file
+ parse_line2 = line2.split("\t");
+ name2 = parse_line2[0] + ":" + parse_line2[2] + ":" + parse_line2[3] + ":" + parse_line2[4] + ":" + parse_line2[5] + ":" + parse_line2[6] + ":" + parse_line2[7];
+ read2 = parse_line2[8];
+ quality2 = parse_line2[9];
+ } else if (readsInputFormat == 2) { // FASTA file
+ name2 = nextName2;
+ read2 = "";
+ while ((line2 != null) && ((line2.length() == 0) || (line2.charAt(0) != '>'))) {
+ read2 += line2;
+ line2 = reader2.readLine();
+ }
+ if (line2 == null) nextName2 = "";
+ else if (line2.startsWith(">")) nextName2 = line2.substring(1);
+ else nextName2 = ""; // Case should never be reached
+ if (quality_fasta2.length() != read2.length()) quality_fasta2 = new String(new char[read2.length()]).replace('\0', '(');
+ quality2 = quality_fasta2;
+ }
+ }
+ }
+ }
+
+ if (readsInputFormat == 3) { // SAM file (single-end)
+ parse_line = sam.parseAlignmentLine_SAM(line);
+ if (parse_line == SamOps.emptyStringArray) continue;
+ if (parse_line[0].startsWith("U")) {
+ read = parse_line[9];
+ quality = parse_line[10];
+ } else if (samWriter != null) { // Output to SAM file
+ name = parse_line[0].substring(1);
+ while (name.startsWith("@")) name = name.substring(1);
+ int flag = 4;
+ synchronized(samWriter) {
+ samWriter.println(name + "\t" + flag + "\t" + "*" + "\t" + "0" + "\t" + "255" + "\t" + "*" + "\t" + "*" + "\t" + "0" + "\t" + "0" + "\t" + parse_line[9] + "\t" + parse_line[10]);
+ }
+ continue;
+ } else continue;
+ } else if (readsInputFormat == 4) { // SAM file (paired-end)
+ parse_line = sam.parseAlignmentLine_SAM(line);
+ parse_line2 = sam.parseAlignmentLine_SAM(line2);
+ if ((parse_line == SamOps.emptyStringArray) || (parse_line2 == SamOps.emptyStringArray)) continue;
+ if ((parse_line[0].startsWith("U")) || parse_line2[0].startsWith("U")) {
+ read = parse_line[9];
+ quality = parse_line[10];
+ read2 = parse_line2[9];
+ quality2 = parse_line2[10];
+ } else if (samWriter != null) {
+ name = parse_line[0].substring(1);
+ while (name.startsWith("@")) name = name.substring(1);
+ name2 = parse_line2[0].substring(1);
+ while (name2.startsWith("@")) name2 = name2.substring(1);
+ int flag = 77; // 01001101
+ int flag2 = 141; // 10001101
+ synchronized(samWriter) {
+ samWriter.println(name + "\t" + flag + "\t" + "*" + "\t" + "0" + "\t" + "255" + "\t" + "*" + "\t" + "*" + "\t" + "0" + "\t" + "0" + "\t" + parse_line[9] + "\t" + parse_line[10]);
+ samWriter.println(name2 + "\t" + flag2 + "\t" + "*" + "\t" + "0" + "\t" + "255" + "\t" + "*" + "\t" + "*" + "\t" + "0" + "\t" + "0" + "\t" + parse_line2[9] + "\t" + parse_line2[10]);
+ }
+ continue;
+ } else continue;
+ }
+
+ // Output to SAM file
+ if ((samWriter != null) && (!mapFullReadsToTranscriptome)) {
+ while (name.startsWith("@")) name = name.substring(1);
+ if (isPairedEnd || ((sam != null) && (sam.isPairedEnd()))) { // Paired-end
+ while (name2.startsWith("@")) name2 = name2.substring(1);
+ if (name.length() == 0) {
+ name = "r" + nameCount.getAndIncrement();
+ name2 = name;
+ }
+ int flag = 77; // 01001101
+ int flag2 = 141; // 10001101
+ synchronized(samWriter) {
+ samWriter.println(name + "\t" + flag + "\t" + "*" + "\t" + "0" + "\t" + "255" + "\t" + "*" + "\t" + "*" + "\t" + "0" + "\t" + "0" + "\t" + read + "\t" + quality);
+ samWriter.println(name2 + "\t" + flag2 + "\t" + "*" + "\t" + "0" + "\t" + "255" + "\t" + "*" + "\t" + "*" + "\t" + "0" + "\t" + "0" + "\t" + read2 + "\t" + quality2);
+ }
+ } else { // Single-end
+ if (name.length() == 0) name = "r" + nameCount.getAndIncrement();
+ int flag = 4;
+ synchronized(samWriter) {
+ samWriter.println(name + "\t" + flag + "\t" + "*" + "\t" + "0" + "\t" + "255" + "\t" + "*" + "\t" + "*" + "\t" + "0" + "\t" + "0" + "\t" + read + "\t" + quality);
+ }
+ }
+ }
+
+ // Process read
+ read = read.toUpperCase();
+ boolean ambiguous = false;
+ for (int i=0; i<read.length(); i++) {
+ if ((read.charAt(i) != 'A') && (read.charAt(i) != 'C') &&
+ (read.charAt(i) != 'G') && (read.charAt(i) != 'T'))
+ ambiguous = true;
+ }
+ if (isPairedEnd || ((sam != null) && (sam.isPairedEnd()))) { // Using paired-end reads
+ read2 = read2.toUpperCase();
+ for (int i=0; i<read2.length(); i++) {
+ if ((read2.charAt(i) != 'A') && (read2.charAt(i) != 'C') &&
+ (read2.charAt(i) != 'G') && (read2.charAt(i) != 'T'))
+ ambiguous = true;
+ }
+ // Orient paired-end reads (0=ff, 1=fr, 2=rf, 3=rr)
+ if (pairedEndOrientation.charAt(0) == 'r') { // Reverse first read
+ read = reverseComplement(read);
+ quality = reverse(quality);
+ }
+ if (pairedEndOrientation.charAt(1) == 'r') { // Reverse second read
+ read2 = reverseComplement(read2);
+ quality2 = reverse(quality2);
+ }
+ } else { // Using single-end reads
+ // Orient single-end reads (true=reverse_complement, false=nothing)
+ if (singleEndOrientationReverseComplement) { // Reverse complement read
+ read = reverseComplement(read);
+ quality = reverse(quality);
+ }
+ }
+
+ // Process quality
+ if (quality.length() != read.length()) {
+ output("Quality sequence has different length than read sequence.\n");
+ continue;
+ }
+ int endIndex = quality.length()-1;
+ while ((endIndex >= 0) && ((int)(quality.charAt(endIndex))-PHRED_offset == 2)) endIndex--;
+ quality = quality.substring(0, endIndex+1);
+ read = read.substring(0, endIndex+1);
+ if (qualities.length != read.length()) qualities = new int[read.length()];
+ boolean invalid = false;
+ for (int i=0; i<quality.length(); i++) {
+ qualities[i] = (int)(quality.charAt(i)) - PHRED_offset;
+ if ((qualities[i] < 0) || (qualities[i] > 93)) invalid = true;
+ }
+ if (isPairedEnd || ((sam != null) && (sam.isPairedEnd()))) { // Using paired-end reads
+ if (quality2.length() != read2.length()) {
+ output("Quality sequence has different length than read sequence.\n");
+ continue;
+ }
+ int endIndex2 = quality2.length()-1;
+ while ((endIndex2 >= 0) && ((int)(quality2.charAt(endIndex2))-PHRED_offset == 2)) endIndex2--;
+ quality2 = quality2.substring(0, endIndex2+1);
+ read2 = read2.substring(0, endIndex2+1);
+ if (qualities2.length != read2.length()) qualities2 = new int[read2.length()];
+ for (int i=0; i<quality2.length(); i++) {
+ qualities2[i] = (int)(quality2.charAt(i)) - PHRED_offset;
+ if ((qualities2[i] < 0) || (qualities2[i] > 93)) invalid = true;
+ }
+ }
+
+ // Process sequencing reads.
+ totalReads.getAndIncrement();
+ if (ambiguous) ambiguousReads.getAndIncrement();
+ else if ((quality.length() < minReadLength) || (isPairedEnd && (quality2.length() < minReadLength)) || ((sam != null) && (sam.isPairedEnd()) && (quality2.length() < minReadLength))) lowQualityReads.getAndIncrement(); // Minimum read length
+ else if (invalid) invalidQualityReads.getAndIncrement(); // Invalid quality score
+ else {
+ if (!mapFullReadsToTranscriptome) { // First pass. Assemble transcriptome.
+ kDict.add(read); // Add read to dictionary!
+ if (isPairedEnd || ((sam != null) && (sam.isPairedEnd()))) kDict.add(read2); // Using paired-end reads
+ } else { // Second pass. Map full length reads to assembled transcripts.
+ if (isPairedEnd || ((sam != null) && (sam.isPairedEnd()))) { // Using paired-end reads
+ kDict.mapFullLengthRead(read, read2);
+ } else { // Using single-end reads
+ kDict.mapFullLengthRead(read);
+ if (unstranded) kDict.mapFullLengthRead(reverseComplement(read));
+ }
+ }
+ }
+ }
+ } catch (IOException e) {
+ output("Error - could not read in from sequencing reads file.\n\n");
+ System.exit(0);
+ }
+ }
+
+ /**
+ * Return the base file name for the compressed transcripts file.
+ * For example, if A,B,C are replicates in conditions 1 and
+ * X,Y,Z are replicates in condition 2, then the base file name
+ * would be ABC_XYZ__parameters
+ */
+ public String getCompressedFileName() {
+ StringBuilder sb = new StringBuilder();
+ for (int i=0; i<conditionFiles.size(); i++) {
+ String[] files = conditionFiles.get(i).split(",");
+ for (int j=0; j<files.length; j++) sb.append(encode(files[j]));
+ sb.append("_");
+ }
+ sb.append(parametersToString());
+ return sb.toString();
+ }
+
+
+
+ /**********************************************
+ ********** Public Class Methods **********
+ **********************************************/
+
+ public static void output(String s) {
+ if (summaryWriter != null) summaryWriter.print(s);
+ if (output == null) System.out.print(s);
+ else {
+ output.append(s);
+ output.setCaretPosition(output.getDocument().getLength());
+ }
+ }
+
+ /**
+ * Returns a reversed version of String s.
+ */
+ public static String reverse(String s) {
+ return (new StringBuilder(s)).reverse().toString();
+ }
+
+ /**
+ * Returns a reverse complemented version of String s.
+ */
+ public static String reverseComplement(String s) {
+ StringBuilder sb = new StringBuilder(s.length());
+ for (int i=s.length()-1; i>=0; i--) {
+ if (s.charAt(i) == 'A') sb.append('T');
+ else if (s.charAt(i) == 'C') sb.append('G');
+ else if (s.charAt(i) == 'G') sb.append('C');
+ else if (s.charAt(i) == 'T') sb.append('A');
+ else sb.append(s.charAt(i));
+ }
+ return sb.toString();
+ }
+
+
+
+ /**************************************************
+ ********** Private Instance Methods **********
+ **************************************************/
+
+ /**
+ * Read in sequencing reads from file.
+ */
+ private void readInSequencingReads(String readsFile) {
+
+ try {
+ if (isCompressedFile) reader = new BufferedReader(new InputStreamReader(new GZIPInputStream(new FileInputStream(readsFile))));
+ else reader = new BufferedReader(new FileReader(readsFile));
+ if (isPairedEnd) {
+ if (FileOps.isGZIP(pairedEndFile)) reader2 = new BufferedReader(new InputStreamReader(new GZIPInputStream(new FileInputStream(pairedEndFile))));
+ else reader2 = new BufferedReader(new FileReader(pairedEndFile));
+ }
+ Thread[] threads = new Thread[numThreads];
+ for (int i=0; i<numThreads; i++) {
+ threads[i] = new ProcessReadsDeNovo_Thread(this);
+ threads[i].start();
+ }
+ for (int i=0; i<numThreads; i++) threads[i].join();
+ reader.close();
+ if (isPairedEnd) reader2.close();
+ } catch (IOException e) {
+ output("Error - could not read from " + readsFile + "\n\n");
+ System.exit(0);
+ } catch (InterruptedException e) {
+ output("Error - thread execution was interrupted.\n\n");
+ System.exit(0);
+ }
+ }
+
+ /**
+ * Outputs to STDOUT stats on sequencing reads.
+ */
+ private void outputResults() {
+ output("Total number of assembled transcripts:\t\t" + transcripts.getNumTranscripts() + "\n");
+ output("\tAverage transcript length: \t" + transcripts.getAverageTranscriptLength() + "\n");
+ output("\tMedian transcript length: \t" + transcripts.getMedianTranscriptLength() + "\n");
+ output("\tTotal number of assembled bases: \t" + transcripts.getTotalAssembledBases() + "\n");
+ output("\n");
+ output("Summary of results written to file: \t" + output_DIR + summaryFile + "\n");
+ output("Details of assembled transcripts written to file: \t" + output_DIR + expressionFile + "\n");
+ output("\n");
+ output("FINSIHED.\n\n");
+ }
+
+ /**
+ * Determines the file format of the input reads file.
+ * Returns 0 if the file is in FASTQ format.
+ * Returns 1 if the file is in QSEQ format.
+ * Returns 2 if the file is in FASTA format.
+ * Returns 3 if the file is in SAM single-end format.
+ * Returns 4 if the file is in SAM paired-end format.
+ * Returns 5 if the file is in BAM single-end format.
+ * Returns 6 if the file is in BAM paired-end format.
+ */
+ private int getReadsInputFileType(String readsFile) {
+ int MAX_LINES = 10000;
+ int lineCounter = 0;
+ int fastqCount = 0;
+ int qseqCount = 0;
+ int fastaCount = 0;
+ try {
+ // First check if we have a SAM file
+ sam = new SamOps(readsFile, MAX_LINES, true);
+ if (sam.isValidSam() || sam.isValidBam()) {
+ String[] replicons = sam.getReplicons();
+ if (sam.isValidSam() && !sam.isPairedEnd()) return 3; // Single-end SAM file
+ else if (sam.isValidSam()) return 4; // Paired-end SAM file
+ else if (sam.isValidBam() && !sam.isPairedEnd()) return 5; // Single-end BAM file
+ else if (sam.isValidBam()) return 6; // Paired-end BAM file
+ else return -1; // This case should never be reached
+ } else sam = null;
+
+ Scanner reader = null;
+ isCompressedFile = FileOps.isGZIP(readsFile);
+ if (isCompressedFile) reader = new Scanner(new GZIPInputStream(new FileInputStream(readsFile)));
+ else reader = new Scanner(new File(readsFile));
+ String line;
+ while (reader.hasNextLine() && (lineCounter < MAX_LINES)) {
+ line = reader.nextLine();
+ if (line.length() > 0) {
+ if (line.charAt(0) == '@') fastqCount++;
+ else if (line.split("\t").length >= 11) qseqCount++;
+ else if (line.charAt(0) == '>') fastaCount++;
+ }
+ lineCounter++;
+ }
+ reader.close();
+ if (fastqCount > Math.max(qseqCount, fastaCount)) return 0;
+ else if (qseqCount > fastaCount) return 1;
+ else if (fastaCount > 0) return 2;
+ else {
+ output("Error - could not recognize format of file " + readsFile + "\n\n");
+ System.exit(0);
+ }
+ } catch (IOException e) {
+ output("\nError - could not open sequencing reads file: " + readsFile + "\n\n");
+ System.exit(0);
+ }
+ return -1;
+ }
+
+ /**
+ * Depending on version of Solexa machine used, the quality
+ * score may range from 35 (or 37) up to 73, or it may range
+ * from 66 up to 104. To obtain the Phred score, we subtract
+ * either 33 or 64, depending on the version. Here, we get the
+ * maximum quality score over all nucleotides in the first
+ * 100,000 reads (it should be either 73 or 104). The offset
+ * is the number we must subtract from this maximum to
+ * obtain 40, i.e., either 33 or 64.
+ */
+ private int getPhredOffset(String readsFile) {
+ int lineCounter = 0;
+ try {
+ int maxQuality = Integer.MIN_VALUE;
+ if ((readsInputFormat == 5) || (readsInputFormat == 6)) { // BAM file
+ maxQuality = sam.getMaxQuality();
+ } else {
+ Scanner reader = null;
+ if (isCompressedFile) reader = new Scanner(new GZIPInputStream(new FileInputStream(readsFile)));
+ else reader = new Scanner(new File(readsFile));
+ String line;
+ String read = "";
+ String quality = "";
+ while (reader.hasNextLine() && (lineCounter < 100000)) {
+
+ line = reader.nextLine();
+ if (readsInputFormat == 0) { // FASTQ file
+ read = reader.nextLine();
+ line = reader.nextLine();
+ quality = reader.nextLine();
+ } else if (readsInputFormat == 1) { // QSEQ file
+ String[] parse_line = line.split("\t");
+ read = parse_line[8];
+ quality = parse_line[9];
+ } else if (readsInputFormat == 2) { // FASTA file
+ read = reader.nextLine();
+ quality = "("; // ASCII value of 40
+ } else if ((readsInputFormat == 3) || (readsInputFormat == 4)) { // SAM file
+ if (line.startsWith("@")) {
+ read = "";
+ quality = "";
+ } else {
+ String[] parse_line = line.split("\t");
+ read = parse_line[9];
+ quality = parse_line[10];
+ if (quality.equals("*")) quality = "";
+ }
+ }
+
+ // Process quality
+ for (int i=0; i<quality.length(); i++)
+ maxQuality = Math.max(maxQuality, (int)(quality.charAt(i)));
+
+ lineCounter++;
+ }
+ reader.close();
+ }
+
+ // Are we Phred+33 or Phred+64?
+ if (Math.abs(maxQuality - 40 - 33) < Math.abs(maxQuality - 40 - 64))
+ return 33;
+ else
+ return 64;
+ } catch (IOException e) {
+ output("\nError - could not open file " + readsFile + "\n\n");
+ System.exit(0);
+ }
+ return -1;
+ }
+
+ /**
+ * Open SAM file for writing.
+ * Output header information to SAM file.
+ */
+ private void outputSamHeader(String readsFile) {
+ String samFileName = output_DIR + getFileNameBase(readsFile) + ".sam";
+ if (readsFile.equals(samFileName)) return; // Do not read and write same file at same time
+ nameCount = new AtomicInteger(1);
+ try {
+ samWriter = new PrintWriter(new File(samFileName));
+ samWriter.println("@HD" + "\t" + "VN:1.0" + "\t" + "SO:unsorted");
+ samWriter.println("@PG" + "\t" + "ID:Rockhopper" + "\t" + "PN:Rockhopper" + "\t" + "VN:" + Rockhopper.version);
+ } catch (IOException f) {
+ samWriter = null;
+ }
+ }
+
+ /**
+ * Return a String representation of the parameter settings.
+ */
+ private String parametersToString() {
+ return "_k" + k + "_e" + ("" + computeExpression).toUpperCase().charAt(0) + "_a" + ("" + stopAfterOneHit).toUpperCase().charAt(0) + "_d" + maxPairedEndLength + "_j" + minReadLength + "_n" + CAPACITY_POWER + "_b" + MIN_READS_MAPPING + "_u" + minTranscriptLength + "_w" + minSeedExpression + "_x" + minExpression + "_" + pairedEndOrientation + "_s" + ("" + unstranded).toUpperCase().charAt(0) + "_c" + ("" + singleEndOrientationReverseComplement).toUpperCase().charAt(0);
+ }
+
+
+
+ /***********************************************
+ ********** Private Class Methods **********
+ ***********************************************/
+
+ /**
+ * Returns the base of the specified file name, i.e.,
+ * the file extension and path to the file are excluded.
+ */
+ private static String getFileNameBase(String fileName) {
+ int slashIndex = fileName.lastIndexOf(separator());
+ if (slashIndex == -1) slashIndex = fileName.lastIndexOf("/");
+ int periodIndex = fileName.indexOf('.', slashIndex+1);
+ if (periodIndex == -1) periodIndex = fileName.length();
+ return fileName.substring(slashIndex+1, periodIndex);
+ }
+
+ /**
+ * Returns the system-dependent file separator that
+ * can be used as a RegEx.
+ */
+ private static String separator() {
+ if (File.separatorChar == '\\') return "\\\\";
+ else return File.separator;
+ }
+
+ /**
+ * Returns the file name with the leading path removed.
+ */
+ private static String removePath(String fileName) {
+ int slashIndex = fileName.lastIndexOf(separator());
+ if (slashIndex == -1) slashIndex = fileName.lastIndexOf("/");
+ return fileName.substring(slashIndex+1);
+ }
+
+ /**
+ * Returns a 2 character encoding of the String s.
+ * First, s is converted to an integer via hashing.
+ * Then, the integer is converted into a 2 character
+ * encoding, where each character takes on one of
+ * 52 different values (a-z, A-Z).
+ */
+ private static String encode(String s) {
+ int encoding = s.hashCode() % 2704; // 52*52=2704
+ if (encoding < 0) encoding += 2704;
+ int digit1 = encoding / 52;
+ int digit2 = encoding % 52;
+ if (digit2 < 0) digit2 += 52;
+ char char1 = '?';
+ char char2 = '?';
+ if (digit1 < 26) char1 = (char)('A' + digit1);
+ else char1 = (char)('a' - 26 + digit1);
+ if (digit2 < 26) char2 = (char)('A' + digit2);
+ else char2 = (char)('a' - 26 + digit2);
+ return char1 + "" + char2;
+ }
+
+ /**
+ * Output the specified string s to the specified file.
+ */
+ private static void outputToFile(String fileName, String s) {
+ try {
+ PrintWriter writer = new PrintWriter(new File(fileName));
+ writer.print(s);
+ writer.close();
+ } catch (FileNotFoundException e) {
+ output("\nError - could not open file " + fileName + "\n\n");
+ }
+ }
+
+ /**
+ * Checks if quality scores specified by parameter String
+ * need to be adjusted by a Phred offset of 33. If not,
+ * the original String is returned. If so, a new
+ * adjusted String is returned.
+ */
+ private static String mapPhred(String qualities) {
+ int offset = 33;
+ int maxPhred = 104;
+ boolean needsAdjusting = false;
+ boolean needsResetting = false;
+ for (int i=0; i<qualities.length(); i++) {
+ if ((int)(qualities.charAt(i)) < offset) needsAdjusting = true;
+ if ((int)(qualities.charAt(i)) > maxPhred) needsResetting = true;
+ }
+ if (!needsAdjusting && !needsResetting) return qualities;
+ StringBuilder sb = new StringBuilder(qualities.length());
+ for (int i=0; i<qualities.length(); i++) {
+ if (needsAdjusting) sb.append((char)(offset + qualities.charAt(i)));
+ else if (needsResetting) sb.append('(');
+ }
+ return sb.toString();
+ }
+
+ private static void commandLineArguments(String[] args) {
+ if (args.length < 1) {
+ output("\nThe Assembler application takes one or more files of RNA-seq reads and it assembles the reads (de novo) into a transcriptome map.\n");
+ output("\nThe Assembler application has one required command line argument.\n");
+ output("\nREQUIRED ARGUMENT\n\n");
+ output("\t" + "a FASTQ file of RNA-seq reads\n");
+
+ output("\nOPTIONAL ARGUMENTS\n\n");
+ output("\t" + "-k <integer>" + "\t" + "size of k-mer, range of values is 15 to 31 (default is 25)\n");
+ output("\t" + "-c <boolean>" + "\t" + "reverse complement single-end reads (default is false)\n");
+ output("\t" + "-ff/fr/rf/rr" + "\t" + "orientation of two mate reads for paired-end read, f=forward and r=reverse_complement (default is fr)\n");
+ output("\t" + "-s <boolean>" + "\t" + "RNA-seq experiments are strand specific (true) or strand ambiguous (false) (default is true)\n");
+ output("\t" + "-p <integer>" + "\t" + "number of processors (default is self-identify)\n");
+ output("\t" + "-e <boolean>" + "\t" + "compute differential expression for transcripts in pairs of experimental conditions (default is true)\n");
+ output("\t" + "-a <boolean>" + "\t" + "report 1 alignment (true) or report all optimal alignments (false), (default is true)\n");
+ output("\t" + "-d <integer>" + "\t" + "maximum number of bases between mate pairs for paired-end reads (default is 500)\n");
+ output("\t" + "-j <integer>" + "\t" + "minimum length required to use a sequencing read after trimming/processing (default is 35)\n");
+ output("\t" + "-n <integer>" + "\t" + "size of k-mer hashtable is ~ 2^n (default is 25). HINT: should normally be 25 or, if more memory is available, 26. WARNING: if increased above 25 then more than 1.2M of memory must be allocated\n");
+ output("\t" + "-b <integer>" + "\t" + "minimum number of full length reads required to map to a de novo assembled trancript (default is 20)\n");
+ output("\t" + "-u <integer>" + "\t" + "minimum length of de novo assembled transcripts (default is 2*k)\n");
+ output("\t" + "-w <integer>" + "\t" + "minimum count of k-mer to use it to seed a new de novo assembled transcript (default is 50)\n");
+ output("\t" + "-x <integer>" + "\t" + "minimum count of k-mer to use it to extend an existing de novo assembled transcript (default is 5)\n");
+ output("\t" + "-L <comma separated list>" + "\t" + "labels for each condition\n");
+ output("\t" + "-v <boolean>" + "\t" + "verbose output including raw/normalized counts aligning to each transcript (default is false)\n");
+ output("\t" + "-TIME " + "\t" + "output time taken to execute program\n");
+
+ output("\nEXAMPLE EXECUTION: SINGLE-END READS\n");
+ output("\njava Assembler <options> aerobic_replicate1.fastq,aerobic_replicate2.fastq anaerobic_replicate1.fastq,anaerobic_replicate2.fastq\n");
+ output("\nEXAMPLE EXECUTION: PAIRED-END READS\n");
+ output("\njava Assembler <options> aerobic_replicate1_pairedend1.fastq%aerobic_replicate1_pairedend2.fastq,aerobic_replicate2_pairedend1.fastq%aerobic_replicate2_pairedend2.fastq anaerobic_replicate1_pairedend1.fastq%anaerobic_replicate1_pairedend2.fastq,anaerobic_replicate2_pairedend1.fastq%anaerobic_replicate2_pairedend2.fastq\n");
+ output("\n");
+ System.exit(0);
+ }
+
+ // Initially set the number of threads
+ Assembler.numThreads = Runtime.getRuntime().availableProcessors();
+ if (Assembler.numThreads > 4) Assembler.numThreads = (int)Math.min(Assembler.numThreads * 0.75, 8.0);
+
+ int i=0;
+ while (i < args.length) {
+ if (args[i].startsWith("-k")) {
+ if ((i == args.length-2) || (args[i+1].startsWith("-"))) {
+ output("Error - command line argument -k must be followed by an integer.\n");
+ System.exit(0);
+ }
+ Assembler.k = Integer.parseInt(args[i+1]);
+ if (Assembler.minTranscriptLength == 0) Assembler.minTranscriptLength = 2*Assembler.k;
+ i += 2;
+ } else if (args[i].startsWith("-c")) {
+ if ((i == args.length-2) || (args[i+1].startsWith("-"))) {
+ output("Error - command line argument -c must be followed by a boolean.\n");
+ System.exit(0);
+ }
+ Assembler.singleEndOrientationReverseComplement = Boolean.valueOf(args[i+1]);
+ i += 2;
+ } else if (args[i].startsWith("-s")) {
+ if ((i == args.length-2) || (args[i+1].startsWith("-"))) {
+ output("Error - command line argument -s must be followed by a boolean.\n");
+ System.exit(0);
+ }
+ Assembler.unstranded = !Boolean.valueOf(args[i+1]);
+ i += 2;
+ } else if (args[i].startsWith("-p")) {
+ if ((i == args.length-2) || (args[i+1].startsWith("-"))) {
+ output("Error - command line argument -p must be followed by an integer.\n");
+ System.exit(0);
+ }
+ Assembler.numThreads = Integer.parseInt(args[i+1]);
+ i += 2;
+ } else if (args[i].startsWith("-e")) {
+ if ((i == args.length-2) || (args[i+1].startsWith("-"))) {
+ output("Error - command line argument -e must be followed by a boolean.\n");
+ System.exit(0);
+ }
+ Assembler.computeExpression = Boolean.valueOf(args[i+1]);
+ i += 2;
+ } else if (args[i].startsWith("-a")) {
+ if ((i == args.length-2) || (args[i+1].startsWith("-"))) {
+ output("Error - command line argument -a must be followed by a boolean.\n");
+ System.exit(0);
+ }
+ Assembler.stopAfterOneHit = Boolean.valueOf(args[i+1]);
+ i += 2;
+ } else if (args[i].startsWith("-d")) {
+ if ((i == args.length-2) || (args[i+1].startsWith("-"))) {
+ output("Error - command line argument -d must be followed by an integer.\n");
+ System.exit(0);
+ }
+ Assembler.maxPairedEndLength = Integer.parseInt(args[i+1]);
+ SamOps.maxPairedEndLength = Integer.parseInt(args[i+1]);
+ i += 2;
+ } else if (args[i].startsWith("-j")) {
+ if ((i == args.length-2) || (args[i+1].startsWith("-"))) {
+ output("Error - command line argument -j must be followed by an integer.\n");
+ System.exit(0);
+ }
+ Assembler.minReadLength = Integer.parseInt(args[i+1]);
+ i += 2;
+ } else if (args[i].startsWith("-n")) {
+ if ((i == args.length-2) || (args[i+1].startsWith("-"))) {
+ output("Error - command line argument -n must be followed by an integer.\n");
+ System.exit(0);
+ }
+ Assembler.CAPACITY_POWER = Integer.parseInt(args[i+1]);
+ i += 2;
+ } else if (args[i].startsWith("-b")) {
+ if ((i == args.length-2) || (args[i+1].startsWith("-"))) {
+ output("Error - command line argument -b must be followed by an integer.\n");
+ System.exit(0);
+ }
+ Assembler.MIN_READS_MAPPING = Integer.parseInt(args[i+1]);
+ i += 2;
+ } else if (args[i].startsWith("-u")) {
+ if ((i == args.length-2) || (args[i+1].startsWith("-"))) {
+ output("Error - command line argument -u must be followed by an integer.\n");
+ System.exit(0);
+ }
+ Assembler.minTranscriptLength = Integer.parseInt(args[i+1]);
+ i += 2;
+ } else if (args[i].startsWith("-w")) {
+ if ((i == args.length-2) || (args[i+1].startsWith("-"))) {
+ output("Error - command line argument -w must be followed by an integer.\n");
+ System.exit(0);
+ }
+ Assembler.minSeedExpression = Integer.parseInt(args[i+1]);
+ i += 2;
+ } else if (args[i].startsWith("-x")) {
+ if ((i == args.length-2) || (args[i+1].startsWith("-"))) {
+ output("Error - command line argument -x must be followed by an integer.\n");
+ System.exit(0);
+ }
+ Assembler.minExpression = Integer.parseInt(args[i+1]);
+ i += 2;
+ } else if (args[i].startsWith("-L")) {
+ if ((i == args.length-2) || (args[i+1].startsWith("-"))) {
+ output("Error - command line argument -L must be followed by a comma separated list of names for the conditions.\n");
+ System.exit(0);
+ }
+ Assembler.labels = args[i+1].split(",");
+ i += 2;
+ } else if (args[i].startsWith("-v")) {
+ if ((i == args.length-2) || (args[i+1].startsWith("-"))) {
+ output("Error - command line argument -v must be followed by a boolean.\n");
+ System.exit(0);
+ }
+ Assembler.verbose = Boolean.valueOf(args[i+1]);
+ i += 2;
+ } else if (args[i].equals("-ff")) {
+ Assembler.pairedEndOrientation = "ff";
+ i++;
+ } else if (args[i].equals("-fr")) {
+ Assembler.pairedEndOrientation = "fr";
+ i++;
+ } else if (args[i].equals("-rf")) {
+ Assembler.pairedEndOrientation = "rf";
+ i++;
+ } else if (args[i].equals("-rr")) {
+ Assembler.pairedEndOrientation = "rr";
+ i++;
+ } else if (args[i].equals("-TIME")) {
+ time = true;
+ i++;
+ } else { // Sequencing reads files
+ Assembler.conditionFiles.add(args[i]);
+ i++;
+ }
+ }
+
+ // Handle erroneous command line arguments
+ if (conditionFiles.size() == 0) {
+ output("Error - sequencing reads files (in FASTQ, QSEQ, or FASTA format) are required as command line arguments.\n");
+ System.exit(0);
+ }
+ for (int j=0; j<conditionFiles.size(); j++) {
+ String[] files = conditionFiles.get(j).split(",");
+ for (int k=0; k<files.length; k++) {
+ String[] pairedEnd_files = files[k].split("%");
+ if (!(new File(pairedEnd_files[0]).exists())) {
+ output("Error - file " + pairedEnd_files[0] + " does not exist.\n");
+ System.exit(0);
+ }
+ if ((pairedEnd_files.length > 1) && (!(new File(pairedEnd_files[1]).exists()))) {
+ output("Error - file " + pairedEnd_files[1] + " does not exist.\n");
+ System.exit(0);
+ }
+ if (pairedEnd_files.length > 1) Assembler.unstranded = false; // Assume paired-end reads are strand specific
+ }
+ }
+
+ // If not set by command line arguments, set de novo assembled transcript length
+ if (Assembler.minTranscriptLength == 0) Assembler.minTranscriptLength = 2*Assembler.k;
+
+ // Output directory does not exist. Create it.
+ if (!(new File(output_DIR).exists())) {
+ if (!(new File(output_DIR).mkdir())) {
+ output("Error - could not create directory " + output_DIR + "." + "\n");
+ System.exit(0);
+ }
+ }
+
+ try {
+ summaryWriter = new PrintWriter(new File(output_DIR + summaryFile));
+ } catch (FileNotFoundException e) {
+ output("Error - could not create file " + (output_DIR+summaryFile) + "\n");
+ System.exit(0);
+ }
+ }
+
+
+
+ /*************************************
+ ********** Main Method **********
+ *************************************/
+
+ public static void main(String[] args) {
+
+ commandLineArguments(args);
+ Assembler a = new Assembler();
+
+ }
+
+}
+
+
+
+/***************************************************
+ ********** ProcessReadsDeNovo_Thread **********
+ ***************************************************/
+
+class ProcessReadsDeNovo_Thread extends Thread {
+
+ private Assembler a;
+
+ public ProcessReadsDeNovo_Thread(Assembler a) {
+ this.a = a;
+ }
+
+ public void run() {
+ a.processReads();
+ }
+}
diff --git a/Condition.java b/Condition.java
new file mode 100644
index 0000000..7c7585e
--- /dev/null
+++ b/Condition.java
@@ -0,0 +1,185 @@
+/*
+ * Copyright 2013 Brian Tjaden
+ *
+ * This file is part of Rockhopper.
+ *
+ * Rockhopper is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * any later version.
+ *
+ * Rockhopper is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * (in the file gpl.txt) along with Rockhopper.
+ * If not, see <http://www.gnu.org/licenses/>.
+ */
+
+import java.util.ArrayList;
+
+/**
+ * A Condition keeps track of the RNA-seq data in each
+ * replicate experiment for a given condition.
+ */
+public class Condition {
+
+ /********************************************
+ ********** INSTANCE VARIABLES **********
+ ********************************************/
+
+ private ArrayList<Replicate> replicates;
+ private int partner; // If there are no replicates, index of most similar other condition.
+ private int minDiffExpressionLevel; // Used for differentially expressed p-value correction
+
+
+
+ /*****************************************
+ ********** CLASS VARIABLES **********
+ *****************************************/
+
+ private static long avgUpperQuartile; // Avg upper quartile over all replicates in all conditions
+
+
+
+ /**************************************
+ ********** CONSTRUCTORS **********
+ **************************************/
+
+ public Condition() {
+ this.replicates = new ArrayList<Replicate>();
+ this.partner = -1;
+ }
+
+
+
+ /*************************************************
+ ********** PUBLIC INSTANCE METHODS **********
+ *************************************************/
+
+ /**
+ * Return the Replicate at the specified index.
+ */
+ public Replicate getReplicate(int i) {
+ if ((i >= 0) && (i < replicates.size()))
+ return replicates.get(i);
+ return null;
+ }
+
+ /**
+ * Adds a replicate to this Condition.
+ */
+ public void addReplicate(Replicate r) {
+ this.replicates.add(r);
+ }
+
+ /**
+ * Return the number of Replicates performed for this Condition.
+ */
+ public int numReplicates() {
+ return replicates.size();
+ }
+
+ /**
+ * Sets the partner of this Condition, i.e., the index of the other
+ * condition that is most similar to this Condition.
+ */
+ public void setPartner(int partner) {
+ this.partner = partner;
+ }
+
+ /**
+ * Return the partner of this Condition, i.e., the index of the other
+ * condition that is most similar to this Condition.
+ */
+ public int getPartner() {
+ return this.partner;
+ }
+
+ /**
+ * Estimates the minimum expression level, across all replicates,
+ * necessary to compute a p-value for differential expression.
+ */
+ public int getMinDiffExpressionLevel() {
+ return minDiffExpressionLevel;
+ }
+
+ /**
+ * The background probability decreases as the number of reads increases.
+ * We use this fact to estimate a minimum level of expression necessary
+ * for us to be able to compute a p-value of differential expression.
+ * For a given Condition, we ensure that all Replicates meet the
+ * expression threshold.
+ * Currently, the expression threshold is set (based on anecdote and
+ * experience) to 0.005.
+ */
+ public void setMinDiffExpressionLevel() {
+ double THRESHOLD = 0.005;
+ minDiffExpressionLevel = 0;
+ while (true) {
+ boolean foundThreshold = true;
+ for (int i=0; i<replicates.size(); i++) {
+ if (replicates.get(i).getBackgroundProb(minDiffExpressionLevel) >= THRESHOLD)
+ foundThreshold = false;
+ }
+ if (foundThreshold) return;
+ minDiffExpressionLevel++;
+ }
+ }
+
+ /**
+ * Returns a String representation of a this object.
+ */
+ public String toString() {
+ StringBuilder sb = new StringBuilder();
+ for (int i=0; i<replicates.size(); i++) {
+ sb.append(replicates.get(i).toString() + "\n");
+ }
+ return sb.toString();
+ }
+
+
+
+ /**********************************************
+ ********** PUBLIC CLASS METHODS **********
+ **********************************************/
+
+ /**
+ * Set the average upper quartile gene expression over
+ * all replicates in all all conditions.
+ */
+ public static void setAvgUpperQuartile(long avgUpperQuartile) {
+ Condition.avgUpperQuartile = avgUpperQuartile;
+ }
+
+ /**
+ * Returns the average upper quartile gene expression over
+ * all replicates in all conditions.
+ */
+ public static long getAvgUpperQuartile() {
+ return Condition.avgUpperQuartile;
+ }
+
+
+
+ /**************************************************
+ ********** PRIVATE INSTANCE METHODS **********
+ **************************************************/
+
+
+
+ /*************************************
+ ********** MAIN METHOD **********
+ *************************************/
+
+ /**
+ * The main method is used to test the methods of this class.
+ */
+ public static void main(String[] args) {
+
+ }
+
+}
+
diff --git a/DeNovoIndex.java b/DeNovoIndex.java
new file mode 100644
index 0000000..3103507
--- /dev/null
+++ b/DeNovoIndex.java
@@ -0,0 +1,568 @@
+/*
+ * Copyright 2014 Brian Tjaden
+ *
+ * This file is part of Rockhopper.
+ *
+ * Rockhopper is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * any later version.
+ *
+ * Rockhopper is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * (in the file gpl.txt) along with Rockhopper.
+ * If not, see <http://www.gnu.org/licenses/>.
+ */
+
+import java.util.ArrayList;
+import java.util.Random;
+import java.util.concurrent.atomic.AtomicIntegerArray;
+import java.util.concurrent.atomic.AtomicLongArray;
+
+public class DeNovoIndex {
+
+ /********************************************
+ ********** Instance Variables **********
+ ********************************************/
+
+ public String sequence; // Concatenated transcripts (separated by '^' with '$' at end)
+ private int length; // Length of sequence
+ private int[] rotations; // Burrows-Wheeler matrix of cyclic rotations
+ private String BWT; // Borrows-Wheeler transform of original sequence
+ private boolean stopAfterOneHit; // Report only one mapping as opposed to all mappings
+ public AtomicIntegerArray[] readCounts; // Number of reads mapping to each nt of each transcript from each sequencing reads file
+ private AtomicIntegerArray numReads; // Num reads from each file
+ private AtomicIntegerArray numMappingReads; // Num reads from each file mapping to transcripts
+ private AtomicLongArray avgLengthReads; // Avg length of mapping reads from each file
+
+ private int[] C; // Number of chars lexicographically less than...
+ private int[][] occ; // Number of occurrences of char up to row...
+
+
+
+ /*****************************************
+ ********** Class Variables **********
+ *****************************************/
+
+ private static Random rand = new Random();
+
+
+
+ /**************************************
+ ********** Constructors **********
+ **************************************/
+
+ public DeNovoIndex(ArrayList<StringBuilder> transcripts) {
+ StringBuilder sb = new StringBuilder();
+ for (StringBuilder transcript : transcripts) {
+ sb.append(transcript);
+ sb.append('^');
+ }
+ sb.append('$');
+ this.sequence = sb.toString();
+ this.length = sequence.length();
+ this.rotations = rotations();
+ this.BWT = getTransform();
+ precomputeCharacterInfo(); // Populate "C" and "occ" instance variables
+ }
+
+
+
+ /*************************************************
+ ********** Public Instance Methods **********
+ *************************************************/
+
+ /**
+ * Returns true if s is in index, false otherwise.
+ */
+ public boolean exactMatch(String s) {
+ return exactMatch(s, 0, s.length());
+ }
+
+ /**
+ * Returns true if s[start:end] is in index, false otherwise.
+ * Note "start" is inclusive and "end" is exclusive.
+ */
+ public boolean exactMatch(String s, int start, int end) {
+ int i = end - 1;
+ char c = s.charAt(i);
+ int sp = getC(Dictionary.charToInt(c));
+ int ep = -1;
+ if (Dictionary.charToInt(c) < 4) ep = getC(Dictionary.charToInt(c)+1);
+ else ep = length;
+ i--;
+ while ((sp < ep) && (i >= start)) {
+ int index = Dictionary.charToInt(s.charAt(i));
+ sp = getC(index) + getOcc(index, sp);
+ ep = getC(index) + getOcc(index, ep);
+ i--;
+ }
+ if (ep > sp) return true;
+ return false;
+ }
+
+ /**
+ * Tallies the number of full length reads mapping to
+ * each nucleotide of each transcript.
+ * If full length read does not map EXACTLY, then the
+ * tally is not incremented.
+ */
+ public void exactMatch_fullRead(String s) {
+ numReads.getAndIncrement(Assembler.readsFileIndex);
+ int start = 0;
+ int end = s.length();
+ int i = end - 1;
+ char c = s.charAt(i);
+ int sp = getC(Dictionary.charToInt(c));
+ int ep = -1;
+ if (Dictionary.charToInt(c) < 4) ep = getC(Dictionary.charToInt(c)+1);
+ else ep = length;
+ i--;
+ while ((sp < ep) && (i >= start)) {
+ int index = Dictionary.charToInt(s.charAt(i));
+ sp = getC(index) + getOcc(index, sp);
+ ep = getC(index) + getOcc(index, ep);
+ i--;
+ }
+ if (!stopAfterOneHit) { // Report all mappings of read
+ for (int j=sp; j<ep; j++) {
+ for (int k=getRotations(j); k<getRotations(j)+s.length(); k++) readCounts[Assembler.readsFileIndex].incrementAndGet(k);
+ }
+ if (ep > sp) {
+ avgLengthReads.getAndAdd(Assembler.readsFileIndex, s.length());
+ numMappingReads.getAndIncrement(Assembler.readsFileIndex);
+ }
+ } else { // Report only one mapping of read
+ if (ep > sp) {
+ int randIndex = sp + rand.nextInt(ep-sp);
+ for (int k=getRotations(randIndex); k<getRotations(randIndex)+s.length(); k++) readCounts[Assembler.readsFileIndex].incrementAndGet(k);
+ avgLengthReads.getAndAdd(Assembler.readsFileIndex, s.length());
+ numMappingReads.getAndIncrement(Assembler.readsFileIndex);
+ }
+ }
+ }
+
+ /**
+ * Tallies the number of full length *paired-end* reads mapping to
+ * each nucleotide of each transcript.
+ * If full length *paired-end* read does not map EXACTLY, then the
+ * tally is not incremented.
+ */
+ public void exactMatch_fullRead(String s, String s2) {
+ numReads.getAndIncrement(Assembler.readsFileIndex);
+
+ // Read 1
+ int start = 0;
+ int end = s.length();
+ int i = end - 1;
+ char c = s.charAt(i);
+ int sp = getC(Dictionary.charToInt(c));
+ int ep = -1;
+ if (Dictionary.charToInt(c) < 4) ep = getC(Dictionary.charToInt(c)+1);
+ else ep = length;
+ i--;
+ while ((sp < ep) && (i >= start)) {
+ int index = Dictionary.charToInt(s.charAt(i));
+ sp = getC(index) + getOcc(index, sp);
+ ep = getC(index) + getOcc(index, ep);
+ i--;
+ }
+ if (sp >= ep) return;
+
+ // Read 2
+ start = 0;
+ end = s2.length();
+ i = end - 1;
+ c = s2.charAt(i);
+ int sp2 = getC(Dictionary.charToInt(c));
+ int ep2 = -1;
+ if (Dictionary.charToInt(c) < 4) ep2 = getC(Dictionary.charToInt(c)+1);
+ else ep2 = length;
+ i--;
+ while ((sp2 < ep2) && (i >= start)) {
+ int index = Dictionary.charToInt(s2.charAt(i));
+ sp2 = getC(index) + getOcc(index, sp2);
+ ep2 = getC(index) + getOcc(index, ep2);
+ i--;
+ }
+ if (sp2 >= ep2) return;
+
+ // Combine paired-end hits
+ ArrayList<Integer> hits1 = new ArrayList<Integer>(ep-sp);
+ for (int j=sp; j<ep; j++) hits1.add(getRotations(j));
+ ArrayList<Integer> hits2 = new ArrayList<Integer>(ep2-sp2);
+ for (int j=sp2; j<ep2; j++) hits2.add(getRotations(j));
+ ArrayList<Integer> starts = new ArrayList<Integer>();
+ ArrayList<Integer> ends = new ArrayList<Integer>();
+ combinePairedEndHits(s.length(), s2.length(), hits1, hits2, starts, ends);
+
+ if (!stopAfterOneHit) { // Report all mappings of read
+ int sum = 0;
+ for (int j=0; j<starts.size(); j++) {
+ for (int k=starts.get(j); k<ends.get(j); k++) readCounts[Assembler.readsFileIndex].incrementAndGet(k);
+ sum += ends.get(j) - starts.get(j);
+ }
+ if (starts.size() > 0) {
+ avgLengthReads.getAndAdd(Assembler.readsFileIndex, sum/starts.size());
+ numMappingReads.getAndIncrement(Assembler.readsFileIndex);
+ }
+ } else { // Report only one mapping of read
+ if (starts.size() > 0) {
+ int randIndex = rand.nextInt(starts.size());
+ for (int k=starts.get(randIndex); k<ends.get(randIndex); k++) readCounts[Assembler.readsFileIndex].incrementAndGet(k);
+ avgLengthReads.getAndAdd(Assembler.readsFileIndex, ends.get(randIndex)-starts.get(randIndex));
+ numMappingReads.getAndIncrement(Assembler.readsFileIndex);
+ }
+ }
+ }
+
+ /**
+ * Creates infrastructure to store information about
+ * full length reads mapping to the length (rather
+ * than just k-mers).
+ */
+ public void initializeReadMapping(boolean stopAfterOneHit) {
+ int numReadsFiles = Assembler.readsFileIndex;
+ readCounts = new AtomicIntegerArray[numReadsFiles];
+ numReads = new AtomicIntegerArray(numReadsFiles);
+ avgLengthReads = new AtomicLongArray(numReadsFiles);
+ numMappingReads = new AtomicIntegerArray(numReadsFiles);
+ for (int i=0; i<numReadsFiles; i++) readCounts[i] = new AtomicIntegerArray(length);
+ this.stopAfterOneHit = stopAfterOneHit;
+ }
+
+ public int[] getAvgLengthOfReads() {
+ int[] avgLengths = new int[avgLengthReads.length()];
+ for (int i=0; i<avgLengths.length; i++) {
+ if (numMappingReads.get(i) == 0) avgLengths[i] = 0;
+ else avgLengths[i] = (int)(avgLengthReads.get(i)/numMappingReads.get(i));
+ }
+ return avgLengths;
+ }
+
+ /**
+ * In the case of unstranded (strand ambiguous) reads,
+ * we invoke exactMatch_fullRead twice, once per strand,
+ * thereby double counting each read. Here we fix the
+ * double dip.
+ */
+ public void halveReads(int fileIndex) {
+ numReads.set(fileIndex, numReads.get(fileIndex)/2);
+ }
+
+ /**
+ * Returns an array containing the total number of full-length reads
+ * in each file.
+ */
+ public int[] getNumReads() {
+ int[] reads = new int[numReads.length()];
+ for (int i=0; i<reads.length; i++)
+ reads[i] = numReads.get(i);
+ return reads;
+ }
+
+ /**
+ * Returns an array containing the number of full-length reads
+ * in each file mapping to assembled transcripts.
+ */
+ public int[] getNumMappingReads() {
+ int[] mappingReads = new int[numMappingReads.length()];
+ for (int i=0; i<mappingReads.length; i++)
+ mappingReads[i] = numMappingReads.get(i);
+ return mappingReads;
+ }
+
+ /**
+ * Returns the total number of full-length reads
+ * in the specified file.
+ */
+ public int getNumReads(int fileIndex) {
+ return numReads.get(fileIndex);
+ }
+
+ /**
+ * Returns the number of full-length reads
+ * in the specified file mapping to assembled transcripts.
+ */
+ public int getNumMappingReads(int fileIndex) {
+ return numMappingReads.get(fileIndex);
+ }
+
+ /**
+ * Returns a 2D array representating the total number of reads mapping to every nt
+ * in each replicate.
+ */
+ public ArrayList<ArrayList<Long>> getTotalReads() {
+ ArrayList<ArrayList<Long>> totalReads = new ArrayList<ArrayList<Long>>(Assembler.conditionFiles.size());
+ int linearIndex = 0;
+ for (int i=0; i<Assembler.conditionFiles.size(); i++) {
+ String[] files = Assembler.conditionFiles.get(i).split(",");
+ totalReads.add(new ArrayList<Long>(files.length));
+ for (int j=0; j<files.length; j++) {
+ totalReads.get(i).add((long)0);
+ for (int k=0; k<readCounts[linearIndex].length(); k++) {
+ totalReads.get(i).set(j, totalReads.get(i).get(j) + readCounts[linearIndex].get(k));
+ }
+ linearIndex++;
+ }
+ }
+ return totalReads;
+ }
+
+
+
+ /**************************************************
+ ********** Private Instance Methods **********
+ **************************************************/
+
+ // Return a row of the cyclic rotations matrix.
+ private String getStringInRotationsMatrix(int row) {
+ return sequence.substring(rotations[row]) + sequence.substring(0, rotations[row]);
+ }
+
+ // Reverse the BWT transform
+ private String unpermute() {
+ StringBuilder sb = new StringBuilder();
+ int r = 0;
+ while (BWT.charAt(r) != '$') {
+ sb.append(BWT.charAt(r));
+ r = stepLeft(r);
+ }
+ return sb.reverse().toString();
+ }
+
+ /**
+ * Returns number of characters lexographically less than x.
+ */
+ private int getC(int x) {
+ return this.C[x];
+ }
+
+ /**
+ * Returns number of occurrences of character x up to row y.
+ */
+ private int getOcc(int x, int y) {
+ return this.occ[x][y];
+ }
+
+ /**
+ * Returns index in Burrows-Wheeler rotations matrix at row x.
+ */
+ private int getRotations(int x) {
+ return this.rotations[x];
+ }
+
+ /**
+ * Compute the Burrows-Wheeler matrix of cyclic rotations.
+ * Rather than return a matrix, we return an array of integers
+ * where each value in the array is an index into the sequence.
+ * So a "row" of the matrix corresponds to the cyclic sequence
+ * beginnning at the specified index. All rows of the matrix
+ * have length equal to the length of the sequence.
+ */
+ private int[] rotations() {
+ int[] indices = new int[this.length];
+ for (int i=0; i<length; i++) indices[i] = i;
+ quicksort(indices, 0, length-1);
+ return indices;
+ }
+
+ /**
+ * Compute the Burrows-Wheeler transform from the "rotations"
+ * matrix, i.e., the last column of the matrix.
+ */
+ private String getTransform() {
+ StringBuilder sb = new StringBuilder(length);
+ for (int i=0; i<length; i++) {
+ sb.append(sequence.charAt((rotations[i]-1+length) % length));;
+ }
+ return sb.toString();
+ }
+
+ /**
+ * Precompute information about how often each character occurs in BWT
+ */
+ private void precomputeCharacterInfo() {
+
+ // Populate instance variable "C"
+ this.C = new int[6]; // All characters in DNA sequence have
+ // ASCII value less than 123.
+ for (int i=0; i<length; i++) C[Dictionary.charToInt(BWT.charAt(i))] += 1;
+
+ // Cumulative
+ int[] temp = new int[6];
+ temp[0] = C[0] + C[5]; // Number of characters <= 'A'
+ temp[5] = C[5]; // Number of characters <= '$'
+ for (int i=1; i<5; i++) temp[i] = C[i] + temp[i-1];
+
+ // Strictly less than
+ for (int i=0; i<6; i++) C[i] = temp[i] - C[i];
+
+ // Populate instance variable "occ"
+ this.occ = new int[5][length+1];
+ for (int i=0; i<length; i++) {
+ for (int j=0; j<5; j++) {
+ occ[j][i+1] = occ[j][i];
+ }
+ int index = Dictionary.charToInt(BWT.charAt(i));
+ if ((index >= 0) && (index < 5)) occ[index][i+1]++;
+ }
+ }
+
+ /**
+ * Helper method for Burrows-Wheeler transform.
+ * Taken from appendix of Bowtie article.
+ */
+ private int stepLeft(int r) {
+ int index = Dictionary.charToInt(BWT.charAt(r));
+ return C[index] + occ[index][r];
+ }
+
+ /**
+ * We quicksort the array. But we don't sort the values at
+ * each array index, since each value is an index
+ * corresponding to a String. We sort the Strings specified
+ * by each array index.
+ */
+ private void quicksort(int[] a, int p, int r) {
+ if (p < r) {
+ int q = partition(a, p, r);
+ quicksort(a, p, q-1);
+ quicksort(a, q+1, r);
+ }
+ }
+
+ /**
+ * Quicksort helper method
+ */
+ private int partition(int[] a, int p, int r) {
+ int x = rand.nextInt(r - p + 1) + p;
+ swap(a, x, r);
+ x = a[r];
+ int i = p-1;
+ for (int j=p; j<r; j++) {
+ if (lessThanOrEqualTo(a[j], x)) { // a[j] <= x
+ i++;
+ swap(a, i, j);
+ }
+ }
+ swap(a, i+1, r);
+ return i+1;
+ }
+
+ /**
+ * Quicksort partition helper method
+ */
+ private void swap(int a[], int i, int j) {
+ int temp = a[i];
+ a[i] = a[j];
+ a[j] = temp;
+ }
+
+ /**
+ * Given two indices in "sequence", determine whether the
+ * cyclic String corresponding to the first index is less
+ * than or equal to the cyclic String corresponding to
+ * the second index.
+ */
+ private boolean lessThanOrEqualTo(int i, int j) {
+ for (int z=0; z<length; z++) {
+ if (sequence.charAt((i+z)%length) < sequence.charAt((j+z)%length))
+ return true;
+ if (sequence.charAt((i+z)%length) > sequence.charAt((j+z)%length))
+ return false;
+
+ }
+ return true; // We have equality of the two Strings
+ }
+
+
+
+ /**********************************************
+ ********** Public Class Methods **********
+ **********************************************/
+
+
+
+ /***********************************************
+ ********** Private Class Methods **********
+ ***********************************************/
+
+ /**
+ * Combines two lists of exact matches, one for each read in a paired-end read,
+ * into parallel lists of coordinates of paired-end matches. A combined match occurs when
+ * there are matches from each of the two input lists that are
+ * within the specified distance from each other.
+ */
+ private static void combinePairedEndHits(int length1, int length2, ArrayList<Integer> hits1, ArrayList<Integer> hits2, ArrayList<Integer> starts, ArrayList<Integer> ends) {
+ for (Integer start1 : hits1) {
+ for (int z=0; z<hits2.size(); z++) {
+ Integer start2 = hits2.get(z);
+ if ((start1.compareTo(start2) <= 0) && (start2+length2-start1 <= Assembler.maxPairedEndLength)) {
+ starts.add(start1);
+ ends.add(start2+length2);
+ hits2.remove(z);
+ break;
+ }
+ if ((start2.compareTo(start1) <= 0) && (start1+length1-start2 <= Assembler.maxPairedEndLength)) {
+ starts.add(start2);
+ ends.add(start1+length1);
+ hits2.remove(z);
+ break;
+ }
+ }
+ }
+ }
+
+
+
+ /*************************************
+ ********** Main Method **********
+ *************************************/
+
+ public static void main(String[] args) {
+
+ // Test DeNovoIndex class
+ StringBuilder sb1 = new StringBuilder("AAAAACCCCCGGGGGTTTTT");
+ StringBuilder sb2 = new StringBuilder("AAAAAAAAAAAAAAAAAAAA");
+ StringBuilder sb3 = new StringBuilder("CCCCCCCCCCCCCCCCCCCC");
+ StringBuilder sb4 = new StringBuilder("GTGTGTGTGTGTGTGTGTGT");
+ ArrayList<StringBuilder> v = new ArrayList<StringBuilder>();
+ v.add(sb1);
+ v.add(sb2);
+ v.add(sb3);
+ v.add(sb4);
+ Dictionary d = new Dictionary(25); // Needed to populate alphabet_2
+ DeNovoIndex index = new DeNovoIndex(v);
+ System.out.println(index.sequence);
+ System.out.println("Length:\t" + index.length);
+ System.out.println();
+ System.out.println(index.BWT);
+ System.out.println();
+ System.out.println(index.unpermute());
+ System.out.println();
+
+ String s1 = "AAAAA";
+ System.out.println("Is exact match:\t" + s1 + "\t" + index.exactMatch(s1));
+ String s2 = "TGTGT";
+ System.out.println("Is exact match:\t" + s2 + "\t" + index.exactMatch(s2));
+ String s3 = "CCGTG";
+ System.out.println("Is exact match:\t" + s3 + "\t" + index.exactMatch(s3));
+ String s4 = "ACAC";
+ System.out.println("Is exact match:\t" + s4 + "\t" + index.exactMatch(s4));
+ String s5 = "CCCCCCCCCCCCCCCCCCCC";
+ System.out.println("Is exact match:\t" + s5 + "\t" + index.exactMatch(s5));
+ String s6 = "CCCCCCCCCCCCCCCCCCCCC";
+ System.out.println("Is exact match:\t" + s6 + "\t" + index.exactMatch(s6));
+ String s7 = "AAAAAAAAAACCCCCCCCCC";
+ System.out.println("Is exact match:\t" + s7 + "\t" + index.exactMatch(s7));
+ String s8 = "GGGGGAAAAA";
+ System.out.println("Is exact match:\t" + s8 + "\t" + index.exactMatch(s8));
+ }
+
+}
+
diff --git a/DeNovoTranscript.java b/DeNovoTranscript.java
new file mode 100644
index 0000000..2398ffa
--- /dev/null
+++ b/DeNovoTranscript.java
@@ -0,0 +1,451 @@
+/*
+ * Copyright 2014 Brian Tjaden
+ *
+ * This file is part of Rockhopper.
+ *
+ * Rockhopper is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * any later version.
+ *
+ * Rockhopper is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * (in the file gpl.txt) along with Rockhopper.
+ * If not, see <http://www.gnu.org/licenses/>.
+ */
+
+import java.util.ArrayList;
+
+/**
+ * An instance of the DeNovoTranscript class represents
+ * a de novo assembled transcript.
+ */
+public class DeNovoTranscript {
+
+ /********************************************
+ ********** Instance Variables **********
+ ********************************************/
+
+ private String sequence;
+ private ArrayList<ArrayList<Long>> rawCounts_nts;
+ private ArrayList<ArrayList<Long>> rawCounts_reads;
+ private ArrayList<ArrayList<Long>> normalizedCounts;
+ private ArrayList<Long> RPKMs;
+ private ArrayList<Long> means;
+ public long[][] variances; // 2D array
+ public long[][] lowess; // 2D array
+ private ArrayList<Double> pValues; // Differential expression
+ private ArrayList<Double> qValues; // Differential expression (corrected)
+
+
+
+ /**************************************
+ ********** CONSTRUCTORS **********
+ **************************************/
+
+ public DeNovoTranscript(String sequence, long[] readCounts_nts_linear) {
+ this.sequence = sequence;
+
+ // Convert linear array to 2D ArrayList based on Conditions/Replicates.
+ rawCounts_nts = new ArrayList<ArrayList<Long>>(Assembler.conditionFiles.size());
+ rawCounts_reads = new ArrayList<ArrayList<Long>>(Assembler.conditionFiles.size());
+ normalizedCounts = new ArrayList<ArrayList<Long>>(Assembler.conditionFiles.size());
+ RPKMs = new ArrayList<Long>(Assembler.conditionFiles.size());
+ means = new ArrayList<Long>(Assembler.conditionFiles.size());
+ int linearIndex = 0;
+ for (int i=0; i<Assembler.conditionFiles.size(); i++) {
+ String[] files = Assembler.conditionFiles.get(i).split(",");
+ rawCounts_nts.add(new ArrayList<Long>(files.length));
+ rawCounts_reads.add(new ArrayList<Long>(files.length));
+ normalizedCounts.add(new ArrayList<Long>(files.length));
+ RPKMs.add((long)0);
+ means.add((long)0);
+ for (int j=0; j<files.length; j++) {
+ rawCounts_nts.get(i).add(readCounts_nts_linear[linearIndex]);
+ rawCounts_reads.get(i).add(readCounts_nts_linear[linearIndex] / DeNovoTranscripts.avgLengthOfReads[linearIndex]);
+ normalizedCounts.get(i).add((long)0);
+ linearIndex++;
+ }
+ }
+ }
+
+ /**
+ * Used when reading in from compressed file.
+ */
+ public DeNovoTranscript(String sequence, ArrayList<ArrayList<Long>> rawCounts_nts, ArrayList<ArrayList<Long>> rawCounts_reads, ArrayList<ArrayList<Long>> normalizedCounts, ArrayList<Long> RPKMs, ArrayList<Long> means, long[][] variances, long[][] lowess, ArrayList<Double> pValues, ArrayList<Double> qValues) {
+ this.sequence = sequence;
+ this.rawCounts_nts = rawCounts_nts;
+ this.rawCounts_reads = rawCounts_reads;
+ this.normalizedCounts = normalizedCounts;
+ this.RPKMs = RPKMs;
+ this.means = means;
+ this.variances = variances;
+ this.lowess = lowess;
+ this.pValues = pValues;
+ this.qValues = qValues;
+ }
+
+
+
+ /*************************************************
+ ********** Public Instance Methods **********
+ *************************************************/
+
+ /**
+ * Returns the length of the transcript sequence.
+ */
+ public int length() {
+ return sequence.length();
+ }
+
+ /**
+ * Returns the sequence of this transcript.
+ */
+ public String sequence() {
+ return this.sequence;
+ }
+
+ /**
+ * Returns the raw count of nts reads mapping to
+ * this transcript for the specified condition and
+ * replicate.
+ */
+ public long getRawCountNTs(int condition, int replicate) {
+ return rawCounts_nts.get(condition).get(replicate);
+ }
+
+ /**
+ * Returns the raw count of full length reads mapping
+ * to this transcript for the specified condition and
+ * replicate.
+ */
+ public long getRawCountReads(int condition, int replicate) {
+ return rawCounts_reads.get(condition).get(replicate);
+ }
+
+ /**
+ * Returns the mean expression of this transcript in
+ * the specified condition.
+ */
+ public long getMean(int condition) {
+ return means.get(condition);
+ }
+
+ /**
+ * Returns the p-value of this transcript for
+ * the specified pair of conditions.
+ */
+ public double getPvalue(int conditionPair) {
+ return pValues.get(conditionPair);
+ }
+
+ /**
+ * Returns the number of p-values, i.e.,
+ * the number of pairs of conditions,
+ * for this transcript.
+ */
+ public int getNumPvalues() {
+ return pValues.size();
+ }
+
+ /**
+ * Set the normalized number of reads mapping to this
+ * transcript in the specified condition and replicate.
+ */
+ public void setNormalizedCount(int condition, int replicate, double scalingFactor, long upperQuartile) {
+ double multiplier = scalingFactor / (double)upperQuartile;
+ long normalizedCount = (long)(multiplier * getRawCountNTs(condition, replicate));
+ normalizedCounts.get(condition).set(replicate, normalizedCount);
+ }
+
+ /**
+ * Sets the q-value for the specified pair of conditions.
+ */
+ public void setQvalue(int conditionPair, double value) {
+ qValues.set(conditionPair, value);
+ }
+
+ /**
+ * Returns an array representation of rawCounts_nts
+ * in the specified condition.
+ */
+ public long[] getRawCounts_nts_array(int condition) {
+ return listToArray_long(rawCounts_nts.get(condition));
+ }
+
+ /**
+ * Returns an array representation of rawCounts_reads
+ * in the specified condition.
+ */
+ public long[] getRawCounts_reads_array(int condition) {
+ return listToArray_long(rawCounts_reads.get(condition));
+ }
+
+ /**
+ * Returns an array representation of normalizedCounts
+ * in the specified condition.
+ */
+ public long[] getNormalizedCounts_array(int condition) {
+ return listToArray_long(normalizedCounts.get(condition));
+ }
+
+ /**
+ * Returns an array representation of RPKMs.
+ */
+ public long[] getRPKMs() {
+ return listToArray_long(RPKMs);
+ }
+
+ /**
+ * Returns an array representation of means.
+ */
+ public long[] getMeans() {
+ return listToArray_long(means);
+ }
+
+ /**
+ * Returns a 1D array representation of variances.
+ */
+ public long[] getVariances() {
+ return array2D_to_1D_long(variances);
+ }
+
+ /**
+ * Returns a 1D array representation of lowess.
+ */
+ public long[] getLowess() {
+ return array2D_to_1D_long(lowess);
+ }
+
+ /**
+ * Returns an array representation of pValues.
+ */
+ public double[] getPvalues() {
+ return listToArray_double(pValues);
+ }
+
+ /**
+ * Returns an array representation of qValues.
+ */
+ public double[] getQvalues() {
+ return listToArray_double(qValues);
+ }
+
+ /**
+ * Calculates the RPKM and mean expression for
+ * this transcript in the specified condition.
+ */
+ public void computeExpression(int condition) {
+ long sumRawCounts = 0;
+ long totalCounts = 0;
+ long mean = 0;
+ for (int j=0; j<rawCounts_nts.get(condition).size(); j++) {
+ sumRawCounts += rawCounts_nts.get(condition).get(j);
+ totalCounts += DeNovoTranscripts.totalReads.get(condition).get(j);
+ mean += normalizedCounts.get(condition).get(j);
+ }
+ sumRawCounts /= rawCounts_nts.get(condition).size();
+ totalCounts /= rawCounts_nts.get(condition).size();
+ mean /= normalizedCounts.get(condition).size();
+ if (totalCounts == 0) RPKMs.set(condition, (long)0); // Avoid divide-by-zero error
+ else RPKMs.set(condition, (long)(1000000000 * sumRawCounts / (totalCounts * sequence.length())));
+ means.set(condition, mean);
+ }
+
+ /**
+ * Calculates the variance for
+ * this transcript in the specified condition.
+ */
+ public void computeVariance(int numConditions) {
+ double varianceAdjustmentNoReplicates = 1.10;
+ double varianceAdjustmentReplicates = 1.20;
+ variances = new long[numConditions][numConditions];
+ lowess = new long[numConditions][numConditions];
+
+ for (int x=0; x<numConditions; x++) { // First of pair
+ for (int y=0; y<numConditions; y++) { // Second of pair
+
+ if (x == y) continue; // No need to compute variance with self
+
+ if (normalizedCounts.get(x).size() == 1) { // No replicates. Use partner surrogate.
+ int partner = y;
+ long mean = (means.get(x) + means.get(partner)) / 2;
+ long variance = ((means.get(x)-mean)*(means.get(x)-mean) + (means.get(partner)-mean)*(means.get(partner)-mean)) / 1; // Sample standard deviation
+ //variances[x][y] = variance;
+ variances[x][y] = (long)Math.pow(variance, varianceAdjustmentNoReplicates);
+ } else { // We have replicates. Use the replicates to compute the variance.
+ long variance = 0;
+ for (int j=0; j<normalizedCounts.get(x).size(); j++) {
+ variance += (long)(normalizedCounts.get(x).get(j) - means.get(x)) * (long)(normalizedCounts.get(x).get(j) - means.get(x));
+ }
+ variance /= (normalizedCounts.get(x).size() - 1); // Sample standard deviation
+ //variances[x][y] = variance;
+ variances[x][y] = (long)Math.pow(variance, varianceAdjustmentReplicates);
+ }
+ }
+ }
+ }
+
+ /**
+ * For each pair of conditions, compute the p-value of differntial
+ * expression for this transcript.
+ */
+ public void computeDifferentialExpression() {
+ pValues = new ArrayList<Double>();
+ qValues = new ArrayList<Double>();
+ for (int x=0; x<normalizedCounts.size()-1; x++) { // First of two conditions
+ for (int y=x+1; y<normalizedCounts.size(); y++) { // Second of two conditions
+
+ double k_A = 0.0;
+ double k_B = 0.0;
+ for (int j=0; j<normalizedCounts.get(x).size(); j++) k_A += normalizedCounts.get(x).get(j);
+ for (int j=0; j<normalizedCounts.get(y).size(); j++) k_B += normalizedCounts.get(y).get(j);
+
+ if (normalizedCounts.get(x).size() < normalizedCounts.get(y).size())
+ k_B *= normalizedCounts.get(x).size() / (double)(normalizedCounts.get(y).size());
+ else if (normalizedCounts.get(x).size() > normalizedCounts.get(y).size())
+ k_A *= normalizedCounts.get(y).size() / (double)(normalizedCounts.get(x).size());
+
+ double q = k_A + k_B;
+
+ double mean_A = q;
+ double mean_B = q;
+ double variance_A = lowess[x][y];
+ double variance_B = lowess[y][x];
+
+ double p_a = mean_A / variance_A;
+ double p_b = mean_B / variance_B;
+ double r_a = Math.max(mean_A*mean_A / (variance_A - mean_A), 1.0); // r should not be < 1
+ double r_b = Math.max(mean_B*mean_B / (variance_B - mean_B), 1.0); // r should not be < 1
+
+ if ((p_a < 0.0) || (p_b < 0.0) || (p_a > 1.0) || (p_b > 1.0) || (variance_A == 0.0) || (variance_B == 0.0)) {
+ pValues.add(1.0);
+ qValues.add(1.0);
+ continue;
+ }
+
+ // Compute p-value of differential expression in two conditions
+ double p_ab = NegativeBinomial.pmf(r_a-1, k_A+r_a-1, p_a) * NegativeBinomial.pmf(r_b-1, k_B+r_b-1, p_b);
+ long k_sum = (long)(k_A + k_B);
+
+ // Fast p-value estimation
+ double numerator = 0.0;
+ double denominator = 0.0;
+ long mode = (long)k_B;
+
+ long a = mode; // Begin near middle
+ long increment = 1;
+ long alpha = 1000; // Number of times we increment by 1 (raising alpha raises precision but slows down computation)
+ double previous_p = 0.0;
+ while (a <= k_sum) {
+ long b = k_sum - a;
+ double current_p = NegativeBinomial.pmf(r_a-1, a+r_a-1, p_a) * NegativeBinomial.pmf(r_b-1, b+r_b-1, p_b);
+ denominator += current_p;
+ if (current_p <= p_ab) numerator += current_p;
+ if (increment > 1) {
+ double average_p = (current_p+previous_p)/2.0;
+ denominator += average_p * (increment-1);
+ if (average_p <= p_ab) numerator += average_p * (increment-1);
+ }
+ previous_p = current_p;
+ if (a - mode >= alpha) {
+ alpha *= 2;
+ increment *= 2;
+ }
+ a += increment;
+ }
+ a = mode; // Begin near middle
+ long decrement = 1;
+ alpha = 1000; // Number of times we increment by 1 (raising alpha raises precision but slows down computation)
+ previous_p = 0.0;
+ while (a >= 0) {
+ long b = k_sum - a;
+ double current_p = NegativeBinomial.pmf(r_a-1, a+r_a-1, p_a) * NegativeBinomial.pmf(r_b-1, b+r_b-1, p_b);
+ denominator += current_p;
+ if (current_p <= p_ab) numerator += current_p;
+ if (decrement > 1) {
+ double average_p = (previous_p + current_p) / 2.0;
+ denominator += average_p * (decrement-1);
+ if (average_p <= p_ab) numerator += average_p * (decrement-1);
+ }
+ previous_p = current_p;
+ if (mode - a >= alpha) {
+ alpha *= 2;
+ decrement *= 2;
+ }
+ a -= decrement;
+ }
+ double p_value = 1.0;
+ if (denominator != 0.0) p_value = numerator / denominator;
+ pValues.add(p_value);
+ qValues.add(1.0);
+ }
+ }
+ }
+
+ /**
+ * Returns a String representation of this transcript.
+ */
+ public String toString() {
+ StringBuilder sb = new StringBuilder();
+ sb.append(sequence + "\t" + sequence.length());
+ for (int i=0; i<normalizedCounts.size(); i++) {
+ if (Assembler.verbose) { // Verbose output
+ for (int j=0; j<normalizedCounts.get(i).size(); j++) sb.append("\t" + rawCounts_reads.get(i).get(j));
+ for (int j=0; j<normalizedCounts.get(i).size(); j++) sb.append("\t" + normalizedCounts.get(i).get(j));
+ sb.append("\t" + RPKMs.get(i));
+ }
+ sb.append("\t" + (means.get(i)/sequence.length()));
+ }
+ for (int i=0; i<qValues.size(); i++) {
+ if (Assembler.verbose) sb.append("\t" + pValues.get(i).toString());
+ sb.append("\t" + qValues.get(i).toString());
+ }
+ return sb.toString();
+ }
+
+
+
+ /**************************************************
+ ********** Private Instance Methods **********
+ **************************************************/
+
+ /**
+ * Returns an array representation of a list of longs.
+ */
+ private long[] listToArray_long(ArrayList<Long> x) {
+ long[] a = new long[x.size()];
+ for (int i=0; i<x.size(); i++) a[i] = x.get(i);
+ return a;
+ }
+
+ /**
+ * Returns an array representation of a list of doubles.
+ */
+ private double[] listToArray_double(ArrayList<Double> x) {
+ double[] a = new double[x.size()];
+ for (int i=0; i<x.size(); i++) a[i] = x.get(i);
+ return a;
+ }
+
+ /**
+ * Returns a 1D array representation of a 2D array of longs.
+ */
+ private long[] array2D_to_1D_long(long[][] x) {
+ long[] a = new long[x.length*x.length];
+ int index = 0;
+ for (int i=0; i<x.length; i++) {
+ for (int j=0; j<x.length; j++) {
+ a[index] = x[i][j];
+ index++;
+ }
+ }
+ return a;
+ }
+
+}
+
diff --git a/DeNovoTranscripts.java b/DeNovoTranscripts.java
new file mode 100644
index 0000000..74afd1e
--- /dev/null
+++ b/DeNovoTranscripts.java
@@ -0,0 +1,452 @@
+/*
+ * Copyright 2014 Brian Tjaden
+ *
+ * This file is part of Rockhopper.
+ *
+ * Rockhopper is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * any later version.
+ *
+ * Rockhopper is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * (in the file gpl.txt) along with Rockhopper.
+ * If not, see <http://www.gnu.org/licenses/>.
+ */
+
+import java.util.ArrayList;
+import java.util.Random;
+import java.util.concurrent.atomic.AtomicIntegerArray;
+
+/**
+ * An instance of the DeNovoTranscripts class represents
+ * a collection of de novo assembled transcripts.
+ */
+public class DeNovoTranscripts {
+
+ /********************************************
+ ********** Instance Variables **********
+ ********************************************/
+
+ private ArrayList<DeNovoTranscript> transcripts;
+ private ArrayList<ArrayList<Long>> upperQuartiles;
+ private ArrayList<Integer> minDiffExpressionLevels; // Min diff expression level per condition
+
+
+
+ /*****************************************
+ ********** Class Variables **********
+ *****************************************/
+
+ public static int[] avgLengthOfReads; // Avg length of mapping reads in each file
+ public static int[] numReads; // Total reads in each file
+ public static int[] numMappingReads; // Reads mapping to transcripts in each file
+ public static ArrayList<ArrayList<Long>> totalReads; // Total number of nt reads in each replicate
+ private static Random rand = new Random(); // Random number generator
+
+
+
+ /**************************************
+ ********** CONSTRUCTORS **********
+ **************************************/
+
+ public DeNovoTranscripts(DeNovoIndex bwtIndex) {
+ DeNovoTranscripts.avgLengthOfReads = bwtIndex.getAvgLengthOfReads();
+ DeNovoTranscripts.numReads = bwtIndex.getNumReads();
+ DeNovoTranscripts.numMappingReads = bwtIndex.getNumMappingReads();
+ DeNovoTranscripts.totalReads = bwtIndex.getTotalReads();
+ transcripts = determineTranscripts(bwtIndex.sequence, bwtIndex.readCounts);
+ computeExpression();
+ }
+
+ /**
+ * Used when reading transcripts in from compressed file.
+ */
+ public DeNovoTranscripts(ArrayList<DeNovoTranscript> transcripts) {
+ this.transcripts = transcripts;
+ }
+
+
+
+ /*************************************************
+ ********** Public Instance Methods **********
+ *************************************************/
+
+ public int getNumTranscripts() {
+ return transcripts.size();
+ }
+
+ public DeNovoTranscript getTranscript(int i) {
+ return transcripts.get(i);
+ }
+
+ /**
+ * Returns the average transcript length.
+ */
+ public int getAverageTranscriptLength() {
+ long length = 0;
+ if (transcripts.size() == 0) return 0;
+ for (DeNovoTranscript transcript : transcripts) length += transcript.length();
+ return (int)(length/transcripts.size());
+ }
+
+ /**
+ * Returns the median transcript length.
+ */
+ public int getMedianTranscriptLength() {
+ ArrayList<Long> a = new ArrayList<Long>(transcripts.size());
+ for (DeNovoTranscript transcript : transcripts) a.add((long)transcript.length());
+ return (int)Misc.select_Long(a, a.size()/2);
+ }
+
+ /**
+ * Returns the sum of all transcript lengths.
+ */
+ public long getTotalAssembledBases() {
+ long sum = 0;
+ for (DeNovoTranscript transcript : transcripts) sum += transcript.length();
+ return sum;
+ }
+
+ public String getTranscriptSequences() {
+ StringBuilder sb = new StringBuilder();
+ for (int z=0; z<transcripts.size(); z++) sb.append(transcripts.get(z).sequence() + "\n");
+ return sb.toString();
+ }
+
+ public void computeDifferentialExpression() {
+ computeVarianceAndLowess();
+ for (DeNovoTranscript transcript : transcripts) transcript.computeDifferentialExpression();
+ correctPvalues();
+ }
+
+ /**
+ * The background probabilty decreases as the number of reads increases.
+ * We use this fact to estimate a minimum level of expression necessary
+ * for us to be able to compute a p-value of differential expression.
+ * For a given Condition, we ensure that all Replicates meet the
+ * expression threshold.
+ * Currently, the expression threshold is set (based on anecdote and
+ * experience) to 0.005.
+ */
+ public void setMinDiffExpressionLevels(DeNovoIndex bwtIndex) {
+ double THRESHOLD = 0.005;
+ String allSequences = bwtIndex.sequence;
+ AtomicIntegerArray[] readCounts = bwtIndex.readCounts;
+ int backgroundLength = 2;
+ int linearIndex = 0;
+ minDiffExpressionLevels = new ArrayList<Integer>(Assembler.conditionFiles.size());
+ for (int i=0; i<Assembler.conditionFiles.size(); i++) { // For each condition
+ String[] files = Assembler.conditionFiles.get(i).split(",");
+ int[][] background = new int[files.length][backgroundLength];
+ double[] backgroundParameter = new double[files.length]; // Parameter of geometric distribution of background reads. One per replicate in current condition.
+ for (int j=0; j<files.length; j++) { // For each replicate
+
+ // Populate background for current replicate
+ for (int z=0; z<allSequences.length()-1; z++) { // We go to length-1 to ignore final '$'
+ if (readCounts[linearIndex].get(z) < background[j].length) background[j][readCounts[linearIndex].get(z)]++;
+ else background[j][background[j].length-1]++;
+ }
+
+ // Compute background parameter for current replicate
+ for (int k=0; k<backgroundLength-1; k++) backgroundParameter[j] += background[j][k];
+ backgroundParameter[j] /= (3.0*1.0*allSequences.length()); // We use 3.0*1.0 since there is only one strand
+
+ linearIndex++;
+ }
+
+ // Compute minDiffExpressionLevel for current condition
+ int minDiffExpressionLevel = 0;
+ while (true) {
+ boolean foundThreshold = true;
+ for (int j=0; j<files.length; j++) {
+ double backgroundProb = Math.pow(1.0 - backgroundParameter[j], minDiffExpressionLevel) * backgroundParameter[j]; // Based on geometric distribution
+ if (backgroundProb >= THRESHOLD)
+ foundThreshold = false;
+ }
+ if (foundThreshold) break;
+ minDiffExpressionLevel++;
+ }
+ minDiffExpressionLevels.add(minDiffExpressionLevel);
+ }
+ }
+
+ public String toString(String[] labels) {
+
+ // Include Header
+ StringBuilder sb = new StringBuilder();
+ sb.append("Sequence" + "\t" + "Length");
+ for (int i=0; i<Assembler.conditionFiles.size(); i++) {
+ String conditionName = "" + (i+1);
+ if ((labels != null) && (labels.length == Assembler.conditionFiles.size())) conditionName = labels[i];
+ if (Assembler.verbose) { // Verbose output
+ String[] files = Assembler.conditionFiles.get(i).split(",");
+ if (files.length == 1) {
+ sb.append("\t" + "Raw Counts " + conditionName);
+ sb.append("\t" + "Normalized Counts " + conditionName);
+ } else {
+ for (int j=0; j<files.length; j++) sb.append("\t" + "Raw Counts " + conditionName + " Replicate " + (j+1));
+ for (int j=0; j<files.length; j++) sb.append("\t" + "Normalized Counts " + conditionName + " Replicate " + (j+1));
+ }
+ sb.append("\t" + "RPKM " + conditionName);
+ }
+ sb.append("\t" + "Expression " + conditionName);
+ }
+ for (int x=0; x<Assembler.conditionFiles.size()-1; x++) { // First in pair
+ String conditionName1 = "" + (x+1);
+ if ((labels != null) && (labels.length == Assembler.conditionFiles.size())) conditionName1 = labels[x];
+ for (int y=x+1; y<Assembler.conditionFiles.size(); y++) { // Second in pair
+ String conditionName2 = "" + (y+1);
+ if ((labels != null) && (labels.length == Assembler.conditionFiles.size())) conditionName2 = labels[y];
+
+ if (Assembler.verbose) // Verbose output
+ sb.append("\t" + "pValue " + conditionName1 + " vs " + conditionName2);
+ sb.append("\t" + "qValue " + conditionName1 + " vs " + conditionName2);
+ }
+ }
+ sb.append("\n");
+
+ // Output each transcript
+ for (int z=0; z<transcripts.size(); z++) sb.append(transcripts.get(z) + "\n");
+ return sb.toString();
+ }
+
+
+
+ /**************************************************
+ ********** Private Instance Methods **********
+ **************************************************/
+
+ /**
+ * Determine transcripts based on DeNovoIndex.
+ */
+ private ArrayList<DeNovoTranscript> determineTranscripts(String allSequences, AtomicIntegerArray[] readCounts) {
+ ArrayList<DeNovoTranscript> transcripts = new ArrayList<DeNovoTranscript>();
+ int start = -1; // -1 is sentinel indicating no transcript
+ int end = -1; // inclusive
+ long[] readCounts_nts = new long[readCounts.length];
+ for (int i=0; i<allSequences.length()-1; i++) { // We go to length-1 to ignore final '$'
+ if (allSequences.charAt(i) == '^') { // End of transcript.
+ if ((start >= 0) && (end-start+1 >= Assembler.minTranscriptLength)) transcripts.add(new DeNovoTranscript(allSequences.substring(start, end+1), readCounts_nts));
+ start = -1;
+ end = -1;
+ for (int j=0; j<readCounts.length; j++) readCounts_nts[j] = 0;
+ } else { // Within transcript
+ if ((start < 0) && (getReadCountAtIndex(readCounts, i) >= Assembler.MIN_READS_MAPPING)) { // Start of new expressed transcript
+ start = i;
+ for (int j=0; j<readCounts.length; j++) readCounts_nts[j] += readCounts[j].get(i);
+ }
+ if (getReadCountAtIndex(readCounts, i) >= Assembler.MIN_READS_MAPPING) { // Within expressed transcript
+ end = i;
+ for (int j=0; j<readCounts.length; j++) readCounts_nts[j] += readCounts[j].get(i);
+ } else { // It is possible expressed transcript just ended
+ if ((start >= 0) && (end-start+1 >= Assembler.minTranscriptLength)) transcripts.add(new DeNovoTranscript(allSequences.substring(start, end+1), readCounts_nts));
+ start = -1;
+ end = -1;
+ for (int j=0; j<readCounts.length; j++) readCounts_nts[j] = 0;
+ }
+ }
+ }
+ return transcripts;
+ }
+
+ /**
+ * For each transcript, compute its normalized expression, RPKM, and
+ * mean expression in each condition and/or replicate.
+ */
+ private void computeExpression() {
+ upperQuartiles = new ArrayList<ArrayList<Long>>(Assembler.conditionFiles.size());
+ for (int i=0; i<Assembler.conditionFiles.size(); i++) {
+ String[] files = Assembler.conditionFiles.get(i).split(",");
+ upperQuartiles.add(new ArrayList<Long>(files.length));
+ for (int j=0; j<files.length; j++) {
+ ArrayList<Long> expressions = new ArrayList<Long>(transcripts.size());
+ for (int k=0; k<transcripts.size(); k++) expressions.add(transcripts.get(k).getRawCountNTs(i, j));
+ long upperQuartile = Misc.select_Long(expressions, (int)(0.75*transcripts.size()));
+ upperQuartiles.get(i).add(upperQuartile);
+ for (int k=0; k<transcripts.size(); k++) transcripts.get(k).setNormalizedCount(i, j, 100000.0, upperQuartile);
+ }
+ for (int k=0; k<transcripts.size(); k++) transcripts.get(k).computeExpression(i);
+ }
+ }
+
+ /**
+ * For each transcripts, compute its expression variance and lowess
+ * in each condition.
+ */
+ private void computeVarianceAndLowess() {
+ // Compute variance
+ for (int k=0; k<transcripts.size(); k++) transcripts.get(k).computeVariance(Assembler.conditionFiles.size());
+
+ // Compute Lowess
+ for (int x=0; x<Assembler.conditionFiles.size(); x++) { // First of pair
+ String[] files = Assembler.conditionFiles.get(x).split(",");
+ for (int y=0; y<Assembler.conditionFiles.size(); y++) { // Second of pair
+
+ if (x == y) continue; // No need to compute lowess for self
+ /*
+ if ((x > 0) && (files.length > 1)) { // We have replicates
+ for (DeNovoTranscript transcript : transcripts)
+ transcript.lowess[x][y] = transcript.lowess[0][y];
+ continue;
+ }
+ */
+ /* (x,y) lowess is NOT the same as (y,x) lowess
+ String[] files2 = Assembler.conditionFiles.get(y).split(",");
+ if ((x > y) && (files.length == 1) && (files2.length == 1)) { // Already computed lowess[y][x], which is same as lowess[x][y]
+ for (DeNovoTranscript transcript : transcripts)
+ transcript.lowess[x][y] = transcript.lowess[y][x];
+ continue;
+ }
+ */
+
+ double b = 0.0; // Bias correction term
+ for (int j=0; j<files.length; j++) {
+ b += 100000.0 / (double)upperQuartiles.get(x).get(j);
+ }
+ b /= files.length;
+
+ // Create list of gene expressions and list of gene variances
+ ArrayList<Long> expression = new ArrayList<Long>();
+ ArrayList<Long> variance = new ArrayList<Long>();
+ for (DeNovoTranscript transcript : transcripts) {
+ expression.add(transcript.getMean(x));
+ variance.add(transcript.variances[x][y]);
+ }
+
+ // Perform Lowess computation
+ ArrayList<Long> lowessVariance = Lowess.lowess(expression, variance);
+
+ // Uncomment to output data for Lowess graph to StdOut
+ //System.out.println("Mean" + "\t" + "Variance" + "\t" + "Lowess");
+ //for (int k=0; k<lowessVariance.size(); k++) System.out.println(expression.get(k) + "\t" + variance.get(k) + "\t" + ((long)(lowessVariance.get(k) - expression.get(k)*b)));
+
+ // Assign each gene its lowess variances (after subtracting bias correction term)
+ for (int k=0; k<transcripts.size(); k++) {
+ transcripts.get(k).lowess[x][y] = (long)(lowessVariance.get(k) - transcripts.get(k).getMean(x) * b);
+ }
+ }
+ }
+ }
+
+ /**
+ * Computes q-values for each transcript, i.e., corrected p-values,
+ * using Benjamini Hochberg correction.
+ */
+ private void correctPvalues() {
+ if (transcripts.size() == 0) return;
+ int pValue_index = 0;
+ for (int x=0; x<transcripts.get(0).variances.length-1; x++) { // First in pair
+ for (int y=x+1; y<transcripts.get(0).variances.length; y++) { // Second in pair
+
+ int[] indices = new int[transcripts.size()];
+ double[] pvalues = new double[transcripts.size()];
+ for (int j=0; j<transcripts.size(); j++) {
+ DeNovoTranscript transcript = transcripts.get(j);
+ pvalues[j] = transcript.getPvalue(pValue_index);
+ indices[j] = j;
+
+ // Check if there is too little expression to compute a p-value
+ double e1 = transcript.getMean(x);
+ double e2 = transcript.getMean(y);
+ e1 /= transcript.length();
+ e2 /= transcript.length();
+ if ((e1 < minDiffExpressionLevels.get(x)) && (e2 < minDiffExpressionLevels.get(y)))
+ pvalues[j] = 1.0;
+ }
+ mergesort(pvalues, indices, 0, transcripts.size()-1);
+ double previous_BH_value = 0.0;
+ for (int k=0; k<pvalues.length; k++) {
+ double BH_value = pvalues[k] * transcripts.size() / (k+1);
+ BH_value = Math.min(BH_value, 1.0); // Disallow values greater than 1
+
+ // To preserve monotonicity, we take maximum to ensure we don't
+ // generate a value less than the previous value.
+ BH_value = Math.max(BH_value, previous_BH_value);
+ previous_BH_value = BH_value;
+ transcripts.get(indices[k]).setQvalue(pValue_index, BH_value);
+ }
+ pValue_index++;
+ }
+ }
+ }
+
+ /**
+ * For each condition, determines the other condition that is most similar,
+ * i.e., its "partner". If there are no replicate experiments then the
+ * partner of each condition is used as a surrogate replicate.
+ * Similarity between two conditions is measured by Pearson correlation
+ * coefficient of normalized gene expression.
+ * This method sets the "partner" of each condition.
+ */
+ private void identifySimilarConditions() {
+ // Unused.
+ }
+
+ /**
+ * Returns the number of reads mapping to nucleotide index i
+ * summed over all sequencing read files.
+ */
+ private int getReadCountAtIndex(AtomicIntegerArray[] readCounts, int index) {
+ int sum = 0;
+ for (int i=0; i<readCounts.length; i++) sum += readCounts[i].get(index);
+ return sum;
+ }
+
+ /**
+ * Mergesort parallel arrays "a" and "b" based on values in "a"
+ */
+ private static void mergesort(double[] a, int[] b, int lo, int hi) {
+ if (lo < hi) {
+ int q = (lo+hi)/2;
+ mergesort(a, b, lo, q);
+ mergesort(a, b, q+1, hi);
+ merge(a, b, lo, q, hi);
+ }
+ }
+
+ /**
+ * Mergesort helper method
+ */
+ private static void merge(double[] a, int[] b, int lo, int q, int hi) {
+ double[] a1 = new double[q-lo+1];
+ double[] a2 = new double[hi-q];
+ int[] b1 = new int[q-lo+1];
+ int[] b2 = new int[hi-q];
+ for (int i=0; i<a1.length; i++) {
+ a1[i] = a[lo+i];
+ b1[i] = b[lo+i];
+ }
+ for (int j=0; j<a2.length; j++) {
+ a2[j] = a[q+1+j];
+ b2[j] = b[q+1+j];
+ }
+ int i=0; // Index for first half arrays
+ int j=0; // Index for second half arrays
+ for (int k=lo; k<=hi; k++) {
+ if (i >= a1.length) {
+ a[k] = a2[j];
+ b[k] = b2[j];
+ j++;
+ } else if (j >= a2.length) {
+ a[k] = a1[i];
+ b[k] = b1[i];
+ i++;
+ } else if (a1[i] <= a2[j]) {
+ a[k] = a1[i];
+ b[k] = b1[i];
+ i++;
+ } else {
+ a[k] = a2[j];
+ b[k] = b2[j];
+ j++;
+ }
+ }
+ }
+
+}
+
diff --git a/Dictionary.java b/Dictionary.java
new file mode 100644
index 0000000..8c11835
--- /dev/null
+++ b/Dictionary.java
@@ -0,0 +1,430 @@
+/*
+ * Copyright 2014 Brian Tjaden
+ *
+ * This file is part of Rockhopper.
+ *
+ * Rockhopper is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * any later version.
+ *
+ * Rockhopper is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * (in the file gpl.txt) along with Rockhopper.
+ * If not, see <http://www.gnu.org/licenses/>.
+ */
+
+/**
+ * A Dictionary instance represents a dictionary of k-mers
+ * found in a set of sequencing reads.
+ */
+
+import java.util.HashMap;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Arrays;
+
+public class Dictionary {
+
+ /********************************************
+ ********** Instance Variables **********
+ ********************************************/
+
+ public Table dict;
+ private int size;
+ private ArrayList<StringBuilder> transcripts = new ArrayList<StringBuilder>();
+ private ArrayList<KMer> seeds;
+ private int seedIndex;
+ public DeNovoIndex bwtIndex;
+
+
+
+ /*****************************************
+ ********** Class Variables **********
+ *****************************************/
+
+ private static int k; // Size of k-mer
+ private static char[] alphabet_1 = {'A', 'C', 'G', 'T'};
+ private static int[] alphabet_2 = new int[128]; // ASCII values
+
+
+
+ /**************************************
+ ********** Constructors **********
+ **************************************/
+
+ public Dictionary(int k) {
+ Dictionary.k = k;
+ dict = new Table();
+ alphabet_2['A'] = 0;
+ alphabet_2['C'] = 1;
+ alphabet_2['G'] = 2;
+ alphabet_2['T'] = 3;
+ alphabet_2['^'] = 4;
+ alphabet_2['$'] = 5;
+ bwtIndex = new DeNovoIndex(new ArrayList<StringBuilder>()); // Empty transcript index initially
+ }
+
+
+
+ /*************************************************
+ ********** Public Instance Methods **********
+ *************************************************/
+
+ public void add(String read) {
+ String read_RC = "";
+ if (Assembler.unstranded) read_RC = Assembler.reverseComplement(read);
+ for (int i=0; i<read.length()-k+1; i++) {
+ if (!bwtIndex.exactMatch(read, i, i+k)) { // k-mer not in BWT transcript index
+ if (Assembler.unstranded) { // Strand ambiguous
+ if (!bwtIndex.exactMatch(read_RC, read.length()-i-k, read.length()-i)) { // revComp of k-mer not in index
+ Long k_mer = stringToLong(read, i, i+k);
+ Long k_mer_RC = stringToLong(read_RC, read.length()-i-k, read.length()-i);
+ dict.add(k_mer, k_mer_RC);
+ }
+ } else { // Strand specific
+ Long k_mer = stringToLong(read, i, i+k);
+ dict.add(k_mer);
+ }
+ }
+ }
+ if (dict.exceedsLoadFactor()) buildTranscriptsAndClearTable(); // Table is full
+ }
+
+ /**
+ * Returns the number of unique elements in the dictionary.
+ */
+ public int getSize() {
+ return size;
+ }
+
+ /**
+ * Returns the number of transcripts.
+ */
+ public int getNumTranscripts() {
+ int size = 0;
+ for (StringBuilder sb : transcripts) {
+ if (sb.length() >= Assembler.minTranscriptLength) size++;
+ }
+ return size;
+ }
+
+ /**
+ * Returns the average transcript length.
+ */
+ public int getAverageTranscriptLength() {
+ long length = 0;
+ int count = 0;
+ if (transcripts.size() == 0) return 0;
+ for (StringBuilder sb : transcripts) {
+ if (sb.length() >= Assembler.minTranscriptLength) {
+ length += sb.length();
+ count++;
+ }
+ }
+ if (count == 0) return 0;
+ else return (int)(length/count);
+ }
+
+ public void initializeReadMapping(boolean stopAfterOneHit) {
+ bwtIndex.initializeReadMapping(stopAfterOneHit);
+ }
+
+ /**
+ * Map the full length read to the index of assembled transcripts.
+ */
+ public void mapFullLengthRead(String read) {
+ bwtIndex.exactMatch_fullRead(read);
+ }
+
+ /**
+ * Map the full length *paired-end* read to the index of assembled transcripts.
+ */
+ public void mapFullLengthRead(String read, String read2) {
+ bwtIndex.exactMatch_fullRead(read, read2);
+ }
+
+ public void assembleTranscripts() {
+ size = dict.size(); // Compute size
+
+ // Extend existing transcripts
+ for (int i=0; i<transcripts.size(); i++) {
+ extendSeedForward(transcripts.get(i));
+ extendSeedBackward(transcripts.get(i));
+ }
+
+ // Create new transcripts
+ prepareSeeds();
+ Long seed = getSeed();
+ while (seed != null) {
+ StringBuilder transcript = new StringBuilder(longToString(seed));
+ dict.remove(seed); // Remove seed from dict
+ extendSeedForward(transcript);
+ extendSeedBackward(transcript);
+ seed = getSeed();
+ transcripts.add(transcript);
+ }
+ dict = new Table();
+ bwtIndex = new DeNovoIndex(transcripts);
+ System.gc();
+ }
+
+
+
+ /**************************************************
+ ********** Private Instance Methods **********
+ **************************************************/
+
+ /**
+ * Check if the table is full.
+ * If so, assemble transcripts via deBruijn graph and
+ * clear the dictionary.
+ */
+ private synchronized void buildTranscriptsAndClearTable() {
+ if (dict.exceedsLoadFactor()) { // Table is full
+ assembleTranscripts();
+ }
+ }
+
+ /**
+ * Returns the most frequently occurring k-mer subject
+ * to the following restrictions:
+ * - The seed is sufficiently expressed, i.e., sufficiently many reads supporting the k-mer
+ * - The information content is at least 1.5
+ * - The k-mer is not palindromic (deleted).
+ */
+ private Long getSeed() {
+ while (seedIndex < seeds.size()) {
+ Long key = seeds.get(seedIndex).key;
+ seedIndex++;
+ if (dict.containsKey(key) && (informationContent(key) >= 1.5)) return key;
+ }
+ return null;
+ }
+
+ /**
+ * Since we need to repeatedly determine the best seed in the
+ * dictionary (an expensive operation for a hashtable), we
+ * create a sorted vector so that finding the best seed is
+ * efficient.
+ */
+ private void prepareSeeds() {
+ seeds = new ArrayList<KMer>();
+ for (int i=0; i<dict.capacity; i++) {
+ int value = dict.getValueAtIndex(i);
+ if (value == 0) continue;
+ Long key = dict.getKeyAtIndex(i);
+ if (value >= Assembler.minSeedExpression) seeds.add(new KMer(key, value));
+ }
+ Collections.sort(seeds, Collections.reverseOrder());
+ seedIndex = 0;
+ }
+
+ /**
+ * Extends transcript 5' to 3'.
+ */
+ private void extendSeedForward(StringBuilder transcript) {
+ boolean done = false;
+ while (!done) {
+ int max = Assembler.minExpression-1;
+ int maxIndex = -1;
+ transcript.append('?');
+ for (int i=0; i<alphabet_1.length; i++) {
+ transcript.setCharAt(transcript.length()-1, alphabet_1[i]);
+ Long k_mer = stringToLong(transcript, transcript.length()-k, transcript.length());
+ if (dict.containsKey(k_mer) && (dict.get(k_mer) > max)) {
+ max = dict.get(k_mer);
+ maxIndex = i;
+ }
+ if (Assembler.unstranded) { // Strand ambiguous
+ Long k_mer_RC = stringToLong(Assembler.reverseComplement(transcript.substring(transcript.length()-k)), 0, k);
+ if (dict.containsKey(k_mer_RC) && (dict.get(k_mer_RC) > max)) {
+ max = dict.get(k_mer_RC);
+ maxIndex = i;
+ }
+ }
+ }
+ if (maxIndex >= 0) { // Found an extension
+ transcript.setCharAt(transcript.length()-1, alphabet_1[maxIndex]);
+ Long key = stringToLong(transcript, transcript.length()-k, transcript.length());
+ dict.remove(key); // Remove k-mer from dict
+ if (Assembler.unstranded) { // Strand ambiguous
+ Long key_RC = stringToLong(Assembler.reverseComplement(transcript.substring(transcript.length()-k)), 0, k);
+ dict.remove(key_RC); // Remove k-mer from dict
+ }
+ } else { // No extension
+ transcript.deleteCharAt(transcript.length()-1);
+ done = true;
+ }
+ }
+ }
+
+ /**
+ * Extends transcript 3' to 5'.
+ */
+ private void extendSeedBackward(StringBuilder transcript) {
+ transcript.reverse();
+ boolean done = false;
+ while (!done) {
+ int max = Assembler.minExpression-1;
+ int maxIndex = -1;
+ transcript.append('?');
+ for (int i=0; i<alphabet_1.length; i++) {
+ transcript.setCharAt(transcript.length()-1, alphabet_1[i]);
+ Long k_mer = stringToLong_Reverse(transcript, transcript.length()-k, transcript.length());
+ if (dict.containsKey(k_mer) && (dict.get(k_mer) > max)) {
+ max = dict.get(k_mer);
+ maxIndex = i;
+ }
+ if (Assembler.unstranded) { // Strand ambiguous
+ Long k_mer_RC = stringToLong_Reverse(Assembler.reverseComplement(transcript.substring(transcript.length()-k)), 0, k);
+ if (dict.containsKey(k_mer_RC) && (dict.get(k_mer_RC) > max)) {
+ max = dict.get(k_mer_RC);
+ maxIndex = i;
+ }
+ }
+ }
+ if (maxIndex >= 0) { // Found an extension
+ transcript.setCharAt(transcript.length()-1, alphabet_1[maxIndex]);
+ Long key = stringToLong_Reverse(transcript, transcript.length()-k, transcript.length());
+ dict.remove(key); // Remove k-mer from dict
+ if (Assembler.unstranded) { // Strand ambiguous
+ Long key_RC = stringToLong_Reverse(Assembler.reverseComplement(transcript.substring(transcript.length()-k)), 0, k);
+ dict.remove(key_RC); // Remove k-mer from dict
+ }
+ } else { // No extension
+ transcript.deleteCharAt(transcript.length()-1);
+ done = true;
+ }
+ }
+ transcript.reverse();
+ }
+
+
+
+ /***********************************************
+ ********** Private Class Methods **********
+ ***********************************************/
+
+ private static Long stringToLong(String s, int index1, int index2) {
+ long num = 0;
+ for (int i=index1; i<index2; i++) {
+ num = num << 2;
+ num += charToInt(s.charAt(i));
+ }
+ return new Long(num);
+ }
+
+ private static Long stringToLong(StringBuilder sb, int index1, int index2) {
+ long num = 0;
+ for (int i=index1; i<index2; i++) {
+ num = num << 2;
+ num += charToInt(sb.charAt(i));
+ }
+ return new Long(num);
+ }
+
+ private static Long stringToLong_Reverse(String s, int index1, int index2) {
+ long num = 0;
+ for (int i=index2-1; i>=index1; i--) {
+ num = num << 2;
+ num += charToInt(s.charAt(i));
+ }
+ return new Long(num);
+ }
+
+ private static Long stringToLong_Reverse(StringBuilder sb, int index1, int index2) {
+ long num = 0;
+ for (int i=index2-1; i>=index1; i--) {
+ num = num << 2;
+ num += charToInt(sb.charAt(i));
+ }
+ return new Long(num);
+ }
+
+ private static String longToString(Long key) {
+ long num = key.longValue();
+ StringBuilder sb = new StringBuilder(k+1);
+ for (int i=0; i<k; i++) {
+ sb.append(intToChar((int)num & 3));
+ num = num >>> 2;
+ }
+ return sb.reverse().toString();
+ }
+
+ public static int charToInt(char c) {
+ return alphabet_2[c];
+ }
+
+ private static char intToChar(int num) {
+ return alphabet_1[num];
+ }
+
+ private static double informationContent(Long k_mer) {
+ double[] counts = new double[4];
+ long num = k_mer.longValue();
+ for (int i=0; i<k; i++) {
+ counts[((int)num & 3)] += 1.0;
+ num = num >>> 2;
+ }
+
+ double sum = 0.0;
+ for (int i=0; i<counts.length; i++) sum += counts[i];
+
+ double informationContent = 0.0;
+ for (int i=0; i<counts.length; i++) {
+ if (counts[i] > 0.0) {
+ double frequency = counts[i] / sum;
+ informationContent += frequency * Math.log(frequency) / Math.log(2.0);
+ }
+ }
+ return 0.0 - informationContent;
+ }
+
+
+
+ /*************************************
+ ********** Main Method **********
+ *************************************/
+
+ public static void main(String[] args) {
+
+ int k = 25;
+ Dictionary d = new Dictionary(k);
+
+ String s = "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAG";
+ System.out.println(s);
+ for (int i=0; i<d.dict.capacity; i++) {
+ int value = d.dict.getValueAtIndex(i);
+ if (value == 0) continue;
+ Long key = d.dict.getKeyAtIndex(i);
+ System.out.println(longToString(key) + "\t" + value);
+ }
+ }
+
+}
+
+
+
+/**************************************
+ ********** Helper Class **********
+ **************************************/
+
+class KMer implements Comparable<KMer> {
+
+ public Long key;
+ public Integer count;
+
+ public KMer(Long key, Integer count) {
+ this.key = key;
+ this.count = count;
+ }
+
+ public int compareTo(KMer k) {
+ return count.compareTo(k.count);
+ }
+}
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diff --git a/ExperimentsGUI.java b/ExperimentsGUI.java
new file mode 100644
index 0000000..fb7e104
--- /dev/null
+++ b/ExperimentsGUI.java
@@ -0,0 +1,525 @@
+/*
+ * Copyright 2013 Brian Tjaden
+ *
+ * This file is part of Rockhopper.
+ *
+ * Rockhopper is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * any later version.
+ *
+ * Rockhopper is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * (in the file gpl.txt) along with Rockhopper.
+ * If not, see <http://www.gnu.org/licenses/>.
+ */
+
+import java.util.ArrayList;
+import java.awt.*;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseListener;
+import javax.swing.*;
+import javax.swing.border.EtchedBorder;
+import java.io.IOException;
+import java.io.File;
+
+public class ExperimentsGUI {
+
+ private JApplet applet;
+ private JFileChooser fc;
+ private int numExperiments;
+ private int currentExperimentNumber;
+ private JPanel panel;
+ private JScrollPane scrollPane;
+ private ArrayList<ArrayList<JTextField>> fileNames;
+ private ArrayList<ArrayList<File>> files;
+ private ArrayList<ArrayList<File>> pairedEndFiles;
+ private ArrayList<ArrayList<JLabel>> replicateBrowseLabels;
+ private ArrayList<JLabel> replicateAddLabels;
+ private ArrayList<ArrayList<JLabel>> replicateRemoveLabels;
+ private ArrayList<ArrayList<JLabel>> pairedEndLabels;
+ private ArrayList<JTextField> experimentNames;
+ private JLabel experimentAddLabel;
+ private ImageIcon experimentAddButton, experimentAddButtonPressed, replicateAddButton, replicateAddButtonPressed, experimentRemoveButton, experimentRemoveButtonPressed, replicateRemoveButton, replicateRemoveButtonPressed, browseButton, browseButtonPressed, pairedEndNoButton, pairedEndYesButton, pairedEndNoButtonPressed, pairedEndYesButtonPressed;
+ private ArrayList<JLabel> experimentRemoveLabels;
+ private ArrayList<JPanel> experimentPanels;
+
+ public ExperimentsGUI(JApplet applet) {
+ this.applet = applet;
+ fc = new JFileChooser();
+ numExperiments = 0;
+ currentExperimentNumber = 0;
+ panel = new JPanel(new FlowLayout(FlowLayout.CENTER,5,5));
+ scrollPane = new JScrollPane(panel);
+ scrollPane.setPreferredSize(new Dimension(720, 500));
+ scrollPane.setBorder(BorderFactory.createEmptyBorder());
+ fileNames = new ArrayList<ArrayList<JTextField>>();
+ files = new ArrayList<ArrayList<File>>();
+ pairedEndFiles = new ArrayList<ArrayList<File>>();
+ replicateBrowseLabels = new ArrayList<ArrayList<JLabel>>();
+ replicateAddLabels = new ArrayList<JLabel>();
+ replicateRemoveLabels = new ArrayList<ArrayList<JLabel>>();
+ pairedEndLabels = new ArrayList<ArrayList<JLabel>>();
+ experimentNames = new ArrayList<JTextField>();
+ experimentAddButton = RockhopperGUI.getScaledImage("images/addExp.gif", 20, 20);
+ experimentAddButtonPressed = RockhopperGUI.getScaledImage("images/addExpPressed.gif", 20, 20);
+ replicateAddButton = RockhopperGUI.getScaledImage("images/addRep.gif", 20, 20);
+ replicateAddButtonPressed = RockhopperGUI.getScaledImage("images/addRepPressed.gif", 20, 20);
+ experimentRemoveButton = RockhopperGUI.getScaledImage("images/removeExp.gif", 20, 20);
+ experimentRemoveButtonPressed = RockhopperGUI.getScaledImage("images/removeExpPressed.gif", 20, 20);
+ replicateRemoveButton = RockhopperGUI.getScaledImage("images/removeRep.gif", 20, 20);
+ replicateRemoveButtonPressed = RockhopperGUI.getScaledImage("images/removeRepPressed.gif", 20, 20);
+ browseButton = RockhopperGUI.getScaledImage("images/browse.gif", 77, 29);
+ browseButtonPressed = RockhopperGUI.getScaledImage("images/browsePressed.gif", 77, 29);
+ pairedEndNoButton = RockhopperGUI.getScaledImage("images/pairedEndRed.gif", 20, 20);
+ pairedEndYesButton = RockhopperGUI.getScaledImage("images/pairedEndGreen.gif", 20, 20);
+ pairedEndNoButtonPressed = RockhopperGUI.getScaledImage("images/pairedEndRedPressed.gif", 20, 20);
+ pairedEndYesButtonPressed = RockhopperGUI.getScaledImage("images/pairedEndGreenPressed.gif", 20, 20);
+ experimentAddLabel = new JLabel(experimentAddButton);
+ experimentAddLabel.setToolTipText("Add experiment");
+ experimentAddLabel.addMouseListener((MouseListener)applet);
+ experimentRemoveLabels = new ArrayList<JLabel>();
+ experimentPanels = new ArrayList<JPanel>();
+ }
+
+ public int getNumExperiments() {
+ return numExperiments;
+ }
+
+ public JScrollPane getScrollPane() {
+ return scrollPane;
+ }
+
+ public boolean isSource(Object source) {
+ if (source.equals(experimentAddLabel)) return true;
+ for (int i=0; i<numExperiments; i++) {
+ if (source.equals(experimentRemoveLabels.get(i))) return true;
+ if (source.equals(replicateAddLabels.get(i))) return true;
+ for (int j=0; j<fileNames.get(i).size(); j++) {
+ if (source.equals(replicateBrowseLabels.get(i).get(j))) return true;
+ if (source.equals(replicateRemoveLabels.get(i).get(j))) return true;
+ if (source.equals(pairedEndLabels.get(i).get(j))) return true;
+ }
+ }
+ return false;
+ }
+
+ public void handleEvent(Object source) {
+ if (source.equals(experimentAddLabel)) {
+ addExperiment();
+ return;
+ }
+ for (int i=0; i<numExperiments; i++) {
+ if (source.equals(experimentRemoveLabels.get(i))) {
+ removeExperiment(i);
+ return;
+ }
+ if (source.equals(replicateAddLabels.get(i))) {
+ addReplicate(i);
+ return;
+ }
+ for (int j=0; j<fileNames.get(i).size(); j++) {
+ if (source.equals(replicateBrowseLabels.get(i).get(j))) {
+ fileChooser(i,j);
+ return;
+ }
+ if (source.equals(replicateRemoveLabels.get(i).get(j))) {
+ removeReplicate(i,j);
+ return;
+ }
+ if (source.equals(pairedEndLabels.get(i).get(j))) {
+ addMatePairFile(i, j);
+ }
+ }
+ }
+ }
+
+ public void mousePressed(Object source) {
+ if (source.equals(experimentAddLabel)) {
+ experimentAddLabel.setIcon(experimentAddButtonPressed);
+ return;
+ }
+ for (int i=0; i<numExperiments; i++) {
+ if (source.equals(experimentRemoveLabels.get(i))) {
+ experimentRemoveLabels.get(i).setIcon(experimentRemoveButtonPressed);
+ return;
+ }
+ if (source.equals(replicateAddLabels.get(i))) {
+ replicateAddLabels.get(i).setIcon(replicateAddButtonPressed);
+ return;
+ }
+ for (int j=0; j<fileNames.get(i).size(); j++) {
+ if (source.equals(replicateBrowseLabels.get(i).get(j))) {
+ replicateBrowseLabels.get(i).get(j).setIcon(browseButtonPressed);
+ return;
+ }
+ if (source.equals(replicateRemoveLabels.get(i).get(j))) {
+ replicateRemoveLabels.get(i).get(j).setIcon(replicateRemoveButtonPressed);
+ return;
+ }
+ if (source.equals(pairedEndLabels.get(i).get(j))) {
+ if (pairedEndLabels.get(i).get(j).getIcon().equals(pairedEndNoButton))
+ pairedEndLabels.get(i).get(j).setIcon(pairedEndNoButtonPressed);
+ if (pairedEndLabels.get(i).get(j).getIcon().equals(pairedEndYesButton))
+ pairedEndLabels.get(i).get(j).setIcon(pairedEndYesButtonPressed);
+ return;
+ }
+ }
+ }
+ }
+
+ public void mouseReleased(Object source) {
+ if (source.equals(experimentAddLabel)) {
+ experimentAddLabel.setIcon(experimentAddButton);
+ return;
+ }
+ for (int i=0; i<numExperiments; i++) {
+ if (source.equals(experimentRemoveLabels.get(i))) {
+ experimentRemoveLabels.get(i).setIcon(experimentRemoveButton);
+ return;
+ }
+ if (source.equals(replicateAddLabels.get(i))) {
+ replicateAddLabels.get(i).setIcon(replicateAddButton);
+ return;
+ }
+ for (int j=0; j<fileNames.get(i).size(); j++) {
+ if (source.equals(replicateBrowseLabels.get(i).get(j))) {
+ replicateBrowseLabels.get(i).get(j).setIcon(browseButton);
+ return;
+ }
+ if (source.equals(replicateRemoveLabels.get(i).get(j))) {
+ replicateRemoveLabels.get(i).get(j).setIcon(replicateRemoveButton);
+ return;
+ }
+ if (source.equals(pairedEndLabels.get(i).get(j))) {
+ if (pairedEndLabels.get(i).get(j).getIcon().equals(pairedEndNoButtonPressed))
+ pairedEndLabels.get(i).get(j).setIcon(pairedEndNoButton);
+ if (pairedEndLabels.get(i).get(j).getIcon().equals(pairedEndYesButtonPressed))
+ pairedEndLabels.get(i).get(j).setIcon(pairedEndYesButton);
+ return;
+ }
+ }
+ }
+ }
+
+ public void addExperiment() {
+ scrollPane.remove(panel);
+ numExperiments++;
+ currentExperimentNumber++;
+ fileNames.add(new ArrayList<JTextField>());
+ fileNames.get(fileNames.size()-1).add(new JTextField(30));
+ fileNames.get(fileNames.size()-1).get(fileNames.get(fileNames.size()-1).size()-1).setBackground(RockhopperGUI.gold);
+ files.add(new ArrayList<File>());
+ files.get(files.size()-1).add(null);
+ pairedEndFiles.add(new ArrayList<File>());
+ pairedEndFiles.get(pairedEndFiles.size()-1).add(null);
+ replicateBrowseLabels.add(new ArrayList<JLabel>());
+ JLabel repBrowse = new JLabel(browseButton);
+ repBrowse.setToolTipText("Search for file");
+ repBrowse.addMouseListener((MouseListener)applet);
+ replicateBrowseLabels.get(replicateBrowseLabels.size()-1).add(repBrowse);
+ JLabel repAdd = new JLabel(replicateAddButton);
+ repAdd.setToolTipText("Add replicate");
+ repAdd.addMouseListener((MouseListener)applet);
+ replicateAddLabels.add(repAdd);
+ replicateRemoveLabels.add(new ArrayList<JLabel>());
+ JLabel repRemove = new JLabel(replicateRemoveButton);
+ repRemove.setToolTipText("Remove replicate");
+ repRemove.addMouseListener((MouseListener)applet);
+ replicateRemoveLabels.get(replicateRemoveLabels.size()-1).add(repRemove);
+ pairedEndLabels.add(new ArrayList<JLabel>());
+ JLabel pairedEndAdd = new JLabel(pairedEndNoButton);
+ pairedEndAdd.setToolTipText("Using paired-end reads; add file of mate-pair reads");
+ pairedEndAdd.addMouseListener((MouseListener)applet);
+ pairedEndLabels.get(pairedEndLabels.size()-1).add(pairedEndAdd);
+ JTextField expName = new JTextField("" + currentExperimentNumber, 15);
+ expName.addActionListener((ActionListener)applet);
+ experimentNames.add(expName);
+ JLabel expRemove = new JLabel(experimentRemoveButton);
+ expRemove.setToolTipText("Remove experiment");
+ expRemove.addMouseListener((MouseListener)applet);
+ experimentRemoveLabels.add(expRemove);
+ experimentPanels.add(generateExperimentPanel(experimentNames.size()-1));
+ populateScrollPane();
+ }
+
+ public void removeExperiment(int i) {
+ scrollPane.remove(panel);
+ numExperiments--;
+ fileNames.remove(i);
+ files.remove(i);
+ pairedEndFiles.remove(i);
+ replicateBrowseLabels.remove(i);
+ replicateAddLabels.remove(i);
+ replicateRemoveLabels.remove(i);
+ pairedEndLabels.remove(i);
+ experimentNames.remove(i);
+ experimentRemoveLabels.remove(i);
+ experimentPanels.remove(i);
+ populateScrollPane();
+ }
+
+ public void fileChooser(int i, int j) {
+ fc.setSelectedFile(null);
+ int returnVal = fc.showOpenDialog(SwingUtilities.getAncestorOfClass(JFrame.class,applet));
+ if (returnVal == JFileChooser.APPROVE_OPTION) {
+ files.get(i).set(j, fc.getSelectedFile());
+ fileNames.get(i).get(j).setText(files.get(i).get(j).getName());
+ fileNames.get(i).get(j).setBackground(Color.WHITE);
+ }
+ }
+
+ public void addMatePairFile(int i, int j) {
+ // First show pop-up information message about paired-end reads
+ String title = "Use mate-pair file for paired-end reads?";
+ String message = "If you are using paired-end reads, use this option if you have two mate-pair files for a particular replicate experiment.";
+ Object[] options = {"OK", "Cancel"};
+ int n = JOptionPane.showOptionDialog(SwingUtilities.getAncestorOfClass(JFrame.class,applet), message, title, JOptionPane.YES_NO_OPTION, JOptionPane.INFORMATION_MESSAGE, pairedEndYesButton, options, options[0]);
+
+ // Select mate-pair file
+ if (n == 0) {
+ fc.setSelectedFile(null);
+ int returnVal = fc.showOpenDialog(SwingUtilities.getAncestorOfClass(JFrame.class,applet));
+ if (returnVal == JFileChooser.APPROVE_OPTION) {
+ pairedEndFiles.get(i).set(j, fc.getSelectedFile());
+ pairedEndLabels.get(i).get(j).setIcon(pairedEndYesButton);
+ }
+ }
+ }
+
+ public void addReplicate(int i) {
+ scrollPane.remove(panel);
+ fileNames.get(i).add(new JTextField(30));
+ fileNames.get(i).get(fileNames.get(i).size()-1).setBackground(RockhopperGUI.gold);
+ files.get(i).add(null);
+ pairedEndFiles.get(i).add(null);
+ JLabel repBrowse = new JLabel(browseButton);
+ repBrowse.setToolTipText("Search for file");
+ repBrowse.addMouseListener((MouseListener)applet);
+ replicateBrowseLabels.get(i).add(repBrowse);
+ JLabel repRemove = new JLabel(replicateRemoveButton);
+ repRemove.setToolTipText("Remove replicate");
+ repRemove.addMouseListener((MouseListener)applet);
+ replicateRemoveLabels.get(i).add(repRemove);
+ JLabel pairedEndAdd = new JLabel(pairedEndNoButton);
+ pairedEndAdd.setToolTipText("Using paired-end reads; add file of mate-pair reads");
+ pairedEndAdd.addMouseListener((MouseListener)applet);
+ pairedEndLabels.get(i).add(pairedEndAdd);
+ experimentPanels.remove(i);
+ experimentPanels.add(i, generateExperimentPanel(i));
+ populateScrollPane();
+ }
+
+ public void removeReplicate(int i, int j) {
+ scrollPane.remove(panel);
+ fileNames.get(i).remove(j);
+ files.get(i).remove(j);
+ pairedEndFiles.get(i).remove(j);
+ replicateBrowseLabels.get(i).remove(j);
+ replicateRemoveLabels.get(i).remove(j);
+ pairedEndLabels.get(i).remove(j);
+ experimentPanels.remove(i);
+ experimentPanels.add(i, generateExperimentPanel(i));
+ populateScrollPane();
+ }
+
+ /**
+ * Returns a String representation of the experiments' names and
+ * all replicate files (including paths to files) for each experiment.
+ * This String is output to a file, which can be read in to populate
+ * the set of experiments and replicate files.
+ *
+ * There is one line per experiment. Each line is tab-delimited.
+ * A line contains the name of an experiment
+ * followed by the path to each replicate file for the experiment.
+ * If mate-pair files are included for paired-end reads, each
+ * replicate file is followed by a comma and the path to the mate-pair file.
+ */
+ public String experimentsToString() {
+ StringBuilder sb = new StringBuilder();
+ for (int i=0; i<files.size(); i++) {
+
+ boolean validExperiment = false;
+ int count = 0; // Count replicate file names for an experiment
+ for (int j=0; j<files.get(i).size(); j++) {
+ if (files.get(i).get(j) != null) count++;
+ }
+ if (count > 0) {
+ // Output name of experiment
+ String experimentName = experimentNames.get(i).getText();
+ if (experimentName.length() == 0) experimentName = "N/A";
+ if (files.get(i).size() > 0) {
+ sb.append(experimentName);
+ validExperiment = true;
+ }
+ }
+ for (int j=0; j<files.get(i).size(); j++) {
+ if (files.get(i).get(j) != null)
+ sb.append("\t" + files.get(i).get(j).getAbsolutePath());
+ if (pairedEndFiles.get(i).get(j) != null)
+ sb.append("%" + pairedEndFiles.get(i).get(j).getAbsolutePath());
+ }
+ if (validExperiment) sb.append("\n");
+ }
+ return sb.toString();
+ }
+
+ public void experimentsFromString(String s) {
+ String[] experiments = s.split("\n");
+ for (int i=0; i<experiments.length; i++) {
+ String[] replicates = experiments[i].split("\t");
+ addExperiment();
+ experimentNames.get(i).setText(replicates[0]);
+ removeReplicate(i, 0);
+ for (int j=1; j<replicates.length; j++) {
+ addReplicate(i);
+ String[] parse_replicates = replicates[j].split("%");
+ File f = new File(parse_replicates[0]);
+ fileNames.get(i).get(j-1).setText(f.getName());
+ fileNames.get(i).get(j-1).setBackground(Color.WHITE);
+ files.get(i).set(j-1, f);
+ if (parse_replicates.length > 1) { // Using paired-end reads
+ pairedEndFiles.get(i).set(j-1, new File(parse_replicates[1]));
+ pairedEndLabels.get(i).get(j-1).setIcon(pairedEndYesButton);
+ }
+ }
+ }
+ }
+
+ /**
+ * Returns a comma-separated list of experiment names.
+ */
+ public String getExperimentsList() {
+ StringBuilder sb = new StringBuilder();
+ if (experimentNames.size() > 0) sb.append(experimentNames.get(0).getText());
+ for (int i=1; i<experimentNames.size(); i++)
+ sb.append("," + experimentNames.get(i).getText());
+ return sb.toString();
+ }
+
+ /**
+ * Returns an array where each entry corresponds to one experiment.
+ * Each entry is a comma-separated list of replicate files for the experiment.
+ * If paired-end reads are used, each comma-separated entry is a percent-separated
+ * list of mate pair files.
+ */
+ public String[] getReplicatesList() {
+ ArrayList<String> repsList = new ArrayList<String>();
+ for (int i=0; i<files.size(); i++) {
+ ArrayList<String> reps = new ArrayList<String>();
+ for (int j=0; j<files.get(i).size(); j++) {
+ if (files.get(i).get(j) != null) {
+ if (files.get(i).get(j).getAbsolutePath().length() > 0) {
+ StringBuilder sb = new StringBuilder(files.get(i).get(j).getAbsolutePath());
+ if (pairedEndFiles.get(i).get(j) != null) {
+ if (pairedEndFiles.get(i).get(j).getAbsolutePath().length() > 0)
+ sb.append("%" + pairedEndFiles.get(i).get(j).getAbsolutePath());
+ }
+ reps.add(sb.toString());
+ }
+ }
+ }
+ if (reps.size() > 0) {
+ StringBuilder sb = new StringBuilder();
+ sb.append(reps.get(0));
+ for (int j=1; j<reps.size(); j++) sb.append("," + reps.get(j));
+ repsList.add(sb.toString());
+ }
+ }
+ return repsList.toArray(new String[repsList.size()]);
+ }
+
+ private JPanel generateExperimentPanel(int i) {
+ Color color = RockhopperGUI.lightPurple;
+ int numReplicates = fileNames.get(i).size();
+ JPanel newPanel = new JPanel(new GridLayout(numReplicates+2,1,0,0));
+ newPanel.setPreferredSize(new Dimension(680, 30*numReplicates+70));
+ newPanel.setBackground(color);
+ JPanel p1 = new JPanel(new GridLayout(1,2,0,0));
+ p1.setBackground(color);
+ JPanel leftPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
+ leftPanel.setBackground(color);
+ JLabel expLabel = new JLabel("Experiment Name:");
+ expLabel.setForeground(Color.red);
+ leftPanel.add(expLabel);
+ leftPanel.add(experimentNames.get(i));
+ JPanel rightPanel = new JPanel(new FlowLayout(FlowLayout.RIGHT));
+ rightPanel.setBackground(color);
+ rightPanel.add(experimentRemoveLabels.get(i));
+ p1.add(leftPanel);
+ p1.add(rightPanel);
+ newPanel.add(p1);
+ for (int j=0; j<numReplicates; j++) {
+ JPanel p2 = new JPanel(new FlowLayout(FlowLayout.LEFT));
+ p2.setBackground(color);
+ JLabel spacer2 = new JLabel("");
+ spacer2.setPreferredSize(new Dimension(70,0));
+ p2.add(spacer2);
+ JLabel repLabel = new JLabel("Replicate #" + (j+1) + ":");
+ repLabel.setForeground(Color.blue);
+ p2.add(repLabel);
+ p2.add(fileNames.get(i).get(j));
+ p2.add(replicateBrowseLabels.get(i).get(j));
+ p2.add(replicateRemoveLabels.get(i).get(j));
+ p2.add(pairedEndLabels.get(i).get(j));
+ newPanel.add(p2);
+ }
+ JPanel p3 = new JPanel(new FlowLayout(FlowLayout.LEFT));
+ p3.setBackground(color);
+ JLabel spacer3 = new JLabel("");
+ spacer3.setPreferredSize(new Dimension(70, 0));
+ p3.add(spacer3);
+ p3.add(replicateAddLabels.get(i));
+ newPanel.add(p3);
+ return newPanel;
+ }
+
+ private void populateScrollPane() {
+ panel = new JPanel(new FlowLayout(FlowLayout.CENTER,2,2));
+ int height = 0;
+ for (int i=0; i<experimentPanels.size(); i++) height += experimentPanels.get(i).getPreferredSize().height;
+ panel.setPreferredSize(new Dimension(700, height + (experimentPanels.size()*14) + 40));
+ panel.setBackground(RockhopperGUI.lightBlue);
+ for (int i=0; i<experimentPanels.size(); i+=2) {
+ if (i > 0) panel.add(RockhopperGUI.getSpacerPanel(700, 10));
+ JPanel twoPanel = new JPanel(new FlowLayout(FlowLayout.CENTER,3,3));
+ int twoHeight = experimentPanels.get(i).getPreferredSize().height + 6;
+ if (i < experimentPanels.size()-1) twoHeight += experimentPanels.get(i+1).getPreferredSize().height + 6;
+ else twoHeight += 3;
+ twoPanel.setPreferredSize(new Dimension(690, twoHeight));
+ twoPanel.setBackground(RockhopperGUI.lightBlue);
+ twoPanel.setBorder(BorderFactory.createEtchedBorder(EtchedBorder.RAISED));
+ twoPanel.add(experimentPanels.get(i));
+ if (i < experimentPanels.size()-1) twoPanel.add(experimentPanels.get(i+1));
+ panel.add(twoPanel);
+ }
+
+ JPanel p4 = new JPanel(new FlowLayout(FlowLayout.LEFT,5,5));
+ p4.setPreferredSize(new Dimension(700, 30));
+ p4.setBackground(RockhopperGUI.lightBlue);
+ p4.add(experimentAddLabel);
+ panel.add(p4);
+ scrollPane = new JScrollPane(panel);
+ scrollPane.setPreferredSize(new Dimension(720, 500));
+ scrollPane.setBorder(BorderFactory.createEmptyBorder());
+
+ // Force scroll to bottom
+ SwingUtilities.invokeLater( new Runnable() {
+ public void run()
+ {
+ JScrollBar v = scrollPane.getVerticalScrollBar();
+ v.setValue(v.getMaximum());
+ }
+ } );
+ }
+
+ private void error(String title, String message) {
+ JOptionPane.showMessageDialog(SwingUtilities.getAncestorOfClass(JFrame.class,applet), message, title, JOptionPane.ERROR_MESSAGE);
+ }
+
+}
+
diff --git a/FileOps.java b/FileOps.java
new file mode 100644
index 0000000..51db1bb
--- /dev/null
+++ b/FileOps.java
@@ -0,0 +1,765 @@
+/*
+ * Copyright 2013 Brian Tjaden
+ *
+ * This file is part of Rockhopper.
+ *
+ * Rockhopper is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * any later version.
+ *
+ * Rockhopper is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * (in the file gpl.txt) along with Rockhopper.
+ * If not, see <http://www.gnu.org/licenses/>.
+ */
+
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.File;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.util.ArrayList;
+import java.util.zip.GZIPOutputStream;
+import java.util.zip.GZIPInputStream;
+
+/**
+ * Supports reading and writing of compressed files.
+ */
+public class FileOps {
+
+ /********************************************
+ ********** Instance Variables **********
+ ********************************************/
+
+ private String readFileName;
+ private long readFileLength;
+ private long readFileDate;
+ private String repliconFileName;
+ private long repliconFileLength;
+ private long repliconFileDate;
+ private String repliconHeader;
+ private int repliconLength;
+ private long avgLengthReads;
+ private int[] coordinates_plus;
+ private int[] coordinates_minus;
+ private ArrayList<DeNovoTranscript> transcripts; // For de novo assembly
+ private boolean isValid;
+
+ // Results
+ private int totalReads;
+ private int invalidQualityReads; // Reads containing an invalid quality score
+ private int ambiguousReads; // Reads with ambiguous nucleotides
+ private int lowQualityReads; // Reads with quality scores too low for mapping
+ private int mappedOnceReads; // Reads mapping to one location
+ private int mappedMoreThanOnceReads; // Reads mapping to multiple locations
+ private int exactMappedReads; // Reads mapping without mismatches/errors
+ private int inexactMappedReads; // Reads mapping with mismatches/errors
+
+
+
+ /*****************************************
+ ********** Class Variables **********
+ *****************************************/
+
+ private static String DIR = Rockhopper.output_DIR + "intermediary/";
+ private static byte[] buffer1 = new byte[1]; // Temp array used when reading in GZIP file
+
+
+
+ /**************************************
+ ********** Constructors **********
+ **************************************/
+
+ public FileOps(String inFileName) {
+ isValid = readCompressedFile(inFileName);
+ }
+
+ public FileOps(String inFileName, String readFileName, String repliconFileName) {
+ isValid = readCompressedFile(inFileName);
+ File readFile = new File(readFileName);
+ File repliconFile = new File(repliconFileName);
+ isValid = isValid && (readFile.getName().equals(this.readFileName)) && (readFile.length() == readFileLength) && (readFile.lastModified() == readFileDate) && (repliconFile.getName().equals(this.repliconFileName)) && (repliconFile.length() == repliconFileLength) && (repliconFile.lastModified() == repliconFileDate);
+ }
+
+ /**
+ * Constructor used for de novo transcript assembly.
+ */
+ public FileOps(String inFileName, ArrayList<String> conditionFiles) {
+ isValid = readCompressedFile_DeNovo(inFileName, conditionFiles);
+ }
+
+
+
+ /*************************************************
+ ********** Public Instance Methods **********
+ *************************************************/
+
+ /**
+ * Returns true if the input file is valid, i.e.,
+ * the stats of the read-file and replicon-file file
+ * correspond to the stats from the input file.
+ * Returns false otherwise.
+ */
+ public boolean isValid() {
+ return this.isValid;
+ }
+
+ /**
+ * Returns the name of the sequencing read file.
+ */
+ public String getReadFileName() {
+ return this.readFileName;
+ }
+
+ /**
+ * Returns the average length of sequencing reads
+ * in the sequencing reads file.
+ */
+ public long getAvgLengthReads() {
+ return avgLengthReads;
+ }
+
+ /**
+ * Returns plus strand coordinates.
+ */
+ public int[] getCoordinates_plus() {
+ return this.coordinates_plus;
+ }
+
+ /**
+ * Returns minus strand coordinates.
+ */
+ public int[] getCoordinates_minus() {
+ return this.coordinates_minus;
+ }
+
+ /**
+ * Returns the total reads
+ */
+ public int getTotalReads() {
+ return this.totalReads;
+ }
+
+ /**
+ * Returns the invalide quality reads
+ */
+ public int getInvalidQualityReads() {
+ return this.invalidQualityReads;
+ }
+
+ /**
+ * Returns the ambiguous reads
+ */
+ public int getAmbiguousReads() {
+ return this.ambiguousReads;
+ }
+
+ /**
+ * Returns the low quality reads
+ */
+ public int getLowQualityReads() {
+ return this.lowQualityReads;
+ }
+
+ /**
+ * Returns the mapped once reads
+ */
+ public int getMappedOnceReads() {
+ return this.mappedOnceReads;
+ }
+
+ /**
+ * Returns the mapped more than once reads
+ */
+ public int getMappedMoreThanOnceReads() {
+ return this.mappedMoreThanOnceReads;
+ }
+
+ /**
+ * Returns the exact mapped reads
+ */
+ public int getExactMappedReads() {
+ return this.exactMappedReads;
+ }
+
+ /**
+ * Returns the inexact mapped reads
+ */
+ public int getInexactMappedReads() {
+ return this.inexactMappedReads;
+ }
+
+ /**
+ * Returns the de novo assembled transcripts
+ */
+ public ArrayList<DeNovoTranscript> getTranscripts() {
+ return this.transcripts;
+ }
+
+
+
+ /**********************************************
+ ********** Public Class Methods **********
+ **********************************************/
+
+ /**
+ * Converts the specified pair of int arrays to byte arrays
+ * and writes these byte arrays to a compressed file. The following
+ * header information is also written to the compressed output file:
+ * version
+ * read file name
+ * read file length
+ * read file last modified date
+ * replicon file name
+ * replicon file length
+ * replicon file last modified date
+ * replicon FASTA header line
+ * replicon length
+ * average length of reads
+ * total reads
+ * invalid quality reads
+ * ambiguous reads
+ * low quality reads
+ * mapped once reads
+ * mapped more than once reads
+ * exact mapped reads
+ * inexact mapped reads
+ */
+ public static void writeCompressedFile(String outFileName, String readFileName, String repliconFileName, String repliconHeader, int repliconLength, int totalReads, int invalidQualityReads, int ambiguousReads, int lowQualityReads, int mappedOnceReads, int mappedMoreThanOnceReads, int exactMappedReads, int inexactMappedReads, long avgLengthReads, int[] a1, int[] a2) {
+ File readFile = new File(readFileName);
+ File repliconFile = new File(repliconFileName);
+ byte[] header = (Rockhopper.version + "\n" + readFile.getName() + "\n" + readFile.length() + "\n" + readFile.lastModified() + "\n" + repliconFile.getName() + "\n" + repliconFile.length() + "\n" + repliconFile.lastModified() + "\n" + repliconHeader + "\n" + repliconLength + "\n" + avgLengthReads + "\n" + totalReads + "\n" + invalidQualityReads + "\n" + ambiguousReads + "\n" + lowQualityReads + "\n" + mappedOnceReads + "\n" + mappedMoreThanOnceReads + "\n" + exactMappedReads + "\n" + inex [...]
+ byte[] b1 = intArrayToByteArray(a1);
+ byte[] b2 = intArrayToByteArray(a2);
+ try {
+ // Set up directory
+ File d = new File(DIR);
+ if (!d.isDirectory()) d.mkdir();
+ GZIPOutputStream gzos = new GZIPOutputStream(new FileOutputStream(DIR + outFileName + ".gz"));
+ gzos.write(header, 0, header.length);
+ gzos.write(b1, 0, b1.length);
+ gzos.write(b2, 0, b2.length);
+ gzos.close();
+ } catch (IOException e) {
+ Rockhopper.output("Could not write to file " + outFileName + ".gz" + "\n");
+ }
+ }
+
+ /**
+ * Writes a list of de novo assembled transcripts to a compressed file.
+ * The following header information is also written to the compressed file:
+ * version
+ * number of conditions
+ * number of replicates in each condition
+ * for each read file: its name, its length, and its last modified time
+ * number of files
+ * for each file: total reads, total mapping reads
+ * number of transcripts in list
+ * number of p-values per transcript
+ * for each transcript:
+ * sequence
+ * for each condition: rawCounts_nts, rawCounts_reads, normalizedCounts
+ * RPKMs, means, variances, lowess, pValues, qValues
+ */
+ public static void writeCompressedFile(String outFileName, ArrayList<String> conditionFiles, int[] numReads, int[] numMappingReads, DeNovoTranscripts transcripts) {
+
+ // Version, number of conditions, and number of replicates in each condition
+ StringBuilder header = new StringBuilder();
+ header.append(Rockhopper.version + "\n");
+ header.append(conditionFiles.size() + "\n");
+ for (int i=0; i<conditionFiles.size(); i++) {
+ header.append(conditionFiles.get(i).split(",").length + "\n");
+ }
+
+ // Name, length, and last modified time of each file (including mate-pair files)
+ for (int i=0; i<conditionFiles.size(); i++) {
+ String[] files = conditionFiles.get(i).split(",");
+ for (int j=0; j<files.length; j++) {
+ String[] parse_readFiles = files[j].split("%");
+ if (parse_readFiles.length == 1) { // Using single-end reads
+ String file1 = parse_readFiles[0];
+ File readFile = new File(file1);
+ header.append(readFile.getName() + "\n" + readFile.length() + "\n" + readFile.lastModified() + "\n");
+ } else { // Using paired-end reads
+ String file1 = parse_readFiles[0];
+ File readFile1 = new File(file1);
+ header.append(readFile1.getName() + "\n" + readFile1.length() + "\n" + readFile1.lastModified() + "\n");
+ String file2 = parse_readFiles[1];
+ File readFile2 = new File(file2);
+ header.append(readFile2.getName() + "\n" + readFile2.length() + "\n" + readFile2.lastModified() + "\n");
+ }
+ }
+ }
+
+ // Number of files. Total reads per file and total number of mapping reads per file
+ header.append(numReads.length + "\n");
+ for (int i=0; i<numReads.length; i++) header.append(numReads[i] + "\n" + numMappingReads[i] + "\n");
+
+ // Number of transcripts and number of p-values per transcript
+ header.append(transcripts.getNumTranscripts() + "\n");
+ if (transcripts.getNumTranscripts() == 0) header.append("0" + "\n");
+ else header.append(transcripts.getTranscript(0).getNumPvalues() + "\n");
+
+ // Write header information and information for each transcript
+ try {
+ // Set up directory
+ File d = new File(DIR);
+ if (!d.isDirectory()) d.mkdir();
+ GZIPOutputStream gzos = new GZIPOutputStream(new FileOutputStream(DIR + outFileName + ".gz"));
+ byte[] header_bytes = header.toString().getBytes();
+ gzos.write(header_bytes, 0, header_bytes.length);
+ for (int i=0; i<transcripts.getNumTranscripts(); i++) {
+ DeNovoTranscript transcript = transcripts.getTranscript(i);
+ byte[] b = (transcript.sequence() + "\n").getBytes(); // Add new line to sequence
+ gzos.write(b, 0, b.length);
+ for (int j=0; j<conditionFiles.size(); j++) {
+ b = longArrayToByteArray(transcript.getRawCounts_nts_array(j));
+ gzos.write(b, 0, b.length);
+ b = longArrayToByteArray(transcript.getRawCounts_reads_array(j));
+ gzos.write(b, 0, b.length);
+ b = longArrayToByteArray(transcript.getNormalizedCounts_array(j));
+ gzos.write(b, 0, b.length);
+ }
+ b = longArrayToByteArray(transcript.getRPKMs());
+ gzos.write(b, 0, b.length);
+ b = longArrayToByteArray(transcript.getMeans());
+ gzos.write(b, 0, b.length);
+ b = longArrayToByteArray(transcript.getVariances());
+ gzos.write(b, 0, b.length);
+ b = longArrayToByteArray(transcript.getLowess());
+ gzos.write(b, 0, b.length);
+ b = doubleArrayToByteArray(transcript.getPvalues());
+ gzos.write(b, 0, b.length);
+ b = doubleArrayToByteArray(transcript.getQvalues());
+ gzos.write(b, 0, b.length);
+ }
+ gzos.close();
+ } catch (IOException e) {
+ Rockhopper.output("Could not write to file " + outFileName + ".gz" + "\n");
+ }
+ }
+
+ /**
+ * Returns true is file is successfully read. False otherwise.
+ */
+ public boolean readCompressedFile(String inFileName) {
+ try {
+ GZIPInputStream in = new GZIPInputStream(new FileInputStream(DIR + inFileName + ".gz"));
+
+ // Read in header information
+ String version = getLine(in);
+ if (!version.equals(Rockhopper.version)) return false;
+ this.readFileName = getLine(in);
+ this.readFileLength = Long.parseLong(getLine(in));
+ this.readFileDate = Long.parseLong(getLine(in));
+ this.repliconFileName = getLine(in);
+ this.repliconFileLength = Long.parseLong(getLine(in));
+ this.repliconFileDate = Long.parseLong(getLine(in));
+ this.repliconHeader = getLine(in);
+ this.repliconLength = Integer.parseInt(getLine(in));
+ this.avgLengthReads = Long.parseLong(getLine(in));
+ this.totalReads = Integer.parseInt(getLine(in));
+ this.invalidQualityReads = Integer.parseInt(getLine(in));
+ this.ambiguousReads = Integer.parseInt(getLine(in));
+ this.lowQualityReads = Integer.parseInt(getLine(in));
+ this.mappedOnceReads = Integer.parseInt(getLine(in));
+ this.mappedMoreThanOnceReads = Integer.parseInt(getLine(in));
+ this.exactMappedReads = Integer.parseInt(getLine(in));
+ this.inexactMappedReads = Integer.parseInt(getLine(in));
+
+ // Retrieve data
+ this.coordinates_plus = new int[repliconLength];
+ for (int i=0; i<repliconLength; i++) coordinates_plus[i] = getInt(in);
+ this.coordinates_minus = new int[repliconLength];
+ for (int i=0; i<repliconLength; i++) coordinates_minus[i] = getInt(in);
+ in.close();
+ return true;
+ } catch (IOException e) {
+ return false;
+ }
+ }
+
+ /**
+ * Returns true is file is successfully read and is valid. False otherwise.
+ */
+ public boolean readCompressedFile_DeNovo(String inFileName, ArrayList<String> conditionFiles) {
+ try {
+
+ // Read in file
+ GZIPInputStream in = new GZIPInputStream(new FileInputStream(DIR + inFileName + ".gz"));
+ ArrayList<Byte> bytes = new ArrayList<Byte>(1000000);
+ byte[] buffer = new byte[1024];
+ int len;
+ while ((len = in.read(buffer)) >= 0) {
+ for (int i=0; i<len; i++)
+ bytes.add(buffer[i]);
+ }
+ in.close();
+
+ // First header line: version
+ int startIndex = 0;
+ int stopIndex = getStopIndex(bytes, startIndex);
+ String version = getLine(bytes, startIndex, stopIndex);
+ if (!version.equals(Rockhopper.version)) return false;
+
+ // Second header line: number of conditions
+ startIndex = stopIndex + 1;
+ stopIndex = getStopIndex(bytes, startIndex);
+ int numConditions = Integer.parseInt(getLine(bytes, startIndex, stopIndex));
+ startIndex = stopIndex + 1;
+
+ // One line for each condition indicating number of replicates in condition
+ int[] numReplicates = new int[numConditions];
+ for (int i=0; i<numConditions; i++) {
+ stopIndex = getStopIndex(bytes, startIndex);
+ numReplicates[i] = Integer.parseInt(getLine(bytes, startIndex, stopIndex));
+ startIndex = stopIndex + 1;
+ }
+
+ // For each read file, we have its name, length, and last modified time
+ String[][][] names = new String[2][numConditions][]; // First coordinate is mate-pair
+ long[][][] lengths = new long[2][numConditions][]; // First coordinate is mate-pair
+ long[][][] times = new long[2][numConditions][]; // First coordinate is mate-pair
+ for (int i=0; i<numConditions; i++) {
+ names[0][i] = new String[numReplicates[i]];
+ lengths[0][i] = new long[numReplicates[i]];
+ times[0][i] = new long[numReplicates[i]];
+ names[1][i] = new String[numReplicates[i]];
+ lengths[1][i] = new long[numReplicates[i]];
+ times[1][i] = new long[numReplicates[i]];
+ String[] files = conditionFiles.get(i).split(",");
+ for (int j=0; j<numReplicates[i]; j++) {
+ stopIndex = getStopIndex(bytes, startIndex);
+ names[0][i][j] = getLine(bytes, startIndex, stopIndex);
+ startIndex = stopIndex + 1;
+ stopIndex = getStopIndex(bytes, startIndex);
+ lengths[0][i][j] = Long.parseLong(getLine(bytes, startIndex, stopIndex));
+ startIndex = stopIndex + 1;
+ stopIndex = getStopIndex(bytes, startIndex);
+ times[0][i][j] = Long.parseLong(getLine(bytes, startIndex, stopIndex));
+ startIndex = stopIndex + 1;
+
+ // Handle mate-pair files, if any
+ String[] parse_readFiles = files[j].split("%");
+ if (parse_readFiles.length > 1) { // Using paired-end reads
+ stopIndex = getStopIndex(bytes, startIndex);
+ names[1][i][j] = getLine(bytes, startIndex, stopIndex);
+ startIndex = stopIndex + 1;
+ stopIndex = getStopIndex(bytes, startIndex);
+ lengths[1][i][j] = Long.parseLong(getLine(bytes, startIndex, stopIndex));
+ startIndex = stopIndex + 1;
+ stopIndex = getStopIndex(bytes, startIndex);
+ times[1][i][j] = Long.parseLong(getLine(bytes, startIndex, stopIndex));
+ startIndex = stopIndex + 1;
+ }
+ }
+ }
+
+ // Number of files. For each file, number of reads and number of mapping reads
+ stopIndex = getStopIndex(bytes, startIndex);
+ int numFiles = Integer.parseInt(getLine(bytes, startIndex, stopIndex));
+ startIndex = stopIndex + 1;
+ int[] numReads = new int[numFiles];
+ int[] numMappingReads = new int[numFiles];
+ for (int i=0; i<numFiles; i++) {
+ stopIndex = getStopIndex(bytes, startIndex);
+ numReads[i] = Integer.parseInt(getLine(bytes, startIndex, stopIndex));
+ startIndex = stopIndex + 1;
+ stopIndex = getStopIndex(bytes, startIndex);
+ numMappingReads[i] = Integer.parseInt(getLine(bytes, startIndex, stopIndex));
+ startIndex = stopIndex + 1;
+ }
+
+ // Final two header lines
+ stopIndex = getStopIndex(bytes, startIndex);
+ int numTranscripts = Integer.parseInt(getLine(bytes, startIndex, stopIndex));
+ startIndex = stopIndex + 1;
+ stopIndex = getStopIndex(bytes, startIndex);
+ int numPvalues = Integer.parseInt(getLine(bytes, startIndex, stopIndex));
+ startIndex = stopIndex + 1;
+
+ // Transcripts
+ ArrayList<DeNovoTranscript> transcripts = new ArrayList<DeNovoTranscript>(numTranscripts);
+ for (int i=0; i<numTranscripts; i++) { // For each transcript
+ stopIndex = getStopIndex(bytes, startIndex);
+ String sequence = getLine(bytes, startIndex, stopIndex);
+ startIndex = stopIndex + 1;
+ ArrayList<ArrayList<Long>> rawCounts_nts = new ArrayList<ArrayList<Long>>(numConditions);
+ ArrayList<ArrayList<Long>> rawCounts_reads = new ArrayList<ArrayList<Long>>(numConditions);
+ ArrayList<ArrayList<Long>> normalizedCounts = new ArrayList<ArrayList<Long>>(numConditions);
+ for (int j=0; j<numConditions; j++) {
+ byte[] tempData = new byte[numReplicates[j]*8];
+ for (int k=startIndex; k<startIndex+numReplicates[j]*8; k++) tempData[k-startIndex] = bytes.get(k).byteValue();
+ rawCounts_nts.add(byteToLongList(tempData));
+ startIndex += numReplicates[j]*8;
+ for (int k=startIndex; k<startIndex+numReplicates[j]*8; k++) tempData[k-startIndex] = bytes.get(k).byteValue();
+ rawCounts_reads.add(byteToLongList(tempData));
+ startIndex += numReplicates[j]*8;
+ for (int k=startIndex; k<startIndex+numReplicates[j]*8; k++) tempData[k-startIndex] = bytes.get(k).byteValue();
+ normalizedCounts.add(byteToLongList(tempData));
+ startIndex += numReplicates[j]*8;
+ }
+ byte[] tempData = new byte[numConditions*8];
+ for (int k=startIndex; k<startIndex+numConditions*8; k++) tempData[k-startIndex] = bytes.get(k).byteValue();
+ ArrayList<Long> RPKMs = byteToLongList(tempData);
+ startIndex += numConditions*8;
+ for (int k=startIndex; k<startIndex+numConditions*8; k++) tempData[k-startIndex] = bytes.get(k).byteValue();
+ ArrayList<Long> means = byteToLongList(tempData);
+ startIndex += numConditions*8;
+ tempData = new byte[numConditions*numConditions*8];
+ for (int k=startIndex; k<startIndex+numConditions*numConditions*8; k++) tempData[k-startIndex] = bytes.get(k).byteValue();
+ long[][] variances = byteToLong2Darray(tempData);
+ startIndex += numConditions*numConditions*8;
+ for (int k=startIndex; k<startIndex+numConditions*numConditions*8; k++) tempData[k-startIndex] = bytes.get(k).byteValue();
+ long[][] lowess = byteToLong2Darray(tempData);
+ startIndex += numConditions*numConditions*8;
+ tempData = new byte[numPvalues*8];
+ for (int k=startIndex; k<startIndex+numPvalues*8; k++) tempData[k-startIndex] = bytes.get(k).byteValue();
+ ArrayList<Double> pValues = byteToDoubleList(tempData);
+ startIndex += numPvalues*8;
+ for (int k=startIndex; k<startIndex+numPvalues*8; k++) tempData[k-startIndex] = bytes.get(k).byteValue();
+ ArrayList<Double> qValues = byteToDoubleList(tempData);
+ startIndex += numPvalues*8;
+ transcripts.add(new DeNovoTranscript(sequence, rawCounts_nts, rawCounts_reads, normalizedCounts, RPKMs, means, variances, lowess, pValues, qValues));
+ }
+
+ // Check validity
+ if (numConditions != conditionFiles.size()) return false;
+ for (int i=0; i<numConditions; i++) {
+ String[] files = conditionFiles.get(i).split(",");
+ if (numReplicates[i] != files.length) return false;
+ for (int j=0; j<numReplicates[i]; j++) {
+ String[] parse_readFiles = files[j].split("%");
+ if (parse_readFiles.length == 1) { // Using single-end reads
+ String file1 = parse_readFiles[0];
+ File f = new File(file1);
+ if (!names[0][i][j].equals(f.getName())) return false;
+ if (lengths[0][i][j] != f.length()) return false;
+ if (times[0][i][j] != f.lastModified()) return false;
+ } else { // Using paired-end reads
+ String file1 = parse_readFiles[0];
+ String file2 = parse_readFiles[1];
+ File f1 = new File(file1);
+ if (!names[0][i][j].equals(f1.getName())) return false;
+ if (lengths[0][i][j] != f1.length()) return false;
+ if (times[0][i][j] != f1.lastModified()) return false;
+ File f2 = new File(file2);
+ if (!names[1][i][j].equals(f2.getName())) return false;
+ if (lengths[1][i][j] != f2.length()) return false;
+ if (times[1][i][j] != f2.lastModified()) return false;
+ }
+ }
+ }
+ this.transcripts = transcripts;
+ DeNovoTranscripts.numReads = numReads;
+ DeNovoTranscripts.numMappingReads = numMappingReads;
+ return true;
+ } catch (Exception e) {
+ return false;
+ }
+ }
+
+ /**
+ * Returns true if the specified file is in gzip format.
+ * Returns false otherwise.
+ */
+ public static boolean isGZIP(String fileName) {
+ try {
+ GZIPInputStream in = new GZIPInputStream(new FileInputStream(fileName));
+ in.close();
+ return true;
+ } catch (Exception e) {
+ return false;
+ }
+ }
+
+
+
+ /**************************************************
+ ********** Private Instance Methods **********
+ **************************************************/
+
+ /**
+ * Returns the first index after the specified startIndex in the Byte list
+ * corresponding to a new line (end of line).
+ */
+ private int getStopIndex(ArrayList<Byte> bytes, int startIndex) {
+ int stopIndex = startIndex;
+ while ((stopIndex < bytes.size()) && (bytes.get(stopIndex).byteValue() != 10)) stopIndex++;
+ return stopIndex;
+ }
+
+ /**
+ * Returns a String corresponding to one line, i.e., the bytes from
+ * startIndex to stopIndex.
+ */
+ private String getLine(ArrayList<Byte> bytes, int startIndex, int stopIndex) {
+ // Convert sequence of bytes to a String representing a line
+ byte[] bytesInLine = new byte[stopIndex - startIndex];
+ for (int i=startIndex; i<stopIndex; i++) bytesInLine[i - startIndex] = bytes.get(i).byteValue();
+ return (new String(bytesInLine));
+ }
+
+
+
+ /***********************************************
+ ********** Private Class Methods **********
+ ***********************************************/
+
+ /**
+ * Returns one line from the specified input stream.
+ */
+ private static String getLine(GZIPInputStream in) {
+ try {
+ int len = -1;
+ ArrayList<Byte> buffer = new ArrayList<Byte>();
+ while (((len = in.read(buffer1)) >= 0) && (buffer1[0] != 10)) {
+ buffer.add(buffer1[0]);
+ }
+ byte[] buffer_bytes = new byte[buffer.size()];
+ for (int i=0; i<buffer.size(); i++) buffer_bytes[i] = buffer.get(i).byteValue();
+ return (new String(buffer_bytes));
+ } catch (IOException e) {
+ return "";
+ }
+ }
+
+ /**
+ * Returns one integer from the specified input stream.
+ */
+ private static int getInt(GZIPInputStream in) {
+ try {
+ int result = 0;
+ in.read(buffer1);
+ result += (buffer1[0] & 0xFF) << 24;
+ in.read(buffer1);
+ result += (buffer1[0] & 0xFF) << 16;
+ in.read(buffer1);
+ result += (buffer1[0] & 0xFF) << 8;
+ in.read(buffer1);
+ result += (buffer1[0] & 0xFF);
+ return result;
+ } catch (IOException e) {
+ return -1;
+ }
+ }
+
+ /**
+ * Returns a byte array representation of the specified int array.
+ */
+ private static byte[] intArrayToByteArray(int[] a) {
+ byte[] b = new byte[a.length*4];
+ for (int i=0; i<a.length; i++) {
+ b[4*i+0] = (byte)(a[i] >>> 24);
+ b[4*i+1] = (byte)(a[i] >>> 16);
+ b[4*i+2] = (byte)(a[i] >>> 8);
+ b[4*i+3] = (byte)(a[i] >>> 0);
+ }
+ return b;
+ }
+
+ /**
+ * Returns a byte array representation of the specified long array.
+ */
+ private static byte[] longArrayToByteArray(long[] a) {
+ byte[] b = new byte[a.length*8];
+ for (int i=0; i<a.length; i++) {
+ b[8*i+0] = (byte)(a[i] >>> 56);
+ b[8*i+1] = (byte)(a[i] >>> 48);
+ b[8*i+2] = (byte)(a[i] >>> 40);
+ b[8*i+3] = (byte)(a[i] >>> 32);
+ b[8*i+4] = (byte)(a[i] >>> 24);
+ b[8*i+5] = (byte)(a[i] >>> 16);
+ b[8*i+6] = (byte)(a[i] >>> 8);
+ b[8*i+7] = (byte)(a[i] >>> 0);
+ }
+ return b;
+ }
+
+ /**
+ * Returns a byte array representation of the specified double array.
+ */
+ private static byte[] doubleArrayToByteArray(double[] a) {
+ byte[] b = new byte[a.length*8];
+ for (int i=0; i<a.length; i++) {
+ b[8*i+0] = (byte)(Double.doubleToRawLongBits(a[i]) >>> 56);
+ b[8*i+1] = (byte)(Double.doubleToRawLongBits(a[i]) >>> 48);
+ b[8*i+2] = (byte)(Double.doubleToRawLongBits(a[i]) >>> 40);
+ b[8*i+3] = (byte)(Double.doubleToRawLongBits(a[i]) >>> 32);
+ b[8*i+4] = (byte)(Double.doubleToRawLongBits(a[i]) >>> 24);
+ b[8*i+5] = (byte)(Double.doubleToRawLongBits(a[i]) >>> 16);
+ b[8*i+6] = (byte)(Double.doubleToRawLongBits(a[i]) >>> 8);
+ b[8*i+7] = (byte)(Double.doubleToRawLongBits(a[i]) >>> 0);
+ }
+ return b;
+ }
+
+ /**
+ * Returns an int array representation of the specified byte array.
+ */
+ private static int[] byteToIntArray(byte[] b) {
+ int[] a = new int[b.length/4];
+ for (int i=0; i<b.length; i+=4) {
+ a[i/4] = (b[i+0] << 24) + ((b[i+1] & 0xFF) << 16) + ((b[i+2] & 0xFF) << 8) + (b[i+3] & 0xFF);
+ }
+ return a;
+ }
+
+ /**
+ * Returns a long list representation of the specified byte array.
+ */
+ private static ArrayList<Long> byteToLongList(byte[] b) {
+ ArrayList<Long> a = new ArrayList<Long>(b.length/8);
+ for (int i=0; i<b.length; i+=8) {
+ a.add(((long)(b[i+0] & 0xFF) << 56) | ((long)(b[i+1] & 0xFF) << 48) | ((long)(b[i+2] & 0xFF) << 40) | ((long)(b[i+3] & 0xFF) << 32) | ((long)(b[i+4] & 0xFF) << 24) | ((long)(b[i+5] & 0xFF) << 16) | ((long)(b[i+6] & 0xFF) << 8) | ((long)(b[i+7] & 0xFF) << 0));
+ }
+ return a;
+ }
+
+ /**
+ * Returns a double list representation of the specified byte array.
+ */
+ private static ArrayList<Double> byteToDoubleList(byte[] b) {
+ ArrayList<Double> a = new ArrayList<Double>(b.length/8);
+ for (int i=0; i<b.length; i+=8) {
+ a.add(Double.longBitsToDouble(((long)(b[i+0] & 0xFF) << 56) | ((long)(b[i+1] & 0xFF) << 48) | ((long)(b[i+2] & 0xFF) << 40) | ((long)(b[i+3] & 0xFF) << 32) | ((long)(b[i+4] & 0xFF) << 24) | ((long)(b[i+5] & 0xFF) << 16) | ((long)(b[i+6] & 0xFF) << 8) | ((long)(b[i+7] & 0xFF) << 0)));
+ }
+ return a;
+ }
+
+ /**
+ * Returns a 2D long array representation of the specified byte array.
+ */
+ private static long[][] byteToLong2Darray(byte[] b) {
+ ArrayList<Long> a = byteToLongList(b);
+
+ // Convert 1D long list into 2D long array
+ int size = (int)(Math.sqrt(a.size()));
+ long[][] c = new long[size][size];
+ int index = 0;
+ for (int x=0; x<size; x++) {
+ for (int y=0; y<size; y++) {
+ c[x][y] = a.get(index);
+ index++;
+ }
+ }
+ return c;
+ }
+
+
+
+ /*************************************
+ ********** Main Method **********
+ *************************************/
+
+ public static void main(String[] args) {
+
+ }
+
+}
+
diff --git a/Gene.java b/Gene.java
new file mode 100644
index 0000000..1a1cae4
--- /dev/null
+++ b/Gene.java
@@ -0,0 +1,787 @@
+/*
+ * Copyright 2013 Brian Tjaden
+ *
+ * This file is part of Rockhopper.
+ *
+ * Rockhopper is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * any later version.
+ *
+ * Rockhopper is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * (in the file gpl.txt) along with Rockhopper.
+ * If not, see <http://www.gnu.org/licenses/>.
+ */
+
+import java.util.ArrayList;
+import java.util.Random;
+import java.util.Collections;
+
+/**
+ * A Gene object represents a gene (either protein-coding or RNA).
+ * A Gene object consists of a variety of data about a gene,
+ * including its coordinates, strand, name, product, and
+ * expression information in each replicate (raw counts mapping
+ * to gene and normalized counts mapping to gene) or in each
+ * condition (mean, variance, lowess, RPKM) or in a pair of
+ * conditions (p-value of differential expression).
+ */
+public class Gene {
+
+ /*****************************************
+ ********** CLASS VARIABLES **********
+ *****************************************/
+
+ private static Random rand = new Random(); // Random number generator
+
+
+
+ /********************************************
+ ********** INSTANCE VARIABLES **********
+ ********************************************/
+
+ private int start; // Translation start
+ private int stop; // Translation stop
+ private char strand;
+ private String ID;
+ private String name;
+ private String synonym;
+ private String product;
+ private String type; // ORF or RNA
+ private int tStart; // Transcription start
+ private int tStop; // Transcription stop
+
+ private ArrayList<ArrayList<Long>> rawCounts; // Reads mapping to each NT of gene
+ private ArrayList<ArrayList<Long>> rawCounts_reads; // Reads mapping to gene
+ private ArrayList<ArrayList<Long>> normalizedCounts;
+ private ArrayList<Long> RPKMs;
+ private ArrayList<Long> means;
+ private long[][] variances; // 2D array
+ private long[][] lowess; // 2D array
+ private ArrayList<Double> pValues; // Differential expression
+ private ArrayList<Double> qValues; // Differential expression (corrected)
+
+
+
+ /**************************************
+ ********** CONSTRUCTORS **********
+ **************************************/
+
+ /**
+ * Constructs a new Genome object based on a line from a
+ * gene file (either *.ptt or *.rnt).
+ */
+ public Gene(String line, String type) {
+ String[] parse_line = line.split("\t");
+ if (parse_line.length < 9) {
+ Rockhopper.output("Error - expecting 9 columns of gene information but found less than 9:\t" + line + "\n");
+ return;
+ }
+ String[] parse_coords = parse_line[0].split("\\.");
+ this.type = type;
+ this.strand = parse_line[1].charAt(0);
+ this.ID = parse_line[3];
+ this.name = parse_line[4];
+ this.synonym = parse_line[5];
+ this.product = parse_line[8];
+
+ // Set coordinates based on strand and type
+ int x = Integer.parseInt(parse_coords[0]); // First coord
+ int y = Integer.parseInt(parse_coords[2]); // Second coord
+ if (type.equals("ORF") && (strand == '+')) { // Plus strand ORF
+ start = x;
+ stop = y;
+ tStart = 0;
+ tStop = 0;
+ } else if (type.equals("ORF") && (strand == '-')) { // Minus strand ORF
+ start = y;
+ stop = x;
+ tStart = 0;
+ tStop = 0;
+ } else if (type.equals("RNA") && (strand == '+')) { // Plus strand RNA
+ start = 0;
+ stop = 0;
+ tStart = x;
+ tStop = y;
+ } else if (type.equals("RNA") && (strand == '-')) { // Minus strand RNA
+ start = 0;
+ stop = 0;
+ tStart = y;
+ tStop = x;
+ } else if (type.equals("RNA") && (strand == '?')) { // Ambiguous strand RNA
+ start = 0;
+ stop = 0;
+ tStart = x;
+ tStop = y;
+ } else
+ Rockhopper.output("Error - this case should be unreachable!\n");
+ }
+
+
+
+ /*************************************************
+ ********** PUBLIC INSTANCE METHODS **********
+ *************************************************/
+
+ /**
+ * Return the gene's strand.
+ */
+ public char getStrand() {
+ return strand;
+ }
+
+ /**
+ * Return the gene's start coordinate of translation.
+ */
+ public int getStart() {
+ return start;
+ }
+
+ /**
+ * Return the gene's stop coordinate of translation.
+ */
+ public int getStop() {
+ return stop;
+ }
+
+ /**
+ * Reeturn the gene's name.
+ */
+ public String getName() {
+ if (name.length() > 1) return name;
+ return synonym;
+ }
+
+ /**
+ * Returns true if this gene is a protein coding gene,
+ * false otherwise.
+ */
+ public boolean isORF() {
+ return type.equals("ORF");
+ }
+
+ /**
+ * Returns this gene's product.
+ */
+ public String getProduct() {
+ return product;
+ }
+
+ /**
+ * Set the transcription start coordinate.
+ */
+ public void setStartT(int tStart) {
+ this.tStart = tStart;
+ }
+
+ /**
+ * Set the transcription stop coordinate.
+ */
+ public void setStopT(int tStop) {
+ this.tStop = tStop;
+ }
+
+ /**
+ * Return the gene's start coordinate of transcription.
+ */
+ public int getStartT() {
+ return this.tStart;
+ }
+
+ /**
+ * Return the gene's stop coordinate of transcription.
+ */
+ public int getStopT() {
+ return this.tStop;
+ }
+
+ /**
+ * Returns the first (smallest) coordinate of this Gene.
+ * If this Gene is an ORF it returns the smallest translation coordinate.
+ * If this Gene is an RNA it returns the smallest transcription coordinate.
+ */
+ public int getFirst() {
+ if (isORF()) return Math.min(start, stop);
+ return Math.min(tStart, tStop);
+ }
+
+ /**
+ * Returns the last (largest) coordinate of this Gene.
+ * If this Gene is an ORF it returns the largest translation coordinate.
+ * If this Gene is an RNA it returns the largest transcription coordinate.
+ */
+ public int getLast() {
+ if (isORF()) return Math.max(start, stop);
+ return Math.max(tStart, tStop);
+ }
+
+ /**
+ * Return the number of reads mapping to the gene in the
+ * specified condition and specified replicate.
+ */
+ public long getRawCount(int condition, int replicate) {
+ if (condition < rawCounts.size()) {
+ if (replicate < rawCounts.get(condition).size())
+ return rawCounts.get(condition).get(replicate);
+ }
+ return 0;
+ }
+
+ /**
+ * Return the number of reads mapping to the gene in the
+ * specified condition and specified replicate.
+ */
+ public long getRawCount_reads(int condition, int replicate) {
+ if (condition < rawCounts_reads.size()) {
+ if (replicate < rawCounts_reads.get(condition).size())
+ return rawCounts_reads.get(condition).get(replicate);
+ }
+ return 0;
+ }
+
+ /**
+ * Return the normalized number of reads mapping to the gene in the
+ * specified condition and specified replicate.
+ */
+ public long getNormalizedCount(int condition, int replicate) {
+ if (condition < normalizedCounts.size()) {
+ if (replicate < normalizedCounts.get(condition).size())
+ return normalizedCounts.get(condition).get(replicate);
+ }
+ return 0;
+ }
+
+ /**
+ * Return the mean reads mapping to the gene in the
+ * specified condition.
+ */
+ public long getMean(int condition) {
+ if (condition < means.size())
+ return means.get(condition);
+ return 0;
+ }
+
+ /**
+ * Returns the average expression of the gene (averaged
+ * over the length of the gene) in the specified
+ * condition.
+ */
+ public long getAvg(int condition) {
+ long avg = 0;
+ if (type.compareTo("ORF") == 0)
+ avg = means.get(condition)/(Math.max(this.start,this.stop)-Math.min(this.start,this.stop)+1);
+ if (type.compareTo("RNA") == 0)
+ avg = means.get(condition)/(Math.max(this.tStart,this.tStop)-Math.min(this.tStart,this.tStop)+1);
+ return avg;
+ }
+
+ /**
+ * Return the number of replicates in the specified condition.
+ */
+ public int getNumReplicates(int condition) {
+ if (condition >= rawCounts.size()) return 0;
+ else return rawCounts.get(condition).size();
+ }
+
+ /**
+ * Returns the minimum q-value for this Gene.
+ */
+ public double getMinQvalue() {
+ double min = 1.0;
+ for (int i=0; i<qValues.size(); i++) min = Math.min(min, qValues.get(i));
+ return min;
+ }
+
+ public boolean hasQvalue(int c) {
+ return ((qValues != null) && (qValues.size() > c));
+ }
+
+ /**
+ * Returns a String representation of a a Gene's expression
+ * in each condition and p-values of differential expression.
+ */
+ public String expressionToString() {
+ StringBuilder sb = new StringBuilder();
+ for (int i=0; i<means.size(); i++) {
+ if (Rockhopper.verbose) { // Verbose output
+ for (int j=0; j<rawCounts.get(i).size(); j++)
+ sb.append("\t" + rawCounts_reads.get(i).get(j));
+ for (int j=0; j<normalizedCounts.get(i).size(); j++)
+ sb.append("\t" + normalizedCounts.get(i).get(j));
+ sb.append("\t" + RPKMs.get(i));
+ }
+ sb.append("\t" + getAvg(i));
+ }
+ for (int i=0; i<qValues.size(); i++) {
+ if (Rockhopper.verbose) sb.append("\t" + pValues.get(i).toString());
+ sb.append("\t" + qValues.get(i).toString());
+ }
+ return sb.toString();
+ }
+
+ /**
+ * Returns a String representation of a Gene.
+ */
+ public String toString() {
+ StringBuilder sb = new StringBuilder();
+ String tStart = "";
+ String start = "";
+ String stop = "";
+ String tStop = "";
+ if (this.tStart > 0) tStart += this.tStart;
+ if (this.start > 0) start += this.start;
+ if (this.stop > 0) stop += this.stop;
+ if (this.tStop > 0) tStop += this.tStop;
+ sb.append(tStart + "\t" + start + "\t" + stop + "\t" + tStop + "\t" + strand + "\t" + name + "\t" + synonym + "\t" + product);
+ return sb.toString();
+ }
+
+ /**
+ * Returns the coordinate (among transcription start/stop coordinates
+ * and translation start/stop coordinates) with minimum value.
+ */
+ public int getMinCoordinate() {
+ int minCoord = Integer.MAX_VALUE;
+ if (tStart > 0) minCoord = Math.min(minCoord, tStart);
+ if (start > 0) minCoord = Math.min(minCoord, start);
+ if (stop > 0) minCoord = Math.min(minCoord, stop);
+ if (tStop > 0) minCoord = Math.min(minCoord, tStop);
+ return minCoord;
+ }
+
+ /**
+ * Returns the coordinate (among transcription start/stop coordinates
+ * and translation start/stop coordinates) with maximum value.
+ */
+ public int getMaxCoordinate() {
+ int maxCoord = -1;
+ if (tStart > 0) maxCoord = Math.max(maxCoord, tStart);
+ if (start > 0) maxCoord = Math.max(maxCoord, start);
+ if (stop > 0) maxCoord = Math.max(maxCoord, stop);
+ if (tStop > 0) maxCoord = Math.max(maxCoord, tStop);
+ return maxCoord;
+ }
+
+ /**
+ * Set the number of reads mapping to this Gene in the specified
+ * replicate in the specified condition.
+ */
+ public void setRawCount(int condition, int replicate, long readsForGene) {
+ // Initialize instance variables
+ if (rawCounts == null) {
+ rawCounts = new ArrayList<ArrayList<Long>>();
+ rawCounts_reads = new ArrayList<ArrayList<Long>>();
+ normalizedCounts = new ArrayList<ArrayList<Long>>();
+ RPKMs = new ArrayList<Long>();
+ means = new ArrayList<Long>();
+ }
+ while (rawCounts.size() < condition+1) {
+ rawCounts.add(new ArrayList<Long>());
+ rawCounts_reads.add(new ArrayList<Long>());
+ normalizedCounts.add(new ArrayList<Long>());
+ RPKMs.add((long)0);
+ means.add((long)0);
+ }
+ while (rawCounts.get(condition).size() < replicate+1) {
+ rawCounts.get(condition).add((long)0);
+ rawCounts_reads.get(condition).add((long)0);
+ normalizedCounts.get(condition).add((long)0);
+ }
+
+ // Populate rawCounts
+ rawCounts.get(condition).set(replicate, readsForGene);
+ }
+
+ /**
+ * Set the number of reads mapping to this Gene in the specified
+ * replicate in the specified condition.
+ */
+ public void setRawCount_reads(int condition, int replicate, long readsForGene) {
+ if (condition < normalizedCounts.size()) {
+ if (replicate < normalizedCounts.get(condition).size()) {
+ rawCounts_reads.get(condition).set(replicate, readsForGene);
+ }
+ }
+ }
+
+ /**
+ * Set the normalized number of reads mapping to this Gene in the specified
+ * replicate in the specified condition.
+ */
+ public void setNormalizedCount(int condition, int replicate, double scalingFactor, long upperQuartile) {
+ if (condition < normalizedCounts.size()) {
+ if (replicate < normalizedCounts.get(condition).size()) {
+ double multiplier = scalingFactor / (double)upperQuartile;
+ long normalizedCount = (long)(multiplier * getRawCount(condition, replicate));
+ normalizedCounts.get(condition).set(replicate, normalizedCount);
+ }
+ }
+ }
+
+ /**
+ * For each condition, across all replicates of the conditions, compute
+ * the mean and RPKM for this Gene.
+ */
+ public void computeExpression(ArrayList<Condition> conditions) {
+ for (int i=0; i<means.size(); i++) { // For each condition
+
+ // Compute RPKM and mean
+ long sumRawCounts = 0;
+ long totalCounts = 0;
+ long mean = 0;
+ for (int j=0; j<rawCounts.get(i).size(); j++) {
+ sumRawCounts += rawCounts.get(i).get(j);
+ totalCounts += conditions.get(i).getReplicate(j).getTotalReads();
+ mean += normalizedCounts.get(i).get(j);
+ }
+ sumRawCounts /= rawCounts.get(i).size();
+ totalCounts /= rawCounts.get(i).size();
+ mean /= normalizedCounts.get(i).size();
+ if (totalCounts == 0) RPKMs.set(i, (long)0); // Avoid divide-by-zero error
+ else RPKMs.set(i, (long)(1000000000 * sumRawCounts / (totalCounts * (getMaxCoordinate()-getMinCoordinate()+1))));
+ means.set(i, mean);
+ }
+ }
+
+ /**
+ * For each condition, across all replicates of the conditions, compute
+ * the variance for this Gene.
+ */
+ public void computeVariance(ArrayList<Condition> conditions) {
+ double varianceAdjustmentNoReplicates = 1.10;
+ double varianceAdjustmentReplicates = 1.20;
+ variances = new long[conditions.size()][conditions.size()];
+ lowess = new long[conditions.size()][conditions.size()];
+
+ for (int x=0; x<conditions.size(); x++) { // First of pair
+ for (int y=0; y<conditions.size(); y++) { // Second of pair
+
+ if (x == y) continue; // No need to compute variance with self
+
+ if (conditions.get(x).numReplicates() == 1) { // No replicates. Use partner surrogate.
+ int partner = y;
+ long mean = (means.get(x) + means.get(partner)) / 2;
+ long variance = ((means.get(x)-mean)*(means.get(x)-mean) + (means.get(partner)-mean)*(means.get(partner)-mean)) / 1; // Sample standard deviation
+ variances[x][y] = (long)Math.pow(variance, varianceAdjustmentNoReplicates);
+ } else { // We have replicates. Use the replicates to compute the variance.
+ long variance = 0;
+ for (int j=0; j<conditions.get(x).numReplicates(); j++) {
+ variance += (long)(normalizedCounts.get(x).get(j) - means.get(x)) * (long)(normalizedCounts.get(x).get(j) - means.get(x));
+ }
+ variance /= (conditions.get(x).numReplicates() - 1); // Sample standard deviation
+ variances[x][y] = (long)Math.pow(variance, varianceAdjustmentReplicates);
+ }
+ }
+ }
+ }
+
+ /**
+ * For each pair of conditions, compute the p-value of differntial
+ * expression for this Gene.
+ */
+ public void computeDifferentialExpression() {
+ pValues = new ArrayList<Double>();
+ qValues = new ArrayList<Double>();
+ for (int x=0; x<normalizedCounts.size()-1; x++) { // First of two conditions
+ for (int y=x+1; y<normalizedCounts.size(); y++) { // Second of two conditions
+
+ double k_A = 0.0;
+ double k_B = 0.0;
+ for (int j=0; j<normalizedCounts.get(x).size(); j++) k_A += normalizedCounts.get(x).get(j);
+ for (int j=0; j<normalizedCounts.get(y).size(); j++) k_B += normalizedCounts.get(y).get(j);
+
+ if (normalizedCounts.get(x).size() < normalizedCounts.get(y).size())
+ k_B *= normalizedCounts.get(x).size() / (double)(normalizedCounts.get(y).size());
+ else if (normalizedCounts.get(x).size() > normalizedCounts.get(y).size())
+ k_A *= normalizedCounts.get(y).size() / (double)(normalizedCounts.get(x).size());
+
+ double q = k_A + k_B;
+
+ double mean_A = q;
+ double mean_B = q;
+ double variance_A = lowess[x][y];
+ double variance_B = lowess[y][x];
+
+ double p_a = mean_A / variance_A;
+ double p_b = mean_B / variance_B;
+ double r_a = Math.max(mean_A*mean_A / (variance_A - mean_A), 1.0); // r should not be < 1
+ double r_b = Math.max(mean_B*mean_B / (variance_B - mean_B), 1.0); // r should not be < 1
+
+ if ((p_a < 0.0) || (p_b < 0.0) || (p_a > 1.0) || (p_b > 1.0) || (variance_A == 0.0) || (variance_B == 0.0)) {
+ pValues.add(1.0);
+ qValues.add(1.0);
+ continue;
+ }
+
+ // Compute p-value of differential expression in two conditions
+ double p_ab = NegativeBinomial.pmf(r_a-1, k_A+r_a-1, p_a) * NegativeBinomial.pmf(r_b-1, k_B+r_b-1, p_b);
+ long k_sum = (long)(k_A + k_B);
+
+ // Fast p-value estimation
+ double numerator = 0.0;
+ double denominator = 0.0;
+ long mode = (long)k_B;
+
+ long a = mode; // Begin near middle
+ long increment = 1;
+ long alpha = 1000; // Number of times we increment by 1 (raising alpha raises precision but slows down computation)
+ double previous_p = 0.0;
+ while (a <= k_sum) {
+ long b = k_sum - a;
+ double current_p = NegativeBinomial.pmf(r_a-1, a+r_a-1, p_a) * NegativeBinomial.pmf(r_b-1, b+r_b-1, p_b);
+ denominator += current_p;
+ if (current_p <= p_ab) numerator += current_p;
+ if (increment > 1) {
+ double average_p = (current_p+previous_p)/2.0;
+ denominator += average_p * (increment-1);
+ if (average_p <= p_ab) numerator += average_p * (increment-1);
+ }
+ previous_p = current_p;
+ if (a - mode >= alpha) {
+ alpha *= 2;
+ increment *= 2;
+ }
+ a += increment;
+ }
+ a = mode; // Begin near middle
+ long decrement = 1;
+ alpha = 1000; // Number of times we increment by 1 (raising alpha raises precision but slows down computation)
+ previous_p = 0.0;
+ while (a >= 0) {
+ long b = k_sum - a;
+ double current_p = NegativeBinomial.pmf(r_a-1, a+r_a-1, p_a) * NegativeBinomial.pmf(r_b-1, b+r_b-1, p_b);
+ denominator += current_p;
+ if (current_p <= p_ab) numerator += current_p;
+ if (decrement > 1) {
+ double average_p = (previous_p + current_p) / 2.0;
+ denominator += average_p * (decrement-1);
+ if (average_p <= p_ab) numerator += average_p * (decrement-1);
+ }
+ previous_p = current_p;
+ if (mode - a >= alpha) {
+ alpha *= 2;
+ decrement *= 2;
+ }
+ a -= decrement;
+ }
+ double p_value = 1.0;
+ if (denominator != 0.0) p_value = numerator / denominator;
+ pValues.add(p_value);
+ qValues.add(1.0);
+ }
+ }
+ }
+
+ /**
+ * Returns true is this Gene is an ORF and if it is differentially
+ * expressed in at least one pair of conditions at the specified
+ * significance level. Returns false otherwise.
+ */
+ public boolean isDifferntiallyExpressedORF(double significance) {
+ if (!isORF()) return false;
+ for (int i=0; i<qValues.size(); i++) {
+ if (qValues.get(i) <= significance) return true;
+ }
+ return false;
+ }
+
+
+
+ /**********************************************
+ ********** PUBLIC CLASS METHODS **********
+ **********************************************/
+
+ /**
+ * Computes the Lowess variance for each Gene in the Genome.
+ */
+ public static void setLowessVariances(ArrayList<Genome> genomes, ArrayList<Condition> conditions) {
+ for (int x=0; x<conditions.size(); x++) { // First of pair
+ for (int y=0; y<conditions.size(); y++) { // Second of pair
+
+ if (x == y) continue; // No need to compute lowess for self
+ /*
+ if ((x > 0) && (conditions.get(x).numReplicates() > 1)) { // We have replicates
+ for (int z=0; z<genomes.size(); z++) {
+ Genome genome = genomes.get(z);
+ for (int j=0; j<genome.numGenes(); j++)
+ genome.getGene(j).lowess[x][y] = genome.getGene(j).lowess[0][y];
+ }
+ continue;
+ }
+ */
+ /* (x,y) lowess is NOT the same as (y,x) lowess
+ if ((x > y) && (conditions.get(x).numReplicates() == 1) && (conditions.get(y).numReplicates() == 1)) { // Already computed lowess[y][x], which is same as lowess[x][y]
+ for (int z=0; z<genomes.size(); z++) {
+ Genome genome = genomes.get(z);
+ for (int j=0; j<genome.numGenes(); j++)
+ genome.getGene(j).lowess[x][y] = genome.getGene(j).lowess[y][x];
+ }
+ continue;
+ }
+ */
+
+ double b = 0.0; // Bias correction term
+ for (int j=0; j<conditions.get(x).numReplicates(); j++) {
+ b += 100000.0 / (double)conditions.get(x).getReplicate(j).getUpperQuartile();
+ }
+ b /= conditions.get(x).numReplicates();
+
+ // Create list of gene expressions and list of gene variances
+ ArrayList<Long> expression = new ArrayList<Long>();
+ ArrayList<Long> variance = new ArrayList<Long>();
+ for (int z=0; z<genomes.size(); z++) {
+ Genome genome = genomes.get(z);
+ for (int j=0; j<genome.numGenes(); j++) {
+ expression.add(genome.getGene(j).means.get(x));
+ variance.add(genome.getGene(j).variances[x][y]);
+ }
+ }
+
+ // Perform Lowess computation
+ ArrayList<Long> lowessVariance = Lowess.lowess(expression, variance);
+
+ // Uncomment to output data for Lowess graph to StdOut
+ //System.out.println("Mean" + "\t" + "Variance" + "\t" + "Lowess");
+ //for (int k=0; k<lowessVariance.size(); k++) System.out.println(expression.get(k) + "\t" + variance.get(k) + "\t" + ((long)(lowessVariance.get(k) - expression.get(k)*b)));
+
+ // Assign each gene its lowess variances (after subtracting bias correction term)
+ int previousGenomeSizes = 0;
+ for (int z=0; z<genomes.size(); z++) {
+ Genome genome = genomes.get(z);
+ for (int j=0; j<genome.numGenes(); j++)
+ genome.getGene(j).lowess[x][y] = (long)(lowessVariance.get(previousGenomeSizes + j) - (genome.getGene(j).getMean(x) * b));
+ previousGenomeSizes += genome.numGenes();
+ }
+ }
+ }
+ }
+
+ /**
+ * Computes q-values for each gene, i.e., corrected p-values,
+ * using Benjamini Hochberg correction.
+ */
+ public static void correctPvalues(ArrayList<Genome> genomes, ArrayList<Condition> conditions) {
+ int totalGenes = 0;
+ for (int z=0; z<genomes.size(); z++) totalGenes += genomes.get(z).numGenes();
+
+ int pValue_index = 0;
+ for (int x=0; x<genomes.get(0).getGene(0).means.size()-1; x++) { // First in pair
+ for (int y=x+1; y<genomes.get(0).getGene(0).means.size(); y++) { // Second in pair
+
+ int[] indices = new int[totalGenes];
+ int[] genomeIndices = new int[totalGenes];
+ double[] pvalues = new double[totalGenes];
+ int previousGenomeSizes = 0;
+ for (int z=0; z<genomes.size(); z++) {
+ Genome genome = genomes.get(z);
+ for (int j=0; j<genome.numGenes(); j++) {
+ pvalues[previousGenomeSizes + j] = genome.getGene(j).pValues.get(pValue_index);
+ indices[previousGenomeSizes + j] = j;
+ genomeIndices[previousGenomeSizes + j] = z;
+
+ // Check if there is too little expression to compute a p-value
+ Gene g = genome.getGene(j);
+ double e1 = g.means.get(x);
+ double e2 = g.means.get(y);
+ if (g.isORF()) { // ORF
+ e1 /= Math.max(g.start, g.stop) - Math.min(g.start, g.stop) + 1;
+ e2 /= Math.max(g.start, g.stop) - Math.min(g.start, g.stop) + 1;
+ } else { // RNA
+ e1 /= Math.max(g.tStart, g.tStop) - Math.min(g.tStart, g.tStop) + 1;
+ e2 /= Math.max(g.tStart, g.tStop) - Math.min(g.tStart, g.tStop) + 1;
+ }
+ if ((e1 < conditions.get(x).getMinDiffExpressionLevel()) &&
+ (e2 < conditions.get(y).getMinDiffExpressionLevel()))
+ pvalues[previousGenomeSizes + j] = 1.0;
+ }
+ previousGenomeSizes += genome.numGenes();
+ }
+ mergesort(pvalues, indices, genomeIndices, 0, totalGenes-1);
+ double previous_BH_value = 0.0;
+ for (int k=0; k<pvalues.length; k++) {
+ double BH_value = pvalues[k] * totalGenes / (k+1);
+ BH_value = Math.min(BH_value, 1.0); // Disallow values greater than 1
+
+ // To preserve monotonicity, we take maximum to ensure we don't
+ // generate a value less than the previous value.
+ BH_value = Math.max(BH_value, previous_BH_value);
+ previous_BH_value = BH_value;
+ genomes.get(genomeIndices[k]).getGene(indices[k]).qValues.set(pValue_index, BH_value);
+ }
+ pValue_index++;
+ }
+ }
+ }
+
+
+
+ /***********************************************
+ ********** PRIVATE CLASS METHODS **********
+ ***********************************************/
+
+ /**
+ * Mergesort parallel arrays "a" and "b" and "c" based on values in "a"
+ */
+ private static void mergesort(double[] a, int[] b, int[] c, int lo, int hi) {
+ if (lo < hi) {
+ int q = (lo+hi)/2;
+ mergesort(a, b, c, lo, q);
+ mergesort(a, b, c, q+1, hi);
+ merge(a, b, c, lo, q, hi);
+ }
+ }
+
+ /**
+ * Mergesort helper method
+ */
+ private static void merge(double[] a, int[] b, int[] c, int lo, int q, int hi) {
+ double[] a1 = new double[q-lo+1];
+ double[] a2 = new double[hi-q];
+ int[] b1 = new int[q-lo+1];
+ int[] b2 = new int[hi-q];
+ int[] c1 = new int[q-lo+1];
+ int[] c2 = new int[hi-q];
+ for (int i=0; i<a1.length; i++) {
+ a1[i] = a[lo+i];
+ b1[i] = b[lo+i];
+ c1[i] = c[lo+i];
+ }
+ for (int j=0; j<a2.length; j++) {
+ a2[j] = a[q+1+j];
+ b2[j] = b[q+1+j];
+ c2[j] = c[q+1+j];
+ }
+ int i=0; // Index for first half arrays
+ int j=0; // Index for second half arrays
+ for (int k=lo; k<=hi; k++) {
+ if (i >= a1.length) {
+ a[k] = a2[j];
+ b[k] = b2[j];
+ c[k] = c2[j];
+ j++;
+ } else if (j >= a2.length) {
+ a[k] = a1[i];
+ b[k] = b1[i];
+ c[k] = c1[i];
+ i++;
+ } else if (a1[i] <= a2[j]) {
+ a[k] = a1[i];
+ b[k] = b1[i];
+ c[k] = c1[i];
+ i++;
+ } else {
+ a[k] = a2[j];
+ b[k] = b2[j];
+ c[k] = c2[j];
+ j++;
+ }
+ }
+ }
+
+}
+
diff --git a/Genome.java b/Genome.java
new file mode 100644
index 0000000..5c41db2
--- /dev/null
+++ b/Genome.java
@@ -0,0 +1,420 @@
+/*
+ * Copyright 2013 Brian Tjaden
+ *
+ * This file is part of Rockhopper.
+ *
+ * Rockhopper is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * any later version.
+ *
+ * Rockhopper is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * (in the file gpl.txt) along with Rockhopper.
+ * If not, see <http://www.gnu.org/licenses/>.
+ */
+
+import java.util.ArrayList;
+import java.util.Scanner;
+import java.io.PrintWriter;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+
+/**
+ * An instance of the Genome class represents a genome and its
+ * annotation, including the genome sequence, protein-coding
+ * genes, and RNA genes in the genome.
+ */
+public class Genome {
+
+ /********************************************
+ ********** INSTANCE VARIABLES **********
+ ********************************************/
+
+ private String ID;
+ private String name;
+ private String genome; // We add a '?' character so it is 1-indexed
+ private String formalGenomeName = ""; // First token of FASTA header line, e.g., gi|49175990|ref|NC_000913.2|
+ private String baseFileName = ""; // Path and name of genome file sans .fna extension
+ private ArrayList<Gene> codingGenes = new ArrayList<Gene>();
+ private ArrayList<Gene> rnas = new ArrayList<Gene>();
+ private ArrayList<Gene> genes = new ArrayList<Gene>(); // Merged coding genes and RNAs
+
+
+
+ /**************************************
+ ********** CONSTRUCTORS **********
+ **************************************/
+
+ /**
+ * Constructs a new Genome object based on files in the specified
+ * directory (e.g., genome.fna, genes.ptt, rna.rnt).
+ */
+ public Genome(String directory) {
+ String genomeFileName = null;
+ String geneFileName = null;
+ String rnaFileName = null;
+
+ if (!directory.endsWith("/")) directory += "/";
+ File dir = new File(directory);
+ String[] files = dir.list();
+ for (int i=0; i<files.length; i++) {
+ if (files[i].endsWith(".fna")) genomeFileName = files[i];
+ if (files[i].endsWith(".ptt")) geneFileName = files[i];
+ if (files[i].endsWith(".rnt")) rnaFileName = files[i];
+ }
+
+ if (genomeFileName != null) readInGenome(directory + genomeFileName);
+ if (geneFileName != null) this.codingGenes = readInGenes(directory + geneFileName, "ORF");
+ if (rnaFileName != null) this.rnas = readInGenes(directory + rnaFileName, "RNA");
+ this.genes = mergeGenes(this.codingGenes, this.rnas);
+ if (genomeFileName != null) create_GFF_file(this.genes, directory + genomeFileName, this.genome.length()-1);
+ if (genomeFileName != null) baseFileName = directory + genomeFileName.substring(0, genomeFileName.length()-4);
+ }
+
+ /**
+ * Constructs a new Genome object based on the specified files
+ * (e.g., genome.fna, genes.ptt, rna.rnt). If any of the file
+ * names are empty, then they are simply ignored.
+ */
+ public Genome(String genomeFileName, String geneFileName, String rnaFileName) {
+ if (genomeFileName != null) readInGenome(genomeFileName);
+ if (geneFileName != null) this.codingGenes = readInGenes(geneFileName, "ORF");
+ if (rnaFileName != null) this.rnas = readInGenes(rnaFileName, "RNA");
+ this.genes = mergeGenes(this.codingGenes, this.rnas);
+ if (genomeFileName != null) create_GFF_file(this.genes, genomeFileName, this.genome.length()-1);
+ }
+
+
+
+ /*************************************************
+ ********** PUBLIC INSTANCE METHODS **********
+ *************************************************/
+
+ /**
+ * Returns the size in nucleotides of the genome
+ * sequence. Note: the returned size will be 1
+ * bigger than the actual genome size since we
+ * add a character to the beginning of the
+ * genome sequence to ensure 1-indexing.
+ */
+ public int size() {
+ return genome.length();
+ }
+
+ /**
+ * Returns the ID of the genome.
+ */
+ public String getID() {
+ return ID;
+ }
+
+ /**
+ * Returns the name of the genome.
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * Returns the path and name of the genome file sans .fna extension.
+ */
+ public String getBaseFileName() {
+ return baseFileName;
+ }
+
+ /**
+ * Returns a subsequence of the (1-indexed) genome
+ * as specified by the two coordinates, inclusive.
+ */
+ public String getSeq(int start, int stop) {
+ return genome.substring(Math.max(start, 1), Math.min(stop+1, genome.length()));
+ }
+
+ /**
+ * Return the number of genes in the genome.
+ */
+ public int numGenes() {
+ return genes.size();
+ }
+
+ /**
+ * Returns the formal genome name, e.g., gi|49175990|ref|NC_000913.2|
+ */
+ public String getFormalGenomeName() {
+ return this.formalGenomeName;
+ }
+
+ /**
+ * Return the Gene at the specified index.
+ */
+ public Gene getGene(int i) {
+ if ((i >= 0) && (i < genes.size()))
+ return genes.get(i);
+ return null;
+ }
+
+ /**
+ * Return the collection of protein coding genes.
+ */
+ public ArrayList<Gene> getCodingGenes() {
+ return this.codingGenes;
+ }
+
+ public void addPredictedRNAs(ArrayList<Gene> predictedRNAs) {
+ this.genes = mergeGenes(this.genes, predictedRNAs);
+ }
+
+ /**
+ * Return the collection of all genes.
+ */
+ public ArrayList<Gene> getGenes() {
+ return this.genes;
+ }
+
+ /**
+ * Returns a String[] representing the annotation
+ * (gene, rRNA, tRNA, RNA, "") for each
+ * coordinate in the genome on the specified strand.
+ */
+ public String[] getAnnotations(char strand) {
+ String[] annotation = new String[genome.length()];
+ for (int i=0; i<annotation.length; i++) annotation[i] = ""; // Initialize
+ for (int i=0; i<codingGenes.size(); i++) {
+ Gene g = codingGenes.get(i);
+ if (g.getStrand() == strand) {
+ for (int j=g.getFirst(); j<=g.getLast(); j++) annotation[j] = g.getName();
+ }
+ }
+ for (int i=0; i<rnas.size(); i++) {
+ Gene g = rnas.get(i);
+ if (g.getStrand() == strand) {
+ for (int j=g.getFirst(); j<=g.getLast(); j++) {
+ if (g.getProduct().contains("tRNA")) annotation[j] = "tRNA";
+ else if ((g.getProduct().contains("rRNA")) || (g.getProduct().contains("ribosomal"))) annotation[j] = "rRNA";
+ else annotation[j] = "RNA"; // Miscellaneous RNA
+ }
+ }
+ }
+ return annotation;
+ }
+
+ /**
+ * Return a String representation of all genes in the genome.
+ */
+ public String genesToString(ArrayList<Condition> conditions, String[] labels) {
+ StringBuilder sb = new StringBuilder();
+ sb.append("Transcription Start" + "\t" + "Translation Start" + "\t" + "Translation Stop" + "\t" + "Transcription Stop" + "\t" + "Strand" + "\t" + "Name" + "\t" + "Synonym" + "\t" + "Product");
+ for (int j=0; j<conditions.size(); j++) {
+ String conditionName = "" + (j+1);
+ if ((labels != null) && (labels.length == conditions.size())) conditionName = labels[j];
+ if (Rockhopper.verbose) { // Verbose output
+ if (conditions.get(j).numReplicates() == 1) {
+ sb.append("\t" + "Raw Counts " + conditionName);
+ sb.append("\t" + "Normalized Counts " + conditionName);
+ } else {
+ for (int k=0; k<conditions.get(j).numReplicates(); k++)
+ sb.append("\t" + "Raw Counts " + conditionName + " Replicate " + (k+1));
+ for (int k=0; k<conditions.get(j).numReplicates(); k++)
+ sb.append("\t" + "Normalized Counts " + conditionName + " Replicate " + (k+1));
+ }
+ sb.append("\t" + "RPKM " + conditionName);
+ }
+ sb.append("\t" + "Expression " + conditionName); // Label experiment conditions
+ }
+ int numQvalues = 0;
+ for (int x=0; x<conditions.size()-1; x++) { // First in pair
+ for (int y=x+1; y<conditions.size(); y++) { // Second in pair
+ if (Rockhopper.verbose) { // Verbose output
+ if ((labels != null) && (labels.length == conditions.size())) // Use labels
+ sb.append("\t" + "pValue " + labels[x] + " vs " + labels[y]);
+ else // Do not use labels
+ sb.append("\t" + "pValue " + (x+1) + " vs " + (y+1));
+ }
+ if ((numGenes() > 0) && (genes.get(0).hasQvalue(numQvalues))) {
+ if ((labels != null) && (labels.length == conditions.size())) // Use labels
+ sb.append("\t" + "qValue " + labels[x] + " vs " + labels[y]);
+ else // Do not use labels
+ sb.append("\t" + "qValue " + (x+1) + " vs " + (y+1));
+ }
+ numQvalues++;
+ }
+ }
+ sb.append("\n");
+ for (int i=0; i<numGenes(); i++) {
+ sb.append(genes.get(i).toString() + genes.get(i).expressionToString() + "\n");
+ }
+ return sb.toString();
+ }
+
+
+
+ /**************************************************
+ ********** PRIVATE INSTANCE METHODS **********
+ **************************************************/
+
+ /* Sets the "genome" instance variable with the FASTA formatted
+ * sequence found in the specified file. Also, sets the "ID"
+ * instance variable and the "name" instance variable based
+ * on the FASTA header line.
+ */
+ private void readInGenome(String fileName) {
+ this.ID = "";
+ this.name = "";
+ this.genome = "";
+
+ StringBuilder sequence = new StringBuilder();
+ try {
+ Scanner reader = new Scanner(new File(fileName));
+
+ // Extract header info
+ String header = reader.nextLine(); // Header line of FASTA file
+ if ((header.length() == 0) || (header.charAt(0) != '>')) {
+ Rockhopper.output("Error - first line of file " + fileName + " is not in FASTA format.\n");
+ return;
+ }
+ String[] parse_header = header.split("\\|");
+ if (parse_header.length >= 5) {
+ String[] parse_ID = parse_header[3].split("\\.");
+ this.ID = parse_ID[0];
+ String[] parse_name = parse_header[4].split(",");
+ this.name = parse_name[0].trim();
+ }
+
+ // Read in sequence
+ sequence.append('?');
+ while (reader.hasNext()) { // continue until we reach end of file
+ sequence.append(reader.nextLine());
+ }
+ reader.close();
+ this.genome = sequence.toString();
+ } catch (FileNotFoundException e) {
+ Rockhopper.output("Error - the file " + fileName + " could not be found and opened.\n");
+ }
+ }
+
+ /**
+ * Reads in a file of genes (either *.ptt or *.rnt) and returns
+ * an ArrayList of gene objects.
+ */
+ private ArrayList<Gene> readInGenes(String fileName, String type) {
+ ArrayList<Gene> listOfGenes = new ArrayList<Gene>();
+ try {
+ Scanner reader = new Scanner(new File(fileName));
+ for (int i=0; i<3; i++) reader.nextLine(); // Ignore 3 header lines
+ while (reader.hasNext()) { // Continue until end of file
+ listOfGenes.add(new Gene(reader.nextLine(), type)); // Create new gene
+ }
+ reader.close();
+ } catch (FileNotFoundException e) {
+ Rockhopper.output("Error - the file " + fileName + " could not be found and opened.\n");
+ }
+ return listOfGenes;
+ }
+
+ /**
+ * Given two lists of Genes, creates a new list of Genes containing
+ * all the Genes from the two specified lists combined and sorted
+ * by their coordinates.
+ */
+ private ArrayList<Gene> mergeGenes(ArrayList<Gene> genes1, ArrayList<Gene> genes2) {
+ ArrayList<Gene> listOfGenes = new ArrayList<Gene>();
+ int i=0; // Index for genes1
+ int j=0; // Index for genes2
+ while ((i < genes1.size()) && (j < genes2.size())) {
+ if (genes1.get(i).getMinCoordinate() < genes2.get(j).getMinCoordinate()) {
+ listOfGenes.add(genes1.get(i));
+ i++;
+ } else {
+ listOfGenes.add(genes2.get(j));
+ j++;
+ }
+ }
+ while (i < genes1.size()) {
+ listOfGenes.add(genes1.get(i));
+ i++;
+ }
+ while (j < genes2.size()) {
+ listOfGenes.add(genes2.get(j));
+ j++;
+ }
+ return listOfGenes;
+ }
+
+ /**
+ * Based on a list of genes and a FASTA genome file,
+ * create a GFF file that can be read by genome browser.
+ * The newly created file is output to the same directory
+ * as the FASTA genome file and has the same name except
+ * with the extension *.gff.
+ */
+ private void create_GFF_file(ArrayList<Gene> genes, String genomeFileName, int genomeSize) {
+ String GFF_fileName = genomeFileName.substring(0, genomeFileName.length()-4) + ".gff";
+ try {
+
+ // Get info from FASTA genome file
+ Scanner reader = new Scanner(new File(genomeFileName));
+ String line = reader.nextLine(); // Header line
+ this.formalGenomeName = line.split("\\s+")[0].substring(1);
+ reader.close();
+
+ // Create GFF file
+ PrintWriter writer = new PrintWriter(new File(GFF_fileName));
+ writer.println("track name=Genes color=255,0,255");
+ writer.println("##gff-version 3"); // Header line
+ writer.println("##sequence-region " + formalGenomeName + " 1 " + genomeSize);
+ for (int i=0; i<genes.size(); i++) {
+ Gene g = genes.get(i);
+ String type = "RNA";
+ int start = g.getMinCoordinate();
+ int stop = g.getMaxCoordinate();
+ if (g.isORF()) {
+ type = "Coding gene";
+ start = Math.min(g.getStart(), g.getStop());
+ stop = Math.max(g.getStart(), g.getStop());
+ }
+ writer.println(formalGenomeName + "\t" + "RefSeq" + "\t" + type + "\t" + start + "\t" + stop + "\t" + "." + "\t" + g.getStrand() + "\t" + "." + "\t" + "name=" + g.getName() + ";" + "product=" + "\"" + g.getProduct() + "\"");
+ }
+ writer.close();
+ } catch (IOException e) {
+ Rockhopper.output("Error - could not create GFF file " + GFF_fileName + "\n");
+ return;
+ }
+ }
+
+
+
+ /*************************************
+ ********** MAIN METHOD **********
+ *************************************/
+
+ /**
+ * The main method is used to test the methods of this class.
+ */
+ public static void main(String[] args) {
+
+ if (args.length == 0) {
+ System.err.println("\nThe Genome application must be invoked with a command line argument corresponding to the name of a directory containing genome files (e.g., *.fna, *.ptt, *.rnt).\n");
+ System.exit(0);
+ }
+
+ Genome g = new Genome(args[0]);
+ System.out.println();
+ System.out.println("Genome ID:\t\t" + g.ID);
+ System.out.println("Genome name:\t\t" + g.name);
+ System.out.println("Size of genome is:\t" + g.genome.length());
+ System.out.println("First 10 nucleotides:\t" + g.genome.substring(0, 10));
+ System.out.println("Final 10 nucleotides:\t" + g.genome.substring(g.genome.length()-10));
+ System.out.println("Number of ORFs:\t\t" + g.codingGenes.size());
+ System.out.println("Number of RNAs:\t\t" + g.rnas.size());
+ System.out.println("Number of all genes:\t" + g.genes.size());
+ System.out.println();
+ }
+
+}
+
diff --git a/Hit.java b/Hit.java
new file mode 100644
index 0000000..55ff3df
--- /dev/null
+++ b/Hit.java
@@ -0,0 +1,132 @@
+/*
+ * Copyright 2013 Brian Tjaden
+ *
+ * This file is part of Rockhopper.
+ *
+ * Rockhopper is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * any later version.
+ *
+ * Rockhopper is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * (in the file gpl.txt) along with Rockhopper.
+ * If not, see <http://www.gnu.org/licenses/>.
+ */
+
+import java.util.ArrayList;
+
+/**
+ * A Hit represents an alignment between a read and a genome.
+ */
+public class Hit implements Comparable<Hit> {
+
+ private int start; // Start coordinate of alignment in genome
+ private int stop; // Stop coordinate of alignment in genome
+ private char strand; // Strand of alignment in genome
+ private int errors; // Number of errors/mismatches in alignment
+ private int repliconIndex; // The index of the replicon to which the read was mapped
+
+ public Hit(int start, int stop, char strand, int errors, int repliconIndex) {
+ this.start = start;
+ this.stop = stop;
+ this.strand = strand;
+ this.errors = errors;
+ this.repliconIndex = repliconIndex;
+ }
+
+ public String getFormattedHit(String sequence, String read) {
+ StringBuilder sb = new StringBuilder(read.length()*3 + 40);
+ sb.append("\t" + (start+1) + "\t");
+ String subSequence = sequence.substring(start-1, stop);
+ if (strand == '-') subSequence = Index.reverseComplement(subSequence);
+ sb.append(subSequence);
+ sb.append("\t" + (stop+1) + "\t" + "(" + strand + ")" + "\n" + "\t" + "\t");
+ for (int i=0; i<read.length(); i++) {
+ if (subSequence.charAt(i) == read.charAt(i)) sb.append('|');
+ else sb.append(' ');
+ }
+ sb.append("\t" + errors + "\n" + "\t" + "\t");
+ sb.append(read);
+ sb.append("\n");
+ return sb.toString();
+ }
+
+ public String toString() {
+ return start + "\t" + stop + "\t" + strand + "\t" + errors;
+ }
+
+ public int getStart() {
+ return start;
+ }
+
+ public int getStop() {
+ return stop;
+ }
+
+ public char getStrand() {
+ return strand;
+ }
+
+ public int getErrors() {
+ return errors;
+ }
+
+ public int getRepliconIndex() {
+ return this.repliconIndex;
+ }
+
+ public int getLength() {
+ return stop - start + 1;
+ }
+
+ public int compareTo(Hit h) {
+ if (this.repliconIndex < h.repliconIndex) return -1;
+ else if (this.repliconIndex > h.repliconIndex) return 1;
+ else { // Same replicon
+ if (this.start < h.start) return -1;
+ else if (this.start > h.start) return 1;
+ else { // start coordinates are equal
+ if (this.stop < h.stop) return -1;
+ else if (this.stop > h.stop) return -1;
+ else { // stop coordinates are equal
+ if ((this.strand == '+') && (h.strand == '-')) return -1;
+ else if ((this.strand == '-') && (h.strand == '+')) return 1;
+ else return 0;
+ }
+ }
+ }
+ }
+
+
+
+ /**********************************************
+ ********** Public Class Methods **********
+ **********************************************/
+
+ /**
+ * Combines two lists of Hits, one for each read in a paired-end read,
+ * into a list of paired-end Hits. A combined Hit occurs when
+ * there are Hits from each of the two input lists that are
+ * on the same strand and within the specified distance from each other.
+ */
+ public static void combinePairedEndHits(ArrayList<Hit> combinedHits, ArrayList<Hit> hits1, ArrayList<Hit> hits2, int maxPairedEndLength) {
+ combinedHits.clear();
+ for (Hit h1 : hits1) {
+ for (Hit h2 : hits2) {
+ if ((h1.strand == h2.strand) && (h1.repliconIndex == h2.repliconIndex)) {
+ if (Math.max(h1.stop, h2.stop) - Math.min(h1.start, h2.start) <= maxPairedEndLength) {
+ combinedHits.add(new Hit(Math.min(h1.start, h2.start), Math.max(h1.stop, h2.stop), h1.strand, Math.max(h1.errors, h2.errors), h1.repliconIndex));
+ break;
+ }
+ }
+ }
+ }
+ }
+
+}
+
diff --git a/IGV_Ops.java b/IGV_Ops.java
new file mode 100644
index 0000000..e33cd77
--- /dev/null
+++ b/IGV_Ops.java
@@ -0,0 +1,88 @@
+/*
+ * Copyright 2013 Brian Tjaden
+ *
+ * This file is part of Rockhopper.
+ *
+ * Rockhopper is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * any later version.
+ *
+ * Rockhopper is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * (in the file gpl.txt) along with Rockhopper.
+ * If not, see <http://www.gnu.org/licenses/>.
+ */
+
+import java.util.ArrayList;
+import java.io.PrintWriter;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import org.broad.igv.feature.genome.GenomeImporter;
+
+public class IGV_Ops {
+
+ /**
+ * Creates a genome registry for IGV. File is named genomes.txt.
+ */
+ public static boolean createGenomeRegistry(File genomeRegistryFile, ArrayList<Genome> genomes) {
+ try {
+ PrintWriter writer = new PrintWriter(genomeRegistryFile);
+ writer.println("<Server-Side Genome List>");
+ for (Genome genome : genomes)
+ writer.println(getGenomeDisplayName(genome.getName()) + "\t" + genome.getBaseFileName() + ".genome" + "\t" + genome.getName().replace(' ', '_'));
+ writer.close();
+ return true;
+ } catch (FileNotFoundException ex) {
+ return false;
+ }
+ }
+
+ /**
+ * Creates a genome archive file for use by IGV. This method
+ * utilizes IGV code.
+ */
+ public static boolean createGenomeArchive(String genomeArchiveFileName, String genomeName, String fastaFileName, String geneFileName) {
+ try {
+ (new GenomeImporter()).createGenomeArchive(new File(genomeArchiveFileName), genomeName.replace(' ', '_'), getGenomeDisplayName(genomeName), fastaFileName, new File(geneFileName), null, null);
+ return true;
+ } catch (IOException ex) {
+ return false;
+ }
+ }
+
+ /**
+ * Create a batch script to execute when IGV launches to load
+ * the sequencing reads data.
+ */
+ public static boolean createBatchFileToLoadData(String batchFileName, String genomeName, String dataFiles, String rockhopperFiles) {
+ try {
+ PrintWriter writer = new PrintWriter(new File(batchFileName));
+ writer.println("new");
+ writer.println("genome " + genomeName.replace(' ', '_'));
+ if (dataFiles.length() > 0) writer.println("load " + dataFiles);
+ if (rockhopperFiles.length() > 0) writer.println("load " + rockhopperFiles);
+ writer.close();
+ return true;
+ } catch (FileNotFoundException ex) {
+ return false;
+ }
+ }
+
+ /**
+ * Returns the name of the genome to display in IGV's drop-down menu.
+ */
+ private static String getGenomeDisplayName(String genomeName) {
+ genomeName = genomeName.trim();
+ int indexOfSpace = genomeName.indexOf(' ');
+ if (indexOfSpace >= 0) genomeName = genomeName.charAt(0) + "." + genomeName.substring(indexOfSpace);
+ return genomeName;
+ }
+
+}
+
diff --git a/Index.java b/Index.java
new file mode 100644
index 0000000..8d995e7
--- /dev/null
+++ b/Index.java
@@ -0,0 +1,324 @@
+/*
+ * Copyright 2013 Brian Tjaden
+ *
+ * This file is part of Rockhopper.
+ *
+ * Rockhopper is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * any later version.
+ *
+ * Rockhopper is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * (in the file gpl.txt) along with Rockhopper.
+ * If not, see <http://www.gnu.org/licenses/>.
+ */
+
+import java.util.Collections;
+import java.util.ArrayList;
+import java.util.Random;
+
+public class Index {
+
+ /********************************************
+ ********** Instance Variables **********
+ ********************************************/
+
+ private int numReplicons; // Number of indexed replicons
+ private ArrayList<Replicon> replicons; // Index for each replicon
+ private boolean stopAfterOneHit; // Terminate the search when the first hit is found
+
+
+
+ /*****************************************
+ ********** Class Variables **********
+ *****************************************/
+
+ public static Random rand = new Random(); // Random number generator
+
+
+
+ /**************************************
+ ********** Constructors **********
+ **************************************/
+
+ public Index(String[] sequenceFiles) {
+ replicons = new ArrayList<Replicon>(sequenceFiles.length);
+ for (int i=0; i<sequenceFiles.length; i++)
+ replicons.add(new Replicon(sequenceFiles[i]));
+ this.numReplicons = replicons.size();
+ this.stopAfterOneHit = true;
+ }
+
+
+
+ /*************************************************
+ ********** Public Instance Methods **********
+ *************************************************/
+
+ /**
+ * Set whether the search should terminate after finding the first hit,
+ * even if there are other hits with the same score.
+ */
+ public void setStopAfterOneHit(boolean stopAfterOneHit) {
+ this.stopAfterOneHit = stopAfterOneHit;
+ }
+
+ /**
+ * Return the number of indexed replicons.
+ */
+ public int getNumReplicons() {
+ return this.numReplicons;
+ }
+
+ /**
+ * Returns the ith Replicon index.
+ */
+ public Replicon getReplicon(int i) {
+ return this.replicons.get(i);
+ }
+
+ /**
+ * Return all hits of s to the genome sequence.
+ */
+ public void exactMatch(String s, ArrayList<Hit> hits) {
+ hits.clear();
+ if (!stopAfterOneHit) { // Find all optimal hits
+ for (int i=0; i<numReplicons; i++) {
+ exactMatch(s, '+', i, 0, hits); // Align to plus strand
+ exactMatch(reverseComplement(s), '-', i, 0, hits); // Align to minus strand
+ }
+ Collections.sort(hits);
+ return;
+ } else { // Find only one hit
+ for (int i=0; i<numReplicons; i++) {
+ if (rand.nextBoolean()) { // Randomly align first to plus strand
+ exactMatch(s, '+', i, 0, hits);
+ if (hits.isEmpty()) exactMatch(reverseComplement(s), '-', i, 0, hits);
+ return;
+ } else { // Randomly align first to minus strand
+ exactMatch(reverseComplement(s), '-', i, 0, hits);
+ if (hits.isEmpty()) exactMatch(s, '+', i, 0, hits);
+ return;
+ }
+ }
+ }
+ return; // This line should never be executed.
+ }
+
+ /**
+ * Return all hits of s to the genome sequence.
+ */
+ public void inexactMatch(String s, int[] qualities, Alignment a, ArrayList<Hit> hits, ArrayList<Hit> seedHits) {
+ hits.clear();
+ seedHits.clear();
+ inexactMatch(s, qualities, 0, a, hits, seedHits);
+ Collections.sort(hits);
+ return;
+ }
+
+
+
+ /**************************************************
+ ********** Private Instance Methods **********
+ **************************************************/
+
+ // Find indices of all occurrences of s in the sequence.
+ private void exactMatch(String s, char strand, int repliconIndex, int errors, ArrayList<Hit> hits) {
+ exactMatch(s, strand, repliconIndex, errors, hits, this.stopAfterOneHit);
+ }
+
+ // Find indices of all occurrences of s in the sequence.
+ private void exactMatch(String s, char strand, int repliconIndex, int errors, ArrayList<Hit> hits, boolean stopAfterOneHit_local) {
+ Replicon r = replicons.get(repliconIndex);
+ int i = s.length() - 1;
+ char c = s.charAt(i);
+ int sp = r.getC(charToInt(c));
+ int ep = -1;
+ if (charToInt(c) < 4) ep = r.getC(charToInt(c)+1);
+ else ep = r.getLength();
+ i--;
+ while ((sp < ep) && (i >= 0)) {
+ int index = charToInt(s.charAt(i));
+ sp = r.getC(index) + r.getOcc(index, sp);
+ ep = r.getC(index) + r.getOcc(index, ep);
+ i--;
+ }
+ if (!stopAfterOneHit_local) { // Find all optimal hits
+ for (int z=sp; z<ep; z++) hits.add(new Hit(r.getRotations(z)+1, r.getRotations(z)+1+s.length()-1, strand, errors, repliconIndex)); // 1-indexed
+ } else { // Find only one hit
+ if (ep > sp) {
+ int randIndex = sp + rand.nextInt(ep-sp);
+ hits.add(new Hit(r.getRotations(randIndex)+1, r.getRotations(randIndex)+1+s.length()-1, strand, errors, repliconIndex)); // 1-indexed
+ }
+ }
+ }
+
+ /**
+ * Find all indices in the sequence (with the same
+ * best score) that match the specified query String
+ * with errors that sum to a value at or below the threshold.
+ */
+ private void inexactMatch(String s, int[] qualities, int threshold, Alignment a, ArrayList<Hit> hits, ArrayList<Hit> seedHits) {
+
+ // Exact match search
+ if (!stopAfterOneHit) { // Find all optimal hits
+ for (int i=0; i<numReplicons; i++) {
+ exactMatch(s, '+', i, 0, hits); // Align to plus strand
+ exactMatch(reverseComplement(s), '-', i, 0, hits); // Align to minus strand
+ }
+ } else { // Find only one hit
+ for (int i=0; i<numReplicons; i++) {
+ if (rand.nextBoolean()) { // Randomly align first to plus strand
+ exactMatch(s, '+', i, 0, hits);
+ if (hits.isEmpty()) exactMatch(reverseComplement(s), '-', i, 0, hits);
+ } else { // Randomly align first to minus strand
+ exactMatch(reverseComplement(s), '-', i, 0, hits);
+ if (hits.isEmpty()) exactMatch(s, '+', i, 0, hits);
+ }
+ if (!hits.isEmpty()) return;
+ }
+ }
+ if (!hits.isEmpty()) return;
+
+ // Inexact search via alignment
+ int qualityThreshold = (int)(40 * s.length() * Peregrine.percentMismatches);
+ int mismatches = (int)(s.length() * Peregrine.percentMismatches);
+ int minSeedLength = Math.max((int)(s.length() * Peregrine.percentSeedLength), Peregrine.minReadLength);
+ a.setNumErrors(mismatches);
+ a.setThreshold(qualityThreshold);
+ if ((mismatches == 0) || (s.length() < minSeedLength)) return;
+ int minScore = Integer.MAX_VALUE;
+ int numSeeds = Math.min(mismatches+1, (int)Math.ceil((s.length()+1)/(double)minSeedLength));
+ int increment = s.length()/numSeeds;
+ int seedLength = Math.max(increment, minSeedLength);
+ int[] reverseQualities = new int[qualities.length];
+ for (int q=0; q<qualities.length; q++) reverseQualities[qualities.length-1-q] = qualities[q];
+ for (int i=0; i<numReplicons; i++) { // Find seed in each replicon
+
+ // Determine all seeds from read
+ int x = 0;
+ int count = 0;
+ while (count < numSeeds) { // Try each seed from read
+ int start = x;
+ int stop = x+seedLength-1;
+ if (count == numSeeds-1) { // Final read
+ start = s.length()-seedLength;
+ stop = s.length()-1;
+ }
+ x += increment;
+ count++;
+
+ seedHits.clear();
+ exactMatch(s.substring(start, stop+1), '+', i, 0, seedHits, false);
+ exactMatch(reverseComplement(s.substring(start, stop+1)), '-', i, 0, seedHits, false); // Align to minus strand
+
+ // Align read to replicon sequence based on seedHits
+ for (int j=0; j<seedHits.size(); j++) {
+ if (seedHits.get(j).getStrand() == '+') // Plus strand
+ a.align(replicons.get(i).getSequence(), seedHits.get(j).getStart()-2, seedHits.get(j).getStop(), s, start-1, stop+1, qualities);
+ else // Minus strand
+ a.align(replicons.get(i).getSequence(), seedHits.get(j).getStart()-2, seedHits.get(j).getStop(), reverseComplement(s), s.length()-1-stop-1, s.length()-1-start+1, reverseQualities);
+ // Add alignment (if found and if among *best* scoring hits found so far) to "hits"
+ if ((a.getScore() >= 0) && (a.getScore() <= qualityThreshold) && (a.getErrors() <= mismatches)) { // Valid alignment
+ if (a.getScore() < minScore) { // This is the new best scoring alignment
+ hits.clear();
+ hits.add(new Hit(a.getStart(), a.getStop(), seedHits.get(j).getStrand(), a.getErrors(), i));
+ minScore = a.getScore();
+ } else if (a.getScore() == minScore) { // This is another best scoring alignment
+ hits.add(new Hit(a.getStart(), a.getStop(), seedHits.get(j).getStrand(), a.getErrors(), i));
+ } else { // We have previously found a better scoring alignment
+ // Do nothing.
+ }
+ }
+ }
+ }
+
+ // Remove neighboring Hits
+ Collections.sort(hits);
+ int j=1;
+ while (j < hits.size()) {
+ if (hits.get(j).getStart() - hits.get(j-1).getStop() < s.length()) hits.remove(j);
+ else j++;
+ }
+ }
+
+ // Randomly choose one best hit to return (as opposed to all best hits)
+ if ((hits.size() > 1) && stopAfterOneHit) { // Find only one hit (not all optimal hits)
+ Hit randomBest = hits.get(rand.nextInt(hits.size()));
+ hits.clear();
+ hits.add(randomBest);
+ }
+ }
+
+
+
+ /**********************************************
+ ********** Public Class Methods **********
+ **********************************************/
+
+ /**
+ * Set seed for pseudorandom number generator.
+ */
+ public static void setRandomSeed(long seed) {
+ rand = new Random(seed);
+ }
+
+ // Convert a nucleotide character to an integer
+ public static int charToInt(char c) {
+ if (c == 'A') return 0;
+ if (c == 'C') return 1;
+ if (c == 'G') return 2;
+ if (c == 'T') return 3;
+ if (c == '^') return 4;
+ if (c == '$') return 5;
+ return -1;
+ }
+
+ /**
+ * Return the reverse complement of the input sequence.
+ */
+ public static String reverseComplement(String s) {
+ StringBuilder sb = new StringBuilder(s.length());
+ for (int i=s.length()-1; i>=0; i--) {
+ if (s.charAt(i) == 'A') sb.append('T');
+ else if (s.charAt(i) == 'C') sb.append('G');
+ else if (s.charAt(i) == 'G') sb.append('C');
+ else if (s.charAt(i) == 'T') sb.append('A');
+ else if (s.charAt(i) == '^') sb.append('^');
+ else Peregrine.output("Invalid DNA nucleotide character: " + s.charAt(i) + "\n");
+ }
+ return sb.toString();
+ }
+
+
+
+ /***********************************************
+ ********** Private Class Methods **********
+ ***********************************************/
+
+
+
+ /*************************************
+ ********** Main Method **********
+ *************************************/
+
+ public static void main(String[] args) {
+
+ if (args.length < 1) {
+ System.err.println("\nUSAGE: java Index <index1.fna,index2.fna,index3.fna>" + "\n");
+ System.err.println("Index takes a comma-separated set of sequence files (such as FASTA genome files) to be indexed and it computes the Burrows-Wheeler transformed index for each sequence. If run from the command line, it simply outputs the size of each index to STDOUT. The Index class is meant to be instantiated from another application. \n");
+ System.exit(0);
+ }
+
+ Index index = new Index(args[0].split(","));
+ for (int i=0; i<index.getNumReplicons(); i++)
+ System.out.println(index.getReplicon(i).getName() + " has size " + index.getReplicon(i).getLength());
+ }
+
+}
+
diff --git a/Jama/CholeskyDecomposition.class b/Jama/CholeskyDecomposition.class
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index 0000000..231760e
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diff --git a/Jama/EigenvalueDecomposition.class b/Jama/EigenvalueDecomposition.class
new file mode 100644
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diff --git a/Jama/Matrix.class b/Jama/Matrix.class
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diff --git a/Jama/QRDecomposition.class b/Jama/QRDecomposition.class
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diff --git a/Jama/SingularValueDecomposition.class b/Jama/SingularValueDecomposition.class
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diff --git a/Jama/examples/MagicSquareExample.class b/Jama/examples/MagicSquareExample.class
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diff --git a/Jama/test/TestMatrix.class b/Jama/test/TestMatrix.class
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diff --git a/Jama/util/Maths.class b/Jama/util/Maths.class
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diff --git a/LICENSE.sun b/LICENSE.sun
new file mode 100644
index 0000000..76b40b1
--- /dev/null
+++ b/LICENSE.sun
@@ -0,0 +1,10 @@
+Copyright 2000 by Sun Microsystems, Inc. All Rights Reserved.
+
+Sun grants you ("Licensee") a non-exclusive, royalty free, license to use, and redistribute this software graphics artwork, as individual graphics or as a collection, as part of software code or programs that you develop, provided that i) this copyright notice and license accompany the software graphics artwork; and ii) you do not utilize the software graphics artwork in a manner which is disparaging to Sun. Unless enforcement is prohibited by applicable law, you may not modify the graph [...]
+
+This software graphics artwork is provided "AS IS," without a warranty of any kind. ALL EXPRESS OR IMPLIED CONDITIONS, REPRESENTATIONS AND WARRANTIES, INCLUDING ANY IMPLIED WARRANTY OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE OR NON-INFRINGEMENT, ARE HEREBY EXCLUDED. SUN AND ITS LICENSORS SHALL NOT BE LIABLE FOR ANY DAMAGES SUFFERED BY LICENSEE AS A RESULT OF USING, MODIFYING OR DISTRIBUTING THE SOFTWARE GRAPHICS ARTWORK.
+
+IN NO EVENT WILL SUN OR ITS LICENSORS BE LIABLE FOR ANY LOST REVENUE, PROFIT OR DATA, OR FOR DIRECT, INDIRECT, SPECIAL, CONSEQUENTIAL, INCIDENTAL OR PUNITIVE DAMAGES, HOWEVER CAUSED AND REGARDLESS OF THE THEORY OF LIABILITY, ARISING OUT OF THE USE OF OR INABILITY TO USE SOFTWARE GRAPHICS ARTWORK, EVEN IF SUN HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
+
+If any of the above provisions are held to be in violation of applicable law, void, or unenforceable in any jurisdiction, then such provisions are waived to the extent necessary for this Disclaimer to be otherwise enforceable in such jurisdiction.
+
diff --git a/LICENSE.txt b/LICENSE.txt
new file mode 100644
index 0000000..5ebe92c
--- /dev/null
+++ b/LICENSE.txt
@@ -0,0 +1,27 @@
+BSD License
+
+Copyright (c) 2000-2006, www.hamcrest.org
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+Redistributions of source code must retain the above copyright notice, this list of
+conditions and the following disclaimer. Redistributions in binary form must reproduce
+the above copyright notice, this list of conditions and the following disclaimer in
+the documentation and/or other materials provided with the distribution.
+
+Neither the name of Hamcrest nor the names of its contributors may be used to endorse
+or promote products derived from this software without specific prior written
+permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY
+EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT
+SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
+INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
+TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY
+WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+DAMAGE.
diff --git a/Lowess.java b/Lowess.java
new file mode 100644
index 0000000..cb12b38
--- /dev/null
+++ b/Lowess.java
@@ -0,0 +1,293 @@
+/*
+ * Copyright 2013 Brian Tjaden
+ *
+ * This file is part of Rockhopper.
+ *
+ * Rockhopper is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * any later version.
+ *
+ * Rockhopper is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * (in the file gpl.txt) along with Rockhopper.
+ * If not, see <http://www.gnu.org/licenses/>.
+ */
+
+import java.util.ArrayList;
+import java.util.Collections;
+
+public class Lowess {
+
+ /**
+ * Lowess smoother. Robust locally weighted regression.
+ * The lowess function fits a nonparametric regression curve to a
+ * scatterplot. x and y must be of equal length. Returns the
+ * estimatad smooth values of y.
+ */
+ public static ArrayList<Long> lowess(ArrayList<Long> x, ArrayList<Long> y) {
+ return lowess(x, y, 0.1, 1); // Default parameters
+ }
+
+ /**
+ * Lowess smoother. Robust locally weighted regression.
+ * The lowess function fits a nonparametric regression curve to a
+ * scatterplot. x and y must be of equal length. Returns the
+ * estimatad smooth values of y.
+ *
+ * A larger smoothing span results in a smoother curve.
+ * The number of iterations can be increased to improve robustness
+ * at a cost to running time.
+ */
+ public static ArrayList<Long> lowess(ArrayList<Long> x, ArrayList<Long> y, double smoothingSpan, int iterations) {
+ if (x.size() != y.size()) {
+ Rockhopper.output("Error - cannot compute lowess of two matrices with differing sizes.\n");
+ return new ArrayList<Long>();
+ }
+
+ // Create lists of nonzero elements
+ ArrayList<Long> X1 = new ArrayList<Long>();
+ ArrayList<Long> Y1 = new ArrayList<Long>();
+ ArrayList<Long> X1_sorted = new ArrayList<Long>();
+ for (int i=0; i<x.size(); i++) {
+ if (x.get(i) > 0) {
+ X1.add(x.get(i));
+ Y1.add(y.get(i));
+ X1_sorted.add(x.get(i));
+ }
+ }
+
+ // "process" method creates a 2D array based on the size of X1.
+ // If X1 is too large, then we run out of memory and crash.
+ // Here we attempt to limit the size of the dimensions, i.e., the X1 array.
+ int power = 0;
+ int threshold = 0;
+ while ((X1.size() >= 10000) && (Runtime.getRuntime().maxMemory() < 1300000000) && (power < 31)) {
+ threshold = (int)Math.pow(2, power);
+ X1.clear();
+ Y1.clear();
+ X1_sorted.clear();
+ for (int i=0; i<x.size(); i++) {
+ if (x.get(i) > threshold) {
+ X1.add(x.get(i));
+ Y1.add(y.get(i));
+ X1_sorted.add(x.get(i));
+ }
+ }
+ power++;
+ }
+
+ // Sort X1 in reverse order
+ Collections.sort(X1_sorted);
+ Collections.reverse(X1_sorted);
+
+ ArrayList<Long> h = new ArrayList<Long>();
+ ArrayList<Long> dist = new ArrayList<Long>();
+ for (int i=0; i<X1.size(); i++) {
+ Long p = X1.get(i);
+ dist.clear();
+ double fraction = (X1_sorted.size() - X1_sorted.indexOf(p)) / (double)(X1_sorted.size());
+ int r = (int)(Math.ceil(Math.min(2.0*fraction, 0.4)*X1.size()));
+ for (int j=0; j<X1.size(); j++) dist.add(Math.abs(p.longValue() - X1.get(j).longValue()));
+ Collections.sort(dist);
+ if (r < dist.size()) h.add(dist.get(r));
+ else h.add(dist.get(dist.size()-1));
+ }
+
+ double[][] w = process(X1, h);
+ cube(w);
+ oneMinus(w);
+ cube(w);
+
+ double[] yest = new double[X1.size()];
+ double[] delta = new double[X1.size()];
+
+ for (int z=0; z<iterations; z++) {
+ for (int i=0; i<X1.size(); i++) {
+ ArrayList<Double> weights = new ArrayList<Double>();
+ for (int j=0; j<w.length; j++) weights.add(w[j][i]);
+ double b1 = sum(product(weights, Y1));
+ double b2 = sum(product(product(weights, Y1), X1));
+ double A1 = sum(weights);
+ double A2 = sum(product(weights, X1));
+ double A3 = A2;
+ double A4 = sum(product(product(weights, X1), X1));
+ double[][] b = {{b1}, {b2}};
+ double[][] A = {{A1, A2}, {A3, A4}};
+ Matrix b_Matrix = new Matrix(b);
+ Matrix A_Matrix = new Matrix(A);
+ double[][] beta = A_Matrix.solve(b_Matrix).getArray(); // Linear algebra solver
+ yest[i] = beta[0][0] + (beta[1][0] * X1.get(i));
+ }
+ double[] residuals = new double[Y1.size()];
+ ArrayList<Double> residuals_absValue = new ArrayList<Double>();
+ for (int i=0; i<Y1.size(); i++) {
+ residuals[i] = Y1.get(i) - yest[i];
+ residuals_absValue.add(Math.abs(Y1.get(i) - yest[i]));
+ }
+ double s = 1.0;
+ if (residuals.length > 0) s = Misc.select_Double(residuals_absValue, 1+(residuals.length/2));
+
+ for (int i=0; i<delta.length; i++) {
+ delta[i] = residuals[i] / (6.0 * s);
+ if (delta[i] < -1) delta[i] = -1.0;
+ if (delta[i] > 1) delta[i] = 1.0;
+ }
+ oneMinus(product(delta, delta));
+ delta = product(delta, delta);
+ }
+
+ double minPositive = Double.MAX_VALUE;
+ for (int i=0; i<yest.length; i++) {
+ if (yest[i] > threshold) {
+ if (yest[i] < minPositive)
+ minPositive = yest[i];
+ }
+ }
+
+ ArrayList<Long> yest_Long = new ArrayList<Long>();
+ int j=0;
+ for (int i=0; i<x.size(); i++) {
+ if (x.get(i) <= threshold)
+ yest_Long.add((long)minPositive);
+ else {
+ yest_Long.add((long)yest[j]);
+ j++;
+ }
+ }
+ return yest_Long;
+ }
+
+
+
+ /************************************************
+ ********** PRIVATE STATIC METHODS **********
+ ************************************************/
+
+ /**
+ * clip(abs(([x]-transpose([x]))/h),0.0,1.0)
+ */
+ private static double[][] process(ArrayList<Long> x, ArrayList<Long> h) {
+ double[][] w = new double[x.size()][x.size()];
+ for (int i=0; i<x.size(); i++) {
+ for (int j=0; j<x.size(); j++) {
+ double value = Math.abs(((double)(x.get(i) - x.get(j)))/h.get(i));
+ if (value < 0.0) value = 0.0;
+ if (value > 1.0) value = 1.0;
+ w[j][i] = value;
+ }
+ }
+ return w;
+ }
+
+ /**
+ * Cube every element in a 2D array.
+ */
+ private static void cube(double[][] w) {
+ for (int i=0; i<w.length; i++)
+ for (int j=0; j<w[0].length; j++)
+ w[i][j] = w[i][j] * w[i][j] * w[i][j];
+ }
+
+ /**
+ * w = 1 - w
+ */
+ private static void oneMinus(double[][] w) {
+ for (int i=0; i<w.length; i++)
+ for (int j=0; j<w[0].length; j++)
+ w[i][j] = 1.0 - w[i][j];
+ }
+
+ /**
+ * w = 1 - w
+ */
+ private static void oneMinus(double[] w) {
+ for (int i=0; i<w.length; i++)
+ w[i] = 1.0 - w[i];
+ }
+
+ /**
+ * Return a new ArrayList where each element is the product of the corresponding
+ * elements in the two specified ArrayLists.
+ */
+ private static ArrayList<Double> product(ArrayList<Double> x, ArrayList<Long> y) {
+ ArrayList<Double> result = new ArrayList<Double>();
+ for (int i=0; i<x.size(); i++)
+ result.add(x.get(i) * y.get(i));
+ return result;
+ }
+
+ /**
+ * Returns a new array where each element is the product of the corresponding
+ * elements in the two specified arrays.
+ */
+ private static double[] product(double[] x, double[] y) {
+ double[] result = new double[x.length];
+ for (int i=0; i<x.length; i++)
+ result[i] = x[i] * y[i];
+ return result;
+ }
+
+ /**
+ * Returns the sum of all elements in an ArrayList.
+ */
+ private static double sum(ArrayList<Double> x) {
+ double sum = 0.0;
+ for (int i=0; i<x.size(); i++) sum += x.get(i);
+ return sum;
+ }
+
+ /**
+ * Output to Stdout a 2D array.
+ */
+ private static void print(double[][] w) {
+ Rockhopper.output("\n");
+ for (int i=0; i<w.length; i++) {
+ for (int j=0; j<w[0].length; j++) {
+ Rockhopper.output("\t" + w[i][j]);
+ }
+ Rockhopper.output("\n");
+ }
+ Rockhopper.output("\n");
+ }
+
+
+
+ /*************************************
+ ********** MAIN METHOD **********
+ *************************************/
+ /**
+ * The main method is used to test the methods of this class.
+ */
+ public static void main(String[] args) {
+ ArrayList<Long> a = new ArrayList<Long>();
+ a.add((long)1);
+ a.add((long)2);
+ a.add((long)5);
+ a.add((long)8);
+ a.add((long)7);
+ a.add((long)3);
+ a.add((long)20);
+ a.add((long)13);
+ a.add((long)10);
+ ArrayList<Long> b = new ArrayList<Long>();
+ b.add((long)4);
+ b.add((long)9);
+ b.add((long)6);
+ b.add((long)0);
+ b.add((long)1);
+ b.add((long)5);
+ b.add((long)15);
+ b.add((long)11);
+ b.add((long)18);
+ System.out.println("\n" + lowess(a, b) + "\n");
+
+
+ }
+
+}
+
diff --git a/Matrix.java b/Matrix.java
new file mode 100644
index 0000000..133a49c
--- /dev/null
+++ b/Matrix.java
@@ -0,0 +1,310 @@
+/*
+ * Copyright 2013 Brian Tjaden
+ *
+ * This file is part of Rockhopper.
+ *
+ * Rockhopper is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * any later version.
+ *
+ * Rockhopper is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * (in the file gpl.txt) along with Rockhopper.
+ * If not, see <http://www.gnu.org/licenses/>.
+ */
+
+public class Matrix {
+
+ /********************************************
+ ********** INSTANCE VARIABLES **********
+ ********************************************/
+
+ private double[][] M;
+ private int rows, cols; // Number or rows and columns
+
+
+
+ /**************************************
+ ********** CONSTRUCTORS **********
+ **************************************/
+
+ public Matrix (int rows, int cols) {
+ M = new double[rows][cols];
+ this.rows = rows;
+ this.cols = cols;
+ }
+
+ public Matrix (double[][] M) {
+ this.M = M;
+ rows = M.length;
+ cols = M[0].length;
+ }
+
+
+
+ /*************************************************
+ ********** PUBLIC INSTANCE METHODS **********
+ *************************************************/
+
+ /**
+ * Returns the number of rows in this Matrix.
+ */
+ public int getRows () {
+ return rows;
+ }
+
+ /**
+ * Returns the number of columns in this Matrix.
+ */
+ public int getCols () {
+ return cols;
+ }
+
+ /**
+ * Returns the 2D array representing this Matrix.
+ */
+ public double[][] getArray () {
+ return M;
+ }
+
+ /**
+ * Returns a copy of the 2D array representing this Matrix.
+ */
+
+ public double[][] getArrayCopy () {
+ double[][] M2 = new double[rows][cols];
+ for (int i = 0; i < rows; i++)
+ for (int j = 0; j < cols; j++)
+ M2[i][j] = M[i][j];
+ return M2;
+ }
+
+ /**
+ * Return a submatrix of this Matrix.
+ */
+ public Matrix getMatrix (int[] r, int x, int y) {
+ Matrix mtrx = new Matrix(r.length,y-x+1);
+ double[][] M2 = mtrx.getArray();
+ for (int i = 0; i < r.length; i++)
+ for (int j = x; j <= y; j++)
+ M2[i][j-x] = M[r[i]][j];
+ return mtrx;
+ }
+
+ /**
+ * Return a submatrix of this Matrix.
+ */
+ public Matrix getMatrix (int x1, int x2, int y1, int y2) {
+ Matrix mtrx = new Matrix(x2-x1+1,y2-y1+1);
+ double[][] M2 = mtrx.getArray();
+ for (int i = x1; i <= x2; i++)
+ for (int j = y1; j <= y2; j++)
+ M2[i-x1][j-y1] = M[i][j];
+ return mtrx;
+ }
+
+ public Matrix solve (Matrix B) {
+ if (rows == cols) return (new LUDecomposition(this)).solve(B);
+ else return (new QRDecomposition(this)).solve(B);
+ }
+
+
+
+ /***************************************
+ ********** CLASS METHODS **********
+ ***************************************/
+
+ public static double hypot(double x, double y) {
+ double r;
+ if (Math.abs(x) > Math.abs(y)) {
+ r = y/x;
+ r = Math.abs(x)*Math.sqrt(1+r*r);
+ } else if (y != 0) {
+ r = x/y;
+ r = Math.abs(y)*Math.sqrt(1+r*r);
+ } else {
+ r = 0.0;
+ }
+ return r;
+ }
+
+}
+
+
+
+/*****************************************
+ ********** LU MATRIX CLASS **********
+ *****************************************/
+
+class LUDecomposition {
+
+ /********************************************
+ ********** INSTANCE VARIABLES **********
+ ********************************************/
+
+ private double[][] LU;
+ private int rows;
+ private int cols;
+ private int signOfPivot;
+ private int[] pivot;
+
+
+
+ /**************************************
+ ********** CONSTRUCTORS **********
+ **************************************/
+
+ public LUDecomposition (Matrix A) {
+
+ LU = A.getArrayCopy();
+ rows = A.getRows();
+ cols = A.getCols();
+ pivot = new int[rows];
+ for (int i = 0; i < rows; i++) pivot[i] = i;
+ signOfPivot = 1;
+ double[] LUrowi;
+ double[] LUcolj = new double[rows];
+
+ for (int j = 0; j < cols; j++) {
+ for (int i = 0; i < rows; i++) LUcolj[i] = LU[i][j];
+ for (int i = 0; i < rows; i++) {
+ LUrowi = LU[i];
+ int kmax = Math.min(i,j);
+ double s = 0.0;
+ for (int k = 0; k < kmax; k++) s += LUrowi[k]*LUcolj[k];
+ LUrowi[j] = LUcolj[i] -= s;
+ }
+ int p = j;
+ for (int i = j+1; i < rows; i++) {
+ if (Math.abs(LUcolj[i]) > Math.abs(LUcolj[p])) p = i;
+ }
+ if (p != j) {
+ for (int k = 0; k < cols; k++) {
+ double t = LU[p][k];
+ LU[p][k] = LU[j][k];
+ LU[j][k] = t;
+ }
+ int k = pivot[p]; pivot[p] = pivot[j]; pivot[j] = k;
+ signOfPivot = -signOfPivot;
+ }
+ if (j < rows & LU[j][j] != 0.0) {
+ for (int i = j+1; i < rows; i++) LU[i][j] /= LU[j][j];
+ }
+ }
+ }
+
+
+
+ /*************************************************
+ ********** PUBLIC INSTANCE METHODS **********
+ *************************************************/
+
+ public Matrix solve (Matrix B) {
+
+ int cols2 = B.getCols();
+ Matrix mtrx = B.getMatrix(pivot,0,cols2-1);
+ double[][] M2 = mtrx.getArray();
+
+ for (int k = 0; k < cols; k++)
+ for (int i = k+1; i < cols; i++)
+ for (int j = 0; j < cols2; j++)
+ M2[i][j] -= M2[k][j]*LU[i][k];
+
+ for (int k = cols-1; k >= 0; k--) {
+ for (int j = 0; j < cols2; j++)
+ M2[k][j] /= LU[k][k];
+ for (int i = 0; i < k; i++)
+ for (int j = 0; j < cols2; j++)
+ M2[i][j] -= M2[k][j]*LU[i][k];
+ }
+ return mtrx;
+ }
+
+}
+
+
+
+/*****************************************
+ ********** QR MATRIX CLASS **********
+ *****************************************/
+
+class QRDecomposition {
+
+ /********************************************
+ ********** INSTANCE VARIABLES **********
+ ********************************************/
+
+ private double[][] QR;
+ private int rows;
+ private int cols;
+ private double[] Rdiag;
+
+
+
+ /**************************************
+ ********** CONSTRUCTORS **********
+ **************************************/
+
+ public QRDecomposition (Matrix A) {
+ QR = A.getArrayCopy();
+ rows = A.getRows();
+ cols = A.getCols();
+ Rdiag = new double[cols];
+ for (int k = 0; k < cols; k++) {
+ double nrm = 0;
+ for (int i = k; i < rows; i++) nrm = Matrix.hypot(nrm,QR[i][k]);
+ if (nrm != 0.0) {
+ if (QR[k][k] < 0) nrm = -nrm;
+ for (int i = k; i < rows; i++) QR[i][k] /= nrm;
+ QR[k][k] += 1.0;
+ for (int j = k+1; j < cols; j++) {
+ double s = 0.0;
+ for (int i = k; i < rows; i++) s += QR[i][k]*QR[i][j];
+ s = -s/QR[k][k];
+ for (int i = k; i < rows; i++) QR[i][j] += s*QR[i][k];
+ }
+ }
+ Rdiag[k] = -nrm;
+ }
+ }
+
+
+
+ /*************************************************
+ ********** PUBLIC INSTANCE METHODS **********
+ *************************************************/
+
+ public boolean isFullRank () {
+ for (int j = 0; j < cols; j++) {
+ if (Rdiag[j] == 0) return false;
+ }
+ return true;
+ }
+
+ public Matrix solve (Matrix B) {
+ int cols2 = B.getCols();
+ double[][] M2 = B.getArrayCopy();
+ for (int k = 0; k < cols; k++) {
+ for (int j = 0; j < cols2; j++) {
+ double s = 0.0;
+ for (int i = k; i < rows; i++) s += QR[i][k]*M2[i][j];
+ s = -s/QR[k][k];
+ for (int i = k; i < rows; i++) M2[i][j] += s*QR[i][k];
+ }
+ }
+ for (int k = cols-1; k >= 0; k--) {
+ for (int j = 0; j < cols2; j++) M2[k][j] /= Rdiag[k];
+ for (int i = 0; i < k; i++)
+ for (int j = 0; j < cols2; j++)
+ M2[i][j] -= M2[k][j]*QR[i][k];
+ }
+ return (new Matrix(M2).getMatrix(0,cols-1,0,cols2-1));
+ }
+}
+
+
diff --git a/Misc.java b/Misc.java
new file mode 100644
index 0000000..2475fef
--- /dev/null
+++ b/Misc.java
@@ -0,0 +1,179 @@
+/*
+ * Copyright 2013 Brian Tjaden
+ *
+ * This file is part of Rockhopper.
+ *
+ * Rockhopper is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * any later version.
+ *
+ * Rockhopper is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * (in the file gpl.txt) along with Rockhopper.
+ * If not, see <http://www.gnu.org/licenses/>.
+ */
+
+import java.util.ArrayList;
+import java.util.Random;
+import java.util.Iterator;
+
+public class Misc {
+
+ /*************************************************
+ ********** PRIVATE CLASS VARIABLES **********
+ *************************************************/
+
+ private static Random rand; // Random number generator
+
+
+
+ /***********************************************
+ ********** PUBLIC STATIC METHODS **********
+ ***********************************************/
+
+ /**
+ * Return the element in the ArrayList corresponding to
+ * the specified order statistic.
+ */
+ public static long select_Long(ArrayList<Long> a, int orderStatistic) {
+ return select_Long(a, 0, a.size()-1, orderStatistic);
+ }
+
+ /**
+ * Return the element in the ArrayList corresponding to
+ * the specified order statistic.
+ */
+ public static double select_Double(ArrayList<Double> a, int orderStatistic) {
+ return select_Double(a, 0, a.size()-1, orderStatistic);
+ }
+
+ /**
+ * Returns the correlation coefficient of two ArrayLists.
+ */
+ public static double correlation(ArrayList<Long> x, ArrayList<Long> y) {
+ if (x.size() != y.size()) return 0.0; // Lists have different lengths
+ double meanX = mean(x);
+ double meanY = mean(y);
+ double sumXY = 0.0;
+ double sumXX = 0.0;
+ double sumYY = 0.0;
+ for (int i=0; i<x.size(); i++) {
+ sumXY += (x.get(i) - meanX) * (y.get(i) - meanY);
+ sumXX += (x.get(i) - meanX) * (x.get(i) - meanX);
+ sumYY += (y.get(i) - meanY) * (y.get(i) - meanY);
+ }
+ if ((sumXX == 0.0) || (sumYY == 0.0)) return 0.0;
+ return sumXY / (Math.sqrt(sumXX) * Math.sqrt(sumYY));
+ }
+
+ /**
+ * Returns the mean of an ArrayList.
+ */
+ public static double mean(ArrayList<Long> a) {
+ double sum = 0;
+ for (Iterator<Long> iter = a.iterator(); iter.hasNext(); )
+ sum += iter.next();
+ return sum / a.size();
+ }
+
+
+
+ /************************************************
+ ********** PRIVATE STATIC METHODS **********
+ ************************************************/
+
+ /**
+ * Return the element in the ArrayList corresponding to
+ * the specified order statistic.
+ */
+ private static long select_Long(ArrayList<Long> a, int lo, int hi, int orderStatistic) {
+ if (lo >= hi) {
+ if (a.size() == 0) return 0;
+ return a.get(lo);
+ }
+ int p = partition(a, lo, hi);
+ if (orderStatistic == p-lo+1) return a.get(p);
+ else if (orderStatistic < p-lo+1) return select_Long(a, lo, p-1, orderStatistic);
+ else return select_Long(a, p+1, hi, orderStatistic-(p-lo+1));
+ }
+
+ /**
+ * Partitions "a" around random pivot element.
+ * Returns the index of the pivot.
+ */
+ private static int partition(ArrayList<Long> a, int lo, int hi) {
+ if (rand == null) rand = new Random();
+ swap(a, rand.nextInt(hi-lo+1)+lo, hi); // Choose pivot randomly and place at end of "a"
+ long x = a.get(hi);
+ int i = lo-1;
+ for (int j=lo; j<hi; j++) {
+ if (a.get(j) <= x) {
+ i++;
+ swap(a, i, j);
+ }
+ }
+ swap(a, i+1, hi);
+ return i+1;
+ }
+
+ /**
+ * Return the element in the ArrayList corresponding to
+ * the specified order statistic.
+ */
+ private static double select_Double(ArrayList<Double> a, int lo, int hi, int orderStatistic) {
+ if (lo == hi) return a.get(lo);
+ int p = partitionDouble(a, lo, hi);
+ if (orderStatistic == p-lo+1) return a.get(p);
+ else if (orderStatistic < p-lo+1) return select_Double(a, lo, p-1, orderStatistic);
+ else return select_Double(a, p+1, hi, orderStatistic-(p-lo+1));
+ }
+
+ /**
+ * Partitions "a" around random pivot element.
+ * Returns the index of the pivot.
+ */
+ private static int partitionDouble(ArrayList<Double> a, int lo, int hi) {
+ if (rand == null) rand = new Random();
+ swap(a, rand.nextInt(hi-lo+1)+lo, hi); // Choose pivot randomly and place at end of "a"
+ double x = a.get(hi);
+ int i = lo-1;
+ for (int j=lo; j<hi; j++) {
+ if (a.get(j) <= x) {
+ i++;
+ swap(a, i, j);
+ }
+ }
+ swap(a, i+1, hi);
+ return i+1;
+ }
+
+ /**
+ * Swaps two elements in an ArrayList at the specified indices.
+ */
+ private static <E> void swap(ArrayList<E> a, int i, int j) {
+ E temp = a.get(i);
+ a.set(i, a.get(j));
+ a.set(j, temp);
+ }
+
+
+ /*************************************
+ ********** MAIN METHOD **********
+ *************************************/
+
+ public static void main(String[] args) {
+
+ System.err.println("\nClass Methods:\n");
+ System.err.println("\t" + "select(ArrayList<Integer or Double> a, int orderStatistic)" + "\t" + "Computes the specified order statistic in the list.\n");
+ System.err.println("\t" + "correlation(ArrayList<Integer> x, ArrayList<Integer> y)" + "\t" + "Computes the correlation coefficient of two lists.\n");
+ System.err.println("\t" + "mean(ArrayList<Integer> a)" + "\t" + "Computes the mean of a list.\n");
+
+ }
+
+}
+
diff --git a/NCBI.java b/NCBI.java
new file mode 100644
index 0000000..93eb9ba
--- /dev/null
+++ b/NCBI.java
@@ -0,0 +1,283 @@
+/*
+ * Copyright 2013 Brian Tjaden
+ *
+ * This file is part of Rockhopper.
+ *
+ * Rockhopper is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * any later version.
+ *
+ * Rockhopper is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * (in the file gpl.txt) along with Rockhopper.
+ * If not, see <http://www.gnu.org/licenses/>.
+ */
+
+import java.util.Collections;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Scanner;
+import java.net.URL;
+import java.net.URLConnection;
+import java.io.IOException;
+import java.io.File;
+import java.io.PrintWriter;
+
+/**
+ * Maintains a list of bacterial genomes and their annotations available from NCBI.
+ */
+public class NCBI {
+
+ /*****************************************
+ ********** CLASS VARIABLES **********
+ *****************************************/
+
+ public static int HASH_SIZE = 3;
+ private static String fileName = "replicons.txt";
+ private static String Genome_url = "http://cs.wellesley.edu/~btjaden/genomes/";
+ private static String Rockhopper_url = "http://cs.wellesley.edu/~btjaden/Rockhopper/";
+ public static String genome_DIR = Rockhopper.output_DIR + "genomes/";
+
+
+
+ /********************************************
+ ********** INSTANCE VARIABLES **********
+ ********************************************/
+
+ private boolean Genome_valid; // We are able to establish a connection to the server.
+ private boolean Rockhopper_valid; // We are able to establish a connection to the server.
+ private ArrayList<String> repliconList;
+ private HashMap<String,HashMap<Integer,Boolean>> repliconDictionary;
+
+
+
+ /**************************************
+ ********** CONSTRUCTORS **********
+ **************************************/
+
+ public NCBI() {
+ Rockhopper_valid = establishServerConnection(Rockhopper_url + fileName);
+ repliconList = readInRepliconList();
+ repliconDictionary = createRepliconDictionary(repliconList);
+ }
+
+
+
+ /*************************************************
+ ********** PUBLIC INSTANCE METHODS **********
+ *************************************************/
+
+ /**
+ * Returns true if a connection to the Genome server has been successfully established.
+ * Returns false otherwise.
+ */
+ public boolean isValid_Genome() {
+ return this.Genome_valid;
+ }
+
+ /**
+ * Returns true if a connection to the NCBI server has been successfully established.
+ * Returns false otherwise.
+ */
+ public boolean isValid_Rockhopper() {
+ return this.Rockhopper_valid;
+ }
+
+ /**
+ * Return a list of all replicon names that contain
+ * the substring s.
+ */
+ public ArrayList<String> getRepliconNames(String s) {
+ s = s.toLowerCase();
+ ArrayList<String> reps = new ArrayList<String>();
+ if (s.length() < HASH_SIZE) return reps;
+ String seed = s.substring(0, HASH_SIZE);
+ if (!repliconDictionary.containsKey(seed)) return reps;
+ HashMap<Integer,Boolean> list = repliconDictionary.get(seed);
+ for (Integer i : list.keySet()) {
+ String repliconName = repliconList.get(i.intValue()).split("\t")[0];
+ if (repliconName.toLowerCase().indexOf(s) >= 0) reps.add(repliconName);
+ }
+ Collections.sort(reps);
+ return reps;
+ }
+
+ /**
+ * Return the name of a FASTA file on the Genome server corresponding
+ * to the given replicon name.
+ */
+ public String getRepliconFileName(String repliconName) {
+ repliconName = repliconName.toLowerCase();
+ if (repliconName.length() < HASH_SIZE) return "";
+ String seed = repliconName.substring(0, HASH_SIZE);
+ if (!repliconDictionary.containsKey(seed)) return "";
+ HashMap<Integer,Boolean> list = repliconDictionary.get(seed);
+ for (Integer i : list.keySet()) {
+ String[] parse_repliconInfo = repliconList.get(i.intValue()).split("\t");
+ if (repliconName.equalsIgnoreCase(parse_repliconInfo[0])) return parse_repliconInfo[1];
+ }
+ return "";
+ }
+
+ /**
+ * Ensures the appropriate genomes files (*.fna, *.ptt, *.rnt) are
+ * available locally for the specified replicon. If not, the
+ * files are copied from the server and created locally.
+ * Returns true if successful, false otherwise (in which
+ * case the user must specifify the files locally).
+ */
+ public boolean prepGenomeFiles(String repliconName) {
+ boolean successful = true;
+ String serverFileName = getRepliconFileName(repliconName);
+ if (serverFileName.length() == 0) return false;
+ int slashIndex = serverFileName.lastIndexOf("/");
+ int periodIndex = serverFileName.lastIndexOf(".");
+ String baseFileName = serverFileName.substring(slashIndex+1, periodIndex);
+ String replicon_DIR = getRepliconDir(repliconName);
+ File resultsDIR = new File(Rockhopper.output_DIR);
+ if (!resultsDIR.exists()) resultsDIR.mkdir();
+ File genDIR = new File(genome_DIR);
+ if (!genDIR.exists()) genDIR.mkdir();
+ File repliconDIR = new File(genome_DIR + replicon_DIR);
+ if (!repliconDIR.exists()) repliconDIR.mkdir();
+ File genomeFile = new File(genome_DIR + replicon_DIR + baseFileName + ".fna");
+ if (!genomeFile.exists()) successful = downloadFile(serverFileName, genome_DIR + replicon_DIR + baseFileName + ".fna");
+ File geneFile = new File(genome_DIR + replicon_DIR + baseFileName + ".ptt");
+ if (!geneFile.exists()) downloadFile(serverFileName.substring(0, serverFileName.length()-4) + ".ptt", genome_DIR + replicon_DIR + baseFileName + ".ptt");
+ File rnaFile = new File(genome_DIR + replicon_DIR + baseFileName + ".rnt");
+ if (!rnaFile.exists()) downloadFile(serverFileName.substring(0, serverFileName.length()-4) + ".rnt", genome_DIR + replicon_DIR + baseFileName + ".rnt");
+ return successful;
+ }
+
+
+
+ /**************************************************
+ ********** PRIVATE INSTANCE METHODS **********
+ **************************************************/
+
+ /**
+ * Returns true if we can connect to the servers, false otherwise.
+ */
+ private boolean establishServerConnection(String url) {
+ try {
+ Scanner reader = new Scanner(new URL(url).openStream());
+ return true;
+ } catch (IOException e) {
+ return false;
+ }
+ }
+
+ /**
+ * Read in the list of replicons either from a local file or from
+ * the Rockhopper server. If there is no local file or its file
+ * size differs from that of the server file, then a new local
+ * file is created. Returns an empty list if neither a local
+ * file nor the server file could be found/accessed.
+ */
+ private ArrayList<String> readInRepliconList() {
+ ArrayList<String> repliconList = new ArrayList<String>();
+
+ try {
+ // Local file
+ File resultsDIR = new File(Rockhopper.output_DIR);
+ if (!resultsDIR.exists()) resultsDIR.mkdir();
+ File genDIR = new File(genome_DIR);
+ if (!genDIR.exists()) genDIR.mkdir();
+ File repFile = new File(genome_DIR + fileName);
+ long fileLength = 0;
+ if (repFile.exists()) fileLength = repFile.length();
+
+ // Server file
+ long serverLength = 0;
+ if (isValid_Rockhopper())
+ serverLength = new URL(Rockhopper_url + fileName).openConnection().getContentLength();
+
+ // Neither local file nor server file is available.
+ if (!repFile.exists() && !isValid_Rockhopper()) return repliconList;
+
+ // Use appropriate file (local or server) to read in replicon information.
+ Scanner reader;
+ PrintWriter writer = null;
+ if (serverLength == fileLength) reader = new Scanner(repFile);
+ else { // Read from server rather than local file. Create new local file.
+ reader = new Scanner(new URL(Rockhopper_url + fileName).openStream());
+ writer = new PrintWriter(repFile);
+ }
+ while (reader.hasNextLine()) {
+ String repliconInfo = reader.nextLine();
+ repliconList.add(repliconInfo);
+ if (serverLength != fileLength) writer.println(repliconInfo);
+ }
+ reader.close();
+ if (serverLength != fileLength) writer.close();
+ } catch (IOException e) {
+ Rockhopper.output("Could not process file " + genome_DIR + fileName + " and file " + Rockhopper_url + fileName + "\n");
+ }
+ return repliconList;
+ }
+
+ /**
+ * Create dictionary of replicon tokens. Values are indices in ArrayList.
+ */
+ private HashMap<String,HashMap<Integer,Boolean>> createRepliconDictionary(ArrayList<String> repliconList) {
+ HashMap<String,HashMap<Integer,Boolean>> repliconDictionary = new HashMap<String,HashMap<Integer,Boolean>>();
+ for (int i=0; i<repliconList.size(); i++) {
+ String name = repliconList.get(i).split("\t")[0].toLowerCase();
+ for (int j=0; j<name.length()-HASH_SIZE+1; j++) {
+ String key = name.substring(j, j+HASH_SIZE);
+ if (!repliconDictionary.containsKey(key)) repliconDictionary.put(key, new HashMap<Integer,Boolean>());
+ repliconDictionary.get(key).put(i, true);
+ }
+ }
+ return repliconDictionary;
+ }
+
+ /**
+ * Retrieves a file from a server and stores it locally.
+ * Returns true on success, false otherwise.
+ */
+ private boolean downloadFile(String serverFileName, String localFileName) {
+ try {
+ //System.setProperty("java.net.preferIPv4Stack", "true"); // Windows firewall bug
+ Scanner reader = new Scanner(new URL(serverFileName).openStream());
+ PrintWriter writer = new PrintWriter(new File(localFileName));
+ while (reader.hasNextLine()) writer.println(reader.nextLine());
+ reader.close();
+ writer.close();
+ return true;
+ } catch (IOException e) {
+ return false;
+ }
+ }
+
+
+
+ /**********************************************
+ ********** PUBLIC CLASS METHODS **********
+ **********************************************/
+
+ public static String getRepliconDir(String repliconName) {
+ for (int i=0; i<repliconName.length(); i++) {
+ char ch = repliconName.charAt(i);
+ if (!Character.isLetterOrDigit(ch)) repliconName = repliconName.replace(ch, '_');
+ }
+ return repliconName + "/";
+ }
+
+
+
+ /*************************************
+ ********** MAIN METHOD **********
+ *************************************/
+
+ public static void main(String[] args) {
+
+ }
+
+}
+
diff --git a/NegativeBinomial.java b/NegativeBinomial.java
new file mode 100644
index 0000000..93d993f
--- /dev/null
+++ b/NegativeBinomial.java
@@ -0,0 +1,138 @@
+/*
+ * Copyright 2013 Brian Tjaden
+ *
+ * This file is part of Rockhopper.
+ *
+ * Rockhopper is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * any later version.
+ *
+ * Rockhopper is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * (in the file gpl.txt) along with Rockhopper.
+ * If not, see <http://www.gnu.org/licenses/>.
+ */
+
+/**
+ * Probability mass function of negative binomial distribution.
+ * Based on saddle point algorithm found in "Fast and Accurate
+ * Computation of Binomial Probabilities" by Catherine Loader, 2000.
+ */
+public class NegativeBinomial {
+
+ /*****************************************
+ ********** CLASS VARIABLES **********
+ *****************************************/
+
+ private static double S0 = 0.08333333333333333333;
+ private static double S1 = 0.00277777777777777778;
+ private static double S2 = 0.00079365079365079365;
+ private static double S3 = 0.00059523809523809524;
+ private static double S4 = 0.00084175084175084175;
+ private static double[] sfe = {0.0, 0.081061466795327258219670264, 0.041340695955409294093822081, 0.0276779256849983391487892927, 0.020790672103765093111522771, 0.0166446911898211921631948653, 0.013876128823070747998945727, 0.0118967099458917700950557241, 0.010411265261972096497478567, 0.0092554621827127329177286366, 0.008330563433362871256469318, 0.0075736754879518407949720242, 0.006942840107209529865664152, 0.0064089941880042070684396370, 0.005951370112758847735624416, 0.0055547335 [...]
+
+
+
+ /**********************************************
+ ********** PUBLIC CLASS METHODS **********
+ **********************************************/
+
+ public static double pmf(double k, double n, double p, boolean b) {
+ if (p == 0.0) {
+ if (k == 0) return 1.0;
+ else return 0.0;
+ } else if (p == 1.0) {
+ if (k == n) return 1.0;
+ else return 0.0;
+ } else if (k == 0) {
+ return Math.exp(n * Math.log(1.0 - p));
+ } else if (k == n) {
+ return Math.exp(n * Math.log(p));
+ } else {
+ double lc = stirlerr(n) - stirlerr(k) - stirlerr(n - k) - bd0(k, n*p) - bd0(n-k, n*(1.0-p));
+ return p * Math.exp(lc) * Math.sqrt(n / (2.0*Math.PI*k*(n-k))); // We multiply by "p" here
+ }
+ }
+
+ public static double pmf(double k, double n, double p) {
+ if (p == 0.0) {
+ if (k == 0) return 1.0;
+ else return 0.0;
+ } else if (p == 1.0) {
+ if (k == n) return 1.0;
+ else return 0.0;
+ } else if (k == 0) {
+ return Math.exp(n * Math.log(1.0 - p));
+ } else if (k == n) {
+ return Math.exp(n * Math.log(p));
+ } else {
+ double lc = stirlerr(n) - stirlerr(k) - stirlerr(n - k) - bd0(k, n*p) - bd0(n-k, n*(1.0-p));
+ return p * Math.exp(lc) * Math.sqrt(n / (2.0*Math.PI*k*(n-k))); // We multiply by "p" here
+ }
+ }
+
+
+
+ /***********************************************
+ ********** PRIVATE CLASS METHODS **********
+ ***********************************************/
+
+ /**
+ * log(n!) - log(sqrt(2*pi*n)*(n/e)^n)
+ */
+ private static double stirlerr(double n) {
+ if (n < 16) return sfe[(int)n];
+ double nn = n*n;
+ if (n > 500) return (S0 - S1/nn)/n;
+ if (n > 80) return (S0 - (S1/S2/nn)/nn)/n;
+ if (n > 35) return (S0 - (S1 - (S2-S3/nn)/nn)/nn)/n;
+ return (S0 - (S1 - (S2 - (S3 - S4/nn)/nn)/nn)/nn)/n;
+ }
+
+ /**
+ * Deviance term: k*lg(k/np) + np - k
+ */
+ private static double bd0(double k, double np) {
+ if (Math.abs(k-np) < 0.1*(k+np)) {
+ double s = (k-np)*(k-np)/(k+np);
+ double v = (k-np)/(k+np);
+ double ej = 2*k*v;
+ int j = 1;
+ while (true) {
+ ej = ej*v*v;
+ double s1 = s+ej/(2*j+1);
+ if (s1 == s) return s;
+ s = s1;
+ j += 1;
+ }
+
+ }
+ return (k*Math.log(k/np)+np-k);
+ }
+
+
+
+ /*************************************
+ ********** MAIN METHOD **********
+ *************************************/
+
+ public static void main(String[] args) {
+
+ if (args.length < 3) {
+ System.err.println("\nUSAGE: java NegativeBinomial <k> <r> <p>" + "\n");
+ System.err.println("NegativeBinomial computes the probability mass function for the negative binomial distribution with parameters (r,p) at value k.\n");
+ System.exit(0);
+ }
+
+ int k = Integer.parseInt(args[0]);
+ int r = Integer.parseInt(args[1]);
+ double p = Double.parseDouble(args[2]);
+ System.out.println(pmf(r-1, k+r-1, p));
+ }
+
+}
diff --git a/Operons.java b/Operons.java
new file mode 100644
index 0000000..fab8c94
--- /dev/null
+++ b/Operons.java
@@ -0,0 +1,575 @@
+/*
+ * Copyright 2013 Brian Tjaden
+ *
+ * This file is part of Rockhopper.
+ *
+ * Rockhopper is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * any later version.
+ *
+ * Rockhopper is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * (in the file gpl.txt) along with Rockhopper.
+ * If not, see <http://www.gnu.org/licenses/>.
+ */
+
+import java.util.ArrayList;
+import java.util.Scanner;
+import java.util.Collections;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.PrintWriter;
+
+public class Operons {
+
+ /********************************************
+ ********** INSTANCE VARIABLES **********
+ ********************************************/
+
+ private SmoothDistribution lengthSame;
+ private SmoothDistribution lengthOpp;
+ private SmoothDistribution corrSame;
+ private SmoothDistribution corrOpp;
+ private double operonPrior;
+ private double nonOperonPrior;
+ private double[] operonIGexpression; // Distribution of IG expression for operons
+ private double[] nonOperonIGexpression; // Distribution of IG expression for non-operons
+ private ArrayList<Double> p_values;
+
+
+
+ /**************************************
+ ********** CONSTRUCTORS **********
+ **************************************/
+
+ public Operons(String geneFileName) {
+ this(readInGenes(geneFileName), readInGenes(geneFileName));
+ }
+
+ public Operons(ArrayList<Gene> codingGenes, ArrayList<Gene> genes) {
+ setOperonPrior(codingGenes);
+ }
+
+
+
+ /*************************************************
+ ********** PUBLIC INSTANCE METHODS **********
+ *************************************************/
+
+ /**
+ * Returns the number of gene pairs predicted to be co-transcribed
+ * as part of an operon.
+ */
+ public int getNumOperonGenePairs(ArrayList<Gene> genes) {
+ int numOperonGenePairs = 0;
+ for (int i=1; i<genes.size(); i++) {
+ if (isGenePairAnOperon(genes, i-1, i)) numOperonGenePairs++;
+ }
+ return numOperonGenePairs;
+ }
+
+ /**
+ * Returns true if the two genes at the specified indices, which must be consecutive,
+ * are predicted to be co-transcribed. Returns false otherwise.
+ */
+ public boolean isGenePairAnOperon(ArrayList<Gene> genes, int x, int y) {
+ if (x != y-1) {
+ Rockhopper.output("Error - two indices must be consecutive.\n");
+ return false;
+ }
+ if (genes.get(x).getStrand() != genes.get(y).getStrand()) return false; // Genes on different strands
+ int length = getIGlength(genes.get(x), genes.get(y));
+ if ((length < 40) || ((length < 100) && (getCorrelation(genes.get(x), genes.get(y)) >= 0.5))) return true;
+ return false;
+ }
+
+ /**
+ * Output to file gene-pairs predicted to be part of the same operon.
+ */
+ public void outputGenePairOperons(String operonOutputFile, ArrayList<Gene> genes) {
+ try {
+ PrintWriter writer = new PrintWriter(new File(operonOutputFile));
+ writer.println("Transcription Start" + "\t" + "Translation Start" + "\t" + "Translation Stop" + "\t" + "Transcription Stop" + "\t" + "Strand" + "\t" + "Name" + "\t" + "Synonym" + "\t" + "Product" + "\t" + "Transcription Start" + "\t" + "Translation Start" + "\t" + "Translation Stop" + "\t" + "Transcription Stop" + "\t" + "Strand" + "\t" + "Name" + "\t" + "Synonym" + "\t" + "Product" + "\t" + "Predicted Polycistronic?");
+ for (int i=1; i<genes.size(); i++) {
+ int length = getIGlength(genes.get(i-1), genes.get(i));
+ writer.print(genes.get(i-1).toString() + "\t" + genes.get(i).toString());
+ if (genes.get(i-1).getStrand() != genes.get(i).getStrand()) writer.print("\n");
+ else if (length < 40) writer.print("\t" + "YES" + "\n");
+ else if (length >= 100) writer.print("\n");
+ else if (getCorrelation(genes.get(i-1), genes.get(i)) >= 0.5) writer.print("\t" + "YES" + "\n");
+ else writer.print("\n");
+ }
+ writer.close();
+ } catch (FileNotFoundException e) {
+ Rockhopper.output("\nError - could not open file " + operonOutputFile + "\n\n");
+ System.exit(0);
+ }
+ }
+
+ /**
+ * Output to file merged operons.
+ * Return the number of predicted merged operons.
+ */
+ public int outputMergedOperons(String operonOutputFile, String browserOutputFile, String genomeName, ArrayList<Gene> genes, int size) {
+ int numMergedOperons = 0;
+ ArrayList<Integer> operonCoordinates = new ArrayList<Integer>(size);
+ try {
+ PrintWriter writer = new PrintWriter(new File(operonOutputFile));
+ writer.println("Start" + "\t" + "Stop" + "\t" + "Strand" + "\t" + "Number of Genes" + "\t" + "Genes");
+ ArrayList<String> genesInOperon = new ArrayList<String>();
+ int start = -1;
+ int stop = -1;
+ char strand = '?';
+ for (int i=1; i<genes.size(); i++) {
+ if (isGenePairAnOperon(genes, i-1, i)) { // Operon
+ if (start == -1) { // Start of new operon
+ start = Math.min(genes.get(i-1).getFirst(), genes.get(i).getFirst());
+ stop = Math.max(genes.get(i-1).getLast(), genes.get(i).getLast());
+ strand = genes.get(i).getStrand();
+ genesInOperon.clear();
+ genesInOperon.add(genes.get(i-1).getName());
+ genesInOperon.add(genes.get(i).getName());
+ } else if (strand == genes.get(i).getStrand()) { // Within operon
+ start = Math.min(start, genes.get(i).getFirst());
+ stop = Math.max(stop, genes.get(i).getLast());
+ genesInOperon.add(genes.get(i).getName());
+ } else { // New operon
+ writer.print(start + "\t" + stop + "\t" + strand + "\t" + genesInOperon.size() + "\t");
+ for (int z = 0; z<genesInOperon.size(); z++) {
+ if (z == 0) writer.print(genesInOperon.get(z));
+ else writer.print(", " + genesInOperon.get(z));
+ }
+ writer.println();
+ numMergedOperons++;
+ for (int j=start; j<=stop; j++) { // Keep track of multi-gene operon coords
+ while (operonCoordinates.size() <= stop) operonCoordinates.add(0);
+ if (strand == '+') operonCoordinates.set(j, 1);
+ if (strand == '-') operonCoordinates.set(j, -1);
+ }
+ start = -1;
+ stop = -1;
+ strand = '?';
+ genesInOperon.clear();
+ genesInOperon.add(genes.get(i-1).getName());
+ genesInOperon.add(genes.get(i).getName());
+ }
+ } else { // Non-operon
+ if (start >= 0) { // End of operon
+ writer.print(start + "\t" + stop + "\t" + strand + "\t" + genesInOperon.size() + "\t");
+ for (int z = 0; z<genesInOperon.size(); z++) {
+ if (z == 0) writer.print(genesInOperon.get(z));
+ else writer.print(", " + genesInOperon.get(z));
+ }
+ writer.println();
+ numMergedOperons++;
+ for (int j=start; j<=stop; j++) { // Keep track of multi-gene operon coords
+ while (operonCoordinates.size() <= stop) operonCoordinates.add(0);
+ if (strand == '+') operonCoordinates.set(j, 1);
+ if (strand == '-') operonCoordinates.set(j, -1);
+ }
+ start = -1;
+ stop = -1;
+ strand = '?';
+ genesInOperon.clear();
+ } else { // Within non-operon
+ // Do nothing.
+ }
+ }
+ }
+ if (start >= 0) { // Include final operon
+ writer.print(start + "\t" + stop + "\t" + strand + "\t" + genesInOperon.size() + "\t");
+ for (int z = 0; z<genesInOperon.size(); z++) {
+ if (z == 0) writer.print(genesInOperon.get(z));
+ else writer.print(", " + genesInOperon.get(z));
+ }
+ writer.println();
+ numMergedOperons++;
+ for (int j=start; j<=stop; j++) { // Keep track of multi-gene operon coords
+ while (operonCoordinates.size() <= stop) operonCoordinates.add(0);
+ if (strand == '+') operonCoordinates.set(j, 1);
+ if (strand == '-') operonCoordinates.set(j, -1);
+ }
+ start = -1;
+ stop = -1;
+ strand = '?';
+ genesInOperon.clear();
+ }
+ writer.close();
+ } catch (FileNotFoundException e) {
+ Rockhopper.output("\nError - could not open file " + operonOutputFile + "\n\n");
+ System.exit(0);
+ }
+
+ // Output genome browser file with multi-gene operon information
+ try {
+ PrintWriter browserWriter = new PrintWriter(new File(browserOutputFile));
+ browserWriter.println("track name=" + "\"" + "Multi-gene Operons" + "\"" + " color=255,0,255 altColor=255,0,255 graphType=bar viewLimits=-1:1");
+ browserWriter.println("fixedStep chrom=" + genomeName + " start=1 step=1");
+ for (int j=1; j<operonCoordinates.size(); j++) browserWriter.println(operonCoordinates.get(j));
+ browserWriter.close();
+ } catch (FileNotFoundException e) {
+ Rockhopper.output("\nError - could not open file " + browserOutputFile + "\n\n");
+ System.exit(0);
+ }
+
+ return numMergedOperons;
+ }
+
+
+
+ /**************************************************
+ ********** PRIVATE INSTANCE METHODS **********
+ **************************************************/
+
+ /**
+ * Determine the distribution of lengths between gene pairs.
+ * One distribution for consecutive genes on the same strand and
+ * one distribution for consecutive genes on the opposite strand.
+ */
+ private void determineOperonLengthDistributions(ArrayList<Gene> genes) {
+ ArrayList<Integer> length_same = new ArrayList<Integer>();
+ ArrayList<Integer> length_opp = new ArrayList<Integer>();
+ for (int i=1; i<genes.size(); i++) {
+ int length = Math.min(genes.get(i).getStart(),genes.get(i).getStop()) - Math.max(genes.get(i-1).getStart(),genes.get(i-1).getStop()) - 1;
+ if (genes.get(i).getStrand() == genes.get(i-1).getStrand()) length_same.add(length);
+ else length_opp.add(length);
+ }
+
+ // Uncomment the below lines to output operon length distributions
+ /*
+ lengthSame = new SmoothDistribution(length_same, 30.0, 10, -100, 300);
+ lengthOpp = new SmoothDistribution(length_opp, 30.0, 10, -100, 300);
+ Rockhopper.output(lengthSame.toString() + "\n" + lengthOpp.toString() + "\n");
+ */
+
+ lengthSame = new SmoothDistribution(length_same, 30.0, 1, -50, 200);
+ lengthOpp = new SmoothDistribution(length_opp, 30.0, 1);
+ lengthSame.setPseudocount(0.0);
+ }
+
+ /**
+ * Determine the distribution of correlations between gene pairs.
+ * One distribution for consecutive genes on the same strand and
+ * one distribution for consecutive genes on the opposite strand.
+ */
+ private void determineOperonCorrelationDistributions(ArrayList<Gene> genes) {
+ ArrayList<Integer> corr_same = new ArrayList<Integer>();
+ ArrayList<Integer> corr_opp = new ArrayList<Integer>();
+ for (int i=1; i<genes.size(); i++) {
+ double corr = getCorrelation(genes.get(i-1), genes.get(i));
+ if (genes.get(i).getStrand() == genes.get(i-1).getStrand()) corr_same.add((int)(corr*20));
+ else corr_opp.add((int)(corr*20));
+ }
+
+ // Uncomment the below lines to output operon correlation distributions
+ /*
+ corrSame = new SmoothDistribution(corr_same, 5.0, 1, -20, 20);
+ corrOpp = new SmoothDistribution(corr_opp, 5.0, 1, -20, 20);
+ Rockhopper.output(corrSame.toString() + "\n" + corrOpp.toString() + "\n");
+ */
+
+ corrSame = new SmoothDistribution(corr_same, 5.0, 1, -20, 20);
+ corrOpp = new SmoothDistribution(corr_opp, 5.0, 1, -20, 20);
+ corrSame.setPseudocount(0.0);
+ }
+
+ private double getCorrelation(Gene g1, Gene g2) {
+ ArrayList<Long> e1 = new ArrayList<Long>();
+ ArrayList<Long> e2 = new ArrayList<Long>();
+ for (int i=0; i<Rockhopper.numConditions; i++) {
+ e1.add(g1.getAvg(i));
+ e2.add(g2.getAvg(i));
+ }
+ return Misc.correlation(e1, e2);
+ }
+
+ /**
+ * Set prior probability of same-strand gene pair being an operon
+ * (based on section 2.2 of Westover 2005).
+ */
+ private void setOperonPrior(ArrayList<Gene> genes) {
+ int numberDirectons = 0; // Two or more consecutive genes on the same strand
+ int numberPairs = 0; // Pair of consecutive genes on the same strand
+ char previousStrand = '?';
+ int currentDirectonLength = 1; // Length of current directon under consideration
+ for (int i=0; i<genes.size(); i++) {
+ Gene g = genes.get(i);
+ if ((g.getStrand() != previousStrand) && (currentDirectonLength > 1)) {
+ numberDirectons += 1;
+ previousStrand = g.getStrand();
+ currentDirectonLength = 1;
+ } else if ((g.getStrand() != previousStrand) && (currentDirectonLength == 1)) {
+ previousStrand = g.getStrand();
+ currentDirectonLength = 1;
+ } else if ((g.getStrand() == previousStrand) && (currentDirectonLength > 1)) {
+ numberPairs += 1;
+ previousStrand = g.getStrand();
+ currentDirectonLength += 1;
+ } else if ((g.getStrand() == previousStrand) && (currentDirectonLength == 1)) {
+ numberPairs += 1;
+ previousStrand = g.getStrand();
+ currentDirectonLength += 1;
+ } else {
+ // Do nothing
+ }
+ }
+ if (currentDirectonLength > 1) numberDirectons += 1;
+ operonPrior = 1.0 - numberDirectons/(double)numberPairs;
+ nonOperonPrior = 1.0 - operonPrior;
+ //Rockhopper.output("Prior probability of operon:\t" + operonPrior + "\n"); // Output operon prior
+ }
+
+ /**
+ * Compute probability that two consecutive genes are co-transcribed.
+ * Return a list of p-values for all gene pairs.
+ */
+ private ArrayList<Double> operonExpression(ArrayList<Gene> genes) {
+ ArrayList<Double> p_values = new ArrayList<Double>(genes.size());
+ for (int i=0; i<genes.size(); i++) p_values.add(Double.MAX_VALUE);
+ p_values.set(0, 0.0);
+ ArrayList<ArrayList<Double>> all_p_values = new ArrayList<ArrayList<Double>>();
+ for (int i=0; i<genes.size(); i++) all_p_values.add(new ArrayList<Double>());
+ for (int i=0; i<Rockhopper.numConditions; i++) {
+ ArrayList<Double> means = new ArrayList<Double>(genes.size());
+ ArrayList<Double> variances = new ArrayList<Double>(genes.size());
+ for (int z=0; z<genes.size(); z++) {
+ means.add(0.0);
+ variances.add(0.0);
+ }
+ for (int z=1; z<genes.size(); z++) {
+ int numReplicates = genes.get(z).getNumReplicates(i);
+
+ // Compute mean expression in each condition.
+ for (int j=0; j<numReplicates; j++) {
+ means.set(z, means.get(z) + 1000.0*genes.get(z).getNormalizedCount(i,j)/(Math.abs(genes.get(z).getStop()-genes.get(z).getStart())+1));
+ }
+ means.set(z, means.get(z) / numReplicates);
+
+ // Compute variance.
+ double varianceAdjustment = 1.15;
+ // If we have NO replicates, then we use neighboring genes.
+ if (numReplicates == 1) { // We have no replicates. Use neighboring gene
+ double mean = (1000.0*genes.get(z-1).getNormalizedCount(i,0)/(Math.abs(genes.get(z-1).getStop()-genes.get(z-1).getStart())-1) + 1000.0*genes.get(z).getNormalizedCount(i,0)/(Math.abs(genes.get(z).getStop()-genes.get(z).getStart())+1)) / 2.0;
+ variances.set(z, Math.pow(1000.0*genes.get(z-1).getNormalizedCount(i,0)/(Math.abs(genes.get(z-1).getStop()-genes.get(z-1).getStart())+1) - mean, 2.0) + Math.pow(1000.0*genes.get(z).getNormalizedCount(i,0)/(Math.abs(genes.get(z).getStop()-genes.get(z).getStart())+1) - mean, 2.0));
+ variances.set(z, variances.get(z) / (2-1));
+ variances.set(z, Math.pow(variances.get(z), varianceAdjustment));
+ }
+
+ // Compute variance.
+ // If we DO have replicates, then we use the replicates.
+ if (numReplicates > 1) { // We have replicates. Use them
+ for (int j=0; j<numReplicates; j++) {
+ variances.set(z, Math.pow(1000.0*genes.get(z).getNormalizedCount(i,j)/(Math.abs(genes.get(z).getStop()-genes.get(z).getStart())+1) - means.get(z), 2.0));
+ }
+ variances.set(z, variances.get(z) / (numReplicates-1));
+ variances.set(z, Math.pow(variances.get(z), varianceAdjustment));
+ }
+ }
+
+ // Generate Lowess variances
+ means.set(0, means.get(1));
+ variances.set(0, variances.get(1));
+ ArrayList<Long> means_Long = new ArrayList<Long>(means.size());
+ ArrayList<Long> variances_Long = new ArrayList<Long>(variances.size());
+ for (int w=0; w<means.size(); w++) {
+ means_Long.add((long)(double)means.get(w));
+ variances_Long.add((long)(double)variances.get(w));
+ }
+ ArrayList<Long> lowessVariance = Lowess.lowess(means_Long, variances_Long);
+
+ // Determine operon probabilities
+ for (int z=1; z<genes.size(); z++) {
+ double p_value = computeProbabilityOfSameTranscript(genes.get(z-1), genes.get(z), (double)lowessVariance.get(z-1), (double)lowessVariance.get(z), i);
+ p_values.set(z, Math.min(p_values.get(z), p_value));
+ all_p_values.get(z).add(p_value);
+ }
+ }
+ for (int z=1; z<genes.size(); z++) {
+ double avg = 0.0;
+ for (int y=0; y<all_p_values.get(z).size(); y++) avg += all_p_values.get(z).get(y);
+ avg /= all_p_values.get(z).size();
+ p_values.set(z, avg);
+ }
+ return p_values;
+ }
+
+
+
+ /***********************************************
+ ********** PRIVATE CLASS METHODS **********
+ ***********************************************/
+
+ /**
+ * Reads in a file of genes (either *.ptt or *.rnt) and returns
+ * an ArrayList of gene objects.
+ */
+ private static ArrayList<Gene> readInGenes(String fileName) {
+ ArrayList<Gene> listOfGenes = new ArrayList<Gene>();
+ try {
+ Scanner reader = new Scanner(new File(fileName));
+ for (int i=0; i<3; i++) reader.nextLine(); // Ignore 3 header lines
+ while (reader.hasNext()) { // Continue until end of file
+ listOfGenes.add(new Gene(reader.nextLine(), "ORF")); // Create new gene
+ }
+ reader.close();
+ } catch (FileNotFoundException e) {
+ Rockhopper.output("Error - the file " + fileName + " could not be found and opened.\n");
+ }
+ return listOfGenes;
+ }
+
+ /**
+ * Returns the probability, based on expression in the given condition "i", that "g1"
+ * is NOT differentially expressed from "g2".
+ * I.e., return the probability that "g1" is part of the same polycistronic transcript
+ * as "g2" in the specified condition "i".
+ */
+ private static double computeProbabilityOfSameTranscript(Gene g1, Gene g2, double lowessVar1, double lowessVar2, int i) {
+ int numReplicates = g1.getNumReplicates(i);
+
+ double k_A = 0.0;
+ double k_B = 0.0;
+ for (int j=0; j<numReplicates; j++) {
+ k_A += 1000.0*g1.getNormalizedCount(i,j)/(Math.abs(g1.getStop()-g1.getStart())+1);
+ k_B += 1000.0*g2.getNormalizedCount(i,j)/(Math.abs(g2.getStop()-g2.getStart())+1);
+ }
+ double q = k_A + k_B;
+
+ double mean_A = q;
+ double mean_B = q;
+ double variance_A = lowessVar1;
+ double variance_B = lowessVar2;
+ double p_a = mean_A / variance_A;
+ double p_b = mean_B / variance_B;
+ double r_a = Math.max(mean_A*mean_A / (variance_A - mean_A), 1.0); // r should never be below 1
+ double r_b = Math.max(mean_B*mean_B / (variance_B - mean_B), 1.0); // r should never be below 1
+
+ if ((p_a < 0.0) || (p_b < 0.0) || (p_a > 1.0) || (p_b > 1.0) || (variance_A == 0.0) || (variance_B == 0.0)) return 0.0;
+
+ // Compute p-value of differential expression in two conditions
+ double p_ab = NegativeBinomial.pmf(r_a-1, k_A+r_a-1, p_a) * NegativeBinomial.pmf(r_b-1, k_B+r_b-1, p_b);
+ long k_sum = (long)(k_A + k_B);
+
+ // Fast p-value estimation
+ double numerator = 0.0;
+ double denominator = 0.0;
+ long mode = (long)k_B;
+
+ long a = mode; // Begin near middle
+ long increment = 1;
+ long alpha = 1000; // Number of times we increment by 1 (raising alpha raises precision but slows down computation)
+ double previous_p = 0.0;
+ while (a <= k_sum) {
+ long b = k_sum - a;
+ double current_p = NegativeBinomial.pmf(r_a-1, a+r_a-1, p_a) * NegativeBinomial.pmf(r_b-1, b+r_b-1, p_b);
+ denominator += current_p;
+ if (current_p <= p_ab) numerator += current_p;
+ if (increment > 1) {
+ double average_p = (current_p + previous_p) / 2.0;
+ denominator += average_p * (increment-1);
+ if (average_p <= p_ab) numerator += average_p * (increment-1);
+ }
+ previous_p = current_p;
+ if (a - mode >= alpha) {
+ alpha *= 2;
+ increment *= 2;
+ }
+ a += increment;
+ }
+
+ a = mode; // Begin near middle
+ long decrement = 1;
+ alpha = 1000; // Number of times we decrement by 1 (raising alpha raises precision but slows down computation)
+ previous_p = 0.0;
+ while (a >= 0) {
+ long b = k_sum - a;
+ double current_p = NegativeBinomial.pmf(r_a-1, a+r_a-1, p_a) * NegativeBinomial.pmf(r_b-1, b+r_b-1, p_b);
+ denominator += current_p;
+ if (current_p <= p_ab) numerator += current_p;
+ if (decrement > 1) {
+ double average_p = (previous_p + current_p) / 2.0;
+ denominator += average_p * (decrement-1);
+ if (average_p <= p_ab) numerator += average_p * (decrement-1);
+ }
+ previous_p = current_p;
+ if (mode - a >= alpha) {
+ alpha *= 2;
+ decrement *= 2;
+ }
+ a -= decrement;
+ }
+
+ double p_value = 1.0;
+ if (denominator != 0.0) p_value = numerator / denominator;
+ return p_value;
+ }
+
+ /**
+ * Returns the number of nucleotides in the IG region between the
+ * two genes. g1 precede g2. May return a negative number if the
+ * genes overlap.
+ */
+ private static int getIGlength(Gene g1, Gene g2) {
+ int IG_start = -1;
+ if (g1.isORF()) IG_start = Math.max(g1.getStart(), g1.getStop()) + 1;
+ else IG_start = Math.max(g1.getStartT(), g1.getStopT()) + 1;
+ int IG_stop = -1;
+ if (g2.isORF()) IG_stop = Math.min(g2.getStart(), g2.getStop()) - 1;
+ else IG_stop = Math.min(g2.getStartT(), g2.getStopT()) - 1;
+ return IG_stop - IG_start + 1;
+ }
+
+ /**
+ * Returns the percentage of nucleotides in the IG region
+ * that are expressed, i.e., that correspond to predicted
+ * UTRs.
+ */
+ private static double getPercentIGexpressed(Gene g1, Gene g2) {
+ if (!g1.isORF() || !g2.isORF()) return 0.0; // Only consider two ORFs
+ int IG_length = getIGlength(g1, g2);
+ if (IG_length <= 0) return 0.0; // Only consider IGs with non-zero length
+
+ int UTR1 = 0;
+ if ((g1.getStrand() == '+') && (g1.getStopT() > 0))
+ UTR1 = g1.getStopT() - g1.getStop();
+ if ((g1.getStrand() == '-') && (g1.getStartT() > 0))
+ UTR1 = g1.getStartT() - g1.getStart();
+ int UTR2 = 0;
+ if ((g2.getStrand() == '+') && (g2.getStartT() > 0))
+ UTR2 = g2.getStart() - g2.getStartT();
+ if ((g2.getStrand() == '-') && (g2.getStopT() > 0))
+ UTR2 = g2.getStop() - g2.getStopT();
+ int UTR_length = UTR1 + UTR2;
+ return Math.min(UTR_length / (double)IG_length, 1.0);
+ }
+
+
+
+ /*************************************
+ ********** MAIN METHOD **********
+ *************************************/
+
+ /**
+ * The Main method, when invoked with the name of a gene file (*.ptt)
+ * as a command line argument, computes the distribution of lengths between
+ * consecutive genes on the same strand and the distribution of lengths
+ * between consecutive genes on the opposite strand. Output is to same.dist
+ * and opp.dist.
+ */
+ public static void main(String[] args) {
+ if (args.length < 1) {
+ System.err.println("\nThe Operons application requires one command line argument, the name of a gene file (*.ptt). The application computes the distribution of lengths between consecutive genes on the same strand and the distribution of lengths between consecutive genes on the opposite strand. Output is to same.dist and opp.dist.");
+ System.err.println("\n\tjava Operons NC_******.ptt\n");
+ System.exit(0);
+ }
+
+ Operons ops = new Operons(args[0]);
+
+ }
+
+}
diff --git a/ParametersGUI.java b/ParametersGUI.java
new file mode 100644
index 0000000..1d93cb5
--- /dev/null
+++ b/ParametersGUI.java
@@ -0,0 +1,674 @@
+/*
+ * Copyright 2013 Brian Tjaden
+ *
+ * This file is part of Rockhopper.
+ *
+ * Rockhopper is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * any later version.
+ *
+ * Rockhopper is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * (in the file gpl.txt) along with Rockhopper.
+ * If not, see <http://www.gnu.org/licenses/>.
+ */
+
+import java.util.Hashtable;
+import java.util.Scanner;
+import java.awt.*;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseListener;
+import javax.swing.*;
+import java.io.PrintWriter;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.util.NoSuchElementException;
+
+public class ParametersGUI {
+
+ private final String fileName = "parameters.txt";
+ JApplet applet;
+
+ // Default values
+ private final double mismatches_DEFAULT = Peregrine.percentMismatches;
+ private final double minReadLength_DEFAULT = Peregrine.percentSeedLength;
+ private final boolean singleEndOrientation_DEFAULT = Peregrine.singleEndOrientationReverseComplement;
+ private final String matePairOrientation_DEFAULT = Peregrine.pairedEndOrientation;
+ private final int numProcessors_DEFAULT = 0;
+ private final int maxPairedEndLength_DEFAULT = Peregrine.maxPairedEndLength;
+ private final boolean verboseOutput_DEFAULT = Rockhopper.verbose;
+ private final boolean outputSAM_DEFAULT = false;
+ private final boolean isStrandSpecific_DEFAULT = !Rockhopper.unstranded;
+ private final boolean testDifferentialExp_DEFAULT = Rockhopper.computeExpression;
+ private final boolean predictOperons_DEFAULT = Rockhopper.computeOperons;
+ private final boolean transcriptBoundaries_DEFAULT = Rockhopper.computeTranscripts;
+ private final double expressionParameter_DEFAULT = Rockhopper.transcriptSensitivity;
+ private final int minReadsMapping_DEFAULT = Assembler.MIN_READS_MAPPING;
+ private final int minTranscriptLength_DEFAULT = 2 * Assembler.k;
+ private final int minSeedExpression_DEFAULT = Assembler.minSeedExpression;
+ private final int minExtendExpression_DEFAULT = Assembler.minExpression;
+ private final String outputDIR_DEFAULT = Rockhopper.output_DIR;
+
+ // Editable values
+ public double mismatches;
+ public double minReadLength;
+ public boolean singleEndOrientation;
+ public String matePairOrientation;
+ public int numProcessors;
+ public int maxPairedEndLength;
+ public boolean verboseOutput;
+ public boolean outputSAM;
+ public boolean isStrandSpecific;
+ public boolean testDifferentialExp;
+ public boolean predictOperons;
+ public boolean transcriptBoundaries;
+ public double expressionParameter;
+ public int minReadsMapping;
+ public int minTranscriptLength;
+ public int minSeedExpression;
+ public int minExtendExpression;
+ public String outputDIR;
+
+ // GUI components
+ private JFrame parameterFrame;
+ private JTextField qualityTextField;
+ private JTextField mismatchTextField;
+ private JTextField readLengthTextField;
+ private JCheckBox orientationCheckBox;
+ private JComboBox orientationComboBox;
+ private JTextField processorsTextField;
+ private JTextField pairedEndLengthTextField;
+ private JCheckBox verbose;
+ private JCheckBox sam;
+ private JCheckBox strand;
+ private JCheckBox diffExpression;
+ private JCheckBox operons;
+ private JCheckBox boundaries;
+ private JSlider minExpression;
+ private JTextField minReadsMappingTextField;
+ private JTextField minTranscriptLengthTextField;
+ private JTextField minSeedExpressionTextField;
+ private JTextField minExtendExpressionTextField;
+ private JTextField dirTextField;
+ private JLabel browseLabel;
+ private JFileChooser fc;
+ private File f;
+ private ImageIcon browseButton, browseButtonPressed;
+ private JButton defaultButton;
+ private JButton saveButton;
+
+
+
+ /**
+ * Constructor.
+ */
+ public ParametersGUI(JApplet applet) {
+ this.applet = applet;
+ browseButton = RockhopperGUI.getScaledImage("images/browse.gif", 77, 29);
+ browseButtonPressed = RockhopperGUI.getScaledImage("images/browsePressed.gif", 77, 29);
+
+ // Initialize to default values
+ mismatches = mismatches_DEFAULT;
+ minReadLength = minReadLength_DEFAULT;
+ singleEndOrientation = singleEndOrientation_DEFAULT;
+ matePairOrientation = matePairOrientation_DEFAULT;
+ numProcessors = numProcessors_DEFAULT;
+ maxPairedEndLength = maxPairedEndLength_DEFAULT;
+ verboseOutput = verboseOutput_DEFAULT;
+ outputSAM = outputSAM_DEFAULT;
+ isStrandSpecific = isStrandSpecific_DEFAULT;
+ testDifferentialExp = testDifferentialExp_DEFAULT;
+ predictOperons = predictOperons_DEFAULT;
+ transcriptBoundaries = transcriptBoundaries_DEFAULT;
+ expressionParameter = expressionParameter_DEFAULT;
+ minReadsMapping = minReadsMapping_DEFAULT;
+ minTranscriptLength = minTranscriptLength_DEFAULT;
+ minSeedExpression = minSeedExpression_DEFAULT;
+ minExtendExpression = minExtendExpression_DEFAULT;
+ outputDIR = outputDIR_DEFAULT;
+
+ // Read in from file previous parameter values.
+ Scanner reader = null;
+ fc = new JFileChooser();
+ fc.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
+ try {
+ File f = new File(RockhopperGUI.directory + fileName);
+ if (!f.exists()) return;
+ reader = new Scanner(f);
+ } catch (FileNotFoundException ex) {
+ // Do nothing. Use default parameter values.
+ } catch (NoSuchElementException ex) {
+ // Do nothing. Use default parameter values.
+ }
+ if (reader != null) {
+ try {
+ String version = reader.nextLine();
+ if (!version.equals(Rockhopper.version)) throw new Exception();
+ double mismatches_TEMP = Double.parseDouble(reader.nextLine());
+ double minReadLength_TEMP = Double.parseDouble(reader.nextLine());
+ boolean singleEndOrientation_TEMP = Boolean.valueOf(reader.nextLine()).booleanValue();
+ String matePairOrientation_TEMP = reader.nextLine();
+ int numProcessors_TEMP = Integer.parseInt(reader.nextLine());
+ int maxPairedEndLength_TEMP = Integer.parseInt(reader.nextLine());
+ boolean verboseOutput_TEMP = Boolean.valueOf(reader.nextLine()).booleanValue();
+ boolean outputSAM_TEMP = Boolean.valueOf(reader.nextLine()).booleanValue();
+ boolean isStrandSpecific_TEMP = Boolean.valueOf(reader.nextLine()).booleanValue();
+ boolean testDifferentialExp_TEMP = Boolean.valueOf(reader.nextLine()).booleanValue();
+ boolean predictOperons_TEMP = Boolean.valueOf(reader.nextLine()).booleanValue();
+ boolean transcriptBoundaries_TEMP = Boolean.valueOf(reader.nextLine()).booleanValue();
+ double expressionParameter_TEMP = Double.parseDouble(reader.nextLine());
+ int minReadsMapping_TEMP = Integer.parseInt(reader.nextLine());
+ int minTranscriptLength_TEMP = Integer.parseInt(reader.nextLine());
+ int minSeedExpression_TEMP = Integer.parseInt(reader.nextLine());
+ int minExtendExpression_TEMP = Integer.parseInt(reader.nextLine());
+ String outputDIR_TEMP = reader.nextLine();
+ reader.close();
+
+ mismatches = mismatches_TEMP;
+ minReadLength = minReadLength_TEMP;
+ singleEndOrientation = singleEndOrientation_TEMP;
+ matePairOrientation = matePairOrientation_TEMP;
+ numProcessors = numProcessors_TEMP;
+ maxPairedEndLength = maxPairedEndLength_TEMP;
+ verboseOutput = verboseOutput_TEMP;
+ outputSAM = outputSAM_TEMP;
+ isStrandSpecific = isStrandSpecific_TEMP;
+ testDifferentialExp = testDifferentialExp_TEMP;
+ predictOperons = predictOperons_TEMP;
+ transcriptBoundaries = transcriptBoundaries_TEMP;
+ expressionParameter = expressionParameter_TEMP;
+ minReadsMapping = minReadsMapping_TEMP;
+ minTranscriptLength = minTranscriptLength_TEMP;
+ minSeedExpression = minSeedExpression_TEMP;
+ minExtendExpression = minExtendExpression_TEMP;
+ outputDIR = outputDIR_TEMP;
+ } catch (Exception e) { }
+ }
+ }
+
+ public boolean isSource(Object source) {
+ if (source.equals(defaultButton)) return true;
+ if (source.equals(saveButton)) return true;
+ if (source.equals(browseLabel)) return true;
+ return false;
+ }
+
+ public void handleEvent(Object source) {
+ if (source.equals(defaultButton)) {
+ mismatches = mismatches_DEFAULT;
+ minReadLength = minReadLength_DEFAULT;
+ singleEndOrientation = singleEndOrientation_DEFAULT;
+ matePairOrientation = matePairOrientation_DEFAULT;
+ numProcessors = numProcessors_DEFAULT;
+ maxPairedEndLength = maxPairedEndLength_DEFAULT;
+ verboseOutput = verboseOutput_DEFAULT;
+ outputSAM = outputSAM_DEFAULT;
+ isStrandSpecific = isStrandSpecific_DEFAULT;
+ testDifferentialExp = testDifferentialExp_DEFAULT;
+ predictOperons = predictOperons_DEFAULT;
+ transcriptBoundaries = transcriptBoundaries_DEFAULT;
+ expressionParameter = expressionParameter_DEFAULT;
+ minReadsMapping = minReadsMapping_DEFAULT;
+ minTranscriptLength = minTranscriptLength_DEFAULT;
+ minSeedExpression = minSeedExpression_DEFAULT;
+ minExtendExpression = minExtendExpression_DEFAULT;
+ outputDIR = outputDIR_DEFAULT;
+
+ mismatchTextField.setText("" + mismatches);
+ readLengthTextField.setText("" + minReadLength);
+ orientationCheckBox.setSelected(singleEndOrientation);
+ orientationComboBox.setSelectedItem(matePairOrientation);
+ processorsTextField.setText("" + numProcessors);
+ pairedEndLengthTextField.setText("" + maxPairedEndLength);
+ verbose.setSelected(verboseOutput);
+ sam.setSelected(outputSAM);
+ strand.setSelected(isStrandSpecific);
+ diffExpression.setSelected(testDifferentialExp);
+ operons.setSelected(predictOperons);
+ boundaries.setSelected(transcriptBoundaries);
+ minExpression.setValue((int)(expressionParameter*10));
+ minReadsMappingTextField.setText("" + minReadsMapping);
+ minTranscriptLengthTextField.setText("" + minTranscriptLength);
+ minSeedExpressionTextField.setText("" + minSeedExpression);
+ minExtendExpressionTextField.setText("" + minExtendExpression);
+ dirTextField.setText(outputDIR);
+ outputParametersToFile();
+ } else if (source.equals(saveButton)) {
+ try { mismatches = Double.parseDouble(mismatchTextField.getText()); }
+ catch (NumberFormatException ex) {
+ error("Parameter input error", "An invalid number was entered for the allowed mismatches.");
+ return;
+ }
+ try { minReadLength = Double.parseDouble(readLengthTextField.getText()); }
+ catch (NumberFormatException ex) {
+ error("Parameter input error", "An invalid number was entered for the minimum seed.");
+ return;
+ }
+ try { numProcessors = Integer.parseInt(processorsTextField.getText()); }
+ catch (NumberFormatException ex) {
+ error("Parameter input error", "An invalid integer was entered for the number of processors.");
+ return;
+ }
+ try { maxPairedEndLength = Integer.parseInt(pairedEndLengthTextField.getText()); }
+ catch (NumberFormatException ex) {
+ error("Parameter input error", "An invalid integer was entered for the maximum paired end length.");
+ return;
+ }
+ try { minReadsMapping = Integer.parseInt(minReadsMappingTextField.getText()); }
+ catch (NumberFormatException ex) {
+ error("Parameter input error", "An invalid integer was entered for the minimum number of mapping reads.");
+ return;
+ }
+ try { minTranscriptLength = Integer.parseInt(minTranscriptLengthTextField.getText()); }
+ catch (NumberFormatException ex) {
+ error("Parameter input error", "An invalid integer was entered for the minimum transcript length.");
+ return;
+ }
+ try { minSeedExpression = Integer.parseInt(minSeedExpressionTextField.getText()); }
+ catch (NumberFormatException ex) {
+ error("Parameter input error", "An invalid integer was entered for the minimum seed count.");
+ return;
+ }
+ try { minExtendExpression = Integer.parseInt(minExtendExpressionTextField.getText()); }
+ catch (NumberFormatException ex) {
+ error("Parameter input error", "An invalid integer was entered for the minimum extension count.");
+ return;
+ }
+ singleEndOrientation = orientationCheckBox.isSelected();
+ matePairOrientation = (String)orientationComboBox.getSelectedItem();
+ verboseOutput = verbose.isSelected();
+ outputSAM = sam.isSelected();
+ isStrandSpecific = strand.isSelected();
+ testDifferentialExp = diffExpression.isSelected();
+ predictOperons = operons.isSelected();
+ transcriptBoundaries = boundaries.isSelected();
+ expressionParameter = minExpression.getValue()/10.0;
+ outputDIR = dirTextField.getText();
+ outputParametersToFile();
+ } else if (source.equals(browseLabel)) {
+ fileChooser();
+ }
+ }
+
+ public void mousePressed(Object source) {
+ if (source.equals(browseLabel)) {
+ browseLabel.setIcon(browseButtonPressed);
+ }
+ }
+
+ public void mouseReleased(Object source) {
+ if (source.equals(browseLabel)) {
+ browseLabel.setIcon(browseButton);
+ }
+ }
+
+ /**
+ * Open frame to display parameter options.
+ */
+ public void displayParameters() {
+ int width = 700;
+ parameterFrame = new JFrame("Parameter Settings");
+ parameterFrame.setSize(width, 620);
+ parameterFrame.setResizable(false);
+ parameterFrame.setLocationRelativeTo(null);
+ parameterFrame.setIconImage(new ImageIcon(RockhopperGUI.penguin).getImage());
+ JPanel p1 = new JPanel(new FlowLayout(FlowLayout.CENTER));
+ p1.setPreferredSize(new Dimension(width, 620));
+ p1.setBackground(RockhopperGUI.lightBlue);
+ JPanel spacerPanel = new JPanel(new FlowLayout(FlowLayout.CENTER));
+ spacerPanel.setPreferredSize(new Dimension(width, 5));
+ spacerPanel.setBackground(RockhopperGUI.lightBlue);
+ p1.add(spacerPanel);
+
+ JLabel generalLabel = new JLabel("General parameters");
+ generalLabel.setForeground(RockhopperGUI.gold);
+ generalLabel.setFont(new Font("Times", Font.ITALIC, 18));
+ p1.add(generalLabel);
+ JPanel gen = new JPanel(new GridLayout(4,2));
+ gen.setPreferredSize(new Dimension(width-150, 120));
+ gen.setBackground(RockhopperGUI.lightBlue);
+
+ // Strand specific
+ JPanel gen_a = new JPanel(new FlowLayout(FlowLayout.RIGHT));
+ gen_a.setBackground(RockhopperGUI.lightBlue);
+ JLabel strandLabel = new JLabel("Strand specific");
+ strandLabel.setToolTipText("Indicates whether RNA-seq experiments are strand specific (checked) or strand ambiguous (unchecked)");
+ gen_a.add(strandLabel);
+ strand = new JCheckBox();
+ strand.setBackground(RockhopperGUI.lightBlue);
+ strand.setSelected(isStrandSpecific);
+ strand.setToolTipText("Indicates whether RNA-seq experiments are strand specific (checked) or strand ambiguous (unchecked)");
+ gen_a.add(strand);
+ gen.add(gen_a);
+
+ // Test for differential expression
+ JPanel gen_b = new JPanel(new FlowLayout(FlowLayout.RIGHT));
+ gen_b.setBackground(RockhopperGUI.lightBlue);
+ JLabel diffExpressionLabel = new JLabel("Test for differential expression");
+ diffExpressionLabel.setToolTipText("Test for differential expression of each transcripts in pairs of experiments");
+ gen_b.add(diffExpressionLabel);
+ diffExpression = new JCheckBox();
+ diffExpression.setBackground(RockhopperGUI.lightBlue);
+ diffExpression.setSelected(testDifferentialExp);
+ diffExpression.setToolTipText("Test for differential expression of each transcripts in pairs of experiments");
+ gen_b.add(diffExpression);
+ gen.add(gen_b);
+
+ // Single-end orientation
+ JPanel gen_c = new JPanel(new FlowLayout(FlowLayout.RIGHT));
+ gen_c.setBackground(RockhopperGUI.lightBlue);
+ JLabel singleEndReverseComplementLabel = new JLabel("Reverse complement reads");
+ singleEndReverseComplementLabel.setToolTipText("Reverse complement all single-end reads");
+ gen_c.add(singleEndReverseComplementLabel);
+ orientationCheckBox = new JCheckBox();
+ orientationCheckBox.setBackground(RockhopperGUI.lightBlue);
+ orientationCheckBox.setSelected(singleEndOrientation);
+ orientationCheckBox.setToolTipText("Reverse complement all single-end reads");
+ gen_c.add(orientationCheckBox);
+ gen.add(gen_c);
+
+ // Paired-end orientation
+ JPanel gen_d = new JPanel(new FlowLayout(FlowLayout.RIGHT));
+ gen_d.setBackground(RockhopperGUI.lightBlue);
+ JLabel orientationLabel = new JLabel("Orientation of mate-pair reads");
+ orientationLabel.setToolTipText("Orientation of two mate reads for paired-end reads, f=forward and r=reverse_complement");
+ gen_d.add(orientationLabel);
+ orientationComboBox = new JComboBox();
+ orientationComboBox.setToolTipText("Orientation of two mate reads for paired-end reads, f=forward and r=reverse_complement");
+ orientationComboBox.addItem("ff");
+ orientationComboBox.addItem("fr");
+ orientationComboBox.addItem("rf");
+ orientationComboBox.addItem("rr");
+ orientationComboBox.setSelectedItem(matePairOrientation);
+ gen_d.add(orientationComboBox);
+ gen.add(gen_d);
+
+ // Verbose
+ JPanel gen_e = new JPanel(new FlowLayout(FlowLayout.RIGHT));
+ gen_e.setBackground(RockhopperGUI.lightBlue);
+ JLabel verboseLabel = new JLabel("Verbose output");
+ verboseLabel.setToolTipText("Verbose output to transcript.txt file, including raw counts, normalized counts, and expression variances");
+ gen_e.add(verboseLabel);
+ verbose = new JCheckBox();
+ verbose.setBackground(RockhopperGUI.lightBlue);
+ verbose.setSelected(verboseOutput);
+ verbose.setToolTipText("Verbose output to transcripts.txt file, including raw counts, normalized counts, and expression variances");
+ gen_e.add(verbose);
+ gen.add(gen_e);
+
+ // Output SAM
+ JPanel gen_f = new JPanel(new FlowLayout(FlowLayout.RIGHT));
+ gen_f.setBackground(RockhopperGUI.lightBlue);
+ JLabel samLabel = new JLabel("Output SAM file");
+ samLabel.setToolTipText("Output sequencing reads to a SAM file");
+ gen_f.add(samLabel);
+ sam = new JCheckBox();
+ sam.setBackground(RockhopperGUI.lightBlue);
+ sam.setSelected(outputSAM);
+ sam.setToolTipText("Output sequencing reads to a SAM file");
+ gen_f.add(sam);
+ gen.add(gen_f);
+
+ // Maximum paired-end length
+ JPanel gen_g = new JPanel(new FlowLayout(FlowLayout.RIGHT));
+ gen_g.setBackground(RockhopperGUI.lightBlue);
+ JLabel pairedEndLengthLabel = new JLabel("Max bases between paired reads");
+ pairedEndLengthLabel.setToolTipText("Maximum number of bases between mate pairs for paired-end reads");
+ gen_g.add(pairedEndLengthLabel);
+ pairedEndLengthTextField = new JTextField("" + maxPairedEndLength, 4);
+ pairedEndLengthTextField.setToolTipText("Maximum number of bases between mate pairs for paired-end reads");
+ gen_g.add(pairedEndLengthTextField);
+ gen.add(gen_g);
+
+ // Number of processors
+ JPanel gen_h = new JPanel(new FlowLayout(FlowLayout.RIGHT));
+ gen_h.setBackground(RockhopperGUI.lightBlue);
+ JLabel processorsLabel = new JLabel("Number of processors");
+ processorsLabel.setToolTipText("Number of parallel processors to use; a value of zero indicates that Rockhopper should determine the number (recommended)");
+ gen_h.add(processorsLabel);
+ processorsTextField = new JTextField("" + numProcessors, 3);
+ processorsTextField.setToolTipText("Number of parallel processors to use; a value of zero indicates that Rockhopper should determine the number (recommended)");
+ gen_h.add(processorsTextField);
+ gen.add(gen_h);
+ p1.add(gen);
+
+ // Output file location
+ JPanel output = new JPanel(new FlowLayout(FlowLayout.CENTER));
+ output.setPreferredSize(new Dimension(width-50, 40));
+ output.setBackground(RockhopperGUI.lightBlue);
+ JLabel dirLabel = new JLabel("Output file location:");
+ dirLabel.setBackground(RockhopperGUI.lightBlue);
+ dirLabel.setToolTipText("Location where output files should be written");
+ dirTextField = new JTextField(outputDIR, 25);
+ dirTextField.setToolTipText("Location where output files should be written");
+ browseLabel = new JLabel(browseButton);
+ browseLabel.setToolTipText("Search for location");
+ browseLabel.addMouseListener((MouseListener)applet);
+ output.add(dirLabel);
+ output.add(dirTextField);
+ output.add(browseLabel);
+
+ // Spacer
+ p1.add(output);
+ spacerPanel = new JPanel(new FlowLayout(FlowLayout.CENTER));
+ spacerPanel.setPreferredSize(new Dimension(width, 10));
+ spacerPanel.setBackground(RockhopperGUI.lightBlue);
+ p1.add(spacerPanel);
+
+ // Parameters for reference based assembly
+ JLabel referenceBasedLabel = new JLabel("Parameters for reference based assembly");
+ referenceBasedLabel.setForeground(RockhopperGUI.gold);
+ referenceBasedLabel.setFont(new Font("Times", Font.ITALIC, 18));
+ p1.add(referenceBasedLabel);
+ JPanel ref = new JPanel(new GridLayout(2,2));
+ ref.setPreferredSize(new Dimension(width-150, 70));
+ ref.setBackground(RockhopperGUI.lightBlue);
+
+ // Allowed mismatches
+ JPanel ref_a = new JPanel(new FlowLayout(FlowLayout.RIGHT));
+ ref_a.setBackground(RockhopperGUI.lightBlue);
+ JLabel mismatchLabel = new JLabel("Allowed mismatches");
+ mismatchLabel.setToolTipText("Maximum number of mismatches/gaps/insertions allowed when aligning read to genome (as percentage of read length)");
+ ref_a.add(mismatchLabel);
+ mismatchTextField = new JTextField("" + mismatches, 4);
+ mismatchTextField.setToolTipText("Maximum number of mismatches/gaps/insertions allowed when aligning read to genome (as percentage of read length)");
+ ref_a.add(mismatchTextField);
+ ref.add(ref_a);
+
+ // Minimum seed length
+ JPanel ref_b = new JPanel(new FlowLayout(FlowLayout.RIGHT));
+ ref_b.setBackground(RockhopperGUI.lightBlue);
+ JLabel readLengthLabel = new JLabel("Minimum seed length");
+ readLengthLabel.setToolTipText("Minimum number of consecutive nucleotides aligning to genome exactly (as percentage of read length)");
+ ref_b.add(readLengthLabel);
+ readLengthTextField = new JTextField("" + minReadLength, 4);
+ readLengthTextField.setToolTipText("Minimum number of consecutive nucleotides aligning to genome exactly (as percentage of read length)");
+ ref_b.add(readLengthTextField);
+ ref.add(ref_b);
+
+ // Transcript boundaries
+ JPanel ref_c = new JPanel(new FlowLayout(FlowLayout.RIGHT));
+ ref_c.setBackground(RockhopperGUI.lightBlue);
+ JLabel boundariesLabel = new JLabel("Identify transcript boundaries");
+ boundariesLabel.setToolTipText("Determine UTRs and novel noncoding RNAs");
+ ref_c.add(boundariesLabel);
+ boundaries = new JCheckBox();
+ boundaries.setBackground(RockhopperGUI.lightBlue);
+ boundaries.setSelected(transcriptBoundaries);
+ boundaries.setToolTipText("Determine UTRs and novel noncoding RNAs");
+ ref_c.add(boundaries);
+ ref.add(ref_c);
+
+ // Operons
+ JPanel ref_d = new JPanel(new FlowLayout(FlowLayout.RIGHT));
+ ref_d.setBackground(RockhopperGUI.lightBlue);
+ JLabel operonsLabel = new JLabel("Predict operons");
+ operonsLabel.setToolTipText("Identify polycistronic messages");
+ ref_d.add(operonsLabel);
+ operons = new JCheckBox();
+ operons.setBackground(RockhopperGUI.lightBlue);
+ operons.setSelected(predictOperons);
+ operons.setToolTipText("Identify polycistronic messages");
+ ref_d.add(operons);
+ ref.add(ref_d);
+
+ // Panel for min expression of UTRs and ncRNAs
+ p1.add(ref);
+ JPanel ref_ef = new JPanel(new FlowLayout(FlowLayout.CENTER));
+ //ref_ef.setPreferredSize(new Dimension(width-50, 75));
+ ref_ef.setBackground(RockhopperGUI.lightBlue);
+ JLabel minExpressionLabel = new JLabel("Minimum expression of UTRs and ncRNAs");
+ minExpressionLabel.setToolTipText("Parameter indicating minimum expression level used to determine UTRs and novel noncoding RNAs");
+ ref_ef.add(minExpressionLabel);
+ minExpression = new JSlider(JSlider.HORIZONTAL, 0, 10, (int)(expressionParameter*10));
+ minExpression.setBackground(RockhopperGUI.lightBlue);
+ minExpression.setForeground(Color.BLACK);
+ minExpression.setMajorTickSpacing(5);
+ minExpression.setMinorTickSpacing(1);
+ minExpression.setPaintTicks(true);
+ Hashtable<Integer, JLabel> labelTable = new Hashtable<Integer, JLabel>();
+ labelTable.put(new Integer(0), new JLabel("0.0"));
+ labelTable.put(new Integer(5), new JLabel("0.5"));
+ labelTable.put(new Integer(10), new JLabel("1.0"));
+ minExpression.setLabelTable(labelTable);
+ minExpression.setPaintLabels(true);
+ minExpression.setToolTipText("Parameter indicating minimum expression level used to determine UTRs and novel noncoding RNAs");
+ ref_ef.add(minExpression);
+
+ // Spacer
+ p1.add(ref_ef);
+ spacerPanel = new JPanel(new FlowLayout(FlowLayout.CENTER));
+ spacerPanel.setPreferredSize(new Dimension(width, 10));
+ spacerPanel.setBackground(RockhopperGUI.lightBlue);
+ p1.add(spacerPanel);
+
+ // Parameters for de novo assembly
+ JLabel denovoLabel = new JLabel("Parameters for de novo assembly");
+ denovoLabel.setForeground(RockhopperGUI.gold);
+ denovoLabel.setFont(new Font("Times", Font.ITALIC, 18));
+ p1.add(denovoLabel);
+ JPanel denovo = new JPanel(new GridLayout(2,2));
+ denovo.setPreferredSize(new Dimension(width-150, 70));
+ denovo.setBackground(RockhopperGUI.lightBlue);
+
+ // Min reads mapping
+ JPanel denovo_a = new JPanel(new FlowLayout(FlowLayout.RIGHT));
+ denovo_a.setBackground(RockhopperGUI.lightBlue);
+ JLabel minReadsMappingLabel = new JLabel("Min reads mapping to a transcript");
+ minReadsMappingLabel.setToolTipText("Minimum number of full length reads required to map to a de novo assembled transcript");
+ denovo_a.add(minReadsMappingLabel);
+ minReadsMappingTextField = new JTextField("" + minReadsMapping, 3);
+ minReadsMappingTextField.setToolTipText("Minimum number of full length reads required to map to a de novo assembled transcript");
+ denovo_a.add(minReadsMappingTextField);
+ denovo.add(denovo_a);
+
+ // Min transcript length
+ JPanel denovo_b = new JPanel(new FlowLayout(FlowLayout.RIGHT));
+ denovo_b.setBackground(RockhopperGUI.lightBlue);
+ JLabel minTranscriptLengthLabel = new JLabel("Minimum transcript length");
+ minTranscriptLengthLabel.setToolTipText("Minimum length of de novo assembled transcripts (in nts)");
+ denovo_b.add(minTranscriptLengthLabel);
+ minTranscriptLengthTextField = new JTextField("" + minTranscriptLength, 3);
+ minTranscriptLengthTextField.setToolTipText("Minimum length of de novo assembled transcripts (in nts)");
+ denovo_b.add(minTranscriptLengthTextField);
+ denovo.add(denovo_b);
+
+ // Min seed expression
+ JPanel denovo_c = new JPanel(new FlowLayout(FlowLayout.RIGHT));
+ denovo_c.setBackground(RockhopperGUI.lightBlue);
+ JLabel minSeedExpressionLabel = new JLabel("Min count to seed a transcript");
+ minSeedExpressionLabel.setToolTipText("Minimum count to seed a new de novo assembled transcript");
+ denovo_c.add(minSeedExpressionLabel);
+ minSeedExpressionTextField = new JTextField("" + minSeedExpression, 3);
+ minSeedExpressionTextField.setToolTipText("Minimum count to seed a new de novo assembled transcript");
+ denovo_c.add(minSeedExpressionTextField);
+ denovo.add(denovo_c);
+
+ // Min extend expression
+ JPanel denovo_d = new JPanel(new FlowLayout(FlowLayout.RIGHT));
+ denovo_d.setBackground(RockhopperGUI.lightBlue);
+ JLabel minExtendExpressionLabel = new JLabel("Min count to extend a transcript");
+ minExtendExpressionLabel.setToolTipText("Minimum count to extend an existing de novo assembled transcript");
+ denovo_d.add(minExtendExpressionLabel);
+ minExtendExpressionTextField = new JTextField("" + minExtendExpression, 3);
+ minExtendExpressionTextField.setToolTipText("Minimum count to extend an existing de novo assembled transcript");
+ denovo_d.add(minExtendExpressionTextField);
+ denovo.add(denovo_d);
+
+ // Spacer
+ p1.add(denovo);
+ spacerPanel = new JPanel(new FlowLayout(FlowLayout.CENTER));
+ spacerPanel.setPreferredSize(new Dimension(width, 25));
+ spacerPanel.setBackground(RockhopperGUI.lightBlue);
+ p1.add(spacerPanel);
+
+ // Defaults and Save buttons
+ JPanel buttons = new JPanel(new GridLayout(1,2,30,0));
+ buttons.setPreferredSize(new Dimension(width-400, 25));
+ buttons.setBackground(RockhopperGUI.lightBlue);
+ defaultButton = new JButton("DEFAULTS");
+ defaultButton.setToolTipText("Restore default parameters values");
+ defaultButton.setForeground(Color.red);
+ defaultButton.setBackground(RockhopperGUI.gold);
+ defaultButton.addActionListener((ActionListener)applet);
+ saveButton = new JButton("SAVE");
+ saveButton.setToolTipText("Save parameter values");
+ saveButton.setForeground(RockhopperGUI.gold);
+ saveButton.setBackground(Color.red);
+ saveButton.addActionListener((ActionListener)applet);
+ buttons.add(defaultButton);
+ buttons.add(saveButton);
+ p1.add(buttons);
+ parameterFrame.add(p1);
+ parameterFrame.setVisible(true);
+ saveButton.requestFocus();
+ }
+
+ private void fileChooser() {
+ fc.setSelectedFile(null);
+ int returnVal = fc.showOpenDialog(SwingUtilities.getAncestorOfClass(JFrame.class,applet));
+ f = fc.getSelectedFile();
+ if (f != null) dirTextField.setText(f.getAbsolutePath());
+ }
+
+ private void outputParametersToFile() {
+ try {
+ File f = new File(RockhopperGUI.directory);
+ if (!f.exists()) f.mkdir();
+ PrintWriter writer = new PrintWriter(new File(RockhopperGUI.directory + fileName));
+ writer.println(Rockhopper.version);
+ writer.println(mismatches);
+ writer.println(minReadLength);
+ writer.println(singleEndOrientation);
+ writer.println(matePairOrientation);
+ writer.println(numProcessors);
+ writer.println(maxPairedEndLength);
+ writer.println(verboseOutput);
+ writer.println(outputSAM);
+ writer.println(isStrandSpecific);
+ writer.println(testDifferentialExp);
+ writer.println(predictOperons);
+ writer.println(transcriptBoundaries);
+ writer.println(expressionParameter);
+ writer.println(minReadsMapping);
+ writer.println(minTranscriptLength);
+ writer.println(minSeedExpression);
+ writer.println(minExtendExpression);
+ writer.println(outputDIR);
+ writer.close();
+ } catch (FileNotFoundException ex) {
+ // Do nothing if parameter file could not be written.
+ }
+ }
+
+ private void error(String title, String message) {
+ JOptionPane.showMessageDialog(parameterFrame, message, title, JOptionPane.ERROR_MESSAGE);
+ }
+
+}
+
diff --git a/Peregrine.java b/Peregrine.java
new file mode 100644
index 0000000..ec4da84
--- /dev/null
+++ b/Peregrine.java
@@ -0,0 +1,1379 @@
+/*
+ * Copyright 2013 Brian Tjaden
+ *
+ * This file is part of Rockhopper.
+ *
+ * Rockhopper is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * any later version.
+ *
+ * Rockhopper is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * (in the file gpl.txt) along with Rockhopper.
+ * If not, see <http://www.gnu.org/licenses/>.
+ */
+
+import java.util.Scanner;
+import java.io.File;
+import java.util.ArrayList;
+import java.io.PrintWriter;
+import java.io.BufferedReader;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.FileInputStream;
+import java.io.InputStreamReader;
+import java.util.zip.GZIPInputStream;
+import java.util.concurrent.atomic.AtomicInteger;
+import java.util.concurrent.atomic.AtomicIntegerArray;
+import java.util.concurrent.atomic.AtomicLong;
+import javax.swing.JTextArea;
+
+public class Peregrine {
+
+ /********************************************
+ ********** Instance Variables **********
+ ********************************************/
+
+ private Index index;
+ private AtomicIntegerArray[] coordinates_plus; // Number of reads mapping to each coordinate in each sequence
+ private AtomicIntegerArray[] coordinates_minus; // Number of reads mapping to each coordinate in each sequence
+ private int PHRED_offset;
+ private BufferedReader reader;
+ private BufferedReader reader2; // Mate-pair file if using paired-end reads
+ private PrintWriter samWriter; // Output reads to SAM file
+ private boolean isCompressedFile; // True if gzip file. False otherwise.
+ private SamOps sam; // Used if reads file is in SAM/BAM format
+ private boolean firstLineDone; // Used when reading in the first line of FASTA files
+ private String parametersString;
+ private String[] genomeNames; // Used when outputting SAM files
+ private long runningTime; // Time taken to execute program
+
+ // Results
+ public AtomicInteger totalReads;
+ private AtomicInteger invalidQualityReads; // Reads containing an invalid quality score
+ private AtomicInteger ambiguousReads; // Reads with ambiguous nucleotides
+ private AtomicInteger lowQualityReads; // Reads with quality scores too low for mapping
+ private AtomicInteger mappedOnceReads; // Reads mapping to one location
+ private AtomicInteger mappedMoreThanOnceReads; // Reads mapping to multiple locations
+ public AtomicIntegerArray exactMappedReads; // Reads mapping without mismatches/errors to each sequence
+ public AtomicIntegerArray inexactMappedReads; // Reads mapping with mismatches/errors to each sequence
+ public AtomicLong avgLengthReads; // Avg length of mapping reads
+ private AtomicInteger numMappingReads; // Number of reads mapping
+ private AtomicInteger nameCount; // Used when outputting SAM file and reads have no name
+
+
+
+ /*****************************************
+ ********** Class Variables **********
+ *****************************************/
+
+ // Parameters
+ public static JTextArea output; // Output to GUI or, if null, to System.out
+ public static PrintWriter summaryWriter = null; // For outputting summary file
+ public static int numSequences;
+ private static int readsInputFormat; // 0=FASTQ, 1=QSEQ, 2=FASTA, 3=SAM(single), 4=SAM(paired), 5=BAM(single), 6=BAM(paired)
+ public static String[] sequenceFiles;
+ public static String[][] annotationsPlus = null; // Gene/RNA coords for each replicon
+ public static String[][] annotationsMinus = null; // Gene/RNA coords for each replicon
+ public static String readsFile;
+ public static double percentMismatches = 0.15;
+ public static boolean stopAfterOneHit = true;
+ public static double percentSeedLength = 0.33; // Minimum allowed seed (read) length
+ public static int minReadLength = 20;
+ public static boolean isPairedEnd = false; // Do we have paired-end reads?
+ public static String pairedEndFile; // Name of mate-pair file if using paired-end reads
+ public static int maxPairedEndLength = 500;
+ public static boolean singleEndOrientationReverseComplement = false; // RevComp reads
+ public static String pairedEndOrientation = "fr"; // ff, fr, rf, rr
+ public static int numThreads = 1; // Number of threads
+ public static boolean outputSAM = false; // Output reads to SAM file
+ public static String outputDIR = "Peregrine_Results/"; // Output directory
+ private static long randomSeed = -1; // Seed for the random number generator
+ private static boolean time = false; // Output time taken to execute program
+
+ public static String browserDIR = "genomeBrowserFiles/"; // Files for genome browser
+ public static ArrayList<String> wigFiles; // List of comma-delimited set of wig files for IGV
+ public static boolean outputBrowserFile = true; // Should we output a browser file?
+
+
+
+ /**************************************
+ ********** Constructors **********
+ **************************************/
+
+ public Peregrine() {
+
+ runningTime = System.currentTimeMillis();
+ this.coordinates_plus = new AtomicIntegerArray[Peregrine.numSequences];
+ this.coordinates_minus = new AtomicIntegerArray[Peregrine.numSequences];
+ this.exactMappedReads = new AtomicIntegerArray(Peregrine.numSequences);
+ this.inexactMappedReads = new AtomicIntegerArray(Peregrine.numSequences);
+ if (wigFiles == null) {
+ wigFiles = new ArrayList<String>(numSequences);
+ for (int i=0; i<numSequences; i++) wigFiles.add("");
+ }
+ parametersString = parametersToString();
+ // For paired-end reads, we must consider all optimal alignments
+ if (Peregrine.isPairedEnd) Peregrine.stopAfterOneHit = false;
+
+ // Check if reads hits have been pre-computed
+ boolean isValid = true;
+ for (int i=0; i<numSequences; i++) {
+ String inFileName = getCompressedFileName(readsFile, sequenceFiles[i]);
+ FileOps foo = new FileOps(inFileName, readsFile, sequenceFiles[i]);
+ if (foo.isValid()) {
+ coordinates_plus[i] = new AtomicIntegerArray(foo.getCoordinates_plus());
+ coordinates_minus[i] = new AtomicIntegerArray(foo.getCoordinates_minus());
+ totalReads = new AtomicInteger(foo.getTotalReads());
+ invalidQualityReads = new AtomicInteger(foo.getInvalidQualityReads());
+ ambiguousReads = new AtomicInteger(foo.getAmbiguousReads());
+ lowQualityReads = new AtomicInteger(foo.getLowQualityReads());
+ mappedOnceReads = new AtomicInteger(foo.getMappedOnceReads());
+ mappedMoreThanOnceReads = new AtomicInteger(foo.getMappedMoreThanOnceReads());
+ avgLengthReads = new AtomicLong(foo.getAvgLengthReads());
+ numMappingReads = new AtomicInteger(0);
+ nameCount = new AtomicInteger(1);
+ exactMappedReads.set(i, foo.getExactMappedReads());
+ inexactMappedReads.set(i, foo.getInexactMappedReads());
+ runningTime = System.currentTimeMillis() - runningTime;
+ if (i == numSequences-1) outputResults();
+ } else {
+ isValid = false;
+ totalReads = new AtomicInteger(0);
+ invalidQualityReads = new AtomicInteger(0);
+ ambiguousReads = new AtomicInteger(0);
+ lowQualityReads = new AtomicInteger(0);
+ mappedOnceReads = new AtomicInteger(0);
+ mappedMoreThanOnceReads = new AtomicInteger(0);
+ avgLengthReads = new AtomicLong(0);
+ numMappingReads = new AtomicInteger(0);
+ nameCount = new AtomicInteger(1);
+ exactMappedReads.set(i, 0);
+ inexactMappedReads.set(i, 0);
+ }
+ if (wigFiles.get(i).length() > 0) wigFiles.set(i, wigFiles.get(i) + ",");
+ wigFiles.set(i, wigFiles.get(i) + outputDIR + browserDIR + inFileName + ".plus" + ".wig");
+ wigFiles.set(i, wigFiles.get(i) + "," + outputDIR + browserDIR + inFileName + ".minus" + ".wig");
+ }
+
+ if (isValid && outputSAM) output("Rockhopper did not output a SAM file since sequencing read alignments were previously cached. If you want a SAM file to be output, you must first clear the cache." + "\n\n");
+
+ if (!isValid) {
+ this.index = new Index(sequenceFiles);
+ readsInputFormat = getReadsInputFileType(readsFile);
+ int numThreads_OLD = numThreads;
+ if ((readsInputFormat == 5) || (readsInputFormat == 6)) numThreads = 1; // BAM file
+ for (int i=0; i<numSequences; i++) {
+ coordinates_plus[i] = new AtomicIntegerArray(index.getReplicon(i).getLength());
+ coordinates_minus[i] = new AtomicIntegerArray(index.getReplicon(i).getLength());
+ }
+ this.PHRED_offset = getPhredOffset(readsFile);
+ firstLineDone = false;
+ if (outputSAM) outputSamHeader();
+
+ // Set parameters
+ index.setStopAfterOneHit(Peregrine.stopAfterOneHit);
+ if (randomSeed >= 0) Index.setRandomSeed(Peregrine.randomSeed);
+
+ mapReads();
+ runningTime = System.currentTimeMillis() - runningTime;
+ numThreads = numThreads_OLD; // Reset the number of threads
+ if (numMappingReads.get() > 0) avgLengthReads.set(avgLengthReads.get() / numMappingReads.get());
+ avgLengthReads.set(Math.max(avgLengthReads.get(), 72)); // Minimum of 72 nts
+
+ // Incorporate results from SAM file
+ if (sam != null) {
+ int samAlignedReads = 0;
+ for (int i=0; i<sam.alignedReads.length(); i++) samAlignedReads += sam.alignedReads.get(i);
+ if (samAlignedReads > 0) avgLengthReads.set(Math.max(avgLengthReads.get(), sam.avgLengthReads.get() / samAlignedReads));
+ totalReads.addAndGet(sam.badReads.get());
+ invalidQualityReads.addAndGet(sam.badReads.get());
+ for (int i=0; i<Math.min(exactMappedReads.length(), sam.alignedReads.length()); i++) {
+ totalReads.addAndGet(sam.alignedReads.get(i));
+ exactMappedReads.addAndGet(i, sam.alignedReads.get(i));
+ for (int j=0; j<Math.min(coordinates_plus[i].length(), sam.coordinates_plus[i].length()); j++) {
+ coordinates_plus[i].addAndGet(j, sam.coordinates_plus[i].get(j));
+ coordinates_minus[i].addAndGet(j, sam.coordinates_minus[i].get(j));
+ }
+ }
+ }
+
+ if (samWriter != null) samWriter.close();
+ outputResults();
+ outputReadsToFile();
+ }
+ }
+
+
+
+ /*************************************************
+ ********** Public Instance Methods **********
+ *************************************************/
+
+ /**
+ * Read from reads file and map any reads from file to
+ * reference index.
+ */
+ public void processReads() {
+ String line = "";;
+ String name = "";
+ String nextName = ""; // Special case (FASTA)
+ String read = "";
+ String quality = "";
+ String quality_fasta = ""; // Special case (FASTA)
+ int[] qualities = new int[0];
+ String[] parse_line = null;
+ ArrayList<Hit> hits = new ArrayList<Hit>();
+ ArrayList<Hit> seedHits = new ArrayList<Hit>();
+ Alignment a = new Alignment();
+ // Using paired-end reads
+ String line2 = "";;
+ String name2 = "";
+ String nextName2 = ""; // Special case (FASTA)
+ String read2 = "";
+ String quality2 = "";
+ String quality_fasta2 = ""; // Special case (FASTA)
+ int[] qualities2 = new int[0];
+ String[] parse_line2 = null;
+ ArrayList<Hit> hits2 = new ArrayList<Hit>();
+ ArrayList<Hit> seedHits2 = new ArrayList<Hit>();
+ ArrayList<Hit> combinedHits = new ArrayList<Hit>();
+ Alignment a2 = new Alignment();
+
+ try {
+ synchronized(reader) {
+ if ((readsInputFormat == 2) && !firstLineDone) { // Special case (FASTA)
+ line = reader.readLine(); // Special case (FASTA)
+ if (line.startsWith(">")) nextName = line.substring(1);
+ if (isPairedEnd) {
+ line2 = reader2.readLine();
+ if (line2.startsWith(">")) nextName2 = line2.substring(1);
+ }
+ }
+ firstLineDone = true;
+ }
+
+ while (line != null) {
+
+ synchronized(reader) { // Thread safe reading from file
+ if (readsInputFormat < 5) line = reader.readLine(); // Not a BAM file
+ if (line == null) continue;
+ if (readsInputFormat == 0) { // FASTQ file
+ name = line;
+ read = reader.readLine();
+ line = reader.readLine();
+ quality = reader.readLine();
+ } else if (readsInputFormat == 1) { // QSEQ file
+ parse_line = line.split("\t");
+ name = parse_line[0] + ":" + parse_line[2] + ":" + parse_line[3] + ":" + parse_line[4] + ":" + parse_line[5] + ":" + parse_line[6] + ":" + parse_line[7];
+ read = parse_line[8];
+ quality = parse_line[9];
+ } else if (readsInputFormat == 2) { // FASTA file
+ name = nextName;
+ read = "";
+ while ((line != null) && ((line.length() == 0) || (line.charAt(0) != '>'))) {
+ read += line;
+ line = reader.readLine();
+ }
+ if (line == null) nextName = "";
+ else if (line.startsWith(">")) nextName = line.substring(1);
+ else nextName = ""; // Case should never be reached
+ if (quality_fasta.length() != read.length()) quality_fasta = new String(new char[read.length()]).replace('\0', '(');
+ quality = quality_fasta;
+ } else if (readsInputFormat == 3) { // SAM file (single-end)
+ if (SamOps.isHeaderLine(line)) continue;
+ } else if (readsInputFormat == 4) { // SAM file (paired-end)
+ if (SamOps.isHeaderLine(line)) continue;
+ line2 = reader.readLine();
+ } else if (readsInputFormat == 5) { // BAM file (single-end)
+ parse_line = sam.parseAlignmentLine_BAM();
+ if (parse_line == null) {
+ line = null;
+ continue;
+ }
+ if (parse_line == SamOps.emptyStringArray) continue;
+ if (parse_line[0].startsWith("U")) {
+ read = parse_line[9];
+ quality = mapPhred(parse_line[10]);
+ } else if (samWriter != null) {
+ name = parse_line[0].substring(1);
+ while (name.startsWith("@")) name = name.substring(1);
+ mapBamNames(parse_line);
+ synchronized(samWriter) {
+ samWriter.println(name + "\t" + parse_line[1] + "\t" + parse_line[2] + "\t" + parse_line[3] + "\t" + parse_line[4] + "\t" + parse_line[5] + "\t" + parse_line[6] + "\t" + parse_line[7] + "\t" + parse_line[8] + "\t" + parse_line[9] + "\t" + mapPhred(parse_line[10]));
+ continue;
+ }
+ } else continue;
+ } else if (readsInputFormat == 6) { // BAM file (paired-end)
+ parse_line = sam.parseAlignmentLine_BAM();
+ if (parse_line == null) {
+ line = null;
+ continue;
+ }
+ parse_line2 = sam.parseAlignmentLine_BAM();
+ if (parse_line2 == null) {
+ line = null;
+ continue;
+ }
+ if ((parse_line == SamOps.emptyStringArray) || (parse_line2 == SamOps.emptyStringArray)) continue;
+ if ((parse_line[0].startsWith("U")) || parse_line2[0].startsWith("U")) {
+ read = parse_line[9];
+ quality = mapPhred(parse_line[10]);
+ read2 = parse_line2[9];
+ quality2 = mapPhred(parse_line2[10]);
+ } else if (samWriter != null) {
+ name = parse_line[0].substring(1);
+ while (name.startsWith("@")) name = name.substring(1);
+ name2 = parse_line2[0].substring(1);
+ while (name2.startsWith("@")) name2 = name2.substring(1);
+ mapBamNames(parse_line);
+ mapBamNames(parse_line2);
+ synchronized(samWriter) {
+ samWriter.println(name + "\t" + parse_line[1] + "\t" + parse_line[2] + "\t" + parse_line[3] + "\t" + parse_line[4] + "\t" + parse_line[5] + "\t" + parse_line[6] + "\t" + parse_line[7] + "\t" + parse_line[8] + "\t" + parse_line[9] + "\t" + mapPhred(parse_line[10]));
+ samWriter.println(name2 + "\t" + parse_line2[1] + "\t" + parse_line2[2] + "\t" + parse_line2[3] + "\t" + parse_line2[4] + "\t" + parse_line2[5] + "\t" + parse_line2[6] + "\t" + parse_line2[7] + "\t" + parse_line2[8] + "\t" + parse_line2[9] + "\t" + mapPhred(parse_line2[10]));
+ continue;
+ }
+ } else continue;
+ }
+
+ if (isPairedEnd) { // Using paired-end reads
+ synchronized(reader2) { // Thread safe reading from file
+ line2 = reader2.readLine();
+ if (line2 == null) {
+ output("Error - the two files of mate-pair reads contain different numbers of sequencing reads.");
+ continue;
+ }
+ if (readsInputFormat == 0) { // FASTQ file
+ name2 = line;
+ read2 = reader2.readLine();
+ line2 = reader2.readLine();
+ quality2 = reader2.readLine();
+ } else if (readsInputFormat == 1) { // QSEQ file
+ parse_line2 = line2.split("\t");
+ name2 = parse_line2[0] + ":" + parse_line2[2] + ":" + parse_line2[3] + ":" + parse_line2[4] + ":" + parse_line2[5] + ":" + parse_line2[6] + ":" + parse_line2[7];
+ read2 = parse_line2[8];
+ quality2 = parse_line2[9];
+ } else if (readsInputFormat == 2) { // FASTA file
+ name2 = nextName2;
+ read2 = "";
+ while ((line2 != null) && ((line2.length() == 0) || (line2.charAt(0) != '>'))) {
+ read2 += line2;
+ line2 = reader2.readLine();
+ }
+ if (line2 == null) nextName2 = "";
+ else if (line2.startsWith(">")) nextName2 = line2.substring(1);
+ else nextName2 = ""; // Case should never be reached
+ if (quality_fasta2.length() != read2.length()) quality_fasta2 = new String(new char[read2.length()]).replace('\0', '(');
+ quality2 = quality_fasta2;
+ }
+ }
+ }
+ }
+
+ if (readsInputFormat == 3) { // SAM file (single-end)
+ parse_line = sam.parseAlignmentLine_SAM(line);
+ if (parse_line == SamOps.emptyStringArray) continue;
+ if (parse_line[0].startsWith("U")) {
+ read = parse_line[9];
+ quality = parse_line[10];
+ } else if (samWriter != null) { // Output to SAM file
+ name = parse_line[0].substring(1);
+ while (name.startsWith("@")) name = name.substring(1);
+ synchronized(samWriter) {
+ samWriter.println(name + "\t" + parse_line[1] + "\t" + parse_line[2] + "\t" + parse_line[3] + "\t" + parse_line[4] + "\t" + parse_line[5] + "\t" + parse_line[6] + "\t" + parse_line[7] + "\t" + parse_line[8] + "\t" + parse_line[9] + "\t" + parse_line[10]);
+ }
+ continue;
+ } else continue;
+ } else if (readsInputFormat == 4) { // SAM File (paired-end)
+ parse_line = sam.parseAlignmentLine_SAM(line);
+ parse_line2 = sam.parseAlignmentLine_SAM(line2);
+ if ((parse_line == SamOps.emptyStringArray) || (parse_line2 == SamOps.emptyStringArray)) continue;
+ if ((parse_line[0].startsWith("U")) || parse_line2[0].startsWith("U")) {
+ read = parse_line[9];
+ quality = parse_line[10];
+ read2 = parse_line2[9];
+ quality2 = parse_line2[10];
+ } else if (samWriter != null) {
+ name = parse_line[0].substring(1);
+ while (name.startsWith("@")) name = name.substring(1);
+ name2 = parse_line2[0].substring(1);
+ while (name2.startsWith("@")) name2 = name2.substring(1);
+ synchronized(samWriter) {
+ samWriter.println(name + "\t" + parse_line[1] + "\t" + parse_line[2] + "\t" + parse_line[3] + "\t" + parse_line[4] + "\t" + parse_line[5] + "\t" + parse_line[6] + "\t" + parse_line[7] + "\t" + parse_line[8] + "\t" + parse_line[9] + "\t" + parse_line[10]);
+ samWriter.println(name2 + "\t" + parse_line2[1] + "\t" + parse_line2[2] + "\t" + parse_line2[3] + "\t" + parse_line2[4] + "\t" + parse_line2[5] + "\t" + parse_line2[6] + "\t" + parse_line2[7] + "\t" + parse_line2[8] + "\t" + parse_line2[9] + "\t" + parse_line2[10]);
+ }
+ continue;
+ } else continue;
+ }
+
+ // Process read
+ read = read.toUpperCase();
+ boolean ambiguous = false;
+ for (int i=0; i<read.length(); i++) {
+ if ((read.charAt(i) != 'A') && (read.charAt(i) != 'C') &&
+ (read.charAt(i) != 'G') && (read.charAt(i) != 'T'))
+ ambiguous = true;
+ }
+ if (isPairedEnd || ((sam != null) && (sam.isPairedEnd()))) { // Using paired-end reads
+ read2 = read2.toUpperCase();
+ for (int i=0; i<read2.length(); i++) {
+ if ((read2.charAt(i) != 'A') && (read2.charAt(i) != 'C') &&
+ (read2.charAt(i) != 'G') && (read2.charAt(i) != 'T'))
+ ambiguous = true;
+ }
+
+ // Orient paired-end reads (0=ff, 1=fr, 2=rf, 3=rr)
+ if (pairedEndOrientation.charAt(0) == 'r') { // Reverse first read
+ read = reverseComplement(read);
+ quality = reverse(quality);
+ }
+ if (pairedEndOrientation.charAt(1) == 'r') { // Reverse second read
+ read2 = reverseComplement(read2);
+ quality2 = reverse(quality2);
+ }
+ } else { // Using single-end reads
+ // Orient single-end reads (true=reverse_complement, false=nothing)
+ if (singleEndOrientationReverseComplement) { // Reverse complement read
+ read = reverseComplement(read);
+ quality = reverse(quality);
+ }
+ }
+
+ // Process quality
+ if (quality.length() != read.length()) {
+ output("Quality sequence has different length than read sequence.\n");
+ continue;
+ }
+ int endIndex = quality.length()-1;
+ while ((endIndex >= 0) && ((int)(quality.charAt(endIndex))-PHRED_offset == 2)) endIndex--;
+ quality = quality.substring(0, endIndex+1);
+ read = read.substring(0, endIndex+1);
+ if (qualities.length != read.length()) qualities = new int[read.length()];
+ boolean invalid = false;
+ for (int i=0; i<quality.length(); i++) {
+ qualities[i] = (int)(quality.charAt(i)) - PHRED_offset;
+ if ((qualities[i] < 0) || (qualities[i] > 93)) invalid = true;
+ }
+ if (isPairedEnd || ((sam != null) && (sam.isPairedEnd()))) { // Using paired-end reads
+ if (quality2.length() != read2.length()) {
+ output("Quality sequence has different length than read sequence.\n");
+ continue;
+ }
+ int endIndex2 = quality2.length()-1;
+ while ((endIndex2 >= 0) && ((int)(quality2.charAt(endIndex2))-PHRED_offset == 2)) endIndex2--;
+ quality2 = quality2.substring(0, endIndex2+1);
+ read2 = read2.substring(0, endIndex2+1);
+ if (qualities2.length != read2.length()) qualities2 = new int[read2.length()];
+ for (int i=0; i<quality2.length(); i++) {
+ qualities2[i] = (int)(quality2.charAt(i)) - PHRED_offset;
+ if ((qualities2[i] < 0) || (qualities2[i] > 93)) invalid = true;
+ }
+ }
+
+ // Align read to genome
+ totalReads.getAndIncrement();
+ if (ambiguous) ambiguousReads.getAndIncrement();
+ else if ((quality.length() < minReadLength) || (isPairedEnd && (quality2.length() < minReadLength)) || ((sam != null) && (sam.isPairedEnd()) && (quality2.length() < minReadLength))) lowQualityReads.getAndIncrement(); // Minimum read length
+ else if (invalid || (read.length() < minReadLength)) invalidQualityReads.getAndIncrement(); // Invalid quality score
+ else {
+ index.inexactMatch(read, qualities, a, hits, seedHits);
+ if ((isPairedEnd && (hits.size()>0)) || ((sam != null) && (sam.isPairedEnd()) && (hits.size()>0))) { // Using paired-end reads
+ index.inexactMatch(read2, qualities2, a2, hits2, seedHits2);
+ Hit.combinePairedEndHits(combinedHits, hits, hits2, maxPairedEndLength);
+ // Swap "hits" and "combinedHits"
+ ArrayList<Hit> temp = hits;
+ hits = combinedHits;
+ combinedHits = temp;
+ }
+ for (int i=0; i<hits.size(); i++) { // Update coordinates
+ mapHitsToCoordinates(hits.get(i));
+ }
+ if (hits.size() > 0) { // Update stats
+ if (hits.get(0).getErrors() == 0) exactMappedReads.getAndIncrement(hits.get(0).getRepliconIndex());
+ else inexactMappedReads.getAndIncrement(hits.get(0).getRepliconIndex());
+ if (hits.size() == 1) mappedOnceReads.getAndIncrement();
+ else mappedMoreThanOnceReads.getAndIncrement();
+ avgLengthReads.addAndGet(hits.get(0).getLength());
+ numMappingReads.incrementAndGet();
+ }
+ }
+
+ // Output to SAM file
+ if (samWriter != null) {
+ synchronized(samWriter) {
+ int flag = 0;
+ int flag2 = 0;
+ if ((quality.length() < minReadLength) || (isPairedEnd && (quality2.length() < minReadLength)) || ((sam != null) && (sam.isPairedEnd()) && (quality2.length() < minReadLength))) { // READ TOO SHORT, DON'T USE
+ // Do nothing.
+ }
+ else if (ambiguous || invalid || (hits.size() == 0)) { // UNALIGNED
+ if (isPairedEnd || ((sam != null) && (sam.isPairedEnd()))) { // Paired-end
+ if (readsInputFormat == 6) { // BAM
+ mapBamNames(parse_line);
+ mapBamNames(parse_line2);
+ parse_line[10] = mapPhred(parse_line[10]);
+ parse_line2[10] = mapPhred(parse_line2[10]);
+ }
+ if ((readsInputFormat == 4) || (readsInputFormat == 6)) { // SAM/BAM
+ name = parse_line[0].substring(1);
+ while (name.startsWith("@")) name = name.substring(1);
+ name2 = parse_line2[0].substring(1);
+ while (name2.startsWith("@")) name2 = name2.substring(1);
+ samWriter.println(name + "\t" + parse_line[1] + "\t" + parse_line[2] + "\t" + parse_line[3] + "\t" + parse_line[4] + "\t" + parse_line[5] + "\t" + parse_line[6] + "\t" + parse_line[7] + "\t" + parse_line[8] + "\t" + parse_line[9] + "\t" + parse_line[10]);
+ samWriter.println(name2 + "\t" + parse_line2[1] + "\t" + parse_line2[2] + "\t" + parse_line2[3] + "\t" + parse_line2[4] + "\t" + parse_line2[5] + "\t" + parse_line2[6] + "\t" + parse_line2[7] + "\t" + parse_line2[8] + "\t" + parse_line2[9] + "\t" + parse_line2[10]);
+ } else { // FASTA, QSEQ, FASTQ
+ flag = 77; // 01001101
+ if (pairedEndOrientation.charAt(0) == 'r') { // Reverse first read
+ read = reverseComplement(read);
+ quality = reverse(quality);
+ }
+ while (name.startsWith("@")) name = name.substring(1);
+ if (name.length() == 0) {
+ name = "r" + nameCount.getAndIncrement();
+ name2 = name;
+ }
+ samWriter.println(name + "\t" + flag + "\t" + "*" + "\t" + "0" + "\t" + "0" + "\t" + "*" + "\t" + "*" + "\t" + "0" + "\t" + "0" + "\t" + read + "\t" + quality);
+ flag2 = 141; // 10001101
+ if (pairedEndOrientation.charAt(1) == 'r') { // Reverse second read
+ read2 = reverseComplement(read2);
+ quality2 = reverse(quality2);
+ }
+ while (name2.startsWith("@")) name2 = name2.substring(1);
+ samWriter.println(name2 + "\t" + flag2 + "\t" + "*" + "\t" + "0" + "\t" + "0" + "\t" + "*" + "\t" + "*" + "\t" + "0" + "\t" + "0" + "\t" + read2 + "\t" + quality2);
+ }
+ } else { // Single-end
+ if (readsInputFormat == 5) { // BAM
+ mapBamNames(parse_line);
+ parse_line[10] = mapPhred(parse_line[10]);
+ }
+ if ((readsInputFormat == 3) || (readsInputFormat == 5)) { // SAM/BAM
+ name = parse_line[0].substring(1);
+ while (name.startsWith("@")) name = name.substring(1);
+ samWriter.println(name + "\t" + parse_line[1] + "\t" + parse_line[2] + "\t" + parse_line[3] + "\t" + parse_line[4] + "\t" + parse_line[5] + "\t" + parse_line[6] + "\t" + parse_line[7] + "\t" + parse_line[8] + "\t" + parse_line[9] + "\t" + parse_line[10]);
+ } else { // FASTA, QSEQ, FASTQ
+ flag = 4; // Unmapped
+ if (singleEndOrientationReverseComplement) { // Reverse complement read
+ read = reverseComplement(read);
+ quality = reverse(quality);
+ }
+ while (name.startsWith("@")) name = name.substring(1);
+ if (name.length() == 0) name = "r" + nameCount.getAndIncrement();
+ samWriter.println(name + "\t" + flag + "\t" + "*" + "\t" + "0" + "\t" + "0" + "\t" + "*" + "\t" + "*" + "\t" + "0" + "\t" + "0" + "\t" + read + "\t" + quality);
+ }
+ }
+ } else { // ALIGNED
+ if (isPairedEnd || ((sam != null) && (sam.isPairedEnd()))) { // Paired-end (FASTA, QSEQ, FASTQ, SAM, BAM)
+ flag = 67; // 01000011
+ flag2 = 131; // 10000011
+ if (pairedEndOrientation.charAt(0) == 'r') { // Reverse first read
+ read = reverseComplement(read);
+ quality = reverse(quality);
+ if (hits.get(0).getStrand() == '+') {
+ flag += 16;
+ flag2 += 32;
+ }
+ } else {
+ if (hits.get(0).getStrand() == '-') {
+ flag += 16;
+ flag2 += 32;
+ }
+ }
+ if (pairedEndOrientation.charAt(1) == 'r') { // Reverse second read
+ read2 = reverseComplement(read2);
+ quality2 = reverse(quality2);
+ if (hits.get(0).getStrand() == '+') {
+ flag2 += 16;
+ flag += 32;
+ }
+ } else {
+ if (hits.get(0).getStrand() == '+') {
+ flag2 += 16;
+ flag += 32;
+ }
+ }
+ if ((readsInputFormat == 4) || (readsInputFormat == 6)) { // SAM/BAM
+ name = parse_line[0].substring(1);
+ name2 = parse_line2[0].substring(1);
+ }
+ while (name.startsWith("@")) name = name.substring(1);
+ while (name2.startsWith("@")) name2 = name2.substring(1);
+ if (name.length() == 0) {
+ name = "r" + nameCount.getAndIncrement();
+ name2 = name;
+ }
+ samWriter.println(name + "\t" + flag + "\t" + genomeNames[hits.get(0).getRepliconIndex()] + "\t" + hits.get(0).getStart() + "\t" + "255" + "\t" + read.length() + "M" + "\t" + "=" + "\t" + (hits.get(0).getStop()-read2.length()+1) + "\t" + hits.get(0).getLength() + "\t" + read + "\t" + quality);
+ samWriter.println(name2 + "\t" + flag2 + "\t" + genomeNames[hits.get(0).getRepliconIndex()] + "\t" + (hits.get(0).getStop()-read2.length()+1) + "\t" + "255" + "\t" + read2.length() + "M" + "\t" + "=" + "\t" + hits.get(0).getStart() + "\t" + (0-hits.get(0).getLength()) + "\t" + read2 + "\t" + quality2);
+ } else { // Single-end (FASTA, QSEQ, FASTQ, SAM, BAM)
+ flag = 0;
+ if (singleEndOrientationReverseComplement) { // Reverse complement read
+ read = reverseComplement(read);
+ quality = reverse(quality);
+ if (hits.get(0).getStrand() == '+') flag += 16;
+ } else {
+ if (hits.get(0).getStrand() == '-') flag += 16;
+ }
+ if ((readsInputFormat == 3) || (readsInputFormat == 5)) // SAM/BAM
+ name = parse_line[0].substring(1);
+ while (name.startsWith("@")) name = name.substring(1);
+ if (name.length() == 0) name = "r" + nameCount.getAndIncrement();
+ samWriter.println(name + "\t" + flag + "\t" + genomeNames[hits.get(0).getRepliconIndex()] + "\t" + hits.get(0).getStart() + "\t" + "255" + "\t" + read.length() + "M" + "\t" + "*" + "\t" + "0" + "\t" + "0" + "\t" + read + "\t" + quality);
+ }
+ }
+ }
+ }
+ }
+ } catch (IOException e) {
+ output("Error - could not read in from file " + readsFile + "\n\n");
+ System.exit(0);
+ }
+ }
+
+ /**
+ * Return the base file name for the compressed sequencing reads file.
+ */
+ public String getCompressedFileName(String readsFile, String genomeFile) {
+ if (!isPairedEnd) return getFileNameBase(readsFile) + "_" + getFileNameBase(genomeFile) + parametersString;
+ else return getFileNameBase(readsFile) + "_" + getFileNameBase(pairedEndFile) + "_" + getFileNameBase(genomeFile) + parametersString;
+ }
+
+ /**
+ * Return a list of the base file names for the compressed sequencing reads files.
+ */
+ public ArrayList<String> getListOfCompressedFileNames(String readsFile) {
+ ArrayList<String> fileNames = new ArrayList<String>(numSequences);
+ for (int i=0; i<numSequences; i++) {
+ fileNames.add(getCompressedFileName(readsFile, sequenceFiles[i]));
+ }
+ return fileNames;
+ }
+
+
+
+ /**********************************************
+ ********** Public Class Methods **********
+ **********************************************/
+
+ /**
+ * Output mapped reads to WIG file that can be loaded
+ * by a genome browser.
+ */
+ public static void outputBrowserFile(String readsFile, String genomeFile, String dir1, String dir2, String outFileName, int[] coordinates_plus, int[] coordinates_minus, int trackRange) {
+
+ try {
+ // Set up directory
+ File d = new File(dir1);
+ if (!d.isDirectory()) d.mkdir();
+ d = new File(dir1 + dir2);
+ if (!d.isDirectory()) d.mkdir();
+ PrintWriter out = new PrintWriter(new File(dir1 + dir2 + outFileName + ".plus" + ".wig"));
+ out.println("track name=" + getFileNameBase(readsFile) + "_PLUS color=0,0,255 graphType=bar viewLimits=0:" + trackRange);
+ out.println("fixedStep chrom=" + getGenomeName(genomeFile) + " start=1 step=1");
+ for (int j=1; j<coordinates_plus.length; j++) out.println(coordinates_plus[j]);
+ out.close();
+ out = new PrintWriter(new File(dir1 + dir2 + outFileName + ".minus" + ".wig"));
+ out.println("track name=" + getFileNameBase(readsFile) + "_MINUS color=255,0,0 graphType=bar viewLimits=0:" + trackRange);
+ out.println("fixedStep chrom=" + getGenomeName(genomeFile) + " start=1 step=1");
+ for (int j=1; j<coordinates_minus.length; j++) out.println(coordinates_minus[j]);
+ out.close();
+ } catch (IOException e) {
+ output("Could not write wiggle file in directory " + (dir1 + dir2) + "\n");
+ }
+ }
+
+ public static void output(String s) {
+ if (summaryWriter != null) summaryWriter.print(s);
+ if (output == null) System.out.print(s);
+ else output.append(s);
+ }
+
+
+
+ /**************************************************
+ ********** Private Instance Methods **********
+ **************************************************/
+
+ /**
+ * Read in reads file and map all reads to reference
+ * index using multiple threads.
+ */
+ private void mapReads() {
+
+ try {
+ if (isCompressedFile) reader = new BufferedReader(new InputStreamReader(new GZIPInputStream(new FileInputStream(readsFile))));
+ else reader = new BufferedReader(new FileReader(readsFile));
+ if (isPairedEnd) {
+ if (FileOps.isGZIP(pairedEndFile)) reader2 = new BufferedReader(new InputStreamReader(new GZIPInputStream(new FileInputStream(pairedEndFile))));
+ else reader2 = new BufferedReader(new FileReader(pairedEndFile));
+ }
+ Thread[] threads = new Thread[numThreads];
+ for (int i=0; i<numThreads; i++) {
+ threads[i] = new ProcessReads_Thread(this);
+ threads[i].start();
+ }
+ for (int i=0; i<numThreads; i++) threads[i].join();
+ reader.close();
+ if (isPairedEnd) reader2.close();
+ } catch (IOException e) {
+ output("Error - could not read from " + readsFile + "\n\n");
+ System.exit(0);
+ } catch (InterruptedException e) {
+ output("Error - thread execution was interrupted.\n\n");
+ System.exit(0);
+ }
+ }
+
+ /**
+ * Output the reads aligning to each replicon to a file.
+ */
+ private void outputReadsToFile() {
+ for (int i=0; i<numSequences; i++) {
+ String outFileName = getCompressedFileName(readsFile, sequenceFiles[i]);
+ FileOps.writeCompressedFile(outFileName, readsFile, sequenceFiles[i], index.getReplicon(i).getName(), index.getReplicon(i).getLength(), totalReads.get(), invalidQualityReads.get(), ambiguousReads.get(), lowQualityReads.get(), mappedOnceReads.get(), mappedMoreThanOnceReads.get(), exactMappedReads.get(i), inexactMappedReads.get(i), avgLengthReads.get(), toArray(coordinates_plus[i]), toArray(coordinates_minus[i]));
+
+ // Write Wiggle files
+ if (Peregrine.outputBrowserFile) {
+ int[] plusCoords = new int[coordinates_plus[i].length()];
+ int[] minusCoords = new int[coordinates_minus[i].length()];
+ for (int j=0; j<plusCoords.length; j++) plusCoords[j] = coordinates_plus[i].get(j);
+ for (int j=0; j<minusCoords.length; j++) minusCoords[j] = coordinates_minus[i].get(j);
+ int lengthOfAllReplicons = 0;
+ for (int k=0; k<index.getNumReplicons(); k++) lengthOfAllReplicons += index.getReplicon(k).getLength();
+ long trackRange = 2 * avgLengthReads.get() * (long)(exactMappedReads.get(i) + inexactMappedReads.get(i)) / lengthOfAllReplicons;
+ outputBrowserFile(readsFile, sequenceFiles[i], outputDIR, browserDIR, outFileName, plusCoords, minusCoords, (int)trackRange);
+ }
+ }
+ }
+
+ /**
+ * Outputs to STDOUT stats on how many reads align to the genomic sequence.
+ */
+ private void outputResults() {
+ output("Total reads: \t" + totalReads + "\n");
+ //output("Invalid quality reads: \t" + invalidQualityReads + "\t" + Math.round((100.0*invalidQualityReads.get())/totalReads.get()) + "%" + "\n");
+ //output("Ambiguous reads: \t" + ambiguousReads + "\t" + Math.round((100.0*ambiguousReads.get())/totalReads.get()) + "%" + "\n");
+ //output("Low quality reads: \t" + lowQualityReads + "\t" + Math.round((100.0*lowQualityReads.get())/totalReads.get()) + "%" + "\n");
+ //output("Aligned 1 time reads: \t" + mappedOnceReads + "\t" + Math.round((100.0*mappedOnceReads.get())/totalReads.get()) + "%" + "\n");
+ //output("Aligned >1 time reads: \t" + mappedMoreThanOnceReads + "\t" + Math.round((100.0*mappedMoreThanOnceReads.get())/totalReads.get()) + "%" + "\n");
+ //output("Exact alignment reads: \t" + exactMappedReads + "\t" + Math.round((100.0*exactMappedReads.get())/totalReads.get(i)) + "%" + "\n");
+ //output("Inexact alignment reads:\t" + inexactMappedReads + "\t" + Math.round((100.0*inexactMappedReads.get(i))/totalReads.get()) + "%" + "\n");
+ //output("\n");
+ for (int i=0; i<Peregrine.numSequences; i++) {
+ output("Successfully aligned reads:\t" + (exactMappedReads.get(i) + inexactMappedReads.get(i)) + "\t" + Math.round((100.0*(exactMappedReads.get(i)+inexactMappedReads.get(i)))/totalReads.get()) + "%" + "\t" + "(" + getInformalName(sequenceFiles[i]) + ")" + "\n");
+ outputAnnotationStats(i); // Number of reads aligning genes and RNAs
+ }
+ output("\n");
+
+ if (samWriter != null) output("Sequencing reads written to SAM file:\t" + outputDIR + getFileNameBase(readsFile) + ".sam" + "\n\n");
+
+ if (time) { // Output time taken to execute program
+ output("Time taken to align reads:\t" + (runningTime/60000) + " minutes " + ((runningTime%60000)/1000) + " seconds\n");
+ }
+ }
+
+ /**
+ * Determines the file format of the input reads file.
+ * Returns 0 if the file is in FASTQ format.
+ * Returns 1 if the file is in QSEQ format.
+ * Returns 2 if the file is in FASTA format.
+ * Returns 3 if the file is in SAM single-end format.
+ * Returns 4 if the file is in SAM paired-end format.
+ * Returns 5 if the file is in BAM single-end format.
+ * Returns 6 if the file is in BAM paired-end format.
+ */
+ private int getReadsInputFileType(String readsFile) {
+ int MAX_LINES = 10000;
+ int lineCounter = 0;
+ int fastqCount = 0;
+ int qseqCount = 0;
+ int fastaCount = 0;
+ try {
+ // First check if we have a SAM file
+ sam = new SamOps(readsFile, MAX_LINES, false);
+ if (sam.isValidSam() || sam.isValidBam()) {
+ String[] replicons = sam.getReplicons();
+ output("\nUser should make sure that reference replicons input by the user correspond to those in SAM/BAM file.\n");
+ output("\tReference replicons input by user:\n");
+ for (int i=0; i<numSequences; i++) output("\t\t" + getGenomeName(sequenceFiles[i]) + " with length " + (index.getReplicon(i).getLength()-1) + " nts\n");
+ output("\tReference replicons found in SAM file:\n");
+ for (int i=0; i<replicons.length; i++) output("\t\t" + replicons[i] + " with length " + sam.getRepliconLength(i) + " nts\n");
+ output("\n");
+ if (sam.isValidSam() && !sam.isPairedEnd()) return 3; // Single-end SAM file
+ else if (sam.isValidSam()) { // Paired-end SAM file
+ Peregrine.stopAfterOneHit = false;
+ return 4;
+ } else if (sam.isValidBam() && !sam.isPairedEnd()) return 5; // Single-end BAM file
+ else if (sam.isValidBam()) { // Paired-end BAM file
+ Peregrine.stopAfterOneHit = false;
+ return 6;
+ } else return -1; // This case should never be reached
+ } else sam = null;
+
+ Scanner reader = null;
+ isCompressedFile = FileOps.isGZIP(readsFile);
+ if (isCompressedFile) reader = new Scanner(new GZIPInputStream(new FileInputStream(readsFile)));
+ else reader = new Scanner(new File(readsFile));
+ String line;
+ while (reader.hasNextLine() && (lineCounter < MAX_LINES)) {
+ line = reader.nextLine();
+ if (line.length() > 0) {
+ if (line.charAt(0) == '@') fastqCount++;
+ else if (line.split("\t").length >= 11) qseqCount++;
+ else if (line.charAt(0) == '>') fastaCount++;
+ }
+ lineCounter++;
+ }
+ reader.close();
+ if (fastqCount > Math.max(qseqCount, fastaCount)) return 0;
+ else if (qseqCount > fastaCount) return 1;
+ else if (fastaCount > 0) return 2;
+ else {
+ output("Error - could not recognize format of file " + readsFile + "\n\n");
+ System.exit(0);
+ }
+ } catch (IOException e) {
+ output("\nError - could not open file " + readsFile + "\n\n");
+ System.exit(0);
+ }
+ return -1;
+ }
+
+ /**
+ * Depending on version of Solexa machine used, the quality
+ * score may range from 35 (or 37) up to 73, or it may range
+ * from 66 up to 104. To obtain the Phred score, we subtract
+ * either 33 or 64, depending on the version. Here, we get the
+ * maximum quality score over all nucleotides in the first
+ * 100,000 reads (it should be either 73 or 104). The offset
+ * is the number we must subtract from this maximum to
+ * obtain 40, i.e., either 33 or 64.
+ */
+ private int getPhredOffset(String readsFile) {
+ int lineCounter = 0;
+ try {
+ int maxQuality = Integer.MIN_VALUE;
+ if ((readsInputFormat == 5) || (readsInputFormat == 6)) { // BAM file
+ maxQuality = sam.getMaxQuality();
+ } else {
+ Scanner reader = null;
+ if (isCompressedFile) reader = new Scanner(new GZIPInputStream(new FileInputStream(readsFile)));
+ else reader = new Scanner(new File(readsFile));
+ String line;
+ String read = "";
+ String quality = "";
+
+ while (reader.hasNextLine() && (lineCounter < 100000)) {
+
+ line = reader.nextLine();
+ if (readsInputFormat == 0) { // FASTQ file
+ read = reader.nextLine();
+ line = reader.nextLine();
+ quality = reader.nextLine();
+ } else if (readsInputFormat == 1) { // QSEQ file
+ String[] parse_line = line.split("\t");
+ read = parse_line[8];
+ quality = parse_line[9];
+ } else if (readsInputFormat == 2) { // FASTA file
+ read = reader.nextLine();
+ quality = "("; // ASCII value of 40
+ } else if ((readsInputFormat == 3) || (readsInputFormat == 4)) { // SAM file
+ if (line.startsWith("@")) {
+ read = "";
+ quality = "";
+ } else {
+ String[] parse_line = line.split("\t");
+ read = parse_line[9];
+ quality = parse_line[10];
+ if (quality.equals("*")) quality = "";
+ }
+ }
+
+ // Process quality
+ for (int i=0; i<quality.length(); i++)
+ maxQuality = Math.max(maxQuality, (int)(quality.charAt(i)));
+
+ lineCounter++;
+ }
+ reader.close();
+ }
+
+ // Are we Phred+33 or Phred+64?
+ if (Math.abs(maxQuality - 40 - 33) < Math.abs(maxQuality - 40 - 64))
+ return 33;
+ else
+ return 64;
+ } catch (IOException e) {
+ output("\nError - could not open file " + readsFile + "\n\n");
+ System.exit(0);
+ }
+ return -1;
+ }
+
+ /**
+ * Given the hit of a read mapping to the genome, we update
+ * the coordinates corresponding to the read hit.
+ */
+ private void mapHitsToCoordinates(Hit a) {
+ AtomicIntegerArray coordinates = this.coordinates_plus[a.getRepliconIndex()]; // Plus strand
+ if (a.getStrand() == '-') coordinates = this.coordinates_minus[a.getRepliconIndex()]; // Minus strand
+ for (int i=a.getStart(); i<=a.getStop(); i++)
+ coordinates.getAndIncrement(i);
+ }
+
+ /**
+ * Output number of reads aligning sense/antisense to
+ * annotated genes and RNAs in replicon i.
+ */
+ private void outputAnnotationStats(int i) {
+ if ((annotationsPlus == null) || annotationsMinus == null) return;
+ if ((i >= annotationsPlus.length) || (i >= annotationsMinus.length)) return;
+
+ long gene_sense = 0;
+ long gene_antisense = 0;
+ long rRNA_sense = 0;
+ long rRNA_antisense = 0;
+ long tRNA_sense = 0;
+ long tRNA_antisense = 0;
+ long miscRNA_sense = 0;
+ long miscRNA_antisense = 0;
+ long IG = 0;
+
+ String[] annotationPlus = annotationsPlus[i];
+ String[] annotationMinus = annotationsMinus[i];
+ AtomicIntegerArray coordinate_plus = coordinates_plus[i];
+ AtomicIntegerArray coordinate_minus = coordinates_minus[i];
+ for (int j=1; j<coordinate_plus.length(); j++) { // 1-indexed
+ // There are five possibilities on each strand (rRNA, tRNA, RNA, gene, empty).
+ // We handle all twenty-five cases.
+ if (annotationPlus[j].equals("rRNA")) { // Plus rRNA
+ rRNA_sense += coordinate_plus.get(j);
+ if (annotationMinus[j].length() == 0) rRNA_antisense += coordinate_minus.get(j);
+ else if (annotationMinus[j].equals("rRNA")) rRNA_sense += coordinate_minus.get(j);
+ else if (annotationMinus[j].equals("tRNA")) tRNA_sense += coordinate_minus.get(j);
+ else if (annotationMinus[j].equals("RNA")) miscRNA_sense += coordinate_minus.get(j);
+ else gene_sense += coordinate_minus.get(j);
+ } else if (annotationPlus[j].equals("tRNA")) { // Plus tRNA
+ tRNA_sense += coordinate_plus.get(j);
+ if (annotationMinus[j].length() == 0) tRNA_antisense += coordinate_minus.get(j);
+ else if (annotationMinus[j].equals("rRNA")) rRNA_sense += coordinate_minus.get(j);
+ else if (annotationMinus[j].equals("tRNA")) tRNA_sense += coordinate_minus.get(j);
+ else if (annotationMinus[j].equals("RNA")) miscRNA_sense += coordinate_minus.get(j);
+ else gene_sense += coordinate_minus.get(j);
+ } else if (annotationPlus[j].equals("RNA")) { // Plus misc RNA
+ miscRNA_sense += coordinate_plus.get(j);
+ if (annotationMinus[j].length() == 0) miscRNA_antisense += coordinate_minus.get(j);
+ else if (annotationMinus[j].equals("rRNA")) rRNA_sense += coordinate_minus.get(j);
+ else if (annotationMinus[j].equals("tRNA")) tRNA_sense += coordinate_minus.get(j);
+ else if (annotationMinus[j].equals("RNA")) miscRNA_sense += coordinate_minus.get(j);
+ else gene_sense += coordinate_minus.get(j);
+ } else if (annotationPlus[j].length() > 0) { // Plus protein-coding gene
+ gene_sense += coordinate_plus.get(j);
+ if (annotationMinus[j].length() == 0) gene_antisense += coordinate_minus.get(j);
+ else if (annotationMinus[j].equals("rRNA")) rRNA_sense += coordinate_minus.get(j);
+ else if (annotationMinus[j].equals("tRNA")) tRNA_sense += coordinate_minus.get(j);
+ else if (annotationMinus[j].equals("RNA")) miscRNA_sense += coordinate_minus.get(j);
+ else gene_sense += coordinate_minus.get(j);
+ } else { // Plus no annotation
+ if (annotationMinus[j].equals("rRNA")) {
+ rRNA_sense += coordinate_minus.get(j);
+ rRNA_antisense += coordinate_plus.get(j);
+ } else if (annotationMinus[j].equals("tRNA")) {
+ tRNA_sense += coordinate_minus.get(j);
+ tRNA_antisense += coordinate_plus.get(j);
+ } else if (annotationMinus[j].equals("RNA")) {
+ miscRNA_sense += coordinate_minus.get(j);
+ miscRNA_antisense += coordinate_plus.get(j);
+ } else if (annotationMinus[j].length() > 0) {
+ gene_sense += coordinate_minus.get(j);
+ gene_antisense += coordinate_plus.get(j);
+ } else {
+ IG += coordinate_minus.get(j);
+ IG += coordinate_plus.get(j);
+ }
+ }
+ }
+
+ // Output stats
+ long total = gene_sense + gene_antisense + rRNA_sense + rRNA_antisense + tRNA_sense + tRNA_antisense + miscRNA_sense + miscRNA_antisense + IG;
+ output("\t" + "Aligning (sense) to protein-coding genes:\t" + Math.round(100.0*gene_sense/total) + "%" + "\n");
+ output("\t" + "Aligning (antisense) to protein-coding genes:\t" + Math.round(100.0*gene_antisense/total) + "%" + "\n");
+ output("\t" + "Aligning (sense) to ribosomal RNAs:\t" + Math.round(100.0*rRNA_sense/total) + "%" + "\n");
+ output("\t" + "Aligning (antisense) to ribosomal RNAs:\t" + Math.round(100.0*rRNA_antisense/total) + "%" + "\n");
+ output("\t" + "Aligning (sense) to transfer RNAs:\t" + Math.round(100.0*tRNA_sense/total) + "%" + "\n");
+ output("\t" + "Aligning (antisense) to transfer RNAs:\t" + Math.round(100.0*tRNA_antisense/total) + "%" + "\n");
+ output("\t" + "Aligning (sense) to miscellaneous RNAs:\t" + Math.round(100.0*miscRNA_sense/total) + "%" + "\n");
+ output("\t" + "Aligning (antisense) to miscellaneous RNAs:\t" + Math.round(100.0*miscRNA_antisense/total) + "%" + "\n");
+ output("\t" + "Aligning to unannotated regions: \t" + Math.round(100.0*IG/total) + "%" + "\n");
+ }
+
+ /**
+ * Open SAM file for writing.
+ * Output header information to SAM file.
+ */
+ private void outputSamHeader() {
+ String samFileName = outputDIR + getFileNameBase(readsFile) + ".sam";
+ if (readsFile.equals(samFileName)) return; // Do not read and write same file at same time
+ try {
+ samWriter = new PrintWriter(new File(samFileName));
+ samWriter.println("@HD" + "\t" + "VN:1.0" + "\t" + "SO:unsorted");
+ genomeNames = new String[sequenceFiles.length];
+ for (int i=0; i<sequenceFiles.length; i++) {
+ samWriter.println("@SQ" + "\t" + "SN:" + getGenomeName(sequenceFiles[i]) + "\t" + "LN:" + (index.getReplicon(i).getLength()-1) + "\t" + "SP:" + getInformalName(sequenceFiles[i]));
+ genomeNames[i] = getGenomeName(sequenceFiles[i]);
+ }
+ samWriter.println("@PG" + "\t" + "ID:Rockhopper" + "\t" + "PN:Rockhopper" + "\t" + "VN:" + Rockhopper.version);
+ } catch (IOException f) {
+ samWriter = null;
+ }
+ }
+
+ /**
+ * Takes a String array representing one line from a BAM file and
+ * we map the repliconIndex (at parse_line[2] and parse_line[6])
+ * to the corresponding replicon name.
+ */
+ private void mapBamNames(String[] parse_line) {
+ if (parse_line[2].equals("*")) parse_line[6] = "*";
+ else {
+ int repliconIndex = 0;
+ try {
+ repliconIndex = Integer.parseInt(parse_line[2]);
+ } catch (NumberFormatException e) {
+ parse_line[2] = "*";
+ parse_line[6] = "*";
+ return;
+ }
+ if (repliconIndex < 0) {
+ parse_line[2] = "*";
+ parse_line[6] = "*";
+ } else parse_line[2] = genomeNames[repliconIndex];
+ if (!parse_line[6].equals("*")) {
+ if (parse_line[2].equals(parse_line[6])) parse_line[6] = "=";
+ else {
+ try {
+ repliconIndex = Integer.parseInt(parse_line[6]);
+ } catch (NumberFormatException e) {
+ parse_line[6] = "*";
+ return;
+ }
+ if (repliconIndex < 0) parse_line[6] = "*";
+ else parse_line[6] = genomeNames[repliconIndex];
+ }
+ }
+ }
+ }
+
+ /**
+ * Return a String representation of the parameter settings.
+ */
+ private String parametersToString() {
+ return "_v" + numSequences + "_m" + (int)(100*percentMismatches) + "_a" + ("" + stopAfterOneHit).toUpperCase().charAt(0) + "_d" + maxPairedEndLength + "_l" + (int)(100*percentSeedLength) + "_" + pairedEndOrientation + "_c" + ("" + singleEndOrientationReverseComplement).toUpperCase().charAt(0);
+ }
+
+ /**
+ * Returns an int[] version of an atomic integer array.
+ */
+ private int[] toArray(AtomicIntegerArray a) {
+ int[] b = new int[a.length()];
+ for (int i=0; i<a.length(); i++) b[i] = a.get(i);
+ return b;
+ }
+
+ /**
+ * Returns a reversed version of String s.
+ */
+ private String reverse(String s) {
+ return (new StringBuilder(s)).reverse().toString();
+ }
+
+ /**
+ * Returns a reverse complemented version of String s.
+ */
+ private String reverseComplement(String s) {
+ StringBuilder sb = new StringBuilder(s.length());
+ for (int i=s.length()-1; i>=0; i--) {
+ if (s.charAt(i) == 'A') sb.append('T');
+ else if (s.charAt(i) == 'C') sb.append('G');
+ else if (s.charAt(i) == 'G') sb.append('C');
+ else if (s.charAt(i) == 'T') sb.append('A');
+ else sb.append(s.charAt(i));
+ }
+ return sb.toString();
+ }
+
+
+
+ /***********************************************
+ ********** Private Class Methods **********
+ ***********************************************/
+
+ /**
+ * Free up memory by deleting class variables that
+ * we are finished with.
+ */
+ public static void releaseMemory() {
+ annotationsPlus = null;
+ annotationsMinus = null;
+ }
+
+
+
+ /***********************************************
+ ********** Private Class Methods **********
+ ***********************************************/
+
+ /**
+ * Returns the base of the specified file name, i.e.,
+ * the file extension and path to the file are excluded.
+ */
+ private static String getFileNameBase(String fileName) {
+ int slashIndex = fileName.lastIndexOf(File.separator);
+ if (slashIndex == -1) slashIndex = fileName.lastIndexOf("/");
+ int periodIndex = fileName.indexOf('.', slashIndex+1);
+ if (periodIndex == -1) periodIndex = fileName.length();
+ return fileName.substring(slashIndex+1, periodIndex);
+ }
+
+ /**
+ * Returns the name of the replicon from the FASTA header line,
+ * e.g., gi|59800473|ref|NC_002946.2|
+ */
+ private static String getGenomeName(String fileName) {
+ String genomeName = "";
+ try {
+ Scanner reader = new Scanner(new File(fileName));
+ String line = reader.nextLine();
+ String[] parse_line = line.split("\\s+");
+ genomeName = parse_line[0].substring(1);
+ reader.close();
+ } catch (IOException e) {
+ output("Error - could not read in from file " + fileName + "\n\n");
+ System.exit(0);
+ }
+ return genomeName;
+ }
+
+ /**
+ * Returns the informal name of the replicon from the FASTA header line,
+ * e.g., Escherichia coli str. K-12 substr. MG1655 chromosome
+ */
+ private static String getInformalName(String fileName) {
+ String genomeName = "";
+ try {
+ Scanner reader = new Scanner(new File(fileName));
+ String line = reader.nextLine();
+ String[] parse_line = line.split("\\|");
+ if (parse_line.length > 4) { // Appropriately formatted FASTA header
+ String[] parse_name = parse_line[4].split(",");
+ genomeName = parse_name[0].trim();
+ } else { // Unexpected format for FASTA header
+ genomeName = line.trim();
+ }
+ reader.close();
+ } catch (IOException e) {
+ output("Error - could not read in from file " + fileName + "\n\n");
+ System.exit(0);
+ }
+ return genomeName;
+ }
+
+ /**
+ * Checks if quality scores specified by parameter String
+ * need to be adjusted by a Phred offset of 33. If not,
+ * the original String is returned. If so, a new
+ * adjusted String is returned.
+ */
+ private static String mapPhred(String qualities) {
+ int offset = 33;
+ int maxPhred = 104;
+ boolean needsAdjusting = false;
+ boolean needsResetting = false;
+ for (int i=0; i<qualities.length(); i++) {
+ if ((int)(qualities.charAt(i)) < offset) needsAdjusting = true;
+ if ((int)(qualities.charAt(i)) > maxPhred) needsResetting = true;
+ }
+ if (!needsAdjusting && !needsResetting) return qualities;
+ StringBuilder sb = new StringBuilder(qualities.length());
+ for (int i=0; i<qualities.length(); i++) {
+ if (needsAdjusting) sb.append((char)(offset + qualities.charAt(i)));
+ else if (needsResetting) sb.append('(');
+ }
+ return sb.toString();
+ }
+
+ private static void commandLineArguments(String[] args) {
+ if (args.length < 2) {
+ System.err.println("\nThe Peregrine application takes one or more files of genomic sequences (such as FASTA genome files) and a file of RNA-seq reads and it aligns the reads to the genomic sequences.");
+ System.err.println("\nThe Peregrine application has two required command line arguments.");
+ System.err.println("\nREQUIRED ARGUMENTS\n");
+ System.err.println("\t" + "a comma-separated list of files containing replicon sequences in FASTA format");
+ System.err.println("\t" + "a file <FASTQ,QSEQ,FASTA> of RNA-seq reads");
+
+ System.err.println("\nOPTIONAL ARGUMENTS\n");
+ System.err.println("\t" + "-2 <file>" + "\t" + "a file <FASTQ,QSEQ,FASTA> of mate-paired RNA-seq reads, (default is single-end rather than paired-end reads)");
+ System.err.println("\t" + "-c <boolean>" + "\t" + "reverse complement single-end reads (default is false)");
+ System.err.println("\t" + "-ff/fr/rf/rr" + "\t" + "orientation of two mate reads for each paired-end read, f=forward and r=reverse_complement (default is fr)");
+ System.err.println("\t" + "-m <number>" + "\t" + "allowed mismatches as percent of read length (default is 0.15)");
+ System.err.println("\t" + "-a <boolean>" + "\t" + "report 1 alignment (true) or report all optimal alignments (false), (default is true)");
+ System.err.println("\t" + "-d <integer>" + "\t" + "maximum number of bases between mate pairs for paired-end reads (default is 500)");
+ System.err.println("\t" + "-l <number>" + "\t" + "minimum seed as percent of read length (default is 0.33)");
+ System.err.println("\t" + "-p <integer>" + "\t" + "number of processors (default is self-identification of processors)");
+ System.err.println("\t" + "-o <DIR>" + "\t" + "directory where output files are written (default is Peregrine_Results/)");
+ System.err.println("\t" + "-time " + "\t" + "output time taken to execute program");
+
+ System.err.println("\njava Peregrine <options> NC_002505.fna,NC_002506.fna reads.fastq\n");
+ System.exit(0);
+ }
+
+ // Initially set the number of threads
+ Peregrine.numThreads = Runtime.getRuntime().availableProcessors();
+ if (Peregrine.numThreads > 4) Peregrine.numThreads *= 0.75;
+
+ int i=0;
+ while (i < args.length - 2) {
+ if (args[i].startsWith("-2")) {
+ if ((i == args.length-3) || (args[i+1].startsWith("-"))) {
+ System.err.println("Error - command line argument -2 must be followed by a mate-paired sequencing read file.");
+ System.exit(0);
+ }
+ Peregrine.isPairedEnd = true;
+ Peregrine.pairedEndFile = args[i+1];
+ i += 2;
+ } else if (args[i].startsWith("-c")) {
+ if ((i == args.length-3) || (args[i+1].startsWith("-"))) {
+ System.err.println("Error - command line argument -c must be followed by a boolean.");
+ System.exit(0);
+ }
+ Peregrine.singleEndOrientationReverseComplement = Boolean.valueOf(args[i+1]);
+ i += 2;
+ } else if (args[i].equals("-ff")) {
+ Peregrine.pairedEndOrientation = "ff";
+ i += 1;
+ } else if (args[i].equals("-fr")) {
+ Peregrine.pairedEndOrientation = "fr";
+ i += 1;
+ } else if (args[i].equals("-rf")) {
+ Peregrine.pairedEndOrientation = "rf";
+ i += 1;
+ } else if (args[i].equals("-rr")) {
+ Peregrine.pairedEndOrientation = "rr";
+ i += 1;
+ } else if (args[i].startsWith("-m")) {
+ if ((i == args.length-3) || (args[i+1].startsWith("-"))) {
+ System.err.println("Error - command line argument -m must be followed by a decimal number.");
+ System.exit(0);
+ }
+ Peregrine.percentMismatches = Double.parseDouble(args[i+1]);
+ i += 2;
+ } else if (args[i].startsWith("-a")) {
+ if ((i == args.length-3) || (args[i+1].startsWith("-"))) {
+ System.err.println("Error - command line argument -a must be followed by a boolean.");
+ System.exit(0);
+ }
+ Peregrine.stopAfterOneHit = Boolean.valueOf(args[i+1]);
+ i += 2;
+ } else if (args[i].startsWith("-d")) {
+ if ((i == args.length-3) || (args[i+1].startsWith("-"))) {
+ System.err.println("Error - command line argument -d must be followed by an integer.");
+ System.exit(0);
+ }
+ Peregrine.maxPairedEndLength = Integer.parseInt(args[i+1]);
+ SamOps.maxPairedEndLength = Integer.parseInt(args[i+1]);
+ i += 2;
+ } else if (args[i].startsWith("-l")) {
+ if ((i == args.length-3) || (args[i+1].startsWith("-"))) {
+ System.err.println("Error - command line argument -l must be followed by a decimal number.");
+ System.exit(0);
+ }
+ Peregrine.percentSeedLength = Double.parseDouble(args[i+1]);
+ i += 2;
+ } else if (args[i].startsWith("-p")) {
+ if ((i == args.length-3) || (args[i+1].startsWith("-"))) {
+ System.err.println("Error - command line argument -p must be followed by an integer.");
+ System.exit(0);
+ }
+ Peregrine.numThreads = Integer.parseInt(args[i+1]);
+ i += 2;
+ } else if (args[i].startsWith("-o")) {
+ if ((i == args.length-3) || (args[i+1].startsWith("-"))) {
+ System.err.println("Error - command line argument -o must be followed by a directory path.");
+ System.exit(0);
+ }
+ Peregrine.outputDIR = args[i+1];
+ if (Peregrine.outputDIR.charAt(outputDIR.length()-1) != '/') outputDIR += '/';
+ i += 2;
+ } else if (args[i].startsWith("-r")) {
+ if ((i == args.length-3) || (args[i+1].startsWith("-"))) {
+ System.err.println("Error - command line argument -r must be followed by a long integer.");
+ System.exit(0);
+ }
+ Peregrine.randomSeed = Long.parseLong(args[i+1]);
+ i += 2;
+ } else if (args[i].equals("-time")) {
+ Peregrine.time = true;
+ i += 1;
+ } else {
+ System.err.println("Error - could not recognize command line argument: " + args[i]);
+ System.exit(0);
+ }
+ }
+
+ // Determine required input files
+ Peregrine.sequenceFiles = args[i].split(",");
+ Peregrine.readsFile = args[i+1];
+ Peregrine.numSequences = Peregrine.sequenceFiles.length;
+
+ // Handle erroneous command line arguments
+ for (int j=0; j<sequenceFiles.length; j++) {
+ if (!(new File(sequenceFiles[j]).exists())) {
+ System.err.println("Error - file " + sequenceFiles[j] + " does not exist.");
+ System.exit(0);
+ }
+ }
+ if (!(new File(readsFile).exists())) {
+ System.err.println("Error - file " + readsFile + " does not exist.");
+ System.exit(0);
+ }
+ if (isPairedEnd && !(new File(pairedEndFile).exists())) {
+ System.err.println("Error - file " + pairedEndFile + " does not exist.");
+ System.exit(0);
+ }
+ }
+
+
+
+ /*************************************
+ ********** Main Method **********
+ *************************************/
+
+ public static void main(String[] args) {
+
+ commandLineArguments(args);
+ Peregrine p = new Peregrine();
+
+ }
+
+}
+
+
+
+/*********************************************
+ ********** ProcessReads_Thread **********
+ *********************************************/
+
+class ProcessReads_Thread extends Thread {
+
+ private Peregrine p;
+
+ public ProcessReads_Thread(Peregrine p) {
+ this.p = p;
+ }
+
+ public void run() {
+ p.processReads();
+ }
+}
diff --git a/ProgressGUI.java b/ProgressGUI.java
new file mode 100644
index 0000000..b0a6a99
--- /dev/null
+++ b/ProgressGUI.java
@@ -0,0 +1,122 @@
+/*
+ * Copyright 2013 Brian Tjaden
+ *
+ * This file is part of Rockhopper.
+ *
+ * Rockhopper is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * any later version.
+ *
+ * Rockhopper is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * (in the file gpl.txt) along with Rockhopper.
+ * If not, see <http://www.gnu.org/licenses/>.
+ */
+
+import java.awt.Dimension;
+import java.awt.FlowLayout;
+import java.awt.event.MouseListener;
+import java.beans.PropertyChangeListener;
+import java.beans.PropertyChangeEvent;
+import javax.swing.*;
+
+public class ProgressGUI implements PropertyChangeListener {
+
+ private JFrame progressFrame;
+ private JApplet applet;
+ public JTextArea progressArea;
+ public JProgressBar progressBar;
+ private JLabel IGV_Label;
+ private ImageIcon IGV_Button, IGV_ButtonPressed;
+ private int width = 620;
+ private int height = 650;
+
+
+
+ /**
+ * Constructor.
+ */
+ public ProgressGUI(JApplet applet) {
+ this.applet = applet;
+ }
+
+
+
+ public void createProgressWindow() {
+
+ progressFrame = new JFrame("Progress");
+ progressFrame.setSize(width,height);
+ progressFrame.setResizable(false);
+ progressFrame.setLocationRelativeTo(null);
+ progressFrame.setIconImage(new ImageIcon(RockhopperGUI.penguin).getImage());
+ progressFrame.setVisible(true);
+ JPanel progressPanel = new JPanel(new FlowLayout(FlowLayout.CENTER));
+ progressPanel.setPreferredSize(new Dimension(width,height));
+ progressPanel.setBackground(RockhopperGUI.lightBlue);
+
+ progressBar = new JProgressBar(0, 100);
+ progressBar.setValue(0);
+ progressBar.setStringPainted(true);
+
+ progressArea = new JTextArea();
+ progressArea.setEditable(false);
+ progressArea.setText("Initializing RNAseq analysis...\n");
+
+ IGV_Button = RockhopperGUI.getScaledImage("images/IGV_button.gif", 130, 57);
+ IGV_ButtonPressed = RockhopperGUI.getScaledImage("images/IGV_buttonPressed.gif", 130, 57);
+ IGV_Label = new JLabel(IGV_Button);
+ IGV_Label.setToolTipText("Launch the Integrative Genomics Viewer from the Broad Institute");
+ IGV_Label.addMouseListener((MouseListener)applet);
+ IGV_Label.setVisible(false);
+
+ JScrollPane scrollPane = new JScrollPane(progressArea);
+ scrollPane.setPreferredSize(new Dimension(width-20,height-130));
+ scrollPane.setBorder(BorderFactory.createEmptyBorder());
+
+ progressPanel.add(progressBar);
+ progressPanel.add(scrollPane);
+ progressPanel.add(IGV_Label);
+ progressFrame.add(progressPanel);
+
+ progressFrame.validate();
+ progressFrame.repaint();
+ }
+
+ /**
+ * Add button to launch IGV.
+ */
+ public void addIGV() {
+ IGV_Label.setVisible(true);
+ }
+
+ public void propertyChange(PropertyChangeEvent event) {
+ if ("progress" == event.getPropertyName()) {
+ int progress = (Integer) event.getNewValue();
+ progressBar.setValue(progress);
+ }
+ }
+
+ public boolean isSource(Object source) {
+ if (source.equals(IGV_Label)) return true;
+ return false;
+ }
+
+ public void mousePressed(Object source) {
+ if (source.equals(IGV_Label)) {
+ IGV_Label.setIcon(IGV_ButtonPressed);
+ }
+ }
+
+ public void mouseReleased(Object source) {
+ if (source.equals(IGV_Label)) {
+ IGV_Label.setIcon(IGV_Button);
+ }
+ }
+
+}
+
diff --git a/Replicate.java b/Replicate.java
new file mode 100644
index 0000000..f46ba68
--- /dev/null
+++ b/Replicate.java
@@ -0,0 +1,330 @@
+/*
+ * Copyright 2013 Brian Tjaden
+ *
+ * This file is part of Rockhopper.
+ *
+ * Rockhopper is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * any later version.
+ *
+ * Rockhopper is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * (in the file gpl.txt) along with Rockhopper.
+ * If not, see <http://www.gnu.org/licenses/>.
+ */
+
+import java.util.ArrayList;
+import java.util.Scanner;
+import java.io.File;
+import java.io.FileNotFoundException;
+
+/**
+ * A Replicate object represents information about a
+ * single RNA-seq experiment, including information
+ * about all reads from the experiment.
+ */
+public class Replicate {
+
+ /********************************************
+ ********** INSTANCE VARIABLES **********
+ ********************************************/
+
+ private String fileName; // Path to sequencing reads file
+ private ArrayList<String> compressedFileNames; // List of compressed (WIG) file names
+ private String name; // Name of experiment
+ private int[][] plusReads; // Reads on the plus strand for each genome
+ private int[][] minusReads; // Reads on the minus strand for each genome
+ private long totalReads;
+ private long upperQuartile; // Number of reads for 75% most expressed gene
+ private ArrayList<Integer> background; // Number of nucleotides with few or no reads
+ private double backgroundParameter; // Parameter of geometric distribution of background reads
+ private double avgReads; // Average number of reads mapping to nucleotides throughout genome
+ private double minExpressionUTR; // Minimum expression for a UTR region to be deemed expressed
+ private double minExpressionRNA; // Minimum expression for a ncRNA to be deemed expressed
+ private long avgLengthReads; // Avg length of mapping reads in this replicate file
+
+
+
+ /**************************************
+ ********** CONSTRUCTORS **********
+ **************************************/
+
+ /**
+ * Constructs a new Replicate object based on compressed sequencing reads files.
+ */
+ public Replicate(ArrayList<String> fileNames, String readFile, boolean unstranded) {
+ compressedFileNames = new ArrayList<String>();
+ plusReads = new int[Peregrine.numSequences][];
+ minusReads = new int[Peregrine.numSequences][];
+ this.totalReads = 0;
+ int backgroundLength = 2;
+ this.background = new ArrayList<Integer>(backgroundLength);
+ for (int i=0; i<backgroundLength; i++) background.add(0);
+ for (int z=0; z<Peregrine.numSequences; z++) {
+ String compressedFileName = fileNames.get(z);
+ compressedFileNames.add(compressedFileName);
+ readInAlignmentFile(z, compressedFileName, unstranded);
+ }
+ for (int i=0; i<backgroundLength-1; i++) backgroundParameter += background.get(i);
+ backgroundParameter /= (3.0*2.0*Rockhopper.genomeSize);
+ if (unstranded) backgroundParameter /= (3.0*1.0*Rockhopper.genomeSize);
+ avgReads = totalReads / (2.0 * Rockhopper.genomeSize);
+ if (unstranded) avgReads = totalReads / (1.0 * Rockhopper.genomeSize);
+ }
+
+
+
+ /*************************************************
+ ********** PUBLIC INSTANCE METHODS **********
+ *************************************************/
+
+ /**
+ * Return the name of this Replicate.
+ */
+ public String getName() {
+ return this.name;
+ }
+
+ /**
+ * Return the name of the compressed WIG file for this Replicate
+ * for the specified genome at index z.
+ */
+ public String getCompressedFileName(int z) {
+ return this.compressedFileNames.get(z);
+ }
+
+ /**
+ * Return total number of reads in this Replicate.
+ */
+ public long getTotalReads() {
+ return this.totalReads;
+ }
+
+ /**
+ * Return average number of reads in this Replicate.
+ */
+ public double getAvgReads() {
+ return this.avgReads;
+ }
+
+ /**
+ * Return the number of reads mapping to the specified coordinate
+ * on the specified strand for the specified genome at index z.
+ */
+ public int getReads(int z, int coord, char strand) {
+ if (strand == '+') return plusReads[z][coord];
+ else if (strand == '-') return minusReads[z][coord];
+ else return plusReads[z][coord] + minusReads[z][coord];
+ }
+
+ /**
+ * Return the number of reads on the given strand mapping
+ * to the given range of genomic coordinates for the specified
+ * genome at index z.
+ */
+ public long getReadsInRange(int z, int start, int stop, char strand) {
+ if (stop < start) { // Swap
+ int temp = start;
+ start = stop;
+ stop = temp;
+ }
+
+ long sum = 0;
+ for (int i=Math.max(start, 1); i<Math.min(stop+1, plusReads[z].length); i++) {
+ if (strand == '+') // Plus strand
+ sum += this.plusReads[z][i];
+ else if (strand == '-') // Minus strand
+ sum += this.minusReads[z][i];
+ else // Ambiguous strand
+ sum += this.plusReads[z][i] + this.minusReads[z][i];
+ }
+ return sum;
+ }
+
+ /**
+ * Return the upper quartile for this Replicate.
+ */
+ public long getUpperQuartile() {
+ return upperQuartile;
+ }
+
+ /**
+ * Set the upper quartile, i.e., the number of reads mapping
+ * to the 75% most expressed gene (not counting genes with
+ * zero reads mapping to them).
+ */
+ public void setUpperQuartile(long upperQuartile) {
+ this.upperQuartile = upperQuartile;
+ }
+
+ /**
+ * Sets the minimum level of expression (for a UTR region and
+ * ncRNA to be considered expressed) in this Replicate based on
+ * the average number of reads per nucleotide in this Replicate
+ * and the specified transcript sensitivity between 0.0 and 1.0,
+ * inclusive.
+ */
+ public void setMinExpression(double transcriptSensitivity) {
+ minExpressionUTR = transformation(Math.pow(transcriptSensitivity, 3.3));
+ minExpressionRNA = transformation(Math.pow(transcriptSensitivity, 0.4));
+ }
+
+ /**
+ * Return the minimum level of expression for a UTR region to be
+ * considered expressed in this Replicate.
+ */
+ public double getMinExpressionUTR() {
+ return this.minExpressionUTR;
+ }
+
+ /**
+ * Return the minimum level of expression for a ncRNA to be
+ * considered expressed in this Replicate.
+ */
+ public double getMinExpressionRNA() {
+ return this.minExpressionRNA;
+ }
+
+ /**
+ * Return average length of sequencing reads in this Replicate.
+ */
+ public long getAvgLengthReads() {
+ return this.avgLengthReads;
+ }
+
+ /**
+ * Returns the probability that the given number of reads
+ * at some nucleotide corresponds to the background, i.e.,
+ * a non-transcript.
+ */
+ public double getBackgroundProb(int numReads) {
+ // Based on geometric distribution
+ return Math.pow(1.0 - this.backgroundParameter, numReads) * this.backgroundParameter;
+ }
+
+ /**
+ * Return the mean number of reads on the given strand mapping
+ * to the given range of genomic coordinates in the specified
+ * genome at index z.
+ */
+ public double getMeanOfRange(int z, int start, int stop, char strand) {
+ return getReadsInRange(z, start, stop, strand) / (double)(Math.abs(stop-start)+1);
+ }
+
+ /**
+ * Return the standard deviation of reads on the given strand mapping
+ * to the given range of genomic coordinates in the specified genome
+ * at index z.
+ */
+ public double getStdevOfRange(int z, int start, int stop, char strand, double mean) {
+ if (stop < start) { // Swap
+ int temp = start;
+ start = stop;
+ stop = temp;
+ }
+
+ double stdev = 0.0;
+ for (int i=Math.max(start, 1); i<Math.min(stop+1, plusReads[z].length); i++) {
+ if (strand == '+') // Plus strand
+ stdev += Math.pow(plusReads[z][i] - mean, 2.0);
+ else if (strand == '-') // Minus strand
+ stdev += Math.pow(minusReads[z][i] - mean, 2.0);
+ else // Ambiguous strand
+ stdev += Math.pow(plusReads[z][i] + minusReads[z][i] - mean, 2.0);
+ }
+ return stdev / Math.sqrt(Math.min(stop, plusReads[z].length-1) - Math.max(start, 1) + 1);
+ }
+
+ /**
+ * Returns a String representation of this object.
+ */
+ public String toString() {
+ return name;
+ }
+
+
+
+ /**************************************************
+ ********** PRIVATE INSTANCE METHODS **********
+ **************************************************/
+
+ /**
+ * Reads in a compressed alignment file for a genome with
+ * the specified index z. Stores the
+ * RNA-seq data in two lists, one for the plus strand
+ * and one for the minus strand. Also computes the
+ * total reads in the file.
+ */
+ private void readInAlignmentFile(int z, String inFile, boolean unstranded) {
+ FileOps foo = new FileOps(inFile);
+ if (!foo.isValid()) {
+ Rockhopper.output("Error - could not read in file " + inFile + "\n");
+ return;
+ }
+
+ this.fileName = foo.getReadFileName();
+ int slashIndex = fileName.lastIndexOf(File.separator);
+ int periodIndex = fileName.lastIndexOf(".");
+ if (periodIndex < 0) periodIndex = fileName.length();
+ this.name = fileName.substring(slashIndex+1, periodIndex);
+ this.avgLengthReads = foo.getAvgLengthReads();
+ int[] coordinates_plus = foo.getCoordinates_plus();
+ int[] coordinates_minus = foo.getCoordinates_minus();
+ this.plusReads[z] = new int[Rockhopper.genomeSizes.get(z)];
+ this.minusReads[z] = new int[Rockhopper.genomeSizes.get(z)];
+ for (int i=0; i<Rockhopper.genomeSizes.get(z); i++) {
+ int reads_plus = coordinates_plus[i];
+ int reads_minus = coordinates_minus[i];
+ plusReads[z][i] = reads_plus;
+ minusReads[z][i] = reads_minus;
+ totalReads += reads_plus + reads_minus;
+ if (!unstranded) { // Strand specific
+ if (reads_plus < background.size()) background.set(reads_plus, background.get(reads_plus) + 1);
+ else background.set(background.size()-1, background.get(background.size()-1) + 1);
+ if (reads_minus < background.size()) background.set(reads_minus, background.get(reads_minus) + 1);
+ else background.set(background.size()-1, background.get(background.size()-1) + 1);
+ } else { // Strand ambiguous
+ if (reads_plus + reads_minus < background.size()) background.set(reads_plus + reads_minus, background.get(reads_plus + reads_minus) + 1);
+ else background.set(background.size()-1, background.get(background.size()-1) + 1);
+ }
+ }
+ }
+
+ /**
+ * Helper method for setting the minimum expression level for UTRs and ncRNAs.
+ */
+ private double transformation(double transcriptSensitivity) {
+ if (transcriptSensitivity <= 0.5) { // less than or equal to 0.5
+ return Math.pow(avgReads/2, Math.pow(transcriptSensitivity/0.5, 0.25));
+ } else { // greater than 0.5
+ return Math.pow(avgReads/2, 1 + Math.pow(2.0*(transcriptSensitivity - 0.5), 2));
+ }
+ }
+
+
+
+ /*************************************
+ ********** MAIN METHOD **********
+ *************************************/
+
+ /**
+ * The main method is used to test the methods of this class.
+ */
+ public static void main(String[] args) {
+ /*
+ if (args.length == 0) {
+ System.err.println("\nThe Replicate application must be invoked with a single command line argument corresponding to the name of a WIG file.\n");
+ System.exit(0);
+ }
+
+ Replicate r = new Replicate(args[0], false);
+ System.out.println(r);
+ */
+ }
+}
+
diff --git a/Replicon.java b/Replicon.java
new file mode 100644
index 0000000..55a6a2d
--- /dev/null
+++ b/Replicon.java
@@ -0,0 +1,298 @@
+/*
+ * Copyright 2013 Brian Tjaden
+ *
+ * This file is part of Rockhopper.
+ *
+ * Rockhopper is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * any later version.
+ *
+ * Rockhopper is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * (in the file gpl.txt) along with Rockhopper.
+ * If not, see <http://www.gnu.org/licenses/>.
+ */
+
+import java.util.Scanner;
+import java.io.File;
+import java.io.FileNotFoundException;
+
+public class Replicon {
+
+ /********************************************
+ ********** Instance Variables **********
+ ********************************************/
+
+ private String name; // Name of replicon (first line of FASTA file)
+ private String sequence; // Original DNA sequence with '$' appended
+ private int length; // Length of sequence
+ private int[] rotations; // Burrows-Wheeler matrix of cyclic rotations
+ private String BWT; // Borrows-Wheeler transform of original sequence
+
+ private int[] C; // Number of chars lexicographically less than...
+ private int[][] occ; // Number of occurrences of char up to row...
+
+
+
+ /**************************************
+ ********** Constructors **********
+ **************************************/
+
+ public Replicon(String fastaFile) {
+ this.sequence = readInFastaFile(fastaFile);
+ this.sequence = this.sequence.toUpperCase();
+ this.sequence = this.sequence.replace('U', 'T');
+ this.sequence = replaceAmbiguousCharacters();
+ this.sequence = this.sequence + "$";
+ this.length = sequence.length();
+ this.rotations = rotations();
+ this.BWT = getTransform();
+
+ precomputeCharacterInfo(); // Populate "C" and "occ" instance variables
+ }
+
+
+
+ /*************************************************
+ ********** Public Instance Methods **********
+ *************************************************/
+
+ // Return a row of the cyclic rotations matrix.
+ public String getStringInRotationsMatrix(int row) {
+ return sequence.substring(rotations[row]) + sequence.substring(0, rotations[row]);
+ }
+
+ // Reverse the BWT transform
+ public String unpermute() {
+ StringBuilder sb = new StringBuilder();
+ int r = 0;
+ while (BWT.charAt(r) != '$') {
+ sb.append(BWT.charAt(r));
+ r = stepLeft(r);
+ }
+ return sb.reverse().toString();
+ }
+
+ /**
+ * Returns the name of the genome sequence (FASTA header line).
+ */
+ public String getName() {
+ return this.name;
+ }
+
+ /**
+ * Returns the DNA sequence of this Replicon.
+ */
+ public String getSequence() {
+ return this.sequence;
+ }
+
+ /**
+ * Returns the length of the genome sequence (plus 1).
+ */
+ public int getLength() {
+ return this.length;
+ }
+
+ /**
+ * Returns number of characters lexographically less than x.
+ */
+ public int getC(int x) {
+ return this.C[x];
+ }
+
+ /**
+ * Returns number of occurrences of character x up to row y.
+ */
+ public int getOcc(int x, int y) {
+ return this.occ[x][y];
+ }
+
+ /**
+ * Returns index in Burrows-Wheeler rotations matrix at row x.
+ */
+ public int getRotations(int x) {
+ return this.rotations[x];
+ }
+
+
+
+ /**************************************************
+ ********** Private Instance Methods **********
+ **************************************************/
+
+ // Read in sequence from from file.
+ private String readInFastaFile(String fastaFile) {
+ try {
+ Scanner reader = new Scanner(new File(fastaFile));
+ StringBuilder sb = new StringBuilder();
+
+ // Handle header line
+ if (reader.hasNextLine()) {
+ String line = reader.nextLine();
+ if (line.startsWith(">")) { // Header line
+ this.name = line.substring(1).trim();
+ } else { // Not header line
+ sb.append(line);
+ }
+ }
+
+ // Read in file
+ while (reader.hasNextLine()) {
+ sb.append(reader.nextLine());
+ }
+
+ reader.close();
+ return sb.toString();
+ } catch (FileNotFoundException e) {
+ Peregrine.output("\nError - could not open file " + fastaFile + "\n\n");
+ System.exit(0);
+ }
+ return "";
+ }
+
+ // Replace any non-nucleotide character with '^'.
+ // We use '^' because its ASCII value is greater than A,C,G,T
+ private String replaceAmbiguousCharacters() {
+ StringBuilder sb = new StringBuilder(this.sequence);
+ for (int i=0; i<sb.length(); i++) {
+ if ((sb.charAt(i) != 'A') && (sb.charAt(i) != 'C') &&
+ (sb.charAt(i) != 'G') && (sb.charAt(i) != 'T'))
+ sb.setCharAt(i, '^');
+ }
+ return sb.toString();
+ }
+
+ // Compute the Burrows-Wheeler matrix of cyclic rotations.
+ // Rather than return a matrix, we return an array of integers
+ // where each value in the array is an index into the sequence.
+ // So a "row" of the matrix corresponds to the cyclic sequence
+ // beginnning at the specified index. All rows of the matrix
+ // have length equal to the length of the sequence.
+ private int[] rotations() {
+ int[] indices= new int[this.length];
+ for (int i=0; i<length; i++) indices[i] = i;
+ quicksort(indices, 0, length-1);
+ return indices;
+ }
+
+ // Compute the Burrows-Wheeler transform from the "rotations"
+ // matrix, i.e., the last column of the matrix.
+ private String getTransform() {
+ StringBuilder sb = new StringBuilder();
+ for (int i=0; i<length; i++) {
+ sb.append(sequence.charAt((rotations[i]-1+length) % length));;
+ }
+ return sb.toString();
+ }
+
+ // Precompute information about how often each character occurs in BWT
+ private void precomputeCharacterInfo() {
+
+ // Populate instance variable "C"
+ this.C = new int[6]; // All characters in DNA sequence have
+ // ASCII value less than 123.
+ for (int i=0; i<length; i++) C[Index.charToInt(BWT.charAt(i))] += 1;
+
+ // Cumulative
+ int[] temp = new int[6];
+ temp[0] = C[0] + C[5]; // Number of characters <= 'A'
+ temp[5] = C[5]; // Number of characters <= '$'
+ for (int i=1; i<5; i++) temp[i] = C[i] + temp[i-1];
+
+ // Strictly less than
+ for (int i=0; i<6; i++) C[i] = temp[i] - C[i];
+
+ // Populate instance variable "occ"
+ this.occ = new int[5][length+1];
+ for (int i=0; i<length; i++) {
+ for (int j=0; j<5; j++) {
+ occ[j][i+1] = occ[j][i];
+ }
+ int index = Index.charToInt(BWT.charAt(i));
+ if ((index >= 0) && (index < 5)) occ[index][i+1]++;
+ }
+ }
+
+ // Helper method for Burrows-Wheeler transform.
+ // Taken from appendix of Bowtie article.
+ private int stepLeft(int r) {
+ int index = Index.charToInt(BWT.charAt(r));
+ return C[index] + occ[index][r];
+ }
+
+ // We quicksort the array. But we don't sort the values at
+ // each array index, since each value is an index
+ // corresponding to a String. We sort the Strings specified
+ // by each array index.
+ private void quicksort(int[] a, int p, int r) {
+ if (p < r) {
+ int q = partition(a, p, r);
+ quicksort(a, p, q-1);
+ quicksort(a, q+1, r);
+ }
+ }
+
+ // Quicksort helper method
+ private int partition(int[] a, int p, int r) {
+ int x = Index.rand.nextInt(r - p + 1) + p;
+ swap(a, x, r);
+ x = a[r];
+ int i = p-1;
+ for (int j=p; j<r; j++) {
+ if (lessThanOrEqualTo(a[j], x)) { // a[j] <= x
+ i++;
+ swap(a, i, j);
+ }
+ }
+ swap(a, i+1, r);
+ return i+1;
+ }
+
+ // Quicksort partition helper method
+ private void swap(int a[], int i, int j) {
+ int temp = a[i];
+ a[i] = a[j];
+ a[j] = temp;
+ }
+
+ // Given two indices in "sequence", determine whether the
+ // cyclic String corresponding to the first index is less
+ // than or equal to the cyclic String corresponding to
+ // the second index.
+ private boolean lessThanOrEqualTo(int i, int j) {
+ for (int z=0; z<length; z++) {
+ if (sequence.charAt((i+z)%length) < sequence.charAt((j+z)%length))
+ return true;
+ if (sequence.charAt((i+z)%length) > sequence.charAt((j+z)%length))
+ return false;
+
+ }
+ return true; // We have equality of the two Strings
+ }
+
+
+
+ /*************************************
+ ********** Main Method **********
+ *************************************/
+
+ public static void main(String[] args) {
+
+ if (args.length < 1) {
+ System.err.println("\nUSAGE: java Replicon <index.fna>" + "\n");
+ System.err.println("Replicon takes a sequence file (such as a FASTA genome) to be indexed and it computes the Burrows-Wheeler transformed index. If run from the command line, it simply outputs the size of the index to STDOUT. The Replicon class is meant to be instantiated from another application. \n");
+ System.exit(0);
+ }
+
+ Replicon index = new Replicon(args[0]);
+ System.out.println("Size of index is:\t" + index.BWT.length());
+ }
+
+}
+
diff --git a/Rockhopper.java b/Rockhopper.java
new file mode 100644
index 0000000..f2c85e2
--- /dev/null
+++ b/Rockhopper.java
@@ -0,0 +1,916 @@
+/*
+ * Copyright 2013 Brian Tjaden
+ *
+ * This file is part of Rockhopper.
+ *
+ * Rockhopper is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * any later version.
+ *
+ * Rockhopper is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * (in the file gpl.txt) along with Rockhopper.
+ * If not, see <http://www.gnu.org/licenses/>.
+ */
+
+import java.util.ArrayList;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.PrintWriter;
+import javax.swing.JTextArea;
+import javax.swing.SwingWorker;
+
+/**
+ * The Rockhopper application reads in RNA-seq data, aligns the
+ * sequencing reads to a genome, and then analyzes the data to
+ * identify the expression of genes in each condition, differential
+ * gene expression between conditions, transcript boundaries, and
+ * operons. Rockhopper can also assemble transcripts de novo
+ * without a reference genome.
+ */
+public class Rockhopper {
+
+ /*****************************************
+ ********** CLASS VARIABLES **********
+ *****************************************/
+
+ public static final String version = "2.03";
+ public static JTextArea output; // Output to GUI or, if null, to System.out
+ public static SwingWorker worker; // Update progress bar if using GUI.
+ private static int stagesProcessed; // Number of files (stages) processed. Needed for GUI progress bar.
+ public static ArrayList<Integer> genomeSizes; // Sizes of each 1-indexed genome in nucleotides
+ public static int genomeSize; // Size of all genomes combined
+ public static int numConditions; // Number of experimental conditions
+ private static ArrayList<String> genome_DIRs; // PARAM: directories of geneome files
+ public static String output_DIR = "Rockhopper_Results/"; // PARAM: write output files to this directory
+ public static String browser_DIR = "genomeBrowserFiles/"; // Write browser files to this sub-directory
+ private static ArrayList<String> conditionFiles; // PARAM: list of seq-read files for each condition
+ public static boolean computeExpression = true; // PARAM: compute differential expression
+ public static boolean computeOperons = true; // PARAM: compute operons
+ public static boolean computeTranscripts = true; // PARAM: compute transcript boundaries
+ private static PrintWriter summaryWriter = null; // For outputting summary file
+ private static String summaryFile = "summary.txt";
+ private static String expressionFile = "transcripts.txt";
+ private static String operonGenePairFile = "operonGenePairs.txt";
+ private static String operonMergedFile = "operons.txt";
+ public static boolean unstranded = false; // Is RNA-seq data strand specific or ambiguous?
+ public static double transcriptSensitivity = 0.5;
+ public static boolean verbose = false;
+ private static String[] labels;
+ private static boolean time = false;
+ private static boolean isDeNovo = false; // Reference based (false) or de novo (true) assembly
+
+
+
+ /********************************************
+ ********** INSTANCE VARIABLES **********
+ ********************************************/
+
+ private ArrayList<Genome> genomes = new ArrayList<Genome>();
+ private ArrayList<Transcripts> transcripts = new ArrayList<Transcripts>();
+ private ArrayList<Condition> conditions; // RNA-seq data for each condition
+
+
+
+ /**************************************
+ ********** CONSTRUCTORS **********
+ **************************************/
+
+ /**
+ * Constructs a new Rockhopper object.
+ */
+ public Rockhopper() {
+
+ stagesProcessed = 0;
+ if (isDeNovo) { // De novo assembly
+ Assembler a = new Assembler();
+ return;
+ }
+
+ // Read in genome
+ Rockhopper.genomeSizes = new ArrayList<Integer>();
+ Rockhopper.genomeSize = 0;
+ for (String genome_DIR : genome_DIRs) {
+ Genome genome = new Genome(genome_DIR);
+ this.genomes.add(genome);
+ Rockhopper.genomeSizes.add(genome.size());
+ Rockhopper.genomeSize += genome.size();
+ }
+
+ // Align sequencing reads to genome and compute basic expression information
+ this.conditions = new ArrayList<Condition>();
+ Peregrine.sequenceFiles = new String[genomes.size()];
+ Peregrine.annotationsPlus = new String[genomes.size()][];
+ Peregrine.annotationsMinus = new String[genomes.size()][];
+ for (int z=0; z<genomes.size(); z++) {
+ String genome_DIR = genome_DIRs.get(z);
+ File dir = new File(genome_DIR);
+ String[] files = dir.list();
+ for (int i=0; i<files.length; i++) {
+ if (files[i].endsWith(".fna")) {
+ Peregrine.sequenceFiles[z] = genome_DIR + files[i];
+ Peregrine.annotationsPlus[z] = genomes.get(z).getAnnotations('+');
+ Peregrine.annotationsMinus[z] = genomes.get(z).getAnnotations('-');
+ }
+ }
+ }
+ Peregrine.numSequences = genomes.size();
+ Peregrine.outputBrowserFile = false;
+ output("\n");
+ for (int i=0; i<conditionFiles.size(); i++) { // For each condition
+ String[] readFiles = conditionFiles.get(i).split(",");
+ Condition C = new Condition();
+ for (int j=0; j<readFiles.length; j++) { // For each replicate
+ String[] parse_readFiles = readFiles[j].split("%");
+ if (parse_readFiles.length == 1) { // Using single-end reads (except maybe SAM/BAM)
+ String file1 = parse_readFiles[0];
+ output("Aligning sequencing reads from file:\t" + file1.split(separator())[file1.split(separator()).length-1] + "\n");
+ Peregrine.isPairedEnd = false;
+ Peregrine.pairedEndFile = null;
+ Peregrine.readsFile = file1;
+ Peregrine p = new Peregrine();
+ updateProgress();
+ C.addReplicate(new Replicate(p.getListOfCompressedFileNames(file1), file1, unstranded));
+ } else { // Using paired-end reads
+ String file1 = parse_readFiles[0];
+ String file2 = parse_readFiles[1];
+ output("Aligning sequencing reads from files:\n");
+ output("\t" + file1.split(separator())[file1.split(separator()).length-1] + "\n");
+ output("\t" + file2.split(separator())[file2.split(separator()).length-1] + "\n");
+ Peregrine.isPairedEnd = true;
+ Peregrine.readsFile = file1;
+ Peregrine.pairedEndFile = file2;
+ Peregrine p = new Peregrine();
+ updateProgress();
+ C.addReplicate(new Replicate(p.getListOfCompressedFileNames(file1), file1, unstranded));
+ }
+ }
+ C.setMinDiffExpressionLevel();
+ conditions.add(C);
+ }
+ Rockhopper.numConditions = conditions.size();
+ computeGeneExpression();
+
+ // Output mapped reads to WIG files that can be loaded by genome browser
+ double trackRange = 0.0;
+ int totalReplicates = 0;
+ for (int i=0; i<conditions.size(); i++) {
+ for (int j=0; j<conditions.get(i).numReplicates(); j++) {
+ trackRange += conditions.get(i).getReplicate(j).getAvgReads();
+ totalReplicates++;
+ }
+ }
+ trackRange = (2*trackRange) / totalReplicates; // Range for display in genome browser
+ for (int i=0; i<conditionFiles.size(); i++) { // For each condition
+ String[] readFiles = conditionFiles.get(i).split(",");
+ for (int j=0; j<readFiles.length; j++) { // For each replicate
+ Replicate r = conditions.get(i).getReplicate(j);
+ double multiplier = 100000.0 / (double)r.getUpperQuartile();
+ for (int z=0; z<genomes.size(); z++) {
+ int[] coordinates_plus = new int[Rockhopper.genomeSizes.get(z)];
+ int[] coordinates_minus = new int[Rockhopper.genomeSizes.get(z)];
+ for (int k=0; k<Rockhopper.genomeSizes.get(z); k++) {
+ coordinates_plus[k] = (int)(multiplier * r.getReads(z, k, '+'));
+ coordinates_minus[k] = (int)(multiplier * r.getReads(z, k, '-'));
+ }
+ Peregrine.outputBrowserFile(readFiles[j].split("%")[0], Peregrine.sequenceFiles[z], output_DIR, browser_DIR, r.getCompressedFileName(z), coordinates_plus, coordinates_minus, (int)trackRange);
+ }
+ }
+ }
+ Peregrine.releaseMemory();
+
+ output("Analyzing transcripts..." + "\n");
+
+ // Compute transcript boundaries
+ if (computeTranscripts) {
+ for (int z=0; z<genomes.size(); z++) {
+ Genome genome = genomes.get(z);
+ if (genome.numGenes() > 0) {
+ Transcripts t = new Transcripts(z, genome, conditions, unstranded);
+ t.identifyUTRs();
+ t.identifyRNAs();
+ transcripts.add(t);
+ }
+ }
+ }
+
+ // Compute gene differential expression
+ if (computeExpression) {
+ Gene.setLowessVariances(genomes, conditions); // Compute lowess variance for each gene
+ for (Genome genome : genomes) {
+ if (genome.numGenes() > 0) computeDifferentialExpression(genome);
+ }
+ Gene.correctPvalues(genomes, conditions); // Compute q-values, Benjamini-Hochberg correction
+ }
+
+ for (int z=0; z<genomes.size(); z++) runRockhopper(z);
+ output("\nSummary of results written to file:\t" + output_DIR + summaryFile + "\n");
+ for (int z=0; z<genomes.size(); z++) {
+ output("Expression of transcripts written to file:\t" + output_DIR + genomes.get(z).getID() + "_" + expressionFile + "\n");
+ if (computeOperons) {
+ //output("Pairs of operon genes written to file:\t" + output_DIR + genome.getID() + "_" + operonGenePairFile + "\n");
+ output("Operons written to file:\t\t" + output_DIR + genomes.get(z).getID() + "_" + operonMergedFile + "\n");
+ }
+ }
+ output("\nFINISHED.\n\n");
+ summaryWriter.close();
+ updateProgress();
+ }
+
+
+
+ /*************************************************
+ ********** PUBLIC INSTANCE METHODS **********
+ *************************************************/
+
+ public void runRockhopper(int z) {
+ Genome genome = genomes.get(z);
+
+ output("\n");
+ output("************************************************************\n");
+ output(genome.getName() + "\n");
+ output("************************************************************\n");
+ output("\n");
+
+ // Compute transcript boundaries
+ if (computeTranscripts && (genome.numGenes() > 0)) {
+ Transcripts t = transcripts.get(z);
+ output("Computing transcript boundaries...\n");
+ output("\tNumber of 5'UTRs:\t\t\t" + t.getNum5UTRs() + "\n");
+ output("\tNumber of 3'UTRs:\t\t\t" + t.getNum3UTRs() + "\n");
+ output("\tNumber of predicted RNAs:\t\t\t" + (t.getNumSenseRNAs() + t.getNumAntisenseRNAs()) + "\n");
+ if (!unstranded) {
+ output("\tNumber of predicted RNAs (not antisense):\t\t" + t.getNumSenseRNAs() + "\n");
+ output("\tNumber of predicted RNAs (antisense):\t\t" + t.getNumAntisenseRNAs() + "\n");
+ }
+ output("\n");
+ outputUTRsForBrowser(output_DIR + browser_DIR + genome.getID() + "_UTRs.wig", genome.getFormalGenomeName(), genome.getGenes(), genome.size());
+ outputRNAsForBrowser(output_DIR + browser_DIR + genome.getID() + "_ncRNAs.wig", genome.getFormalGenomeName(), genome.getGenes(), genome.size());
+ }
+
+ // Compute gene differential expression
+ if (computeExpression && (genome.numGenes() > 0)) {
+ output("Computing differential gene expression...\n");
+ output("\tNumber of differentially expressed protein coding genes:\t" + getNumOfDifferentiallyExpressedGenes(genome, 0.01) + "\n\n");
+ outputDifferentiallyExpressedGenesForBrowser(output_DIR + browser_DIR + genome.getID() + "_diffExpressedGenes.wig", genome.getFormalGenomeName(), genome.getGenes(), genome.size());
+ }
+
+ // Output transcript file
+ try {
+ PrintWriter writer = new PrintWriter(new File(output_DIR + genome.getID() + "_" + expressionFile));
+ writer.println(genome.genesToString(conditions, labels));
+ writer.close();
+ } catch (FileNotFoundException e) {
+ output("\nError - could not open file " + genome.getID() + "_" + expressionFile + "\n\n");
+ }
+
+ // Compute operons
+ if (computeOperons && (genome.numGenes() > 0)) {
+ output("Computing likely operons...\n");
+ Operons ops = new Operons(genome.getCodingGenes(), genome.getGenes());
+ output("\tNumber of gene-pairs predicted to be part of the same operon:\t" + ops.getNumOperonGenePairs(genome.getCodingGenes()) + "\n");
+ //ops.outputGenePairOperons(output_DIR + genome.getID() + "_" + operonGenePairFile, genome.getCodingGenes());
+ int numMergedOperons = ops.outputMergedOperons(output_DIR + genome.getID() + "_" + operonMergedFile, output_DIR + browser_DIR + genome.getID() + "_operons.wig", genome.getFormalGenomeName(), genome.getCodingGenes(), genome.size());
+ output("\tNumber of predicted multi-gene operons:\t\t" + numMergedOperons + "\n\n");
+ }
+ }
+
+ /**
+ * Returns a list of Genome objects.
+ */
+ public ArrayList<Genome> getGenomes() {
+ return genomes;
+ }
+
+
+
+ /**************************************************
+ ********** PRIVATE INSTANCE METHODS **********
+ **************************************************/
+
+ /**
+ * For each gene, compute its raw read counts, normalized read
+ * counts, mean, variance, and RPKM.
+ */
+ private void computeGeneExpression() {
+ int totalReplicates = 0;
+ long sumUpperQuartile = 0;
+ for (int j=0; j<conditions.size(); j++) {
+ for (int k=0; k<conditions.get(j).numReplicates(); k++) {
+ Replicate r = conditions.get(j).getReplicate(k);
+ r.setMinExpression(transcriptSensitivity);
+ ArrayList<Long> currentGeneReads = new ArrayList<Long>(); // For normalization
+ int zeroCountGenes = 0; // For normalization, keep track of genes with zero reads
+ int totalGenes = 0;
+ for (int z=0; z<genomes.size(); z++) {
+ Genome genome = genomes.get(z);
+ for (int i=0; i<genome.numGenes(); i++) {
+ Gene g = genome.getGene(i);
+
+ long readsForGene = r.getReadsInRange(z, g.getMinCoordinate(), g.getMaxCoordinate(), g.getStrand());
+ if (unstranded) // Strand ambiguous. Count reads on both strands.
+ readsForGene = r.getReadsInRange(z, g.getMinCoordinate(), g.getMaxCoordinate(), '+') + r.getReadsInRange(z, g.getMinCoordinate(), g.getMaxCoordinate(), '-');
+ g.setRawCount(j, k, readsForGene); // Set raw counts for gene
+ if (r.getAvgLengthReads() == 0) g.setRawCount_reads(j, k, 0);
+ else g.setRawCount_reads(j, k, readsForGene/r.getAvgLengthReads());
+ currentGeneReads.add(readsForGene); // Populate list for normalization
+ if (readsForGene == 0) zeroCountGenes++; // Genes with zero reads for normalization
+ }
+ totalGenes += genome.numGenes();
+ }
+ long upperQuartile = Misc.select_Long(currentGeneReads, (int)(zeroCountGenes+0.75*(totalGenes-zeroCountGenes)));
+ r.setUpperQuartile(upperQuartile);
+ sumUpperQuartile += upperQuartile;
+ totalReplicates++;
+ }
+ }
+ Condition.setAvgUpperQuartile(sumUpperQuartile / totalReplicates);
+
+ // Set normalized read counts for each gene
+ for (int j=0; j<conditions.size(); j++) {
+ for (int k=0; k<conditions.get(j).numReplicates(); k++) {
+ for (int z=0; z<genomes.size(); z++) {
+ Genome genome = genomes.get(z);
+ for (int i=0; i<genome.numGenes(); i++) { // Set normalized counts
+ genome.getGene(i).setNormalizedCount(j, k, 100000.0, conditions.get(j).getReplicate(k).getUpperQuartile());
+ }
+ }
+ }
+ }
+
+ // Compute mean and RPKM for each gene in each condition
+ for (int z=0; z<genomes.size(); z++) {
+ Genome genome = genomes.get(z);
+ for (int i=0; i<genome.numGenes(); i++) genome.getGene(i).computeExpression(conditions);
+ }
+
+ identifySimilarConditions(); // We require means to identify similar conditions
+
+ // Compute variance for each gene in each condition
+ for (int z=0; z<genomes.size(); z++) {
+ Genome genome = genomes.get(z);
+ for (int i=0; i<genome.numGenes(); i++) genome.getGene(i).computeVariance(conditions);
+ }
+ }
+
+ private void computeDifferentialExpression(Genome genome) {
+ // Compute differential expression for each gene in pairs of conditions
+ for (int i=0; i<genome.numGenes(); i++) genome.getGene(i).computeDifferentialExpression();
+ }
+
+ /**
+ * Returns the number of significantly differentially expressed
+ * protein-coding genes.
+ * The significance threshold is specified by the parameter.
+ */
+ private int getNumOfDifferentiallyExpressedGenes(Genome genome, double significance) {
+ int numDiffExpressedGenes = 0;
+ for (int i=0; i<genome.numGenes(); i++) {
+ if (genome.getGene(i).isDifferntiallyExpressedORF(significance))
+ numDiffExpressedGenes++;
+ }
+ return numDiffExpressedGenes;
+ }
+
+ /**
+ * For each condition, determines the other condition that is most similar,
+ * i.e., its "partner". If there are no replicate experiments then the
+ * partner of each condition is used as a surrogate replicate.
+ * Similarity between two conditions is measured by the Pearson correlation
+ * coefficient of normalized gene expression.
+ * This method sets the "partner" of each condition.
+ */
+ private void identifySimilarConditions() {
+ if (conditions.size() == 1) { // Special case. Only 1 condition. It partners itself.
+ conditions.get(0).setPartner(0);
+ return;
+ }
+
+ double[][] correlationMatrix = new double[conditions.size()][conditions.size()];
+ for (int i=0; i<conditions.size(); i++) {
+ for (int j=0; j<conditions.size(); j++) {
+ ArrayList<Long> e1 = new ArrayList<Long>(); // Gene expression values 1
+ ArrayList<Long> e2 = new ArrayList<Long>(); // Gene expression values 2
+ for (Genome genome : genomes) {
+ for (int k=0; k<genome.numGenes(); k++) {
+ int geneLength = genome.getGene(k).getMaxCoordinate() - genome.getGene(k).getMinCoordinate() + 1;
+ e1.add(genome.getGene(k).getMean(i)/geneLength);
+ e2.add(genome.getGene(k).getMean(j)/geneLength);
+ }
+ }
+ correlationMatrix[i][j] = Misc.correlation(e1, e2);
+ }
+ }
+
+ // Determine partner for each condition
+ int partner = -1;
+ for (int i=0; i<conditions.size(); i++) {
+ if (i == 0) partner = 1;
+ else partner = 0;
+ for (int j=0; j<conditions.size(); j++) {
+ if ((i != j) && (correlationMatrix[i][j] > correlationMatrix[i][partner]))
+ partner = j;
+ }
+ conditions.get(i).setPartner(partner);
+ }
+ }
+
+
+
+ /***********************************************
+ ********** PRIVATE CLASS METHODS **********
+ ***********************************************/
+
+ /**
+ * Create WIG file of predicted UTRs that
+ * can be loaded into a genome browser.
+ */
+ private static void outputUTRsForBrowser(String outputFile, String genomeName, ArrayList<Gene> genes, int size) {
+ // Determine coordinates of UTRs
+ int[] geneCoordinates = new int[size];
+ for (int i=0; i<genes.size(); i++) {
+ Gene g = genes.get(i);
+
+ // UTRs
+ if (g.isORF() && (g.getStartT() > 0) && (g.getStrand() == '+')) // 5'UTR on plus strand
+ for (int j=g.getStartT(); j<g.getStart(); j++) geneCoordinates[j] = 1;
+ if (g.isORF() && (g.getStartT() > 0) && (g.getStrand() == '-')) // 5'UTR on minus strand
+ for (int j=g.getStart()+1; j<=g.getStartT(); j++) geneCoordinates[j] = -1;
+ if (g.isORF() && (g.getStopT() > 0) && (g.getStrand() == '+')) // 3'UTR on plus strand
+ for (int j=g.getStop()+1; j<=g.getStopT(); j++) geneCoordinates[j] = 1;
+ if (g.isORF() && (g.getStopT() > 0) && (g.getStrand() == '-')) // 3'UTR on minus strand
+ for (int j=g.getStopT(); j<g.getStop(); j++) geneCoordinates[j] = -1;
+ }
+
+ // Output differentially expressed genes to genome browser file
+ try {
+ PrintWriter writer = new PrintWriter(new File(outputFile));
+ writer.println("track name=" + "\"" + "UTRs" + "\"" + " color=255,0,255 altColor=255,0,255 graphType=bar viewLimits=-1:1");
+ writer.println("fixedStep chrom=" + genomeName + " start=1 step=1");
+ for (int j=1; j<geneCoordinates.length; j++) writer.println(geneCoordinates[j]);
+ writer.close();
+ } catch (FileNotFoundException e) {
+ output("\nError - could not open file " + outputFile + "\n\n");
+ }
+ }
+
+ /**
+ * Create WIG file of predicted RNAs that
+ * can be loaded into a genome browser.
+ */
+ private static void outputRNAsForBrowser(String outputFile, String genomeName, ArrayList<Gene> genes, int size) {
+ // Determine coordinates of ncRNAs
+ int[] geneCoordinates = new int[size];
+ for (int i=0; i<genes.size(); i++) {
+ Gene g = genes.get(i);
+
+ // ncRNAs
+ if (!g.isORF() && (g.getName().equals("predicted RNA"))) { // novel RNA
+ int value = 1;
+ if (g.getStrand() == '-') value = -1;
+ for (int j=g.getFirst(); j<=g.getLast(); j++) geneCoordinates[j] = value;
+ }
+ }
+
+ // Output differentially expressed genes to genome browser file
+ try {
+ PrintWriter writer = new PrintWriter(new File(outputFile));
+ writer.println("track name=" + "\"" + "Novel RNAs" + "\"" + " color=0,255,0 altColor=0,255,0 graphType=bar viewLimits=-1:1");
+ writer.println("fixedStep chrom=" + genomeName + " start=1 step=1");
+ for (int j=1; j<geneCoordinates.length; j++) writer.println(geneCoordinates[j]);
+ writer.close();
+ } catch (FileNotFoundException e) {
+ output("\nError - could not open file " + outputFile + "\n\n");
+ }
+ }
+
+ /**
+ * Create WIG file of differentially expressed genes that
+ * can be loaded into a genome browser.
+ */
+ private static void outputDifferentiallyExpressedGenesForBrowser(String outputFile, String genomeName, ArrayList<Gene> genes, int size) {
+ // Determine coordinates of differentially expressed genes
+ int[] geneCoordinates = new int[size];
+ for (int i=0; i<genes.size(); i++) {
+ Gene g = genes.get(i);
+ double qValue = g.getMinQvalue();
+ int value = 0;
+ if (qValue == 0.0) value = 300; // Special case. We cannot take log of zero.
+ else value = (int)(-Math.log10(qValue));
+ if (g.getStrand() == '-') value = -value;
+ for (int j=g.getFirst(); j<=g.getLast(); j++) geneCoordinates[j] = value;
+ }
+
+ // Output differentially expressed genes to genome browser file
+ try {
+ PrintWriter writer = new PrintWriter(new File(outputFile));
+ writer.println("track name=" + "\"" + "Differentially expressed genes" + "\"" + " color=0,255,0 altColor=0,255,0 graphType=bar viewLimits=-10:10");
+ writer.println("fixedStep chrom=" + genomeName + " start=1 step=1");
+ for (int j=1; j<geneCoordinates.length; j++) writer.println(geneCoordinates[j]);
+ writer.close();
+ } catch (FileNotFoundException e) {
+ output("\nError - could not open file " + outputFile + "\n\n");
+ }
+ }
+
+ /**
+ * Returns the system-dependent file separator that
+ * can be used as a RegEx.
+ */
+ private static String separator() {
+ if (File.separatorChar == '\\') return "\\\\";
+ else return File.separator;
+ }
+
+
+
+ /**********************************************
+ ********** PUBLIC CLASS METHODS **********
+ **********************************************/
+
+ // Used for updating the GUI progress bar.
+ public static void updateProgress() {
+ if (worker != null) {
+ double totalStages = 0.0;
+ for (String files : conditionFiles) totalStages += files.split(",").length;
+ if (isDeNovo) {
+ for (String files : conditionFiles) totalStages += files.split(",").length;
+ for (String files : conditionFiles) totalStages += files.split(",").length;
+ }
+ totalStages += 1.0; // For analyzing transcripts and computing expression
+ stagesProcessed++;
+ worker.firePropertyChange("progress", worker.getProgress(), (int)(100.0*stagesProcessed/totalStages));
+ }
+ }
+
+ public static void commandLineArguments(String[] args) {
+ if (args.length < 1) {
+ output("\n*************************************************\n");
+ output("********** Rockhopper version " + Rockhopper.version + " **********\n");
+ output("*************************************************\n");
+ output("\nThe Rockhopper application has the following required command line arguments.\n");
+
+ output("\nREQUIRED ARGUMENTS\n\n");
+ output("\t" + "exp1A.fastq,exp1B.fastq,exp1C.fastq exp2A.fastq,exp2B.fastq" + "\t" + "a comma separated list of sequencing files (in FASTQ, QSEQ, FASTA, SAM, or BAM format) for replicate experiments, one list per experimental condition (mate-pair files should be delimited by '%')\n");
+
+ output("\nREFERENCE BASED ASSEMBLY VS. DE NONO ASSEMBLY:\n");
+ output("IF THE -g OPTION IS USED THEN ROCKHOPPER ALIGNS READS TO ONE OR MORE REFERENCE GENOMES,\n");
+ output("OTHERWISE, ROCKHOPPER PERFORMS DE NOVO TRANSCRIPT ASSEMBLY.\n\n");
+ output("\t" + "-g <DIR1,DIR2>" + "\t" + "a comma separated list of directories, each containing a genome file (*.fna), gene file (*.ptt), and rna file (*.rnt)\n");
+
+ output("\nOPTIONAL ARGUMENTS FOR EITHER REFERENCE BASED ASSEMBLY OR DE NOVO ASSEMBLY\n\n");
+ output("\t" + "-c <boolean>" + "\t" + "reverse complement single-end reads (default is false)\n");
+ output("\t" + "-ff/fr/rf/rr" + "\t" + "orientation of two mate reads for paired-end read, f=forward and r=reverse_complement (default is fr)\n");
+ output("\t" + "-d <integer>" + "\t" + "maximum number of bases between mate pairs for paired-end reads (default is 500)\n");
+ output("\t" + "-a <boolean>" + "\t" + "identify 1 alignment (true) or identify all optimal alignments (false), (default is true)\n");
+ output("\t" + "-p <integer>" + "\t" + "number of processors (default is self-identification of processors)\n");
+ output("\t" + "-e <boolean>" + "\t" + "compute differential expression for transcripts in pairs of experimental conditions (default is true)\n");
+ output("\t" + "-s <boolean>" + "\t" + "RNA-seq experiments are strand specific (true) or strand ambiguous (false), (default is true)\n");
+ output("\t" + "-L <comma separated list>" + "\t" + "labels for each condition\n");
+ output("\t" + "-o <DIR>" + "\t" + "directory where output files are written (default is Rockhopper_Results/)\n");
+ output("\t" + "-v <boolean>" + "\t" + "verbose output including raw/normalized counts aligning to each gene (default is false)\n");
+ output("\t" + "-SAM " + "\t" + "output a SAM format file\n");
+ output("\t" + "-TIME " + "\t" + "output time taken to execute program\n");
+
+ output("\nOPTIONAL ARGUMENTS FOR REFERENCE BASED ASSEMBLY ONLY\n\n");
+ output("\t" + "-m <number>" + "\t" + "allowed mismatches as percent of read length (default is 0.15)\n");
+ output("\t" + "-l <number>" + "\t" + "minimum seed as percent of read length (default is 0.33)\n");
+ output("\t" + "-y <boolean>" + "\t" + "compute operons (default is true)\n");
+ output("\t" + "-t <boolean>" + "\t" + "identify transcript boundaries including UTRs and ncRNAs (default is true)\n");
+ output("\t" + "-z <number>" + "\t" + "minimum expression of UTRs and ncRNAs, a number in range [0.0, 1.0] (default is 0.5)\n");
+
+ output("\nOPTIONAL ARGUMENTS FOR DE NOVO ASSEMBLY ONLY\n\n");
+ output("\t" + "-k <integer>" + "\t" + "size of k-mer, range of values is 15 to 31 (default is 25)\n");
+ output("\t" + "-j <integer>" + "\t" + "minimum length required to use a sequencing read after trimming/processing (default is 35)\n");
+ output("\t" + "-n <integer>" + "\t" + "size of k-mer hashtable is ~ 2^n (default is 25). HINT: should normally be 25 or, if more memory is available, 26. WARNING: if increased above 25 then more than 1.2M of memory must be allocated\n");
+ output("\t" + "-b <integer>" + "\t" + "minimum number of full length reads required to map to a de novo assembled trancript (default is 20)\n");
+ output("\t" + "-u <integer>" + "\t" + "minimum length of de novo assembled transcripts (default is 2*k)\n");
+ output("\t" + "-w <integer>" + "\t" + "minimum count of k-mer to use it to seed a new de novo assembled transcript (default is 50)\n");
+ output("\t" + "-x <integer>" + "\t" + "minimum count of k-mer to use it to extend an existing de novo assembled transcript (default is 5)\n");
+
+ output("\nEXAMPLE EXECUTION: REFERENCE BASED ASSEMBLY WITH SINGLE-END READS\n");
+ output("\njava Rockhopper <options> -g genome_DIR1,genome_DIR2 aerobic_replicate1.fastq,aerobic_replicate2.fastq anaerobic_replicate1.fastq,anaerobic_replicate2.fastq\n");
+ output("\nEXAMPLE EXECUTION: REFERENCE BASED ASSEMBLY WITH PAIRED-END READS\n");
+ output("\njava Rockhopper <options> -g genome_DIR1,genome_DIR2 aerobic_replicate1_pairedend1.fastq%aerobic_replicate1_pairedend2.fastq,aerobic_replicate2_pairedend1.fastq%aerobic_replicate2_pairedend2.fastq anaerobic_replicate1_pairedend1.fastq%anaerobic_replicate1_pairedend2.fastq,anaerobic_replicate2_pairedend1.fastq%anaerobic_replicate2_pairedend2.fastq\n");
+ output("\nEXAMPLE EXECUTION: DE NOVO ASSEMBLY WITH SINGLE-END READS\n");
+ output("\njava Rockhopper <options> aerobic_replicate1.fastq,aerobic_replicate2.fastq anaerobic_replicate1.fastq,anaerobic_replicate2.fastq\n");
+ output("\nEXAMPLE EXECUTION: DE NOVO ASSEMBLY WITH PAIRED-END READS\n");
+ output("\njava Rockhopper <options> aerobic_replicate1_pairedend1.fastq%aerobic_replicate1_pairedend2.fastq,aerobic_replicate2_pairedend1.fastq%aerobic_replicate2_pairedend2.fastq anaerobic_replicate1_pairedend1.fastq%anaerobic_replicate1_pairedend2.fastq,anaerobic_replicate2_pairedend1.fastq%anaerobic_replicate2_pairedend2.fastq\n");
+
+ output("\n");
+ System.exit(0);
+ }
+
+ // Initially set the number of threads
+ Peregrine.numThreads = Runtime.getRuntime().availableProcessors();
+ if (Peregrine.numThreads > 4) Peregrine.numThreads *= 0.75;
+ Assembler.numThreads = Runtime.getRuntime().availableProcessors();
+ if (Assembler.numThreads > 4) Assembler.numThreads = (int)Math.min(Assembler.numThreads * 0.75, 8.0);
+
+ int i = 0;
+ conditionFiles = new ArrayList<String>();
+ genome_DIRs = null;
+ while (i < args.length) {
+ if (args[i].equals("-g")) {
+ if ((i == args.length-1) || (args[i+1].startsWith("-"))) {
+ output("Error - command line argument -g must be followed by the name of one or more directories.\n");
+ System.exit(0);
+ }
+ String[] parse_dirs = args[i+1].split(",");
+ genome_DIRs = new ArrayList<String>();
+ for (String s : parse_dirs) {
+ if (s.endsWith(File.separator)) genome_DIRs.add(s);
+ else genome_DIRs.add(s + File.separatorChar);
+ }
+ isDeNovo = false;
+ i += 2;
+ } else if (args[i].startsWith("-a")) {
+ if ((i == args.length-1) || (args[i+1].startsWith("-"))) {
+ output("Error - command line argument -a must be followed by a boolean.\n");
+ System.exit(0);
+ }
+ Peregrine.stopAfterOneHit = Boolean.valueOf(args[i+1]);
+ Assembler.stopAfterOneHit = Boolean.valueOf(args[i+1]);
+ i += 2;
+ } else if (args[i].startsWith("-p")) {
+ if ((i == args.length-1) || (args[i+1].startsWith("-"))) {
+ output("Error - command line argument -p must be followed by an integer.\n");
+ System.exit(0);
+ }
+ Peregrine.numThreads = Integer.parseInt(args[i+1]);
+ Assembler.numThreads = Integer.parseInt(args[i+1]);
+ i += 2;
+ } else if (args[i].startsWith("-e")) {
+ if ((i == args.length-1) || (args[i+1].startsWith("-"))) {
+ output("Error - command line argument -e must be followed by a boolean.\n");
+ System.exit(0);
+ }
+ computeExpression = Boolean.valueOf(args[i+1]);
+ Assembler.computeExpression = Boolean.valueOf(args[i+1]);
+ i += 2;
+ } else if (args[i].startsWith("-s")) {
+ if ((i == args.length-1) || (args[i+1].startsWith("-"))) {
+ output("Error - command line argument -s must be followed by a boolean.\n");
+ System.exit(0);
+ }
+ unstranded = !Boolean.valueOf(args[i+1]);
+ Assembler.unstranded = !Boolean.valueOf(args[i+1]);
+ i += 2;
+ } else if (args[i].startsWith("-d")) {
+ if ((i == args.length-1) || (args[i+1].startsWith("-"))) {
+ output("Error - command line argument -d must be followed by an integer.\n");
+ System.exit(0);
+ }
+ Peregrine.maxPairedEndLength = Integer.parseInt(args[i+1]);
+ Assembler.maxPairedEndLength = Integer.parseInt(args[i+1]);
+ SamOps.maxPairedEndLength = Integer.parseInt(args[i+1]);
+ i += 2;
+ } else if (args[i].equals("-L")) {
+ if (i == args.length-1) {
+ output("Error - command line argument -L must be followed by a comma separated list of names for the conditions.\n");
+ System.exit(0);
+ }
+ labels = args[i+1].split(",");
+ Assembler.labels = args[i+1].split(",");
+ i += 2;
+ } else if (args[i].equals("-o")) {
+ if ((i == args.length-1) || (args[i+1].startsWith("-"))) {
+ output("Error - command line argument -o must be followed the name of a directory.\n");
+ System.exit(0);
+ }
+ if (args[i+1].endsWith("/")) output_DIR = args[i+1];
+ else output_DIR = args[i+1] + "/";
+ Peregrine.outputDIR = output_DIR;
+ Assembler.output_DIR = output_DIR;
+ i += 2;
+ } else if (args[i].startsWith("-v")) {
+ if ((i == args.length-1) || (args[i+1].startsWith("-"))) {
+ output("Error - command line argument -v must be followed by a boolean.\n");
+ System.exit(0);
+ }
+ verbose = Boolean.valueOf(args[i+1]);
+ Assembler.verbose = Boolean.valueOf(args[i+1]);
+ i += 2;
+ } else if (args[i].startsWith("-m")) {
+ if ((i == args.length-1) || (args[i+1].startsWith("-"))) {
+ output("Error - command line argument -m must be followed by a decimal number.\n");
+ System.exit(0);
+ }
+ Peregrine.percentMismatches = Double.parseDouble(args[i+1]);
+ i += 2;
+ } else if (args[i].startsWith("-l")) {
+ if ((i == args.length-1) || (args[i+1].startsWith("-"))) {
+ output("Error - command line argument -l must be followed by a decimal number.\n");
+ System.exit(0);
+ }
+ Peregrine.percentSeedLength = Double.parseDouble(args[i+1]);
+ i += 2;
+ } else if (args[i].startsWith("-y")) {
+ if ((i == args.length-1) || (args[i+1].startsWith("-"))) {
+ output("Error - command line argument -y must be followed by a boolean.\n");
+ System.exit(0);
+ }
+ computeOperons = Boolean.valueOf(args[i+1]);
+ i += 2;
+ } else if (args[i].startsWith("-t")) {
+ if ((i == args.length-1) || (args[i+1].startsWith("-"))) {
+ output("Error - command line argument -t must be followed by a boolean.\n");
+ System.exit(0);
+ }
+ computeTranscripts = Boolean.valueOf(args[i+1]);
+ i += 2;
+ } else if (args[i].equals("-z")) {
+ if ((i == args.length-1) || (args[i+1].startsWith("-"))) {
+ output("Error - command line argument -z must be followed by a number in the range [0.0,1.0].\n");
+ System.exit(0);
+ }
+ transcriptSensitivity = Double.parseDouble(args[i+1]);
+ i += 2;
+ } else if (args[i].startsWith("-k")) {
+ if ((i == args.length-2) || (args[i+1].startsWith("-"))) {
+ output("Error - command line argument -k must be followed by an integer.\n");
+ System.exit(0);
+ }
+ Assembler.k = Integer.parseInt(args[i+1]);
+ if (Assembler.minTranscriptLength == 0) Assembler.minTranscriptLength = 2*Assembler.k;
+ i += 2;
+ } else if (args[i].startsWith("-j")) {
+ if ((i == args.length-2) || (args[i+1].startsWith("-"))) {
+ output("Error - command line argument -j must be followed by an integer.\n");
+ System.exit(0);
+ }
+ Assembler.minReadLength = Integer.parseInt(args[i+1]);
+ i += 2;
+ } else if (args[i].startsWith("-n")) {
+ if ((i == args.length-2) || (args[i+1].startsWith("-"))) {
+ output("Error - command line argument -n must be followed by an integer.\n");
+ System.exit(0);
+ }
+ Assembler.CAPACITY_POWER = Integer.parseInt(args[i+1]);
+ i += 2;
+ } else if (args[i].startsWith("-b")) {
+ if ((i == args.length-2) || (args[i+1].startsWith("-"))) {
+ output("Error - command line argument -b must be followed by an integer.\n");
+ System.exit(0);
+ }
+ Assembler.MIN_READS_MAPPING = Integer.parseInt(args[i+1]);
+ i += 2;
+ } else if (args[i].startsWith("-u")) {
+ if ((i == args.length-2) || (args[i+1].startsWith("-"))) {
+ output("Error - command line argument -u must be followed by an integer.\n");
+ System.exit(0);
+ }
+ Assembler.minTranscriptLength = Integer.parseInt(args[i+1]);
+ i += 2;
+ } else if (args[i].startsWith("-w")) {
+ if ((i == args.length-2) || (args[i+1].startsWith("-"))) {
+ output("Error - command line argument -w must be followed by an integer.\n");
+ System.exit(0);
+ }
+ Assembler.minSeedExpression = Integer.parseInt(args[i+1]);
+ i += 2;
+ } else if (args[i].startsWith("-x")) {
+ if ((i == args.length-2) || (args[i+1].startsWith("-"))) {
+ output("Error - command line argument -x must be followed by an integer.\n");
+ System.exit(0);
+ }
+ Assembler.minExpression = Integer.parseInt(args[i+1]);
+ i += 2;
+ } else if (args[i].startsWith("-c")) {
+ if ((i == args.length-1) || (args[i+1].startsWith("-"))) {
+ output("Error - command line argument -c must be followed by a boolean.\n");
+ System.exit(0);
+ }
+ Peregrine.singleEndOrientationReverseComplement = Boolean.valueOf(args[i+1]);
+ Assembler.singleEndOrientationReverseComplement = Boolean.valueOf(args[i+1]);
+ i += 2;
+ } else if (args[i].equals("-ff")) {
+ Peregrine.pairedEndOrientation = "ff";
+ Assembler.pairedEndOrientation = "ff";
+ i++;
+ } else if (args[i].equals("-fr")) {
+ Peregrine.pairedEndOrientation = "fr";
+ Assembler.pairedEndOrientation = "fr";
+ i++;
+ } else if (args[i].equals("-rf")) {
+ Peregrine.pairedEndOrientation = "rf";
+ Assembler.pairedEndOrientation = "rf";
+ i++;
+ } else if (args[i].equals("-rr")) {
+ Peregrine.pairedEndOrientation = "rr";
+ Assembler.pairedEndOrientation = "rr";
+ i++;
+ } else if (args[i].equals("-TIME")) {
+ time = true;
+ Assembler.time = true;
+ i++;
+ } else if (args[i].equals("-SAM")) {
+ Peregrine.outputSAM = true;
+ Assembler.outputSAM = true;
+ i++;
+ } else {
+ conditionFiles.add(args[i]);
+ i++;
+ }
+ }
+
+ // Handle erroneous command line arguments
+ if (genome_DIRs == null) {
+ isDeNovo = true;
+ } else {
+ for (int j=0; j<genome_DIRs.size(); j++) {
+ if (!(new File(genome_DIRs.get(j)).exists())) {
+ output("Error - directory " + genome_DIRs.get(j) + " does not exist.\n");
+ System.exit(0);
+ }
+ }
+ }
+ if (conditionFiles.size() == 0) {
+ output("Error - sequencing reads files (in FASTQ, QSEQ, FASTA, SAM, or BAM format) are required as command line arguments.\n");
+ System.exit(0);
+ }
+ Assembler.conditionFiles = conditionFiles;
+ Assembler.expressionFile = expressionFile;
+ Assembler.output_DIR = output_DIR;
+ Peregrine.outputDIR = output_DIR;
+ for (int j=0; j<conditionFiles.size(); j++) {
+ String[] files = conditionFiles.get(j).split(",");
+ for (int k=0; k<files.length; k++) {
+ String[] pairedEnd_files = files[k].split("%");
+ if (!(new File(pairedEnd_files[0]).exists())) {
+ output("Error - file " + pairedEnd_files[0] + " does not exist.\n");
+ System.exit(0);
+ }
+ if ((pairedEnd_files.length > 1) && (!(new File(pairedEnd_files[1]).exists()))) {
+ output("Error - file " + pairedEnd_files[1] + " does not exist.\n");
+ System.exit(0);
+ }
+ if (pairedEnd_files.length > 1) Assembler.unstranded = false; // Assume paired-end reads are strand specific
+ }
+ }
+
+ // If not set by command line arguments, set de novo assembled transcript length
+ if (Assembler.minTranscriptLength == 0) Assembler.minTranscriptLength = 2*Assembler.k;
+
+ // Output directory does not exist. Create it.
+ if (!(new File(output_DIR).exists())) {
+ if (!(new File(output_DIR).mkdir())) {
+ output("Error - could not create directory " + output_DIR + "." + "\n");
+ System.exit(0);
+ }
+ }
+ Peregrine.browserDIR = Rockhopper.browser_DIR;
+ if (!(new File(output_DIR + browser_DIR).exists())) {
+ if (!(new File(output_DIR + browser_DIR).mkdir())) {
+ output("Error - could not create directory " + (output_DIR+browser_DIR) + "." + "\n");
+ System.exit(0);
+ }
+ }
+ try {
+ summaryWriter = new PrintWriter(new File(output_DIR + summaryFile));
+ Peregrine.summaryWriter = summaryWriter;
+ Assembler.summaryWriter = summaryWriter;
+ } catch (FileNotFoundException e) {
+ output("Error - could not create file " + (output_DIR+summaryFile) + "\n");
+ System.exit(0);
+ }
+
+ }
+
+ public static void output(String s) {
+ if (summaryWriter != null) summaryWriter.print(s);
+ if (output == null) System.out.print(s);
+ else {
+ output.append(s);
+ output.setCaretPosition(output.getDocument().getLength());
+ }
+ }
+
+
+
+ /*************************************
+ ********** MAIN METHOD **********
+ *************************************/
+
+ /**
+ * The Main method, when invoked with the appropriate command line
+ * arguments, executes the Rockhopper application for the purpose
+ * of analyzing RNA-seq data.
+ */
+ public static void main(String[] args) {
+ commandLineArguments(args);
+ long runningTime = System.currentTimeMillis();
+ Rockhopper rh = new Rockhopper();
+ runningTime = System.currentTimeMillis() - runningTime;
+ if (time) { // Output time taken to execute program
+ System.out.println("Execution time:\t" + (runningTime/60000) + " minutes " + ((runningTime%60000)/1000) + " seconds" + "\n");
+ }
+ }
+
+}
+
diff --git a/RockhopperGUI.java b/RockhopperGUI.java
new file mode 100644
index 0000000..36eaf7e
--- /dev/null
+++ b/RockhopperGUI.java
@@ -0,0 +1,993 @@
+/*
+ * Copyright 2013 Brian Tjaden
+ *
+ * This file is part of Rockhopper.
+ *
+ * Rockhopper is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * any later version.
+ *
+ * Rockhopper is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * (in the file gpl.txt) along with Rockhopper.
+ * If not, see <http://www.gnu.org/licenses/>.
+ */
+
+import java.util.ArrayList;
+import java.util.Scanner;
+import javax.swing.*;
+import java.awt.*;
+import java.awt.event.ActionListener;
+import java.awt.event.ActionEvent;
+import javax.swing.event.DocumentListener;
+import javax.swing.event.DocumentEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseEvent;
+import java.io.File;
+import java.io.PrintWriter;
+import java.io.FileNotFoundException;
+import java.net.URL;
+import java.net.URI;
+import java.io.IOException;
+
+public class RockhopperGUI extends JApplet implements ActionListener,DocumentListener,MouseListener {
+
+ /*****************************************
+ ********** CLASS VARIABLES **********
+ *****************************************/
+
+ public static final String directory = Rockhopper.output_DIR + "intermediary/";
+ public static final String fileName = "experiments.txt";
+
+ private static final Color white = Color.white;
+ public static final Color lightBlue = new Color(150,200,255);
+ public static final Color gold = new Color(255,215,0);
+ public static final Color lightPurple = new Color(240,240,255);
+ public static ClassLoader cl;
+ public static URL penguin;
+ private static JFrame frame;
+
+
+
+ /********************************************
+ ********** INSTANCE VARIABLES **********
+ ********************************************/
+
+ private NCBI ncbi;
+ private String genome_DIR;
+ private JMenuBar menuBar;
+ private JMenuItem parameterMenuItem;
+ private JMenuItem cacheMenuItem;
+ private JMenuItem exitMenuItem;
+ private JMenuItem userGuideMenuItem;
+ private JMenuItem aboutMenuItem;
+
+ private JPanel mainPanel;
+ private JScrollPane outerRepliconPanel;
+ private JPanel innerRepliconPanel;
+ private ArrayList<JTextField> genomeTextFields;
+ private JPopupMenu popupMenu;
+ private int currentReplicon; // Replicon associated with popup menu
+ private ArrayList<IndexedMenuItem> popupReplicons;
+ private ArrayList<JLabel> genomeLabels;
+ private ArrayList<JLabel> customGenomeLabels;
+ private ArrayList<String> customGenomeDirs;
+ private JLabel genomeAddLabel;
+ private JPanel denovoPanel;
+ private JLabel denovoLabel;
+ private boolean isDenovo; // Performing de novo assembly (true) or reference based assembly (false)
+ private JPanel denovoInfo;
+ private JLabel submitLabel;
+ private ImageIcon submitButton, submitButtonPressed, genomeAddButton, genomeAddButtonPressed, genomeRemoveButton, genomeRemoveButtonPressed, customGenomeButton, customGenomeButtonPressed, denovoNoButton, denovoYesButton, denovoNoButtonPressed, denovoYesButtonPressed;
+ private JPanel spacer;
+ private boolean readingFromFile;
+ private JFileChooser fc;
+
+ // RNAseq files
+ private ExperimentsGUI exps;
+ private ParametersGUI params;
+ private ProgressGUI progress;
+ private Rockhopper rh;
+
+
+
+ /**************************************
+ ********** CONSTRUCTORS **********
+ **************************************/
+
+ public RockhopperGUI() {
+ cl = this.getClass().getClassLoader();
+ penguin = cl.getResource("images/Rockhopper.jpg");
+ fc = new JFileChooser();
+ fc.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
+ customGenomeDirs = new ArrayList<String>();
+ ncbi = new NCBI();
+ exps = new ExperimentsGUI(this);
+ params = new ParametersGUI(this);
+ progress = new ProgressGUI(this);
+ makeMenuBar();
+ makeMainPanel();
+ readExperimentsFromFile();
+ }
+
+
+
+ /*************************************************
+ ********** PUBLIC INSTANCE METHODS **********
+ *************************************************/
+
+ public void init() {
+ this.setJMenuBar(menuBar);
+ add(mainPanel);
+ }
+
+ public void actionPerformed(ActionEvent event) {
+ Object source = event.getSource();
+
+ if (source.equals(aboutMenuItem)) newDialogAbout();
+ else if (source.equals(parameterMenuItem)) params.displayParameters();
+ else if (source.equals(cacheMenuItem)) clearCache();
+ else if (source.equals(exitMenuItem)) System.exit(0);
+ else if (source.equals(userGuideMenuItem)) openUserGuide();
+ else if (params.isSource(source)) params.handleEvent(source);
+ else { // Pop up menu selection
+ // Check if event was one of the replicon text fields and, if so, get index.
+ int z = -1;
+ for (int i=0; i<genomeTextFields.size(); i++) {
+ if (source.equals(genomeTextFields.get(i))) z = i;
+ }
+ if (z >= 0) handleGenomeTextField(z); // Replicon text field
+ else { // Replicon popup menu
+ for (IndexedMenuItem item : popupReplicons) {
+ if (source.equals(item)) {
+ if (item.getText().indexOf("*** MORE ***") >= 0) {
+ updateRepliconMenu(currentReplicon, item.index);
+ } else {
+ genomeTextFields.get(currentReplicon).setText(item.getText());
+ //removePopupMenu();
+ customGenomeDirs.set(currentReplicon, null);
+ handleGenomeTextField(currentReplicon);
+ }
+ break;
+ }
+ }
+ }
+ }
+ }
+
+ public void insertUpdate(DocumentEvent event) {
+ for (int i=0; i<genomeTextFields.size(); i++) {
+ if (event.getDocument().equals(genomeTextFields.get(i).getDocument()) && !readingFromFile) updateRepliconMenu(i, 0);
+ }
+ }
+
+ public void removeUpdate(DocumentEvent event) {
+ for (int i=0; i<genomeTextFields.size(); i++) {
+ if (event.getDocument().equals(genomeTextFields.get(i).getDocument())) updateRepliconMenu(i, 0);
+ }
+ }
+
+ public void changedUpdate(DocumentEvent event) {
+ // Plain text components do not fire these events.
+ }
+
+ public void mouseClicked(MouseEvent event) {
+ Object source = event.getSource();
+ if (exps.isSource(source)) {
+ mainPanel.remove(exps.getScrollPane());
+ mainPanel.remove(submitLabel);
+ exps.handleEvent(source);
+ updateSeqFilePanel();
+ } else if (params.isSource(source)) {
+ params.handleEvent(source);
+ } else if (source.equals(genomeAddLabel) && !isDenovo) { // Genome add button is pressed
+ addReplicon();
+ if (exps.getNumExperiments() > 0) {
+ mainPanel.remove(exps.getScrollPane());
+ mainPanel.remove(submitLabel);
+ updateSeqFilePanel();
+ } else {
+ validate();
+ repaint();
+ }
+ } else if (source.equals(denovoLabel)) { // Toggle de novo assembly vs. reference based assembly
+ if (isDenovo) { // Changing from de novo to reference based assembly
+ toggleRepliconDeNovoPanels(denovoInfo, innerRepliconPanel);
+ } else { // Changing from reference based to de novo assembly
+ toggleRepliconDeNovoPanels(innerRepliconPanel, denovoInfo);
+ }
+ isDenovo = !isDenovo;
+ mainPanel.remove(exps.getScrollPane());
+ mainPanel.remove(submitLabel);
+ if (exps.getNumExperiments() == 0) exps.addExperiment();
+ updateSeqFilePanel();
+ } else if (source.equals(submitLabel)) { // Submit button is pressed
+ if (!isDenovo) { // Check replicons if performing reference based assembly
+ if (!prepareRepliconFiles()) return;
+ }
+ if (!outputExperimentsToFile()) return;
+ progress.createProgressWindow();
+ Peregrine.output = progress.progressArea;
+ Assembler.output = progress.progressArea;
+ Rockhopper.output = progress.progressArea;
+ Rockhopper.commandLineArguments(generateCommandLineArguments());
+ Peregrine.wigFiles = null;
+
+ class Worker extends SwingWorker<Void, Void> {
+ public Void doInBackground() {
+ Rockhopper.worker = this;
+ rh = new Rockhopper();
+ return null;
+ }
+ public void done() {
+ setProgress(100);
+ if (!isDenovo) progress.addIGV(); // Add IGV button only if NOT de novo assembly
+ validate();
+ repaint();
+ }
+ }
+ Worker w = new Worker();
+ w.addPropertyChangeListener(progress);
+ w.execute();
+ } else if (progress.isSource(source)) {
+ if (isDenovo) return; // No need to launch IGV if completed de novo assembly
+ // Launch IGV!
+ try {
+ boolean success = true;
+ ArrayList<Genome> genomes = rh.getGenomes();
+ File genomeRegistryFile = new File(directory + "genomes.txt");
+ success &= IGV_Ops.createGenomeRegistry(genomeRegistryFile, genomes);
+ for (int i=0; i<genomes.size(); i++) {
+ Genome genome = genomes.get(i);
+ String baseFileName = genome.getBaseFileName();
+ success &= IGV_Ops.createGenomeArchive(baseFileName + ".genome", genome.getName(), baseFileName + ".fna", baseFileName + ".gff");
+ success &= IGV_Ops.createBatchFileToLoadData(directory + "batch_" + genome.getName().replace(' ', '_') + ".txt", genome.getName(), formatWigFiles(Peregrine.wigFiles.get(i)), getRockhopperWigFiles(genome));
+ }
+ final String firstBatchFile = directory + "batch_" + genomes.get(0).getName().replace(' ', '_') + ".txt";
+ rh = null;
+ System.gc(); // Clean up memory before launching IGV
+
+ class Worker extends SwingWorker<Void, Void> {
+ public Void doInBackground() {
+ String[] args = {"-u", "file:" + directory + "genomes.txt", "-b", firstBatchFile};
+ org.broad.igv.ui.Main.main(args);
+ return null;
+ }
+ public void done() { }
+ }
+ (new Worker()).execute();
+ if (!success) error("IGV error", "There was an error launching and initializing IGV for viewing results.");
+ } catch (Exception ex) {
+ error("IGV error", "Could not open IGV for viewing results.");
+ }
+ } else { // Check if replicon remove button was clicked
+ for (int i=0; i<genomeLabels.size(); i++) {
+ if (source.equals(genomeLabels.get(i)) && !isDenovo) {
+ removeReplicon(i);
+ if (exps.getNumExperiments() > 0) {
+ mainPanel.remove(exps.getScrollPane());
+ mainPanel.remove(submitLabel);
+ updateSeqFilePanel();
+ } else {
+ validate();
+ repaint();
+ }
+ }
+ }
+ for (int i=0; i<customGenomeLabels.size(); i++) {
+ if (source.equals(customGenomeLabels.get(i)) && !isDenovo) {
+ addCustomGenome(i);
+ }
+ }
+ }
+ }
+
+ public void mousePressed(MouseEvent event) {
+ Object source = event.getSource();
+ exps.mousePressed(source);
+ params.mousePressed(source);
+ progress.mousePressed(source);
+ if (source.equals(genomeAddLabel) && !isDenovo) genomeAddLabel.setIcon(genomeAddButtonPressed);
+ if (source.equals(submitLabel)) submitLabel.setIcon(submitButtonPressed);
+ for (JLabel genomeLabel : genomeLabels) {
+ if (source.equals(genomeLabel) && !isDenovo) genomeLabel.setIcon(genomeRemoveButtonPressed);
+ }
+ for (JLabel customGenomeLabel : customGenomeLabels) {
+ if (source.equals(customGenomeLabel) && !isDenovo) customGenomeLabel.setIcon(customGenomeButtonPressed);
+ }
+ if (source.equals(denovoLabel)) {
+ if (isDenovo) denovoLabel.setIcon(denovoYesButtonPressed);
+ else denovoLabel.setIcon(denovoNoButtonPressed);
+ }
+
+ }
+
+ public void mouseReleased(MouseEvent event) {
+ Object source = event.getSource();
+ exps.mouseReleased(source);
+ params.mouseReleased(source);
+ progress.mouseReleased(source);
+ if (source.equals(genomeAddLabel) && !isDenovo) genomeAddLabel.setIcon(genomeAddButton);
+ if (source.equals(submitLabel)) submitLabel.setIcon(submitButton);
+ for (JLabel genomeLabel : genomeLabels) {
+ if (source.equals(genomeLabel) && !isDenovo) genomeLabel.setIcon(genomeRemoveButton);
+ }
+ for (JLabel customGenomeLabel : customGenomeLabels) {
+ if (source.equals(customGenomeLabel) && !isDenovo) customGenomeLabel.setIcon(customGenomeButton);
+ }
+ if (source.equals(denovoLabel)) {
+ if (isDenovo) denovoLabel.setIcon(denovoNoButton);
+ else denovoLabel.setIcon(denovoYesButton);
+ }
+ }
+
+ public void mouseEntered(MouseEvent event) { }
+
+ public void mouseExited(MouseEvent event) { }
+
+
+
+ /**************************************************
+ ********** PRIVATE INSTANCE METHODS **********
+ **************************************************/
+
+ private void makeMenuBar() {
+ menuBar = new JMenuBar();
+ menuBar.setOpaque(true);
+ menuBar.setBackground(gold);
+ menuBar.setPreferredSize(new Dimension(200,20));
+
+ JMenu fileMenu = new JMenu("Options");
+ menuBar.add(fileMenu);
+ fileMenu.setBackground(gold);
+ fileMenu.addSeparator();
+ parameterMenuItem = new JMenuItem("Parameter settings");
+ parameterMenuItem.setBackground(gold);
+ fileMenu.add(parameterMenuItem);
+ parameterMenuItem.addActionListener(this);
+ fileMenu.addSeparator();
+ cacheMenuItem = new JMenuItem("Clear cache");
+ cacheMenuItem.setBackground(gold);
+ fileMenu.add(cacheMenuItem);
+ cacheMenuItem.addActionListener(this);
+ fileMenu.addSeparator();
+ exitMenuItem = new JMenuItem("Exit");
+ exitMenuItem.setBackground(gold);
+ fileMenu.add(exitMenuItem);
+ exitMenuItem.addActionListener(this);
+
+ JMenu helpMenu = new JMenu("Help");
+ menuBar.add(helpMenu);
+ helpMenu.setBackground(gold);
+ userGuideMenuItem = new JMenuItem("User guide");
+ userGuideMenuItem.setBackground(gold);
+ helpMenu.add(userGuideMenuItem);
+ userGuideMenuItem.addActionListener(this);
+ helpMenu.addSeparator();
+ aboutMenuItem = new JMenuItem("About Rockhopper");
+ aboutMenuItem.setBackground(gold);
+ helpMenu.add(aboutMenuItem);
+ aboutMenuItem.addActionListener(this);
+ }
+
+ private void newDialogAbout() {
+ JPanel panel = new JPanel();
+ panel.setBackground(lightBlue);
+ panel.setLayout(new GridLayout(1,2));
+ JLabel picLabel = new JLabel();
+ picLabel.setIcon(new ImageIcon(penguin));
+ JPanel textPanel = new JPanel();
+ textPanel.setBackground(lightBlue);
+ textPanel.setLayout(new GridLayout(7,1));
+ textPanel.add(new JLabel());
+ JLabel textLabel1 = new JLabel("Rockhopper", SwingConstants.CENTER);
+ textLabel1.setFont(new Font("Times", Font.ITALIC, 30));
+ textPanel.add(textLabel1);
+ JLabel textLabel2 = new JLabel("version " + Rockhopper.version, SwingConstants.CENTER);
+ textLabel2.setFont(new Font("Times", Font.PLAIN, 16));
+ textPanel.add(textLabel2);
+ textPanel.add(new JLabel());
+ JLabel textLabel3 = new JLabel("A tool for analyzing", SwingConstants.CENTER);
+ textLabel3.setFont(new Font("Times", Font.PLAIN, 12));
+ textPanel.add(textLabel3);
+ JLabel textLabel4 = new JLabel("bacterial RNAseq data", SwingConstants.CENTER);
+ textLabel4.setFont(new Font("Times", Font.PLAIN, 12));
+ textPanel.add(textLabel4);
+ panel.add(picLabel);
+ panel.add(textPanel);
+ JDialog about = new JDialog(frame, "About Rockhopper", true);
+ about.setSize(500,200);
+ about.setResizable(false);
+ about.setLocationRelativeTo(this);
+ about.add(panel);
+ about.setVisible(true);
+ }
+
+ private void makeMainPanel() {
+ mainPanel = new JPanel(new FlowLayout(FlowLayout.CENTER));
+ mainPanel.setBackground(lightBlue);
+ mainPanel.add(getSpacerPanel(790,20));
+ genomeAddButton = RockhopperGUI.getScaledImage("images/addGenome.gif", 20, 20);
+ genomeAddButtonPressed = RockhopperGUI.getScaledImage("images/addGenomePressed.gif", 20, 20);
+ genomeRemoveButton = RockhopperGUI.getScaledImage("images/removeGenome.gif", 20, 20);
+ genomeRemoveButtonPressed = RockhopperGUI.getScaledImage("images/removeGenomePressed.gif", 20, 20);
+ customGenomeButton = RockhopperGUI.getScaledImage("images/customGenome.gif", 20, 20);
+ customGenomeButtonPressed = RockhopperGUI.getScaledImage("images/customGenomePressed.gif", 20, 20);
+ denovoNoButton = RockhopperGUI.getScaledImage("images/denovoNoButton.png", 20, 20);
+ denovoNoButtonPressed = RockhopperGUI.getScaledImage("images/denovoNoButtonPressed.png", 20, 20);
+ denovoYesButton = RockhopperGUI.getScaledImage("images/denovoYesButton.png", 20, 20);
+ denovoYesButtonPressed = RockhopperGUI.getScaledImage("images/denovoYesButtonPressed.png", 20, 20);
+ isDenovo = false;
+ denovoInfo = new JPanel(new GridBagLayout());
+ denovoInfo.setBackground(lightBlue);
+ denovoInfo.setBorder(BorderFactory.createEmptyBorder());
+ JLabel denovoInfoLabel = new JLabel("Perform de novo transcript assembly without reference replicons");
+ denovoInfoLabel.setFont(new Font("Times", Font.BOLD, 14));
+ denovoInfoLabel.setForeground(gold);
+ denovoInfo.add(denovoInfoLabel);
+ innerRepliconPanel = new JPanel(new FlowLayout(FlowLayout.LEFT,2,2));
+ outerRepliconPanel = new JScrollPane(innerRepliconPanel);
+ outerRepliconPanel.setPreferredSize(new Dimension(500, 100));
+ outerRepliconPanel.setBackground(lightBlue);
+ outerRepliconPanel.setBorder(BorderFactory.createEmptyBorder());
+ genomeAddLabel = new JLabel(genomeAddButton);
+ genomeAddLabel.setToolTipText("Add replicon");
+ genomeAddLabel.addMouseListener(this);
+ genomeTextFields = new ArrayList<JTextField>();
+ genomeLabels = new ArrayList<JLabel>();
+ customGenomeLabels = new ArrayList<JLabel>();
+ denovoLabel = new JLabel(denovoNoButton);
+ denovoLabel.setToolTipText("Press here to toggle between de novo transcript assembly and reference based transcript assembly");
+ denovoLabel.addMouseListener(this);
+ denovoPanel = new JPanel();
+ denovoPanel.setPreferredSize(new Dimension(20, 100));
+ denovoPanel.setBackground(lightBlue);
+ denovoPanel.setBorder(BorderFactory.createEmptyBorder());
+ denovoPanel.add(denovoLabel);
+ addReplicon();
+ popupReplicons = new ArrayList<IndexedMenuItem>();
+ mainPanel.add(outerRepliconPanel);
+ mainPanel.add(denovoPanel);
+
+ submitButton = getScaledImage("images/Submit.gif", 117, 41);
+ submitButtonPressed = getScaledImage("images/SubmitPressed.gif", 117, 41);
+ submitLabel = new JLabel(submitButton);
+ submitLabel.setToolTipText("Submit RNAseq files for analysis");
+ submitLabel.addMouseListener(this);
+ spacer = getSpacerPanel(790,5);
+ }
+
+ public void addReplicon() {
+ outerRepliconPanel.remove(innerRepliconPanel);
+ genomeTextFields.add(new JTextField("", 25));
+ genomeTextFields.get(genomeTextFields.size()-1).setBackground(gold);
+ genomeTextFields.get(genomeTextFields.size()-1).addActionListener(this);
+ genomeTextFields.get(genomeTextFields.size()-1).getDocument().addDocumentListener(this);
+ genomeLabels.add(new JLabel(genomeRemoveButton));
+ genomeLabels.get(genomeLabels.size()-1).setToolTipText("Remove replicon");
+ genomeLabels.get(genomeLabels.size()-1).addMouseListener(this);
+ customGenomeLabels.add(new JLabel(customGenomeButton));
+ customGenomeLabels.get(customGenomeLabels.size()-1).setToolTipText("Use a replicon whose sequence is not available from GenBank");
+ customGenomeLabels.get(customGenomeLabels.size()-1).addMouseListener(this);
+ customGenomeDirs.add(null);
+ currentReplicon = genomeTextFields.size()-1;
+ populateOuterRepliconPanel();
+ }
+
+ public void removeReplicon(int i) {
+ outerRepliconPanel.remove(innerRepliconPanel);
+ genomeTextFields.remove(i);
+ genomeLabels.remove(i);
+ customGenomeLabels.remove(i);
+ customGenomeDirs.remove(i);
+ populateOuterRepliconPanel();
+ }
+
+ private JPanel generateRepliconPanel(int i) {
+ JPanel newPanel = new JPanel(new FlowLayout(FlowLayout.CENTER));
+ newPanel.setPreferredSize(new Dimension(480, 27));
+ newPanel.setBackground(lightBlue);
+ newPanel.add(new JLabel("Replicon name: "));
+ newPanel.add(genomeTextFields.get(i));
+ newPanel.add(genomeLabels.get(i));
+ newPanel.add(customGenomeLabels.get(i));
+ JLabel spacer = new JLabel("");
+ spacer.setPreferredSize(new Dimension(70, 0));
+ newPanel.add(spacer);
+ return newPanel;
+ }
+
+ private void populateOuterRepliconPanel() {
+ innerRepliconPanel = new JPanel(new FlowLayout(FlowLayout.LEFT,2,2));
+ innerRepliconPanel.setPreferredSize(new Dimension(480, genomeTextFields.size()*29 + 40));
+ innerRepliconPanel.setBackground(lightBlue);
+ innerRepliconPanel.setBorder(BorderFactory.createEmptyBorder());
+ for (int i=0; i<genomeTextFields.size(); i++) innerRepliconPanel.add(generateRepliconPanel(i));
+ innerRepliconPanel.add(getSpacerPanel(25, 20));
+ innerRepliconPanel.add(genomeAddLabel);
+ toggleRepliconDeNovoPanels(innerRepliconPanel, innerRepliconPanel);
+
+ // Force scroll to bottom
+ SwingUtilities.invokeLater( new Runnable() {
+ public void run()
+ {
+ JScrollBar v = outerRepliconPanel.getVerticalScrollBar();
+ v.setValue(v.getMaximum());
+ }
+ } );
+
+ validate();
+ repaint();
+ }
+
+ /**
+ * Update panel containing the tree of RNAseq file names.
+ */
+ private void updateSeqFilePanel() {
+ mainPanel.add(exps.getScrollPane());
+ mainPanel.add(spacer);
+ mainPanel.add(submitLabel);
+ validate();
+ repaint();
+ }
+
+ /**
+ * Action performed on genome text field.
+ */
+ private void handleGenomeTextField(int index) {
+ if (genomeTextFields.get(index).getText().length() > 0) genomeTextFields.get(index).setBackground(white);
+ removePopupMenu();
+ if (exps.getNumExperiments() == 0) {
+ exps.addExperiment();
+ updateSeqFilePanel();
+ }
+ }
+
+ private void addCustomGenome(int i) {
+ // First show pop-up information message about custom replicon
+ String title = "Use replicon whose sequence is not available from GenBank?";
+ String message = "If the sequence of your replicon is avilable in GenBank, do not use this option, instead select the Cancel button \nand type the name of your replicon in the Replicon name field. \n\nIf the sequence of your replicion is NOT available in GenBank, select the OK button and indicate a folder that contains \na single FASTA file containing the replicon genomic sequence as well as a gene annotation file (in PTT format).";
+ Object[] options = {"OK", "Cancel"};
+ int n = JOptionPane.showOptionDialog(SwingUtilities.getAncestorOfClass(JFrame.class,this), message, title, JOptionPane.YES_NO_OPTION, JOptionPane.INFORMATION_MESSAGE, customGenomeButtonPressed, options, options[0]);
+
+ // Select replicon folder
+ if (n == 0) {
+ fc.setSelectedFile(null);
+ int returnVal = fc.showOpenDialog(SwingUtilities.getAncestorOfClass(JFrame.class,this));
+ if (returnVal == JFileChooser.APPROVE_OPTION) {
+ try {
+ File dir = fc.getSelectedFile();
+ String genomeFileName = null;
+ String geneFileName = null;
+ String rnaFileName = null;
+ String[] files = dir.list();
+ for (String f : files) {
+ if (f.toLowerCase().endsWith(".fna") || f.toLowerCase().endsWith(".fa") || f.toLowerCase().endsWith(".fasta")) genomeFileName = f;
+ if (f.toLowerCase().endsWith(".ptt")) geneFileName = f;
+ if (f.toLowerCase().endsWith(".rnt")) rnaFileName = f;
+ }
+ String genomeName = validateFastaFile(dir, genomeFileName);
+ if (genomeName != null) genomeFileName = getBaseFileName(genomeFileName) + ".fna";
+ if (genomeFileName == null) {
+ error("Problem reading in FASTA file", "Could not identify in the specified folder a FASTA file with appropriate extension (fna, fa, or fasta) and in the expected format");
+ return;
+ }
+ if (geneFileName == null) {
+ error("Problem reading in gene annotation file", "Could not identify in the specified folder a gene annotation file with appropriate extension (ptt) and in the expected format");
+ return;
+ }
+
+ genomeTextFields.get(i).setText(genomeName); // Fill in custom replicon name in text field
+ customGenomeDirs.set(i, dir.getAbsolutePath());
+ handleGenomeTextField(i);
+
+ } catch (Exception e) {
+ error("Problem reading replicon files", "Unable to read replicon files in supplied folder");
+ }
+ }
+ }
+ }
+
+ /**
+ * Switch between replicon panel and de novo panel.
+ */
+ private void toggleRepliconDeNovoPanels(JPanel p1, JPanel p2) {
+ outerRepliconPanel.remove(p1);
+ mainPanel.remove(outerRepliconPanel);
+ mainPanel.remove(denovoPanel);
+ outerRepliconPanel = new JScrollPane(p2);
+ outerRepliconPanel.setPreferredSize(new Dimension(500, 100));
+ outerRepliconPanel.setBackground(lightBlue);
+ outerRepliconPanel.setBorder(BorderFactory.createEmptyBorder());
+ mainPanel.add(outerRepliconPanel);
+ mainPanel.add(denovoPanel);
+ }
+
+ /**
+ * Check FASTA file is in correct format. Rename the file's extension
+ * to ".fna". If not in the correct format, return null. If in the
+ * correct format, return the name of the genome.
+ */
+ private String validateFastaFile(File dir, String genomeFileName) {
+ if (genomeFileName == null) return null;
+ String baseFileName = getBaseFileName(genomeFileName);
+ try {
+ File f = new File(dir, genomeFileName);
+ Scanner reader = new Scanner(f);
+ String line = reader.nextLine();
+ String name = baseFileName;
+ if (line.length() > 0) {
+ if (line.charAt(0) == '>') {
+ name = line.substring(1);
+ if (name.split("\\|").length >= 5) {
+ reader.close();
+ boolean result = f.renameTo(new File(dir, baseFileName + ".fna"));
+ String[] parse_line = name.split("\\|");
+ if (result) return parse_line[4].trim();
+ return null;
+ } else { // Modify header line of FASTA file
+ StringBuilder sequence = new StringBuilder();
+ while (reader.hasNext()) sequence.append(reader.nextLine());
+ reader.close();
+ PrintWriter writer = new PrintWriter(new File(dir, baseFileName + ".fna"));
+ writer.println(">gi|99999999|ref|NC_999999.9|" + name);
+ writer.println(sequence.toString());
+ writer.close();
+ return name.trim();
+ }
+ } else { // Read in file
+ StringBuilder sequence = new StringBuilder(line);
+ while (reader.hasNext()) sequence.append(reader.nextLine());
+ reader.close();
+ PrintWriter writer = new PrintWriter(new File(dir, baseFileName + ".fna"));
+ writer.println(">gi|99999999|ref|NC_999999.9|" + baseFileName);
+ writer.println(sequence.toString());
+ writer.close();
+ return baseFileName;
+ }
+ }
+ reader.close();
+ } catch (FileNotFoundException e) {
+ return null;
+ }
+ return null;
+ }
+
+ private String getBaseFileName(String fileName) {
+ if (fileName == null) return null;
+ int slashIndex = fileName.lastIndexOf(File.separatorChar);
+ int periodIndex = fileName.lastIndexOf('.');
+ if (periodIndex == -1) return fileName.substring(slashIndex+1);
+ else return fileName.substring(slashIndex+1, periodIndex);
+ }
+
+ /**
+ * Update the popup menu for the replicon name.
+ */
+ private void updateRepliconMenu(int z, int index) {
+ String s = genomeTextFields.get(z).getText();
+ if (s.length() >= NCBI.HASH_SIZE) {
+ popupMenu = new JPopupMenu("Replicons");
+ mainPanel.add(popupMenu);
+ currentReplicon = z;
+ for (IndexedMenuItem item : popupReplicons) item.removeActionListener(this);
+ popupReplicons.clear();
+ ArrayList<String> reps = ncbi.getRepliconNames(s);
+ for (int i=index; i<Math.min(reps.size(), index+25); i++) {
+ IndexedMenuItem item = new IndexedMenuItem(reps.get(i));
+ item.setBackground(white);
+ popupReplicons.add(item);
+ popupMenu.add(item);
+ item.addActionListener(this);
+ }
+ if (reps.size() > index+25) {
+ IndexedMenuItem item = new IndexedMenuItem(" *** MORE ***");
+ item.setBackground(white);
+ item.index = index+25;
+ popupReplicons.add(item);
+ popupMenu.add(item);
+ item.addActionListener(this);
+ }
+ int popupHeight = Math.min(genomeTextFields.get(z).getHeight()+37+z*27, 95);
+ popupMenu.show(mainPanel, genomeTextFields.get(z).getX()+147, popupHeight);
+ genomeTextFields.get(z).requestFocusInWindow();
+ } else removePopupMenu();
+ }
+
+ /**
+ * Delete the popup menu.
+ */
+ private void removePopupMenu() {
+ if (popupMenu != null) popupMenu.setVisible(false);
+ popupMenu = null;
+ currentReplicon = -1;
+ for (IndexedMenuItem item : popupReplicons) item.removeActionListener(this);
+ popupReplicons.clear();
+ validate();
+ repaint();
+ }
+
+ private boolean outputExperimentsToFile() {
+ try {
+ File f = new File(directory);
+ if (!f.exists()) f.mkdir();
+ PrintWriter writer = new PrintWriter(new File(directory + fileName));
+ writer.println(Rockhopper.version);
+ writer.println("" + isDenovo);
+ if (!isDenovo) { // Only write replicon info if we are performing reference based assembly
+ writer.println(genomeTextFields.size());
+ for (int i=0; i<genomeTextFields.size(); i++) {
+ if (customGenomeDirs.get(i) == null) writer.println(genomeTextFields.get(i).getText());
+ else writer.println(genomeTextFields.get(i).getText() + "\t" + customGenomeDirs.get(i));
+ }
+ }
+ String s = exps.experimentsToString();
+ writer.print(s);
+ writer.close();
+ if (s.trim().length() == 0) {
+ error("Invalid experiment files", "Please choose one or more valid experiment files");
+ return false;
+ }
+ } catch (FileNotFoundException ex) {
+ // Do nothing if experiment file could not be written.
+ }
+ return true;
+ }
+
+ private void readExperimentsFromFile() {
+ try {
+ Scanner reader = new Scanner(new File(directory + fileName));
+ String version = reader.nextLine();
+ if (!version.equals(Rockhopper.version)) return;
+ isDenovo = Boolean.parseBoolean(reader.nextLine());
+ if (isDenovo) { // De novo assembly
+ denovoLabel.setIcon(denovoYesButton);
+ toggleRepliconDeNovoPanels(innerRepliconPanel, denovoInfo);
+ } else { // Reference based assembly
+ denovoLabel.setIcon(denovoNoButton);
+ int numReplicons = Integer.parseInt(reader.nextLine().trim());
+ readingFromFile = true;
+ if (numReplicons > 0) {
+ String repliconLine = reader.nextLine();
+ String[] parse_line = repliconLine.split("\t");
+ genomeTextFields.get(0).setText(parse_line[0]);
+ genomeTextFields.get(0).setBackground(white);
+ if (parse_line.length > 1) customGenomeDirs.set(0, parse_line[1]);
+ }
+ for (int i=1; i<numReplicons; i++) {
+ addReplicon();
+ String repliconLine = reader.nextLine();
+ String[] parse_line = repliconLine.split("\t");
+ genomeTextFields.get(genomeTextFields.size()-1).setText(parse_line[0]);
+ genomeTextFields.get(genomeTextFields.size()-1).setBackground(white);
+ if (parse_line.length > 1) customGenomeDirs.set(customGenomeDirs.size()-1, parse_line[1]);
+ }
+ }
+ readingFromFile = false;
+ StringBuilder sb = new StringBuilder();
+ while (reader.hasNext()) sb.append(reader.nextLine() + "\n");
+ exps.experimentsFromString(sb.toString());
+ updateSeqFilePanel();
+ reader.close();
+ } catch (Exception ex) {
+ // Do nothing if experiment file could not be read.
+ }
+ }
+
+ private boolean prepareRepliconFiles() {
+ if (genomeTextFields.size() == 0) {
+ error("No replicons selected", "Please designate one or more replicons");
+ return false;
+ }
+ for (int i=0; i<genomeTextFields.size(); i++) {
+ String repliconName = genomeTextFields.get(i).getText();
+ if ((customGenomeDirs.get(i) == null) && !ncbi.prepGenomeFiles(repliconName)) {
+ error("Invalid replicon name", "Please enter a valid replicon name");
+ return false;
+ }
+ if (customGenomeDirs.get(i) == null) { // Use NCBI replicon
+ if (i == 0) genome_DIR = NCBI.genome_DIR + NCBI.getRepliconDir(repliconName);
+ else genome_DIR += "," + NCBI.genome_DIR + NCBI.getRepliconDir(repliconName);
+ } else { // Use custom replicon
+ if (i == 0) genome_DIR = customGenomeDirs.get(0);
+ else genome_DIR += "," + customGenomeDirs.get(i);
+ }
+ }
+ return true;
+ }
+
+ /**
+ * Returns a comma-delimited String of the WIG files generated
+ * by Rockhopper that can be viewed in IGV.
+ */
+ private String getRockhopperWigFiles(Genome genome) {
+ String s = "";
+ String dir = Rockhopper.output_DIR + Rockhopper.browser_DIR;
+ if (params.testDifferentialExp) s += "," + dir + genome.getID() + "_diffExpressedGenes.wig";
+ if (params.transcriptBoundaries) s += "," + dir + genome.getID() + "_UTRs.wig";
+ if (params.transcriptBoundaries) s += "," + dir + genome.getID() + "_ncRNAs.wig";
+ if (params.predictOperons) s += "," + dir + genome.getID() + "_operons.wig";
+ if (s.length() == 0) return s;
+ else return s.substring(1);
+ }
+
+ /**
+ * Given a comma-delimited list of WIG files representing
+ * reads mapped to a genome by Peregrine, we clean/format
+ * the comma-delimited list and return the
+ * cleaned/formatted version.
+ */
+ private String formatWigFiles(String wigFiles) {
+ if (wigFiles.length() == 0) return "";
+ ArrayList<String> wigs_plus = new ArrayList<String>();
+ ArrayList<String> wigs_minus = new ArrayList<String>();
+ String[] wigList = wigFiles.split(",");
+ for (int i=0; i<wigList.length; i++) {
+ if (wigList[i].indexOf(".minus.") >= 0) wigs_minus.add(wigList[i]);
+ else wigs_plus.add(wigList[i]);
+ }
+ String s = "";
+ for (int i=0; i<wigs_plus.size(); i++) {
+ if (s.length() > 0) s += ",";
+ s += wigs_plus.get(i);
+ }
+ for (int i=0; i<wigs_minus.size(); i++) {
+ if (s.length() > 0) s += ",";
+ s += wigs_minus.get(i);
+ }
+ return s;
+ }
+
+ private void clearCache() {
+ removeAllFiles(new File(Rockhopper.output_DIR));
+ File f = new File(Rockhopper.output_DIR); // Create "Rockhopper_Results" directory
+ f.mkdir();
+ f = new File(directory); // Create "intermediary" directory
+ f.mkdir();
+ mainPanel.removeAll();
+ mainPanel.add(getSpacerPanel(790,20));
+ ncbi = new NCBI();
+ exps = new ExperimentsGUI(this);
+ params = new ParametersGUI(this);
+ progress = new ProgressGUI(this);
+ removePopupMenu();
+ genomeTextFields.clear();
+ genomeLabels.clear();
+ customGenomeLabels.clear();
+ customGenomeDirs.clear();
+ addReplicon();
+ if (isDenovo) { // Clearing cache in de novo assembly mode
+ toggleRepliconDeNovoPanels(innerRepliconPanel, denovoInfo);
+ exps.addExperiment();
+ updateSeqFilePanel();
+ }
+ }
+
+ private void openUserGuide() {
+ String address = "http://cs.wellesley.edu/~btjaden/Rockhopper/user_guide.html";
+ if (Desktop.isDesktopSupported()) {
+ try {
+ Desktop.getDesktop().browse(new URI(address));
+ } catch (Exception e) {
+ JOptionPane.showMessageDialog(frame, "The user guide is available at the following URL:<BR><u>" + address + "</u>", "User Guide", JOptionPane.INFORMATION_MESSAGE);
+ }
+ } else {
+ JOptionPane.showMessageDialog(frame, "The user guide is available at the following URL:<BR><u>" + address + "</u>", "User Guide", JOptionPane.INFORMATION_MESSAGE);
+ }
+ }
+
+ /**
+ * Recursively deletes all files in the specified directory.
+ */
+ private void removeAllFiles(File f) {
+ if (!f.exists()) return;
+ if (f.isDirectory()) { // We have a directory. Look inside directory.
+ for (File x : f.listFiles()) removeAllFiles(x);
+ }
+ f.delete(); // Remove file or empty directory.
+ }
+
+ private String[] generateCommandLineArguments() {
+ ArrayList<String> args = new ArrayList<String>();
+ args.add("-m");
+ args.add("" + params.mismatches);
+ args.add("-l");
+ args.add("" + params.minReadLength);
+ args.add("-c");
+ args.add("" + params.singleEndOrientation);
+ args.add("-" + params.matePairOrientation);
+ if (params.numProcessors > 0) {
+ args.add("-p");
+ args.add("" + params.numProcessors);
+ }
+ args.add("-d");
+ args.add("" + params.maxPairedEndLength);
+ args.add("-v");
+ args.add("" + params.verboseOutput);
+ args.add("-s");
+ args.add("" + params.isStrandSpecific);
+ args.add("-e");
+ args.add("" + params.testDifferentialExp);
+ args.add("-y");
+ args.add("" + params.predictOperons);
+ args.add("-t");
+ args.add("" + params.transcriptBoundaries);
+ args.add("-z");
+ args.add("" + params.expressionParameter);
+ args.add("-o");
+ args.add("" + params.outputDIR);
+ args.add("-L");
+ args.add(exps.getExperimentsList());
+ if (!isDenovo) {
+ args.add("-g");
+ args.add(genome_DIR);
+ }
+ args.add("-b");
+ args.add("" + params.minReadsMapping);
+ args.add("-u");
+ args.add("" + params.minTranscriptLength);
+ args.add("-w");
+ args.add("" + params.minSeedExpression);
+ args.add("-x");
+ args.add("" + params.minExtendExpression);
+ if (params.outputSAM) args.add("-SAM");
+ String[] reps = exps.getReplicatesList();
+ for (int i=0; i<reps.length; i++) args.add(reps[i]);
+ return args.toArray(new String[args.size()]);
+ }
+
+ public static JPanel getSpacerPanel(int x, int y) {
+ JPanel spacer = new JPanel(new FlowLayout(FlowLayout.CENTER));
+ spacer.setPreferredSize(new Dimension(x, y));
+ spacer.setBackground(RockhopperGUI.lightBlue);
+ return spacer;
+ }
+
+ public static ImageIcon getScaledImage(String fileName, int x, int y) {
+ return new ImageIcon(new ImageIcon(cl.getResource(fileName)).getImage().getScaledInstance(x,y,java.awt.Image.SCALE_SMOOTH));
+ }
+
+ private void error(String title, String message) {
+ JOptionPane.showMessageDialog(frame, message, title, JOptionPane.ERROR_MESSAGE);
+ }
+
+
+
+ /*************************************
+ ********** MAIN METHOD **********
+ *************************************/
+
+ private static void createAndShowGUI() {
+ RockhopperGUI applet = new RockhopperGUI();
+ //JFrame.setDefaultLookAndFeelDecorated(true);
+ frame = new JFrame("Rockhopper");
+ frame.setSize(800, 750);
+ frame.setResizable(false);
+ frame.setLocationRelativeTo(null);
+ frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
+ frame.setIconImage(new ImageIcon(penguin).getImage());
+ applet.init();
+ frame.add(applet);
+ frame.setVisible(true);
+ }
+
+ public static void main(String[] args) {
+ javax.swing.SwingUtilities.invokeLater(new Runnable() {
+ public void run() { createAndShowGUI();}
+ });
+ }
+
+}
+
+
+
+class IndexedMenuItem extends JMenuItem {
+ public int index;
+ public IndexedMenuItem(String s) { super(s); }
+}
+
diff --git a/SamOps.java b/SamOps.java
new file mode 100644
index 0000000..d3b8a52
--- /dev/null
+++ b/SamOps.java
@@ -0,0 +1,987 @@
+/*
+ * Copyright 2014 Brian Tjaden
+ *
+ * This file is part of Rockhopper.
+ *
+ * Rockhopper is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * any later version.
+ *
+ * Rockhopper is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * (in the file gpl.txt) along with Rockhopper.
+ * If not, see <http://www.gnu.org/licenses/>.
+ */
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Scanner;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.io.FileInputStream;
+import java.util.concurrent.atomic.AtomicInteger;
+import java.util.concurrent.atomic.AtomicLong;
+import java.util.concurrent.atomic.AtomicIntegerArray;
+import java.util.zip.GZIPInputStream;
+import java.lang.reflect.Field;
+
+/**
+ * An instance of the SamOps class supports operations
+ * on SAM/BAM files. It is assumed that a SAM/BAM file contains
+ * information about a single RNA-seq experiment.
+ * Java 7 is required for properly handling BAM files.
+ */
+public class SamOps {
+
+ /********************************************
+ ********** INSTANCE VARIABLES **********
+ ********************************************/
+
+ private String fileName;
+ private boolean isValidSam;
+ private boolean isValidBam;
+ private boolean isPairedEnd;
+ private boolean isDenovo;
+ private HashMap<String, Integer> replicons;
+ private ArrayList<Integer> repliconLengths;
+ public AtomicIntegerArray alignedReads;
+ public AtomicInteger unalignedReads;
+ public AtomicInteger badReads;
+ public AtomicLong avgLengthReads;
+ public AtomicIntegerArray[] coordinates_plus;
+ public AtomicIntegerArray[] coordinates_minus;
+ private int maxQuality;
+ private long pairedEndCount; // Temp counter used when reading in first lines
+ private String qualities; // Temp String used when reading in unaligned reads
+ private int[] cigarMap; // Indexed by ASCII char values {M,I,D,N,S,H,P,=,X}
+ private char[] cigarChars = {'M', 'I', 'D', 'N', 'S', 'H', 'P', '=', 'X'};
+ private static byte[] intBuffer = new byte[4]; // Temp array used for reading bam files
+ private static byte[] buffer1 = new byte[1]; // Temp array used for reading bam files
+ private static char[] NT_code = {'=','A','C','M','G','R','S','V','T','W','Y','H','K','D','B','N'};
+ public static final String[] emptyStringArray = new String[0];
+ private GZIPInputStream in; // Used for reading BAM files
+ public static int maxPairedEndLength = 500;
+
+
+
+ /**************************************
+ ********** CONSTRUCTORS **********
+ **************************************/
+
+ /**
+ * Constructor for reading in a subset of lines in
+ * SAM/BAM file to check if file is valid.
+ */
+ public SamOps(String fileName, long numLines, boolean isDenovo) {
+ this.fileName = fileName;
+ this.replicons = new HashMap<String, Integer>();
+ this.repliconLengths = new ArrayList<Integer>();
+ this.alignedReads = new AtomicIntegerArray(1);
+ this.unalignedReads = new AtomicInteger(0);
+ this.badReads = new AtomicInteger(0);
+ this.avgLengthReads = new AtomicLong(0);
+ this.isPairedEnd = false;
+ this.isDenovo = isDenovo;
+ this.pairedEndCount = 0;
+ this.qualities = "";
+ if (isTextFile(fileName)) this.isValidSam = prepSAM(numLines);
+ else this.isValidBam = prepBAM(numLines);
+ if (isValidSam || isValidBam) {
+ if ((replicons.size() > 0) && (!isDenovo)) {
+ alignedReads = new AtomicIntegerArray(replicons.size());
+ coordinates_plus = new AtomicIntegerArray[replicons.size()];
+ coordinates_minus = new AtomicIntegerArray[replicons.size()];
+ for (int i=0; i<repliconLengths.size(); i++) {
+ coordinates_plus[i] = new AtomicIntegerArray(repliconLengths.get(i)+1);
+ coordinates_minus[i] = new AtomicIntegerArray(repliconLengths.get(i)+1);
+ }
+ } else {
+ coordinates_plus = new AtomicIntegerArray[1];
+ coordinates_minus = new AtomicIntegerArray[1];
+ coordinates_plus[0] = new AtomicIntegerArray(0);
+ coordinates_minus[0] = new AtomicIntegerArray(0);
+ }
+ }
+ }
+
+
+
+ /*************************************************
+ ********** PUBLIC INSTANCE METHODS **********
+ *************************************************/
+
+ /**
+ * Returns true if the first lines of the input SAM
+ * file are valid (correspond to what we are expecting
+ * from a SAM file) and false otherwise.
+ */
+ public boolean isValidSam() {
+ return this.isValidSam;
+ }
+
+ /**
+ * Returns true if the first lines of the input BAM
+ * file are valid (correspond to what we are expecting
+ * from a BAM file) and false otherwise.
+ */
+ public boolean isValidBam() {
+ return this.isValidBam;
+ }
+
+ /**
+ * Returns true if file contains paired end reads.
+ * False otherwise.
+ * Only defined if file is valid.
+ */
+ public boolean isPairedEnd() {
+ return isPairedEnd;
+ }
+
+ /**
+ * Returns the maximum quality score found in the first lines of the file.
+ */
+ public int getMaxQuality() {
+ return maxQuality;
+ }
+
+ /**
+ * Returns the length of the replicon at the specified index.
+ */
+ public int getRepliconLength(int i) {
+ return repliconLengths.get(i);
+ }
+
+ /**
+ * Returns an array of replicon names. The array is ordered
+ * so that the indices in the array are the same as those
+ * for the repliconLengths list.
+ */
+ public String[] getReplicons() {
+ String[] names = new String[replicons.size()];
+ int[] indices = new int[replicons.size()];
+ int i = 0;
+ for (String key : replicons.keySet()) {
+ names[i] = key;
+ indices[i] = replicons.get(key);
+ i++;
+ }
+ mergesort(indices, names, 0, replicons.size()-1);
+ return names;
+ }
+
+ /**
+ * Return a String containing stats/information about this SamOps object.
+ */
+ public String toString() {
+ if (!isValidSam() && !isValidBam()) return "Not a valid SAM/BAM file.\n";
+ StringBuilder sb = new StringBuilder();
+ sb.append("\n");
+ sb.append("Sam/Bam file contains reads mapping to " + replicons.size() + " replicons." + "\n");
+ if (replicons.size() == 0) { // No replicons in SAM/BAM header
+ int final_NT = 0;
+ int repliconIndex = 0;
+ int count_plus = 0;
+ for (int i=0; i<coordinates_plus[repliconIndex].length(); i++) {
+ if (coordinates_plus[repliconIndex].get(i) > 0) {
+ count_plus++;
+ if (i > final_NT) final_NT = i;
+ }
+ }
+ int count_minus = 0;
+ for (int i=0; i<coordinates_minus[repliconIndex].length(); i++) {
+ if (coordinates_minus[repliconIndex].get(i) > 0) {
+ count_minus++;
+ if (i > final_NT) final_NT = i;
+ }
+ }
+ sb.append("\t\tPercent of plus strand covered: \t" + (int)(100.0*count_plus/final_NT) + "%" + "\n");
+ sb.append("\t\tPercent of minus strand covered:\t" + (int)(100.0*count_minus/final_NT) + "%" + "\n");
+ } else { // We have replicons in SAM/BAM header
+ for (String name : replicons.keySet()) {
+ int repliconIndex = replicons.get(name);
+ sb.append("\tReplicon " + name + " with length " + repliconLengths.get(repliconIndex) + "\n");
+ int count = 0;
+ for (int i=0; i<coordinates_plus[repliconIndex].length(); i++) {
+ if (coordinates_plus[repliconIndex].get(i) > 0) count++;
+ }
+ sb.append("\t\tPercent of plus strand covered: \t" + (int)(100.0*count/coordinates_plus[repliconIndex].length()) + "%" + "\n");
+ count = 0;
+ for (int i=0; i<coordinates_minus[repliconIndex].length(); i++) {
+ if (coordinates_minus[repliconIndex].get(i) > 0) count++;
+ }
+ sb.append("\t\tPercent of minus strand covered:\t" + (int)(100.0*count/coordinates_minus[repliconIndex].length()) + "%" + "\n");
+ }
+ }
+ sb.append("\n");
+ sb.append("Bad reads: \t\t" + badReads.get() + "\n");
+ sb.append("Unaligned reads:\t\t" + unalignedReads.get() + "\n");
+ String[] orderedReplicons = getReplicons();
+ for (int i=0; i<orderedReplicons.length; i++)
+ sb.append("Aligned reads in " + orderedReplicons[i] + ": \t" + alignedReads.get(i) + "\n");
+ int count = 0;
+ return sb.toString();
+ }
+
+ /**
+ * Parse one line of alignment information from the SAM file.
+ * Returns empty String array if line should be skipped.
+ * Returns parsed String array with "U" prepended at index 0 if
+ * read is unaligned and alignment should be attempted.
+ * Returns parsed String array with "A" prepended at index 0 if
+ * read has already been aligned.
+ */
+ public String[] parseAlignmentLine_SAM(String line) {
+ try {
+ if (isHeaderLine(line)) return emptyStringArray; // We have a header line
+ String[] parse_line = line.split("\t");
+ //String qname = parse_line[0]; // QNAME
+ int flag = Integer.parseInt(parse_line[1]); // FLAG
+ String rname = parse_line[2]; // RNAME
+ int pos = Integer.parseInt(parse_line[3]); // POS
+ //int mapq = Integer.parseInt(parse_line[4]); // MAPQ
+ //String rnext = parse_line[6]; // RNEXT
+ //int pnext = Integer.parseInt(parse_line[7]); // PNEXT
+ int tlen = Integer.parseInt(parse_line[8]); // TLEN
+ String seq = parse_line[9]; // SEQ
+ String qual = parse_line[10]; // QUAL
+
+ if (flag >= 256) { // Bad or chimeric read
+ badReads.incrementAndGet();
+ return emptyStringArray;
+ } else if ((((flag >>> 2) & 1) == 1) || (rname.equals("*")) || (pos == 0) || (((flag & 1) == 1) && (tlen == 0)) || isDenovo) { // Unaligned read
+ unalignedReads.incrementAndGet();
+ if (seq.equals("*")) return emptyStringArray;
+ if (isDenovo && (((flag >>> 2) & 1) == 0) && (((flag >>> 4) & 1) == 0)) parse_line[9] = reverseComplement(seq);
+ parse_line[0] = "U" + parse_line[0];
+ if (qual.length() == seq.length()) return parse_line;
+ else if (qualities.length() != seq.length()) qualities = new String(new char[seq.length()]).replace('\0', '(');
+ parse_line[10] = qualities;
+ return parse_line;
+ } else if ((flag & 1) == 0) { // Single-end aligned read
+ int length = seq.length();
+ boolean isRevComp = (((flag >>> 4) & 1) == 1);
+ int repliconIndex = 0;
+ if (replicons.containsKey(rname)) repliconIndex = replicons.get(rname);
+ mapReadToCoords(repliconIndex, pos, length, isRevComp);
+ alignedReads.incrementAndGet(repliconIndex);
+ avgLengthReads.addAndGet(length);
+ parse_line[0] = "A" + parse_line[0];
+ return parse_line;
+ } else if (((flag & 1) == 1) && (tlen != 0) && (((flag >>> 6) & 1) == 1) && (((flag >>> 7) & 1) == 0) && (Math.abs(tlen) <= maxPairedEndLength)) { // First of paired-end aligned read
+ boolean isRevComp = (((flag >>> 4) & 1) == 1);
+ int repliconIndex = 0;
+ if (replicons.containsKey(rname)) repliconIndex = replicons.get(rname);
+ mapReadToCoords(repliconIndex, pos, tlen, isRevComp);
+ alignedReads.incrementAndGet(repliconIndex);
+ avgLengthReads.addAndGet(Math.abs(tlen));
+ parse_line[0] = "A" + parse_line[0];
+ return parse_line;
+ } else if (((flag & 1) == 1) && (tlen != 0) && (((flag >>> 6) & 1) == 0) && (((flag >>> 7) & 1) == 1) && (Math.abs(tlen) <= maxPairedEndLength)) { // Second of paired-end aligned read
+ parse_line[0] = "A" + parse_line[0];
+ return parse_line;
+ }
+ return emptyStringArray;
+ } catch (Exception e) {
+ return emptyStringArray;
+ }
+ }
+
+ /**
+ * Parse one line of alignment information from the BAM file.
+ * Return null if there is an error or if we reach the end
+ * of the file.
+ * Returns empty String array if line should be skipped.
+ * Returns parsed String array with "U" prepended at index 0 if
+ * read is unaligned and alignment should be attempted.
+ * Returns parsed String array with "A" prepended at index 0 if
+ * read has already been aligned.
+ */
+ public String[] parseAlignmentLine_BAM() {
+ try {
+ if (this.in == null) {
+ this.in = new GZIPInputStream(new FileInputStream(fileName));
+ disregardHeader_BAM(this.in);
+ }
+ int lengthOfAlignmentSection = readInt(in);
+ int repliconIndex = readInt(in);
+ int pos = readInt(in) + 1;
+ int bin_mq_nl = readInt(in);
+ //int bin = bin_mq_nl >>> 16;
+ int mapq = (bin_mq_nl >>> 8) & 0xFF;
+ int l_read_name = bin_mq_nl & 0xFF;
+ int flag_nc = readInt(in);
+ int flag = flag_nc >>> 16;
+ int numCigarOps = flag_nc & 0xFFFF;
+ int seqLength = readInt(in);
+ int nextRefID = readInt(in);
+ int pnext = readInt(in) + 1;
+ int tlen = readInt(in);
+ String readName = readString(in, l_read_name);
+ String qname = readName.substring(0, readName.length()-1);
+ String cigar = readCigarString(in, numCigarOps);
+ String seq = readSequence(in, seqLength);
+ String qual = readString(in, seqLength);
+ int partialLengthOfAlignmentSection = 8*4 + l_read_name + numCigarOps*4 + ((seqLength+1)/2) + seqLength;
+ String remainder = readString(in, lengthOfAlignmentSection - partialLengthOfAlignmentSection);
+
+ if (flag >= 256) { // Bad or chimeric read
+ badReads.incrementAndGet();
+ return emptyStringArray;
+ } else if ((((flag >>> 2) & 1) == 1) || (repliconIndex < 0) || (pos == 0) || (((flag & 1) == 1) && (tlen == 0)) || isDenovo) { // Unaligned read
+ unalignedReads.incrementAndGet();
+ if (seq.length() <= 1) return emptyStringArray;
+ if (isDenovo && (((flag >>> 2) & 1) == 0) && (((flag >>> 4) & 1) == 0)) seq = reverseComplement(seq);
+ String[] parse_line = new String[11];
+ parse_line[0] = "U" + qname; // QNAME; Sentinel: "unaligned"
+ parse_line[1] = flag + ""; // FLAG
+ parse_line[2] = repliconIndex + ""; // RNAME
+ parse_line[3] = pos + ""; // POS
+ parse_line[4] = mapq + ""; // MAPQ
+ parse_line[5] = cigar; // CIGAR
+ parse_line[6] = nextRefID + ""; // RNEXT
+ parse_line[7] = pnext + ""; // PNEXT
+ parse_line[8] = tlen + ""; // TLEN
+ parse_line[9] = seq; // SEQ
+ parse_line[10] = qual; // QUAL
+ if ((qual.length() == seq.length()) && (qual.indexOf('\t') == -1)) return parse_line;
+ else if (qualities.length() != seq.length()) qualities = new String(new char[seq.length()]).replace('\0', '(');
+ parse_line[10] = qualities;
+ return parse_line;
+ } else if ((flag & 1) == 0) { // Single-end aligned read
+ int length = seq.length();
+ boolean isRevComp = (((flag >>> 4) & 1) == 1);
+ mapReadToCoords(repliconIndex, pos, length, isRevComp);
+ alignedReads.incrementAndGet(repliconIndex);
+ avgLengthReads.addAndGet(length);
+ String[] parse_line = new String[11];
+ parse_line[0] = "A" + qname; // QNAME; Sentinel: "aligned"
+ parse_line[1] = flag + ""; // FLAG
+ parse_line[2] = repliconIndex + ""; // RNAME
+ parse_line[3] = pos + ""; // POS
+ parse_line[4] = mapq + ""; // MAPQ
+ parse_line[5] = cigar; // CIGAR
+ parse_line[6] = nextRefID + ""; // RNEXT
+ parse_line[7] = pnext + ""; // PNEXT
+ parse_line[8] = tlen + ""; // TLEN
+ parse_line[9] = seq; // SEQ
+ parse_line[10] = qual; // QUAL
+ return parse_line;
+ } else if (((flag & 1) == 1) && (tlen != 0) && (((flag >>> 6) & 1) == 1) && (((flag >>> 7) & 1) == 0) && (Math.abs(tlen) <= maxPairedEndLength)) { // First of paired-end aligned read
+ boolean isRevComp = (((flag >>> 4) & 1) == 1);
+ mapReadToCoords(repliconIndex, pos, tlen, isRevComp);
+ alignedReads.incrementAndGet(repliconIndex);
+ avgLengthReads.addAndGet(Math.abs(tlen));
+ String[] parse_line = new String[11];
+ parse_line[0] = "A" + qname; // QNAME; Sentinel: "aligned"
+ parse_line[1] = flag + ""; // FLAG
+ parse_line[2] = repliconIndex + ""; // RNAME
+ parse_line[3] = pos + ""; // POS
+ parse_line[4] = mapq + ""; // MAPQ
+ parse_line[5] = cigar; // CIGAR
+ parse_line[6] = nextRefID + ""; // RNEXT
+ parse_line[7] = pnext + ""; // PNEXT
+ parse_line[8] = tlen + ""; // TLEN
+ parse_line[9] = seq; // SEQ
+ parse_line[10] = qual; // QUAL
+ return parse_line;
+ } else if (((flag & 1) == 1) && (tlen != 0) && (((flag >>> 6) & 1) == 0) && (((flag >>> 7) & 1) == 1) && (Math.abs(tlen) <= maxPairedEndLength)) { // Second of paired-end aligned read
+ String[] parse_line = new String[11];
+ parse_line[0] = "A" + qname; // QNAME; Sentinel: "aligned"
+ parse_line[1] = flag + ""; // FLAG
+ parse_line[2] = repliconIndex + ""; // RNAME
+ parse_line[3] = pos + ""; // POS
+ parse_line[4] = mapq + ""; // MAPQ
+ parse_line[5] = cigar; // CIGAR
+ parse_line[6] = nextRefID + ""; // RNEXT
+ parse_line[7] = pnext + ""; // PNEXT
+ parse_line[8] = tlen + ""; // TLEN
+ parse_line[9] = seq; // SEQ
+ parse_line[10] = qual; // QUAL
+ return parse_line;
+ }
+ return emptyStringArray;
+ } catch (Exception e) {
+ try {
+ if (this.in != null) {
+ in.close();
+ in = null;
+ }
+ } catch (IOException e2) {
+ return null;
+ }
+ return null;
+ }
+ }
+
+
+
+ /**************************************************
+ ********** PRIVATE INSTANCE METHODS **********
+ **************************************************/
+
+ /**
+ * Read in the first lines of the SAM file, extract useful header info,
+ * and check validity.
+ */
+ private boolean prepSAM(long numLines) {
+ cigarMap = new int[91]; // Converts cigar characters to counts
+ File f = new File(fileName);
+ if (!f.exists()) { // File does not exist
+ //output("Error - file " + fileName + " does not exist.\n");
+ return false;
+ }
+ try {
+ Scanner reader = new Scanner(f);
+ long lineCount = (long)0;
+ int totalAlignmentLines = 0; // Total number of non-header lines
+ while (reader.hasNextLine() && (lineCount < numLines)) {
+ String line = reader.nextLine();
+ boolean isValidLine;
+ if (isHeaderLine(line)) isValidLine = parseHeaderLine_SAM(line);
+ else {
+ isValidLine = checkAlignmentLine_SAM(line);
+ totalAlignmentLines++;
+ }
+ if (!isValidLine) {
+ if (pairedEndCount == totalAlignmentLines) isPairedEnd = true;
+ return false;
+ }
+ lineCount++;
+ }
+ reader.close();
+ if (pairedEndCount == totalAlignmentLines) isPairedEnd = true;
+ return true;
+ } catch (FileNotFoundException e) {
+ //output("Error - could not read in from file " + fileName + "\n");
+ return false;
+ }
+ }
+
+ /**
+ * Read in the first lines of the BAM file, extract useful header info,
+ * and check validity.
+ */
+ private boolean prepBAM(long numLines) {
+ File f = new File(fileName);
+ if (!f.exists()) { // File does not exist
+ //output("Error - file " + fileName + " does not exist.\n");
+ return false;
+ }
+ try {
+ this.in = new GZIPInputStream(new FileInputStream(fileName));
+
+ // Read in header info
+ String magicString = readString(in, 4);
+ if (!magicString.substring(0, 3).toLowerCase().equals("bam")) { // Not a bam file
+ in.close();
+ in = null;
+ return false;
+ }
+ int headerTextLength = readInt(in);
+ String samHeaderText = readString(in, headerTextLength);
+ int numRefSeqs = readInt(in);
+ // Read in each replicon (reference sequence) name and length
+ for (int i=0; i<numRefSeqs; i++) {
+ int repliconNameLength = readInt(in);
+ String repliconName = readString(in, repliconNameLength);
+ int repliconLength = readInt(in);
+ replicons.put(repliconName, replicons.size());
+ repliconLengths.add(repliconLength);
+ }
+
+ long lineCount = (long)0;
+ boolean isValidLine = true;
+ while (isValidLine && (lineCount < numLines)) {
+ lineCount++;
+ isValidLine = checkAlignmentLine_BAM();
+ if (!isValidLine) {
+ if (pairedEndCount == lineCount) isPairedEnd = true;
+ in.close();
+ in = null;
+ return false;
+ }
+ }
+ in.close();
+ in = null;
+ if (pairedEndCount == lineCount) isPairedEnd = true;
+ return true;
+ } catch (IOException e) {
+ //output("Error - could not read in from file " + fileName + "\n");
+ try { in.close();
+ } catch (Exception e2) { }
+ in = null;
+ return false;
+ }
+ }
+
+ /**
+ * Read in the entire SAM file.
+ */
+ private boolean readInSAM() {
+ try {
+ File f = new File(fileName);
+ Scanner reader = new Scanner(f);
+ while (reader.hasNextLine()) {
+ parseAlignmentLine_SAM(reader.nextLine());
+ }
+ reader.close();
+ return true;
+ } catch (FileNotFoundException e) {
+ output("Error - could not read in from file " + fileName + "\n");
+ return false;
+ }
+ }
+
+ /**
+ * Read in the entire BAM file.
+ */
+ private void readInBAM() {
+ while (parseAlignmentLine_BAM() != null) { }
+ }
+
+ /**
+ * Parse one line of header information from the SAM file.
+ */
+ private boolean parseHeaderLine_SAM(String line) {
+ try {
+ String[] parse_line = line.split("\t");
+ if (parse_line[0].equals("@HD")) {
+ // Information in header line is currently unused
+ } else if (parse_line[0].equals("@SQ")) {
+ String repliconName = null;
+ Integer repliconLength = null;
+ for (int i=1; i<parse_line.length; i++) {
+ String[] pair = parse_line[i].split(":");
+ String tag = pair[0];
+ String value = pair[1];
+ if (tag.equals("SN")) repliconName = value;
+ if (tag.equals("LN")) repliconLength = Integer.parseInt(value);
+ }
+ if ((repliconName != null) && (repliconLength != null)) {
+ replicons.put(repliconName, replicons.size());
+ repliconLengths.add(repliconLength);
+ } else {
+ //output("Error - reference sequence header line in SAM file is not formatted as expected:\n");
+ //output("\t" + line + "\n\n");
+ return false;
+ }
+ } else if (parse_line[0].equals("@RG")) {
+ // Information in read group line is currently unused
+ } else if (parse_line[0].equals("@PG")) {
+ // Information in program line is currently unused
+ } else if (parse_line[0].equals("@CO")) {
+ // Information in comment line is currently unused
+ } else { // Unrecognized header record type
+ //output("Error - unrecognized SAM record type " + parse_line[0] + " in header line:\n");
+ //output("\t" + line + "\n\n");
+ return false;
+ }
+ return true;
+ } catch (Exception e) {
+ //output("Error - line not in expected SAM format:\n");
+ //output("\t" + line + "\n\n");
+ return false;
+ }
+ }
+
+ /**
+ * Read in and disregard header of BAM file.
+ */
+ private void disregardHeader_BAM(GZIPInputStream in) throws IOException {
+ String magicString = readString(in, 4);
+ int headerTextLength = readInt(in);
+ String samHeaderText = readString(in, headerTextLength);
+ int numRefSeqs = readInt(in);
+
+ // Read in each replicon (reference sequence) name and length
+ for (int i=0; i<numRefSeqs; i++) {
+ int repliconNameLength = readInt(in);
+ String repliconName = readString(in, repliconNameLength);
+ int repliconLength = readInt(in);
+ }
+ }
+
+ /**
+ * Parse one line of alignment information from the SAM file and check its validity.
+ */
+ private boolean checkAlignmentLine_SAM(String line) {
+ try {
+ String[] parse_line = line.split("\t");
+ //String qname = parse_line[0]; // QNAME
+ int flag = Integer.parseInt(parse_line[1]); // FLAG
+ String rname = parse_line[2]; // RNAME
+ int pos = Integer.parseInt(parse_line[3]); // POS
+ //int mapq = Integer.parseInt(parse_line[4]); // MAPQ
+ //String rnext = parse_line[6]; // RNEXT
+ //int pnext = Integer.parseInt(parse_line[7]); // PNEXT
+ int tlen = Integer.parseInt(parse_line[8]); // TLEN
+ String seq = parse_line[9]; // SEQ
+ String qual = parse_line[10]; // QUAL
+ if ((flag & 1) == 1) pairedEndCount++;
+
+ if (flag >= 256) { // Bad or chimeric read
+ // Do nothing
+ } else if ((((flag >>> 2) & 1) == 1) || (rname.equals("*")) || (pos == 0) || (((flag & 1) == 1) && (tlen == 0))) { // Unaligned read
+ if ((!seq.equals("*")) && (!qual.equals("*")) && (seq.length() != qual.length())) {
+ //output("Error - unrecognized format in SAM file - expecting seq length to equal qual length:\n");
+ //output("\t" + line + "\n\n");
+ return false;
+ }
+ } else if ((flag & 1) == 0) { // Single-end aligned read
+ if (!rname.equals("*") && (replicons.size() > 0) && (!replicons.containsKey(rname))) {
+ //output("Error - unrecognized format in SAM file - expecting RNAME to match a SQ-SN tag:\n");
+ //output("\t" + line + "\n\n");
+ return false;
+ }
+ parseCigar(parse_line[5]); // CIGAR
+ int cigarLength = (cigarMap['M'] + cigarMap['I'] + cigarMap['S'] + cigarMap['='] + cigarMap['X']);
+ if (!seq.equals("*") && (seq.length() != cigarLength)) {
+ //output("Error - unrecognized format in SAM file - expecting sequence length to match CIGAR length:\n");
+ //output("\t" + line + "\n\n");
+ return false;
+ }
+ } else if (((flag & 1) == 1) && (tlen > 0) && ((((flag >>> 6) & 1) == 0) || (((flag >>> 7) & 1) == 0))) { // Paired-end aligned read (leftmost mate-pair)
+ if (!rname.equals("*") && (replicons.size() > 0) && (!replicons.containsKey(rname))) {
+ //output("Error - unrecognized format in SAM file - expecting RNAME to match a SQ-SN tag:\n");
+ //output("\t" + line + "\n\n");
+ return false;
+ }
+ }
+ return true;
+ } catch (Exception e) {
+ //output("Error - line not in expected SAM format:\n");
+ //output("\t" + line + "\n\n");
+ return false;
+ }
+ }
+
+ /**
+ * Parse one line of alignment information from the BAM file and check its validity.
+ */
+ private boolean checkAlignmentLine_BAM() {
+ try {
+ int lengthOfAlignmentSection = readInt(in);
+ int repliconIndex = readInt(in);
+ int pos = readInt(in) + 1;
+ int bin_mq_nl = readInt(in);
+ //int bin = bin_mq_nl >>> 16;
+ //int mapq = (bin_mq_nl >>> 8) & 0xFF;
+ int l_read_name = bin_mq_nl & 0xFF;
+ int flag_nc = readInt(in);
+ int flag = flag_nc >>> 16;
+ int numCigarOps = flag_nc & 0xFFFF;
+ int seqLength = readInt(in);
+ int nextRefID = readInt(in);
+ int pnext = readInt(in) + 1;
+ int tlen = readInt(in);
+ String readName = readString(in, l_read_name);
+ //String qname = readName.substring(0, readName.length()-1);
+ for (int i=0; i<numCigarOps; i++) readInt(in); // Ignore CIGAR ops
+ String seq = readSequence(in, seqLength);
+ String qual = readString(in, seqLength);
+ int partialLengthOfAlignmentSection = 8*4 + l_read_name + numCigarOps*4 + ((seqLength+1)/2) + seqLength;
+ String remainder = readString(in, lengthOfAlignmentSection - partialLengthOfAlignmentSection);
+
+ if ((flag & 1) == 1) pairedEndCount++;
+ //this.maxReadLength = Math.max(this.maxReadLength, seq.length());
+ for (int i=0; i<qual.length(); i++)
+ this.maxQuality = Math.max(this.maxQuality, (int)(qual.charAt(i)));
+
+ if (flag >= 256) { // Bad or chimeric read
+ // Do nothing
+ } else if ((((flag >>> 2) & 1) == 1) || (repliconIndex < 0) || (pos == 0) || (((flag & 1) == 1) && (tlen == 0))) { // Unaligned read
+ if ((!seq.equals("*")) && (!qual.equals("*")) && (seq.length() != qual.length())) {
+ //output("Error - unrecognized format in BAM file - expecting seq length to equal qual length:\n");
+ //output("\t" + line + "\n\n");
+ return false;
+ }
+ } else if ((flag & 1) == 0) { // Single-end aligned read
+ if (repliconIndex >= replicons.size()) {
+ //output("Error - unrecognized format in BAM file - expecting valid replicon index:\n");
+ //output("\t" + line + "\n\n");
+ return false;
+ }
+ } else if (((flag & 1) == 1) && (tlen > 0) && ((((flag >>> 6) & 1) == 0) || (((flag >>> 7) & 1) == 0))) { // Paired-end aligned read (leftmost mate-pair)
+ if (repliconIndex >= replicons.size()) {
+ //output("Error - unrecognized format in BAM file - expecting RNAME to match a SQ-SN tag:\n");
+ //output("\t" + line + "\n\n");
+ return false;
+ }
+ }
+ return true;
+ } catch (Exception e) {
+ return false;
+ }
+ }
+
+ /**
+ * Parse a CIGAR string from a SAM file and populate the cigarMap.
+ */
+ private void parseCigar(String s) {
+ for (char ch : cigarChars) cigarMap[ch] = 0; // Initialize cigar map
+ if (s.equals("*")) return;
+ int index = 0;
+ while (index < s.length()) {
+ StringBuilder sb = new StringBuilder();
+ while (Character.isDigit(s.charAt(index))) {
+ sb.append(s.charAt(index));
+ index++;
+ }
+ cigarMap[s.charAt(index)] += Integer.parseInt(sb.toString());
+ index++;
+ }
+ }
+
+ /**
+ * Read in CIGAR information from a BAM file and return the CIGAR string.
+ */
+ private String readCigarString(GZIPInputStream in, int numCigarOps) throws IOException {
+ String cigar = "";
+ for (int i=0; i<numCigarOps; i++) {
+ int bin_cigar_op = readInt(in);
+ int op = bin_cigar_op & 0xF;
+ if (op > 9) return "";
+ int op_len = bin_cigar_op >>> 4;
+ cigar += op_len + "" + cigarChars[op];
+ }
+ return cigar;
+ }
+
+ /**
+ * Map a read to the appropriate loci in the appropriate coords array.
+ */
+ private void mapReadToCoords(int repliconIndex, int pos, int length, boolean isRevComp) {
+ if (length < 0) {
+ pos = pos - length + 1;
+ if (pos < 0) pos = 0;
+ length = -length;
+ }
+ if (coordinates_plus[repliconIndex].length() < (pos+length)) { // Increase size of arrays
+ synchronized (coordinates_plus) {
+ if (coordinates_plus[repliconIndex].length() < (pos+length)) { // Double check if we want to increase size of arrays
+ int new_size = Math.max(pos+length, 2*coordinates_plus[repliconIndex].length());
+ AtomicIntegerArray temp_plus = new AtomicIntegerArray(new_size);
+ AtomicIntegerArray temp_minus = new AtomicIntegerArray(new_size);
+ for (int i=0; i<coordinates_plus[repliconIndex].length(); i++) {
+ temp_plus.set(i, coordinates_plus[repliconIndex].get(i));
+ temp_minus.set(i, coordinates_minus[repliconIndex].get(i));
+ }
+ coordinates_plus[repliconIndex] = temp_plus;
+ coordinates_minus[repliconIndex] = temp_minus;
+ }
+ }
+ }
+ if (!isRevComp) { // Plus strand
+ for (int i=pos; i<pos+length; i++) coordinates_plus[repliconIndex].incrementAndGet(i);
+ } else { // Minus strand
+ for (int i=pos; i<pos+length; i++) coordinates_minus[repliconIndex].incrementAndGet(i);
+ }
+ }
+
+
+
+ /**********************************************
+ ********** PUBLIC CLASS METHODS **********
+ **********************************************/
+
+ /**
+ * Returns true if line is a SAM header line, false otherwise.
+ */
+ public static boolean isHeaderLine(String line) {
+ return line.startsWith("@");
+ }
+
+ /**
+ * Returns true if the file is a text file.
+ * Returns false if the file is a binary file (e.g.,
+ * gzip or bam).
+ */
+ public static boolean isTextFile(String fileName) {
+ try {
+ FileInputStream in = new FileInputStream(new File(fileName));
+ int size = in.available();
+ if (size > 1024) size = 1024;
+ byte[] data = new byte[size];
+ in.read(data);
+ in.close();
+
+ int ascii = 0;
+ int other = 0;
+ for (int i=0; i<data.length; i++) {
+ byte b = data[i];
+ if (b < 0x09) return false;
+ if ((b == 0x09) || (b == 0x0A) || (b == 0x0C) || (b == 0x0D)) ascii++;
+ else if ((b >= 0x20) && (b <= 0x7E)) ascii++;
+ else other++;
+ }
+ return ((100 * ascii / size) > 95);
+ } catch (IOException e) {
+ return false;
+ }
+ }
+
+
+
+ /***********************************************
+ ********** PRIVATE CLASS METHODS **********
+ ***********************************************/
+
+ private static void output(String s) {
+ System.err.print(s);
+ }
+
+ /**
+ * Converts the first four bytes in the specified array into an integer.
+ * Assumes little-endianness.
+ */
+ private static int byteArrayToInt(byte[] b) {
+ if (b.length < 4) return 0;
+ //return (b[0] << 24) + ((b[1] & 0xFF) << 16) + ((b[2] & 0xFF) << 8) + (b[3] & 0xFF);
+ return ((b[3] & 0xFF) << 24) + ((b[2] & 0xFF) << 16) + ((b[1] & 0xFF) << 8) + (b[0] & 0xFF);
+ }
+
+ /**
+ * Reads an integer (little-endian) from a gzip/bam file.
+ */
+ private static int readInt(GZIPInputStream in) throws IOException {
+ in.read(buffer1);
+ intBuffer[0] = buffer1[0];
+ in.read(buffer1);
+ intBuffer[1] = buffer1[0];
+ in.read(buffer1);
+ intBuffer[2] = buffer1[0];
+ in.read(buffer1);
+ intBuffer[3] = buffer1[0];
+ return byteArrayToInt(intBuffer);
+ }
+
+ /**
+ * Reads a String of the specified length from a gzip/bam file.
+ */
+ private static String readString(GZIPInputStream in, int length) throws IOException {
+ byte[] s = new byte[length];
+ for (int i=0; i<length; i++) {
+ in.read(buffer1);
+ s[i] = buffer1[0];
+ }
+ return (new String(s));
+ }
+
+ /**
+ * Reads a nucleotide sequence of the given length from a gzip/bam file.
+ */
+ private static String readSequence(GZIPInputStream in, int length) throws IOException {
+ char[] sequence = new char[length];
+ int NT_index = 15;
+ for (int i=0; i<(length+1)/2; i++) {
+ in.read(buffer1);
+ NT_index = (buffer1[0] >>> 4) & 0xF;
+ sequence[2*i] = NT_code[NT_index];
+ NT_index = buffer1[0] & 0xF;
+ if (2*i+1 < length) sequence[2*i+1] = NT_code[NT_index];
+ }
+ return (new String(sequence));
+ }
+
+ /**
+ * Mergesort parallel arrays "a" and "b" based on values in "a"
+ */
+ private static void mergesort(int[] a, String[] b, int lo, int hi) {
+ if (lo < hi) {
+ int q = (lo+hi)/2;
+ mergesort(a, b, lo, q);
+ mergesort(a, b, q+1, hi);
+ merge(a, b, lo, q, hi);
+ }
+ }
+
+ /**
+ * Mergesort helper method
+ */
+ private static void merge(int[] a, String[] b, int lo, int q, int hi) {
+ int[] a1 = new int[q-lo+1];
+ int[] a2 = new int[hi-q];
+ String[] b1 = new String[q-lo+1];
+ String[] b2 = new String[hi-q];
+ for (int i=0; i<a1.length; i++) {
+ a1[i] = a[lo+i];
+ b1[i] = b[lo+i];
+ }
+ for (int j=0; j<a2.length; j++) {
+ a2[j] = a[q+1+j];
+ b2[j] = b[q+1+j];
+ }
+ int i=0; // Index for first half arrays
+ int j=0; // Index for second half arrays
+ for (int k=lo; k<=hi; k++) {
+ if (i >= a1.length) {
+ a[k] = a2[j];
+ b[k] = b2[j];
+ j++;
+ } else if (j >= a2.length) {
+ a[k] = a1[i];
+ b[k] = b1[i];
+ i++;
+ } else if (a1[i] <= a2[j]) {
+ a[k] = a1[i];
+ b[k] = b1[i];
+ i++;
+ } else {
+ a[k] = a2[j];
+ b[k] = b2[j];
+ j++;
+ }
+ }
+ }
+
+ /**
+ * Returns a reverse complemented version of String s.
+ */
+ private static String reverseComplement(String s) {
+ StringBuilder sb = new StringBuilder(s.length());
+ for (int i=s.length()-1; i>=0; i--) {
+ if (s.charAt(i) == 'A') sb.append('T');
+ else if (s.charAt(i) == 'C') sb.append('G');
+ else if (s.charAt(i) == 'G') sb.append('C');
+ else if (s.charAt(i) == 'T') sb.append('A');
+ else sb.append(s.charAt(i));
+ }
+ return sb.toString();
+ }
+
+
+
+ /*************************************
+ ********** MAIN METHOD **********
+ *************************************/
+
+ public static void main(String[] args) {
+ if (args.length < 1) {
+ System.err.println("\n" + "SamOps requires a SAM/BAM file as a command line argument and it outputs information about the SAM/BAM file." + "\n");
+ System.err.println("\t" + "java SampOps <foo.sam or foo.bam>" + "\n");
+ System.exit(0);
+ }
+ long numLines = 10000;
+ SamOps S = new SamOps(args[0], numLines, false); // Read in first few lines to check validity
+ if (S.isValidSam()) {
+ System.out.println("\n" + "File appears to be in valid SAM format.");
+ System.out.println("Does file contain paired-end reads?\t" + S.isPairedEnd() + "\n");
+ S.readInSAM();
+ System.out.println(S.toString());
+ }
+ if (S.isValidBam()) {
+ System.out.println("\n" + "File appears to be in valid BAM format.");
+ System.out.println("Does file contain paired-end reads?\t" + S.isPairedEnd() + "\n");
+ S.readInBAM();
+ System.out.println(S.toString());
+ }
+ }
+
+}
+
diff --git a/SmoothDistribution.java b/SmoothDistribution.java
new file mode 100644
index 0000000..4b82f88
--- /dev/null
+++ b/SmoothDistribution.java
@@ -0,0 +1,197 @@
+/*
+ * Copyright 2013 Brian Tjaden
+ *
+ * This file is part of Rockhopper.
+ *
+ * Rockhopper is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * any later version.
+ *
+ * Rockhopper is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * (in the file gpl.txt) along with Rockhopper.
+ * If not, see <http://www.gnu.org/licenses/>.
+ */
+
+import java.util.ArrayList;
+import java.util.Collections;
+
+public class SmoothDistribution {
+
+ /********************************************
+ ********** INSTANCE VARIABLES **********
+ ********************************************/
+
+ private ArrayList<Integer> data;
+ private double bandwidth;
+ private int BIN_SIZE;
+ private int minimum;
+ private int maximum;
+ private double pseudocount;
+
+ private ArrayList<Integer> histogram;
+ private ArrayList<Double> histogramNormalized;
+ private ArrayList<Integer> values;
+ private ArrayList<Double> smoothed;
+ private ArrayList<Double> smoothedNormalized;
+
+
+
+ /**************************************
+ ********** CONSTRUCTORS **********
+ **************************************/
+
+ public SmoothDistribution(ArrayList<Integer> data) {
+ this(data, 1.0, 1);
+ }
+
+ public SmoothDistribution(ArrayList<Integer> data, double bandwidth, int BIN_SIZE) {
+ this(data, bandwidth, BIN_SIZE, Collections.min(data), Collections.max(data));
+ }
+
+ public SmoothDistribution(ArrayList<Integer> data, double bandwidth, int BIN_SIZE, int minimum, int maximum) {
+ this.data = data;
+ this.minimum = minimum;
+ this.maximum = maximum;
+ this.bandwidth = bandwidth;
+ this.BIN_SIZE = BIN_SIZE;
+ this.pseudocount = 0.0;
+ generateHistogram();
+ smoothData();
+ normalize();
+ }
+
+
+
+ /*************************************************
+ ********** PUBLIC INSTANCE METHODS **********
+ *************************************************/
+
+ /**
+ * Get smoothed value at point "x".
+ */
+ public double getSmoothedValue(double x) {
+ if (x < this.minimum) return this.pseudocount;
+ if (x > this.maximum) return this.pseudocount;
+ int index = binarySearch(values, x, 0, values.size()-1);
+ // If "x" is not in our discrete distribution, the index may be off by 1.
+ // For example, if our distribution includes 4,5,6,7 and x=5.3, we
+ // may return index 1 (corresponding to 5) or index 2 (corresponding to 6).
+ if (index > 0) {
+ if (Math.abs(x - values.get(index)) > Math.abs(x - values.get(index-1)))
+ return Math.max(smoothedNormalized.get(index-1), this.pseudocount);
+ }
+ if (index < smoothedNormalized.size()-1) {
+ if (Math.abs(x - values.get(index)) > Math.abs(x - values.get(index+1)))
+ return Math.max(smoothedNormalized.get(index+1), this.pseudocount);
+ }
+ return Math.max(smoothedNormalized.get(index), this.pseudocount);
+ }
+
+ /**
+ * Set the pseudocount for this distribution.
+ */
+ public void setPseudocount(double pseudocount) {
+ this.pseudocount = pseudocount;
+ }
+
+ /**
+ * Returns a String representation of this smoothed distribution.
+ */
+ public String toString() {
+ StringBuilder sb = new StringBuilder();
+ sb.append("VALUES" + "\t" + "SMOOTHED" + "\t" + "NORMALIZED" + "\n");
+ for (int i=0; i<smoothedNormalized.size(); i++) {
+ sb.append(values.get(i) + "\t" + histogram.get(i) + "\t" + histogramNormalized.get(i) + "\t" + smoothedNormalized.get(i) + "\n");
+ }
+ return sb.toString();
+ }
+
+
+
+ /**************************************************
+ ********** PRIVATE INSTANCE METHODS **********
+ **************************************************/
+
+ /**
+ * Generate histogram of data.
+ */
+ private void generateHistogram() {
+ this.histogram = new ArrayList<Integer>();
+ this.histogramNormalized = new ArrayList<Double>();
+ for (int i=this.minimum; i<=maximum; i+=BIN_SIZE) {
+ histogram.add(0);
+ histogramNormalized.add(0.0);
+ }
+ for (int i=0; i<data.size(); i++) {
+ if (data.get(i) < minimum) histogram.set(0, histogram.get(0) + 1);
+ else if (data.get(i) > maximum) histogram.set(histogram.size()-1, histogram.get(histogram.size()-1) + 1);
+ else histogram.set((data.get(i)-minimum)/BIN_SIZE, histogram.get((data.get(i)-minimum)/BIN_SIZE) + 1);
+ }
+ for (int i=0; i<histogram.size(); i++) histogramNormalized.set(i, histogram.get(i) / (double)data.size());
+ }
+
+ /**
+ * Generate smooth distibution of data (based on Epanechnikov kernel).
+ */
+ private void smoothData() {
+ values = new ArrayList<Integer>();
+ smoothed = new ArrayList<Double>();
+ int i = this.minimum;
+ while (i <= this.maximum) { // Compute weighted value for index i
+ double sum = 0.0;
+ for (int j=0; j<data.size(); j++) {
+ if (Math.abs(i - data.get(j)) <= this.bandwidth) {
+ double u = (i - data.get(j)) / this.bandwidth;
+ sum += (3.0/4.0) * (1.0 - u*u);
+ }
+ }
+ values.add(i);
+ smoothed.add(sum / (data.size() * this.bandwidth));
+ i += this.BIN_SIZE;
+ }
+ }
+
+ /**
+ * Determine pseudocounts and normalize distribution so it sums to 1.0.
+ */
+ private void normalize() {
+ smoothedNormalized = new ArrayList<Double>();
+ double sum = 0.0;
+ for (int i=0; i<smoothed.size(); i++) sum += smoothed.get(i);
+ double min = Double.MAX_VALUE;
+ for (int i=0; i<smoothed.size(); i++) {
+ double normalizedValue = smoothed.get(i) / sum;
+ smoothedNormalized.add(normalizedValue);
+ if ((normalizedValue > 0) && (normalizedValue < min)) min = normalizedValue;
+ }
+ this.pseudocount = min / 10.0;
+ }
+
+ /**
+ * Perform a binary search for the specified value.
+ */
+ private int binarySearch(ArrayList<Integer> a, double value, int lo, int hi) {
+ if (hi <= lo) return lo;
+ int mid = lo + (hi-lo)/2;
+ if (a.get(mid) > value) return binarySearch(a, value, lo, mid-1);
+ if (a.get(mid) < value) return binarySearch(a, value, mid+1, hi);
+ return mid;
+ }
+
+
+
+ /*************************************
+ ********** MAIN METHOD **********
+ *************************************/
+
+ public static void main(String[] args) {
+ System.err.println("\nThe SmoothDistribution application cannot be executed from the command line. It must be instantiated from another Java application. It takes a set of data and generates a smoothed version of the data distribution based on the Epanechnikov kernel. Smoothing occurs at each point over an interval [-bandwidth,bandwidth]. The BIN_SIZE indicates how big each BIN_SIZE should be.\n");
+ }
+
+}
diff --git a/Table.java b/Table.java
new file mode 100644
index 0000000..70808ae
--- /dev/null
+++ b/Table.java
@@ -0,0 +1,219 @@
+/*
+ * Copyright 2014 Brian Tjaden
+ *
+ * This file is part of Rockhopper.
+ *
+ * Rockhopper is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * any later version.
+ *
+ * Rockhopper is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * (in the file gpl.txt) along with Rockhopper.
+ * If not, see <http://www.gnu.org/licenses/>.
+ */
+
+/**
+ * Hashtable implementation. Uses two parallel arrays.
+ * Uses open addressing for collision resolution.
+ */
+
+import java.util.concurrent.atomic.AtomicIntegerArray;
+import java.util.concurrent.atomic.AtomicLongArray;
+import java.util.concurrent.atomic.AtomicLong;
+import java.util.concurrent.atomic.AtomicInteger;
+
+public class Table {
+
+ public int capacity;
+ private AtomicInteger size = new AtomicInteger(); // Size of table
+ private double loadFactor = 0.90;
+ private AtomicLongArray keys;
+ private AtomicIntegerArray values;
+ private long prime = 16777619;
+ private Long offset = new Long("2166136261");
+ private int hashPower = (int)Math.pow(2, Assembler.k) - 1;
+
+ public Table() {
+ if (Assembler.CAPACITY_POWER == 25) capacity = 30000001;
+ else if (Assembler.CAPACITY_POWER >= 31) capacity = (int)(Math.pow(2, 31) - 7); // Max int
+ else if (Assembler.CAPACITY_POWER % 4 == 0) capacity = (int)(Math.pow(2, Assembler.CAPACITY_POWER) + 1);
+ else capacity = (int)(Math.pow(2, Assembler.CAPACITY_POWER) - 1);
+ keys = new AtomicLongArray(capacity);
+ values = new AtomicIntegerArray(capacity);
+ }
+
+ /**
+ * If "key" is not in table, add it with "value" of 1.
+ * If "key" is in table, increment its "value".
+ */
+ public void add(Long key) {
+ int index = hash(key);
+ while (values.get(index) != 0) {
+ if (keys.get(index) == key.longValue()) {
+ values.incrementAndGet(index);
+ return;
+ }
+ index = (index+1) % capacity;
+ }
+ keys.set(index, key.longValue());
+ values.incrementAndGet(index);
+ size.incrementAndGet();
+ }
+
+ /**
+ * Used for adding strand ambiguous reads.
+ * If "key" is not in table, add it with "value" of 1.
+ * If "key" is in table, increment its "value".
+ */
+ public void add(Long key, Long key_RC) {
+ int index = hash(key);
+ while (values.get(index) != 0) {
+ if (keys.get(index) == key.longValue()) {
+ values.incrementAndGet(index);
+ return;
+ }
+ index = (index+1) % capacity;
+ }
+ int index_RC = hash(key_RC);
+ while (values.get(index_RC) != 0) {
+ if (keys.get(index_RC) == key_RC.longValue()) {
+ values.incrementAndGet(index_RC);
+ return;
+ }
+ index_RC = (index_RC+1) % capacity;
+ }
+ keys.set(index, key.longValue());
+ values.incrementAndGet(index);
+ size.incrementAndGet();
+ }
+
+ public double getLoadFactor() {
+ return (size.get()/(double)capacity);
+ }
+
+ public boolean exceedsLoadFactor() {
+ return ((size.get()/(double)capacity) >= loadFactor);
+ }
+
+ public boolean containsKey(Long key) {
+ int index = hash(key);
+ while (values.get(index) != 0) {
+ if (keys.get(index) == key.longValue()) return true;
+ index = (index+1) % capacity;
+ }
+ return false;
+ }
+
+ public int size() {
+ return size.get();
+ }
+
+ public int get(Long key) {
+ int index = hash(key);
+ while (values.get(index) != 0) {
+ if (keys.get(index) == key.longValue()) return values.get(index);
+ index = (index+1) % capacity;
+ }
+ return -1;
+ }
+
+ public Long getKeyAtIndex(int i) {
+ return (new Long(keys.get(i)));
+ }
+
+ public int getValueAtIndex(int i) {
+ return values.get(i);
+ }
+
+ public void remove(Long key) {
+ int index = hash(key);
+ while (values.get(index) != 0) {
+ if (keys.get(index) == key.longValue()) {
+ keys.set(index, 0);
+ values.set(index, 0);
+ size.decrementAndGet();
+ index = (index+1) % capacity;
+ while (values.get(index) != 0) {
+ // Re-hash
+ int index2 = hash(new Long(keys.get(index)));
+ while ((index2 != index) && (values.get(index2) != 0)) index2 = (index2+1) % capacity;
+ if ((index2 != index) && (values.get(index2) == 0)) {
+ keys.set(index2, keys.get(index));
+ values.set(index2, values.get(index));
+ keys.set(index, 0);
+ values.set(index, 0);
+ }
+ index = (index+1) % capacity;
+ }
+ return;
+ }
+ index = (index+1) % capacity;
+ }
+ }
+
+ private int hash(Long key) {
+
+ // FNV-1a
+ long hash = offset.longValue();
+ long num = key.longValue();
+ for (int i=0; i<2; i++) {
+ hash = hash ^ (num&hashPower);
+ hash *= prime;
+ num = num >>> Assembler.k;
+ }
+ int result = (int)(hash) % capacity;
+ if (result < 0) result += capacity;
+ return result;
+ }
+
+ /*
+ private synchronized void rehash() {
+ double REHASH_FACTOR = 1.5;
+ if (!exceedsLoadFactor()) return; // Another thread already rehashed
+ int capacity2 = (int)(REHASH_FACTOR*capacity + 1.0);
+ AtomicLongArray keys2 = new AtomicLongArray(capacity2);
+ AtomicIntegerArray values2 = new AtomicIntegerArray(capacity2);
+ for (int i=0; i<capacity; i++) {
+ if (values.get(i) != 0) {
+ //int i2 = (new Long(keys.get(i))).hashCode() % capacity2;
+ //if (i2 < 0) i2 += capacity2;
+ int i2 = hash(new Long(keys.get(i)));
+ while (values2.get(i2) != 0) i2 = (i2+1) % capacity2;
+ keys2.set(i2, keys.get(i));
+ values2.set(i2, values.get(i));
+ }
+ }
+ capacity = capacity2;
+ keys = keys2;
+ values = values2;
+ System.gc();
+ }
+ */
+
+ public static void main(String[] args) {
+
+ Table t = new Table();
+ t.add(new Long(40));
+ t.add(new Long(0));
+ t.add(new Long(10));
+ t.add(new Long(40));
+ t.add(new Long(21));
+ t.add(new Long(30));
+ t.add(new Long(30));
+ t.add(new Long(40));
+ t.add(new Long(30));
+ t.add(new Long(21));
+ t.add(new Long(40));
+ t.remove(new Long(30));
+
+ for (int i=0; i<t.capacity; i++) System.out.println(t.keys.get(i) + "\t" + t.values.get(i));
+ }
+
+}
+
diff --git a/Transcripts.java b/Transcripts.java
new file mode 100644
index 0000000..bfc3715
--- /dev/null
+++ b/Transcripts.java
@@ -0,0 +1,1005 @@
+/*
+ * Copyright 2013 Brian Tjaden
+ *
+ * This file is part of Rockhopper.
+ *
+ * Rockhopper is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * any later version.
+ *
+ * Rockhopper is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * (in the file gpl.txt) along with Rockhopper.
+ * If not, see <http://www.gnu.org/licenses/>.
+ */
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.io.File;
+import java.io.PrintWriter;
+import java.io.FileNotFoundException;
+
+/**
+ * The Transcript class identifies UTRs of genes as well
+ * ncRNA transcripts based on RNA-seq data.
+ */
+public class Transcripts {
+
+ /*****************************************
+ ********** CLASS VARIABLES **********
+ *****************************************/
+
+ //private static int WINDOW = 10; // Number of nucleotides in sliding window
+
+
+
+ /********************************************
+ ********** INSTANCE VARIABLES **********
+ ********************************************/
+
+ private Genome genome;
+ private int z; // Index of genome in list of all genomes
+ private ArrayList<Condition> conditions;
+ private boolean unstranded; // Is RNA-seq data strand specific or ambiguous?
+ private int num5UTRs = 0; // Number of 5'UTRs
+ private int num3UTRs = 0; // Number of 3'UTRs
+ private int numSenseRNAs = 0; // Number of sense ncRNAs
+ private int numAntisenseRNAs = 0; // Number of antisense ncRNAs
+ //public long[] distribution = new long[201]; // Distribution of expressed gene reads
+
+
+
+ /**************************************
+ ********** CONSTRUCTORS **********
+ **************************************/
+
+ public Transcripts(int z, Genome genome, ArrayList<Condition> conditions, boolean unstranded) {
+ this.z = z;
+ this.genome = genome;
+ this.conditions = conditions;
+ this.unstranded = unstranded;
+ }
+
+
+
+ /*************************************************
+ ********** PUBLIC INSTANCE METHODS **********
+ *************************************************/
+
+ /**
+ * Returns the number of 5'UTRs.
+ */
+ public int getNum5UTRs() {
+ return this.num5UTRs;
+ }
+
+ /**
+ * Returns the number of 3'UTRs.
+ */
+ public int getNum3UTRs() {
+ return this.num3UTRs;
+ }
+
+ /**
+ * Returns the number of sense ncRNAs.
+ */
+ public int getNumSenseRNAs() {
+ return this.numSenseRNAs;
+ }
+
+ /**
+ * Returns the number of antisense ncRNAs.
+ */
+ public int getNumAntisenseRNAs() {
+ return this.numAntisenseRNAs;
+ }
+
+ /**
+ * For each gene, identify its 5'UTR and 3'UTR based on
+ * the expression data.
+ */
+ public void identifyUTRs() {
+ for (int x=0; x<genome.numGenes()+1; x++) { // For each IG region
+ Gene g1 = null;
+ Gene g2 = null;
+
+ // Identify downstream gene and IG stop coordinate
+ if (x == genome.numGenes()) g2 = new Gene((genome.size()-1) + ".." + (genome.size()-1) + "\t" + genome.getGene(x-1).getStrand() + "\t" + "0" + "\t" + "-" + "\t" + "???" + "\t" + "???" + "\t" + "-" + "\t" + "-" + "\t" + "???", "ORF");
+ else g2 = genome.getGene(x);
+ int stop = Math.min(g2.getStart(), g2.getStop()) - 1;
+ if (!g2.isORF()) stop = g2.getMinCoordinate() - 1;
+
+ // Identify upstream gene and IG start coordinate
+ int start = 1;
+ int upstreamGeneIndex = x-1;
+ while (upstreamGeneIndex >= 0) {
+ if (unstranded) { // Strand ambiguous
+ start = Math.max(genome.getGene(upstreamGeneIndex).getStart(), genome.getGene(upstreamGeneIndex).getStop()) + 1;
+ if (!genome.getGene(upstreamGeneIndex).isORF()) start = genome.getGene(upstreamGeneIndex).getMaxCoordinate() + 1;
+ break;
+ } else { // Strand specific
+ if (g2.getStrand() == genome.getGene(upstreamGeneIndex).getStrand()) {
+ start = Math.max(genome.getGene(upstreamGeneIndex).getStart(), genome.getGene(upstreamGeneIndex).getStop()) + 1;
+ if (!genome.getGene(upstreamGeneIndex).isORF()) start = genome.getGene(upstreamGeneIndex).getMaxCoordinate() + 1;
+ break;
+ }
+ upstreamGeneIndex--;
+ }
+ }
+ if (upstreamGeneIndex < 0) g1 = new Gene(1 + ".." + 1 + "\t" + g2.getStrand() + "\t" + "0" + "\t" + "-" + "\t" + "???" + "\t" + "???" + "\t" + "-" + "\t" + "-" + "\t" + "???", "ORF");
+ else g1 = genome.getGene(upstreamGeneIndex);
+
+ int IG_length = stop - start + 1;
+ if (IG_length <= 0) continue; // No action necessary if there is no IG region.
+
+ int frontUTR_length_merged = -1;
+ int backUTR_length_merged = -1;
+ for (int i=0; i<conditions.size(); i++) {
+ for (int j=0; j<conditions.get(i).numReplicates(); j++) {
+
+ Replicate r = conditions.get(i).getReplicate(j);
+
+ // Get UTR lengths
+ int frontUTR_length = getUTR_length(g1, start, stop, r, true);
+ int backUTR_length = getUTR_length(g2, start, stop, r, false);
+
+ // Distinguish overlapping UTRs
+ if ((frontUTR_length > 0) && (backUTR_length > 0) &&
+ (Math.max(g1.getStart(), g1.getStop()) + frontUTR_length >= Math.min(g2.getStart(), g2.getStop()) - backUTR_length)) {
+
+ // Determine mean of genes' expression
+ double mean1 = r.getMeanOfRange(z, g1.getStart(), g1.getStop(), g1.getStrand());
+ double mean2 = r.getMeanOfRange(z, g2.getStart(), g2.getStop(), g2.getStrand());
+ if (unstranded) {
+ mean1 = r.getMeanOfRange(z, g1.getStart(), g1.getStop(), '?');
+ mean2 = r.getMeanOfRange(z, g2.getStart(), g2.getStop(), '?');
+ }
+
+ int overlapStart = Math.min(g2.getStart(), g2.getStop()) - backUTR_length;
+ int overlapStop = Math.max(g1.getStart(), g1.getStop()) + frontUTR_length;
+ //while ((overlapStart < Math.min(g2.getStart(), g2.getStop())) && (getPoissonPDF(r.getReads(overlapStart, g1.getStrand()), mean1) > getPoissonPDF(r.getReads(overlapStart, g2.getStrand()), mean2))) overlapStart++;
+ if (!unstranded) { // Strand specific
+ while ((overlapStart <= overlapStop) && (Math.abs(r.getReads(z, overlapStart, g1.getStrand()) - mean1) < Math.abs(r.getReads(z, overlapStart, g2.getStrand()) - mean2))) overlapStart++;
+ //while ((overlapStop > Math.max(g1.getStart(), g1.getStop())) && (getPoissonPDF(r.getReads(overlapStop, g1.getStrand()), mean1) < getPoissonPDF(r.getReads(overlapStop, g2.getStrand()), mean2))) overlapStop--;
+ while ((overlapStop >= overlapStart) && (Math.abs(r.getReads(z, overlapStop, g1.getStrand()) - mean1) > Math.abs(r.getReads(z, overlapStop, g2.getStrand()) - mean2))) overlapStop--;
+ } else { // Strand ambiguous
+ while ((overlapStart <= overlapStop) && (Math.abs(r.getReads(z, overlapStart, '?') - mean1) < Math.abs(r.getReads(z, overlapStart, '?') - mean2))) overlapStart++;
+ while ((overlapStop >= overlapStart) && (Math.abs(r.getReads(z, overlapStop, '?') - mean1) > Math.abs(r.getReads(z, overlapStop, '?') - mean2))) overlapStop--;
+ }
+ if (overlapStop - overlapStart < -1)
+ Rockhopper.output("Error - overlapping UTR region has invalid size.\n");
+ else if (overlapStop - overlapStart == -1) {
+ // Do nothing. There is no overlap.
+ } else { // We still have overlapping UTR regions
+ double mean_of_overlap = r.getMeanOfRange(z, overlapStart, overlapStop, g1.getStrand());
+ if (unstranded) mean_of_overlap = r.getMeanOfRange(z, overlapStart, overlapStop, '?');
+ if (Math.abs(mean_of_overlap - mean1) <= Math.abs(mean_of_overlap - mean2))
+ overlapStart = overlapStop + 1;
+ else overlapStop = overlapStart - 1;
+ //double prob1 = 1.0;
+ //double prob2 = 1.0;
+ //for (int y=overlapStart; y<=overlapStop; y++) {
+ //prob1 *= getPoissonPDF(r.getReads(y, g1.getStrand()), mean1);
+ //prob2 *= getPoissonPDF(r.getReads(y, g2.getStrand()), mean2);
+ //}
+ //if (prob1 >= prob2) overlapStart = overlapStop + 1;
+ //else overlapStop = overlapStart - 1;
+ }
+ frontUTR_length = overlapStart - (Math.max(g1.getStart(), g1.getStop()) + 1);
+ backUTR_length = Math.min(g2.getStart(), g2.getStop()) - 1 - overlapStop;
+ }
+
+ // Merge UTRs from different experiments
+ //frontUTR_length_merged = Math.max(frontUTR_length_merged, frontUTR_length);
+ if (frontUTR_length_merged == -1) frontUTR_length_merged = frontUTR_length;
+ else if (frontUTR_length_merged == 0) frontUTR_length_merged = Math.max(frontUTR_length_merged, frontUTR_length);
+ else frontUTR_length_merged = Math.min(frontUTR_length_merged, frontUTR_length);
+ //backUTR_length_merged = Math.max(backUTR_length_merged, backUTR_length);
+ if (backUTR_length_merged == -1) backUTR_length_merged = backUTR_length;
+ else if (backUTR_length_merged == 0) backUTR_length_merged = Math.max(backUTR_length_merged, backUTR_length);
+ else backUTR_length_merged = Math.min(backUTR_length_merged, backUTR_length);
+ }
+ }
+
+ // Update transcription start/stop of genes (if genes are expressed)
+ if (frontUTR_length_merged >= 0) { // Gene is expressed and has flanking IG region
+ if (g1.getStrand() == '+') g1.setStopT(g1.getStop() + frontUTR_length_merged);
+ if (g1.getStrand() == '-') g1.setStartT(g1.getStart() + frontUTR_length_merged);
+ }
+ if (backUTR_length_merged >= 0) { // Gene is expressed and has flanking IG region
+ if (g2.getStrand() == '+') g2.setStartT(g2.getStart() - backUTR_length_merged);
+ if (g2.getStrand() == '-') g2.setStopT(g2.getStop() - backUTR_length_merged);
+ }
+ }
+
+ // Keep track of the number of 5'UTRs and 3'UTRs
+ for (int x=0; x<genome.numGenes(); x++) {
+ Gene g = genome.getGene(x);
+ if (g.isORF() && (g.getStartT() > 0) && (g.getStrand() == '+') && (g.getStart()-g.getStartT() > 0))
+ num5UTRs++;
+ if (g.isORF() && (g.getStartT() > 0) && (g.getStrand() == '-') && (g.getStartT()-g.getStart() > 0))
+ num5UTRs++;
+ if (g.isORF() && (g.getStopT() > 0) && (g.getStrand() == '+') && (g.getStopT()-g.getStop() > 0))
+ num3UTRs++;
+ if (g.isORF() && (g.getStopT() > 0) && (g.getStrand() == '-') && (g.getStop()-g.getStopT() > 0))
+ num3UTRs++;
+ }
+ }
+
+ /**
+ * For each IG, identify ncRNAs based on
+ * the expression data.
+ */
+ public void identifyRNAs() {
+
+ // Generate coordinate map of genes
+ String[] genesPlus = new String[genome.size()+1];
+ String[] genesMinus = new String[genome.size()+1];
+ for (int i=0; i<genesPlus.length; i++) {
+ genesPlus[i] = "";
+ genesMinus[i] = "";
+ }
+ for (int i=0; i<genome.numGenes(); i++) {
+ Gene g = genome.getGene(i);
+ int geneStart = Math.min(g.getStart(), g.getStop());
+ int geneStop = Math.max(g.getStart(), g.getStop());
+ if (!g.isORF()) {
+ geneStart = g.getMinCoordinate();
+ geneStop = g.getMaxCoordinate();
+ }
+ String[] genes = genesPlus; // Plus strand
+ if (g.getStrand() == '-') genes = genesMinus; // Minus strand
+ for (int j=geneStart; j<=geneStop; j++) genes[j] = g.getName();
+ }
+
+ ArrayList<Gene> rnaGenes = new ArrayList<Gene>(); // List of new predicted RNAs
+ for (int x=0; x<genome.numGenes()+1; x++) { // For each IG region
+ Gene g1 = null;
+ Gene g2 = null;
+
+ // Identify downstream gene and IG stop coordinate
+ if (x == genome.numGenes()) g2 = new Gene((genome.size()-1) + ".." + (genome.size()-1) + "\t" + genome.getGene(x-1).getStrand() + "\t" + "0" + "\t" + "-" + "\t" + "???" + "\t" + "???" + "\t" + "-" + "\t" + "-" + "\t" + "???", "ORF");
+ else g2 = genome.getGene(x);
+ if (!g2.isORF()) continue; // Do not predict novel ncRNAs near known RNA genes
+ int stop = g2.getMinCoordinate() - 1;
+
+ // Identify upstream gene and IG start coordinate
+ int start = 1;
+ int upstreamGeneIndex = x-1;
+ while (upstreamGeneIndex >= 0) {
+ if (unstranded) { // Strand ambiguous
+ start = genome.getGene(upstreamGeneIndex).getMaxCoordinate() + 1;
+ break;
+ } else { // Strand specific
+ if (g2.getStrand() == genome.getGene(upstreamGeneIndex).getStrand()) {
+ start = genome.getGene(upstreamGeneIndex).getMaxCoordinate() + 1;
+ break;
+ }
+ upstreamGeneIndex--;
+ }
+ }
+ if (upstreamGeneIndex < 0) g1 = new Gene(1 + ".." + 1 + "\t" + g2.getStrand() + "\t" + "0" + "\t" + "-" + "\t" + "???" + "\t" + "???" + "\t" + "-" + "\t" + "-" + "\t" + "???", "ORF");
+ else g1 = genome.getGene(upstreamGeneIndex);
+ if (!g1.isORF()) continue; // Do not predict novel ncRNAs near known RNA genes
+
+ // Determine strand
+ char strand = '?';
+ if (unstranded) strand = '?'; // Strand ambiguous
+ else if ((g1.getStrand() == '+') || (g2.getStrand() == '+')) strand = '+'; // Plus strand
+ else if ((g1.getStrand() == '-') || (g2.getStrand() == '-')) strand = '-'; // Minus strand
+ else strand = '?';
+
+ // No action necessary if there is no IG region.
+ if (stop - start + 1 <= 0) {
+ //output_IG_to_file(g1, g2, strand, new ArrayList<RNA>(), "IGs/Strep/");
+ continue;
+ }
+
+ ArrayList<RNA> rnas = new ArrayList<RNA>();
+ for (int i=0; i<conditions.size(); i++) {
+ for (int j=0; j<conditions.get(i).numReplicates(); j++) {
+ // Find novel transcripts on both strands separately
+ identifyNovelTranscriptsInIG(rnas, conditions.get(i).getReplicate(j), start, stop, strand);
+ }
+ }
+
+ // Merge novel RNA transcripts (from different experiments and nearby novel RNAs)
+ ArrayList<RNA> merged_RNAs = new ArrayList<RNA>();
+ if (unstranded) { // Strand ambiguous
+ merge_RNAs(g1, g2, '?', rnas, merged_RNAs);
+ } else { // Strand specific
+ merge_RNAs(g1, g2, '+', rnas, merged_RNAs);
+ merge_RNAs(g1, g2, '-', rnas, merged_RNAs);
+ }
+ //output_IG_to_file(g1, g2, strand, merged_RNAs, "IGs/Strep/");
+
+ /*
+ if (merged_RNAs.size() > 0) {
+ int IG_start = Math.max(g1.getStart(), g1.getStop()) + 1;
+ int IG_stop = Math.min(g2.getStart(), g2.getStop()) - 1;
+ if (!g1.isORF()) IG_start = g1.getMaxCoordinate() + 1;
+ if (!g2.isORF()) IG_stop = g2.getMinCoordinate() - 1;
+ Rockhopper.output(IG_start + "_" + IG_stop + "\t" + g1.getName() + "\t" + g1.getStrand() + "\t" + g2.getName() + "\t" + g2.getStrand() + "\t" + rnas.size() + "\t" + merged_RNAs.size() + "\n");
+ }
+ */
+
+ // Convert RNAs to Genes
+ for (int i=0; i<merged_RNAs.size(); i++) {
+ String product = getAntisenseAnnotation(merged_RNAs.get(i), genesPlus, genesMinus);
+ if (product.indexOf("antisense") >= 0) this.numAntisenseRNAs++;
+ rnaGenes.add(new Gene(merged_RNAs.get(i).start + ".." + merged_RNAs.get(i).stop + "\t" + merged_RNAs.get(i).strand + "\t" + "0" + "\t" + "-" + "\t" + "-" + "\t" + "predicted RNA" + "\t" + "-" + "\t" + "-" + "\t" + getAntisenseAnnotation(merged_RNAs.get(i), genesPlus, genesMinus), "RNA"));
+ }
+ }
+ this.numSenseRNAs = rnaGenes.size() - this.numAntisenseRNAs;
+
+ // Compute expression of each predicted RNA
+ for (int i=0; i<rnaGenes.size(); i++) {
+ Gene g = rnaGenes.get(i);
+ for (int j=0; j<conditions.size(); j++) {
+ for (int k=0; k<conditions.get(j).numReplicates(); k++) {
+ Replicate r = conditions.get(j).getReplicate(k);
+ long readsForGene = r.getReadsInRange(z, g.getMinCoordinate(), g.getMaxCoordinate(), g.getStrand());
+ g.setRawCount(j, k, readsForGene); // Set raw counts for gene
+ if (r.getAvgLengthReads() == 0) g.setRawCount_reads(j, k, 0);
+ else g.setRawCount_reads(j, k, readsForGene/r.getAvgLengthReads());
+ //g.setNormalizedCount(j, k, Condition.getAvgUpperQuartile(), r.getUpperQuartile());
+ g.setNormalizedCount(j, k, 100000.0, r.getUpperQuartile());
+ }
+ }
+
+ // Compute mean and RPKM for each gene in each condition
+ g.computeExpression(conditions);
+
+ // Compute variance for each gene in each condition
+ g.computeVariance(conditions);
+ }
+
+ // Add transcripts to list of genes
+ genome.addPredictedRNAs(rnaGenes);
+ }
+
+
+
+ /**************************************************
+ ********** PRIVATE INSTANCE METHODS **********
+ **************************************************/
+
+ private int getUTR_length(Gene g, int start, int stop, Replicate r, boolean isFront) {
+
+ // If we do not have a real gene but merely a place holder, do not compute UTR.
+ if (g.getStart() == g.getStop()) return -1;
+
+ // If we have an RNA gene rather than an ORF, do not compute UTR.
+ if (!g.isORF()) return -1;
+
+ // Determine strand
+ char strand = g.getStrand();
+ if (unstranded) strand = '?';
+
+ // Determine mean of gene's expression
+ double mean = r.getMeanOfRange(z, g.getStart(), g.getStop(), strand);
+ if (mean < r.getMinExpressionUTR()) return -1; // Gene is not expressed
+
+ // Compute expression distribution
+ /*
+ double thresh = 1.0;
+ if (mean >= thresh * r.getMinExpressionUTR()) {
+ int start2 = g.getStart();
+ int stop2 = g.getStop();
+ if (stop2 < start2) { // Swap
+ int temp = start2;
+ start2 = stop2;
+ stop2 = temp;
+ }
+ for (int i=start2; i<=stop2; i++) {
+ int x = (int)Math.round(20000*((r.getMeanOfRange(z, i, i, strand) - mean) / stdev));
+ if (Math.abs(x) >= distribution.length/2) x = (distribution.length/2)*(x/Math.abs(x));
+ distribution[x+distribution.length/2]++;
+ }
+ }
+ */
+
+ //int[] IG = new int[stop-start+1+WINDOW];
+ //if (isFront) { // Front UTR
+ // for (int i=start-WINDOW/2; i<=Math.min(stop+WINDOW/2, genome.size()-1); i++) IG[i-start+WINDOW/2] = r.getReads(i, g.getStrand());
+ //} else { // Back UTR
+ // for (int i=stop+WINDOW/2; i>=Math.max(start-WINDOW/2,1); i--) IG[stop+WINDOW/2-i] = r.getReads(i, g.getStrand());
+ //}
+ int[] IG = new int[stop-start+1];
+ if (isFront) { // Front UTR
+ for (int i=start; i<=Math.min(stop, genome.size()-1); i++) IG[i-start] = r.getReads(z, i, strand);
+ } else { // Back UTR
+ for (int i=stop; i>=Math.max(start, 1); i--) IG[stop-i] = r.getReads(z, i, strand);
+ }
+
+ //for (int i=0; i<IG.length-WINDOW; i++) {
+ for (int i=0; i<IG.length; i++) {
+
+ double SCALE = 1.5;
+ if (IG[i] == 0) return i;
+ if (IG[i] >= SCALE*mean) continue;
+ if (IG[i] >= SCALE*r.getMinExpressionUTR()) continue;
+ if (SCALE*r.getBackgroundProb(IG[i]) > getPoissonPDF(IG[i], mean)) return i;
+ else continue;
+ /*
+ // Quick check to see if we can easily classify the window as IG or UTR
+ int numZeros = 0;
+ int numExpressed = 0;
+ for (int j=i; j<i+WINDOW; j++) {
+ if (IG[j] == 0) numZeros++;
+ if (IG[j] >= mean) numExpressed++;
+ }
+ if (numZeros >= WINDOW/2) return i;
+ if (numExpressed >= WINDOW/2) continue;
+
+ // More extensive check if probability is closer to IG or UTR
+ double probIG = 1.0;
+ double probUTR = 1.0;
+ for (int j=i; j<i+WINDOW; j++) {
+ probIG *= r.getBackgroundProb(IG[j]);
+ probUTR *= getPoissonPDF(IG[j], mean);
+ }
+ if (probIG >= probUTR) return i;
+ */
+ }
+ //return IG.length-WINDOW;
+ return IG.length;
+ }
+
+ /**
+ * For a given IG region, identifies novel transcripts on the specified strand.
+ * Each novel transcript is added to the list of "rnas".
+ */
+ private void identifyNovelTranscriptsInIG(ArrayList<RNA> rnas, Replicate r, int start, int stop, char strand) {
+
+ // Search for a transcript seed, i.e., n consecutive nucleotides above some threshold.
+ // Then we extend this seed in both directions.
+ //int n = WINDOW/2;
+ double THRESHOLD = r.getMinExpressionRNA() * 2.0;
+ int MIN_RNA_LENGTH = 10;
+
+ //int[] IG = new int[stop-start+1+WINDOW];
+ //int startReadsForIG = Math.max(start-WINDOW/2, 1);
+ //for (int i=startReadsForIG; i<=Math.min(stop+WINDOW/2, genome.size()-1); i++) IG[i-startReadsForIG] = r.getReads(i, strand);
+ int[] IG = new int[stop-start+1];
+ int startReadsForIG = Math.max(start, 1);
+ for (int i=startReadsForIG; i<=Math.min(stop, genome.size()-1); i++) IG[i-startReadsForIG] = r.getReads(z, i, strand);
+
+ //int i = WINDOW/2;
+ int i = 0;
+ int startT = -1;
+ int stopT = -1;
+ //while (i < IG.length-WINDOW-n+1) {
+ while (i < IG.length) {
+ if ((IG[i] >= THRESHOLD) && (startT == -1)) { // Start of new possible seed
+ startT = i;
+ stopT = i;
+ } else if ((IG[i] >= THRESHOLD) && (startT >= 0)) { // Within possible seed
+ stopT = i;
+ } else if ((IG[i] < THRESHOLD) && (startT == -1)) { // Within non-seed
+ // Do nothing
+ } else if ((IG[i] < THRESHOLD) && (startT >= 0)) { // Just ended possible seed
+ //if (stopT - startT + 1 >= n) { // We have a seed
+ if (stopT - startT + 1 >= MIN_RNA_LENGTH) { // We have a seed
+
+ // Extend the seed downstream
+ //boolean done = (stopT == IG.length-WINDOW);
+ boolean done = (stopT == IG.length-1);
+ while (!done) {
+ double mean = r.getMeanOfRange(z, startT, stopT, strand);
+ if (mean < THRESHOLD) break;
+
+ if ((IG[stopT+1] >= THRESHOLD) || (r.getBackgroundProb(IG[stopT+1]) <= getPoissonPDF(IG[stopT+1], mean))) stopT++;
+ else break;
+ done = (stopT == IG.length-1);
+ /*
+ double probIG = 1.0;
+ double probRNA = 1.0;
+ for (int j=stopT+1-WINDOW/2+1; j<Math.min(stopT+1+WINDOW/2+1,IG.length); j++) {
+ probIG *= r.getBackgroundProb(IG[j]);
+ probRNA *= getPoissonPDF(IG[j], mean);
+ }
+ if (probIG >= probRNA) break;
+ stopT++;
+ if (stopT == IG.length-1-WINDOW) done = true;
+ */
+ }
+
+ // Extend the seed upstream
+ //done = (startT == WINDOW/2);
+ done = (startT == 0);
+ while (!done) {
+ double mean = r.getMeanOfRange(z, startT, stopT, strand);
+ if (mean < THRESHOLD) break;
+
+ if ((IG[startT-1] >= THRESHOLD) || (r.getBackgroundProb(IG[startT-1]) <= getPoissonPDF(IG[startT-1], mean))) startT--;
+ else break;
+ done = (startT == 0);
+ /*
+ double probIG = 1.0;
+ double probRNA = 1.0;
+ for (int j=startT-1+WINDOW/2-1; j>Math.max(startT-1-WINDOW/2-1,-1); j--) {
+ probIG *= r.getBackgroundProb(IG[j]);
+ probRNA *= getPoissonPDF(IG[j], mean);
+ }
+ if (probIG >= probRNA) break;
+ startT--;
+ if (startT == WINDOW/2) done = true;
+ */
+ }
+
+ // Add transcript to list
+ rnas.add(new RNA(start + startT, start + stopT, strand));
+
+ i = stopT;
+ startT = -1;
+ } else { // Seed is too short, so it is not a seed.
+ startT = -1;
+ }
+ } else {
+ // Impossible to reach this case.
+ }
+ i++;
+ }
+
+ // Handle case where seed extends all the way to end of IG region
+ if (startT >= 0) { // Ended possible seed
+ //if (stopT - startT + 1 >= n) { // We have a seed
+ if (stopT - startT + 1 >= MIN_RNA_LENGTH) { // We have a seed
+
+ // Extend the seed downstream
+ //boolean done = (stopT == IG.length-WINDOW);
+ boolean done = (stopT == IG.length-1);
+ while (!done) {
+ double mean = r.getMeanOfRange(z, startT, stopT, strand);
+ if (mean < THRESHOLD) break;
+
+ if ((IG[stopT+1] >= THRESHOLD) || (r.getBackgroundProb(IG[stopT+1]) <= getPoissonPDF(IG[stopT+1], mean))) stopT++;
+ else break;
+ done = (stopT == IG.length-1);
+ /*
+ double probIG = 1.0;
+ double probRNA = 1.0;
+ for (int j=stopT+1-WINDOW/2+1; j<Math.min(stopT+1+WINDOW/2+1,IG.length); j++) {
+ probIG *= r.getBackgroundProb(IG[j]);
+ probRNA *= getPoissonPDF(IG[j], mean);
+ }
+ if (probIG >= probRNA) break;
+ stopT++;
+ if (stopT == IG.length-1-WINDOW) done = true;
+ */
+ }
+
+ // Extend the seed upstream
+ //done = (startT == WINDOW/2);
+ done = (startT == 0);
+ while (!done) {
+ double mean = r.getMeanOfRange(z, startT, stopT, strand);
+ if (mean < THRESHOLD) break;
+
+ if ((IG[startT-1] >= THRESHOLD) || (r.getBackgroundProb(IG[startT-1]) <= getPoissonPDF(IG[startT-1], mean))) startT--;
+ else break;
+ done = (startT == 0);
+ /*
+ double probIG = 1.0;
+ double probRNA = 1.0;
+ for (int j=startT-1+WINDOW/2-1; j>Math.max(startT-1-WINDOW/2-1,-1); j--) {
+ probIG *= r.getBackgroundProb(IG[j]);
+ probRNA *= getPoissonPDF(IG[j], mean);
+ }
+ if (probIG >= probRNA) break;
+ startT--;
+ if (startT == WINDOW/2) done = true;
+ */
+ }
+
+ // Add transcript to list
+ rnas.add(new RNA(start + startT, start + stopT, strand));
+ }
+ }
+ }
+
+ /**
+ * Given a list of RNAs, merges overlapping RNAs from different experiments
+ * and RNAs that are close in proximity. Adds the merged RNAs to the
+ * list "merged_RNAs".
+ */
+ private void merge_RNAs(Gene g1, Gene g2, char strand, ArrayList<RNA> rnas, ArrayList<RNA> merged_RNAs) {
+ if (rnas.size() == 0) return;
+
+ // Get coordinates of genes flanking the IG region
+ int start1 = g1.getStart();
+ int stop1 = g1.getStop();
+ if (!g1.isORF()) {
+ start1 = g1.getStartT();
+ stop1 = g1.getStopT();
+ }
+ if (start1 > stop1) { // Swap
+ int temp = start1;
+ start1 = stop1;
+ stop1 = temp;
+ }
+ int start2 = g2.getStart();
+ int stop2 = g2.getStop();
+ if (!g2.isORF()) {
+ start2 = g2.getStartT();
+ stop2 = g2.getStopT();
+ }
+ if (start2 > stop2) { // Swap
+ int temp = start2;
+ start2 = stop2;
+ stop2 = temp;
+ }
+
+ int IG_start = stop1 + 1;
+ int IG_stop = start2 - 1;
+ int IG_length = IG_stop - IG_start + 1;
+ if (IG_length <= 0) return; // IG region has length 0. Do not output it.
+
+ // For each nucleotide in an IG region, indicates if a RNA is predicted
+ // for the nucleotide or not.
+ boolean[] IG = new boolean[IG_length];
+ for (int i=0; i<rnas.size(); i++) {
+ if ((rnas.get(i).strand == strand) || unstranded) {
+ for (int j=rnas.get(i).start; j<=rnas.get(i).stop; j++) {
+ if (j < IG_start) return;
+ IG[j-IG_start] = true;
+ }
+ }
+ }
+
+ // Determine set of merged RNAs
+ int PROXIMITY = 50; // RNAs within this many NTs of each other are merged
+ int start = -1;
+ int stop = -1;
+ for (int i=0; i<IG.length; i++) {
+ if (IG[i] && (start == -1)) { // Start of RNA
+ start = i;
+ stop = i;
+ } else if (IG[i] && (start >= 0)) { // Within RNA
+ stop = i;
+ } else if (!IG[i] && (start == -1)) { // Within non-RNA
+ // do nothing
+ } else if (!IG[i] && (start >= 0)) { // RNA just ended
+ for (int j=i; j<Math.min(i+PROXIMITY, IG.length); j++) {
+ if (IG[j]) stop = j;
+ }
+ if (stop > i-1) i = stop; // Continue the loop from the end of the RNA
+ else {
+ // Ignore predicted RNAs that abut annotated RNAs
+ if (((g1.isORF()) || (start > 0)) && ((g2.isORF()) || (stop < IG.length-1)))
+ merged_RNAs.add(new RNA(IG_start + start, IG_start + stop, strand));
+ start = -1;
+ stop = -1;
+ }
+ } else {
+ Rockhopper.output("Error - this case should be unreachable!\n");
+ }
+ }
+ // Check if IG region ends with RNA
+ if (start >= 0) {
+ int previousStop = stop;
+ for (int j=previousStop+1; j<Math.min(previousStop+1+PROXIMITY, IG.length); j++) {
+ if (IG[j]) stop = j;
+ }
+ // Ignore predicted RNAs that abut annotated RNAs
+ if (((g1.isORF()) || (start > 0)) && ((g2.isORF()) || (stop < IG.length-1)))
+ merged_RNAs.add(new RNA(IG_start + start, IG_start + stop, strand));
+ }
+ }
+
+ /**
+ * Given a predicted RNA, determines if it is antisense to any annotated genes.
+ * Returns "-" if it is not antisense to any genes.
+ * Otherwise, returns "antisense" followed by a list of genes it is antisense to.
+ */
+ private String getAntisenseAnnotation(RNA rna, String[] genesPlus, String[] genesMinus) {
+ HashMap<String, String> genes = new HashMap<String, String>();
+ for (int i=rna.start; i<=rna.stop; i++) {
+ if (unstranded || (rna.strand == '+')) genes.put(genesMinus[i], "");
+ if (unstranded || (rna.strand == '-')) genes.put(genesPlus[i], "");
+ }
+
+ String s = "";
+ for (String key : genes.keySet()) {
+ if (key.length() > 0) s += " " + key;
+ }
+
+ if (s.length() == 0) return "-";
+ else return "antisense:" + s;
+ }
+
+ /**
+ * Output reads in IG region along with UTR and RNA annotation of region.
+ */
+ private void output_IG_to_file(Gene g1, Gene g2, char strand, ArrayList<RNA> rnas, String DIR) {
+
+ // Get coordinates of genes flanking the IG region
+ int start1 = g1.getStart();
+ int stop1 = g1.getStop();
+ if (!g1.isORF()) {
+ start1 = g1.getStartT();
+ stop1 = g1.getStopT();
+ }
+ if (start1 > stop1) { // Swap
+ int temp = start1;
+ start1 = stop1;
+ stop1 = temp;
+ }
+ int start2 = g2.getStart();
+ int stop2 = g2.getStop();
+ if (!g2.isORF()) {
+ start2 = g2.getStartT();
+ stop2 = g2.getStopT();
+ }
+ if (start2 > stop2) { // Swap
+ int temp = start2;
+ start2 = stop2;
+ stop2 = temp;
+ }
+
+ int IG_start = stop1 + 1;
+ int IG_stop = start2 - 1;
+ int IG_length = IG_stop - IG_start + 1;
+ if (IG_length <= 0) return; // IG region has length 0. Do not output it.
+
+ int mean1 = 0;
+ int mean2 = 0;
+ for (int x=0; x<conditions.size(); x++)
+ for (int y=0; y<conditions.get(x).numReplicates(); y++) {
+ if (!unstranded) { // Strand specific
+ mean1 = Math.max(mean1, (int)conditions.get(x).getReplicate(y).getMeanOfRange(z, start1, stop1, g1.getStrand()));
+ mean2 = Math.max(mean2, (int)conditions.get(x).getReplicate(y).getMeanOfRange(z, start2, stop2, g2.getStrand()));
+ } else { // Starnd ambiguous
+ mean1 = Math.max(mean1, (int)conditions.get(x).getReplicate(y).getMeanOfRange(z, start1, stop1, '?'));
+ mean2 = Math.max(mean2, (int)conditions.get(x).getReplicate(y).getMeanOfRange(z, start2, stop2, '?'));
+ }
+ }
+ int[] IG = new int[IG_length];
+ for (int i=IG_start; i<=IG_stop; i++) {
+ int maxRead = 0;
+ for (int x=0; x<conditions.size(); x++)
+ for (int y=0; y<conditions.get(x).numReplicates(); y++)
+ maxRead = Math.max(maxRead, conditions.get(x).getReplicate(y).getReads(z, i, strand));
+ IG[i-IG_start] = maxRead;
+ }
+ StringBuilder annotation = getAnnotationOfIG(IG, g1, g2, strand, rnas);
+
+ try {
+
+ // Create directory (if it doesn't exist) to write files to
+ if (DIR.charAt(DIR.length()-1) != '/') DIR += '/';
+ File dir = new File(DIR);
+ if (!dir.exists()) dir.mkdir();
+
+ String fileName = IG_start + "_" + IG_stop + ".txt";
+ PrintWriter writer = new PrintWriter(new File(DIR + fileName));
+ writer.println(g1.getName() + "\t" + g1.getStrand() + "\t" + mean1);
+ writer.println(g2.getName() + "\t" + g2.getStrand() + "\t" + mean2);
+ writer.println("\n");
+ writer.println(annotation.toString());
+ writer.close();
+ } catch (FileNotFoundException ex) {
+ Rockhopper.output("Error - could not output file.\n");
+ System.exit(0);
+ }
+ }
+
+ /**
+ * Output reads in IG region and UTR of specified gene.
+ */
+ /*
+ private void output_IG_to_file(Gene g1, Gene g2, int frontUTR_length, int backUTR_length, int start, int stop, Replicate r, String DIR) {
+
+ int mean1 = (int)r.getMeanOfRange(g1.getStart(), g1.getStop(), g1.getStrand());
+ int mean2 = (int)r.getMeanOfRange(g2.getStart(), g2.getStop(), g2.getStrand());
+ int[] IG1 = new int[stop-start+1];
+ int[] IG2 = null;
+ if ((g1.getStrand() != '+') && (g1.getStrand() != '-')) { // Placeholder gene
+ for (int i=start; i<=stop; i++) IG1[i-start] = r.getReads(i, g2.getStrand());
+ } else if ((g2.getStrand() != '+') && (g2.getStrand() != '-')) { // Placeholder gene
+ for (int i=start; i<=stop; i++) IG1[i-start] = r.getReads(i, g1.getStrand());
+ } else if (g1.getStrand() == g2.getStrand()) { // Same strand
+ for (int i=start; i<=stop; i++) IG1[i-start] = r.getReads(i, g1.getStrand());
+ } else { // Different strands
+ for (int i=start; i<=stop; i++) IG1[i-start] = r.getReads(i, g1.getStrand());
+ IG2 = new int[stop-start+1];
+ for (int i=start; i<=stop; i++) IG2[i-start] = r.getReads(i, g2.getStrand());
+ }
+ StringBuilder annotation1 = getAnnotationOfIG(IG1, g1, g2, frontUTR_length, backUTR_length);
+ StringBuilder annotation2 = getAnnotationOfIG(IG2, g1, g2, frontUTR_length, backUTR_length);
+
+ try {
+
+ // Create directory (if it doesn't exist) to write files to
+ if (DIR.charAt(DIR.length()-1) != '/') DIR += '/';
+ File dir = new File(DIR);
+ if (!dir.exists()) dir.mkdir();
+ dir = new File(DIR + r.getName() + "/");
+ if (!dir.exists()) dir.mkdir();
+ DIR += r.getName() + "/";
+
+ String fileName = start + "_" + stop + ".txt";
+ PrintWriter writer = new PrintWriter(new File(DIR + fileName));
+ writer.println(g1.getName() + "\t" + g1.getStrand() + "\t" + mean1);
+ writer.println(g2.getName() + "\t" + g2.getStrand() + "\t" + mean2);
+ writer.println("\n");
+ writer.println(annotation1.toString());
+ if (annotation2 != null) writer.println("\n" + annotation2.toString());
+ writer.close();
+ } catch (FileNotFoundException ex) {
+ Rockhopper.output("Error - could not output file.\n");
+ System.exit(0);
+ }
+ }
+ */
+
+ /**
+ * Return a StringBuilder representation of an IG region consisting
+ * of reads and an annotation (5'UTR and 3'UTR and RNA) of those reads.
+ */
+ private StringBuilder getAnnotationOfIG(int[] IG, Gene g1, Gene g2, char strand, ArrayList<RNA> rnas) {
+ int FASTA = 25;
+ StringBuilder annotation = new StringBuilder(IG.length);
+ for (int i=0; i<IG.length; i++) annotation.append(".");
+
+ // Front UTR
+ if ((g1.getStrand() == strand) || (this.unstranded)) {
+ int frontUTR_count = g1.getMaxCoordinate() - Math.max(g1.getStart(), g1.getStop());
+ if (!g1.isORF()) frontUTR_count = 0;
+ char UTR_char = '3'; // Plus strand
+ if (g1.getStrand() == '-') UTR_char = '5'; // Minus strand
+ for (int i=0; i<frontUTR_count; i++) annotation.setCharAt(i, UTR_char);
+ }
+
+ // Back UTR
+ if ((g2.getStrand() == strand) || (this.unstranded)) {
+ int backUTR_count = Math.min(g2.getStart(), g2.getStop()) - g2.getMinCoordinate();
+ if (!g2.isORF()) backUTR_count = 0;
+ char UTR_char = '5'; // Plus strand
+ if (g2.getStrand() == '-') UTR_char = '3'; // Minus strand
+ for (int i=0; i<backUTR_count; i++) annotation.setCharAt(annotation.length()-1-i, UTR_char);
+ }
+
+ // RNAs
+ int IG_start = Math.max(g1.getStart(), g1.getStop()) + 1;
+ if (!g1.isORF()) IG_start = g1.getMaxCoordinate() + 1;
+ int IG_stop = Math.min(g2.getStart(), g2.getStop()) - 1;
+ if (!g2.isORF()) IG_stop = g2.getMinCoordinate() - 1;
+ for (int i=0; i<rnas.size(); i++) {
+ RNA rna = rnas.get(i);
+ if ((rna.strand == strand) || (this.unstranded)) {
+ for (int j=rna.start; j<=rna.stop; j++)
+ annotation.setCharAt(j - IG_start, 'R');
+ }
+ }
+
+ StringBuilder IG_annotation = new StringBuilder(IG.length);
+ int i = 0;
+ for (i=0; i<IG.length; i++) {
+ String num = "" + IG[i];
+ if (IG[i] < 10) num = " " + num + " ";
+ else if (IG[i] < 100) num = num + " ";
+ else num = num.charAt(0) + "e" + (num.length()-1);
+ IG_annotation.append(" " + num);
+ if ((i+1) % FASTA == 0) {
+ IG_annotation.append("\n");
+ for (int j=0; j<FASTA; j++) {
+ IG_annotation.append(" " + " " + annotation.charAt((i+1) - FASTA + j) + " ");
+ }
+ IG_annotation.append("\n\n");
+ }
+ }
+ if (i % FASTA != 0) {
+ IG_annotation.append("\n");
+ for (int j=0; j<(i%FASTA); j++) {
+ IG_annotation.append(" " + " " + annotation.charAt(i - (i%FASTA) + j) + " ");
+ }
+ IG_annotation.append("\n\n");
+ }
+ return IG_annotation;
+ }
+
+ /**
+ * Return a StringBuilder representation of an IG region consisting
+ * of reads and an annotation (5'UTR and 3'UTR) of those reads.
+ */
+ /*
+ private StringBuilder getAnnotationOfIG(int[] IG, Gene g1, Gene g2, int frontUTR_length, int backUTR_length) {
+ int FASTA = 25;
+ if (IG == null) return null;
+ StringBuilder annotation = new StringBuilder();
+ int frontUTR_count = 0;
+ int backUTR_count = 0;
+ int i = 0;
+ for (i=0; i<IG.length; i++) {
+ String num = "" + IG[i];
+ if (IG[i] < 10) num = " " + num + " ";
+ else if (IG[i] < 100) num = num + " ";
+ else num = num.charAt(0) + "e" + (num.length()-1);
+ annotation.append(" " + num);
+ if ((i+1) % FASTA == 0) {
+ annotation.append("\n");
+ for (int j=0; j<FASTA; j++) {
+ if (frontUTR_count < frontUTR_length) {
+ if (g1.getStrand() == '+') annotation.append(" " + " 3 ");
+ else annotation.append(" " + " 5 ");
+ frontUTR_count++;
+ }
+ else if (i+1-FASTA+j >= IG.length - backUTR_length) {
+ if (g2.getStrand() == '+') annotation.append(" " + " 5 ");
+ else annotation.append(" " + " 3 ");
+ } else annotation.append(" " + " . ");
+ }
+ annotation.append("\n\n");
+ }
+ }
+ if ((i+1) % FASTA != 0) annotation.append("\n");
+ for (int j=0; j<(IG.length%FASTA); j++) {
+ if (frontUTR_count < frontUTR_length) {
+ if (g1.getStrand() == '+') annotation.append(" " + " 3 ");
+ else annotation.append(" " + " 5 ");
+ frontUTR_count++;
+ }
+ else if (IG.length - (IG.length%FASTA) + j >= IG.length - backUTR_length) {
+ if (g2.getStrand() == '+') annotation.append(" " + " 5 ");
+ else annotation.append(" " + " 3 ");
+ } else annotation.append(" " + " . ");
+ }
+ annotation.append("\n\n");
+ return annotation;
+ }
+ */
+
+
+
+ /***********************************************
+ ********** PRIVATE CLASS METHODS **********
+ ***********************************************/
+
+ /**
+ * Returns the PDF value at x for the specified Poisson distribution.
+ */
+ private static double getPoissonPDF(int x, double lambda) {
+ double result = Math.exp(-lambda);
+ int k = x;
+ while (k >= 1) {
+ result *= lambda/k;
+ k--;
+ }
+ return result;
+ }
+
+}
+
+
+
+
+
+/***********************************
+ ********** RNA CLASS **********
+ ***********************************/
+
+class RNA {
+
+ public int start;
+ public int stop;
+ public char strand;
+
+ public RNA(int start, int stop, char strand) {
+ this.start = start;
+ this.stop = stop;
+ this.strand = strand;
+ }
+
+ public String toString() {
+ return start + "\t" + stop + "\t" + strand;
+ }
+
+}
+
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+++ b/com/jidesoft/converter/converter.properties
@@ -0,0 +1,19 @@
+#
+#Strings for BooleanConverter
+#
+Boolean.true=True
+Boolean.false=False
+
+#
+#Strings for FontConverter
+#
+Font.plain=Plain
+Font.bold=Bold
+Font.italic=Italic
+Font.boldItalic=BoldItalic
+
+#
+#Strings for QuarterConverter
+#
+Quarter.quarter=Qtr {0}
+#Please note, there is a space at the end of Qtr.
\ No newline at end of file
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diff --git a/com/jidesoft/dialog/TreeIconsFactory$CellRenderer.class b/com/jidesoft/dialog/TreeIconsFactory$CellRenderer.class
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index 0000000..45c3918
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diff --git a/com/jidesoft/dialog/buttons.properties b/com/jidesoft/dialog/buttons.properties
new file mode 100644
index 0000000..c66f9ea
--- /dev/null
+++ b/com/jidesoft/dialog/buttons.properties
@@ -0,0 +1,81 @@
+#
+#Buttons
+#
+
+Button.apply=Apply
+Button.apply.mnemonic=A
+
+Button.back=< Back
+Button.back.mnemonic=B
+
+Button.browse=Browse
+Button.browse.mnemonic=B
+
+Button.clear=Clear
+Button.clear.mnemonic=C
+
+Button.close=Close
+Button.close.mnemonic=C
+
+Button.continue=Continue
+Button.continue.mnemonic=C
+
+Button.edit=Edit
+Button.edit.mnemonic=E
+
+Button.exit=Exit
+Button.exit.mnemonic=X
+
+Button.find=Find
+Button.find.mnemonic=F
+
+Button.findNext=Find Next
+Button.findNext.mnemonic=N
+
+Button.finish=Finish
+Button.finish.mnemonic=F
+
+Button.forward=Forward
+Button.forward.mnemonic=F
+
+Button.goback=Go Back
+Button.goback.mnemonic=G
+
+Button.help=Help
+Button.help.mnemonic=H
+
+Button.new=New
+Button.new.mnemonic=N
+
+Button.next=Next >
+Button.next.mnemonic=N
+
+Button.open=Open
+Button.open.mnemonic=O
+
+Button.print=Print
+Button.print.mnemonic=P
+
+Button.replace=Replace
+Button.replace.mnemonic=R
+
+Button.retry=Retry
+Button.retry.mnemonic=R
+
+Button.run=Run
+Button.run.mnemonic=R
+
+Button.save=Save
+Button.save.mnemonic=S
+
+Button.saveAs=Save As
+Button.saveAs.mnemonic=A
+
+Button.stop=Stop
+Button.stop.mnemonic=S
+
+Button.showDetails=Details >>
+Button.showDetails.mnemonic=D
+
+Button.hideDetails=<< Details
+Button.hideDetails.mnemonic=D
\ No newline at end of file
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index 0000000..cbed1da
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index 0000000..0d2ff4a
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diff --git a/com/jidesoft/grouper/group.properties b/com/jidesoft/grouper/group.properties
new file mode 100644
index 0000000..95c1b30
--- /dev/null
+++ b/com/jidesoft/grouper/group.properties
@@ -0,0 +1,12 @@
+#
+# Date related Grouper names
+#
+Date.dayOfYear=Day of Year
+Date.dayOfMonth=Day of Month
+Date.dayOfWeek=Day of Week
+Date.dayOfWeekInMonth=Day of Week in Month
+Date.weekOfMonth=Week of Month
+Date.weekOfYear=Week of Year
+Date.year=Year
+Date.month=Month
+Date.quarter=Quarter
\ No newline at end of file
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diff --git a/com/jidesoft/plaf/basic/basic.properties b/com/jidesoft/plaf/basic/basic.properties
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@@ -0,0 +1,75 @@
+#
+# Strings for DockableFrame TitlePane
+#
+
+#
+# Button actions
+#
+DockableFrameTitlePane.closeText=Close
+DockableFrameTitlePane.closeMnemonic=C
+DockableFrameTitlePane.closeTooltip=Close
+
+DockableFrameTitlePane.hideAutohideText=Hide
+DockableFrameTitlePane.hideAutohideMnemonic=H
+DockableFrameTitlePane.hideAutohideTooltip=Hide active auto-hide window
+
+DockableFrameTitlePane.floatingText=Floating
+DockableFrameTitlePane.floatingMnemonic=F
+DockableFrameTitlePane.floatingTooltip=Toggle floating
+
+DockableFrameTitlePane.autohideText=Auto Hide
+DockableFrameTitlePane.autohideMnemonic=A
+## for both autohide button and stop autohide button since it is a toggle button
+DockableFrameTitlePane.autohideTooltip=Toggle auto-hide
+
+DockableFrameTitlePane.maximizeText=Maximize
+DockableFrameTitlePane.maximizeMnemonic=M
+
+DockableFrameTitlePane.restoreText=Restore
+DockableFrameTitlePane.restoreMnemonic=R
+## for both maximize button and restore button since it is a toggle button
+DockableFrameTitlePane.maximizeTooltip=Maximize/restore
+
+#
+# DockableFrame attributes
+#
+DockableFrameTitlePane.dockableText=Dockable
+DockableFrameTitlePane.dockableMnemonic=D
+DockableFrameTitlePane.dockableTooltip=Toggle Dockable
+
+DockableFrameTitlePane.hidableText=Hidable
+DockableFrameTitlePane.hidableMnemonic=I
+
+DockableFrameTitlePane.floatableText=Floatable
+DockableFrameTitlePane.floatableMnemonic=L
+
+DockableFrameTitlePane.autohidableText=Autohidable
+DockableFrameTitlePane.autohidableMnemonic=U
+
+#
+# Strings for Undo
+#
+Undo.dragging=Dragging
+Undo.hide=Hide
+Undo.toggle=Toggle Floating/Docking Mode
+Undo.toggleAutohide=Toggle Autohidden/Docking Mode
+Undo.maximize=Maximize
+Undo.restore=Restore
+Undo.resizing=Resizing
+Undo.moving=Moving
+
+#
+# Strings for CollapsiblePane
+#
+CollapsiblePane.collapseText=Expand/Collapse
+CollapsiblePane.collapseToolTip=Expand or collapse the content
+
+#
+# Strings for JideTabbedPane
+#
+JideTabbedPane.scrollBackward=Scroll Backward
+JideTabbedPane.scrollForward=Scroll Forward
+JideTabbedPane.showList=Show List
+JideTabbedPane.close=Close
+
+
diff --git a/com/jidesoft/plaf/basic/folderChooser.properties b/com/jidesoft/plaf/basic/folderChooser.properties
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@@ -0,0 +1,16 @@
+#
+# FolderChooser
+#
+FolderChooser.new.title=Create New Folder
+FolderChooser.new.folderName=Enter the name of the new folder:
+FolderChooser.delete.title=Confirm Folder Deletion
+FolderChooser.delete.header=Really delete selected folders?
+FolderChooser.delete.message1=Are you sure you want to permanently delete this folder?
+FolderChooser.delete.message2=Are you sure you want to permanently delete these {0} items?
+FolderChooser.toolbar.desktop=Jump to the Desktop
+FolderChooser.toolbar.home=Jump to Home
+FolderChooser.toolbar.mydocuments=Jump to My Documents
+FolderChooser.toolbar.delete=Delete the selected folder
+FolderChooser.toolbar.new=Create a new folder under the selected folder
+FolderChooser.toolbar.refresh=Refresh the folder view to reflect external folder changes
+FolderChooser.toolbar.recent=Recent:
\ No newline at end of file
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--- /dev/null
+++ b/com/jidesoft/swing/swing.properties
@@ -0,0 +1,30 @@
+#
+# Strings for Searchable classes
+#
+Searchable.searchFor=Search for:
+Searchable.noMatch=(no match)
+
+#
+# Strings for SearchableBar classes
+#
+SearchableBar.find=Find:
+SearchableBar.find.mnemonic=F
+SearchableBar.findNext=Find Next
+SearchableBar.findNext.mnemonic=N
+SearchableBar.findNext.tooltip=Find the next occurrence of the phrase
+SearchableBar.findPrevious=Find Previous
+SearchableBar.findPrevious.mnemonic=P
+SearchableBar.findPrevious.tooltip=Find the previous occurrence of the phrase
+SearchableBar.highlights=Highlight
+SearchableBar.highlights.mnemonic=H
+SearchableBar.highlights.tooltip=Highlights all occurrences of the phrase
+SearchableBar.matchCase=Match Case
+SearchableBar.matchCase.mnemonic=M
+SearchableBar.repeats=Repeats
+SearchableBar.repeats.mnemonic=R
+
+SearchableBar.reachedBottom=Reached bottom of the page
+SearchableBar.reachedTop=Reached top of the page
+SearchableBar.reachedBottomRepeat=Reached bottom of the page, continued from top
+SearchableBar.reachedTopRepeat=Reached top of the page, continued from bottom
+SearchableBar.notFound=Phrase not found
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@@ -0,0 +1,102 @@
+#
+# Charset Mappings
+#
+# Java Encoding MySQL Name (and version, '*'
+# denotes preferred value)
+#
+
+javaToMysqlMappings=\
+ US-ASCII = usa7,\
+ US-ASCII = ascii,\
+ Big5 = big5,\
+ GBK = gbk,\
+ SJIS = sjis,\
+ EUC_CN = gb2312,\
+ EUC_JP = ujis,\
+ EUC_JP_Solaris = >5.0.3 eucjpms,\
+ EUC_KR = euc_kr,\
+ EUC_KR = >4.1.0 euckr,\
+ ISO8859_1 = *latin1,\
+ ISO8859_1 = latin1_de,\
+ ISO8859_1 = german1,\
+ ISO8859_1 = danish,\
+ ISO8859_2 = latin2,\
+ ISO8859_2 = czech,\
+ ISO8859_2 = hungarian,\
+ ISO8859_2 = croat,\
+ ISO8859_7 = greek,\
+ ISO8859_7 = latin7,\
+ ISO8859_8 = hebrew,\
+ ISO8859_9 = latin5,\
+ ISO8859_13 = latvian,\
+ ISO8859_13 = latvian1,\
+ ISO8859_13 = estonia,\
+ Cp437 = *>4.1.0 cp850,\
+ Cp437 = dos,\
+ Cp850 = Cp850,\
+ Cp852 = Cp852,\
+ Cp866 = cp866,\
+ KOI8_R = koi8_ru,\
+ KOI8_R = >4.1.0 koi8r,\
+ TIS620 = tis620,\
+ Cp1250 = cp1250,\
+ Cp1250 = win1250,\
+ Cp1251 = *>4.1.0 cp1251,\
+ Cp1251 = win1251,\
+ Cp1251 = cp1251cias,\
+ Cp1251 = cp1251csas,\
+ Cp1256 = cp1256,\
+ Cp1251 = win1251ukr,\
+ Cp1257 = cp1257,\
+ MacRoman = macroman,\
+ MacCentralEurope = macce,\
+ UTF-8 = utf8,\
+ UnicodeBig = ucs2,\
+ US-ASCII = binary,\
+ Cp943 = sjis,\
+ MS932 = sjis,\
+ MS932 = >4.1.11 cp932,\
+ WINDOWS-31J = sjis,\
+ WINDOWS-31J = >4.1.11 cp932,\
+ CP932 = sjis,\
+ CP932 = *>4.1.11 cp932,\
+ SHIFT_JIS = sjis,\
+ ASCII = ascii,\
+ LATIN5 = latin5,\
+ LATIN7 = latin7,\
+ HEBREW = hebrew,\
+ GREEK = greek,\
+ EUCKR = euckr,\
+ GB2312 = gb2312,\
+ LATIN2 = latin2
+
+#
+# List of multibyte character sets that can not
+# use efficient charset conversion or escaping
+#
+# This map is made case-insensitive inside CharsetMapping
+#
+# Java Name MySQL Name (not currently used)
+
+multibyteCharsets=\
+ Big5 = big5,\
+ GBK = gbk,\
+ SJIS = sjis,\
+ EUC_CN = gb2312,\
+ EUC_JP = ujis,\
+ EUC_JP_Solaris = eucjpms,\
+ EUC_KR = euc_kr,\
+ EUC_KR = >4.1.0 euckr,\
+ Cp943 = sjis,\
+ Cp943 = cp943,\
+ WINDOWS-31J = sjis,\
+ WINDOWS-31J = cp932,\
+ CP932 = cp932,\
+ MS932 = sjis,\
+ MS932 = cp932,\
+ SHIFT_JIS = sjis,\
+ EUCKR = euckr,\
+ GB2312 = gb2312,\
+ UTF-8 = utf8,\
+ utf8 = utf8,\
+ UnicodeBig = ucs2
\ No newline at end of file
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index 0000000..7293f04
Binary files /dev/null and b/com/mysql/jdbc/Field.class differ
diff --git a/com/mysql/jdbc/LicenseConfiguration.class b/com/mysql/jdbc/LicenseConfiguration.class
new file mode 100644
index 0000000..f0a99d3
Binary files /dev/null and b/com/mysql/jdbc/LicenseConfiguration.class differ
diff --git a/com/mysql/jdbc/LocalizedErrorMessages.properties b/com/mysql/jdbc/LocalizedErrorMessages.properties
new file mode 100644
index 0000000..0de00c1
--- /dev/null
+++ b/com/mysql/jdbc/LocalizedErrorMessages.properties
@@ -0,0 +1,404 @@
+#
+# Fixed
+#
+
+ResultSet.Retrieved__1=Retrieved
+ResultSet.Bad_format_for_BigDecimal=Bad format for BigDecimal ''{0}'' in column {1}.
+ResultSet.Bad_format_for_BigInteger=Bad format for BigInteger ''{0}'' in column {1}.
+ResultSet.Column_Index_out_of_range=Column Index out of range, {0} > {1}.
+ResultSet.Value_is_out_of_range=Value ''{0}'' is out of range [{1}, {2}].
+ResultSet.Positioned_Update_not_supported=Positioned Update not supported.
+ResultSet.Bad_format_for_Date=Bad format for DATE ''{0}'' in column {1}.
+ResultSet.Bad_format_for_Column=Bad format for {0} ''{1}'' in column {2} ({3}).
+ResultSet.Bad_format_for_number=Bad format for number ''{0}'' in column {1}.
+ResultSet.Illegal_operation_on_empty_result_set=Illegal operation on empty result set.
+
+Statement.0=Connection is closed.
+Statement.2=Unsupported character encoding ''{0}''
+Statement.5=Illegal value for setFetchDirection().
+Statement.7=Illegal value for setFetchSize().
+Statement.11=Illegal value for setMaxFieldSize().
+Statement.13=Can not set max field size > max allowed packet of {0} bytes.
+Statement.15=setMaxRows() out of range.
+Statement.19=Illegal flag for getMoreResults(int).
+Statement.21=Illegal value for setQueryTimeout().
+Statement.27=Connection is read-only.
+Statement.28=Queries leading to data modification are not allowed.
+Statement.34=Connection is read-only.
+Statement.35=Queries leading to data modification are not allowed.
+Statement.40=Can not issue INSERT/UPDATE/DELETE with executeQuery().
+Statement.42=Connection is read-only.
+Statement.43=Queries leading to data modification are not allowed.
+Statement.46=Can not issue SELECT via executeUpdate().
+Statement.49=No operations allowed after statement closed.
+Statement.57=Can not issue data manipulation statements with executeQuery().
+Statement.59=Can not issue NULL query.
+Statement.61=Can not issue empty query.
+Statement.63=Statement not closed explicitly. You should call close() on created
+Statement.64=Statement instances from your code to be more efficient.
+
+UpdatableResultSet.1=Can not call deleteRow() when on insert row.
+UpdatableResultSet.2=Can not call deleteRow() on empty result set.
+UpdatableResultSet.3=Before start of result set. Can not call deleteRow().
+UpdatableResultSet.4=After end of result set. Can not call deleteRow().
+UpdatableResultSet.7=Not on insert row.
+UpdatableResultSet.8=Can not call refreshRow() when on insert row.
+UpdatableResultSet.9=Can not call refreshRow() on empty result set.
+UpdatableResultSet.10=Before start of result set. Can not call refreshRow().
+UpdatableResultSet.11=After end of result set. Can not call refreshRow().
+UpdatableResultSet.12=refreshRow() called on row that has been deleted or had primary key changed.
+UpdatableResultSet.34=Updatable result set created, but never updated. You should only create updatable result sets when you want to update/insert/delete values using the updateRow(), deleteRow() and insertRow() methods.
+UpdatableResultSet.39=Unsupported character encoding ''{0}''.
+UpdatableResultSet.43=Can not create updatable result sets when there is no currently selected database and MySQL server version < 4.1.
+
+#
+# Possible re-names
+#
+
+ResultSet.Query_generated_no_fields_for_ResultSet_57=Query generated no fields for ResultSet
+ResultSet.Illegal_value_for_fetch_direction_64=Illegal value for fetch direction
+ResultSet.Value_must_be_between_0_and_getMaxRows()_66=Value must be between 0 and getMaxRows()
+ResultSet.Query_generated_no_fields_for_ResultSet_99=Query generated no fields for ResultSet
+ResultSet.Cannot_absolute_position_to_row_0_110=Cannot absolute position to row 0
+ResultSet.Operation_not_allowed_after_ResultSet_closed_144=Operation not allowed after ResultSet closed
+ResultSet.Before_start_of_result_set_146=Before start of result set
+ResultSet.After_end_of_result_set_148=After end of result set
+ResultSet.Query_generated_no_fields_for_ResultSet_133=Query generated no fields for ResultSet
+ResultSet.ResultSet_is_from_UPDATE._No_Data_115=ResultSet is from UPDATE. No Data.
+ResultSet.N/A_159=N/A
+
+#
+# To fix
+#
+
+ResultSet.Invalid_value_for_getFloat()_-____68=Invalid value for getFloat() - \'
+ResultSet.Invalid_value_for_getInt()_-____74=Invalid value for getInt() - \'
+ResultSet.Invalid_value_for_getLong()_-____79=Invalid value for getLong() - \'
+ResultSet.Invalid_value_for_getFloat()_-____200=Invalid value for getFloat() - \'
+ResultSet.___in_column__201=\' in column
+ResultSet.Invalid_value_for_getInt()_-____206=Invalid value for getInt() - \'
+ResultSet.___in_column__207=\' in column
+ResultSet.Invalid_value_for_getLong()_-____211=Invalid value for getLong() - \'
+ResultSet.___in_column__212=\' in column
+ResultSet.Invalid_value_for_getShort()_-____217=Invalid value for getShort() - \'
+ResultSet.___in_column__218=\' in column
+
+ResultSet.Class_not_found___91=Class not found:
+ResultSet._while_reading_serialized_object_92=\ while reading serialized object
+
+ResultSet.Invalid_value_for_getShort()_-____96=Invalid value for getShort() - \'
+ResultSet.Unsupported_character_encoding____101=Unsupported character encoding \'
+
+ResultSet.Malformed_URL____104=Malformed URL \'
+ResultSet.Malformed_URL____107=Malformed URL \'
+ResultSet.Malformed_URL____141=Malformed URL \'
+
+ResultSet.Column____112=Column \'
+ResultSet.___not_found._113=\' not found.
+
+ResultSet.Unsupported_character_encoding____135=Unsupported character encoding \'
+ResultSet.Unsupported_character_encoding____138=Unsupported character encoding \'
+
+ResultSet.ResultSet_implicitly_closed_by_driver._150=ResultSet implicitly closed by driver.
+ResultSet._n_nYou_should_close_ResultSets_explicitly_from_your_code_to_free_up_resources_in_a_more_efficient_manner._151=\n\nYou should close ResultSets explicitly from your code to free up resources in a more efficient manner.
+
+ResultSet.Possible_incomplete_traversal_of_result_set._Cursor_was_left_on_row__154=Possible incomplete traversal of result set. Cursor was left on row
+ResultSet._of__155=\ of
+ResultSet._rows_when_it_was_closed._156=\ rows when it was closed.
+ResultSet._n_nYou_should_consider_re-formulating_your_query_to_return_only_the_rows_you_are_interested_in_using._157=\n\nYou should consider re-formulating your query to return only the rows you are interested in using.
+
+ResultSet.The_following_columns_were__160=The following columns were
+ResultSet._part_of_the_SELECT_statement_for_this_result_set,_but_were_161=\ part of the SELECT statement for this result set, but were
+ResultSet._never_referenced___162=\ never referenced:
+
+ResultSet.Value____173=Value \'
+ResultSetMetaData.46=Column index out of range.
+ResultSet.___is_out_of_range_[-127,127]_174=\' is out of range [-127,127]
+ResultSet.Bad_format_for_Date____180=Bad format for Date \'
+
+ResultSet.Timestamp_too_small_to_convert_to_Time_value_in_column__223=Timestamp too small to convert to Time value in column
+ResultSet.Precision_lost_converting_TIMESTAMP_to_Time_with_getTime()_on_column__227=Precision lost converting TIMESTAMP to Time with getTime() on column
+ResultSet.Precision_lost_converting_DATETIME_to_Time_with_getTime()_on_column__230=Precision lost converting DATETIME to Time with getTime() on column
+ResultSet.Bad_format_for_Time____233=Bad format for Time \'
+ResultSet.___in_column__234=\' in column
+ResultSet.Bad_format_for_Timestamp____244=Bad format for Timestamp \'
+ResultSet.___in_column__245=\' in column
+ResultSet.Cannot_convert_value____249=Cannot convert value \'
+ResultSet.___from_column__250=\' from column
+ResultSet._)_to_TIMESTAMP._252=\ ) to TIMESTAMP.
+ResultSet.Timestamp_too_small_to_convert_to_Time_value_in_column__257=Timestamp too small to convert to Time value in column
+ResultSet.Precision_lost_converting_TIMESTAMP_to_Time_with_getTime()_on_column__261=Precision lost converting TIMESTAMP to Time with getTime() on column
+ResultSet.Precision_lost_converting_DATETIME_to_Time_with_getTime()_on_column__264=Precision lost converting DATETIME to Time with getTime() on column
+ResultSet.Bad_format_for_Time____267=Bad format for Time \'
+ResultSet.___in_column__268=\' in column
+ResultSet.Bad_format_for_Timestamp____278=Bad format for Timestamp \'
+ResultSet.___in_column__279=\' in column
+ResultSet.Cannot_convert_value____283=Cannot convert value \'
+ResultSet.___from_column__284=\' from column
+ResultSet._)_to_TIMESTAMP._286=\ ) to TIMESTAMP.
+CallableStatement.2=Parameter name can not be NULL or zero-length.
+CallableStatement.3=No parameter named '
+CallableStatement.4='
+CallableStatement.5=Parameter named '
+CallableStatement.6=' is not an OUT parameter
+CallableStatement.7=No output parameters registered.
+CallableStatement.8=No output parameters returned by procedure.
+CallableStatement.9=Parameter number
+CallableStatement.10=\ is not an OUT parameter
+CallableStatement.11=Parameter index of
+CallableStatement.12=\ is out of range (1,
+CallableStatement.13=)
+CallableStatement.14=Can not use streaming result sets with callable statements that have output parameters
+CallableStatement.1=Unable to retrieve metadata for procedure.
+CallableStatement.0=Parameter name can not be
+CallableStatement.15=null.
+CallableStatement.16=empty.
+CallableStatement.21=Parameter
+CallableStatement.22=\ is not registered as an output parameter
+CommunicationsException.2=\ is longer than the server configured value of
+CommunicationsException.3='wait_timeout'
+CommunicationsException.4='interactive_timeout'
+CommunicationsException.5=may or may not be greater than the server-side timeout
+CommunicationsException.6=(the driver was unable to determine the value of either the
+CommunicationsException.7='wait_timeout' or 'interactive_timeout' configuration values from
+CommunicationsException.8=the server.
+CommunicationsException.9=The last communications with the server was
+CommunicationsException.10=\ seconds ago, which
+CommunicationsException.11=. You should consider either expiring and/or testing connection validity
+CommunicationsException.12=before use in your application, increasing the server configured values for client timeouts,
+CommunicationsException.13=or using the Connector/J connection property 'autoReconnect=true' to avoid this problem.
+CommunicationsException.14=The driver was unable to create a connection due to
+CommunicationsException.15=an inability to establish the client portion of a socket.\n\n
+CommunicationsException.16=This is usually caused by a limit on the number of sockets imposed by
+CommunicationsException.17=the operating system. This limit is usually configurable. \n\n
+CommunicationsException.18=For Unix-based platforms, see the manual page for the 'ulimit' command. Kernel or system reconfiguration may also be required.
+CommunicationsException.19=\n\nFor Windows-based platforms, see Microsoft Knowledge Base Article 196271 (Q196271).
+CommunicationsException.20=Communications link failure
+CommunicationsException.21=\ due to underlying exception:
+NonRegisteringDriver.3=Hostname of MySQL Server
+NonRegisteringDriver.7=Port number of MySQL Server
+NonRegisteringDriver.13=Username to authenticate as
+NonRegisteringDriver.16=Password to use for authentication
+NonRegisteringDriver.17=Cannot load connection class because of underlying exception: '
+NonRegisteringDriver.18='.
+NonRegisteringDriver.37=Must specify port after ':' in connection string
+SQLError.35=Disconnect error
+SQLError.36=Data truncated
+SQLError.37=Privilege not revoked
+SQLError.38=Invalid connection string attribute
+SQLError.39=Error in row
+SQLError.40=No rows updated or deleted
+SQLError.41=More than one row updated or deleted
+SQLError.42=Wrong number of parameters
+SQLError.43=Unable to connect to data source
+SQLError.44=Connection in use
+SQLError.45=Connection not open
+SQLError.46=Data source rejected establishment of connection
+SQLError.47=Connection failure during transaction
+SQLError.48=Communication link failure
+SQLError.49=Insert value list does not match column list
+SQLError.50=Numeric value out of range
+SQLError.51=Datetime field overflow
+SQLError.52=Division by zero
+SQLError.53=Deadlock found when trying to get lock; Try restarting transaction
+SQLError.54=Invalid authorization specification
+SQLError.55=Syntax error or access violation
+SQLError.56=Base table or view not found
+SQLError.57=Base table or view already exists
+SQLError.58=Base table not found
+SQLError.59=Index already exists
+SQLError.60=Index not found
+SQLError.61=Column already exists
+SQLError.62=Column not found
+SQLError.63=No default for column
+SQLError.64=General error
+SQLError.65=Memory allocation failure
+SQLError.66=Invalid column number
+SQLError.67=Invalid argument value
+SQLError.68=Driver not capable
+SQLError.69=Timeout expired
+ChannelBuffer.0=Unsupported character encoding '
+ChannelBuffer.1='
+Field.12=Unsupported character encoding '
+Field.13='
+Blob.0=indexToWriteAt must be >= 1
+Blob.1=IO Error while writing bytes to blob
+Blob.2=Position 'pos' can not be < 1
+StringUtils.0=Unsupported character encoding '
+StringUtils.1='.
+StringUtils.5=Unsupported character encoding '
+StringUtils.6='.
+StringUtils.10=Unsupported character encoding '
+StringUtils.11='.
+RowDataDynamic.2=WARN: Possible incomplete traversal of result set. Streaming result set had
+RowDataDynamic.3=\ rows left to read when it was closed.
+RowDataDynamic.4=\n\nYou should consider re-formulating your query to
+RowDataDynamic.5=return only the rows you are interested in using.
+RowDataDynamic.6=\n\nResultSet was created at:
+RowDataDynamic.7=\n\nNested Stack Trace:\n
+RowDataDynamic.8=Error retrieving record: Unexpected Exception:
+RowDataDynamic.9=\ message given:
+RowDataDynamic.10=Operation not supported for streaming result sets
+Clob.0=indexToWriteAt must be >= 1
+Clob.1=indexToWriteAt must be >= 1
+Clob.2=Starting position can not be < 1
+Clob.3=String to set can not be NULL
+Clob.4=Starting position can not be < 1
+Clob.5=String to set can not be NULL
+Clob.6=CLOB start position can not be < 1
+Clob.7=CLOB start position + length can not be > length of CLOB
+Clob.8=Illegal starting position for search, '
+Clob.9='
+Clob.10=Starting position for search is past end of CLOB
+Clob.11=Cannot truncate CLOB of length
+Clob.12=\ to length of
+Clob.13=.
+PacketTooBigException.0=Packet for query is too large (
+PacketTooBigException.1=\ >
+PacketTooBigException.2=).
+PacketTooBigException.3=You can change this value on the server by setting the
+PacketTooBigException.4=max_allowed_packet' variable.
+Util.1=\n\n** BEGIN NESTED EXCEPTION ** \n\n
+Util.2=\nMESSAGE:
+Util.3=\n\nSTACKTRACE:\n\n
+Util.4=\n\n** END NESTED EXCEPTION **\n\n
+MiniAdmin.0=Conection can not be null.
+MiniAdmin.1=MiniAdmin can only be used with MySQL connections
+NamedPipeSocketFactory.2=Can not specify NULL or empty value for property '
+NamedPipeSocketFactory.3='.
+NamedPipeSocketFactory.4=Named pipe path can not be null or empty
+MysqlIO.1=Unexpected end of input stream
+MysqlIO.2=Reading packet of length
+MysqlIO.3=\nPacket header:\n
+MysqlIO.4=readPacket() payload:\n
+MysqlIO.8=Slow query explain results for '
+MysqlIO.9=' :\n\n
+MysqlIO.10=\ message from server: "
+MysqlIO.15=SSL Connection required, but not supported by server.
+MysqlIO.17=Attempt to close streaming result set
+MysqlIO.18=\ when no streaming result set was registered. This is an internal error.
+MysqlIO.19=Attempt to close streaming result set
+MysqlIO.20=\ that was not registered.
+MysqlIO.21=\ Only one streaming result set may be open and in use per-connection. Ensure that you have called .close() on
+MysqlIO.22=\ any active result sets before attempting more queries.
+MysqlIO.23=Can not use streaming results with multiple result statements
+MysqlIO.25=\ ... (truncated)
+MysqlIO.26=Slow query (exceeded
+MysqlIO.26a=\ ms., duration:\
+MysqlIO.27=\ ms):
+MysqlIO.28=Not issuing EXPLAIN for query of size >
+MysqlIO.29=\ bytes.
+MysqlIO.33=The following query was executed with a bad index, use 'EXPLAIN' for more details:
+MysqlIO.35=The following query was executed using no index, use 'EXPLAIN' for more details:
+MysqlIO.36=\n\nLarge packet dump truncated at
+MysqlIO.37=\ bytes.
+MysqlIO.39=Streaming result set
+MysqlIO.40=\ is still active.
+MysqlIO.41=\ No statements may be issued when any streaming result sets are open and in use on a given connection.
+MysqlIO.42=\ Ensure that you have called .close() on any active streaming result sets before attempting more queries.
+MysqlIO.43=Unexpected end of input stream
+MysqlIO.44=Reading reusable packet of length
+MysqlIO.45=\nPacket header:\n
+MysqlIO.46=reuseAndReadPacket() payload:\n
+MysqlIO.47=Unexpected end of input stream
+MysqlIO.48=Unexpected end of input stream
+MysqlIO.49=Packets received out of order
+MysqlIO.50=Short read from server, expected
+MysqlIO.51=\ bytes, received only
+MysqlIO.53=Packets received out of order
+MysqlIO.54=Short read from server, expected
+MysqlIO.55=\ bytes, received only
+MysqlIO.57=send() compressed packet:\n
+MysqlIO.58=\n\nOriginal packet (uncompressed):\n
+MysqlIO.59=send() packet payload:\n
+MysqlIO.60=Unable to open file
+MysqlIO.63=for 'LOAD DATA LOCAL INFILE' command.
+MysqlIO.64=Due to underlying IOException:
+MysqlIO.65=Unable to close local file during LOAD DATA LOCAL INFILE command
+MysqlIO.68=\ message from server: "
+MysqlIO.70=Unknown column
+MysqlIO.72=\ message from server: "
+MysqlIO.75=No name specified for socket factory
+MysqlIO.76=Could not create socket factory '
+MysqlIO.77=' due to underlying exception:
+MysqlIO.79=Unexpected end of input stream
+MysqlIO.80=Unexpected end of input stream
+MysqlIO.81=Unexpected end of input stream
+MysqlIO.82=Unexpected end of input stream
+MysqlIO.83=Packets received out of order
+MysqlIO.84=Packets received out of order
+MysqlIO.85=Unexpected end of input stream
+MysqlIO.86=Unexpected end of input stream
+MysqlIO.87=Unexpected end of input stream
+MysqlIO.88=Packets received out of order
+MysqlIO.89=Packets received out of order
+MysqlIO.91=Failed to create message digest 'SHA-1' for authentication.
+MysqlIO.92=\ You must use a JDK that supports JCE to be able to use secure connection authentication
+MysqlIO.93=Failed to create message digest 'SHA-1' for authentication.
+MysqlIO.94=\ You must use a JDK that supports JCE to be able to use secure connection authentication
+MysqlIO.95=Failed to create message digest 'SHA-1' for authentication.
+MysqlIO.96=\ You must use a JDK that supports JCE to be able to use secure connection authentication
+MysqlIO.97=Unknown type '
+MysqlIO.98=\ in column
+MysqlIO.99=\ of
+MysqlIO.100=\ in binary-encoded result set.
+MysqlIO.102=, underlying cause:
+NotImplemented.0=Feature not implemented
+PreparedStatement.0=SQL String can not be NULL
+PreparedStatement.1=SQL String can not be NULL
+PreparedStatement.2=Parameter index out of range (
+PreparedStatement.3=\ >
+PreparedStatement.4=)
+PreparedStatement.16=Unknown Types value
+PreparedStatement.17=Cannot convert
+PreparedStatement.18=\ to SQL type requested due to
+PreparedStatement.19=\ -
+PreparedStatement.20=Connection is read-only.
+PreparedStatement.21=Queries leading to data modification are not allowed
+PreparedStatement.25=Connection is read-only.
+PreparedStatement.26=Queries leading to data modification are not allowed
+PreparedStatement.32=Unsupported character encoding '
+PreparedStatement.33='
+PreparedStatement.34=Connection is read-only.
+PreparedStatement.35=Queries leading to data modification are not allowed
+PreparedStatement.37=Can not issue executeUpdate() for SELECTs
+PreparedStatement.40=No value specified for parameter
+PreparedStatement.43=PreparedStatement created, but used 1 or fewer times. It is more efficient to prepare statements once, and re-use them many times
+PreparedStatement.48=PreparedStatement has been closed. No further operations allowed.
+PreparedStatement.49=Parameter index out of range (
+PreparedStatement.50=\ < 1 ).
+PreparedStatement.51=Parameter index out of range (
+PreparedStatement.52=\ > number of parameters, which is
+PreparedStatement.53=).
+PreparedStatement.54=Invalid argument value:
+PreparedStatement.55=Error reading from InputStream
+PreparedStatement.56=Error reading from InputStream
+PreparedStatement.61=SQL String can not be NULL
+ServerPreparedStatement.2=Connection is read-only.
+ServerPreparedStatement.3=Queries leading to data modification are not allowed
+ServerPreparedStatement.6=\ unable to materialize as string due to underlying SQLException:
+ServerPreparedStatement.7=Not supported for server-side prepared statements.
+ServerPreparedStatement.8=No parameters defined during prepareCall()
+ServerPreparedStatement.9=Parameter index out of bounds.
+ServerPreparedStatement.10=\ is not between valid values of 1 and
+ServerPreparedStatement.11=Driver can not re-execute prepared statement when a parameter has been changed
+ServerPreparedStatement.12=from a streaming type to an intrinsic data type without calling clearParameters() first.
+ServerPreparedStatement.13=Statement parameter
+ServerPreparedStatement.14=\ not set.
+ServerPreparedStatement.15=Slow query (exceeded
+ServerPreparedStatement.15a=\ ms., duration:\
+ServerPreparedStatement.16=\ ms):
+ServerPreparedStatement.18=Unknown LONG DATA type '
+ServerPreparedStatement.22=Unsupported character encoding '
+ServerPreparedStatement.24=Error while reading binary stream:
+ServerPreparedStatement.25=Error while reading binary stream:
+ByteArrayBuffer.0=ByteArrayBuffer has no NIO buffers
+ByteArrayBuffer.1=Unsupported character encoding '
+AssertionFailedException.0=ASSERT FAILS: Exception
+AssertionFailedException.1=\ that should not be thrown, was thrown
+NotUpdatable.0=Result Set not updatable.
+NotUpdatable.1=This result set must come from a statement
+NotUpdatable.2=that was created with a result set type of ResultSet.CONCUR_UPDATABLE,
+NotUpdatable.3=the query must select only one table, and must
+NotUpdatable.4=select all primary keys from that table. See the JDBC 2.1 API Specification,
+NotUpdatable.5=section 5.6 for more details.
diff --git a/com/mysql/jdbc/Messages.class b/com/mysql/jdbc/Messages.class
new file mode 100644
index 0000000..b44a385
Binary files /dev/null and b/com/mysql/jdbc/Messages.class differ
diff --git a/com/mysql/jdbc/MiniAdmin.class b/com/mysql/jdbc/MiniAdmin.class
new file mode 100644
index 0000000..7c4f081
Binary files /dev/null and b/com/mysql/jdbc/MiniAdmin.class differ
diff --git a/com/mysql/jdbc/MysqlDataTruncation.class b/com/mysql/jdbc/MysqlDataTruncation.class
new file mode 100644
index 0000000..babebdb
Binary files /dev/null and b/com/mysql/jdbc/MysqlDataTruncation.class differ
diff --git a/com/mysql/jdbc/MysqlDefs.class b/com/mysql/jdbc/MysqlDefs.class
new file mode 100644
index 0000000..c17e3db
Binary files /dev/null and b/com/mysql/jdbc/MysqlDefs.class differ
diff --git a/com/mysql/jdbc/MysqlErrorNumbers.class b/com/mysql/jdbc/MysqlErrorNumbers.class
new file mode 100644
index 0000000..9a876ed
Binary files /dev/null and b/com/mysql/jdbc/MysqlErrorNumbers.class differ
diff --git a/com/mysql/jdbc/MysqlIO.class b/com/mysql/jdbc/MysqlIO.class
new file mode 100644
index 0000000..8443959
Binary files /dev/null and b/com/mysql/jdbc/MysqlIO.class differ
diff --git a/com/mysql/jdbc/MysqlParameterMetadata.class b/com/mysql/jdbc/MysqlParameterMetadata.class
new file mode 100644
index 0000000..21a9ea8
Binary files /dev/null and b/com/mysql/jdbc/MysqlParameterMetadata.class differ
diff --git a/com/mysql/jdbc/MysqlSavepoint.class b/com/mysql/jdbc/MysqlSavepoint.class
new file mode 100644
index 0000000..0a7981e
Binary files /dev/null and b/com/mysql/jdbc/MysqlSavepoint.class differ
diff --git a/com/mysql/jdbc/NamedPipeSocketFactory$NamedPipeSocket.class b/com/mysql/jdbc/NamedPipeSocketFactory$NamedPipeSocket.class
new file mode 100644
index 0000000..3a0cc27
Binary files /dev/null and b/com/mysql/jdbc/NamedPipeSocketFactory$NamedPipeSocket.class differ
diff --git a/com/mysql/jdbc/NamedPipeSocketFactory$RandomAccessFileInputStream.class b/com/mysql/jdbc/NamedPipeSocketFactory$RandomAccessFileInputStream.class
new file mode 100644
index 0000000..8d0fb72
Binary files /dev/null and b/com/mysql/jdbc/NamedPipeSocketFactory$RandomAccessFileInputStream.class differ
diff --git a/com/mysql/jdbc/NamedPipeSocketFactory$RandomAccessFileOutputStream.class b/com/mysql/jdbc/NamedPipeSocketFactory$RandomAccessFileOutputStream.class
new file mode 100644
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diff --git a/com/mysql/jdbc/configs/3-0-Compat.properties b/com/mysql/jdbc/configs/3-0-Compat.properties
new file mode 100644
index 0000000..eaddc06
--- /dev/null
+++ b/com/mysql/jdbc/configs/3-0-Compat.properties
@@ -0,0 +1,16 @@
+#
+# Settings to maintain Connector/J 3.0.x compatibility
+# (as much as it can be)
+#
+
+emptyStringsConvertToZero=true
+jdbcCompliantTruncation=false
+noDatetimeStringSync=true
+nullCatalogMeansCurrent=true
+nullNamePatternMatchesAll=true
+transformedBitIsBoolean=false
+dontTrackOpenResources=true
+zeroDateTimeBehavior=convertToNull
+useServerPrepStmts=false
+autoClosePStmtStreams=true
+processEscapeCodesForPrepStmts=false
\ No newline at end of file
diff --git a/com/mysql/jdbc/configs/clusterBase.properties b/com/mysql/jdbc/configs/clusterBase.properties
new file mode 100644
index 0000000..e87a604
--- /dev/null
+++ b/com/mysql/jdbc/configs/clusterBase.properties
@@ -0,0 +1,4 @@
+# Basic properties for clusters
+autoReconnect=true
+failOverReadOnly=false
+roundRobinLoadBalance=true
\ No newline at end of file
diff --git a/com/mysql/jdbc/configs/fullDebug.properties b/com/mysql/jdbc/configs/fullDebug.properties
new file mode 100644
index 0000000..c1fcdc8
--- /dev/null
+++ b/com/mysql/jdbc/configs/fullDebug.properties
@@ -0,0 +1,6 @@
+# Settings for 'max-debug' style situations
+profileSQL=true
+gatherPerMetrics=true
+useUsageAdvisor=true
+logSlowQueries=true
+explainSlowQueries=true
\ No newline at end of file
diff --git a/com/mysql/jdbc/configs/maxPerformance.properties b/com/mysql/jdbc/configs/maxPerformance.properties
new file mode 100644
index 0000000..703ad7c
--- /dev/null
+++ b/com/mysql/jdbc/configs/maxPerformance.properties
@@ -0,0 +1,25 @@
+#
+# A configuration that maximizes performance, while
+# still staying JDBC-compliant and not doing anything that
+# would be "dangerous" to run-of-the-mill J2EE applications
+#
+# Note that because we're caching things like callable statements
+# and the server configuration, this bundle isn't appropriate
+# for use with servers that get config'd dynamically without
+# restarting the application using this configuration bundle.
+
+cachePrepStmts=true
+cacheCallableStatements=true
+
+cacheServerConfiguration=true
+
+#
+# Reduces amount of calls to database to set
+# session state. "Safe" as long as application uses
+# Connection methods to set current database, autocommit
+# and transaction isolation
+#
+
+useLocalSessionState=true
+elideSetAutoCommits=true
+alwaysSendSetIsolation=false
\ No newline at end of file
diff --git a/com/mysql/jdbc/configs/solarisMaxPerformance.properties b/com/mysql/jdbc/configs/solarisMaxPerformance.properties
new file mode 100644
index 0000000..b4b31a1
--- /dev/null
+++ b/com/mysql/jdbc/configs/solarisMaxPerformance.properties
@@ -0,0 +1,13 @@
+#
+# Solaris has pretty high syscall overhead, so these configs
+# remove as many syscalls as possible.
+#
+
+# Reduce recv() syscalls
+
+useUnbufferedInput=false
+useReadAheadInput=false
+
+# Reduce number of calls to getTimeOfDay()
+
+maintainTimeStats=false
\ No newline at end of file
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diff --git a/com/mysql/jdbc/util/TimezoneDump.class b/com/mysql/jdbc/util/TimezoneDump.class
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diff --git a/copyright.txt b/copyright.txt
new file mode 100644
index 0000000..fe59b27
--- /dev/null
+++ b/copyright.txt
@@ -0,0 +1,18 @@
+/*
+ * Copyright (c) 2007-2011 by The Broad Institute, Inc. and the Massachusetts Institute of Technology.
+ * All Rights Reserved.
+ *
+ * This software is licensed under the terms of the GNU Lesser General Public License (LGPL), Version 2.1 which
+ * is available at http://www.opensource.org/licenses/lgpl-2.1.php.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS." THE BROAD AND MIT MAKE NO REPRESENTATIONS OR WARRANTIES OF
+ * ANY KIND CONCERNING THE SOFTWARE, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT
+ * OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. IN NO EVENT SHALL THE BROAD OR MIT, OR THEIR
+ * RESPECTIVE TRUSTEES, DIRECTORS, OFFICERS, EMPLOYEES, AND AFFILIATES BE LIABLE FOR ANY DAMAGES OF
+ * ANY KIND, INCLUDING, WITHOUT LIMITATION, INCIDENTAL OR CONSEQUENTIAL DAMAGES, ECONOMIC
+ * DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER THE BROAD OR MIT SHALL
+ * BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE
+ * FOREGOING.
+ */
+
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diff --git a/gpl.txt b/gpl.txt
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--- /dev/null
+++ b/gpl.txt
@@ -0,0 +1,674 @@
+ GNU GENERAL PUBLIC LICENSE
+ Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
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+ 12. No Surrender of Others' Freedom.
+
+ If conditions are imposed on you (whether by court order, agreement or
+otherwise) that contradict the conditions of this License, they do not
+excuse you from the conditions of this License. If you cannot convey a
+covered work so as to satisfy simultaneously your obligations under this
+License and any other pertinent obligations, then as a consequence you may
+not convey it at all. For example, if you agree to terms that obligate you
+to collect a royalty for further conveying from those to whom you convey
+the Program, the only way you could satisfy both those terms and this
+License would be to refrain entirely from conveying the Program.
+
+ 13. Use with the GNU Affero General Public License.
+
+ Notwithstanding any other provision of this License, you have
+permission to link or combine any covered work with a work licensed
+under version 3 of the GNU Affero General Public License into a single
+combined work, and to convey the resulting work. The terms of this
+License will continue to apply to the part which is the covered work,
+but the special requirements of the GNU Affero General Public License,
+section 13, concerning interaction through a network will apply to the
+combination as such.
+
+ 14. Revised Versions of this License.
+
+ The Free Software Foundation may publish revised and/or new versions of
+the GNU General Public License from time to time. Such new versions will
+be similar in spirit to the present version, but may differ in detail to
+address new problems or concerns.
+
+ Each version is given a distinguishing version number. If the
+Program specifies that a certain numbered version of the GNU General
+Public License "or any later version" applies to it, you have the
+option of following the terms and conditions either of that numbered
+version or of any later version published by the Free Software
+Foundation. If the Program does not specify a version number of the
+GNU General Public License, you may choose any version ever published
+by the Free Software Foundation.
+
+ If the Program specifies that a proxy can decide which future
+versions of the GNU General Public License can be used, that proxy's
+public statement of acceptance of a version permanently authorizes you
+to choose that version for the Program.
+
+ Later license versions may give you additional or different
+permissions. However, no additional obligations are imposed on any
+author or copyright holder as a result of your choosing to follow a
+later version.
+
+ 15. Disclaimer of Warranty.
+
+ THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
+APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
+HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
+OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
+IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
+ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+ 16. Limitation of Liability.
+
+ IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
+USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.
+
+ 17. Interpretation of Sections 15 and 16.
+
+ If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+ END OF TERMS AND CONDITIONS
+
+ How to Apply These Terms to Your New Programs
+
+ If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+ To do so, attach the following notices to the program. It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+ <one line to give the program's name and a brief idea of what it does.>
+ Copyright (C) <year> <name of author>
+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+ If the program does terminal interaction, make it output a short
+notice like this when it starts in an interactive mode:
+
+ <program> Copyright (C) <year> <name of author>
+ This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+ This is free software, and you are welcome to redistribute it
+ under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License. Of course, your program's commands
+might be different; for a GUI interface, you would use an "about box".
+
+ You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU GPL, see
+<http://www.gnu.org/licenses/>.
+
+ The GNU General Public License does not permit incorporating your program
+into proprietary programs. If your program is a subroutine library, you
+may consider it more useful to permit linking proprietary applications with
+the library. If this is what you want to do, use the GNU Lesser General
+Public License instead of this License. But first, please read
+<http://www.gnu.org/philosophy/why-not-lgpl.html>.
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diff --git a/license/LICENSE b/license/LICENSE
new file mode 100644
index 0000000..75b5248
--- /dev/null
+++ b/license/LICENSE
@@ -0,0 +1,202 @@
+
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diff --git a/license/LICENSE.dom-documentation.txt b/license/LICENSE.dom-documentation.txt
new file mode 100644
index 0000000..e4226c7
--- /dev/null
+++ b/license/LICENSE.dom-documentation.txt
@@ -0,0 +1,73 @@
+xml-commons/java/external/LICENSE.dom-documentation.txt $Id: LICENSE.dom-documentation.txt 226215 2005-06-03 22:49:13Z mrglavas $
+
+
+This license came from: http://www.w3.org/Consortium/Legal/copyright-documents-20021231
+
+
+W3C� DOCUMENT LICENSE
+http://www.w3.org/Consortium/Legal/2002/copyright-documents-20021231
+
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+
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+ http://www.w3.org/Consortium/Legal/2002/copyright-documents-20021231"
+ 3. If it exists, the STATUS of the W3C document.
+
+When space permits, inclusion of the full text of this NOTICE should be
+provided. We request that authorship attribution be provided in any software,
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+No right to create modifications or derivatives of W3C documents is granted
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+THIS DOCUMENT IS PROVIDED "AS IS," AND COPYRIGHT HOLDERS MAKE NO
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+
+COPYRIGHT HOLDERS WILL NOT BE LIABLE FOR ANY DIRECT, INDIRECT, SPECIAL OR
+CONSEQUENTIAL DAMAGES ARISING OUT OF ANY USE OF THE DOCUMENT OR THE
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+
+The name and trademarks of copyright holders may NOT be used in advertising
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+written prior permission. Title to copyright in this document will at all
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+
+----------------------------------------------------------------------------
+
+This formulation of W3C's notice and license became active on December 31 2002.
+This version removes the copyright ownership notice such that this license can
+be used with materials other than those owned by the W3C, moves information on
+style sheets, DTDs, and schemas to the Copyright FAQ, reflects that ERCIM is
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+common questions about using materials from our site, such as the translating
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+to site-policy at w3.org.
+
+Joseph Reagle <site-policy at w3.org>
+
+Last revised by Reagle $Date: 2005-06-03 18:49:13 -0400 (Fri, 03 Jun 2005) $
diff --git a/license/LICENSE.dom-software.txt b/license/LICENSE.dom-software.txt
new file mode 100644
index 0000000..93a8f4e
--- /dev/null
+++ b/license/LICENSE.dom-software.txt
@@ -0,0 +1,61 @@
+xml-commons/java/external/LICENSE.dom-software.txt $Id: LICENSE.dom-software.txt 226215 2005-06-03 22:49:13Z mrglavas $
+
+
+This license came from: http://www.w3.org/Consortium/Legal/copyright-software-20021231
+
+
+W3C� SOFTWARE NOTICE AND LICENSE
+http://www.w3.org/Consortium/Legal/2002/copyright-software-20021231
+
+This work (and included software, documentation such as READMEs, or other
+related items) is being provided by the copyright holders under the following
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+that you have read, understood, and will comply with the following terms and
+conditions.
+
+Permission to copy, modify, and distribute this software and its documentation,
+with or without modification, for any purpose and without fee or royalty is
+hereby granted, provided that you include the following on ALL copies of the
+software and documentation or portions thereof, including modifications:
+
+ 1. The full text of this NOTICE in a location viewable to users of the
+ redistributed or derivative work.
+ 2. Any pre-existing intellectual property disclaimers, notices, or terms
+ and conditions. If none exist, the W3C Software Short Notice should be
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+ 3. Notice of any changes or modifications to the files, including the date
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+
+THIS SOFTWARE AND DOCUMENTATION IS PROVIDED "AS IS," AND COPYRIGHT HOLDERS MAKE
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+
+COPYRIGHT HOLDERS WILL NOT BE LIABLE FOR ANY DIRECT, INDIRECT, SPECIAL OR
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+
+The name and trademarks of copyright holders may NOT be used in advertising or
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+Title to copyright in this software and any associated documentation will at
+all times remain with copyright holders.
+
+____________________________________
+
+This formulation of W3C's notice and license became active on December 31 2002.
+This version removes the copyright ownership notice such that this license can
+be used with materials other than those owned by the W3C, reflects that ERCIM
+is now a host of the W3C, includes references to this specific dated version of
+the license, and removes the ambiguous grant of "use". Otherwise, this version
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+Software Foundation's assessment of GPL compatibility and OSI's certification
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+this notice can be directed to site-policy at w3.org.
+
+Joseph Reagle <site-policy at w3.org>
+
+Last revised by Reagle $Date: 2005-06-03 18:49:13 -0400 (Fri, 03 Jun 2005) $
diff --git a/license/LICENSE.sac.html b/license/LICENSE.sac.html
new file mode 100644
index 0000000..e203a58
--- /dev/null
+++ b/license/LICENSE.sac.html
@@ -0,0 +1,75 @@
+<?xml version="1.0" encoding="iso-8859-1"?>
+<!-- $Id: LICENSE.sac.html 477037 2006-11-20 04:30:53Z mrglavas $ -->
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+ <title>W3C IPR SOFTWARE NOTICE</title>
+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
+ <style type='text/css'>
+ body { background: white; color: black; }
+ </style>
+</head>
+
+<body>
+<h1>W3C IPR SOFTWARE NOTICE</h1>
+
+<h3>Copyright � 2002 World Wide Web Consortium, (Massachusetts Institute of
+Technology, Institut National de Recherche en Informatique et en Automatique,
+Keio University). All Rights Reserved.</h3>
+
+<p><b>Note:</b> The original version of the W3C Software Copyright Notice and
+License could be found at <a
+href="http://www.w3.org/Consortium/Legal/copyright-software-19980720">http://www.w3.org/Consortium/Legal/copyright-software-19980720</a></p>
+
+<h3>Copyright � 1994-2002 <a href="http://www.w3.org/">World Wide Web
+Consortium</a>, (<a href="http://www.lcs.mit.edu/">Massachusetts Institute of
+Technology</a>, <a href="http://www.inria.fr/">Institut National de Recherche
+en Informatique et en Automatique</a>, <a href="http://www.keio.ac.jp/">Keio
+University</a>). All Rights Reserved. http://www.w3.org/Consortium/Legal/</h3>
+
+<p>This W3C work (including software, documents, or other related items) is
+being provided by the copyright holders under the following license. By
+obtaining, using and/or copying this work, you (the licensee) agree that you
+have read, understood, and will comply with the following terms and
+conditions:</p>
+
+<p>Permission to use, copy, and modify this software and its documentation,
+with or without modification,� for any purpose and without fee or royalty is
+hereby granted, provided that you include the following on ALL copies of the
+software and documentation or portions thereof, including modifications, that
+you make:</p>
+<ol>
+ <li>The full text of this NOTICE in a location viewable to users of the
+ redistributed or derivative work.</li>
+ <li>Any pre-existing intellectual property disclaimers, notices, or terms
+ and conditions. If none exist, a short notice of the following form
+ (hypertext is preferred, text is permitted) should be used within the body
+ of any redistributed or derivative code: "Copyright � 2002
+ <a href="http://www.w3.org/">World Wide Web Consortium</a>, (<a
+ href="http://www.lcs.mit.edu/">Massachusetts Institute of Technology</a>,
+ <a href="http://www.inria.fr/">Institut National de Recherche en
+ Informatique et en Automatique</a>, <a href="http://www.keio.ac.jp/">Keio
+ University</a>). All Rights Reserved.
+ http://www.w3.org/Consortium/Legal/"</li>
+ <li>Notice of any changes or modifications to the W3C files, including the
+ date changes were made. (We recommend you provide URIs to the location
+ from which the code is derived.)</li>
+</ol>
+
+<p>THIS SOFTWARE AND DOCUMENTATION IS PROVIDED "AS IS," AND COPYRIGHT HOLDERS
+MAKE NO REPRESENTATIONS OR WARRANTIES, EXPRESS OR IMPLIED, INCLUDING BUT NOT
+LIMITED TO, WARRANTIES OF MERCHANTABILITY OR FITNESS FOR ANY PARTICULAR
+PURPOSE OR THAT THE USE OF THE SOFTWARE OR DOCUMENTATION WILL NOT INFRINGE ANY
+THIRD PARTY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS.</p>
+
+<p>COPYRIGHT HOLDERS WILL NOT BE LIABLE FOR ANY DIRECT, INDIRECT, SPECIAL OR
+CONSEQUENTIAL DAMAGES ARISING OUT OF ANY USE OF THE SOFTWARE OR
+DOCUMENTATION.</p>
+
+<p>The name and trademarks of copyright holders may NOT be used in advertising
+or publicity pertaining to the software without specific, written prior
+permission. Title to copyright in this software and any associated
+documentation will at all times remain with copyright holders.</p>
+</body>
+</html>
diff --git a/license/LICENSE.sax.txt b/license/LICENSE.sax.txt
new file mode 100644
index 0000000..0738c24
--- /dev/null
+++ b/license/LICENSE.sax.txt
@@ -0,0 +1,23 @@
+xml-commons/java/external/LICENSE.sax.txt $Id: LICENSE.sax.txt 225954 2002-01-31 23:26:48Z curcuru $
+
+
+This license came from: http://www.megginson.com/SAX/copying.html
+ However please note future versions of SAX may be covered
+ under http://saxproject.org/?selected=pd
+
+
+This page is now out of date -- see the new SAX site at
+http://www.saxproject.org/ for more up-to-date
+releases and other information. Please change your bookmarks.
+
+
+SAX2 is Free!
+
+I hereby abandon any property rights to SAX 2.0 (the Simple API for
+XML), and release all of the SAX 2.0 source code, compiled code, and
+documentation contained in this distribution into the Public Domain.
+SAX comes with NO WARRANTY or guarantee of fitness for any
+purpose.
+
+David Megginson, david at megginson.com
+2000-05-05
\ No newline at end of file
diff --git a/license/NOTICE b/license/NOTICE
new file mode 100644
index 0000000..d092366
--- /dev/null
+++ b/license/NOTICE
@@ -0,0 +1,16 @@
+ =========================================================================
+ == NOTICE file corresponding to section 4(d) of the Apache License, ==
+ == Version 2.0, in this case for the Apache xml-commons xml-apis ==
+ == distribution. ==
+ =========================================================================
+
+ Apache XML Commons XML APIs
+ Copyright 2006 The Apache Software Foundation.
+
+ This product includes software developed at
+ The Apache Software Foundation (http://www.apache.org/).
+
+ Portions of this software were originally based on the following:
+ - software copyright (c) 1999, IBM Corporation., http://www.ibm.com.
+ - software copyright (c) 1999, Sun Microsystems., http://www.sun.com.
+ - software copyright (c) 2000 World Wide Web Consortium, http://www.w3.org
diff --git a/license/README.dom.txt b/license/README.dom.txt
new file mode 100644
index 0000000..4f6fb31
--- /dev/null
+++ b/license/README.dom.txt
@@ -0,0 +1,56 @@
+xml-commons/java/external/README.dom.txt $Id: README.dom.txt 477038 2006-11-20 04:40:36Z mrglavas $
+
+
+HEAR YE, HEAR YE!
+
+
+All of the .java software and associated documentation about
+the DOM in this repository are distributed under the license
+from the W3C, which is provided herein.
+
+
+LICENSE.dom-software.txt covers all software from the W3C
+including the following items in the xml-commons project:
+
+ xml-commons/java/external/src/org/w3c
+ and all subdirectories
+
+(Note: SAC (The Simple API for CSS) has been published under an older
+version of the W3C license. The original license file is LICENSE.sac.html.)
+
+LICENSE.dom-documentation.txt covers all documentation from the W3C
+including the following items in the xml-commons project:
+
+ xml-commons/java/external/xdocs/dom
+ and all subdirectories
+
+The actual DOM Java Language Binding classes in xml-commons came from:
+ http://www.w3.org/TR/2004/REC-DOM-Level-3-Core-20040407/java-binding.html
+
+The specification of DOM Level 3's various parts is at:
+ http://www.w3.org/TR/2004/REC-DOM-Level-3-Core-20040407/
+ http://www.w3.org/TR/2004/REC-DOM-Level-3-LS-20040407/
+ http://www.w3.org/TR/2004/NOTE-DOM-Level-3-XPath-20040226/
+
+The specification of DOM Level 2's various parts is at:
+ http://www.w3.org/TR/2000/REC-DOM-Level-2-Events-20001113/
+ http://www.w3.org/TR/2000/REC-DOM-Level-2-Style-20001113/
+ http://www.w3.org/TR/2000/REC-DOM-Level-2-Traversal-Range-20001113/
+ http://www.w3.org/TR/2000/REC-DOM-Level-2-Views-20001113/
+
+The specification of DOM Level 1's various parts is at:
+ http://www.w3.org/TR/1998/REC-DOM-Level-1-19981001/level-one-html.html
+
+Links to all available W3C DOM Java Bindings can be found at:
+ http://www.w3.org/DOM/DOMTR
+
+The actual classes of The Simple API for CSS (SAC) came from:
+ http://www.w3.org/Style/CSS/SAC/
+ http://www.w3.org/2002/06/sacjava-1.3.zip
+
+The actual DOM Java Language Binding classes for SMIL came from:
+ http://dev.w3.org/cvsweb/java/classes/org/w3c/dom/smil/
+ (both ElementTimeControl.java and TimeEvent.java were taken at revision 1.1)
+
+The actual DOM Java Language Binding classes for SVG 1.1 came from:
+ http://www.w3.org/TR/SVG11/java.html
\ No newline at end of file
diff --git a/license/README.sax.txt b/license/README.sax.txt
new file mode 100644
index 0000000..fd87876
--- /dev/null
+++ b/license/README.sax.txt
@@ -0,0 +1,24 @@
+xml-commons/java/external/README.sax.txt $Id: README.sax.txt 225954 2002-01-31 23:26:48Z curcuru $
+
+
+HEAR YE, HEAR YE!
+
+
+All of the .java software and associated documentation about
+SAX in this repository are distributed freely in the
+public domain.
+
+
+LICENSE.sax.txt covers all software and documentation from the
+megginson.com including the following in the xml-commons project:
+
+ xml-commons/java/external/src/org/xml/sax
+ and all subdirectories
+ xml-commons/java/external/xdocs/sax
+ and all subdirectories
+
+
+The actual SAX classes in xml-commons came from:
+ http://www.megginson.com/Software/index.html
+ The original versions are tagged 'SAX-2_0-r2-prerelease'
+
diff --git a/log4j.properties b/log4j.properties
new file mode 100644
index 0000000..36c6b48
--- /dev/null
+++ b/log4j.properties
@@ -0,0 +1,27 @@
+#
+# Copyright (c) 2007-2011 by The Broad Institute of MIT and Harvard. All Rights Reserved.
+#
+# This software is licensed under the terms of the GNU Lesser General Public License (LGPL),
+# Version 2.1 which is available at http://www.opensource.org/licenses/lgpl-2.1.php.
+#
+# THE SOFTWARE IS PROVIDED "AS IS." THE BROAD AND MIT MAKE NO REPRESENTATIONS OR
+# WARRANTES OF ANY KIND CONCERNING THE SOFTWARE, EXPRESS OR IMPLIED, INCLUDING,
+# WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR
+# PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER
+# OR NOT DISCOVERABLE. IN NO EVENT SHALL THE BROAD OR MIT, OR THEIR RESPECTIVE
+# TRUSTEES, DIRECTORS, OFFICERS, EMPLOYEES, AND AFFILIATES BE LIABLE FOR ANY DAMAGES
+# OF ANY KIND, INCLUDING, WITHOUT LIMITATION, INCIDENTAL OR CONSEQUENTIAL DAMAGES,
+# ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER
+# THE BROAD OR MIT SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT
+# SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
+#
+
+log4j.rootLogger=INFO, stdout
+#log4j.rootLogger=DEBUG, stdout
+#log4j.logger.org.broad.igv=DEBUG, stdout
+
+log4j.appender.stdout=org.apache.log4j.ConsoleAppender
+log4j.appender.stdout.layout=org.apache.log4j.PatternLayout
+log4j.appender.stdout.layout.ConversionPattern=%p [%d{ISO8601}] [%F:%L] [%t] %m%n
+
+# The file appender is set in the application
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diff --git a/org/apache/batik/bridge/resources/Messages.properties b/org/apache/batik/bridge/resources/Messages.properties
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--- /dev/null
+++ b/org/apache/batik/bridge/resources/Messages.properties
@@ -0,0 +1,140 @@
+# -----------------------------------------------------------------------------
+#
+# Licensed to the Apache Software Foundation (ASF) under one or more
+# contributor license agreements. See the NOTICE file distributed with
+# this work for additional information regarding copyright ownership.
+# The ASF licenses this file to You under the Apache License, Version 2.0
+# (the "License"); you may not use this file except in compliance with
+# the License. You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+# $Id: Messages.properties 475477 2006-11-15 22:44:28Z cam $
+# -----------------------------------------------------------------------------
+
+attribute.missing = \
+{0}:{1}\n\
+The attribute "{3}" of the element <{2}> is required
+
+attribute.malformed = \
+{0}:{1}\n\
+The attribute "{3}" of the element <{2}> is invalid
+
+attribute.not.animatable = \
+{0}:{1}\n\
+The attribute "{4}" of the element <{3}> is not animatable
+
+type.not.animatable = \
+{0}:{1}\n\
+The attribute "{4}" of the element <{3}> cannot be animated with the \
+<{5}> element
+
+length.negative = \
+{0}:{1}\n\
+The attribute "{3}" of the element <{2}> cannot be negative
+
+css.length.negative = \
+{0}:{1}\n\
+The CSS property "{3}" found on the element <{2}> cannot be negative
+
+css.uri.badTarget = \
+{0}:{1}\n\
+The URI "{3}"\n\
+for a CSS property found on the element <{2}> is invalid
+
+xlink.href.circularDependencies = \
+{0}:{1}\n\
+A circular dependency has been detected on the element <{2}> for the URI:\n\
+"{3}"
+
+uri.malformed = \
+{0}:{1}\n\
+The URI "{3}"\n\
+specified on the element <{2}> is invalid
+
+uri.badTarget = \
+{0}:{1}\n\
+Cannot find the referenced element:\n\
+"{3}"\n\
+specified on the element <{2}> - may be a problem of ''id''
+
+uri.io = \
+{0}:{1}\n\
+An I/O error occured while processing the URI:\n\
+"{3}"\n\
+specified on the element <{2}>
+
+uri.unsecure = \
+{0}:{1}\n\
+A security exception occured while processing the URI:\n\
+"{3}"\n\
+specified on the element <{2}>
+
+uri.referenceDocument = \
+{0}:{1}\n\
+The URI "{3}"\n\
+specified on the element <{2}> references an entire document. \n\
+This is illegal: The element <{2}> must reference an element\n\
+inside a document.
+
+uri.image.invalid = \
+{0}:{1}\n\
+The URI "{3}"\n\
+specified on the element <{2}> is invalid
+
+uri.image.broken = \
+{0}:{1}\n\
+The URI "{3}"\n\
+on element <{2}> can''t be opened because:\n\
+{4}
+
+uri.image.error = \
+The URI can''t be opened:\n\
+{0}
+
+##########################################################################
+# Messages for DefaultScriptSecurity
+##########################################################################
+
+DefaultScriptSecurity.error.cannot.access.document.url = \
+Could not access the current document URL when trying to load script file {0}. Script will not be loaded as it is not possible to verify it comes from the same location as the document.
+
+DefaultScriptSecurity.error.script.from.different.url = \
+The document references a script file ({0}) which comes from different location than the document itself. This is not allowed with the current security settings and that script will not be loaded.
+
+EmbededScriptSecurity.error.script.not.embeded = \
+The document references a script file ({0}) which is not embeded in the document. This is not allowed with the current security settings and that script will not be loaded.
+
+EmbededExternalResourceSecurity.error.external.resource.not.embeded = \
+The document references a resource ({0}) which is not embeded in the document. This is not allowed with the current security settings and that resource cannot be loaded.
+
+NoLoadScriptSecurity.error.no.script.of.type.allowed = \
+Scripts of type ({0}) cannot be loaded and executed with the current security settings.
+
+DefaultExternalResourceSecurity.error.cannot.access.document.url = \
+Could not access the current document URL when trying to load an external resource {0}. The external resource will not be loaded as it is not possible to verify it comes from the same location as the document.
+
+DefaultExternalResourceSecurity.error.external.resource.from.different.url = \
+The document references a external resource ({0}) which comes from different location than the document itself. This is not allowed for security reasons and that resource will not be loaded.
+
+NoLoadExternalResourceSecurity.error.no.external.resource.allowed = \
+The security settings do not allow any external resources to be referenced from the document
+
+##########################################################################
+# Messages for BaseScriptingEnvironment
+##########################################################################
+
+BaseScriptingEnvironment.constant.inline.script.description = \
+Inline {1} {0}:{2}
+
+BaseScriptingEnvironment.constant.event.script.description = \
+Event attribute {0}:{2} {1}
+
+SVG12ScriptingEnvironment.constant.handler.script.description = \
+Handler {0}:{3} {1} {2}
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--- /dev/null
+++ b/org/apache/batik/css/engine/resources/Messages.properties
@@ -0,0 +1,43 @@
+# -----------------------------------------------------------------------------
+#
+# Licensed to the Apache Software Foundation (ASF) under one or more
+# contributor license agreements. See the NOTICE file distributed with
+# this work for additional information regarding copyright ownership.
+# The ASF licenses this file to You under the Apache License, Version 2.0
+# (the "License"); you may not use this file except in compliance with
+# the License. You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+# $Id: Messages.properties 475477 2006-11-15 22:44:28Z cam $
+# -----------------------------------------------------------------------------
+
+syntax.error.at = \
+{0}:\nInvalid CSS document.\n{1}
+
+media.error = \
+Invalid CSS media:\n{1}
+
+property.syntax.error.at = \
+{0}:\n\
+The attribute "{1}" represents an invalid CSS value ("{2}").\n\
+Original message:\n{3}
+
+style.syntax.error.at = \
+{0}:\n\
+The attribute "{1}" represents an invalid CSS declaration ("{2}").\n\
+Original message:\n{3}
+
+stylesheet.syntax.error = \
+{0}:\n\
+The following stylesheet represents an invalid \n\
+CSS document.\n{1}\nOriginal message:\n{2}
+
+invalid.property = \
+{0}:\nThe "{1}" CSS property is not supported.
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diff --git a/org/apache/batik/css/engine/value/resources/Messages.properties b/org/apache/batik/css/engine/value/resources/Messages.properties
new file mode 100644
index 0000000..fe2da25
--- /dev/null
+++ b/org/apache/batik/css/engine/value/resources/Messages.properties
@@ -0,0 +1,98 @@
+# -----------------------------------------------------------------------------
+#
+# Licensed to the Apache Software Foundation (ASF) under one or more
+# contributor license agreements. See the NOTICE file distributed with
+# this work for additional information regarding copyright ownership.
+# The ASF licenses this file to You under the Apache License, Version 2.0
+# (the "License"); you may not use this file except in compliance with
+# the License. You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+# $Id: Messages.properties 475477 2006-11-15 22:44:28Z cam $
+# -----------------------------------------------------------------------------
+
+invalid.access = \
+The invoked method is not enabled for the "{0}" property.
+
+invalid.value.access = \
+The invoked method cannot be called for {0,choice,\
+0#the inherit value|\
+1#a primitive value|\
+2#the value list|\
+3#a custom value\
+} type.
+
+invalid.string.type = \
+The given string type ({1}) is invalid for \
+the "{0}" property \
+(see org.w3c.dom.css.CSSPrimitiveValue).
+
+invalid.identifier = \
+The "{1}" identifier is not a valid value for the "{0}" property.
+
+# !!! choices limited to 30 (java.text bug).
+
+invalid.lexical.unit = \
+The "{0}" property does not support {1,choice,\
+13#integer|\
+14#real|\
+15#em|\
+16#ex|\
+17#pixel|\
+18#inch|\
+19#centimeter|\
+20#millimeter|\
+21#point|\
+22#pica|\
+23#percentage|\
+24#URI|\
+25#counter function|\
+26#counters function|\
+27#RGB color|\
+28#degree|\
+29#gradian|\
+30#radian|\
+31#millisecond|\
+32#second|\
+33#hertz|\
+34#kilohertz|\
+35#identifier|\
+36#string|\
+37#attr function|\
+38#rect function|\
+39#unicode range|\
+40#identifier|\
+41#function|\
+42#dimension\
+} values.
+
+malformed.rect = \
+The ''{0}'' property value is malformed.
+
+invalid.float.type = \
+The given CSS primitive value ({1,choice,\
+0#CSS_UNKNOWN|\
+19#CSS_STRING|\
+20#CSS_URI|\
+30#CSS_IDENT|\
+31#CSS_ATTR|\
+32#CSS_COUNTER|\
+33#CSS_RECT|\
+34#CSS_RGBCOLOR\
+}) represents an invalid type for the "{0}".
+
+invalid.float.value = \
+The number ''{1}'' represents an invalid value for the ''{0}'' property.
+
+invalid.rgb.component.unit = \
+The "{0}" property does not support RGB values with type #{1} components.
+
+malformed.lexical.unit = \
+A malformed value was assigned to a "{0}" property.
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diff --git a/org/apache/batik/css/parser/resources/Messages.properties b/org/apache/batik/css/parser/resources/Messages.properties
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--- /dev/null
+++ b/org/apache/batik/css/parser/resources/Messages.properties
@@ -0,0 +1,88 @@
+# -----------------------------------------------------------------------------
+#
+# Licensed to the Apache Software Foundation (ASF) under one or more
+# contributor license agreements. See the NOTICE file distributed with
+# this work for additional information regarding copyright ownership.
+# The ASF licenses this file to You under the Apache License, Version 2.0
+# (the "License"); you may not use this file except in compliance with
+# the License. You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+# The error messages for the CSS parser.
+#
+# Author: stephane at hillion.org
+# $Id: Messages.properties 569967 2007-08-27 02:54:20Z cam $
+# -----------------------------------------------------------------------------
+
+charset.string = \
+A string was expected in a @charset rule.
+
+semicolon = \
+';' expected.
+
+colon = \
+':' expected.
+
+eof = \
+Unexpected end of file.
+
+eof.expected = \
+End of file expected.
+
+character = \
+Unexpected character.
+
+string.or.uri = \
+String or URI expected.
+
+identifier = \
+Identifier expected.
+
+identifier.character = \
+Invalid identifier start character.
+
+identifier.or.string = \
+Identifier or string expected.
+
+left.curly.brace = \
+'{' expected.
+
+right.curly.brace = \
+'}' expected.
+
+right.brace = \
+')' expected.
+
+right.bracket = \
+']' expected.
+
+token = \
+Unexpected token: {0} (see LexicalUnits).
+
+rgb.color = \
+Invalid RGB color: {0}.
+
+encoding = \
+Invalid encoding: {0}.
+
+number.format = \
+Invalid number.
+
+duplicate.pseudo.element = \
+A pseudo element has already been defined.
+
+pseudo.element.position = \
+Pseudo element cannot occur before the end of the selector.
+
+pseudo.function = \
+Invalid pseudo-function.
+
+empty.source = \
+Empty input source.
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diff --git a/org/apache/batik/dom/resources/Messages.properties b/org/apache/batik/dom/resources/Messages.properties
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--- /dev/null
+++ b/org/apache/batik/dom/resources/Messages.properties
@@ -0,0 +1,181 @@
+# -----------------------------------------------------------------------------
+#
+# Licensed to the Apache Software Foundation (ASF) under one or more
+# contributor license agreements. See the NOTICE file distributed with
+# this work for additional information regarding copyright ownership.
+# The ASF licenses this file to You under the Apache License, Version 2.0
+# (the "License"); you may not use this file except in compliance with
+# the License. You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+# The error messages for DOM.
+#
+# Author: Stephane Hillion
+# $Id: Messages.properties 475477 2006-11-15 22:44:28Z cam $
+# -----------------------------------------------------------------------------
+
+add.ancestor = \
+Cannot add the given node as a child of the current node (type: {0}, \
+name: {1}) since it is an ancestor of (or the same as) this one.
+
+import.document = \
+A Document node cannot be imported.
+
+import.document.type = \
+A DocumentType node cannot be imported.
+
+add.self = \
+Cannot add a node as a child of it's self (name: {1})
+
+attribute.missing = \
+The "{0}" attribute was not found.
+
+attribute.missing.ns = \
+The \{{0}, {1}\} attribute was not found.
+
+attribute.value = \
+The given attribute value "{0}" is invalid.
+
+cdata.section.split = \
+A CDATA section was split.
+
+child.missing = \
+The child node (type: {0}, name: {1}) is missing.
+
+child.type = \
+The current node (type: {0}, name: {1}) do not allow children of the given \
+type (type: {2}, name: {3})
+
+children.not.allowed = \
+The current node (type: {0}, name: {1}) cannot have children.
+
+cloning.error = \
+An error occured while cloning a node (type: {0}, name: {1}). \
+The original error message was: "{2}".
+
+document.child.already.exists = \
+The node (type: {0}, name: {1}) cannot be inserted, since the document \
+node already has a node of type {0}.
+
+detached.iterator = \
+The iterator was detached from the document.
+
+domconfig.param.not.found = \
+The requested DOMConfiguration parameter "{0}" was not found.
+
+domconfig.param.type = \
+Invalid type when setting DOMConfiguration parameter "{0}".
+
+domconfig.param.value = \
+Unsupported value when setting DOMConfiguration parameter "{0}".
+
+import.node = \
+Cannot import node.
+
+import.document = \
+A Document node cannot be imported.
+
+import.document.type = \
+A DocumentType node cannot be imported.
+
+invalid.element = \
+The current document is unable to create an element of the requested type \
+(namespace: {0}, name: {1}).
+
+inuse.attribute = \
+The given attribute "{0}" is already in use.
+
+unspecified.event = \
+Event type was not specified before dispatch.
+
+namespace = \
+The invoked method requires the current node (type: {0}, name: {1}) to be \
+placed in a non-anonymous namespace.
+
+namespace.uri = \
+The namespace URI "{2}" is invalid. Current node type: {0}, name: {1}.
+
+need.parent = \
+A text node needs a parent node in order to be split.
+
+negative.count = \
+The given count ({0}) is negative.
+
+node.from.wrong.document = \
+The given node (type: {0}, name: {1}) was not created by the current document.
+
+node.type = \
+An attempt as been made to invoke an invalid method for the current node \
+(type: {0}, name: {1}).
+
+null.root = \
+Iterators do not support null root nodes.
+
+null.current.node = \
+An attempt was made to set the current node of a tree walker to null.
+
+offset = \
+The given offset ({0}) is out of range.
+
+parent.child.mismatch = \
+The node (type: {0}, name: {1}) must be a child of the 'parent' node
+(type: {2}, name: {3}) but it is not.
+
+parent.not.allowed = \
+The current node (type: {0}, name: {1}) cannot have parent.
+
+prefix = \
+The prefix "{2}" is invalid. Current node type: {0}, name: {1}.
+
+qname = \
+The QName "{2}" is invalid. Current node type: {0}, name: {1}.
+
+readonly.node = \
+The current node (type: {0}, name: {1}) is read-only.
+
+rename.document.element = \
+Cannot rename the document element.
+
+rename.node = \
+The current node (type: {0}, name: {1}) cannot be renamed.
+
+sibling.not.allowed = \
+The current node (type: {0}, name: {1}) cannot have siblings.
+
+unsupported.event = \
+The event object was not created with DocumentEvent.createEvent() or does not \
+support the CustomEvent interface.
+
+wf.invalid.character = \
+Invalid character found in node content (type: {0}, name: {1}): "{2}".
+
+wf.invalid.name = \
+Invalid character found in node name {0}.
+
+xml.version = \
+XML version {0} is not supported.
+
+xml.name = \
+The given name ("{0}") is an invalid XML name.
+
+xpath.invalid.expression = \
+Invalid XPath expression ({0}): "{1}".
+
+xpath.invalid.context.node = \
+Invalid context node (type: {0}, name: {1}) for XPath evaluation.
+
+xpath.invalid.result.type = \
+Invalid XPath result type {0}.
+
+xpath.cannot.convert.result = \
+Cannot convert result of XPath evaluation to type {0}: "{1}".
+
+xpath.error = \
+Error evaluationg XPath expression ({0}): "{1}".
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diff --git a/org/apache/batik/dom/svg/resources/Messages.properties b/org/apache/batik/dom/svg/resources/Messages.properties
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index 0000000..9c0c566
--- /dev/null
+++ b/org/apache/batik/dom/svg/resources/Messages.properties
@@ -0,0 +1,99 @@
+# -----------------------------------------------------------------------------
+#
+# Licensed to the Apache Software Foundation (ASF) under one or more
+# contributor license agreements. See the NOTICE file distributed with
+# this work for additional information regarding copyright ownership.
+# The ASF licenses this file to You under the Apache License, Version 2.0
+# (the "License"); you may not use this file except in compliance with
+# the License. You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+# The error message for SVG DOM.
+#
+# $Id: Messages.properties 475477 2006-11-15 22:44:28Z cam $
+# -----------------------------------------------------------------------------
+
+id.name = \
+"{0}" represents an invalid ID name for SVG.
+
+stylesheet.type = \
+"{0}" represents an unsupported stylesheet type.
+
+zoom.and.pan = \
+The given value ({0}) represents an invalid SVGZoomAndPan value.
+
+preserve.aspect.ratio = \
+The given value ({0}) represents an invalid SVGPreserveAspectRatio value.
+
+preserve.aspect.ratio.align = \
+The given value ({0}) represents an invalid SVGPreserveAspectRatio align value.
+
+preserve.aspect.ratio.meet.or.slice = \
+The given value ({0}) represents an invalid SVGPreserveAspectRatio meet-or-slice value.
+
+index.out.of.bounds = \
+The given index ({0}) is out of bounds.
+
+doctype.not.supported = \
+Cannot create a SVG DocumentType object.
+
+css.parser.class = \
+The CSS parser class {0} cannot be found.
+
+css.parser.creation = \
+The CSS parser class '{0}' cannot be instantiated.
+
+css.parser.access = \
+The CSS parser class '{0}' cannot be accessed.
+
+noninvertiblematrix = \
+The matrix is not invertible.
+
+readonly.length = \
+This SVGLength is readonly.
+
+readonly.length.list = \
+This SVGLength is readonly.
+
+readonly.pathseg.list = \
+This SVGPathSegList is readonly.
+
+readonly.transform.list = \
+This SVGTransformList is readonly.
+
+readonly.preserve.aspect.ratio = \
+This SVGPreserveAspectRatio is readonly.
+
+readonly.point = \
+This SVGPoint is readonly.
+
+readonly.point.list = \
+This SVGPointList is readonly.
+
+readonly.rect = \
+This SVGRect is readonly.
+
+readonly.angle = \
+This SVGAngle is readonly.
+
+animation.dur.indefinite = \
+The simple duration of the animation element is indefinite.
+
+expected.point = \
+Expected an object of type SVGPoint.
+
+expected.length = \
+Expected an object of type SVGLength.
+
+expected.transform = \
+Expected an object of type SVGTransform.
+
+invalid.suspend.handle = \
+Invalid suspend handle ID {0}.
diff --git a/org/apache/batik/dom/svg/resources/UserAgentStyleSheet.css b/org/apache/batik/dom/svg/resources/UserAgentStyleSheet.css
new file mode 100644
index 0000000..8127697
--- /dev/null
+++ b/org/apache/batik/dom/svg/resources/UserAgentStyleSheet.css
@@ -0,0 +1,6 @@
+/*
+ * The default SVG style sheet.
+ */
+svg, symbol, image, marker, pattern, foreignObject { overflow: hidden }
+
+/* svg { width:attr(width); height:attr(height) } */
diff --git a/org/apache/batik/dom/svg/resources/dtdids.properties b/org/apache/batik/dom/svg/resources/dtdids.properties
new file mode 100644
index 0000000..a6e9bfe
--- /dev/null
+++ b/org/apache/batik/dom/svg/resources/dtdids.properties
@@ -0,0 +1,68 @@
+# -----------------------------------------------------------------------------
+#
+# Licensed to the Apache Software Foundation (ASF) under one or more
+# contributor license agreements. See the NOTICE file distributed with
+# this work for additional information regarding copyright ownership.
+# The ASF licenses this file to You under the Apache License, Version 2.0
+# (the "License"); you may not use this file except in compliance with
+# the License. You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+# The publicIds property represents the list of SVG DTD IDs supported by
+# this SVG DOMImplementation.
+#
+# $Id: dtdids.properties 475477 2006-11-15 22:44:28Z cam $
+# -----------------------------------------------------------------------------
+
+publicIds = \
+ -//W3C//DTD SVG 1.0//EN\
+ -//W3C//DTD SVG 20010904//EN\
+ -//W3C//DTD SVG 20001102//EN\
+ -//W3C//DTD SVG 20000802//EN\
+ -//W3C//DTD SVG 20000303 Stylable//EN\
+ -//W3C//DTD SVG 1.1//EN\
+ -//W3C//DTD SVG 1.1 Basic//EN\
+ -//W3C//DTD SVG 1.1 Tiny//EN\
+ -//W3C//DTD SVG 1.2//EN
+
+systemId.-//W3C//DTD_SVG_1.0//EN = resources/svg10.dtd
+systemId.-//W3C//DTD_SVG_20010904//EN = resources/svg10.dtd
+systemId.-//W3C//DTD_SVG_20001102//EN = resources/svg10.dtd
+systemId.-//W3C//DTD_SVG_20000802//EN = resources/svg10.dtd
+systemId.-//W3C//DTD_SVG_20000303_Stylable//EN = resources/svg10.dtd
+
+systemId.-//W3C//DTD_SVG_1.1//EN = resources/svg11-flat.dtd
+systemId.-//W3C//DTD_SVG_1.1_Basic//EN = resources/svg11-basic-flat.dtd
+systemId.-//W3C//DTD_SVG_1.1_Tiny//EN = resources/svg11-tiny-flat.dtd
+systemId.-//W3C//DTD_SVG_1.2//EN = resources/svg12-flat.dtd
+
+#
+# The skippablePublicIds property represents the list of SVG DTD's we
+# can safely skip if we are not validating. Since SVG may move to
+# schema you shouldn't count on any entities from these files anyways.
+#
+skippablePublicIds = \
+ -//W3C//DTD SVG 1.0//EN\
+ -//W3C//DTD SVG 20010904//EN\
+ -//W3C//DTD SVG 20001102//EN\
+ -//W3C//DTD SVG 20000802//EN\
+ -//W3C//DTD SVG 20000303 Stylable//EN\
+ -//W3C//DTD SVG 1.1//EN\
+ -//W3C//DTD SVG 1.1 Basic//EN\
+ -//W3C//DTD SVG 1.1 Tiny//EN\
+ -//W3C//DTD SVG 1.2//EN
+
+#
+# This is an absolutely minimal DTD for SVG 1.0/1.1
+# It just defines the svg and xlink namespaces.
+skipDTD = \
+<!ELEMENT svg (desc|title|metadata|defs)*> \
+<!ATTLIST svg xmlns CDATA #FIXED "http://www.w3.org/2000/svg" \
+ xmlns:xlink CDATA #FIXED "http://www.w3.org/1999/xlink" >
diff --git a/org/apache/batik/dom/svg/resources/svg-animation.mod b/org/apache/batik/dom/svg/resources/svg-animation.mod
new file mode 100644
index 0000000..b540fd0
--- /dev/null
+++ b/org/apache/batik/dom/svg/resources/svg-animation.mod
@@ -0,0 +1,278 @@
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Animation Module .............................................. -->
+<!-- file: svg-animation.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg-animation.mod 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Animation//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-animation.mod"
+
+ ....................................................................... -->
+
+<!-- Animation
+
+ animate, set, animateMotion, animateColor, animateTransform, mpath
+
+ This module declares markup to provide support for animation.
+-->
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.animate.qname "animate" >
+<!ENTITY % SVG.set.qname "set" >
+<!ENTITY % SVG.animateMotion.qname "animateMotion" >
+<!ENTITY % SVG.animateColor.qname "animateColor" >
+<!ENTITY % SVG.animateTransform.qname "animateTransform" >
+<!ENTITY % SVG.mpath.qname "mpath" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Conditional.attrib "" >
+<!ENTITY % SVG.AnimationEvents.attrib "" >
+<!ENTITY % SVG.XLink.attrib "" >
+<!ENTITY % SVG.XLinkRequired.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Animation.class ............................... -->
+
+<!ENTITY % SVG.Animation.extra.class "" >
+
+<!ENTITY % SVG.Animation.class
+ "%SVG.animate.qname; | %SVG.set.qname; | %SVG.animateMotion.qname; |
+ %SVG.animateColor.qname; | %SVG.animateTransform.qname;
+ %SVG.Animation.extra.class;"
+>
+
+<!-- SVG.Animation.attrib .............................. -->
+
+<!ENTITY % SVG.Animation.extra.attrib "" >
+
+<!ENTITY % SVG.Animation.attrib
+ "%SVG.XLink.attrib;
+ %SVG.Animation.extra.attrib;"
+>
+
+<!-- SVG.AnimationAttribute.attrib ..................... -->
+
+<!ENTITY % SVG.AnimationAttribute.extra.attrib "" >
+
+<!ENTITY % SVG.AnimationAttribute.attrib
+ "attributeName CDATA #REQUIRED
+ attributeType CDATA #IMPLIED
+ %SVG.AnimationAttribute.extra.attrib;"
+>
+
+<!-- SVG.AnimationTiming.attrib ........................ -->
+
+<!ENTITY % SVG.AnimationTiming.extra.attrib "" >
+
+<!ENTITY % SVG.AnimationTiming.attrib
+ "begin CDATA #IMPLIED
+ dur CDATA #IMPLIED
+ end CDATA #IMPLIED
+ min CDATA #IMPLIED
+ max CDATA #IMPLIED
+ restart ( always | never | whenNotActive ) 'always'
+ repeatCount CDATA #IMPLIED
+ repeatDur CDATA #IMPLIED
+ fill ( remove | freeze ) 'remove'
+ %SVG.AnimationTiming.extra.attrib;"
+>
+
+<!-- SVG.AnimationValue.attrib ......................... -->
+
+<!ENTITY % SVG.AnimationValue.extra.attrib "" >
+
+<!ENTITY % SVG.AnimationValue.attrib
+ "calcMode ( discrete | linear | paced | spline ) 'linear'
+ values CDATA #IMPLIED
+ keyTimes CDATA #IMPLIED
+ keySplines CDATA #IMPLIED
+ from CDATA #IMPLIED
+ to CDATA #IMPLIED
+ by CDATA #IMPLIED
+ %SVG.AnimationValue.extra.attrib;"
+>
+
+<!-- SVG.AnimationAddtion.attrib ....................... -->
+
+<!ENTITY % SVG.AnimationAddtion.extra.attrib "" >
+
+<!ENTITY % SVG.AnimationAddtion.attrib
+ "additive ( replace | sum ) 'replace'
+ accumulate ( none | sum ) 'none'
+ %SVG.AnimationAddtion.extra.attrib;"
+>
+
+<!-- animate: Animate Element .......................... -->
+
+<!ENTITY % SVG.animate.extra.content "" >
+
+<!ENTITY % SVG.animate.element "INCLUDE" >
+<![%SVG.animate.element;[
+<!ENTITY % SVG.animate.content
+ "( %SVG.Description.class; %SVG.animate.extra.content; )*"
+>
+<!ELEMENT %SVG.animate.qname; %SVG.animate.content; >
+<!-- end of SVG.animate.element -->]]>
+
+<!ENTITY % SVG.animate.attlist "INCLUDE" >
+<![%SVG.animate.attlist;[
+<!ATTLIST %SVG.animate.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.AnimationEvents.attrib;
+ %SVG.External.attrib;
+ %SVG.Animation.attrib;
+ %SVG.AnimationAttribute.attrib;
+ %SVG.AnimationTiming.attrib;
+ %SVG.AnimationValue.attrib;
+ %SVG.AnimationAddtion.attrib;
+>
+<!-- end of SVG.animate.attlist -->]]>
+
+<!-- set: Set Element .................................. -->
+
+<!ENTITY % SVG.set.extra.content "" >
+
+<!ENTITY % SVG.set.element "INCLUDE" >
+<![%SVG.set.element;[
+<!ENTITY % SVG.set.content
+ "( %SVG.Description.class; %SVG.set.extra.content; )*"
+>
+<!ELEMENT %SVG.set.qname; %SVG.set.content; >
+<!-- end of SVG.set.element -->]]>
+
+<!ENTITY % SVG.set.attlist "INCLUDE" >
+<![%SVG.set.attlist;[
+<!ATTLIST %SVG.set.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.AnimationEvents.attrib;
+ %SVG.External.attrib;
+ %SVG.Animation.attrib;
+ %SVG.AnimationAttribute.attrib;
+ %SVG.AnimationTiming.attrib;
+ to CDATA #IMPLIED
+>
+<!-- end of SVG.set.attlist -->]]>
+
+<!-- animateMotion: Animate Motion Element ............. -->
+
+<!ENTITY % SVG.animateMotion.extra.content "" >
+
+<!ENTITY % SVG.animateMotion.element "INCLUDE" >
+<![%SVG.animateMotion.element;[
+<!ENTITY % SVG.animateMotion.content
+ "(( %SVG.Description.class; )*, %SVG.mpath.qname;?
+ %SVG.animateMotion.extra.content; )"
+>
+<!ELEMENT %SVG.animateMotion.qname; %SVG.animateMotion.content; >
+<!-- end of SVG.animateMotion.element -->]]>
+
+<!ENTITY % SVG.animateMotion.attlist "INCLUDE" >
+<![%SVG.animateMotion.attlist;[
+<!ATTLIST %SVG.animateMotion.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.AnimationEvents.attrib;
+ %SVG.External.attrib;
+ %SVG.Animation.attrib;
+ %SVG.AnimationTiming.attrib;
+ %SVG.AnimationAddtion.attrib;
+ calcMode ( discrete | linear | paced | spline ) 'paced'
+ values CDATA #IMPLIED
+ keyTimes CDATA #IMPLIED
+ keySplines CDATA #IMPLIED
+ from CDATA #IMPLIED
+ to CDATA #IMPLIED
+ by CDATA #IMPLIED
+ path CDATA #IMPLIED
+ keyPoints CDATA #IMPLIED
+ rotate CDATA #IMPLIED
+ origin CDATA #IMPLIED
+>
+<!-- end of SVG.animateMotion.attlist -->]]>
+
+<!-- animateColor: Animate Color Element ............... -->
+
+<!ENTITY % SVG.animateColor.extra.content "" >
+
+<!ENTITY % SVG.animateColor.element "INCLUDE" >
+<![%SVG.animateColor.element;[
+<!ENTITY % SVG.animateColor.content
+ "( %SVG.Description.class; %SVG.animateColor.extra.content; )*"
+>
+<!ELEMENT %SVG.animateColor.qname; %SVG.animateColor.content; >
+<!-- end of SVG.animateColor.element -->]]>
+
+<!ENTITY % SVG.animateColor.attlist "INCLUDE" >
+<![%SVG.animateColor.attlist;[
+<!ATTLIST %SVG.animateColor.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.AnimationEvents.attrib;
+ %SVG.External.attrib;
+ %SVG.Animation.attrib;
+ %SVG.AnimationAttribute.attrib;
+ %SVG.AnimationTiming.attrib;
+ %SVG.AnimationValue.attrib;
+ %SVG.AnimationAddtion.attrib;
+>
+<!-- end of SVG.animateColor.attlist -->]]>
+
+<!-- animateTransform: Animate Transform Element ....... -->
+
+<!ENTITY % SVG.animateTransform.extra.content "" >
+
+<!ENTITY % SVG.animateTransform.element "INCLUDE" >
+<![%SVG.animateTransform.element;[
+<!ENTITY % SVG.animateTransform.content
+ "( %SVG.Description.class; %SVG.animateTransform.extra.content; )*"
+>
+<!ELEMENT %SVG.animateTransform.qname; %SVG.animateTransform.content; >
+<!-- end of SVG.animateTransform.element -->]]>
+
+<!ENTITY % SVG.animateTransform.attlist "INCLUDE" >
+<![%SVG.animateTransform.attlist;[
+<!ATTLIST %SVG.animateTransform.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.AnimationEvents.attrib;
+ %SVG.External.attrib;
+ %SVG.Animation.attrib;
+ %SVG.AnimationAttribute.attrib;
+ %SVG.AnimationTiming.attrib;
+ %SVG.AnimationValue.attrib;
+ %SVG.AnimationAddtion.attrib;
+ type ( translate | scale | rotate | skewX | skewY ) 'translate'
+>
+<!-- end of SVG.animateTransform.attlist -->]]>
+
+<!-- mpath: Motion Path Element ........................ -->
+
+<!ENTITY % SVG.mpath.extra.content "" >
+
+<!ENTITY % SVG.mpath.element "INCLUDE" >
+<![%SVG.mpath.element;[
+<!ENTITY % SVG.mpath.content
+ "( %SVG.Description.class; %SVG.mpath.extra.content; )*"
+>
+<!ELEMENT %SVG.mpath.qname; %SVG.mpath.content; >
+<!-- end of SVG.mpath.element -->]]>
+
+<!ENTITY % SVG.mpath.attlist "INCLUDE" >
+<![%SVG.mpath.attlist;[
+<!ATTLIST %SVG.mpath.qname;
+ %SVG.Core.attrib;
+ %SVG.XLinkRequired.attrib;
+ %SVG.External.attrib;
+>
+<!-- end of SVG.mpath.attlist -->]]>
+
+<!-- end of svg-animation.mod -->
diff --git a/org/apache/batik/dom/svg/resources/svg-animevents-attrib.mod b/org/apache/batik/dom/svg/resources/svg-animevents-attrib.mod
new file mode 100644
index 0000000..74e304c
--- /dev/null
+++ b/org/apache/batik/dom/svg/resources/svg-animevents-attrib.mod
@@ -0,0 +1,49 @@
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Animation Events Attribute Module ............................. -->
+<!-- file: svg-animevents-attrib.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg-animevents-attrib.mod 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Animation Events Attribute//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-animevents-attrib.mod"
+
+ ....................................................................... -->
+
+<!-- Animation Events Attribute
+
+ onbegin, onend, onrepeat, onload
+
+ This module defines the AnimationEvents attribute set.
+-->
+
+<!ENTITY % SVG.onbegin.attrib
+ "onbegin %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onend.attrib
+ "onend %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onrepeat.attrib
+ "onrepeat %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onload.attrib
+ "onload %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.AnimationEvents.extra.attrib "" >
+
+<!ENTITY % SVG.AnimationEvents.attrib
+ "%SVG.onbegin.attrib;
+ %SVG.onend.attrib;
+ %SVG.onrepeat.attrib;
+ %SVG.onload.attrib;
+ %SVG.AnimationEvents.extra.attrib;"
+>
+
+<!-- end of svg-animevents-attrib.mod -->
diff --git a/org/apache/batik/dom/svg/resources/svg-basic-clip.mod b/org/apache/batik/dom/svg/resources/svg-basic-clip.mod
new file mode 100644
index 0000000..ffd7bb0
--- /dev/null
+++ b/org/apache/batik/dom/svg/resources/svg-basic-clip.mod
@@ -0,0 +1,101 @@
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Basic Clip Module ............................................. -->
+<!-- file: svg-basic-clip.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg-basic-clip.mod 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Basic Clip//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-basic-clip.mod"
+
+ ....................................................................... -->
+
+<!-- Basic Clip
+
+ clipPath
+
+ This module declares markup to provide support for clipping.
+-->
+
+<!-- 'clip-path' property/attribute value (e.g., 'none', <uri>) -->
+<!ENTITY % ClipPathValue.datatype "CDATA" >
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.clipPath.qname "clipPath" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Conditional.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Text.attrib "" >
+<!ENTITY % SVG.TextContent.attrib "" >
+<!ENTITY % SVG.Font.attrib "" >
+<!ENTITY % SVG.Paint.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Mask.attrib "" >
+<!ENTITY % SVG.Filter.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Clip.class .................................... -->
+
+<!ENTITY % SVG.Clip.extra.class "" >
+
+<!ENTITY % SVG.Clip.class
+ "| %SVG.clipPath.qname; %SVG.Clip.extra.class;"
+>
+
+<!-- SVG.Clip.attrib ................................... -->
+
+<!ENTITY % SVG.Clip.extra.attrib "" >
+
+<!ENTITY % SVG.Clip.attrib
+ "clip-path %ClipPathValue.datatype; #IMPLIED
+ clip-rule %ClipFillRule.datatype; #IMPLIED
+ %SVG.Clip.extra.attrib;"
+>
+
+<!-- clipPath: Clip Path Element ....................... -->
+
+<!ENTITY % SVG.clipPath.extra.content "" >
+
+<!ENTITY % SVG.clipPath.element "INCLUDE" >
+<![%SVG.clipPath.element;[
+<!ENTITY % SVG.clipPath.content
+ "(( %SVG.Description.class; )*, ( %SVG.rect.qname; | %SVG.Animation.class;
+ %SVG.Use.class; %SVG.clipPath.extra.content; )*)"
+>
+<!ELEMENT %SVG.clipPath.qname; %SVG.clipPath.content; >
+<!-- end of SVG.clipPath.element -->]]>
+
+<!ENTITY % SVG.clipPath.attlist "INCLUDE" >
+<![%SVG.clipPath.attlist;[
+<!ATTLIST %SVG.clipPath.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Text.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.External.attrib;
+ transform %TransformList.datatype; #IMPLIED
+ clipPathUnits ( userSpaceOnUse | objectBoundingBox ) #IMPLIED
+>
+<!-- end of SVG.clipPath.attlist -->]]>
+
+<!-- end of svg-basic-clip.mod -->
diff --git a/org/apache/batik/dom/svg/resources/svg-basic-filter.mod b/org/apache/batik/dom/svg/resources/svg-basic-filter.mod
new file mode 100644
index 0000000..a17f674
--- /dev/null
+++ b/org/apache/batik/dom/svg/resources/svg-basic-filter.mod
@@ -0,0 +1,554 @@
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Basic Filter Module ........................................... -->
+<!-- file: svg-basic-filter.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg-basic-filter.mod 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Basic Filter//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-basic-filter.mod"
+
+ ....................................................................... -->
+
+<!-- Basic Filter
+
+ filter, feBlend, feColorMatrix, feComponentTransfer, feComposite,
+ feFlood, feGaussianBlur, feImage, feMerge, feMergeNode, feOffset,
+ feTile, feFuncR, feFuncG, feFuncB, feFuncA
+
+ This module declares markup to provide support for filter effect.
+-->
+
+<!-- 'filter' property/attribute value (e.g., 'none', <uri>) -->
+<!ENTITY % FilterValue.datatype "CDATA" >
+
+<!-- list of <number>s, but at least one and at most two -->
+<!ENTITY % NumberOptionalNumber.datatype "CDATA" >
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.filter.qname "filter" >
+<!ENTITY % SVG.feBlend.qname "feBlend" >
+<!ENTITY % SVG.feColorMatrix.qname "feColorMatrix" >
+<!ENTITY % SVG.feComponentTransfer.qname "feComponentTransfer" >
+<!ENTITY % SVG.feComposite.qname "feComposite" >
+<!ENTITY % SVG.feFlood.qname "feFlood" >
+<!ENTITY % SVG.feGaussianBlur.qname "feGaussianBlur" >
+<!ENTITY % SVG.feImage.qname "feImage" >
+<!ENTITY % SVG.feMerge.qname "feMerge" >
+<!ENTITY % SVG.feMergeNode.qname "feMergeNode" >
+<!ENTITY % SVG.feOffset.qname "feOffset" >
+<!ENTITY % SVG.feTile.qname "feTile" >
+<!ENTITY % SVG.feFuncR.qname "feFuncR" >
+<!ENTITY % SVG.feFuncG.qname "feFuncG" >
+<!ENTITY % SVG.feFuncB.qname "feFuncB" >
+<!ENTITY % SVG.feFuncA.qname "feFuncA" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Container.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Viewport.attrib "" >
+<!ENTITY % SVG.Text.attrib "" >
+<!ENTITY % SVG.TextContent.attrib "" >
+<!ENTITY % SVG.Font.attrib "" >
+<!ENTITY % SVG.Paint.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Marker.attrib "" >
+<!ENTITY % SVG.Profile.attrib "" >
+<!ENTITY % SVG.Gradient.attrib "" >
+<!ENTITY % SVG.Clip.attrib "" >
+<!ENTITY % SVG.Mask.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.XLink.attrib "" >
+<!ENTITY % SVG.XLinkEmbed.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Filter.class .................................. -->
+
+<!ENTITY % SVG.Filter.extra.class "" >
+
+<!ENTITY % SVG.Filter.class
+ "| %SVG.filter.qname; %SVG.Filter.extra.class;"
+>
+
+<!-- SVG.FilterPrimitive.class ......................... -->
+
+<!ENTITY % SVG.FilterPrimitive.extra.class "" >
+
+<!ENTITY % SVG.FilterPrimitive.class
+ "| %SVG.feBlend.qname; | %SVG.feColorMatrix.qname;
+ | %SVG.feComponentTransfer.qname; | %SVG.feComposite.qname;
+ | %SVG.feFlood.qname; | %SVG.feGaussianBlur.qname; | %SVG.feImage.qname;
+ | %SVG.feMerge.qname; | %SVG.feOffset.qname; | %SVG.feTile.qname;
+ %SVG.FilterPrimitive.extra.class;"
+>
+
+<!-- SVG.Filter.attrib ................................. -->
+
+<!ENTITY % SVG.Filter.extra.attrib "" >
+
+<!ENTITY % SVG.Filter.attrib
+ "filter %FilterValue.datatype; #IMPLIED
+ %SVG.Filter.extra.attrib;"
+>
+
+<!-- SVG.FilterColor.attrib ............................ -->
+
+<!ENTITY % SVG.FilterColor.extra.attrib "" >
+
+<!ENTITY % SVG.FilterColor.attrib
+ "color-interpolation-filters ( auto | sRGB | linearRGB | inherit )
+ #IMPLIED
+ %SVG.FilterColor.extra.attrib;"
+>
+
+<!-- SVG.FilterPrimitive.attrib ........................ -->
+
+<!ENTITY % SVG.FilterPrimitive.extra.attrib "" >
+
+<!ENTITY % SVG.FilterPrimitive.attrib
+ "x %Coordinate.datatype; #IMPLIED
+ y %Coordinate.datatype; #IMPLIED
+ width %Length.datatype; #IMPLIED
+ height %Length.datatype; #IMPLIED
+ result CDATA #IMPLIED
+ %SVG.FilterPrimitive.extra.attrib;"
+>
+
+<!-- SVG.FilterPrimitiveWithIn.attrib .................. -->
+
+<!ENTITY % SVG.FilterPrimitiveWithIn.extra.attrib "" >
+
+<!ENTITY % SVG.FilterPrimitiveWithIn.attrib
+ "%SVG.FilterPrimitive.attrib;
+ in CDATA #IMPLIED
+ %SVG.FilterPrimitiveWithIn.extra.attrib;"
+>
+
+<!-- SVG.Presentation.attrib ........................... -->
+
+<!ENTITY % SVG.Presentation.extra.attrib "" >
+
+<!ENTITY % SVG.Presentation.attrib
+ "%SVG.Container.attrib;
+ %SVG.Viewport.attrib;
+ %SVG.Text.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Profile.attrib;
+ %SVG.Gradient.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.Cursor.attrib;
+ flood-color %SVGColor.datatype; #IMPLIED
+ flood-opacity %OpacityValue.datatype; #IMPLIED
+ lighting-color %SVGColor.datatype; #IMPLIED
+ %SVG.Presentation.extra.attrib;"
+>
+
+<!-- filter: Filter Element ............................ -->
+
+<!ENTITY % SVG.filter.extra.content "" >
+
+<!ENTITY % SVG.filter.element "INCLUDE" >
+<![%SVG.filter.element;[
+<!ENTITY % SVG.filter.content
+ "(( %SVG.Description.class; )*, ( %SVG.animate.qname; | %SVG.set.qname;
+ %SVG.FilterPrimitive.class; %SVG.filter.extra.content; )*)"
+>
+<!ELEMENT %SVG.filter.qname; %SVG.filter.content; >
+<!-- end of SVG.filter.element -->]]>
+
+<!ENTITY % SVG.filter.attlist "INCLUDE" >
+<![%SVG.filter.attlist;[
+<!ATTLIST %SVG.filter.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.XLink.attrib;
+ %SVG.External.attrib;
+ x %Coordinate.datatype; #IMPLIED
+ y %Coordinate.datatype; #IMPLIED
+ width %Length.datatype; #IMPLIED
+ height %Length.datatype; #IMPLIED
+ filterRes %NumberOptionalNumber.datatype; #IMPLIED
+ filterUnits ( userSpaceOnUse | objectBoundingBox ) #IMPLIED
+ primitiveUnits ( userSpaceOnUse | objectBoundingBox ) #IMPLIED
+>
+<!-- end of SVG.filter.attlist -->]]>
+
+<!-- feBlend: Filter Effect Blend Element .............. -->
+
+<!ENTITY % SVG.feBlend.extra.content "" >
+
+<!ENTITY % SVG.feBlend.element "INCLUDE" >
+<![%SVG.feBlend.element;[
+<!ENTITY % SVG.feBlend.content
+ "( %SVG.animate.qname; | %SVG.set.qname; %SVG.feBlend.extra.content; )*"
+>
+<!ELEMENT %SVG.feBlend.qname; %SVG.feBlend.content; >
+<!-- end of SVG.feBlend.element -->]]>
+
+<!ENTITY % SVG.feBlend.attlist "INCLUDE" >
+<![%SVG.feBlend.attlist;[
+<!ATTLIST %SVG.feBlend.qname;
+ %SVG.Core.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitiveWithIn.attrib;
+ in2 CDATA #REQUIRED
+ mode ( normal | multiply | screen | darken | lighten ) 'normal'
+>
+<!-- end of SVG.feBlend.attlist -->]]>
+
+<!-- feColorMatrix: Filter Effect Color Matrix Element . -->
+
+<!ENTITY % SVG.feColorMatrix.extra.content "" >
+
+<!ENTITY % SVG.feColorMatrix.element "INCLUDE" >
+<![%SVG.feColorMatrix.element;[
+<!ENTITY % SVG.feColorMatrix.content
+ "( %SVG.animate.qname; | %SVG.set.qname;
+ %SVG.feColorMatrix.extra.content; )*"
+>
+<!ELEMENT %SVG.feColorMatrix.qname; %SVG.feColorMatrix.content; >
+<!-- end of SVG.feColorMatrix.element -->]]>
+
+<!ENTITY % SVG.feColorMatrix.attlist "INCLUDE" >
+<![%SVG.feColorMatrix.attlist;[
+<!ATTLIST %SVG.feColorMatrix.qname;
+ %SVG.Core.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitiveWithIn.attrib;
+ type ( matrix | saturate | hueRotate | luminanceToAlpha ) 'matrix'
+ values CDATA #IMPLIED
+>
+<!-- end of SVG.feColorMatrix.attlist -->]]>
+
+<!-- feComponentTransfer: Filter Effect Component Transfer Element -->
+
+<!ENTITY % SVG.feComponentTransfer.extra.content "" >
+
+<!ENTITY % SVG.feComponentTransfer.element "INCLUDE" >
+<![%SVG.feComponentTransfer.element;[
+<!ENTITY % SVG.feComponentTransfer.content
+ "( %SVG.feFuncR.qname;?, %SVG.feFuncG.qname;?, %SVG.feFuncB.qname;?,
+ %SVG.feFuncA.qname;? %SVG.feComponentTransfer.extra.content; )"
+>
+<!ELEMENT %SVG.feComponentTransfer.qname; %SVG.feComponentTransfer.content; >
+<!-- end of SVG.feComponentTransfer.element -->]]>
+
+<!ENTITY % SVG.feComponentTransfer.attlist "INCLUDE" >
+<![%SVG.feComponentTransfer.attlist;[
+<!ATTLIST %SVG.feComponentTransfer.qname;
+ %SVG.Core.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitiveWithIn.attrib;
+>
+<!-- end of SVG.feComponentTransfer.attlist -->]]>
+
+<!-- feComposite: Filter Effect Composite Element ...... -->
+
+<!ENTITY % SVG.feComposite.extra.content "" >
+
+<!ENTITY % SVG.feComposite.element "INCLUDE" >
+<![%SVG.feComposite.element;[
+<!ENTITY % SVG.feComposite.content
+ "( %SVG.animate.qname; | %SVG.set.qname; %SVG.feComposite.extra.content; )*"
+>
+<!ELEMENT %SVG.feComposite.qname; %SVG.feComposite.content; >
+<!-- end of SVG.feComposite.element -->]]>
+
+<!ENTITY % SVG.feComposite.attlist "INCLUDE" >
+<![%SVG.feComposite.attlist;[
+<!ATTLIST %SVG.feComposite.qname;
+ %SVG.Core.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitiveWithIn.attrib;
+ in2 CDATA #REQUIRED
+ operator ( over | in | out | atop | xor | arithmetic ) 'over'
+ k1 %Number.datatype; #IMPLIED
+ k2 %Number.datatype; #IMPLIED
+ k3 %Number.datatype; #IMPLIED
+ k4 %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.feComposite.attlist -->]]>
+
+<!-- feFlood: Filter Effect Flood Element .............. -->
+
+<!ENTITY % SVG.feFlood.extra.content "" >
+
+<!ENTITY % SVG.feFlood.element "INCLUDE" >
+<![%SVG.feFlood.element;[
+<!ENTITY % SVG.feFlood.content
+ "( %SVG.animate.qname; | %SVG.set.qname; | %SVG.animateColor.qname;
+ %SVG.feFlood.extra.content; )*"
+>
+<!ELEMENT %SVG.feFlood.qname; %SVG.feFlood.content; >
+<!-- end of SVG.feFlood.element -->]]>
+
+<!ENTITY % SVG.feFlood.attlist "INCLUDE" >
+<![%SVG.feFlood.attlist;[
+<!ATTLIST %SVG.feFlood.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Color.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitiveWithIn.attrib;
+ flood-color %SVGColor.datatype; #IMPLIED
+ flood-opacity %OpacityValue.datatype; #IMPLIED
+>
+<!-- end of SVG.feFlood.attlist -->]]>
+
+<!-- feGaussianBlur: Filter Effect Gaussian Blur Element -->
+
+<!ENTITY % SVG.feGaussianBlur.extra.content "" >
+
+<!ENTITY % SVG.feGaussianBlur.element "INCLUDE" >
+<![%SVG.feGaussianBlur.element;[
+<!ENTITY % SVG.feGaussianBlur.content
+ "( %SVG.animate.qname; | %SVG.set.qname;
+ %SVG.feGaussianBlur.extra.content; )*"
+>
+<!ELEMENT %SVG.feGaussianBlur.qname; %SVG.feGaussianBlur.content; >
+<!-- end of SVG.feGaussianBlur.element -->]]>
+
+<!ENTITY % SVG.feGaussianBlur.attlist "INCLUDE" >
+<![%SVG.feGaussianBlur.attlist;[
+<!ATTLIST %SVG.feGaussianBlur.qname;
+ %SVG.Core.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitiveWithIn.attrib;
+ stdDeviation %NumberOptionalNumber.datatype; #IMPLIED
+>
+<!-- end of SVG.feGaussianBlur.attlist -->]]>
+
+<!-- feImage: Filter Effect Image Element .............. -->
+
+<!ENTITY % SVG.feImage.extra.content "" >
+
+<!ENTITY % SVG.feImage.element "INCLUDE" >
+<![%SVG.feImage.element;[
+<!ENTITY % SVG.feImage.content
+ "( %SVG.animate.qname; | %SVG.set.qname; | %SVG.animateTransform.qname;
+ %SVG.feImage.extra.content; )*"
+>
+<!ELEMENT %SVG.feImage.qname; %SVG.feImage.content; >
+<!-- end of SVG.feImage.element -->]]>
+
+<!ENTITY % SVG.feImage.attlist "INCLUDE" >
+<![%SVG.feImage.attlist;[
+<!ATTLIST %SVG.feImage.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.FilterPrimitive.attrib;
+ %SVG.XLinkEmbed.attrib;
+ %SVG.External.attrib;
+ preserveAspectRatio %PreserveAspectRatioSpec.datatype; 'xMidYMid meet'
+>
+<!-- end of SVG.feImage.attlist -->]]>
+
+<!-- feMerge: Filter Effect Merge Element .............. -->
+
+<!ENTITY % SVG.feMerge.extra.content "" >
+
+<!ENTITY % SVG.feMerge.element "INCLUDE" >
+<![%SVG.feMerge.element;[
+<!ENTITY % SVG.feMerge.content
+ "( %SVG.feMergeNode.qname; %SVG.feMerge.extra.content; )*"
+>
+<!ELEMENT %SVG.feMerge.qname; %SVG.feMerge.content; >
+<!-- end of SVG.feMerge.element -->]]>
+
+<!ENTITY % SVG.feMerge.attlist "INCLUDE" >
+<![%SVG.feMerge.attlist;[
+<!ATTLIST %SVG.feMerge.qname;
+ %SVG.Core.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitive.attrib;
+>
+<!-- end of SVG.feMerge.attlist -->]]>
+
+<!-- feMergeNode: Filter Effect Merge Node Element ..... -->
+
+<!ENTITY % SVG.feMergeNode.extra.content "" >
+
+<!ENTITY % SVG.feMergeNode.element "INCLUDE" >
+<![%SVG.feMergeNode.element;[
+<!ENTITY % SVG.feMergeNode.content
+ "( %SVG.animate.qname; | %SVG.set.qname; %SVG.feMergeNode.extra.content; )*"
+>
+<!ELEMENT %SVG.feMergeNode.qname; %SVG.feMergeNode.content; >
+<!-- end of SVG.feMergeNode.element -->]]>
+
+<!ENTITY % SVG.feMergeNode.attlist "INCLUDE" >
+<![%SVG.feMergeNode.attlist;[
+<!ATTLIST %SVG.feMergeNode.qname;
+ %SVG.Core.attrib;
+ in CDATA #IMPLIED
+>
+<!-- end of SVG.feMergeNode.attlist -->]]>
+
+<!-- feOffset: Filter Effect Offset Element ............ -->
+
+<!ENTITY % SVG.feOffset.extra.content "" >
+
+<!ENTITY % SVG.feOffset.element "INCLUDE" >
+<![%SVG.feOffset.element;[
+<!ENTITY % SVG.feOffset.content
+ "( %SVG.animate.qname; | %SVG.set.qname; %SVG.feOffset.extra.content; )*"
+>
+<!ELEMENT %SVG.feOffset.qname; %SVG.feOffset.content; >
+<!-- end of SVG.feOffset.element -->]]>
+
+<!ENTITY % SVG.feOffset.attlist "INCLUDE" >
+<![%SVG.feOffset.attlist;[
+<!ATTLIST %SVG.feOffset.qname;
+ %SVG.Core.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitiveWithIn.attrib;
+ dx %Number.datatype; #IMPLIED
+ dy %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.feOffset.attlist -->]]>
+
+<!-- feTile: Filter Effect Tile Element ................ -->
+
+<!ENTITY % SVG.feTile.extra.content "" >
+
+<!ENTITY % SVG.feTile.element "INCLUDE" >
+<![%SVG.feTile.element;[
+<!ENTITY % SVG.feTile.content
+ "( %SVG.animate.qname; | %SVG.set.qname; %SVG.feTile.extra.content; )*"
+>
+<!ELEMENT %SVG.feTile.qname; %SVG.feTile.content; >
+<!-- end of SVG.feTile.element -->]]>
+
+<!ENTITY % SVG.feTile.attlist "INCLUDE" >
+<![%SVG.feTile.attlist;[
+<!ATTLIST %SVG.feTile.qname;
+ %SVG.Core.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitiveWithIn.attrib;
+>
+<!-- end of SVG.feTile.attlist -->]]>
+
+<!-- feFuncR: Filter Effect Function Red Element ....... -->
+
+<!ENTITY % SVG.feFuncR.extra.content "" >
+
+<!ENTITY % SVG.feFuncR.element "INCLUDE" >
+<![%SVG.feFuncR.element;[
+<!ENTITY % SVG.feFuncR.content
+ "( %SVG.animate.qname; | %SVG.set.qname; %SVG.feFuncR.extra.content; )*"
+>
+<!ELEMENT %SVG.feFuncR.qname; %SVG.feFuncR.content; >
+<!-- end of SVG.feFuncR.element -->]]>
+
+<!ENTITY % SVG.feFuncR.attlist "INCLUDE" >
+<![%SVG.feFuncR.attlist;[
+<!ATTLIST %SVG.feFuncR.qname;
+ %SVG.Core.attrib;
+ type ( identity | table | discrete | linear | gamma ) #REQUIRED
+ tableValues CDATA #IMPLIED
+ slope %Number.datatype; #IMPLIED
+ intercept %Number.datatype; #IMPLIED
+ amplitude %Number.datatype; #IMPLIED
+ exponent %Number.datatype; #IMPLIED
+ offset %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.feFuncR.attlist -->]]>
+
+<!-- feFuncG: Filter Effect Function Green Element ..... -->
+
+<!ENTITY % SVG.feFuncG.extra.content "" >
+
+<!ENTITY % SVG.feFuncG.element "INCLUDE" >
+<![%SVG.feFuncG.element;[
+<!ENTITY % SVG.feFuncG.content
+ "( %SVG.animate.qname; | %SVG.set.qname; %SVG.feFuncG.extra.content; )*"
+>
+<!ELEMENT %SVG.feFuncG.qname; %SVG.feFuncG.content; >
+<!-- end of SVG.feFuncG.element -->]]>
+
+<!ENTITY % SVG.feFuncG.attlist "INCLUDE" >
+<![%SVG.feFuncG.attlist;[
+<!ATTLIST %SVG.feFuncG.qname;
+ %SVG.Core.attrib;
+ type ( identity | table | discrete | linear | gamma ) #REQUIRED
+ tableValues CDATA #IMPLIED
+ slope %Number.datatype; #IMPLIED
+ intercept %Number.datatype; #IMPLIED
+ amplitude %Number.datatype; #IMPLIED
+ exponent %Number.datatype; #IMPLIED
+ offset %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.feFuncG.attlist -->]]>
+
+<!-- feFuncB: Filter Effect Function Blue Element ...... -->
+
+<!ENTITY % SVG.feFuncB.extra.content "" >
+
+<!ENTITY % SVG.feFuncB.element "INCLUDE" >
+<![%SVG.feFuncB.element;[
+<!ENTITY % SVG.feFuncB.content
+ "( %SVG.animate.qname; | %SVG.set.qname; %SVG.feFuncB.extra.content; )*"
+>
+<!ELEMENT %SVG.feFuncB.qname; %SVG.feFuncB.content; >
+<!-- end of SVG.feFuncB.element -->]]>
+
+<!ENTITY % SVG.feFuncB.attlist "INCLUDE" >
+<![%SVG.feFuncB.attlist;[
+<!ATTLIST %SVG.feFuncB.qname;
+ %SVG.Core.attrib;
+ type ( identity | table | discrete | linear | gamma ) #REQUIRED
+ tableValues CDATA #IMPLIED
+ slope %Number.datatype; #IMPLIED
+ intercept %Number.datatype; #IMPLIED
+ amplitude %Number.datatype; #IMPLIED
+ exponent %Number.datatype; #IMPLIED
+ offset %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.feFuncB.attlist -->]]>
+
+<!-- feFuncA: Filter Effect Function Alpha Element ..... -->
+
+<!ENTITY % SVG.feFuncA.extra.content "" >
+
+<!ENTITY % SVG.feFuncA.element "INCLUDE" >
+<![%SVG.feFuncA.element;[
+<!ENTITY % SVG.feFuncA.content
+ "( %SVG.animate.qname; | %SVG.set.qname; %SVG.feFuncA.extra.content; )*"
+>
+<!ELEMENT %SVG.feFuncA.qname; %SVG.feFuncA.content; >
+<!-- end of SVG.feFuncA.element -->]]>
+
+<!ENTITY % SVG.feFuncA.attlist "INCLUDE" >
+<![%SVG.feFuncA.attlist;[
+<!ATTLIST %SVG.feFuncA.qname;
+ %SVG.Core.attrib;
+ type ( identity | table | discrete | linear | gamma ) #REQUIRED
+ tableValues CDATA #IMPLIED
+ slope %Number.datatype; #IMPLIED
+ intercept %Number.datatype; #IMPLIED
+ amplitude %Number.datatype; #IMPLIED
+ exponent %Number.datatype; #IMPLIED
+ offset %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.feFuncA.attlist -->]]>
+
+<!-- end of svg-basic-filter.mod -->
diff --git a/org/apache/batik/dom/svg/resources/svg-basic-font.mod b/org/apache/batik/dom/svg/resources/svg-basic-font.mod
new file mode 100644
index 0000000..cd45b9a
--- /dev/null
+++ b/org/apache/batik/dom/svg/resources/svg-basic-font.mod
@@ -0,0 +1,328 @@
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Basic Font Module ............................................. -->
+<!-- file: svg-basic-font.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg-basic-font.mod 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Basic Font//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-basic-font.mod"
+
+ ....................................................................... -->
+
+<!-- Basic Font
+
+ font, font-face, glyph, missing-glyph, hkern, vkern, font-face-src,
+ font-face-uri, font-face-name
+
+ This module declares markup to provide support for template.
+-->
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.font.qname "font" >
+<!ENTITY % SVG.font-face.qname "font-face" >
+<!ENTITY % SVG.glyph.qname "glyph" >
+<!ENTITY % SVG.missing-glyph.qname "missing-glyph" >
+<!ENTITY % SVG.hkern.qname "hkern" >
+<!ENTITY % SVG.vkern.qname "vkern" >
+<!ENTITY % SVG.font-face-src.qname "font-face-src" >
+<!ENTITY % SVG.font-face-uri.qname "font-face-uri" >
+<!ENTITY % SVG.font-face-name.qname "font-face-name" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Container.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Viewport.attrib "" >
+<!ENTITY % SVG.Text.attrib "" >
+<!ENTITY % SVG.TextContent.attrib "" >
+<!ENTITY % SVG.Font.attrib "" >
+<!ENTITY % SVG.Paint.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Marker.attrib "" >
+<!ENTITY % SVG.Profile.attrib "" >
+<!ENTITY % SVG.Gradient.attrib "" >
+<!ENTITY % SVG.Clip.attrib "" >
+<!ENTITY % SVG.Mask.attrib "" >
+<!ENTITY % SVG.Filter.attrib "" >
+<!ENTITY % SVG.FilterColor.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.XLinkRequired.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Font.class .................................... -->
+
+<!ENTITY % SVG.Font.extra.class "" >
+
+<!ENTITY % SVG.Font.class
+ "| %SVG.font.qname; | %SVG.font-face.qname; %SVG.Font.extra.class;"
+>
+
+<!-- SVG.Presentation.attrib ........................... -->
+
+<!ENTITY % SVG.Presentation.extra.attrib "" >
+
+<!ENTITY % SVG.Presentation.attrib
+ "%SVG.Container.attrib;
+ %SVG.Viewport.attrib;
+ %SVG.Text.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Profile.attrib;
+ %SVG.Gradient.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.Cursor.attrib;
+ flood-color %SVGColor.datatype; #IMPLIED
+ flood-opacity %OpacityValue.datatype; #IMPLIED
+ lighting-color %SVGColor.datatype; #IMPLIED
+ %SVG.Presentation.extra.attrib;"
+>
+
+<!-- font: Font Element ................................ -->
+
+<!ENTITY % SVG.font.extra.content "" >
+
+<!ENTITY % SVG.font.element "INCLUDE" >
+<![%SVG.font.element;[
+<!ENTITY % SVG.font.content
+ "(( %SVG.Description.class; )*, %SVG.font-face.qname;,
+ %SVG.missing-glyph.qname;, ( %SVG.glyph.qname; | %SVG.hkern.qname;
+ | %SVG.vkern.qname; %SVG.font.extra.content; )*)"
+>
+<!ELEMENT %SVG.font.qname; %SVG.font.content; >
+<!-- end of SVG.font.element -->]]>
+
+<!ENTITY % SVG.font.attlist "INCLUDE" >
+<![%SVG.font.attlist;[
+<!ATTLIST %SVG.font.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.External.attrib;
+ horiz-origin-x %Number.datatype; #IMPLIED
+ horiz-origin-y %Number.datatype; #IMPLIED
+ horiz-adv-x %Number.datatype; #REQUIRED
+ vert-origin-x %Number.datatype; #IMPLIED
+ vert-origin-y %Number.datatype; #IMPLIED
+ vert-adv-y %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.font.attlist -->]]>
+
+<!-- font-face: Font Face Element ...................... -->
+
+<!ENTITY % SVG.font-face.extra.content "" >
+
+<!ENTITY % SVG.font-face.element "INCLUDE" >
+<![%SVG.font-face.element;[
+<!ENTITY % SVG.font-face.content
+ "(( %SVG.Description.class; )*, %SVG.font-face-src.qname;?
+ %SVG.font-face.extra.content; )"
+>
+<!ELEMENT %SVG.font-face.qname; %SVG.font-face.content; >
+<!-- end of SVG.font-face.element -->]]>
+
+<!ENTITY % SVG.font-face.attlist "INCLUDE" >
+<![%SVG.font-face.attlist;[
+<!ATTLIST %SVG.font-face.qname;
+ %SVG.Core.attrib;
+ font-family CDATA #IMPLIED
+ font-style CDATA #IMPLIED
+ font-variant CDATA #IMPLIED
+ font-weight CDATA #IMPLIED
+ font-stretch CDATA #IMPLIED
+ font-size CDATA #IMPLIED
+ unicode-range CDATA #IMPLIED
+ units-per-em %Number.datatype; #IMPLIED
+ panose-1 CDATA #IMPLIED
+ stemv %Number.datatype; #IMPLIED
+ stemh %Number.datatype; #IMPLIED
+ slope %Number.datatype; #IMPLIED
+ cap-height %Number.datatype; #IMPLIED
+ x-height %Number.datatype; #IMPLIED
+ accent-height %Number.datatype; #IMPLIED
+ ascent %Number.datatype; #IMPLIED
+ descent %Number.datatype; #IMPLIED
+ widths CDATA #IMPLIED
+ bbox CDATA #IMPLIED
+ ideographic %Number.datatype; #IMPLIED
+ alphabetic %Number.datatype; #IMPLIED
+ mathematical %Number.datatype; #IMPLIED
+ hanging %Number.datatype; #IMPLIED
+ v-ideographic %Number.datatype; #IMPLIED
+ v-alphabetic %Number.datatype; #IMPLIED
+ v-mathematical %Number.datatype; #IMPLIED
+ v-hanging %Number.datatype; #IMPLIED
+ underline-position %Number.datatype; #IMPLIED
+ underline-thickness %Number.datatype; #IMPLIED
+ strikethrough-position %Number.datatype; #IMPLIED
+ strikethrough-thickness %Number.datatype; #IMPLIED
+ overline-position %Number.datatype; #IMPLIED
+ overline-thickness %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.font-face.attlist -->]]>
+
+<!-- glyph: Glyph Element .............................. -->
+
+<!ENTITY % SVG.glyph.extra.content "" >
+
+<!ENTITY % SVG.glyph.element "INCLUDE" >
+<![%SVG.glyph.element;[
+<!ENTITY % SVG.glyph.content
+ "( %SVG.Description.class; %SVG.glyph.extra.content; )*"
+>
+<!ELEMENT %SVG.glyph.qname; %SVG.glyph.content; >
+<!-- end of SVG.glyph.element -->]]>
+
+<!ENTITY % SVG.glyph.attlist "INCLUDE" >
+<![%SVG.glyph.attlist;[
+<!ATTLIST %SVG.glyph.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ unicode CDATA #IMPLIED
+ glyph-name CDATA #IMPLIED
+ d %PathData.datatype; #IMPLIED
+ orientation CDATA #IMPLIED
+ arabic-form CDATA #IMPLIED
+ lang %LanguageCodes.datatype; #IMPLIED
+ horiz-adv-x %Number.datatype; #IMPLIED
+ vert-origin-x %Number.datatype; #IMPLIED
+ vert-origin-y %Number.datatype; #IMPLIED
+ vert-adv-y %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.glyph.attlist -->]]>
+
+<!-- missing-glyph: Missing Glyph Element .............. -->
+
+<!ENTITY % SVG.missing-glyph.extra.content "" >
+
+<!ENTITY % SVG.missing-glyph.element "INCLUDE" >
+<![%SVG.missing-glyph.element;[
+<!ENTITY % SVG.missing-glyph.content
+ "( %SVG.Description.class; %SVG.missing-glyph.extra.content; )*"
+>
+<!ELEMENT %SVG.missing-glyph.qname; %SVG.missing-glyph.content; >
+<!-- end of SVG.missing-glyph.element -->]]>
+
+<!ENTITY % SVG.missing-glyph.attlist "INCLUDE" >
+<![%SVG.missing-glyph.attlist;[
+<!ATTLIST %SVG.missing-glyph.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ d %PathData.datatype; #IMPLIED
+ horiz-adv-x %Number.datatype; #IMPLIED
+ vert-origin-x %Number.datatype; #IMPLIED
+ vert-origin-y %Number.datatype; #IMPLIED
+ vert-adv-y %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.missing-glyph.attlist -->]]>
+
+<!-- hkern: Horizontal Kerning Element ................. -->
+
+<!ENTITY % SVG.hkern.element "INCLUDE" >
+<![%SVG.hkern.element;[
+<!ENTITY % SVG.hkern.content "EMPTY" >
+<!ELEMENT %SVG.hkern.qname; %SVG.hkern.content; >
+<!-- end of SVG.hkern.element -->]]>
+
+<!ENTITY % SVG.hkern.attlist "INCLUDE" >
+<![%SVG.hkern.attlist;[
+<!ATTLIST %SVG.hkern.qname;
+ %SVG.Core.attrib;
+ u1 CDATA #IMPLIED
+ g1 CDATA #IMPLIED
+ u2 CDATA #IMPLIED
+ g2 CDATA #IMPLIED
+ k %Number.datatype; #REQUIRED
+>
+<!-- end of SVG.hkern.attlist -->]]>
+
+<!-- vkern: Vertical Kerning Element ................... -->
+
+<!ENTITY % SVG.vkern.element "INCLUDE" >
+<![%SVG.vkern.element;[
+<!ENTITY % SVG.vkern.content "EMPTY" >
+<!ELEMENT %SVG.vkern.qname; %SVG.vkern.content; >
+<!-- end of SVG.vkern.element -->]]>
+
+<!ENTITY % SVG.vkern.attlist "INCLUDE" >
+<![%SVG.vkern.attlist;[
+<!ATTLIST %SVG.vkern.qname;
+ %SVG.Core.attrib;
+ u1 CDATA #IMPLIED
+ g1 CDATA #IMPLIED
+ u2 CDATA #IMPLIED
+ g2 CDATA #IMPLIED
+ k %Number.datatype; #REQUIRED
+>
+<!-- end of SVG.vkern.attlist -->]]>
+
+<!-- font-face-src: Font Face Source Element ........... -->
+
+<!ENTITY % SVG.font-face-src.extra.content "" >
+
+<!ENTITY % SVG.font-face-src.element "INCLUDE" >
+<![%SVG.font-face-src.element;[
+<!ENTITY % SVG.font-face-src.content
+ "( %SVG.font-face-uri.qname; | %SVG.font-face-name.qname;
+ %SVG.font-face-src.extra.content; )+"
+>
+<!ELEMENT %SVG.font-face-src.qname; %SVG.font-face-src.content; >
+<!-- end of SVG.font-face-src.element -->]]>
+
+<!ENTITY % SVG.font-face-src.attlist "INCLUDE" >
+<![%SVG.font-face-src.attlist;[
+<!ATTLIST %SVG.font-face-src.qname;
+ %SVG.Core.attrib;
+>
+<!-- end of SVG.font-face-src.attlist -->]]>
+
+<!-- font-face-uri: Font Face URI Element .............. -->
+
+<!ENTITY % SVG.font-face-uri.element "INCLUDE" >
+<![%SVG.font-face-uri.element;[
+<!ENTITY % SVG.font-face-uri.content "EMPTY" >
+<!ELEMENT %SVG.font-face-uri.qname; %SVG.font-face-uri.content; >
+<!-- end of SVG.font-face-uri.element -->]]>
+
+<!ENTITY % SVG.font-face-uri.attlist "INCLUDE" >
+<![%SVG.font-face-uri.attlist;[
+<!ATTLIST %SVG.font-face-uri.qname;
+ %SVG.Core.attrib;
+ %SVG.XLinkRequired.attrib;
+>
+<!-- end of SVG.font-face-uri.attlist -->]]>
+
+<!-- font-face-name: Font Face Name Element ............ -->
+
+<!ENTITY % SVG.font-face-name.element "INCLUDE" >
+<![%SVG.font-face-name.element;[
+<!ENTITY % SVG.font-face-name.content "EMPTY" >
+<!ELEMENT %SVG.font-face-name.qname; %SVG.font-face-name.content; >
+<!-- end of SVG.font-face-name.element -->]]>
+
+<!ENTITY % SVG.font-face-name.attlist "INCLUDE" >
+<![%SVG.font-face-name.attlist;[
+<!ATTLIST %SVG.font-face-name.qname;
+ %SVG.Core.attrib;
+ name CDATA #IMPLIED
+>
+<!-- end of SVG.font-face-name.attlist -->]]>
+
+<!-- end of svg-basic-font.mod -->
diff --git a/org/apache/batik/dom/svg/resources/svg-basic-graphics-attrib.mod b/org/apache/batik/dom/svg/resources/svg-basic-graphics-attrib.mod
new file mode 100644
index 0000000..75350bd
--- /dev/null
+++ b/org/apache/batik/dom/svg/resources/svg-basic-graphics-attrib.mod
@@ -0,0 +1,43 @@
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Basic Graphics Attribute Module ............................... -->
+<!-- file: svg-basic-graphics-attrib.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg-basic-graphics-attrib.mod 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Basic Graphics Attribute//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-basic-graphics-attrib.mod"
+
+ ....................................................................... -->
+
+<!-- Basic Graphics Attribute
+
+ display, visibility
+
+ This module defines the Graphics attribute set.
+-->
+
+<!ENTITY % SVG.display.attrib
+ "display ( inline | block | list-item | run-in | compact | marker |
+ table | inline-table | table-row-group | table-header-group |
+ table-footer-group | table-row | table-column-group |
+ table-column | table-cell | table-caption | none | inherit )
+ #IMPLIED"
+>
+
+<!ENTITY % SVG.visibility.attrib
+ "visibility ( visible | hidden | inherit ) #IMPLIED"
+>
+
+<!ENTITY % SVG.Graphics.extra.attrib "" >
+
+<!ENTITY % SVG.Graphics.attrib
+ "%SVG.display.attrib;
+ %SVG.visibility.attrib;
+ %SVG.Graphics.extra.attrib;"
+>
+
+<!-- end of svg-basic-graphics-attrib.mod -->
diff --git a/org/apache/batik/dom/svg/resources/svg-basic-structure.mod b/org/apache/batik/dom/svg/resources/svg-basic-structure.mod
new file mode 100644
index 0000000..7b597cc
--- /dev/null
+++ b/org/apache/batik/dom/svg/resources/svg-basic-structure.mod
@@ -0,0 +1,309 @@
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Basic Structure Module ........................................ -->
+<!-- file: svg-basic-structure.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg-basic-structure.mod 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Basic Structure//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-basic-structure.mod"
+
+ ....................................................................... -->
+
+<!-- Basic Structure
+
+ svg, g, defs, desc, title, metadata, use
+
+ This module declares the major structural elements and their attributes.
+-->
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.svg.qname "svg" >
+<!ENTITY % SVG.g.qname "g" >
+<!ENTITY % SVG.defs.qname "defs" >
+<!ENTITY % SVG.desc.qname "desc" >
+<!ENTITY % SVG.title.qname "title" >
+<!ENTITY % SVG.metadata.qname "metadata" >
+<!ENTITY % SVG.use.qname "use" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Container.attrib "" >
+<!ENTITY % SVG.Conditional.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Viewport.attrib "" >
+<!ENTITY % SVG.Text.attrib "" >
+<!ENTITY % SVG.TextContent.attrib "" >
+<!ENTITY % SVG.Font.attrib "" >
+<!ENTITY % SVG.Paint.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Marker.attrib "" >
+<!ENTITY % SVG.Profile.attrib "" >
+<!ENTITY % SVG.Gradient.attrib "" >
+<!ENTITY % SVG.Clip.attrib "" >
+<!ENTITY % SVG.Mask.attrib "" >
+<!ENTITY % SVG.Filter.attrib "" >
+<!ENTITY % SVG.FilterColor.attrib "" >
+<!ENTITY % SVG.DocumentEvents.attrib "" >
+<!ENTITY % SVG.GraphicalEvents.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.XLinkEmbed.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Description.class ............................. -->
+
+<!ENTITY % SVG.Description.extra.class "" >
+
+<!ENTITY % SVG.Description.class
+ "%SVG.desc.qname; | %SVG.title.qname; | %SVG.metadata.qname;
+ %SVG.Description.extra.class;"
+>
+
+<!-- SVG.Use.class ..................................... -->
+
+<!ENTITY % SVG.Use.extra.class "" >
+
+<!ENTITY % SVG.Use.class
+ "| %SVG.use.qname; %SVG.Use.extra.class;"
+>
+
+<!-- SVG.Structure.class ............................... -->
+
+<!ENTITY % SVG.Structure.extra.class "" >
+
+<!ENTITY % SVG.Structure.class
+ "| %SVG.svg.qname; | %SVG.g.qname; | %SVG.defs.qname; %SVG.Use.class;
+ %SVG.Structure.extra.class;"
+>
+
+<!-- SVG.Presentation.attrib ........................... -->
+
+<!ENTITY % SVG.Presentation.extra.attrib "" >
+
+<!ENTITY % SVG.Presentation.attrib
+ "%SVG.Container.attrib;
+ %SVG.Viewport.attrib;
+ %SVG.Text.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Profile.attrib;
+ %SVG.Gradient.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.Cursor.attrib;
+ flood-color %SVGColor.datatype; #IMPLIED
+ flood-opacity %OpacityValue.datatype; #IMPLIED
+ lighting-color %SVGColor.datatype; #IMPLIED
+ %SVG.Presentation.extra.attrib;"
+>
+
+<!-- svg: SVG Document Element ......................... -->
+
+<!ENTITY % SVG.svg.extra.content "" >
+
+<!ENTITY % SVG.svg.element "INCLUDE" >
+<![%SVG.svg.element;[
+<!ENTITY % SVG.svg.content
+ "( %SVG.Description.class; | %SVG.Animation.class; %SVG.Structure.class;
+ %SVG.Conditional.class; %SVG.Image.class; %SVG.Style.class;
+ %SVG.Shape.class; %SVG.Text.class; %SVG.Marker.class; %SVG.Profile.class;
+ %SVG.Gradient.class; %SVG.Pattern.class; %SVG.Clip.class;
+ %SVG.Mask.class; %SVG.Filter.class; %SVG.Cursor.class;
+ %SVG.Hyperlink.class; %SVG.View.class; %SVG.Script.class;
+ %SVG.Font.class; %SVG.svg.extra.content; )*"
+>
+<!ELEMENT %SVG.svg.qname; %SVG.svg.content; >
+<!-- end of SVG.svg.element -->]]>
+
+<!ENTITY % SVG.svg.attlist "INCLUDE" >
+<![%SVG.svg.attlist;[
+<!ATTLIST %SVG.svg.qname;
+ %SVG.xmlns.attrib;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.DocumentEvents.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.External.attrib;
+ x %Coordinate.datatype; #IMPLIED
+ y %Coordinate.datatype; #IMPLIED
+ width %Length.datatype; #IMPLIED
+ height %Length.datatype; #IMPLIED
+ viewBox %ViewBoxSpec.datatype; #IMPLIED
+ preserveAspectRatio %PreserveAspectRatioSpec.datatype; 'xMidYMid meet'
+ zoomAndPan ( disable | magnify ) 'magnify'
+ version %Number.datatype; #FIXED '1.1'
+ baseProfile %Text.datatype; #IMPLIED
+ contentScriptType %ContentType.datatype; 'text/ecmascript'
+ contentStyleType %ContentType.datatype; 'text/css'
+>
+<!-- end of SVG.svg.attlist -->]]>
+
+<!-- g: Group Element .................................. -->
+
+<!ENTITY % SVG.g.extra.content "" >
+
+<!ENTITY % SVG.g.element "INCLUDE" >
+<![%SVG.g.element;[
+<!ENTITY % SVG.g.content
+ "( %SVG.Description.class; | %SVG.Animation.class; %SVG.Structure.class;
+ %SVG.Conditional.class; %SVG.Image.class; %SVG.Style.class;
+ %SVG.Shape.class; %SVG.Text.class; %SVG.Marker.class; %SVG.Profile.class;
+ %SVG.Gradient.class; %SVG.Pattern.class; %SVG.Clip.class;
+ %SVG.Mask.class; %SVG.Filter.class; %SVG.Cursor.class;
+ %SVG.Hyperlink.class; %SVG.View.class; %SVG.Script.class;
+ %SVG.Font.class; %SVG.g.extra.content; )*"
+>
+<!ELEMENT %SVG.g.qname; %SVG.g.content; >
+<!-- end of SVG.g.element -->]]>
+
+<!ENTITY % SVG.g.attlist "INCLUDE" >
+<![%SVG.g.attlist;[
+<!ATTLIST %SVG.g.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.External.attrib;
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.g.attlist -->]]>
+
+<!-- defs: Definisions Element ......................... -->
+
+<!ENTITY % SVG.defs.extra.content "" >
+
+<!ENTITY % SVG.defs.element "INCLUDE" >
+<![%SVG.defs.element;[
+<!ENTITY % SVG.defs.content
+ "( %SVG.Description.class; | %SVG.Animation.class; %SVG.Structure.class;
+ %SVG.Conditional.class; %SVG.Image.class; %SVG.Style.class;
+ %SVG.Shape.class; %SVG.Text.class; %SVG.Marker.class; %SVG.Profile.class;
+ %SVG.Gradient.class; %SVG.Pattern.class; %SVG.Clip.class;
+ %SVG.Mask.class; %SVG.Filter.class; %SVG.Cursor.class;
+ %SVG.Hyperlink.class; %SVG.View.class; %SVG.Script.class;
+ %SVG.Font.class; %SVG.defs.extra.content; )*"
+>
+<!ELEMENT %SVG.defs.qname; %SVG.defs.content; >
+<!-- end of SVG.defs.element -->]]>
+
+<!ENTITY % SVG.defs.attlist "INCLUDE" >
+<![%SVG.defs.attlist;[
+<!ATTLIST %SVG.defs.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.External.attrib;
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.defs.attlist -->]]>
+
+<!-- desc: Description Element ......................... -->
+
+<!ENTITY % SVG.desc.extra.content "" >
+
+<!ENTITY % SVG.desc.element "INCLUDE" >
+<![%SVG.desc.element;[
+<!ENTITY % SVG.desc.content
+ "( #PCDATA %SVG.desc.extra.content; )*"
+>
+<!ELEMENT %SVG.desc.qname; %SVG.desc.content; >
+<!-- end of SVG.desc.element -->]]>
+
+<!ENTITY % SVG.desc.attlist "INCLUDE" >
+<![%SVG.desc.attlist;[
+<!ATTLIST %SVG.desc.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+>
+<!-- end of SVG.desc.attlist -->]]>
+
+<!-- title: Title Element .............................. -->
+
+<!ENTITY % SVG.title.extra.content "" >
+
+<!ENTITY % SVG.title.element "INCLUDE" >
+<![%SVG.title.element;[
+<!ENTITY % SVG.title.content
+ "( #PCDATA %SVG.title.extra.content; )*"
+>
+<!ELEMENT %SVG.title.qname; %SVG.title.content; >
+<!-- end of SVG.title.element -->]]>
+
+<!ENTITY % SVG.title.attlist "INCLUDE" >
+<![%SVG.title.attlist;[
+<!ATTLIST %SVG.title.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+>
+<!-- end of SVG.title.attlist -->]]>
+
+<!-- metadata: Metadata Element ........................ -->
+
+<!ENTITY % SVG.metadata.extra.content "" >
+
+<!ENTITY % SVG.metadata.element "INCLUDE" >
+<![%SVG.metadata.element;[
+<!ENTITY % SVG.metadata.content
+ "( #PCDATA %SVG.metadata.extra.content; )*"
+>
+<!ELEMENT %SVG.metadata.qname; %SVG.metadata.content; >
+<!-- end of SVG.metadata.element -->]]>
+
+<!ENTITY % SVG.metadata.attlist "INCLUDE" >
+<![%SVG.metadata.attlist;[
+<!ATTLIST %SVG.metadata.qname;
+ %SVG.Core.attrib;
+>
+<!-- end of SVG.metadata.attlist -->]]>
+
+<!-- use: Use Element .................................. -->
+
+<!ENTITY % SVG.use.extra.content "" >
+
+<!ENTITY % SVG.use.element "INCLUDE" >
+<![%SVG.use.element;[
+<!ENTITY % SVG.use.content
+ "(( %SVG.Description.class; )*, ( %SVG.Animation.class;
+ %SVG.use.extra.content; )*)"
+>
+<!ELEMENT %SVG.use.qname; %SVG.use.content; >
+<!-- end of SVG.use.element -->]]>
+
+<!ENTITY % SVG.use.attlist "INCLUDE" >
+<![%SVG.use.attlist;[
+<!ATTLIST %SVG.use.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.XLinkEmbed.attrib;
+ %SVG.External.attrib;
+ x %Coordinate.datatype; #IMPLIED
+ y %Coordinate.datatype; #IMPLIED
+ width %Length.datatype; #IMPLIED
+ height %Length.datatype; #IMPLIED
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.use.attlist -->]]>
+
+<!-- end of svg-basic-structure.mod -->
diff --git a/org/apache/batik/dom/svg/resources/svg-basic-text.mod b/org/apache/batik/dom/svg/resources/svg-basic-text.mod
new file mode 100644
index 0000000..7762373
--- /dev/null
+++ b/org/apache/batik/dom/svg/resources/svg-basic-text.mod
@@ -0,0 +1,194 @@
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Basic Text Module ............................................. -->
+<!-- file: svg-basic-text.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg-basic-text.mod 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Basic Text//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-basic-text.mod"
+
+ ....................................................................... -->
+
+<!-- Basic Text
+
+ text, altGlyph, altGlyphDef, glyphRef
+
+ This module declares markup to provide support for text.
+-->
+
+<!-- 'font-family' property/attribute value (i.e., list of fonts) -->
+<!ENTITY % FontFamilyValue.datatype "CDATA" >
+
+<!-- 'font-size' property/attribute value -->
+<!ENTITY % FontSizeValue.datatype "CDATA" >
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.text.qname "text" >
+<!ENTITY % SVG.altGlyph.qname "altGlyph" >
+<!ENTITY % SVG.altGlyphDef.qname "altGlyphDef" >
+<!ENTITY % SVG.glyphRef.qname "glyphRef" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Conditional.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Paint.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Clip.attrib "" >
+<!ENTITY % SVG.Mask.attrib "" >
+<!ENTITY % SVG.Filter.attrib "" >
+<!ENTITY % SVG.GraphicalEvents.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.XLink.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Text.class .................................... -->
+
+<!ENTITY % SVG.Text.extra.class "" >
+
+<!ENTITY % SVG.Text.class
+ "| %SVG.text.qname; | %SVG.altGlyphDef.qname; %SVG.Text.extra.class;"
+>
+
+<!-- SVG.TextContent.class ............................. -->
+
+<!ENTITY % SVG.TextContent.extra.class "" >
+
+<!ENTITY % SVG.TextContent.class
+ "| %SVG.altGlyph.qname; %SVG.TextContent.extra.class;"
+>
+
+<!-- SVG.Font.attrib ................................... -->
+
+<!ENTITY % SVG.Font.extra.attrib "" >
+
+<!ENTITY % SVG.Font.attrib
+ "font-family %FontFamilyValue.datatype; #IMPLIED
+ font-size %FontSizeValue.datatype; #IMPLIED
+ font-style ( normal | italic | oblique | inherit ) #IMPLIED
+ font-weight ( normal | bold | bolder | lighter | 100 | 200 | 300 | 400 |
+ 500 | 600 | 700 | 800 | 900 | inherit ) #IMPLIED
+ %SVG.Font.extra.attrib;"
+>
+
+<!-- text: Text Element ................................ -->
+
+<!ENTITY % SVG.text.extra.content "" >
+
+<!ENTITY % SVG.text.element "INCLUDE" >
+<![%SVG.text.element;[
+<!ENTITY % SVG.text.content
+ "( #PCDATA | %SVG.Description.class; | %SVG.Animation.class;
+ %SVG.TextContent.class; %SVG.Hyperlink.class;
+ %SVG.text.extra.content; )*"
+>
+<!ELEMENT %SVG.text.qname; %SVG.text.content; >
+<!-- end of SVG.text.element -->]]>
+
+<!ENTITY % SVG.text.attlist "INCLUDE" >
+<![%SVG.text.attlist;[
+<!ATTLIST %SVG.text.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.External.attrib;
+ x %Coordinates.datatype; #IMPLIED
+ y %Coordinates.datatype; #IMPLIED
+ rotate %Numbers.datatype; #IMPLIED
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.text.attlist -->]]>
+
+<!-- altGlyph: Alternate Glyph Element ................. -->
+
+<!ENTITY % SVG.altGlyph.extra.content "" >
+
+<!ENTITY % SVG.altGlyph.element "INCLUDE" >
+<![%SVG.altGlyph.element;[
+<!ENTITY % SVG.altGlyph.content
+ "( #PCDATA %SVG.altGlyph.extra.content; )*"
+>
+<!ELEMENT %SVG.altGlyph.qname; %SVG.altGlyph.content; >
+<!-- end of SVG.altGlyph.element -->]]>
+
+<!ENTITY % SVG.altGlyph.attlist "INCLUDE" >
+<![%SVG.altGlyph.attlist;[
+<!ATTLIST %SVG.altGlyph.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.XLink.attrib;
+ %SVG.External.attrib;
+ glyphRef CDATA #IMPLIED
+ format CDATA #IMPLIED
+>
+<!-- end of SVG.altGlyph.attlist -->]]>
+
+<!-- altGlyphDef: Alternate Glyph Definition Element ... -->
+
+<!ENTITY % SVG.altGlyphDef.extra.content "" >
+
+<!ENTITY % SVG.altGlyphDef.element "INCLUDE" >
+<![%SVG.altGlyphDef.element;[
+<!ENTITY % SVG.altGlyphDef.content
+ "( %SVG.glyphRef.qname;+ %SVG.altGlyphDef.extra.content; )"
+>
+<!ELEMENT %SVG.altGlyphDef.qname; %SVG.altGlyphDef.content; >
+<!-- end of SVG.altGlyphDef.element -->]]>
+
+<!ENTITY % SVG.altGlyphDef.attlist "INCLUDE" >
+<![%SVG.altGlyphDef.attlist;[
+<!ATTLIST %SVG.altGlyphDef.qname;
+ %SVG.Core.attrib;
+>
+<!-- end of SVG.altGlyphDef.attlist -->]]>
+
+<!-- glyphRef: Glyph Reference Element ................. -->
+
+<!ENTITY % SVG.glyphRef.element "INCLUDE" >
+<![%SVG.glyphRef.element;[
+<!ENTITY % SVG.glyphRef.content "EMPTY" >
+<!ELEMENT %SVG.glyphRef.qname; %SVG.glyphRef.content; >
+<!-- end of SVG.glyphRef.element -->]]>
+
+<!ENTITY % SVG.glyphRef.attlist "INCLUDE" >
+<![%SVG.glyphRef.attlist;[
+<!ATTLIST %SVG.glyphRef.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Font.attrib;
+ %SVG.XLink.attrib;
+ glyphRef CDATA #IMPLIED
+ format CDATA #IMPLIED
+>
+<!-- end of SVG.glyphRef.attlist -->]]>
+
+<!-- end of svg-basic-text.mod -->
diff --git a/org/apache/batik/dom/svg/resources/svg-clip.mod b/org/apache/batik/dom/svg/resources/svg-clip.mod
new file mode 100644
index 0000000..989db97
--- /dev/null
+++ b/org/apache/batik/dom/svg/resources/svg-clip.mod
@@ -0,0 +1,101 @@
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Clip Module ................................................... -->
+<!-- file: svg-clip.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg-clip.mod 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Clip//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-clip.mod"
+
+ ....................................................................... -->
+
+<!-- Clip
+
+ clipPath
+
+ This module declares markup to provide support for clipping.
+-->
+
+<!-- 'clip-path' property/attribute value (e.g., 'none', <uri>) -->
+<!ENTITY % ClipPathValue.datatype "CDATA" >
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.clipPath.qname "clipPath" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Conditional.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Text.attrib "" >
+<!ENTITY % SVG.TextContent.attrib "" >
+<!ENTITY % SVG.Font.attrib "" >
+<!ENTITY % SVG.Paint.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Mask.attrib "" >
+<!ENTITY % SVG.Filter.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Clip.class .................................... -->
+
+<!ENTITY % SVG.Clip.extra.class "" >
+
+<!ENTITY % SVG.Clip.class
+ "| %SVG.clipPath.qname; %SVG.Clip.extra.class;"
+>
+
+<!-- SVG.Clip.attrib ................................... -->
+
+<!ENTITY % SVG.Clip.extra.attrib "" >
+
+<!ENTITY % SVG.Clip.attrib
+ "clip-path %ClipPathValue.datatype; #IMPLIED
+ clip-rule %ClipFillRule.datatype; #IMPLIED
+ %SVG.Clip.extra.attrib;"
+>
+
+<!-- clipPath: Clip Path Element ....................... -->
+
+<!ENTITY % SVG.clipPath.extra.content "" >
+
+<!ENTITY % SVG.clipPath.element "INCLUDE" >
+<![%SVG.clipPath.element;[
+<!ENTITY % SVG.clipPath.content
+ "(( %SVG.Description.class; )*, ( %SVG.Animation.class; %SVG.Use.class;
+ %SVG.Shape.class; %SVG.Text.class; %SVG.clipPath.extra.content; )*)"
+>
+<!ELEMENT %SVG.clipPath.qname; %SVG.clipPath.content; >
+<!-- end of SVG.clipPath.element -->]]>
+
+<!ENTITY % SVG.clipPath.attlist "INCLUDE" >
+<![%SVG.clipPath.attlist;[
+<!ATTLIST %SVG.clipPath.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Text.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.External.attrib;
+ transform %TransformList.datatype; #IMPLIED
+ clipPathUnits ( userSpaceOnUse | objectBoundingBox ) #IMPLIED
+>
+<!-- end of SVG.clipPath.attlist -->]]>
+
+<!-- end of svg-clip.mod -->
diff --git a/org/apache/batik/dom/svg/resources/svg-conditional.mod b/org/apache/batik/dom/svg/resources/svg-conditional.mod
new file mode 100644
index 0000000..4e13ddb
--- /dev/null
+++ b/org/apache/batik/dom/svg/resources/svg-conditional.mod
@@ -0,0 +1,133 @@
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Conditional Processing Module ................................. -->
+<!-- file: svg-conditional.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg-conditional.mod 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Conditional Processing//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-conditional.mod"
+
+ ....................................................................... -->
+
+<!-- Conditional Processing
+
+ switch
+
+ This module declares markup to provide support for conditional processing.
+-->
+
+<!-- extension list specification -->
+<!ENTITY % ExtensionList.datatype "CDATA" >
+
+<!-- feature list specification -->
+<!ENTITY % FeatureList.datatype "CDATA" >
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.switch.qname "switch" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Container.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Viewport.attrib "" >
+<!ENTITY % SVG.Text.attrib "" >
+<!ENTITY % SVG.TextContent.attrib "" >
+<!ENTITY % SVG.Font.attrib "" >
+<!ENTITY % SVG.Paint.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Marker.attrib "" >
+<!ENTITY % SVG.Profile.attrib "" >
+<!ENTITY % SVG.Gradient.attrib "" >
+<!ENTITY % SVG.Clip.attrib "" >
+<!ENTITY % SVG.Mask.attrib "" >
+<!ENTITY % SVG.Filter.attrib "" >
+<!ENTITY % SVG.FilterColor.attrib "" >
+<!ENTITY % SVG.GraphicalEvents.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Conditional.class ............................. -->
+
+<!ENTITY % SVG.Conditional.extra.class "" >
+
+<!ENTITY % SVG.Conditional.class
+ "| %SVG.switch.qname; %SVG.Conditional.extra.class;"
+>
+
+<!-- SVG.Conditional.attrib ............................ -->
+
+<!ENTITY % SVG.Conditional.extra.attrib "" >
+
+<!ENTITY % SVG.Conditional.attrib
+ "requiredFeatures %FeatureList.datatype; #IMPLIED
+ requiredExtensions %ExtensionList.datatype; #IMPLIED
+ systemLanguage %LanguageCodes.datatype; #IMPLIED
+ %SVG.Conditional.extra.attrib;"
+>
+
+<!-- SVG.Presentation.attrib ........................... -->
+
+<!ENTITY % SVG.Presentation.extra.attrib "" >
+
+<!ENTITY % SVG.Presentation.attrib
+ "%SVG.Container.attrib;
+ %SVG.Viewport.attrib;
+ %SVG.Text.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Profile.attrib;
+ %SVG.Gradient.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.Cursor.attrib;
+ flood-color %SVGColor.datatype; #IMPLIED
+ flood-opacity %OpacityValue.datatype; #IMPLIED
+ lighting-color %SVGColor.datatype; #IMPLIED
+ %SVG.Presentation.extra.attrib;"
+>
+
+<!-- switch: Switch Element ............................ -->
+
+<!ENTITY % SVG.switch.extra.content "" >
+
+<!ENTITY % SVG.switch.element "INCLUDE" >
+<![%SVG.switch.element;[
+<!ENTITY % SVG.switch.content
+ "(( %SVG.Description.class; )*, ( %SVG.svg.qname; | %SVG.g.qname;
+ | %SVG.use.qname; | %SVG.text.qname; | %SVG.Animation.class;
+ %SVG.Conditional.class; %SVG.Image.class; %SVG.Shape.class;
+ %SVG.Hyperlink.class; %SVG.Extensibility.class;
+ %SVG.switch.extra.content; )*)"
+>
+<!ELEMENT %SVG.switch.qname; %SVG.switch.content; >
+<!-- end of SVG.switch.element -->]]>
+
+<!ENTITY % SVG.switch.attlist "INCLUDE" >
+<![%SVG.switch.attlist;[
+<!ATTLIST %SVG.switch.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.External.attrib;
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.switch.attlist -->]]>
+
+<!-- end of svg-conditional.mod -->
diff --git a/org/apache/batik/dom/svg/resources/svg-container-attrib.mod b/org/apache/batik/dom/svg/resources/svg-container-attrib.mod
new file mode 100644
index 0000000..dd875e4
--- /dev/null
+++ b/org/apache/batik/dom/svg/resources/svg-container-attrib.mod
@@ -0,0 +1,37 @@
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Container Attribute Module .................................... -->
+<!-- file: svg-container-attrib.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg-container-attrib.mod 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Container Attribute//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-container-attrib.mod"
+
+ ....................................................................... -->
+
+<!-- Container Attribute
+
+ enable-background
+
+ This module defines the Container attribute set.
+-->
+
+<!-- 'enable-background' property/attribute value (e.g., 'new', 'accumulate') -->
+<!ENTITY % EnableBackgroundValue.datatype "CDATA" >
+
+<!ENTITY % SVG.enable-background.attrib
+ "enable-background %EnableBackgroundValue.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.Container.extra.attrib "" >
+
+<!ENTITY % SVG.Container.attrib
+ "%SVG.enable-background.attrib;
+ %SVG.Container.extra.attrib;"
+>
+
+<!-- end of svg-container-attrib.mod -->
diff --git a/org/apache/batik/dom/svg/resources/svg-core-attrib.mod b/org/apache/batik/dom/svg/resources/svg-core-attrib.mod
new file mode 100644
index 0000000..190a51f
--- /dev/null
+++ b/org/apache/batik/dom/svg/resources/svg-core-attrib.mod
@@ -0,0 +1,50 @@
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Core Attribute Module ......................................... -->
+<!-- file: svg-core-attrib.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg-core-attrib.mod 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Core Attribute//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-core-attrib.mod"
+
+ ....................................................................... -->
+
+<!-- Core Attribute
+
+ id, xml:base, xml:lang, xml:space
+
+ This module defines the core set of attributes that can be present on
+ any element.
+-->
+
+<!ENTITY % SVG.id.attrib
+ "id ID #IMPLIED"
+>
+
+<!ENTITY % SVG.base.attrib
+ "xml:base %URI.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.lang.attrib
+ "xml:lang %LanguageCode.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.space.attrib
+ "xml:space ( default | preserve ) #IMPLIED"
+>
+
+<!ENTITY % SVG.Core.extra.attrib "" >
+
+<!ENTITY % SVG.Core.attrib
+ "%SVG.id.attrib;
+ %SVG.base.attrib;
+ %SVG.lang.attrib;
+ %SVG.space.attrib;
+ %SVG.Core.extra.attrib;"
+>
+
+<!-- end of svg-core-attrib.mod -->
diff --git a/org/apache/batik/dom/svg/resources/svg-cursor.mod b/org/apache/batik/dom/svg/resources/svg-cursor.mod
new file mode 100644
index 0000000..7802e54
--- /dev/null
+++ b/org/apache/batik/dom/svg/resources/svg-cursor.mod
@@ -0,0 +1,78 @@
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Cursor Module ................................................. -->
+<!-- file: svg-cursor.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg-cursor.mod 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Cursor//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-cursor.mod"
+
+ ....................................................................... -->
+
+<!-- Cursor
+
+ cursor
+
+ This module declares markup to provide support for cursor.
+-->
+
+<!-- 'cursor' property/attribute value (e.g., 'crosshair', <uri>) -->
+<!ENTITY % CursorValue.datatype "CDATA" >
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.cursor.qname "cursor" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Conditional.attrib "" >
+<!ENTITY % SVG.XLinkRequired.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Cursor.class .................................. -->
+
+<!ENTITY % SVG.Cursor.extra.class "" >
+
+<!ENTITY % SVG.Cursor.class
+ "| %SVG.cursor.qname; %SVG.Cursor.extra.class;"
+>
+
+<!-- SVG.Cursor.attrib ................................. -->
+
+<!ENTITY % SVG.Cursor.extra.attrib "" >
+
+<!ENTITY % SVG.Cursor.attrib
+ "cursor %CursorValue.datatype; #IMPLIED
+ %SVG.Cursor.extra.attrib;"
+>
+
+<!-- cursor: Cursor Element ............................ -->
+
+<!ENTITY % SVG.cursor.extra.content "" >
+
+<!ENTITY % SVG.cursor.element "INCLUDE" >
+<![%SVG.cursor.element;[
+<!ENTITY % SVG.cursor.content
+ "( %SVG.Description.class; %SVG.cursor.extra.content; )*"
+>
+<!ELEMENT %SVG.cursor.qname; %SVG.cursor.content; >
+<!-- end of SVG.cursor.element -->]]>
+
+<!ENTITY % SVG.cursor.attlist "INCLUDE" >
+<![%SVG.cursor.attlist;[
+<!ATTLIST %SVG.cursor.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.XLinkRequired.attrib;
+ %SVG.External.attrib;
+ x %Coordinate.datatype; #IMPLIED
+ y %Coordinate.datatype; #IMPLIED
+>
+<!-- end of SVG.cursor.attlist -->]]>
+
+<!-- end of svg-cursor.mod -->
diff --git a/org/apache/batik/dom/svg/resources/svg-datatypes.mod b/org/apache/batik/dom/svg/resources/svg-datatypes.mod
new file mode 100644
index 0000000..b7d05be
--- /dev/null
+++ b/org/apache/batik/dom/svg/resources/svg-datatypes.mod
@@ -0,0 +1,87 @@
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Datatypes Module .............................................. -->
+<!-- file: svg-datatypes.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg-datatypes.mod 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Datatypes//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-datatypes.mod"
+
+ ....................................................................... -->
+
+<!-- Datatypes
+
+ This module declares common data types for properties and attributes.
+-->
+
+<!-- feature specification -->
+<!ENTITY % Boolean.datatype "( false | true )" >
+
+<!-- 'clip-rule' or 'fill-rule' property/attribute value -->
+<!ENTITY % ClipFillRule.datatype "( nonzero | evenodd | inherit )" >
+
+<!-- media type, as per [RFC2045] -->
+<!ENTITY % ContentType.datatype "CDATA" >
+
+<!-- a <coordinate> -->
+<!ENTITY % Coordinate.datatype "CDATA" >
+
+<!-- a list of <coordinate>s -->
+<!ENTITY % Coordinates.datatype "CDATA" >
+
+<!-- a <color> value -->
+<!ENTITY % Color.datatype "CDATA" >
+
+<!-- a <integer> -->
+<!ENTITY % Integer.datatype "CDATA" >
+
+<!-- a language code, as per [RFC3066] -->
+<!ENTITY % LanguageCode.datatype "NMTOKEN" >
+
+<!-- comma-separated list of language codes, as per [RFC3066] -->
+<!ENTITY % LanguageCodes.datatype "CDATA" >
+
+<!-- a <length> -->
+<!ENTITY % Length.datatype "CDATA" >
+
+<!-- a list of <length>s -->
+<!ENTITY % Lengths.datatype "CDATA" >
+
+<!-- a <number> -->
+<!ENTITY % Number.datatype "CDATA" >
+
+<!-- a list of <number>s -->
+<!ENTITY % Numbers.datatype "CDATA" >
+
+<!-- opacity value (e.g., <number>) -->
+<!ENTITY % OpacityValue.datatype "CDATA" >
+
+<!-- a path data specification -->
+<!ENTITY % PathData.datatype "CDATA" >
+
+<!-- 'preserveAspectRatio' attribute specification -->
+<!ENTITY % PreserveAspectRatioSpec.datatype "CDATA" >
+
+<!-- script expression -->
+<!ENTITY % Script.datatype "CDATA" >
+
+<!-- An SVG color value (RGB plus optional ICC) -->
+<!ENTITY % SVGColor.datatype "CDATA" >
+
+<!-- arbitrary text string -->
+<!ENTITY % Text.datatype "CDATA" >
+
+<!-- list of transforms -->
+<!ENTITY % TransformList.datatype "CDATA" >
+
+<!-- a Uniform Resource Identifier, see [URI] -->
+<!ENTITY % URI.datatype "CDATA" >
+
+<!-- 'viewBox' attribute specification -->
+<!ENTITY % ViewBoxSpec.datatype "CDATA" >
+
+<!-- end of svg-datatypes.mod -->
diff --git a/org/apache/batik/dom/svg/resources/svg-docevents-attrib.mod b/org/apache/batik/dom/svg/resources/svg-docevents-attrib.mod
new file mode 100644
index 0000000..5592783
--- /dev/null
+++ b/org/apache/batik/dom/svg/resources/svg-docevents-attrib.mod
@@ -0,0 +1,59 @@
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Document Events Attribute Module .............................. -->
+<!-- file: svg-docevents-attrib.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg-docevents-attrib.mod 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Document Events Attribute//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-docevents-attrib.mod"
+
+ ....................................................................... -->
+
+<!-- Document Events Attribute
+
+ onunload, onabort, onerror, onresize, onscroll, onzoom
+
+ This module defines the DocumentEvents attribute set.
+-->
+
+<!ENTITY % SVG.onunload.attrib
+ "onunload %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onabort.attrib
+ "onabort %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onerror.attrib
+ "onerror %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onresize.attrib
+ "onresize %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onscroll.attrib
+ "onscroll %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onzoom.attrib
+ "onzoom %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.DocumentEvents.extra.attrib "" >
+
+<!ENTITY % SVG.DocumentEvents.attrib
+ "%SVG.onunload.attrib;
+ %SVG.onabort.attrib;
+ %SVG.onerror.attrib;
+ %SVG.onresize.attrib;
+ %SVG.onscroll.attrib;
+ %SVG.onzoom.attrib;
+ %SVG.DocumentEvents.extra.attrib;"
+>
+
+<!-- end of svg-docevents-attrib.mod -->
diff --git a/org/apache/batik/dom/svg/resources/svg-extensibility.mod b/org/apache/batik/dom/svg/resources/svg-extensibility.mod
new file mode 100644
index 0000000..bbe7186
--- /dev/null
+++ b/org/apache/batik/dom/svg/resources/svg-extensibility.mod
@@ -0,0 +1,115 @@
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Extensibility Module .......................................... -->
+<!-- file: svg-extensibility.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg-extensibility.mod 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Extensibility//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-extensibility.mod"
+
+ ....................................................................... -->
+
+<!-- Extensibility
+
+ foreignObject
+
+ This module declares markup to provide support for extensibility.
+-->
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.foreignObject.qname "foreignObject" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Conditional.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Viewport.attrib "" >
+<!ENTITY % SVG.Text.attrib "" >
+<!ENTITY % SVG.TextContent.attrib "" >
+<!ENTITY % SVG.Font.attrib "" >
+<!ENTITY % SVG.Paint.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Marker.attrib "" >
+<!ENTITY % SVG.Gradient.attrib "" >
+<!ENTITY % SVG.Clip.attrib "" >
+<!ENTITY % SVG.Mask.attrib "" >
+<!ENTITY % SVG.Filter.attrib "" >
+<!ENTITY % SVG.FilterColor.attrib "" >
+<!ENTITY % SVG.GraphicalEvents.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Extensibility.class ........................... -->
+
+<!ENTITY % SVG.Extensibility.extra.class "" >
+
+<!ENTITY % SVG.Extensibility.class
+ "| %SVG.foreignObject.qname; %SVG.Extensibility.extra.class;"
+>
+
+<!-- SVG.Presentation.attrib ........................... -->
+
+<!ENTITY % SVG.Presentation.extra.attrib "" >
+
+<!ENTITY % SVG.Presentation.attrib
+ "%SVG.Container.attrib;
+ %SVG.Viewport.attrib;
+ %SVG.Text.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Profile.attrib;
+ %SVG.Gradient.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.Cursor.attrib;
+ flood-color %SVGColor.datatype; #IMPLIED
+ flood-opacity %OpacityValue.datatype; #IMPLIED
+ lighting-color %SVGColor.datatype; #IMPLIED
+ %SVG.Presentation.extra.attrib;"
+>
+
+<!-- foreignObject: Foreign Object Element ............. -->
+
+<!ENTITY % SVG.foreignObject.extra.content "" >
+
+<!ENTITY % SVG.foreignObject.element "INCLUDE" >
+<![%SVG.foreignObject.element;[
+<!ENTITY % SVG.foreignObject.content
+ "( #PCDATA %SVG.foreignObject.extra.content; )*"
+>
+<!ELEMENT %SVG.foreignObject.qname; %SVG.foreignObject.content; >
+<!-- end of SVG.foreignObject.element -->]]>
+
+<!ENTITY % SVG.foreignObject.attlist "INCLUDE" >
+<![%SVG.foreignObject.attlist;[
+<!ATTLIST %SVG.foreignObject.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.External.attrib;
+ x %Coordinate.datatype; #IMPLIED
+ y %Coordinate.datatype; #IMPLIED
+ width %Length.datatype; #REQUIRED
+ height %Length.datatype; #REQUIRED
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.foreignObject.attlist -->]]>
+
+<!-- end of svg-extensibility.mod -->
diff --git a/org/apache/batik/dom/svg/resources/svg-extresources-attrib.mod b/org/apache/batik/dom/svg/resources/svg-extresources-attrib.mod
new file mode 100644
index 0000000..4f41864
--- /dev/null
+++ b/org/apache/batik/dom/svg/resources/svg-extresources-attrib.mod
@@ -0,0 +1,34 @@
+<!-- ....................................................................... -->
+<!-- SVG 1.1 External Resources Attribute Module ........................... -->
+<!-- file: svg-extresources-attrib.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg-extresources-attrib.mod 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 External Resources Attribute//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-extresources-attrib.mod"
+
+ ....................................................................... -->
+
+<!-- External Resources Attribute
+
+ externalResourcesRequired
+
+ This module defines the External attribute set.
+-->
+
+<!ENTITY % SVG.externalResourcesRequired.attrib
+ "externalResourcesRequired %Boolean.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.External.extra.attrib "" >
+
+<!ENTITY % SVG.External.attrib
+ "%SVG.externalResourcesRequired.attrib;
+ %SVG.External.extra.attrib;"
+>
+
+<!-- end of svg-extresources-attrib.mod -->
diff --git a/org/apache/batik/dom/svg/resources/svg-filter.mod b/org/apache/batik/dom/svg/resources/svg-filter.mod
new file mode 100644
index 0000000..c6427c4
--- /dev/null
+++ b/org/apache/batik/dom/svg/resources/svg-filter.mod
@@ -0,0 +1,807 @@
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Filter Module ................................................. -->
+<!-- file: svg-filter.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg-filter.mod 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Filter//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-filter.mod"
+
+ ....................................................................... -->
+
+<!-- Filter
+
+ filter, feBlend, feColorMatrix, feComponentTransfer, feComposite,
+ feConvolveMatrix, feDiffuseLighting, feDisplacementMap, feFlood,
+ feGaussianBlur, feImage, feMerge, feMergeNode, feMorphology, feOffset,
+ feSpecularLighting, feTile, feTurbulence, feDistantLight, fePointLight,
+ feSpotLight, feFuncR, feFuncG, feFuncB, feFuncA
+
+ This module declares markup to provide support for filter effect.
+-->
+
+<!-- 'filter' property/attribute value (e.g., 'none', <uri>) -->
+<!ENTITY % FilterValue.datatype "CDATA" >
+
+<!-- list of <number>s, but at least one and at most two -->
+<!ENTITY % NumberOptionalNumber.datatype "CDATA" >
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.filter.qname "filter" >
+<!ENTITY % SVG.feBlend.qname "feBlend" >
+<!ENTITY % SVG.feColorMatrix.qname "feColorMatrix" >
+<!ENTITY % SVG.feComponentTransfer.qname "feComponentTransfer" >
+<!ENTITY % SVG.feComposite.qname "feComposite" >
+<!ENTITY % SVG.feConvolveMatrix.qname "feConvolveMatrix" >
+<!ENTITY % SVG.feDiffuseLighting.qname "feDiffuseLighting" >
+<!ENTITY % SVG.feDisplacementMap.qname "feDisplacementMap" >
+<!ENTITY % SVG.feFlood.qname "feFlood" >
+<!ENTITY % SVG.feGaussianBlur.qname "feGaussianBlur" >
+<!ENTITY % SVG.feImage.qname "feImage" >
+<!ENTITY % SVG.feMerge.qname "feMerge" >
+<!ENTITY % SVG.feMergeNode.qname "feMergeNode" >
+<!ENTITY % SVG.feMorphology.qname "feMorphology" >
+<!ENTITY % SVG.feOffset.qname "feOffset" >
+<!ENTITY % SVG.feSpecularLighting.qname "feSpecularLighting" >
+<!ENTITY % SVG.feTile.qname "feTile" >
+<!ENTITY % SVG.feTurbulence.qname "feTurbulence" >
+<!ENTITY % SVG.feDistantLight.qname "feDistantLight" >
+<!ENTITY % SVG.fePointLight.qname "fePointLight" >
+<!ENTITY % SVG.feSpotLight.qname "feSpotLight" >
+<!ENTITY % SVG.feFuncR.qname "feFuncR" >
+<!ENTITY % SVG.feFuncG.qname "feFuncG" >
+<!ENTITY % SVG.feFuncB.qname "feFuncB" >
+<!ENTITY % SVG.feFuncA.qname "feFuncA" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Container.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Viewport.attrib "" >
+<!ENTITY % SVG.Text.attrib "" >
+<!ENTITY % SVG.TextContent.attrib "" >
+<!ENTITY % SVG.Font.attrib "" >
+<!ENTITY % SVG.Paint.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Marker.attrib "" >
+<!ENTITY % SVG.Profile.attrib "" >
+<!ENTITY % SVG.Gradient.attrib "" >
+<!ENTITY % SVG.Clip.attrib "" >
+<!ENTITY % SVG.Mask.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.XLink.attrib "" >
+<!ENTITY % SVG.XLinkEmbed.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Filter.class .................................. -->
+
+<!ENTITY % SVG.Filter.extra.class "" >
+
+<!ENTITY % SVG.Filter.class
+ "| %SVG.filter.qname; %SVG.Filter.extra.class;"
+>
+
+<!-- SVG.FilterPrimitive.class ......................... -->
+
+<!ENTITY % SVG.FilterPrimitive.extra.class "" >
+
+<!ENTITY % SVG.FilterPrimitive.class
+ "| %SVG.feBlend.qname; | %SVG.feColorMatrix.qname;
+ | %SVG.feComponentTransfer.qname; | %SVG.feComposite.qname;
+ | %SVG.feConvolveMatrix.qname; | %SVG.feDiffuseLighting.qname;
+ | %SVG.feDisplacementMap.qname; | %SVG.feFlood.qname;
+ | %SVG.feGaussianBlur.qname; | %SVG.feImage.qname; | %SVG.feMerge.qname;
+ | %SVG.feMorphology.qname; | %SVG.feOffset.qname;
+ | %SVG.feSpecularLighting.qname; | %SVG.feTile.qname;
+ | %SVG.feTurbulence.qname; %SVG.FilterPrimitive.extra.class;"
+>
+
+<!-- SVG.Filter.attrib ................................. -->
+
+<!ENTITY % SVG.Filter.extra.attrib "" >
+
+<!ENTITY % SVG.Filter.attrib
+ "filter %FilterValue.datatype; #IMPLIED
+ %SVG.Filter.extra.attrib;"
+>
+
+<!-- SVG.FilterColor.attrib ............................ -->
+
+<!ENTITY % SVG.FilterColor.extra.attrib "" >
+
+<!ENTITY % SVG.FilterColor.attrib
+ "color-interpolation-filters ( auto | sRGB | linearRGB | inherit )
+ #IMPLIED
+ %SVG.FilterColor.extra.attrib;"
+>
+
+<!-- SVG.FilterPrimitive.attrib ........................ -->
+
+<!ENTITY % SVG.FilterPrimitive.extra.attrib "" >
+
+<!ENTITY % SVG.FilterPrimitive.attrib
+ "x %Coordinate.datatype; #IMPLIED
+ y %Coordinate.datatype; #IMPLIED
+ width %Length.datatype; #IMPLIED
+ height %Length.datatype; #IMPLIED
+ result CDATA #IMPLIED
+ %SVG.FilterPrimitive.extra.attrib;"
+>
+
+<!-- SVG.FilterPrimitiveWithIn.attrib .................. -->
+
+<!ENTITY % SVG.FilterPrimitiveWithIn.extra.attrib "" >
+
+<!ENTITY % SVG.FilterPrimitiveWithIn.attrib
+ "%SVG.FilterPrimitive.attrib;
+ in CDATA #IMPLIED
+ %SVG.FilterPrimitiveWithIn.extra.attrib;"
+>
+
+<!-- SVG.Presentation.attrib ........................... -->
+
+<!ENTITY % SVG.Presentation.extra.attrib "" >
+
+<!ENTITY % SVG.Presentation.attrib
+ "%SVG.Container.attrib;
+ %SVG.Viewport.attrib;
+ %SVG.Text.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Profile.attrib;
+ %SVG.Gradient.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.Cursor.attrib;
+ flood-color %SVGColor.datatype; #IMPLIED
+ flood-opacity %OpacityValue.datatype; #IMPLIED
+ lighting-color %SVGColor.datatype; #IMPLIED
+ %SVG.Presentation.extra.attrib;"
+>
+
+<!-- filter: Filter Element ............................ -->
+
+<!ENTITY % SVG.filter.extra.content "" >
+
+<!ENTITY % SVG.filter.element "INCLUDE" >
+<![%SVG.filter.element;[
+<!ENTITY % SVG.filter.content
+ "(( %SVG.Description.class; )*, ( %SVG.animate.qname; | %SVG.set.qname;
+ %SVG.FilterPrimitive.class; %SVG.filter.extra.content; )*)"
+>
+<!ELEMENT %SVG.filter.qname; %SVG.filter.content; >
+<!-- end of SVG.filter.element -->]]>
+
+<!ENTITY % SVG.filter.attlist "INCLUDE" >
+<![%SVG.filter.attlist;[
+<!ATTLIST %SVG.filter.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.XLink.attrib;
+ %SVG.External.attrib;
+ x %Coordinate.datatype; #IMPLIED
+ y %Coordinate.datatype; #IMPLIED
+ width %Length.datatype; #IMPLIED
+ height %Length.datatype; #IMPLIED
+ filterRes %NumberOptionalNumber.datatype; #IMPLIED
+ filterUnits ( userSpaceOnUse | objectBoundingBox ) #IMPLIED
+ primitiveUnits ( userSpaceOnUse | objectBoundingBox ) #IMPLIED
+>
+<!-- end of SVG.filter.attlist -->]]>
+
+<!-- feBlend: Filter Effect Blend Element .............. -->
+
+<!ENTITY % SVG.feBlend.extra.content "" >
+
+<!ENTITY % SVG.feBlend.element "INCLUDE" >
+<![%SVG.feBlend.element;[
+<!ENTITY % SVG.feBlend.content
+ "( %SVG.animate.qname; | %SVG.set.qname; %SVG.feBlend.extra.content; )*"
+>
+<!ELEMENT %SVG.feBlend.qname; %SVG.feBlend.content; >
+<!-- end of SVG.feBlend.element -->]]>
+
+<!ENTITY % SVG.feBlend.attlist "INCLUDE" >
+<![%SVG.feBlend.attlist;[
+<!ATTLIST %SVG.feBlend.qname;
+ %SVG.Core.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitiveWithIn.attrib;
+ in2 CDATA #REQUIRED
+ mode ( normal | multiply | screen | darken | lighten ) 'normal'
+>
+<!-- end of SVG.feBlend.attlist -->]]>
+
+<!-- feColorMatrix: Filter Effect Color Matrix Element . -->
+
+<!ENTITY % SVG.feColorMatrix.extra.content "" >
+
+<!ENTITY % SVG.feColorMatrix.element "INCLUDE" >
+<![%SVG.feColorMatrix.element;[
+<!ENTITY % SVG.feColorMatrix.content
+ "( %SVG.animate.qname; | %SVG.set.qname;
+ %SVG.feColorMatrix.extra.content; )*"
+>
+<!ELEMENT %SVG.feColorMatrix.qname; %SVG.feColorMatrix.content; >
+<!-- end of SVG.feColorMatrix.element -->]]>
+
+<!ENTITY % SVG.feColorMatrix.attlist "INCLUDE" >
+<![%SVG.feColorMatrix.attlist;[
+<!ATTLIST %SVG.feColorMatrix.qname;
+ %SVG.Core.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitiveWithIn.attrib;
+ type ( matrix | saturate | hueRotate | luminanceToAlpha ) 'matrix'
+ values CDATA #IMPLIED
+>
+<!-- end of SVG.feColorMatrix.attlist -->]]>
+
+<!-- feComponentTransfer: Filter Effect Component Transfer Element -->
+
+<!ENTITY % SVG.feComponentTransfer.extra.content "" >
+
+<!ENTITY % SVG.feComponentTransfer.element "INCLUDE" >
+<![%SVG.feComponentTransfer.element;[
+<!ENTITY % SVG.feComponentTransfer.content
+ "( %SVG.feFuncR.qname;?, %SVG.feFuncG.qname;?, %SVG.feFuncB.qname;?,
+ %SVG.feFuncA.qname;? %SVG.feComponentTransfer.extra.content; )"
+>
+<!ELEMENT %SVG.feComponentTransfer.qname; %SVG.feComponentTransfer.content; >
+<!-- end of SVG.feComponentTransfer.element -->]]>
+
+<!ENTITY % SVG.feComponentTransfer.attlist "INCLUDE" >
+<![%SVG.feComponentTransfer.attlist;[
+<!ATTLIST %SVG.feComponentTransfer.qname;
+ %SVG.Core.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitiveWithIn.attrib;
+>
+<!-- end of SVG.feComponentTransfer.attlist -->]]>
+
+<!-- feComposite: Filter Effect Composite Element ...... -->
+
+<!ENTITY % SVG.feComposite.extra.content "" >
+
+<!ENTITY % SVG.feComposite.element "INCLUDE" >
+<![%SVG.feComposite.element;[
+<!ENTITY % SVG.feComposite.content
+ "( %SVG.animate.qname; | %SVG.set.qname; %SVG.feComposite.extra.content; )*"
+>
+<!ELEMENT %SVG.feComposite.qname; %SVG.feComposite.content; >
+<!-- end of SVG.feComposite.element -->]]>
+
+<!ENTITY % SVG.feComposite.attlist "INCLUDE" >
+<![%SVG.feComposite.attlist;[
+<!ATTLIST %SVG.feComposite.qname;
+ %SVG.Core.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitiveWithIn.attrib;
+ in2 CDATA #REQUIRED
+ operator ( over | in | out | atop | xor | arithmetic ) 'over'
+ k1 %Number.datatype; #IMPLIED
+ k2 %Number.datatype; #IMPLIED
+ k3 %Number.datatype; #IMPLIED
+ k4 %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.feComposite.attlist -->]]>
+
+<!-- feConvolveMatrix: Filter Effect Convolve Matrix Element -->
+
+<!ENTITY % SVG.feConvolveMatrix.extra.content "" >
+
+<!ENTITY % SVG.feConvolveMatrix.element "INCLUDE" >
+<![%SVG.feConvolveMatrix.element;[
+<!ENTITY % SVG.feConvolveMatrix.content
+ "( %SVG.animate.qname; | %SVG.set.qname;
+ %SVG.feConvolveMatrix.extra.content; )*"
+>
+<!ELEMENT %SVG.feConvolveMatrix.qname; %SVG.feConvolveMatrix.content; >
+<!-- end of SVG.feConvolveMatrix.element -->]]>
+
+<!ENTITY % SVG.feConvolveMatrix.attlist "INCLUDE" >
+<![%SVG.feConvolveMatrix.attlist;[
+<!ATTLIST %SVG.feConvolveMatrix.qname;
+ %SVG.Core.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitiveWithIn.attrib;
+ order %NumberOptionalNumber.datatype; #REQUIRED
+ kernelMatrix CDATA #REQUIRED
+ divisor %Number.datatype; #IMPLIED
+ bias %Number.datatype; #IMPLIED
+ targetX %Integer.datatype; #IMPLIED
+ targetY %Integer.datatype; #IMPLIED
+ edgeMode ( duplicate | wrap | none ) 'duplicate'
+ kernelUnitLength %NumberOptionalNumber.datatype; #IMPLIED
+ preserveAlpha %Boolean.datatype; #IMPLIED
+>
+<!-- end of SVG.feConvolveMatrix.attlist -->]]>
+
+<!-- feDiffuseLighting: Filter Effect Diffuse Lighting Element -->
+
+<!ENTITY % SVG.feDiffuseLighting.extra.content "" >
+
+<!ENTITY % SVG.feDiffuseLighting.element "INCLUDE" >
+<![%SVG.feDiffuseLighting.element;[
+<!ENTITY % SVG.feDiffuseLighting.content
+ "(( %SVG.feDistantLight.qname; | %SVG.fePointLight.qname;
+ | %SVG.feSpotLight.qname; ), ( %SVG.animate.qname; | %SVG.set.qname;
+ | %SVG.animateColor.qname; %SVG.feDiffuseLighting.extra.content; )*)"
+>
+<!ELEMENT %SVG.feDiffuseLighting.qname; %SVG.feDiffuseLighting.content; >
+<!-- end of SVG.feDiffuseLighting.element -->]]>
+
+<!ENTITY % SVG.feDiffuseLighting.attlist "INCLUDE" >
+<![%SVG.feDiffuseLighting.attlist;[
+<!ATTLIST %SVG.feDiffuseLighting.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Color.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitiveWithIn.attrib;
+ lighting-color %SVGColor.datatype; #IMPLIED
+ surfaceScale %Number.datatype; #IMPLIED
+ diffuseConstant %Number.datatype; #IMPLIED
+ kernelUnitLength %NumberOptionalNumber.datatype; #IMPLIED
+>
+<!-- end of SVG.feDiffuseLighting.attlist -->]]>
+
+<!-- feDisplacementMap: Filter Effect Displacement Map Element -->
+
+<!ENTITY % SVG.feDisplacementMap.extra.content "" >
+
+<!ENTITY % SVG.feDisplacementMap.element "INCLUDE" >
+<![%SVG.feDisplacementMap.element;[
+<!ENTITY % SVG.feDisplacementMap.content
+ "( %SVG.animate.qname; | %SVG.set.qname;
+ %SVG.feDisplacementMap.extra.content; )*"
+>
+<!ELEMENT %SVG.feDisplacementMap.qname; %SVG.feDisplacementMap.content; >
+<!-- end of SVG.feDisplacementMap.element -->]]>
+
+<!ENTITY % SVG.feDisplacementMap.attlist "INCLUDE" >
+<![%SVG.feDisplacementMap.attlist;[
+<!ATTLIST %SVG.feDisplacementMap.qname;
+ %SVG.Core.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitiveWithIn.attrib;
+ in2 CDATA #REQUIRED
+ scale %Number.datatype; #IMPLIED
+ xChannelSelector ( R | G | B | A ) 'A'
+ yChannelSelector ( R | G | B | A ) 'A'
+>
+<!-- end of SVG.feDisplacementMap.attlist -->]]>
+
+<!-- feFlood: Filter Effect Flood Element .............. -->
+
+<!ENTITY % SVG.feFlood.extra.content "" >
+
+<!ENTITY % SVG.feFlood.element "INCLUDE" >
+<![%SVG.feFlood.element;[
+<!ENTITY % SVG.feFlood.content
+ "( %SVG.animate.qname; | %SVG.set.qname; | %SVG.animateColor.qname;
+ %SVG.feFlood.extra.content; )*"
+>
+<!ELEMENT %SVG.feFlood.qname; %SVG.feFlood.content; >
+<!-- end of SVG.feFlood.element -->]]>
+
+<!ENTITY % SVG.feFlood.attlist "INCLUDE" >
+<![%SVG.feFlood.attlist;[
+<!ATTLIST %SVG.feFlood.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Color.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitiveWithIn.attrib;
+ flood-color %SVGColor.datatype; #IMPLIED
+ flood-opacity %OpacityValue.datatype; #IMPLIED
+>
+<!-- end of SVG.feFlood.attlist -->]]>
+
+<!-- feGaussianBlur: Filter Effect Gaussian Blur Element -->
+
+<!ENTITY % SVG.feGaussianBlur.extra.content "" >
+
+<!ENTITY % SVG.feGaussianBlur.element "INCLUDE" >
+<![%SVG.feGaussianBlur.element;[
+<!ENTITY % SVG.feGaussianBlur.content
+ "( %SVG.animate.qname; | %SVG.set.qname;
+ %SVG.feGaussianBlur.extra.content; )*"
+>
+<!ELEMENT %SVG.feGaussianBlur.qname; %SVG.feGaussianBlur.content; >
+<!-- end of SVG.feGaussianBlur.element -->]]>
+
+<!ENTITY % SVG.feGaussianBlur.attlist "INCLUDE" >
+<![%SVG.feGaussianBlur.attlist;[
+<!ATTLIST %SVG.feGaussianBlur.qname;
+ %SVG.Core.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitiveWithIn.attrib;
+ stdDeviation %NumberOptionalNumber.datatype; #IMPLIED
+>
+<!-- end of SVG.feGaussianBlur.attlist -->]]>
+
+<!-- feImage: Filter Effect Image Element .............. -->
+
+<!ENTITY % SVG.feImage.extra.content "" >
+
+<!ENTITY % SVG.feImage.element "INCLUDE" >
+<![%SVG.feImage.element;[
+<!ENTITY % SVG.feImage.content
+ "( %SVG.animate.qname; | %SVG.set.qname; | %SVG.animateTransform.qname;
+ %SVG.feImage.extra.content; )*"
+>
+<!ELEMENT %SVG.feImage.qname; %SVG.feImage.content; >
+<!-- end of SVG.feImage.element -->]]>
+
+<!ENTITY % SVG.feImage.attlist "INCLUDE" >
+<![%SVG.feImage.attlist;[
+<!ATTLIST %SVG.feImage.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.FilterPrimitive.attrib;
+ %SVG.XLinkEmbed.attrib;
+ %SVG.External.attrib;
+ preserveAspectRatio %PreserveAspectRatioSpec.datatype; 'xMidYMid meet'
+>
+<!-- end of SVG.feImage.attlist -->]]>
+
+<!-- feMerge: Filter Effect Merge Element .............. -->
+
+<!ENTITY % SVG.feMerge.extra.content "" >
+
+<!ENTITY % SVG.feMerge.element "INCLUDE" >
+<![%SVG.feMerge.element;[
+<!ENTITY % SVG.feMerge.content
+ "( %SVG.feMergeNode.qname; %SVG.feMerge.extra.content; )*"
+>
+<!ELEMENT %SVG.feMerge.qname; %SVG.feMerge.content; >
+<!-- end of SVG.feMerge.element -->]]>
+
+<!ENTITY % SVG.feMerge.attlist "INCLUDE" >
+<![%SVG.feMerge.attlist;[
+<!ATTLIST %SVG.feMerge.qname;
+ %SVG.Core.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitive.attrib;
+>
+<!-- end of SVG.feMerge.attlist -->]]>
+
+<!-- feMergeNode: Filter Effect Merge Node Element ..... -->
+
+<!ENTITY % SVG.feMergeNode.extra.content "" >
+
+<!ENTITY % SVG.feMergeNode.element "INCLUDE" >
+<![%SVG.feMergeNode.element;[
+<!ENTITY % SVG.feMergeNode.content
+ "( %SVG.animate.qname; | %SVG.set.qname; %SVG.feMergeNode.extra.content; )*"
+>
+<!ELEMENT %SVG.feMergeNode.qname; %SVG.feMergeNode.content; >
+<!-- end of SVG.feMergeNode.element -->]]>
+
+<!ENTITY % SVG.feMergeNode.attlist "INCLUDE" >
+<![%SVG.feMergeNode.attlist;[
+<!ATTLIST %SVG.feMergeNode.qname;
+ %SVG.Core.attrib;
+ in CDATA #IMPLIED
+>
+<!-- end of SVG.feMergeNode.attlist -->]]>
+
+<!-- feMorphology: Filter Effect Morphology Element .... -->
+
+<!ENTITY % SVG.feMorphology.extra.content "" >
+
+<!ENTITY % SVG.feMorphology.element "INCLUDE" >
+<![%SVG.feMorphology.element;[
+<!ENTITY % SVG.feMorphology.content
+ "( %SVG.animate.qname; | %SVG.set.qname;
+ %SVG.feMorphology.extra.content; )*"
+>
+<!ELEMENT %SVG.feMorphology.qname; %SVG.feMorphology.content; >
+<!-- end of SVG.feMorphology.element -->]]>
+
+<!ENTITY % SVG.feMorphology.attlist "INCLUDE" >
+<![%SVG.feMorphology.attlist;[
+<!ATTLIST %SVG.feMorphology.qname;
+ %SVG.Core.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitiveWithIn.attrib;
+ operator ( erode | dilate ) 'erode'
+ radius %NumberOptionalNumber.datatype; #IMPLIED
+>
+<!-- end of SVG.feMorphology.attlist -->]]>
+
+<!-- feOffset: Filter Effect Offset Element ............ -->
+
+<!ENTITY % SVG.feOffset.extra.content "" >
+
+<!ENTITY % SVG.feOffset.element "INCLUDE" >
+<![%SVG.feOffset.element;[
+<!ENTITY % SVG.feOffset.content
+ "( %SVG.animate.qname; | %SVG.set.qname; %SVG.feOffset.extra.content; )*"
+>
+<!ELEMENT %SVG.feOffset.qname; %SVG.feOffset.content; >
+<!-- end of SVG.feOffset.element -->]]>
+
+<!ENTITY % SVG.feOffset.attlist "INCLUDE" >
+<![%SVG.feOffset.attlist;[
+<!ATTLIST %SVG.feOffset.qname;
+ %SVG.Core.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitiveWithIn.attrib;
+ dx %Number.datatype; #IMPLIED
+ dy %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.feOffset.attlist -->]]>
+
+<!-- feSpecularLighting: Filter Effect Specular Lighting Element -->
+
+<!ENTITY % SVG.feSpecularLighting.extra.content "" >
+
+<!ENTITY % SVG.feSpecularLighting.element "INCLUDE" >
+<![%SVG.feSpecularLighting.element;[
+<!ENTITY % SVG.feSpecularLighting.content
+ "(( %SVG.feDistantLight.qname; | %SVG.fePointLight.qname;
+ | %SVG.feSpotLight.qname; ), ( %SVG.animate.qname; | %SVG.set.qname;
+ | %SVG.animateColor.qname; %SVG.feSpecularLighting.extra.content; )*)"
+>
+<!ELEMENT %SVG.feSpecularLighting.qname; %SVG.feSpecularLighting.content; >
+<!-- end of SVG.feSpecularLighting.element -->]]>
+
+<!ENTITY % SVG.feSpecularLighting.attlist "INCLUDE" >
+<![%SVG.feSpecularLighting.attlist;[
+<!ATTLIST %SVG.feSpecularLighting.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Color.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitiveWithIn.attrib;
+ lighting-color %SVGColor.datatype; #IMPLIED
+ surfaceScale %Number.datatype; #IMPLIED
+ specularConstant %Number.datatype; #IMPLIED
+ specularExponent %Number.datatype; #IMPLIED
+ kernelUnitLength %NumberOptionalNumber.datatype; #IMPLIED
+>
+<!-- end of SVG.feSpecularLighting.attlist -->]]>
+
+<!-- feTile: Filter Effect Tile Element ................ -->
+
+<!ENTITY % SVG.feTile.extra.content "" >
+
+<!ENTITY % SVG.feTile.element "INCLUDE" >
+<![%SVG.feTile.element;[
+<!ENTITY % SVG.feTile.content
+ "( %SVG.animate.qname; | %SVG.set.qname; %SVG.feTile.extra.content; )*"
+>
+<!ELEMENT %SVG.feTile.qname; %SVG.feTile.content; >
+<!-- end of SVG.feTile.element -->]]>
+
+<!ENTITY % SVG.feTile.attlist "INCLUDE" >
+<![%SVG.feTile.attlist;[
+<!ATTLIST %SVG.feTile.qname;
+ %SVG.Core.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitiveWithIn.attrib;
+>
+<!-- end of SVG.feTile.attlist -->]]>
+
+<!-- feTurbulence: Filter Effect Turbulence Element .... -->
+
+<!ENTITY % SVG.feTurbulence.extra.content "" >
+
+<!ENTITY % SVG.feTurbulence.element "INCLUDE" >
+<![%SVG.feTurbulence.element;[
+<!ENTITY % SVG.feTurbulence.content
+ "( %SVG.animate.qname; | %SVG.set.qname;
+ %SVG.feTurbulence.extra.content; )*"
+>
+<!ELEMENT %SVG.feTurbulence.qname; %SVG.feTurbulence.content; >
+<!-- end of SVG.feTurbulence.element -->]]>
+
+<!ENTITY % SVG.feTurbulence.attlist "INCLUDE" >
+<![%SVG.feTurbulence.attlist;[
+<!ATTLIST %SVG.feTurbulence.qname;
+ %SVG.Core.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitive.attrib;
+ baseFrequency %NumberOptionalNumber.datatype; #IMPLIED
+ numOctaves %Integer.datatype; #IMPLIED
+ seed %Number.datatype; #IMPLIED
+ stitchTiles ( stitch | noStitch ) 'noStitch'
+ type ( fractalNoise | turbulence ) 'turbulence'
+>
+<!-- end of SVG.feTurbulence.attlist -->]]>
+
+<!-- feDistantLight: Filter Effect Distant Light Element -->
+
+<!ENTITY % SVG.feDistantLight.extra.content "" >
+
+<!ENTITY % SVG.feDistantLight.element "INCLUDE" >
+<![%SVG.feDistantLight.element;[
+<!ENTITY % SVG.feDistantLight.content
+ "( %SVG.animate.qname; | %SVG.set.qname;
+ %SVG.feDistantLight.extra.content; )*"
+>
+<!ELEMENT %SVG.feDistantLight.qname; %SVG.feDistantLight.content; >
+<!-- end of SVG.feDistantLight.element -->]]>
+
+<!ENTITY % SVG.feDistantLight.attlist "INCLUDE" >
+<![%SVG.feDistantLight.attlist;[
+<!ATTLIST %SVG.feDistantLight.qname;
+ %SVG.Core.attrib;
+ azimuth %Number.datatype; #IMPLIED
+ elevation %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.feDistantLight.attlist -->]]>
+
+<!-- fePointLight: Filter Effect Point Light Element ... -->
+
+<!ENTITY % SVG.fePointLight.extra.content "" >
+
+<!ENTITY % SVG.fePointLight.element "INCLUDE" >
+<![%SVG.fePointLight.element;[
+<!ENTITY % SVG.fePointLight.content
+ "( %SVG.animate.qname; | %SVG.set.qname;
+ %SVG.fePointLight.extra.content; )*"
+>
+<!ELEMENT %SVG.fePointLight.qname; %SVG.fePointLight.content; >
+<!-- end of SVG.fePointLight.element -->]]>
+
+<!ENTITY % SVG.fePointLight.attlist "INCLUDE" >
+<![%SVG.fePointLight.attlist;[
+<!ATTLIST %SVG.fePointLight.qname;
+ %SVG.Core.attrib;
+ x %Number.datatype; #IMPLIED
+ y %Number.datatype; #IMPLIED
+ z %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.fePointLight.attlist -->]]>
+
+<!-- feSpotLight: Filter Effect Spot Light Element ..... -->
+
+<!ENTITY % SVG.feSpotLight.extra.content "" >
+
+<!ENTITY % SVG.feSpotLight.element "INCLUDE" >
+<![%SVG.feSpotLight.element;[
+<!ENTITY % SVG.feSpotLight.content
+ "( %SVG.animate.qname; | %SVG.set.qname; %SVG.feSpotLight.extra.content; )*"
+>
+<!ELEMENT %SVG.feSpotLight.qname; %SVG.feSpotLight.content; >
+<!-- end of SVG.feSpotLight.element -->]]>
+
+<!ENTITY % SVG.feSpotLight.attlist "INCLUDE" >
+<![%SVG.feSpotLight.attlist;[
+<!ATTLIST %SVG.feSpotLight.qname;
+ %SVG.Core.attrib;
+ x %Number.datatype; #IMPLIED
+ y %Number.datatype; #IMPLIED
+ z %Number.datatype; #IMPLIED
+ pointsAtX %Number.datatype; #IMPLIED
+ pointsAtY %Number.datatype; #IMPLIED
+ pointsAtZ %Number.datatype; #IMPLIED
+ specularExponent %Number.datatype; #IMPLIED
+ limitingConeAngle %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.feSpotLight.attlist -->]]>
+
+<!-- feFuncR: Filter Effect Function Red Element ....... -->
+
+<!ENTITY % SVG.feFuncR.extra.content "" >
+
+<!ENTITY % SVG.feFuncR.element "INCLUDE" >
+<![%SVG.feFuncR.element;[
+<!ENTITY % SVG.feFuncR.content
+ "( %SVG.animate.qname; | %SVG.set.qname; %SVG.feFuncR.extra.content; )*"
+>
+<!ELEMENT %SVG.feFuncR.qname; %SVG.feFuncR.content; >
+<!-- end of SVG.feFuncR.element -->]]>
+
+<!ENTITY % SVG.feFuncR.attlist "INCLUDE" >
+<![%SVG.feFuncR.attlist;[
+<!ATTLIST %SVG.feFuncR.qname;
+ %SVG.Core.attrib;
+ type ( identity | table | discrete | linear | gamma ) #REQUIRED
+ tableValues CDATA #IMPLIED
+ slope %Number.datatype; #IMPLIED
+ intercept %Number.datatype; #IMPLIED
+ amplitude %Number.datatype; #IMPLIED
+ exponent %Number.datatype; #IMPLIED
+ offset %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.feFuncR.attlist -->]]>
+
+<!-- feFuncG: Filter Effect Function Green Element ..... -->
+
+<!ENTITY % SVG.feFuncG.extra.content "" >
+
+<!ENTITY % SVG.feFuncG.element "INCLUDE" >
+<![%SVG.feFuncG.element;[
+<!ENTITY % SVG.feFuncG.content
+ "( %SVG.animate.qname; | %SVG.set.qname; %SVG.feFuncG.extra.content; )*"
+>
+<!ELEMENT %SVG.feFuncG.qname; %SVG.feFuncG.content; >
+<!-- end of SVG.feFuncG.element -->]]>
+
+<!ENTITY % SVG.feFuncG.attlist "INCLUDE" >
+<![%SVG.feFuncG.attlist;[
+<!ATTLIST %SVG.feFuncG.qname;
+ %SVG.Core.attrib;
+ type ( identity | table | discrete | linear | gamma ) #REQUIRED
+ tableValues CDATA #IMPLIED
+ slope %Number.datatype; #IMPLIED
+ intercept %Number.datatype; #IMPLIED
+ amplitude %Number.datatype; #IMPLIED
+ exponent %Number.datatype; #IMPLIED
+ offset %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.feFuncG.attlist -->]]>
+
+<!-- feFuncB: Filter Effect Function Blue Element ...... -->
+
+<!ENTITY % SVG.feFuncB.extra.content "" >
+
+<!ENTITY % SVG.feFuncB.element "INCLUDE" >
+<![%SVG.feFuncB.element;[
+<!ENTITY % SVG.feFuncB.content
+ "( %SVG.animate.qname; | %SVG.set.qname; %SVG.feFuncB.extra.content; )*"
+>
+<!ELEMENT %SVG.feFuncB.qname; %SVG.feFuncB.content; >
+<!-- end of SVG.feFuncB.element -->]]>
+
+<!ENTITY % SVG.feFuncB.attlist "INCLUDE" >
+<![%SVG.feFuncB.attlist;[
+<!ATTLIST %SVG.feFuncB.qname;
+ %SVG.Core.attrib;
+ type ( identity | table | discrete | linear | gamma ) #REQUIRED
+ tableValues CDATA #IMPLIED
+ slope %Number.datatype; #IMPLIED
+ intercept %Number.datatype; #IMPLIED
+ amplitude %Number.datatype; #IMPLIED
+ exponent %Number.datatype; #IMPLIED
+ offset %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.feFuncB.attlist -->]]>
+
+<!-- feFuncA: Filter Effect Function Alpha Element ..... -->
+
+<!ENTITY % SVG.feFuncA.extra.content "" >
+
+<!ENTITY % SVG.feFuncA.element "INCLUDE" >
+<![%SVG.feFuncA.element;[
+<!ENTITY % SVG.feFuncA.content
+ "( %SVG.animate.qname; | %SVG.set.qname; %SVG.feFuncA.extra.content; )*"
+>
+<!ELEMENT %SVG.feFuncA.qname; %SVG.feFuncA.content; >
+<!-- end of SVG.feFuncA.element -->]]>
+
+<!ENTITY % SVG.feFuncA.attlist "INCLUDE" >
+<![%SVG.feFuncA.attlist;[
+<!ATTLIST %SVG.feFuncA.qname;
+ %SVG.Core.attrib;
+ type ( identity | table | discrete | linear | gamma ) #REQUIRED
+ tableValues CDATA #IMPLIED
+ slope %Number.datatype; #IMPLIED
+ intercept %Number.datatype; #IMPLIED
+ amplitude %Number.datatype; #IMPLIED
+ exponent %Number.datatype; #IMPLIED
+ offset %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.feFuncA.attlist -->]]>
+
+<!-- end of svg-filter.mod -->
diff --git a/org/apache/batik/dom/svg/resources/svg-font.mod b/org/apache/batik/dom/svg/resources/svg-font.mod
new file mode 100644
index 0000000..59b0b76
--- /dev/null
+++ b/org/apache/batik/dom/svg/resources/svg-font.mod
@@ -0,0 +1,378 @@
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Font Module ................................................... -->
+<!-- file: svg-font.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg-font.mod 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Font//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-font.mod"
+
+ ....................................................................... -->
+
+<!-- Font
+
+ font, font-face, glyph, missing-glyph, hkern, vkern, font-face-src,
+ font-face-uri, font-face-format, font-face-name, definition-src
+
+ This module declares markup to provide support for template.
+-->
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.font.qname "font" >
+<!ENTITY % SVG.font-face.qname "font-face" >
+<!ENTITY % SVG.glyph.qname "glyph" >
+<!ENTITY % SVG.missing-glyph.qname "missing-glyph" >
+<!ENTITY % SVG.hkern.qname "hkern" >
+<!ENTITY % SVG.vkern.qname "vkern" >
+<!ENTITY % SVG.font-face-src.qname "font-face-src" >
+<!ENTITY % SVG.font-face-uri.qname "font-face-uri" >
+<!ENTITY % SVG.font-face-format.qname "font-face-format" >
+<!ENTITY % SVG.font-face-name.qname "font-face-name" >
+<!ENTITY % SVG.definition-src.qname "definition-src" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Container.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Viewport.attrib "" >
+<!ENTITY % SVG.Text.attrib "" >
+<!ENTITY % SVG.TextContent.attrib "" >
+<!ENTITY % SVG.Font.attrib "" >
+<!ENTITY % SVG.Paint.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Marker.attrib "" >
+<!ENTITY % SVG.Profile.attrib "" >
+<!ENTITY % SVG.Gradient.attrib "" >
+<!ENTITY % SVG.Clip.attrib "" >
+<!ENTITY % SVG.Mask.attrib "" >
+<!ENTITY % SVG.Filter.attrib "" >
+<!ENTITY % SVG.FilterColor.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.XLinkRequired.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Font.class .................................... -->
+
+<!ENTITY % SVG.Font.extra.class "" >
+
+<!ENTITY % SVG.Font.class
+ "| %SVG.font.qname; | %SVG.font-face.qname; %SVG.Font.extra.class;"
+>
+
+<!-- SVG.Presentation.attrib ........................... -->
+
+<!ENTITY % SVG.Presentation.extra.attrib "" >
+
+<!ENTITY % SVG.Presentation.attrib
+ "%SVG.Container.attrib;
+ %SVG.Viewport.attrib;
+ %SVG.Text.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Profile.attrib;
+ %SVG.Gradient.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.Cursor.attrib;
+ flood-color %SVGColor.datatype; #IMPLIED
+ flood-opacity %OpacityValue.datatype; #IMPLIED
+ lighting-color %SVGColor.datatype; #IMPLIED
+ %SVG.Presentation.extra.attrib;"
+>
+
+<!-- font: Font Element ................................ -->
+
+<!ENTITY % SVG.font.extra.content "" >
+
+<!ENTITY % SVG.font.element "INCLUDE" >
+<![%SVG.font.element;[
+<!ENTITY % SVG.font.content
+ "(( %SVG.Description.class; )*, %SVG.font-face.qname;,
+ %SVG.missing-glyph.qname;, ( %SVG.glyph.qname; | %SVG.hkern.qname;
+ | %SVG.vkern.qname; %SVG.font.extra.content; )*)"
+>
+<!ELEMENT %SVG.font.qname; %SVG.font.content; >
+<!-- end of SVG.font.element -->]]>
+
+<!ENTITY % SVG.font.attlist "INCLUDE" >
+<![%SVG.font.attlist;[
+<!ATTLIST %SVG.font.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.External.attrib;
+ horiz-origin-x %Number.datatype; #IMPLIED
+ horiz-origin-y %Number.datatype; #IMPLIED
+ horiz-adv-x %Number.datatype; #REQUIRED
+ vert-origin-x %Number.datatype; #IMPLIED
+ vert-origin-y %Number.datatype; #IMPLIED
+ vert-adv-y %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.font.attlist -->]]>
+
+<!-- font-face: Font Face Element ...................... -->
+
+<!ENTITY % SVG.font-face.extra.content "" >
+
+<!ENTITY % SVG.font-face.element "INCLUDE" >
+<![%SVG.font-face.element;[
+<!ENTITY % SVG.font-face.content
+ "(( %SVG.Description.class; )*, %SVG.font-face-src.qname;?,
+ %SVG.definition-src.qname;? %SVG.font-face.extra.content; )"
+>
+<!ELEMENT %SVG.font-face.qname; %SVG.font-face.content; >
+<!-- end of SVG.font-face.element -->]]>
+
+<!ENTITY % SVG.font-face.attlist "INCLUDE" >
+<![%SVG.font-face.attlist;[
+<!ATTLIST %SVG.font-face.qname;
+ %SVG.Core.attrib;
+ font-family CDATA #IMPLIED
+ font-style CDATA #IMPLIED
+ font-variant CDATA #IMPLIED
+ font-weight CDATA #IMPLIED
+ font-stretch CDATA #IMPLIED
+ font-size CDATA #IMPLIED
+ unicode-range CDATA #IMPLIED
+ units-per-em %Number.datatype; #IMPLIED
+ panose-1 CDATA #IMPLIED
+ stemv %Number.datatype; #IMPLIED
+ stemh %Number.datatype; #IMPLIED
+ slope %Number.datatype; #IMPLIED
+ cap-height %Number.datatype; #IMPLIED
+ x-height %Number.datatype; #IMPLIED
+ accent-height %Number.datatype; #IMPLIED
+ ascent %Number.datatype; #IMPLIED
+ descent %Number.datatype; #IMPLIED
+ widths CDATA #IMPLIED
+ bbox CDATA #IMPLIED
+ ideographic %Number.datatype; #IMPLIED
+ alphabetic %Number.datatype; #IMPLIED
+ mathematical %Number.datatype; #IMPLIED
+ hanging %Number.datatype; #IMPLIED
+ v-ideographic %Number.datatype; #IMPLIED
+ v-alphabetic %Number.datatype; #IMPLIED
+ v-mathematical %Number.datatype; #IMPLIED
+ v-hanging %Number.datatype; #IMPLIED
+ underline-position %Number.datatype; #IMPLIED
+ underline-thickness %Number.datatype; #IMPLIED
+ strikethrough-position %Number.datatype; #IMPLIED
+ strikethrough-thickness %Number.datatype; #IMPLIED
+ overline-position %Number.datatype; #IMPLIED
+ overline-thickness %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.font-face.attlist -->]]>
+
+<!-- glyph: Glyph Element .............................. -->
+
+<!ENTITY % SVG.glyph.extra.content "" >
+
+<!ENTITY % SVG.glyph.element "INCLUDE" >
+<![%SVG.glyph.element;[
+<!ENTITY % SVG.glyph.content
+ "( %SVG.Description.class; | %SVG.Animation.class; %SVG.Structure.class;
+ %SVG.Conditional.class; %SVG.Image.class; %SVG.Style.class;
+ %SVG.Shape.class; %SVG.Text.class; %SVG.Marker.class; %SVG.Profile.class;
+ %SVG.Gradient.class; %SVG.Pattern.class; %SVG.Clip.class;
+ %SVG.Mask.class; %SVG.Filter.class; %SVG.Cursor.class;
+ %SVG.Hyperlink.class; %SVG.View.class; %SVG.Script.class;
+ %SVG.Font.class; %SVG.glyph.extra.content; )*"
+>
+<!ELEMENT %SVG.glyph.qname; %SVG.glyph.content; >
+<!-- end of SVG.glyph.element -->]]>
+
+<!ENTITY % SVG.glyph.attlist "INCLUDE" >
+<![%SVG.glyph.attlist;[
+<!ATTLIST %SVG.glyph.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ unicode CDATA #IMPLIED
+ glyph-name CDATA #IMPLIED
+ d %PathData.datatype; #IMPLIED
+ orientation CDATA #IMPLIED
+ arabic-form CDATA #IMPLIED
+ lang %LanguageCodes.datatype; #IMPLIED
+ horiz-adv-x %Number.datatype; #IMPLIED
+ vert-origin-x %Number.datatype; #IMPLIED
+ vert-origin-y %Number.datatype; #IMPLIED
+ vert-adv-y %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.glyph.attlist -->]]>
+
+<!-- missing-glyph: Missing Glyph Element .............. -->
+
+<!ENTITY % SVG.missing-glyph.extra.content "" >
+
+<!ENTITY % SVG.missing-glyph.element "INCLUDE" >
+<![%SVG.missing-glyph.element;[
+<!ENTITY % SVG.missing-glyph.content
+ "( %SVG.Description.class; | %SVG.Animation.class; %SVG.Structure.class;
+ %SVG.Conditional.class; %SVG.Image.class; %SVG.Style.class;
+ %SVG.Shape.class; %SVG.Text.class; %SVG.Marker.class; %SVG.Profile.class;
+ %SVG.Gradient.class; %SVG.Pattern.class; %SVG.Clip.class;
+ %SVG.Mask.class; %SVG.Filter.class; %SVG.Cursor.class;
+ %SVG.Hyperlink.class; %SVG.View.class; %SVG.Script.class;
+ %SVG.Font.class; %SVG.missing-glyph.extra.content; )*"
+>
+<!ELEMENT %SVG.missing-glyph.qname; %SVG.missing-glyph.content; >
+<!-- end of SVG.missing-glyph.element -->]]>
+
+<!ENTITY % SVG.missing-glyph.attlist "INCLUDE" >
+<![%SVG.missing-glyph.attlist;[
+<!ATTLIST %SVG.missing-glyph.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ d %PathData.datatype; #IMPLIED
+ horiz-adv-x %Number.datatype; #IMPLIED
+ vert-origin-x %Number.datatype; #IMPLIED
+ vert-origin-y %Number.datatype; #IMPLIED
+ vert-adv-y %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.missing-glyph.attlist -->]]>
+
+<!-- hkern: Horizontal Kerning Element ................. -->
+
+<!ENTITY % SVG.hkern.element "INCLUDE" >
+<![%SVG.hkern.element;[
+<!ENTITY % SVG.hkern.content "EMPTY" >
+<!ELEMENT %SVG.hkern.qname; %SVG.hkern.content; >
+<!-- end of SVG.hkern.element -->]]>
+
+<!ENTITY % SVG.hkern.attlist "INCLUDE" >
+<![%SVG.hkern.attlist;[
+<!ATTLIST %SVG.hkern.qname;
+ %SVG.Core.attrib;
+ u1 CDATA #IMPLIED
+ g1 CDATA #IMPLIED
+ u2 CDATA #IMPLIED
+ g2 CDATA #IMPLIED
+ k %Number.datatype; #REQUIRED
+>
+<!-- end of SVG.hkern.attlist -->]]>
+
+<!-- vkern: Vertical Kerning Element ................... -->
+
+<!ENTITY % SVG.vkern.element "INCLUDE" >
+<![%SVG.vkern.element;[
+<!ENTITY % SVG.vkern.content "EMPTY" >
+<!ELEMENT %SVG.vkern.qname; %SVG.vkern.content; >
+<!-- end of SVG.vkern.element -->]]>
+
+<!ENTITY % SVG.vkern.attlist "INCLUDE" >
+<![%SVG.vkern.attlist;[
+<!ATTLIST %SVG.vkern.qname;
+ %SVG.Core.attrib;
+ u1 CDATA #IMPLIED
+ g1 CDATA #IMPLIED
+ u2 CDATA #IMPLIED
+ g2 CDATA #IMPLIED
+ k %Number.datatype; #REQUIRED
+>
+<!-- end of SVG.vkern.attlist -->]]>
+
+<!-- font-face-src: Font Face Source Element ........... -->
+
+<!ENTITY % SVG.font-face-src.extra.content "" >
+
+<!ENTITY % SVG.font-face-src.element "INCLUDE" >
+<![%SVG.font-face-src.element;[
+<!ENTITY % SVG.font-face-src.content
+ "( %SVG.font-face-uri.qname; | %SVG.font-face-name.qname;
+ %SVG.font-face-src.extra.content; )+"
+>
+<!ELEMENT %SVG.font-face-src.qname; %SVG.font-face-src.content; >
+<!-- end of SVG.font-face-src.element -->]]>
+
+<!ENTITY % SVG.font-face-src.attlist "INCLUDE" >
+<![%SVG.font-face-src.attlist;[
+<!ATTLIST %SVG.font-face-src.qname;
+ %SVG.Core.attrib;
+>
+<!-- end of SVG.font-face-src.attlist -->]]>
+
+<!-- font-face-uri: Font Face URI Element .............. -->
+
+<!ENTITY % SVG.font-face-uri.extra.content "" >
+
+<!ENTITY % SVG.font-face-uri.element "INCLUDE" >
+<![%SVG.font-face-uri.element;[
+<!ENTITY % SVG.font-face-uri.content
+ "( %SVG.font-face-format.qname; %SVG.font-face-uri.extra.content; )*"
+>
+<!ELEMENT %SVG.font-face-uri.qname; %SVG.font-face-uri.content; >
+<!-- end of SVG.font-face-uri.element -->]]>
+
+<!ENTITY % SVG.font-face-uri.attlist "INCLUDE" >
+<![%SVG.font-face-uri.attlist;[
+<!ATTLIST %SVG.font-face-uri.qname;
+ %SVG.Core.attrib;
+ %SVG.XLinkRequired.attrib;
+>
+<!-- end of SVG.font-face-uri.attlist -->]]>
+
+<!-- font-face-format: Font Face Format Element ........ -->
+
+<!ENTITY % SVG.font-face-format.element "INCLUDE" >
+<![%SVG.font-face-format.element;[
+<!ENTITY % SVG.font-face-format.content "EMPTY" >
+<!ELEMENT %SVG.font-face-format.qname; %SVG.font-face-format.content; >
+<!-- end of SVG.font-face-format.element -->]]>
+
+<!ENTITY % SVG.font-face-format.attlist "INCLUDE" >
+<![%SVG.font-face-format.attlist;[
+<!ATTLIST %SVG.font-face-format.qname;
+ %SVG.Core.attrib;
+ string CDATA #IMPLIED
+>
+<!-- end of SVG.font-face-format.attlist -->]]>
+
+<!-- font-face-name: Font Face Name Element ............ -->
+
+<!ENTITY % SVG.font-face-name.element "INCLUDE" >
+<![%SVG.font-face-name.element;[
+<!ENTITY % SVG.font-face-name.content "EMPTY" >
+<!ELEMENT %SVG.font-face-name.qname; %SVG.font-face-name.content; >
+<!-- end of SVG.font-face-name.element -->]]>
+
+<!ENTITY % SVG.font-face-name.attlist "INCLUDE" >
+<![%SVG.font-face-name.attlist;[
+<!ATTLIST %SVG.font-face-name.qname;
+ %SVG.Core.attrib;
+ name CDATA #IMPLIED
+>
+<!-- end of SVG.font-face-name.attlist -->]]>
+
+<!-- definition-src: Definition Source Element ......... -->
+
+<!ENTITY % SVG.definition-src.element "INCLUDE" >
+<![%SVG.definition-src.element;[
+<!ENTITY % SVG.definition-src.content "EMPTY" >
+<!ELEMENT %SVG.definition-src.qname; %SVG.definition-src.content; >
+<!-- end of SVG.definition-src.element -->]]>
+
+<!ENTITY % SVG.definition-src.attlist "INCLUDE" >
+<![%SVG.definition-src.attlist;[
+<!ATTLIST %SVG.definition-src.qname;
+ %SVG.Core.attrib;
+ %SVG.XLinkRequired.attrib;
+>
+<!-- end of SVG.definition-src.attlist -->]]>
+
+<!-- end of svg-font.mod -->
diff --git a/org/apache/batik/dom/svg/resources/svg-framework.mod b/org/apache/batik/dom/svg/resources/svg-framework.mod
new file mode 100644
index 0000000..f6fa0b5
--- /dev/null
+++ b/org/apache/batik/dom/svg/resources/svg-framework.mod
@@ -0,0 +1,51 @@
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Modular Framework Module ...................................... -->
+<!-- file: svg-framework.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg-framework.mod 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Modular Framework//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-framework.mod"
+
+ ....................................................................... -->
+
+<!-- Modular Framework
+
+ This module instantiates the modules needed o support the SVG
+ modularization model, including:
+
+ + Datatypes
+ + Qualified Name
+ + Document Model
+ + Attribute Collection
+-->
+
+<!ENTITY % svg-datatypes.module "INCLUDE" >
+<![%svg-datatypes.module;[
+<!ENTITY % svg-datatypes.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Datatypes//EN"
+ "svg-datatypes.mod" >
+%svg-datatypes.mod;]]>
+
+<!ENTITY % svg-qname.module "INCLUDE" >
+<![%svg-qname.module;[
+<!ENTITY % svg-qname.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Qualified Name//EN"
+ "svg-qname.mod" >
+%svg-qname.mod;]]>
+
+<!ENTITY % svg-model.module "INCLUDE" >
+<![%svg-model.module;[
+<!-- instantiate the Document Model declared in the DTD driver -->
+%svg-model.mod;]]>
+
+<!ENTITY % svg-attribs.module "INCLUDE" >
+<![%svg-attribs.module;[
+<!-- instantiate the Attribute Collection declared in the DTD driver -->
+%svg-attribs.mod;]]>
+
+<!-- end of svg-framework.mod -->
diff --git a/org/apache/batik/dom/svg/resources/svg-gradient.mod b/org/apache/batik/dom/svg/resources/svg-gradient.mod
new file mode 100644
index 0000000..6353b01
--- /dev/null
+++ b/org/apache/batik/dom/svg/resources/svg-gradient.mod
@@ -0,0 +1,150 @@
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Gradient Module ............................................... -->
+<!-- file: svg-gradient.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg-gradient.mod 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Gradient//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-gradient.mod"
+
+ ....................................................................... -->
+
+<!-- Gradient
+
+ linearGradient, radialGradient, stop
+
+ This module declares markup to provide support for gradient fill.
+-->
+
+<!-- a <number> or a <percentage> -->
+<!ENTITY % NumberOrPercentage.datatype "CDATA" >
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.linearGradient.qname "linearGradient" >
+<!ENTITY % SVG.radialGradient.qname "radialGradient" >
+<!ENTITY % SVG.stop.qname "stop" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.XLink.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Gradient.class ................................ -->
+
+<!ENTITY % SVG.Gradient.extra.class "" >
+
+<!ENTITY % SVG.Gradient.class
+ "| %SVG.linearGradient.qname; | %SVG.radialGradient.qname;
+ %SVG.Gradient.extra.class;"
+>
+
+<!-- SVG.Gradient.attrib ............................... -->
+
+<!ENTITY % SVG.Gradient.extra.attrib "" >
+
+<!ENTITY % SVG.Gradient.attrib
+ "stop-color %SVGColor.datatype; #IMPLIED
+ stop-opacity %OpacityValue.datatype; #IMPLIED
+ %SVG.Gradient.extra.attrib;"
+>
+
+<!-- linearGradient: Linear Gradient Element ........... -->
+
+<!ENTITY % SVG.linearGradient.extra.content "" >
+
+<!ENTITY % SVG.linearGradient.element "INCLUDE" >
+<![%SVG.linearGradient.element;[
+<!ENTITY % SVG.linearGradient.content
+ "(( %SVG.Description.class; )*, ( %SVG.stop.qname; | %SVG.animate.qname;
+ | %SVG.set.qname; | %SVG.animateTransform.qname;
+ %SVG.linearGradient.extra.content; )*)"
+>
+<!ELEMENT %SVG.linearGradient.qname; %SVG.linearGradient.content; >
+<!-- end of SVG.linearGradient.element -->]]>
+
+<!ENTITY % SVG.linearGradient.attlist "INCLUDE" >
+<![%SVG.linearGradient.attlist;[
+<!ATTLIST %SVG.linearGradient.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Color.attrib;
+ %SVG.Gradient.attrib;
+ %SVG.XLink.attrib;
+ %SVG.External.attrib;
+ x1 %Coordinate.datatype; #IMPLIED
+ y1 %Coordinate.datatype; #IMPLIED
+ x2 %Coordinate.datatype; #IMPLIED
+ y2 %Coordinate.datatype; #IMPLIED
+ gradientUnits ( userSpaceOnUse | objectBoundingBox ) #IMPLIED
+ gradientTransform %TransformList.datatype; #IMPLIED
+ spreadMethod ( pad | reflect | repeat ) #IMPLIED
+>
+<!-- end of SVG.linearGradient.attlist -->]]>
+
+<!-- radialGradient: Radial Gradient Element ........... -->
+
+<!ENTITY % SVG.radialGradient.extra.content "" >
+
+<!ENTITY % SVG.radialGradient.element "INCLUDE" >
+<![%SVG.radialGradient.element;[
+<!ENTITY % SVG.radialGradient.content
+ "(( %SVG.Description.class; )*, ( %SVG.stop.qname; | %SVG.animate.qname;
+ | %SVG.set.qname; | %SVG.animateTransform.qname;
+ %SVG.radialGradient.extra.content; )*)"
+>
+<!ELEMENT %SVG.radialGradient.qname; %SVG.radialGradient.content; >
+<!-- end of SVG.radialGradient.element -->]]>
+
+<!ENTITY % SVG.radialGradient.attlist "INCLUDE" >
+<![%SVG.radialGradient.attlist;[
+<!ATTLIST %SVG.radialGradient.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Color.attrib;
+ %SVG.Gradient.attrib;
+ %SVG.XLink.attrib;
+ %SVG.External.attrib;
+ cx %Coordinate.datatype; #IMPLIED
+ cy %Coordinate.datatype; #IMPLIED
+ r %Length.datatype; #IMPLIED
+ fx %Coordinate.datatype; #IMPLIED
+ fy %Coordinate.datatype; #IMPLIED
+ gradientUnits ( userSpaceOnUse | objectBoundingBox ) #IMPLIED
+ gradientTransform %TransformList.datatype; #IMPLIED
+ spreadMethod ( pad | reflect | repeat ) #IMPLIED
+>
+<!-- end of SVG.radialGradient.attlist -->]]>
+
+<!-- stop: Stop Element ................................ -->
+
+<!ENTITY % SVG.stop.extra.content "" >
+
+<!ENTITY % SVG.stop.element "INCLUDE" >
+<![%SVG.stop.element;[
+<!ENTITY % SVG.stop.content
+ "( %SVG.animate.qname; | %SVG.set.qname; | %SVG.animateColor.qname;
+ %SVG.stop.extra.content; )*"
+>
+<!ELEMENT %SVG.stop.qname; %SVG.stop.content; >
+<!-- end of SVG.stop.element -->]]>
+
+<!ENTITY % SVG.stop.attlist "INCLUDE" >
+<![%SVG.stop.attlist;[
+<!ATTLIST %SVG.stop.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Color.attrib;
+ %SVG.Gradient.attrib;
+ offset %NumberOrPercentage.datatype; #REQUIRED
+>
+<!-- end of SVG.stop.attlist -->]]>
+
+<!-- end of svg-gradient.mod -->
diff --git a/org/apache/batik/dom/svg/resources/svg-graphevents-attrib.mod b/org/apache/batik/dom/svg/resources/svg-graphevents-attrib.mod
new file mode 100644
index 0000000..d03addc
--- /dev/null
+++ b/org/apache/batik/dom/svg/resources/svg-graphevents-attrib.mod
@@ -0,0 +1,80 @@
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Graphical Element Events Attribute Module ..................... -->
+<!-- file: svg-graphevents-attrib.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg-graphevents-attrib.mod 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Graphical Element Events Attribute//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-graphevents-attrib.mod"
+
+ ....................................................................... -->
+
+<!-- Graphical Element Events Attribute
+
+ onfocusin, onfocusout, onactivate, onclick, onmousedown, onmouseup,
+ onmouseover, onmousemove, onmouseout, onload
+
+ This module defines the GraphicalEvents attribute set.
+-->
+
+<!ENTITY % SVG.onfocusin.attrib
+ "onfocusin %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onfocusout.attrib
+ "onfocusout %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onactivate.attrib
+ "onactivate %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onclick.attrib
+ "onclick %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onmousedown.attrib
+ "onmousedown %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onmouseup.attrib
+ "onmouseup %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onmouseover.attrib
+ "onmouseover %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onmousemove.attrib
+ "onmousemove %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onmouseout.attrib
+ "onmouseout %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onload.attrib
+ "onload %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.GraphicalEvents.extra.attrib "" >
+
+<!ENTITY % SVG.GraphicalEvents.attrib
+ "%SVG.onfocusin.attrib;
+ %SVG.onfocusout.attrib;
+ %SVG.onactivate.attrib;
+ %SVG.onclick.attrib;
+ %SVG.onmousedown.attrib;
+ %SVG.onmouseup.attrib;
+ %SVG.onmouseover.attrib;
+ %SVG.onmousemove.attrib;
+ %SVG.onmouseout.attrib;
+ %SVG.onload.attrib;
+ %SVG.GraphicalEvents.extra.attrib;"
+>
+
+<!-- end of svg-graphevents-attrib.mod -->
diff --git a/org/apache/batik/dom/svg/resources/svg-graphics-attrib.mod b/org/apache/batik/dom/svg/resources/svg-graphics-attrib.mod
new file mode 100644
index 0000000..76dacf4
--- /dev/null
+++ b/org/apache/batik/dom/svg/resources/svg-graphics-attrib.mod
@@ -0,0 +1,69 @@
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Graphics Attribute Module ..................................... -->
+<!-- file: svg-graphics-attrib.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg-graphics-attrib.mod 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Graphics Attribute//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-graphics-attrib.mod"
+
+ ....................................................................... -->
+
+<!-- Graphics Attribute
+
+ display, image-rendering, pointer-events, shape-rendering,
+ text-rendering, visibility
+
+ This module defines the Graphics attribute set.
+-->
+
+<!ENTITY % SVG.display.attrib
+ "display ( inline | block | list-item | run-in | compact | marker |
+ table | inline-table | table-row-group | table-header-group |
+ table-footer-group | table-row | table-column-group |
+ table-column | table-cell | table-caption | none | inherit )
+ #IMPLIED"
+>
+
+<!ENTITY % SVG.image-rendering.attrib
+ "image-rendering ( auto | optimizeSpeed | optimizeQuality | inherit )
+ #IMPLIED"
+>
+
+<!ENTITY % SVG.pointer-events.attrib
+ "pointer-events ( visiblePainted | visibleFill | visibleStroke | visible |
+ painted | fill | stroke | all | none | inherit )
+ #IMPLIED"
+>
+
+<!ENTITY % SVG.shape-rendering.attrib
+ "shape-rendering ( auto | optimizeSpeed | crispEdges | geometricPrecision |
+ inherit ) #IMPLIED"
+>
+
+<!ENTITY % SVG.text-rendering.attrib
+ "text-rendering ( auto | optimizeSpeed | optimizeLegibility |
+ geometricPrecision | inherit ) #IMPLIED"
+>
+
+<!ENTITY % SVG.visibility.attrib
+ "visibility ( visible | hidden | inherit ) #IMPLIED"
+>
+
+<!ENTITY % SVG.Graphics.extra.attrib "" >
+
+<!ENTITY % SVG.Graphics.attrib
+ "%SVG.display.attrib;
+ %SVG.image-rendering.attrib;
+ %SVG.pointer-events.attrib;
+ %SVG.shape-rendering.attrib;
+ %SVG.text-rendering.attrib;
+ %SVG.visibility.attrib;
+ %SVG.Graphics.extra.attrib;"
+>
+
+<!-- end of svg-graphics-attrib.mod -->
diff --git a/org/apache/batik/dom/svg/resources/svg-hyperlink.mod b/org/apache/batik/dom/svg/resources/svg-hyperlink.mod
new file mode 100644
index 0000000..2614c9d
--- /dev/null
+++ b/org/apache/batik/dom/svg/resources/svg-hyperlink.mod
@@ -0,0 +1,123 @@
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Hyperlinking Module ........................................... -->
+<!-- file: svg-hyperlink.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg-hyperlink.mod 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Hyperlinking//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-hyperlink.mod"
+
+ ....................................................................... -->
+
+<!-- Hyperlinking
+
+ a
+
+ This module declares markup to provide support for hyper linking.
+-->
+
+<!-- link to this target -->
+<!ENTITY % LinkTarget.datatype "NMTOKEN" >
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.a.qname "a" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Conditional.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Viewport.attrib "" >
+<!ENTITY % SVG.Text.attrib "" >
+<!ENTITY % SVG.TextContent.attrib "" >
+<!ENTITY % SVG.Font.attrib "" >
+<!ENTITY % SVG.Paint.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Marker.attrib "" >
+<!ENTITY % SVG.Gradient.attrib "" >
+<!ENTITY % SVG.Clip.attrib "" >
+<!ENTITY % SVG.Mask.attrib "" >
+<!ENTITY % SVG.Filter.attrib "" >
+<!ENTITY % SVG.FilterColor.attrib "" >
+<!ENTITY % SVG.GraphicalEvents.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.XLinkReplace.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Hyperlink.class ............................... -->
+
+<!ENTITY % SVG.Hyperlink.extra.class "" >
+
+<!ENTITY % SVG.Hyperlink.class
+ "| %SVG.a.qname; %SVG.Hyperlink.extra.class;"
+>
+
+<!-- SVG.Presentation.attrib ........................... -->
+
+<!ENTITY % SVG.Presentation.extra.attrib "" >
+
+<!ENTITY % SVG.Presentation.attrib
+ "%SVG.Container.attrib;
+ %SVG.Viewport.attrib;
+ %SVG.Text.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Profile.attrib;
+ %SVG.Gradient.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.Cursor.attrib;
+ flood-color %SVGColor.datatype; #IMPLIED
+ flood-opacity %OpacityValue.datatype; #IMPLIED
+ lighting-color %SVGColor.datatype; #IMPLIED
+ %SVG.Presentation.extra.attrib;"
+>
+
+<!-- a: Anchor Element ................................. -->
+
+<!ENTITY % SVG.a.extra.content "" >
+
+<!ENTITY % SVG.a.element "INCLUDE" >
+<![%SVG.a.element;[
+<!ENTITY % SVG.a.content
+ "( #PCDATA | %SVG.Description.class; | %SVG.Animation.class;
+ %SVG.Structure.class; %SVG.Conditional.class; %SVG.Image.class;
+ %SVG.Style.class; %SVG.Shape.class; %SVG.Text.class; %SVG.Marker.class;
+ %SVG.Profile.class; %SVG.Gradient.class; %SVG.Pattern.class;
+ %SVG.Clip.class; %SVG.Mask.class; %SVG.Filter.class; %SVG.Cursor.class;
+ %SVG.Hyperlink.class; %SVG.View.class; %SVG.Script.class;
+ %SVG.Font.class; %SVG.a.extra.content; )*"
+>
+<!ELEMENT %SVG.a.qname; %SVG.a.content; >
+<!-- end of SVG.a.element -->]]>
+
+<!ENTITY % SVG.a.attlist "INCLUDE" >
+<![%SVG.a.attlist;[
+<!ATTLIST %SVG.a.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.XLinkReplace.attrib;
+ %SVG.External.attrib;
+ transform %TransformList.datatype; #IMPLIED
+ target %LinkTarget.datatype; #IMPLIED
+>
+<!-- end of SVG.a.attlist -->]]>
+
+<!-- end of svg-hyperlink.mod -->
diff --git a/org/apache/batik/dom/svg/resources/svg-image.mod b/org/apache/batik/dom/svg/resources/svg-image.mod
new file mode 100644
index 0000000..aa90313
--- /dev/null
+++ b/org/apache/batik/dom/svg/resources/svg-image.mod
@@ -0,0 +1,93 @@
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Image Module .................................................. -->
+<!-- file: svg-image.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg-image.mod 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Image//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-image.mod"
+
+ ....................................................................... -->
+
+<!-- Image
+
+ image
+
+ This module declares markup to provide support for image.
+-->
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.image.qname "image" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Conditional.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Viewport.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Profile.attrib "" >
+<!ENTITY % SVG.Clip.attrib "" >
+<!ENTITY % SVG.Mask.attrib "" >
+<!ENTITY % SVG.Filter.attrib "" >
+<!ENTITY % SVG.GraphicalEvents.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.XLinkEmbed.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Image.class ................................... -->
+
+<!ENTITY % SVG.Image.extra.class "" >
+
+<!ENTITY % SVG.Image.class
+ "| %SVG.image.qname; %SVG.Image.extra.class;"
+>
+
+<!-- image: Image Element .............................. -->
+
+<!ENTITY % SVG.image.extra.content "" >
+
+<!ENTITY % SVG.image.element "INCLUDE" >
+<![%SVG.image.element;[
+<!ENTITY % SVG.image.content
+ "(( %SVG.Description.class; )*, ( %SVG.Animation.class;
+ %SVG.image.extra.content; )*)"
+>
+<!ELEMENT %SVG.image.qname; %SVG.image.content; >
+<!-- end of SVG.image.element -->]]>
+
+<!ENTITY % SVG.image.attlist "INCLUDE" >
+<![%SVG.image.attlist;[
+<!ATTLIST %SVG.image.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Viewport.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Profile.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.XLinkEmbed.attrib;
+ %SVG.External.attrib;
+ x %Coordinate.datatype; #IMPLIED
+ y %Coordinate.datatype; #IMPLIED
+ width %Length.datatype; #REQUIRED
+ height %Length.datatype; #REQUIRED
+ preserveAspectRatio %PreserveAspectRatioSpec.datatype; 'xMidYMid meet'
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.image.attlist -->]]>
+
+<!-- end of svg-image.mod -->
diff --git a/org/apache/batik/dom/svg/resources/svg-marker.mod b/org/apache/batik/dom/svg/resources/svg-marker.mod
new file mode 100644
index 0000000..ad3ba4e
--- /dev/null
+++ b/org/apache/batik/dom/svg/resources/svg-marker.mod
@@ -0,0 +1,135 @@
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Marker Module ................................................. -->
+<!-- file: svg-marker.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg-marker.mod 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Marker//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-marker.mod"
+
+ ....................................................................... -->
+
+<!-- Marker
+
+ marker
+
+ This module declares markup to provide support for marker.
+-->
+
+<!-- 'marker' property/attribute value (e.g., 'none', <uri>) -->
+<!ENTITY % MarkerValue.datatype "CDATA" >
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.marker.qname "marker" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Container.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Viewport.attrib "" >
+<!ENTITY % SVG.Text.attrib "" >
+<!ENTITY % SVG.TextContent.attrib "" >
+<!ENTITY % SVG.Font.attrib "" >
+<!ENTITY % SVG.Paint.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Profile.attrib "" >
+<!ENTITY % SVG.Gradient.attrib "" >
+<!ENTITY % SVG.Clip.attrib "" >
+<!ENTITY % SVG.Mask.attrib "" >
+<!ENTITY % SVG.Filter.attrib "" >
+<!ENTITY % SVG.FilterColor.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Marker.class .................................. -->
+
+<!ENTITY % SVG.Marker.extra.class "" >
+
+<!ENTITY % SVG.Marker.class
+ "| %SVG.marker.qname; %SVG.Marker.extra.class;"
+>
+
+<!-- SVG.Marker.attrib ................................. -->
+
+<!ENTITY % SVG.Marker.extra.attrib "" >
+
+<!ENTITY % SVG.Marker.attrib
+ "marker-start %MarkerValue.datatype; #IMPLIED
+ marker-mid %MarkerValue.datatype; #IMPLIED
+ marker-end %MarkerValue.datatype; #IMPLIED
+ %SVG.Marker.extra.attrib;"
+>
+
+<!-- SVG.Presentation.attrib ........................... -->
+
+<!ENTITY % SVG.Presentation.extra.attrib "" >
+
+<!ENTITY % SVG.Presentation.attrib
+ "%SVG.Container.attrib;
+ %SVG.Viewport.attrib;
+ %SVG.Text.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Profile.attrib;
+ %SVG.Gradient.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.Cursor.attrib;
+ flood-color %SVGColor.datatype; #IMPLIED
+ flood-opacity %OpacityValue.datatype; #IMPLIED
+ lighting-color %SVGColor.datatype; #IMPLIED
+ %SVG.Presentation.extra.attrib;"
+>
+
+<!-- marker: Marker Element ............................ -->
+
+<!ENTITY % SVG.marker.extra.content "" >
+
+<!ENTITY % SVG.marker.element "INCLUDE" >
+<![%SVG.marker.element;[
+<!ENTITY % SVG.marker.content
+ "( %SVG.Description.class; | %SVG.Animation.class; %SVG.Structure.class;
+ %SVG.Conditional.class; %SVG.Image.class; %SVG.Style.class;
+ %SVG.Shape.class; %SVG.Text.class; %SVG.Marker.class; %SVG.Profile.class;
+ %SVG.Gradient.class; %SVG.Pattern.class; %SVG.Clip.class;
+ %SVG.Mask.class; %SVG.Filter.class; %SVG.Cursor.class;
+ %SVG.Hyperlink.class; %SVG.View.class; %SVG.Script.class;
+ %SVG.Font.class; %SVG.marker.extra.content; )*"
+>
+<!ELEMENT %SVG.marker.qname; %SVG.marker.content; >
+<!-- end of SVG.marker.element -->]]>
+
+<!ENTITY % SVG.marker.attlist "INCLUDE" >
+<![%SVG.marker.attlist;[
+<!ATTLIST %SVG.marker.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.External.attrib;
+ refX %Coordinate.datatype; #IMPLIED
+ refY %Coordinate.datatype; #IMPLIED
+ markerUnits ( strokeWidth | userSpaceOnUse ) #IMPLIED
+ markerWidth %Length.datatype; #IMPLIED
+ markerHeight %Length.datatype; #IMPLIED
+ orient CDATA #IMPLIED
+ viewBox %ViewBoxSpec.datatype; #IMPLIED
+ preserveAspectRatio %PreserveAspectRatioSpec.datatype; 'xMidYMid meet'
+>
+<!-- end of SVG.marker.attlist -->]]>
+
+<!-- end of svg-marker.mod -->
diff --git a/org/apache/batik/dom/svg/resources/svg-mask.mod b/org/apache/batik/dom/svg/resources/svg-mask.mod
new file mode 100644
index 0000000..0afe8aa
--- /dev/null
+++ b/org/apache/batik/dom/svg/resources/svg-mask.mod
@@ -0,0 +1,133 @@
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Mask Module ................................................... -->
+<!-- file: svg-mask.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg-mask.mod 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Mask//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-mask.mod"
+
+ ....................................................................... -->
+
+<!-- Mask
+
+ mask
+
+ This module declares markup to provide support for masking.
+-->
+
+<!-- 'mask' property/attribute value (e.g., 'none', <uri>) -->
+<!ENTITY % MaskValue.datatype "CDATA" >
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.mask.qname "mask" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Container.attrib "" >
+<!ENTITY % SVG.Conditional.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Viewport.attrib "" >
+<!ENTITY % SVG.Text.attrib "" >
+<!ENTITY % SVG.TextContent.attrib "" >
+<!ENTITY % SVG.Font.attrib "" >
+<!ENTITY % SVG.Paint.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Marker.attrib "" >
+<!ENTITY % SVG.Profile.attrib "" >
+<!ENTITY % SVG.Gradient.attrib "" >
+<!ENTITY % SVG.Clip.attrib "" >
+<!ENTITY % SVG.Filter.attrib "" >
+<!ENTITY % SVG.FilterColor.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Mask.class .................................... -->
+
+<!ENTITY % SVG.Mask.extra.class "" >
+
+<!ENTITY % SVG.Mask.class
+ "| %SVG.mask.qname; %SVG.Mask.extra.class;"
+>
+
+<!-- SVG.Mask.attrib ................................... -->
+
+<!ENTITY % SVG.Mask.extra.attrib "" >
+
+<!ENTITY % SVG.Mask.attrib
+ "mask %MaskValue.datatype; #IMPLIED
+ %SVG.Mask.extra.attrib;"
+>
+
+<!-- SVG.Presentation.attrib ........................... -->
+
+<!ENTITY % SVG.Presentation.extra.attrib "" >
+
+<!ENTITY % SVG.Presentation.attrib
+ "%SVG.Container.attrib;
+ %SVG.Viewport.attrib;
+ %SVG.Text.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Profile.attrib;
+ %SVG.Gradient.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.Cursor.attrib;
+ flood-color %SVGColor.datatype; #IMPLIED
+ flood-opacity %OpacityValue.datatype; #IMPLIED
+ lighting-color %SVGColor.datatype; #IMPLIED
+ %SVG.Presentation.extra.attrib;"
+>
+
+<!-- mask: Mask Element ................................ -->
+
+<!ENTITY % SVG.mask.extra.content "" >
+
+<!ENTITY % SVG.mask.element "INCLUDE" >
+<![%SVG.mask.element;[
+<!ENTITY % SVG.mask.content
+ "( %SVG.Description.class; | %SVG.Animation.class; %SVG.Structure.class;
+ %SVG.Conditional.class; %SVG.Image.class; %SVG.Style.class;
+ %SVG.Shape.class; %SVG.Text.class; %SVG.Marker.class; %SVG.Profile.class;
+ %SVG.Gradient.class; %SVG.Pattern.class; %SVG.Clip.class;
+ %SVG.Mask.class; %SVG.Filter.class; %SVG.Cursor.class;
+ %SVG.Hyperlink.class; %SVG.View.class; %SVG.Script.class;
+ %SVG.Font.class; %SVG.mask.extra.content; )*"
+>
+<!ELEMENT %SVG.mask.qname; %SVG.mask.content; >
+<!-- end of SVG.mask.element -->]]>
+
+<!ENTITY % SVG.mask.attlist "INCLUDE" >
+<![%SVG.mask.attlist;[
+<!ATTLIST %SVG.mask.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.External.attrib;
+ x %Coordinate.datatype; #IMPLIED
+ y %Coordinate.datatype; #IMPLIED
+ width %Length.datatype; #IMPLIED
+ height %Length.datatype; #IMPLIED
+ maskUnits ( userSpaceOnUse | objectBoundingBox ) #IMPLIED
+ maskContentUnits ( userSpaceOnUse | objectBoundingBox ) #IMPLIED
+>
+<!-- end of SVG.mask.attlist -->]]>
+
+<!-- end of svg-mask.mod -->
diff --git a/org/apache/batik/dom/svg/resources/svg-opacity-attrib.mod b/org/apache/batik/dom/svg/resources/svg-opacity-attrib.mod
new file mode 100644
index 0000000..fae12c7
--- /dev/null
+++ b/org/apache/batik/dom/svg/resources/svg-opacity-attrib.mod
@@ -0,0 +1,44 @@
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Paint Opacity Attribute Module ................................ -->
+<!-- file: svg-opacity-attrib.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg-opacity-attrib.mod 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Paint Opacity Attribute//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-opacity-attrib.mod"
+
+ ....................................................................... -->
+
+<!-- Paint Opacity Attribute
+
+ opacity, fill-opacity, stroke-opacity
+
+ This module defines the Opacity attribute set.
+-->
+
+<!ENTITY % SVG.opacity.attrib
+ "opacity %OpacityValue.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.fill-opacity.attrib
+ "fill-opacity %OpacityValue.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.stroke-opacity.attrib
+ "stroke-opacity %OpacityValue.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.Opacity.extra.attrib "" >
+
+<!ENTITY % SVG.Opacity.attrib
+ "%SVG.opacity.attrib;
+ %SVG.fill-opacity.attrib;
+ %SVG.stroke-opacity.attrib;
+ %SVG.Opacity.extra.attrib;"
+>
+
+<!-- end of svg-opacity-attrib.mod -->
diff --git a/org/apache/batik/dom/svg/resources/svg-paint-attrib.mod b/org/apache/batik/dom/svg/resources/svg-paint-attrib.mod
new file mode 100644
index 0000000..a4db4c3
--- /dev/null
+++ b/org/apache/batik/dom/svg/resources/svg-paint-attrib.mod
@@ -0,0 +1,113 @@
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Paint Attribute Module ........................................ -->
+<!-- file: svg-paint-attrib.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg-paint-attrib.mod 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Paint Attribute//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-paint-attrib.mod"
+
+ ....................................................................... -->
+
+<!-- Paint Attribute
+
+ fill, fill-rule, stroke, stroke-dasharray, stroke-dashoffset,
+ stroke-linecap, stroke-linejoin, stroke-miterlimit, stroke-width, color,
+ color-interpolation, color-rendering
+
+ This module defines the Paint and Color attribute sets.
+-->
+
+<!-- a 'fill' or 'stroke' property/attribute value: <paint> -->
+<!ENTITY % Paint.datatype "CDATA" >
+
+<!-- 'stroke-dasharray' property/attribute value (e.g., 'none', list of <number>s) -->
+<!ENTITY % StrokeDashArrayValue.datatype "CDATA" >
+
+<!-- 'stroke-dashoffset' property/attribute value (e.g., 'none', <legnth>) -->
+<!ENTITY % StrokeDashOffsetValue.datatype "CDATA" >
+
+<!-- 'stroke-miterlimit' property/attribute value (e.g., <number>) -->
+<!ENTITY % StrokeMiterLimitValue.datatype "CDATA" >
+
+<!-- 'stroke-width' property/attribute value (e.g., <length>) -->
+<!ENTITY % StrokeWidthValue.datatype "CDATA" >
+
+<!ENTITY % SVG.fill.attrib
+ "fill %Paint.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.fill-rule.attrib
+ "fill-rule %ClipFillRule.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.stroke.attrib
+ "stroke %Paint.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.stroke-dasharray.attrib
+ "stroke-dasharray %StrokeDashArrayValue.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.stroke-dashoffset.attrib
+ "stroke-dashoffset %StrokeDashOffsetValue.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.stroke-linecap.attrib
+ "stroke-linecap ( butt | round | square | inherit ) #IMPLIED"
+>
+
+<!ENTITY % SVG.stroke-linejoin.attrib
+ "stroke-linejoin ( miter | round | bevel | inherit ) #IMPLIED"
+>
+
+<!ENTITY % SVG.stroke-miterlimit.attrib
+ "stroke-miterlimit %StrokeMiterLimitValue.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.stroke-width.attrib
+ "stroke-width %StrokeWidthValue.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.Paint.extra.attrib "" >
+
+<!ENTITY % SVG.Paint.attrib
+ "%SVG.fill.attrib;
+ %SVG.fill-rule.attrib;
+ %SVG.stroke.attrib;
+ %SVG.stroke-dasharray.attrib;
+ %SVG.stroke-dashoffset.attrib;
+ %SVG.stroke-linecap.attrib;
+ %SVG.stroke-linejoin.attrib;
+ %SVG.stroke-miterlimit.attrib;
+ %SVG.stroke-width.attrib;
+ %SVG.Paint.extra.attrib;"
+>
+
+<!ENTITY % SVG.color.attrib
+ "color %Color.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.color-interpolation.attrib
+ "color-interpolation ( auto | sRGB | linearRGB | inherit ) #IMPLIED"
+>
+
+<!ENTITY % SVG.color-rendering.attrib
+ "color-rendering ( auto | optimizeSpeed | optimizeQuality | inherit )
+ #IMPLIED"
+>
+
+<!ENTITY % SVG.Color.extra.attrib "" >
+
+<!ENTITY % SVG.Color.attrib
+ "%SVG.color.attrib;
+ %SVG.color-interpolation.attrib;
+ %SVG.color-rendering.attrib;
+ %SVG.Color.extra.attrib;"
+>
+
+<!-- end of svg-paint-attrib.mod -->
diff --git a/org/apache/batik/dom/svg/resources/svg-pattern.mod b/org/apache/batik/dom/svg/resources/svg-pattern.mod
new file mode 100644
index 0000000..39d682a
--- /dev/null
+++ b/org/apache/batik/dom/svg/resources/svg-pattern.mod
@@ -0,0 +1,127 @@
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Pattern Module ................................................ -->
+<!-- file: svg-pattern.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg-pattern.mod 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Pattern//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-pattern.mod"
+
+ ....................................................................... -->
+
+<!-- Pattern
+
+ pattern
+
+ This module declares markup to provide support for pattern fill.
+-->
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.pattern.qname "pattern" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Container.attrib "" >
+<!ENTITY % SVG.Conditional.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Viewport.attrib "" >
+<!ENTITY % SVG.Text.attrib "" >
+<!ENTITY % SVG.TextContent.attrib "" >
+<!ENTITY % SVG.Font.attrib "" >
+<!ENTITY % SVG.Paint.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Marker.attrib "" >
+<!ENTITY % SVG.Profile.attrib "" >
+<!ENTITY % SVG.Gradient.attrib "" >
+<!ENTITY % SVG.Clip.attrib "" >
+<!ENTITY % SVG.Mask.attrib "" >
+<!ENTITY % SVG.Filter.attrib "" >
+<!ENTITY % SVG.FilterColor.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.XLink.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Pattern.class ................................. -->
+
+<!ENTITY % SVG.Pattern.extra.class "" >
+
+<!ENTITY % SVG.Pattern.class
+ "| %SVG.pattern.qname; %SVG.Pattern.extra.class;"
+>
+
+<!-- SVG.Presentation.attrib ........................... -->
+
+<!ENTITY % SVG.Presentation.extra.attrib "" >
+
+<!ENTITY % SVG.Presentation.attrib
+ "%SVG.Container.attrib;
+ %SVG.Viewport.attrib;
+ %SVG.Text.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Profile.attrib;
+ %SVG.Gradient.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.Cursor.attrib;
+ flood-color %SVGColor.datatype; #IMPLIED
+ flood-opacity %OpacityValue.datatype; #IMPLIED
+ lighting-color %SVGColor.datatype; #IMPLIED
+ %SVG.Presentation.extra.attrib;"
+>
+
+<!-- pattern: Pattern Element .......................... -->
+
+<!ENTITY % SVG.pattern.extra.content "" >
+
+<!ENTITY % SVG.pattern.element "INCLUDE" >
+<![%SVG.pattern.element;[
+<!ENTITY % SVG.pattern.content
+ "( %SVG.Description.class; | %SVG.Animation.class; %SVG.Structure.class;
+ %SVG.Conditional.class; %SVG.Image.class; %SVG.Style.class;
+ %SVG.Shape.class; %SVG.Text.class; %SVG.Marker.class; %SVG.Profile.class;
+ %SVG.Gradient.class; %SVG.Pattern.class; %SVG.Clip.class;
+ %SVG.Mask.class; %SVG.Filter.class; %SVG.Cursor.class;
+ %SVG.Hyperlink.class; %SVG.View.class; %SVG.Script.class;
+ %SVG.Font.class; %SVG.pattern.extra.content; )*"
+>
+<!ELEMENT %SVG.pattern.qname; %SVG.pattern.content; >
+<!-- end of SVG.pattern.element -->]]>
+
+<!ENTITY % SVG.pattern.attlist "INCLUDE" >
+<![%SVG.pattern.attlist;[
+<!ATTLIST %SVG.pattern.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.XLink.attrib;
+ %SVG.External.attrib;
+ x %Coordinate.datatype; #IMPLIED
+ y %Coordinate.datatype; #IMPLIED
+ width %Length.datatype; #IMPLIED
+ height %Length.datatype; #IMPLIED
+ patternUnits ( userSpaceOnUse | objectBoundingBox ) #IMPLIED
+ patternContentUnits ( userSpaceOnUse | objectBoundingBox ) #IMPLIED
+ patternTransform %TransformList.datatype; #IMPLIED
+ viewBox %ViewBoxSpec.datatype; #IMPLIED
+ preserveAspectRatio %PreserveAspectRatioSpec.datatype; 'xMidYMid meet'
+>
+<!-- end of SVG.pattern.attlist -->]]>
+
+<!-- end of svg-pattern.mod -->
diff --git a/org/apache/batik/dom/svg/resources/svg-profile.mod b/org/apache/batik/dom/svg/resources/svg-profile.mod
new file mode 100644
index 0000000..519b70b
--- /dev/null
+++ b/org/apache/batik/dom/svg/resources/svg-profile.mod
@@ -0,0 +1,73 @@
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Color Profile Module .......................................... -->
+<!-- file: svg-profile.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg-profile.mod 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Color Profile//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-profile.mod"
+
+ ....................................................................... -->
+
+<!-- Color Profile
+
+ color-profile
+
+ This module declares markup to provide support for color profile.
+-->
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.color-profile.qname "color-profile" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.XLink.attrib "" >
+
+<!-- SVG.Profile.class ................................. -->
+
+<!ENTITY % SVG.Profile.extra.class "" >
+
+<!ENTITY % SVG.Profile.class
+ "| %SVG.color-profile.qname; %SVG.Profile.extra.class;"
+>
+
+<!-- SVG.Profile.attrib ................................ -->
+
+<!ENTITY % SVG.Profile.extra.attrib "" >
+
+<!ENTITY % SVG.Profile.attrib
+ "color-profile CDATA #IMPLIED
+ %SVG.Profile.extra.attrib;"
+>
+
+<!-- color-profile: Color Profile Element .............. -->
+
+<!ENTITY % SVG.color-profile.extra.content "" >
+
+<!ENTITY % SVG.color-profile.element "INCLUDE" >
+<![%SVG.color-profile.element;[
+<!ENTITY % SVG.color-profile.content
+ "( %SVG.Description.class; %SVG.color-profile.extra.content; )*"
+>
+<!ELEMENT %SVG.color-profile.qname; %SVG.color-profile.content; >
+<!-- end of SVG.color-profile.element -->]]>
+
+<!ENTITY % SVG.color-profile.attlist "INCLUDE" >
+<![%SVG.color-profile.attlist;[
+<!ATTLIST %SVG.color-profile.qname;
+ %SVG.Core.attrib;
+ %SVG.XLink.attrib;
+ local CDATA #IMPLIED
+ name CDATA #REQUIRED
+ rendering-intent ( auto | perceptual | relative-colorimetric | saturation |
+ absolute-colorimetric ) 'auto'
+>
+<!-- end of SVG.color-profile.attlist -->]]>
+
+<!-- end of svg-profile.mod -->
diff --git a/org/apache/batik/dom/svg/resources/svg-qname.mod b/org/apache/batik/dom/svg/resources/svg-qname.mod
new file mode 100644
index 0000000..933c974
--- /dev/null
+++ b/org/apache/batik/dom/svg/resources/svg-qname.mod
@@ -0,0 +1,257 @@
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Qualified Name Module ......................................... -->
+<!-- file: svg-qname.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg-qname.mod 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Qualified Name//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-qname.mod"
+
+ ....................................................................... -->
+
+<!-- Qualified Name
+
+ This module is contained in two parts, labeled Section 'A' and 'B':
+
+ Section A declares parameter entities to support namespace-
+ qualified names, namespace declarations, and name prefixing
+ for SVG and extensions.
+
+ Section B declares parameter entities used to provide
+ namespace-qualified names for all SVG element types:
+-->
+
+<!-- Section A: SVG XML Namespace Framework :::::::::::::::::::::: -->
+
+<!-- 1. Declare a %SVG.prefixed; conditional section keyword, used
+ to activate namespace prefixing. The default value should
+ inherit '%NS.prefixed;' from the DTD driver, so that unless
+ overridden, the default behaviour follows the overall DTD
+ prefixing scheme.
+-->
+<!ENTITY % NS.prefixed "IGNORE" >
+<!ENTITY % SVG.prefixed "%NS.prefixed;" >
+
+<!-- 2. Declare a parameter entity (eg., %SVG.xmlns;) containing
+ the URI reference used to identify the SVG namespace:
+-->
+<!ENTITY % SVG.xmlns "http://www.w3.org/2000/svg" >
+<!ENTITY % XLINK.xmlns "http://www.w3.org/1999/xlink" >
+
+<!-- 3. Declare parameter entities (eg., %SVG.prefix;) containing
+ the default namespace prefix string(s) to use when prefixing
+ is enabled. This may be overridden in the DTD driver or the
+ internal subset of an document instance. If no default prefix
+ is desired, this may be declared as an empty string.
+-->
+<!ENTITY % SVG.prefix "" >
+<!ENTITY % XLINK.prefix "xlink" >
+
+<!-- 4. Declare parameter entities (eg., %SVG.pfx;) containing the
+ colonized prefix(es) (eg., '%SVG.prefix;:') used when
+ prefixing is active, an empty string when it is not.
+-->
+<![%SVG.prefixed;[
+<!ENTITY % SVG.pfx "%SVG.prefix;:" >
+]]>
+<!ENTITY % SVG.pfx "" >
+<!ENTITY % XLINK.pfx "%XLINK.prefix;:" >
+
+<!-- 5. The parameter entity %SVG.xmlns.extra.attrib; may be
+ redeclared to contain any non-SVG namespace declaration
+ attributes for namespaces embedded in SVG. The default
+ is an empty string.
+-->
+<!ENTITY % SVG.xmlns.extra.attrib "" >
+
+<!-- Declare a parameter entity XLINK.xmlns.attrib containing
+ the XML Namespace declarations for XLink.
+-->
+<!ENTITY % XLINK.xmlns.attrib
+ "xmlns:%XLINK.prefix; %URI.datatype; #FIXED '%XLINK.xmlns;'"
+>
+
+<!-- Declare a parameter entity %NS.decl.attrib; containing
+ all XML Namespace declarations used in the DTD, plus the
+ xmlns declaration for SVG, its form dependent on whether
+ prefixing is active.
+-->
+<![%SVG.prefixed;[
+<!ENTITY % NS.decl.attrib
+ "xmlns:%SVG.prefix; %URI.datatype; #FIXED '%SVG.xmlns;'
+ %XLINK.xmlns.attrib;
+ %SVG.xmlns.extra.attrib;"
+>
+]]>
+<!ENTITY % NS.decl.attrib
+ "%XLINK.xmlns.attrib;
+ %SVG.xmlns.extra.attrib;"
+>
+
+<!-- Declare a parameter entity %SVG.xmlns.attrib; containing
+ all XML namespace declaration attributes used by SVG,
+ including a default xmlns attribute when prefixing is
+ inactive.
+-->
+<![%SVG.prefixed;[
+<!ENTITY % SVG.xmlns.attrib
+ "%NS.decl.attrib;"
+>
+]]>
+<!ENTITY % SVG.xmlns.attrib
+ "xmlns %URI.datatype; #FIXED '%SVG.xmlns;'
+ %XLINK.xmlns.attrib;"
+>
+
+<!-- Section B: SVG Qualified Names :::::::::::::::::::::::::::::: -->
+
+<!-- 6. This section declares parameter entities used to provide
+ namespace-qualified names for all SVG element types.
+-->
+
+<!-- module: svg-structure.mod ......................... -->
+
+<!ENTITY % SVG.svg.qname "%SVG.pfx;svg" >
+<!ENTITY % SVG.g.qname "%SVG.pfx;g" >
+<!ENTITY % SVG.defs.qname "%SVG.pfx;defs" >
+<!ENTITY % SVG.desc.qname "%SVG.pfx;desc" >
+<!ENTITY % SVG.title.qname "%SVG.pfx;title" >
+<!ENTITY % SVG.metadata.qname "%SVG.pfx;metadata" >
+<!ENTITY % SVG.symbol.qname "%SVG.pfx;symbol" >
+<!ENTITY % SVG.use.qname "%SVG.pfx;use" >
+
+<!-- module: svg-conditional.mod ....................... -->
+
+<!ENTITY % SVG.switch.qname "%SVG.pfx;switch" >
+
+<!-- module: svg-image.mod ............................. -->
+
+<!ENTITY % SVG.image.qname "%SVG.pfx;image" >
+
+<!-- module: svg-style.mod ............................. -->
+
+<!ENTITY % SVG.style.qname "%SVG.pfx;style" >
+
+<!-- module: svg-shape.mod ............................. -->
+
+<!ENTITY % SVG.path.qname "%SVG.pfx;path" >
+<!ENTITY % SVG.rect.qname "%SVG.pfx;rect" >
+<!ENTITY % SVG.circle.qname "%SVG.pfx;circle" >
+<!ENTITY % SVG.line.qname "%SVG.pfx;line" >
+<!ENTITY % SVG.ellipse.qname "%SVG.pfx;ellipse" >
+<!ENTITY % SVG.polyline.qname "%SVG.pfx;polyline" >
+<!ENTITY % SVG.polygon.qname "%SVG.pfx;polygon" >
+
+<!-- module: svg-text.mod .............................. -->
+
+<!ENTITY % SVG.text.qname "%SVG.pfx;text" >
+<!ENTITY % SVG.tspan.qname "%SVG.pfx;tspan" >
+<!ENTITY % SVG.tref.qname "%SVG.pfx;tref" >
+<!ENTITY % SVG.textPath.qname "%SVG.pfx;textPath" >
+<!ENTITY % SVG.altGlyph.qname "%SVG.pfx;altGlyph" >
+<!ENTITY % SVG.altGlyphDef.qname "%SVG.pfx;altGlyphDef" >
+<!ENTITY % SVG.altGlyphItem.qname "%SVG.pfx;altGlyphItem" >
+<!ENTITY % SVG.glyphRef.qname "%SVG.pfx;glyphRef" >
+
+<!-- module: svg-marker.mod ............................ -->
+
+<!ENTITY % SVG.marker.qname "%SVG.pfx;marker" >
+
+<!-- module: svg-profile.mod ........................... -->
+
+<!ENTITY % SVG.color-profile.qname "%SVG.pfx;color-profile" >
+
+<!-- module: svg-gradient.mod .......................... -->
+
+<!ENTITY % SVG.linearGradient.qname "%SVG.pfx;linearGradient" >
+<!ENTITY % SVG.radialGradient.qname "%SVG.pfx;radialGradient" >
+<!ENTITY % SVG.stop.qname "stop" >
+
+<!-- module: svg-pattern.mod ........................... -->
+
+<!ENTITY % SVG.pattern.qname "%SVG.pfx;pattern" >
+
+<!-- module: svg-clip.mod .............................. -->
+
+<!ENTITY % SVG.clipPath.qname "%SVG.pfx;clipPath" >
+
+<!-- module: svg-mask.mod .............................. -->
+
+<!ENTITY % SVG.mask.qname "%SVG.pfx;mask" >
+
+<!-- module: svg-filter.mod ............................ -->
+
+<!ENTITY % SVG.filter.qname "%SVG.pfx;filter" >
+<!ENTITY % SVG.feBlend.qname "%SVG.pfx;feBlend" >
+<!ENTITY % SVG.feColorMatrix.qname "%SVG.pfx;feColorMatrix" >
+<!ENTITY % SVG.feComponentTransfer.qname "%SVG.pfx;feComponentTransfer" >
+<!ENTITY % SVG.feComposite.qname "%SVG.pfx;feComposite" >
+<!ENTITY % SVG.feConvolveMatrix.qname "%SVG.pfx;feConvolveMatrix" >
+<!ENTITY % SVG.feDiffuseLighting.qname "%SVG.pfx;feDiffuseLighting" >
+<!ENTITY % SVG.feDisplacementMap.qname "%SVG.pfx;feDisplacementMap" >
+<!ENTITY % SVG.feFlood.qname "%SVG.pfx;feFlood" >
+<!ENTITY % SVG.feGaussianBlur.qname "%SVG.pfx;feGaussianBlur" >
+<!ENTITY % SVG.feImage.qname "%SVG.pfx;feImage" >
+<!ENTITY % SVG.feMerge.qname "%SVG.pfx;feMerge" >
+<!ENTITY % SVG.feMergeNode.qname "%SVG.pfx;feMergeNode" >
+<!ENTITY % SVG.feMorphology.qname "%SVG.pfx;feMorphology" >
+<!ENTITY % SVG.feOffset.qname "%SVG.pfx;feOffset" >
+<!ENTITY % SVG.feSpecularLighting.qname "%SVG.pfx;feSpecularLighting" >
+<!ENTITY % SVG.feTile.qname "%SVG.pfx;feTile" >
+<!ENTITY % SVG.feTurbulence.qname "%SVG.pfx;feTurbulence" >
+<!ENTITY % SVG.feDistantLight.qname "%SVG.pfx;feDistantLight" >
+<!ENTITY % SVG.fePointLight.qname "%SVG.pfx;fePointLight" >
+<!ENTITY % SVG.feSpotLight.qname "%SVG.pfx;feSpotLight" >
+<!ENTITY % SVG.feFuncR.qname "%SVG.pfx;feFuncR" >
+<!ENTITY % SVG.feFuncG.qname "%SVG.pfx;feFuncG" >
+<!ENTITY % SVG.feFuncB.qname "%SVG.pfx;feFuncB" >
+<!ENTITY % SVG.feFuncA.qname "%SVG.pfx;feFuncA" >
+
+<!-- module: svg-cursor.mod ............................ -->
+
+<!ENTITY % SVG.cursor.qname "%SVG.pfx;cursor" >
+
+<!-- module: svg-hyperlink.mod ......................... -->
+
+<!ENTITY % SVG.a.qname "%SVG.pfx;a" >
+
+<!-- module: svg-view.mod .............................. -->
+
+<!ENTITY % SVG.view.qname "%SVG.pfx;view" >
+
+<!-- module: svg-script.mod ............................ -->
+
+<!ENTITY % SVG.script.qname "%SVG.pfx;script" >
+
+<!-- module: svg-animation.mod ......................... -->
+
+<!ENTITY % SVG.animate.qname "%SVG.pfx;animate" >
+<!ENTITY % SVG.set.qname "%SVG.pfx;set" >
+<!ENTITY % SVG.animateMotion.qname "%SVG.pfx;animateMotion" >
+<!ENTITY % SVG.animateColor.qname "%SVG.pfx;animateColor" >
+<!ENTITY % SVG.animateTransform.qname "%SVG.pfx;animateTransform" >
+<!ENTITY % SVG.mpath.qname "%SVG.pfx;mpath" >
+
+<!-- module: svg-font.mod .............................. -->
+
+<!ENTITY % SVG.font.qname "%SVG.pfx;font" >
+<!ENTITY % SVG.font-face.qname "%SVG.pfx;font-face" >
+<!ENTITY % SVG.glyph.qname "%SVG.pfx;glyph" >
+<!ENTITY % SVG.missing-glyph.qname "%SVG.pfx;missing-glyph" >
+<!ENTITY % SVG.hkern.qname "%SVG.pfx;hkern" >
+<!ENTITY % SVG.vkern.qname "%SVG.pfx;vkern" >
+<!ENTITY % SVG.font-face-src.qname "%SVG.pfx;font-face-src" >
+<!ENTITY % SVG.font-face-uri.qname "%SVG.pfx;font-face-uri" >
+<!ENTITY % SVG.font-face-format.qname "%SVG.pfx;font-face-format" >
+<!ENTITY % SVG.font-face-name.qname "%SVG.pfx;font-face-name" >
+<!ENTITY % SVG.definition-src.qname "%SVG.pfx;definition-src" >
+
+<!-- module: svg-extensibility.mod ..................... -->
+
+<!ENTITY % SVG.foreignObject.qname "%SVG.pfx;foreignObject" >
+
+<!-- end of svg-qname.mod -->
diff --git a/org/apache/batik/dom/svg/resources/svg-script.mod b/org/apache/batik/dom/svg/resources/svg-script.mod
new file mode 100644
index 0000000..68f9e52
--- /dev/null
+++ b/org/apache/batik/dom/svg/resources/svg-script.mod
@@ -0,0 +1,63 @@
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Scripting Module .............................................. -->
+<!-- file: svg-script.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg-script.mod 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Scripting//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-script.mod"
+
+ ....................................................................... -->
+
+<!-- Scripting
+
+ script
+
+ This module declares markup to provide support for scripting.
+-->
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.script.qname "script" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.XLink.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Script.class .................................. -->
+
+<!ENTITY % SVG.Script.extra.class "" >
+
+<!ENTITY % SVG.Script.class
+ "| %SVG.script.qname; %SVG.Script.extra.class;"
+>
+
+<!-- script: Script Element ............................ -->
+
+<!ENTITY % SVG.script.extra.content "" >
+
+<!ENTITY % SVG.script.element "INCLUDE" >
+<![%SVG.script.element;[
+<!ENTITY % SVG.script.content
+ "( #PCDATA %SVG.script.extra.content; )*"
+>
+<!ELEMENT %SVG.script.qname; %SVG.script.content; >
+<!-- end of SVG.script.element -->]]>
+
+<!ENTITY % SVG.script.attlist "INCLUDE" >
+<![%SVG.script.attlist;[
+<!ATTLIST %SVG.script.qname;
+ %SVG.Core.attrib;
+ %SVG.XLink.attrib;
+ %SVG.External.attrib;
+ type %ContentType.datatype; #REQUIRED
+>
+<!-- end of SVG.script.attlist -->]]>
+
+<!-- end of svg-script.mod -->
diff --git a/org/apache/batik/dom/svg/resources/svg-shape.mod b/org/apache/batik/dom/svg/resources/svg-shape.mod
new file mode 100644
index 0000000..f4afc2d
--- /dev/null
+++ b/org/apache/batik/dom/svg/resources/svg-shape.mod
@@ -0,0 +1,319 @@
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Shape Module .................................................. -->
+<!-- file: svg-shape.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg-shape.mod 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Shape//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-shape.mod"
+
+ ....................................................................... -->
+
+<!-- Shape
+
+ path, rect, circle, line, ellipse, polyline, polygon
+
+ This module declares markup to provide support for graphical shapes.
+-->
+
+<!-- a list of points -->
+<!ENTITY % Points.datatype "CDATA" >
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.path.qname "path" >
+<!ENTITY % SVG.rect.qname "rect" >
+<!ENTITY % SVG.circle.qname "circle" >
+<!ENTITY % SVG.line.qname "line" >
+<!ENTITY % SVG.ellipse.qname "ellipse" >
+<!ENTITY % SVG.polyline.qname "polyline" >
+<!ENTITY % SVG.polygon.qname "polygon" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Conditional.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Paint.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Marker.attrib "" >
+<!ENTITY % SVG.Clip.attrib "" >
+<!ENTITY % SVG.Mask.attrib "" >
+<!ENTITY % SVG.Filter.attrib "" >
+<!ENTITY % SVG.GraphicalEvents.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Shape.class ................................... -->
+
+<!ENTITY % SVG.Shape.extra.class "" >
+
+<!ENTITY % SVG.Shape.class
+ "| %SVG.path.qname; | %SVG.rect.qname; | %SVG.circle.qname;
+ | %SVG.line.qname; | %SVG.ellipse.qname; | %SVG.polyline.qname;
+ | %SVG.polygon.qname; %SVG.Shape.extra.class;"
+>
+
+<!-- path: Path Element ................................ -->
+
+<!ENTITY % SVG.path.extra.content "" >
+
+<!ENTITY % SVG.path.element "INCLUDE" >
+<![%SVG.path.element;[
+<!ENTITY % SVG.path.content
+ "(( %SVG.Description.class; )*, ( %SVG.Animation.class;
+ %SVG.path.extra.content; )*)"
+>
+<!ELEMENT %SVG.path.qname; %SVG.path.content; >
+<!-- end of SVG.path.element -->]]>
+
+<!ENTITY % SVG.path.attlist "INCLUDE" >
+<![%SVG.path.attlist;[
+<!ATTLIST %SVG.path.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.External.attrib;
+ d %PathData.datatype; #REQUIRED
+ pathLength %Number.datatype; #IMPLIED
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.path.attlist -->]]>
+
+<!-- rect: Rectangle Element ........................... -->
+
+<!ENTITY % SVG.rect.extra.content "" >
+
+<!ENTITY % SVG.rect.element "INCLUDE" >
+<![%SVG.rect.element;[
+<!ENTITY % SVG.rect.content
+ "(( %SVG.Description.class; )*, ( %SVG.Animation.class;
+ %SVG.rect.extra.content; )*)"
+>
+<!ELEMENT %SVG.rect.qname; %SVG.rect.content; >
+<!-- end of SVG.rect.element -->]]>
+
+<!ENTITY % SVG.rect.attlist "INCLUDE" >
+<![%SVG.rect.attlist;[
+<!ATTLIST %SVG.rect.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.External.attrib;
+ x %Coordinate.datatype; #IMPLIED
+ y %Coordinate.datatype; #IMPLIED
+ width %Length.datatype; #REQUIRED
+ height %Length.datatype; #REQUIRED
+ rx %Length.datatype; #IMPLIED
+ ry %Length.datatype; #IMPLIED
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.rect.attlist -->]]>
+
+<!-- circle: Circle Element ............................ -->
+
+<!ENTITY % SVG.circle.extra.content "" >
+
+<!ENTITY % SVG.circle.element "INCLUDE" >
+<![%SVG.circle.element;[
+<!ENTITY % SVG.circle.content
+ "(( %SVG.Description.class; )*, ( %SVG.Animation.class;
+ %SVG.circle.extra.content; )*)"
+>
+<!ELEMENT %SVG.circle.qname; %SVG.circle.content; >
+<!-- end of SVG.circle.element -->]]>
+
+<!ENTITY % SVG.circle.attlist "INCLUDE" >
+<![%SVG.circle.attlist;[
+<!ATTLIST %SVG.circle.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.External.attrib;
+ cx %Coordinate.datatype; #IMPLIED
+ cy %Coordinate.datatype; #IMPLIED
+ r %Length.datatype; #REQUIRED
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.circle.attlist -->]]>
+
+<!-- line: Line Element ................................ -->
+
+<!ENTITY % SVG.line.extra.content "" >
+
+<!ENTITY % SVG.line.element "INCLUDE" >
+<![%SVG.line.element;[
+<!ENTITY % SVG.line.content
+ "(( %SVG.Description.class; )*, ( %SVG.Animation.class;
+ %SVG.line.extra.content; )*)"
+>
+<!ELEMENT %SVG.line.qname; %SVG.line.content; >
+<!-- end of SVG.line.element -->]]>
+
+<!ENTITY % SVG.line.attlist "INCLUDE" >
+<![%SVG.line.attlist;[
+<!ATTLIST %SVG.line.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.External.attrib;
+ x1 %Coordinate.datatype; #IMPLIED
+ y1 %Coordinate.datatype; #IMPLIED
+ x2 %Coordinate.datatype; #IMPLIED
+ y2 %Coordinate.datatype; #IMPLIED
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.line.attlist -->]]>
+
+<!-- ellipse: Ellipse Element .......................... -->
+
+<!ENTITY % SVG.ellipse.extra.content "" >
+
+<!ENTITY % SVG.ellipse.element "INCLUDE" >
+<![%SVG.ellipse.element;[
+<!ENTITY % SVG.ellipse.content
+ "(( %SVG.Description.class; )*, ( %SVG.Animation.class;
+ %SVG.ellipse.extra.content; )*)"
+>
+<!ELEMENT %SVG.ellipse.qname; %SVG.ellipse.content; >
+<!-- end of SVG.ellipse.element -->]]>
+
+<!ENTITY % SVG.ellipse.attlist "INCLUDE" >
+<![%SVG.ellipse.attlist;[
+<!ATTLIST %SVG.ellipse.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.External.attrib;
+ cx %Coordinate.datatype; #IMPLIED
+ cy %Coordinate.datatype; #IMPLIED
+ rx %Length.datatype; #REQUIRED
+ ry %Length.datatype; #REQUIRED
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.ellipse.attlist -->]]>
+
+<!-- polyline: Polyline Element ........................ -->
+
+<!ENTITY % SVG.polyline.extra.content "" >
+
+<!ENTITY % SVG.polyline.element "INCLUDE" >
+<![%SVG.polyline.element;[
+<!ENTITY % SVG.polyline.content
+ "(( %SVG.Description.class; )*, ( %SVG.Animation.class;
+ %SVG.polyline.extra.content; )*)"
+>
+<!ELEMENT %SVG.polyline.qname; %SVG.polyline.content; >
+<!-- end of SVG.polyline.element -->]]>
+
+<!ENTITY % SVG.polyline.attlist "INCLUDE" >
+<![%SVG.polyline.attlist;[
+<!ATTLIST %SVG.polyline.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.External.attrib;
+ points %Points.datatype; #REQUIRED
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.polyline.attlist -->]]>
+
+<!-- polygon: Polygon Element .......................... -->
+
+<!ENTITY % SVG.polygon.extra.content "" >
+
+<!ENTITY % SVG.polygon.element "INCLUDE" >
+<![%SVG.polygon.element;[
+<!ENTITY % SVG.polygon.content
+ "(( %SVG.Description.class; )*, ( %SVG.Animation.class;
+ %SVG.polygon.extra.content; )*)"
+>
+<!ELEMENT %SVG.polygon.qname; %SVG.polygon.content; >
+<!-- end of SVG.polygon.element -->]]>
+
+<!ENTITY % SVG.polygon.attlist "INCLUDE" >
+<![%SVG.polygon.attlist;[
+<!ATTLIST %SVG.polygon.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.External.attrib;
+ points %Points.datatype; #REQUIRED
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.polygon.attlist -->]]>
+
+<!-- end of svg-shape.mod -->
diff --git a/org/apache/batik/dom/svg/resources/svg-structure.mod b/org/apache/batik/dom/svg/resources/svg-structure.mod
new file mode 100644
index 0000000..d43a798
--- /dev/null
+++ b/org/apache/batik/dom/svg/resources/svg-structure.mod
@@ -0,0 +1,341 @@
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Structure Module .............................................. -->
+<!-- file: svg-structure.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg-structure.mod 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Structure//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-structure.mod"
+
+ ....................................................................... -->
+
+<!-- Structure
+
+ svg, g, defs, desc, title, metadata, symbol, use
+
+ This module declares the major structural elements and their attributes.
+-->
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.svg.qname "svg" >
+<!ENTITY % SVG.g.qname "g" >
+<!ENTITY % SVG.defs.qname "defs" >
+<!ENTITY % SVG.desc.qname "desc" >
+<!ENTITY % SVG.title.qname "title" >
+<!ENTITY % SVG.metadata.qname "metadata" >
+<!ENTITY % SVG.symbol.qname "symbol" >
+<!ENTITY % SVG.use.qname "use" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Container.attrib "" >
+<!ENTITY % SVG.Conditional.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Viewport.attrib "" >
+<!ENTITY % SVG.Text.attrib "" >
+<!ENTITY % SVG.TextContent.attrib "" >
+<!ENTITY % SVG.Font.attrib "" >
+<!ENTITY % SVG.Paint.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Marker.attrib "" >
+<!ENTITY % SVG.Profile.attrib "" >
+<!ENTITY % SVG.Gradient.attrib "" >
+<!ENTITY % SVG.Clip.attrib "" >
+<!ENTITY % SVG.Mask.attrib "" >
+<!ENTITY % SVG.Filter.attrib "" >
+<!ENTITY % SVG.FilterColor.attrib "" >
+<!ENTITY % SVG.DocumentEvents.attrib "" >
+<!ENTITY % SVG.GraphicalEvents.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.XLinkEmbed.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Description.class ............................. -->
+
+<!ENTITY % SVG.Description.extra.class "" >
+
+<!ENTITY % SVG.Description.class
+ "%SVG.desc.qname; | %SVG.title.qname; | %SVG.metadata.qname;
+ %SVG.Description.extra.class;"
+>
+
+<!-- SVG.Use.class ..................................... -->
+
+<!ENTITY % SVG.Use.extra.class "" >
+
+<!ENTITY % SVG.Use.class
+ "| %SVG.use.qname; %SVG.Use.extra.class;"
+>
+
+<!-- SVG.Structure.class ............................... -->
+
+<!ENTITY % SVG.Structure.extra.class "" >
+
+<!ENTITY % SVG.Structure.class
+ "| %SVG.svg.qname; | %SVG.g.qname; | %SVG.defs.qname; | %SVG.symbol.qname;
+ %SVG.Use.class; %SVG.Structure.extra.class;"
+>
+
+<!-- SVG.Presentation.attrib ........................... -->
+
+<!ENTITY % SVG.Presentation.extra.attrib "" >
+
+<!ENTITY % SVG.Presentation.attrib
+ "%SVG.Container.attrib;
+ %SVG.Viewport.attrib;
+ %SVG.Text.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Profile.attrib;
+ %SVG.Gradient.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.Cursor.attrib;
+ flood-color %SVGColor.datatype; #IMPLIED
+ flood-opacity %OpacityValue.datatype; #IMPLIED
+ lighting-color %SVGColor.datatype; #IMPLIED
+ %SVG.Presentation.extra.attrib;"
+>
+
+<!-- svg: SVG Document Element ......................... -->
+
+<!ENTITY % SVG.svg.extra.content "" >
+
+<!ENTITY % SVG.svg.element "INCLUDE" >
+<![%SVG.svg.element;[
+<!ENTITY % SVG.svg.content
+ "( %SVG.Description.class; | %SVG.Animation.class; %SVG.Structure.class;
+ %SVG.Conditional.class; %SVG.Image.class; %SVG.Style.class;
+ %SVG.Shape.class; %SVG.Text.class; %SVG.Marker.class; %SVG.Profile.class;
+ %SVG.Gradient.class; %SVG.Pattern.class; %SVG.Clip.class;
+ %SVG.Mask.class; %SVG.Filter.class; %SVG.Cursor.class;
+ %SVG.Hyperlink.class; %SVG.View.class; %SVG.Script.class;
+ %SVG.Font.class; %SVG.svg.extra.content; )*"
+>
+<!ELEMENT %SVG.svg.qname; %SVG.svg.content; >
+<!-- end of SVG.svg.element -->]]>
+
+<!ENTITY % SVG.svg.attlist "INCLUDE" >
+<![%SVG.svg.attlist;[
+<!ATTLIST %SVG.svg.qname;
+ %SVG.xmlns.attrib;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.DocumentEvents.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.External.attrib;
+ x %Coordinate.datatype; #IMPLIED
+ y %Coordinate.datatype; #IMPLIED
+ width %Length.datatype; #IMPLIED
+ height %Length.datatype; #IMPLIED
+ viewBox %ViewBoxSpec.datatype; #IMPLIED
+ preserveAspectRatio %PreserveAspectRatioSpec.datatype; 'xMidYMid meet'
+ zoomAndPan ( disable | magnify ) 'magnify'
+ version %Number.datatype; #FIXED '1.1'
+ baseProfile %Text.datatype; #IMPLIED
+ contentScriptType %ContentType.datatype; 'text/ecmascript'
+ contentStyleType %ContentType.datatype; 'text/css'
+>
+<!-- end of SVG.svg.attlist -->]]>
+
+<!-- g: Group Element .................................. -->
+
+<!ENTITY % SVG.g.extra.content "" >
+
+<!ENTITY % SVG.g.element "INCLUDE" >
+<![%SVG.g.element;[
+<!ENTITY % SVG.g.content
+ "( %SVG.Description.class; | %SVG.Animation.class; %SVG.Structure.class;
+ %SVG.Conditional.class; %SVG.Image.class; %SVG.Style.class;
+ %SVG.Shape.class; %SVG.Text.class; %SVG.Marker.class; %SVG.Profile.class;
+ %SVG.Gradient.class; %SVG.Pattern.class; %SVG.Clip.class;
+ %SVG.Mask.class; %SVG.Filter.class; %SVG.Cursor.class;
+ %SVG.Hyperlink.class; %SVG.View.class; %SVG.Script.class;
+ %SVG.Font.class; %SVG.g.extra.content; )*"
+>
+<!ELEMENT %SVG.g.qname; %SVG.g.content; >
+<!-- end of SVG.g.element -->]]>
+
+<!ENTITY % SVG.g.attlist "INCLUDE" >
+<![%SVG.g.attlist;[
+<!ATTLIST %SVG.g.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.External.attrib;
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.g.attlist -->]]>
+
+<!-- defs: Definisions Element ......................... -->
+
+<!ENTITY % SVG.defs.extra.content "" >
+
+<!ENTITY % SVG.defs.element "INCLUDE" >
+<![%SVG.defs.element;[
+<!ENTITY % SVG.defs.content
+ "( %SVG.Description.class; | %SVG.Animation.class; %SVG.Structure.class;
+ %SVG.Conditional.class; %SVG.Image.class; %SVG.Style.class;
+ %SVG.Shape.class; %SVG.Text.class; %SVG.Marker.class; %SVG.Profile.class;
+ %SVG.Gradient.class; %SVG.Pattern.class; %SVG.Clip.class;
+ %SVG.Mask.class; %SVG.Filter.class; %SVG.Cursor.class;
+ %SVG.Hyperlink.class; %SVG.View.class; %SVG.Script.class;
+ %SVG.Font.class; %SVG.defs.extra.content; )*"
+>
+<!ELEMENT %SVG.defs.qname; %SVG.defs.content; >
+<!-- end of SVG.defs.element -->]]>
+
+<!ENTITY % SVG.defs.attlist "INCLUDE" >
+<![%SVG.defs.attlist;[
+<!ATTLIST %SVG.defs.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.External.attrib;
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.defs.attlist -->]]>
+
+<!-- desc: Description Element ......................... -->
+
+<!ENTITY % SVG.desc.extra.content "" >
+
+<!ENTITY % SVG.desc.element "INCLUDE" >
+<![%SVG.desc.element;[
+<!ENTITY % SVG.desc.content
+ "( #PCDATA %SVG.desc.extra.content; )*"
+>
+<!ELEMENT %SVG.desc.qname; %SVG.desc.content; >
+<!-- end of SVG.desc.element -->]]>
+
+<!ENTITY % SVG.desc.attlist "INCLUDE" >
+<![%SVG.desc.attlist;[
+<!ATTLIST %SVG.desc.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+>
+<!-- end of SVG.desc.attlist -->]]>
+
+<!-- title: Title Element .............................. -->
+
+<!ENTITY % SVG.title.extra.content "" >
+
+<!ENTITY % SVG.title.element "INCLUDE" >
+<![%SVG.title.element;[
+<!ENTITY % SVG.title.content
+ "( #PCDATA %SVG.title.extra.content; )*"
+>
+<!ELEMENT %SVG.title.qname; %SVG.title.content; >
+<!-- end of SVG.title.element -->]]>
+
+<!ENTITY % SVG.title.attlist "INCLUDE" >
+<![%SVG.title.attlist;[
+<!ATTLIST %SVG.title.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+>
+<!-- end of SVG.title.attlist -->]]>
+
+<!-- metadata: Metadata Element ........................ -->
+
+<!ENTITY % SVG.metadata.extra.content "" >
+
+<!ENTITY % SVG.metadata.element "INCLUDE" >
+<![%SVG.metadata.element;[
+<!ENTITY % SVG.metadata.content
+ "( #PCDATA %SVG.metadata.extra.content; )*"
+>
+<!ELEMENT %SVG.metadata.qname; %SVG.metadata.content; >
+<!-- end of SVG.metadata.element -->]]>
+
+<!ENTITY % SVG.metadata.attlist "INCLUDE" >
+<![%SVG.metadata.attlist;[
+<!ATTLIST %SVG.metadata.qname;
+ %SVG.Core.attrib;
+>
+<!-- end of SVG.metadata.attlist -->]]>
+
+<!-- symbol: Symbol Element ............................ -->
+
+<!ENTITY % SVG.symbol.extra.content "" >
+
+<!ENTITY % SVG.symbol.element "INCLUDE" >
+<![%SVG.symbol.element;[
+<!ENTITY % SVG.symbol.content
+ "( %SVG.Description.class; | %SVG.Animation.class; %SVG.Structure.class;
+ %SVG.Conditional.class; %SVG.Image.class; %SVG.Style.class;
+ %SVG.Shape.class; %SVG.Text.class; %SVG.Marker.class; %SVG.Profile.class;
+ %SVG.Gradient.class; %SVG.Pattern.class; %SVG.Clip.class;
+ %SVG.Mask.class; %SVG.Filter.class; %SVG.Cursor.class;
+ %SVG.Hyperlink.class; %SVG.View.class; %SVG.Script.class;
+ %SVG.Font.class; %SVG.symbol.extra.content; )*"
+>
+<!ELEMENT %SVG.symbol.qname; %SVG.symbol.content; >
+<!-- end of SVG.symbol.element -->]]>
+
+<!ENTITY % SVG.symbol.attlist "INCLUDE" >
+<![%SVG.symbol.attlist;[
+<!ATTLIST %SVG.symbol.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.External.attrib;
+ viewBox %ViewBoxSpec.datatype; #IMPLIED
+ preserveAspectRatio %PreserveAspectRatioSpec.datatype; 'xMidYMid meet'
+>
+<!-- end of SVG.symbol.attlist -->]]>
+
+<!-- use: Use Element .................................. -->
+
+<!ENTITY % SVG.use.extra.content "" >
+
+<!ENTITY % SVG.use.element "INCLUDE" >
+<![%SVG.use.element;[
+<!ENTITY % SVG.use.content
+ "(( %SVG.Description.class; )*, ( %SVG.Animation.class;
+ %SVG.use.extra.content; )*)"
+>
+<!ELEMENT %SVG.use.qname; %SVG.use.content; >
+<!-- end of SVG.use.element -->]]>
+
+<!ENTITY % SVG.use.attlist "INCLUDE" >
+<![%SVG.use.attlist;[
+<!ATTLIST %SVG.use.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.XLinkEmbed.attrib;
+ %SVG.External.attrib;
+ x %Coordinate.datatype; #IMPLIED
+ y %Coordinate.datatype; #IMPLIED
+ width %Length.datatype; #IMPLIED
+ height %Length.datatype; #IMPLIED
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.use.attlist -->]]>
+
+<!-- end of svg-structure.mod -->
diff --git a/org/apache/batik/dom/svg/resources/svg-style.mod b/org/apache/batik/dom/svg/resources/svg-style.mod
new file mode 100644
index 0000000..79fe614
--- /dev/null
+++ b/org/apache/batik/dom/svg/resources/svg-style.mod
@@ -0,0 +1,81 @@
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Style Module .................................................. -->
+<!-- file: svg-style.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg-style.mod 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Style//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-style.mod"
+
+ ....................................................................... -->
+
+<!-- Style
+
+ style
+
+ This module declares markup to provide support for stylesheet.
+-->
+
+<!-- list of classes -->
+<!ENTITY % ClassList.datatype "CDATA" >
+
+<!-- comma-separated list of media descriptors. -->
+<!ENTITY % MediaDesc.datatype "CDATA" >
+
+<!-- style sheet data -->
+<!ENTITY % StyleSheet.datatype "CDATA" >
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.style.qname "style" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+
+<!-- SVG.Style.class ................................... -->
+
+<!ENTITY % SVG.Style.extra.class "" >
+
+<!ENTITY % SVG.Style.class
+ "| %SVG.style.qname; %SVG.Style.extra.class;"
+>
+
+<!-- SVG.Style.attrib .................................. -->
+
+<!ENTITY % SVG.Style.extra.attrib "" >
+
+<!ENTITY % SVG.Style.attrib
+ "style %StyleSheet.datatype; #IMPLIED
+ class %ClassList.datatype; #IMPLIED
+ %SVG.Style.extra.attrib;"
+>
+
+<!-- style: Style Element .............................. -->
+
+<!ENTITY % SVG.style.extra.content "" >
+
+<!ENTITY % SVG.style.element "INCLUDE" >
+<![%SVG.style.element;[
+<!ENTITY % SVG.style.content
+ "( #PCDATA %SVG.style.extra.content; )*"
+>
+<!ELEMENT %SVG.style.qname; %SVG.style.content; >
+<!-- end of SVG.style.element -->]]>
+
+<!ENTITY % SVG.style.attlist "INCLUDE" >
+<![%SVG.style.attlist;[
+<!ATTLIST %SVG.style.qname;
+ xml:space ( preserve ) #FIXED 'preserve'
+ %SVG.Core.attrib;
+ type %ContentType.datatype; #REQUIRED
+ media %MediaDesc.datatype; #IMPLIED
+ title %Text.datatype; #IMPLIED
+>
+<!-- end of SVG.style.attlist -->]]>
+
+<!-- end of svg-style.mod -->
diff --git a/org/apache/batik/dom/svg/resources/svg-text.mod b/org/apache/batik/dom/svg/resources/svg-text.mod
new file mode 100644
index 0000000..59c4329
--- /dev/null
+++ b/org/apache/batik/dom/svg/resources/svg-text.mod
@@ -0,0 +1,428 @@
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Text Module ................................................... -->
+<!-- file: svg-text.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg-text.mod 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Text//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-text.mod"
+
+ ....................................................................... -->
+
+<!-- Text
+
+ text, tspan, tref, textPath, altGlyph, altGlyphDef, altGlyphItem,
+ glyphRef
+
+ This module declares markup to provide support for alternate glyph.
+-->
+
+<!-- 'baseline-shift' property/attribute value (e.g., 'baseline', 'sub', etc.) -->
+<!ENTITY % BaselineShiftValue.datatype "CDATA" >
+
+<!-- 'font-family' property/attribute value (i.e., list of fonts) -->
+<!ENTITY % FontFamilyValue.datatype "CDATA" >
+
+<!-- 'font-size' property/attribute value -->
+<!ENTITY % FontSizeValue.datatype "CDATA" >
+
+<!-- 'font-size-adjust' property/attribute value -->
+<!ENTITY % FontSizeAdjustValue.datatype "CDATA" >
+
+<!-- 'glyph-orientation-horizontal' property/attribute value (e.g., <angle>) -->
+<!ENTITY % GlyphOrientationHorizontalValue.datatype "CDATA" >
+
+<!-- 'glyph-orientation-vertical' property/attribute value (e.g., 'auto', <angle>) -->
+<!ENTITY % GlyphOrientationVerticalValue.datatype "CDATA" >
+
+<!-- 'kerning' property/attribute value (e.g., 'auto', <length>) -->
+<!ENTITY % KerningValue.datatype "CDATA" >
+
+<!-- 'letter-spacing' or 'word-spacing' property/attribute value (e.g., 'normal', <length>) -->
+<!ENTITY % SpacingValue.datatype "CDATA" >
+
+<!-- 'text-decoration' property/attribute value (e.g., 'none', 'underline') -->
+<!ENTITY % TextDecorationValue.datatype "CDATA" >
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.text.qname "text" >
+<!ENTITY % SVG.tspan.qname "tspan" >
+<!ENTITY % SVG.tref.qname "tref" >
+<!ENTITY % SVG.textPath.qname "textPath" >
+<!ENTITY % SVG.altGlyph.qname "altGlyph" >
+<!ENTITY % SVG.altGlyphDef.qname "altGlyphDef" >
+<!ENTITY % SVG.altGlyphItem.qname "altGlyphItem" >
+<!ENTITY % SVG.glyphRef.qname "glyphRef" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Conditional.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Paint.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Clip.attrib "" >
+<!ENTITY % SVG.Mask.attrib "" >
+<!ENTITY % SVG.Filter.attrib "" >
+<!ENTITY % SVG.GraphicalEvents.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.XLink.attrib "" >
+<!ENTITY % SVG.XLinkRequired.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Text.class .................................... -->
+
+<!ENTITY % SVG.Text.extra.class "" >
+
+<!ENTITY % SVG.Text.class
+ "| %SVG.text.qname; | %SVG.altGlyphDef.qname; %SVG.Text.extra.class;"
+>
+
+<!-- SVG.TextContent.class ............................. -->
+
+<!ENTITY % SVG.TextContent.extra.class "" >
+
+<!ENTITY % SVG.TextContent.class
+ "| %SVG.tspan.qname; | %SVG.tref.qname; | %SVG.textPath.qname;
+ | %SVG.altGlyph.qname; %SVG.TextContent.extra.class;"
+>
+
+<!-- SVG.Text.attrib ................................... -->
+
+<!ENTITY % SVG.Text.extra.attrib "" >
+
+<!ENTITY % SVG.Text.attrib
+ "writing-mode ( lr-tb | rl-tb | tb-rl | lr | rl | tb | inherit ) #IMPLIED
+ %SVG.Text.extra.attrib;"
+>
+
+<!-- SVG.TextContent.attrib ............................ -->
+
+<!ENTITY % SVG.TextContent.extra.attrib "" >
+
+<!ENTITY % SVG.TextContent.attrib
+ "alignment-baseline ( auto | baseline | before-edge | text-before-edge |
+ middle | central | after-edge | text-after-edge |
+ ideographic | alphabetic | hanging | mathematical |
+ inherit ) #IMPLIED
+ baseline-shift %BaselineShiftValue.datatype; #IMPLIED
+ direction ( ltr | rtl | inherit ) #IMPLIED
+ dominant-baseline ( auto | use-script | no-change | reset-size |
+ ideographic | alphabetic | hanging | mathematical |
+ central | middle | text-after-edge | text-before-edge |
+ inherit ) #IMPLIED
+ glyph-orientation-horizontal %GlyphOrientationHorizontalValue.datatype;
+ #IMPLIED
+ glyph-orientation-vertical %GlyphOrientationVerticalValue.datatype;
+ #IMPLIED
+ kerning %KerningValue.datatype; #IMPLIED
+ letter-spacing %SpacingValue.datatype; #IMPLIED
+ text-anchor ( start | middle | end | inherit ) #IMPLIED
+ text-decoration %TextDecorationValue.datatype; #IMPLIED
+ unicode-bidi ( normal | embed | bidi-override | inherit ) #IMPLIED
+ word-spacing %SpacingValue.datatype; #IMPLIED
+ %SVG.TextContent.extra.attrib;"
+>
+
+<!-- SVG.Font.attrib ................................... -->
+
+<!ENTITY % SVG.Font.extra.attrib "" >
+
+<!ENTITY % SVG.Font.attrib
+ "font-family %FontFamilyValue.datatype; #IMPLIED
+ font-size %FontSizeValue.datatype; #IMPLIED
+ font-size-adjust %FontSizeAdjustValue.datatype; #IMPLIED
+ font-stretch ( normal | wider | narrower | ultra-condensed |
+ extra-condensed | condensed | semi-condensed |
+ semi-expanded | expanded | extra-expanded |
+ ultra-expanded | inherit ) #IMPLIED
+ font-style ( normal | italic | oblique | inherit ) #IMPLIED
+ font-variant ( normal | small-caps | inherit ) #IMPLIED
+ font-weight ( normal | bold | bolder | lighter | 100 | 200 | 300 | 400 |
+ 500 | 600 | 700 | 800 | 900 | inherit ) #IMPLIED
+ %SVG.Font.extra.attrib;"
+>
+
+<!-- text: Text Element ................................ -->
+
+<!ENTITY % SVG.text.extra.content "" >
+
+<!ENTITY % SVG.text.element "INCLUDE" >
+<![%SVG.text.element;[
+<!ENTITY % SVG.text.content
+ "( #PCDATA | %SVG.Description.class; | %SVG.Animation.class;
+ %SVG.TextContent.class; %SVG.Hyperlink.class;
+ %SVG.text.extra.content; )*"
+>
+<!ELEMENT %SVG.text.qname; %SVG.text.content; >
+<!-- end of SVG.text.element -->]]>
+
+<!ENTITY % SVG.text.attlist "INCLUDE" >
+<![%SVG.text.attlist;[
+<!ATTLIST %SVG.text.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Text.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.External.attrib;
+ x %Coordinates.datatype; #IMPLIED
+ y %Coordinates.datatype; #IMPLIED
+ dx %Lengths.datatype; #IMPLIED
+ dy %Lengths.datatype; #IMPLIED
+ rotate %Numbers.datatype; #IMPLIED
+ textLength %Length.datatype; #IMPLIED
+ lengthAdjust ( spacing | spacingAndGlyphs ) #IMPLIED
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.text.attlist -->]]>
+
+<!-- tspan: Text Span Element .......................... -->
+
+<!ENTITY % SVG.tspan.extra.content "" >
+
+<!ENTITY % SVG.tspan.element "INCLUDE" >
+<![%SVG.tspan.element;[
+<!ENTITY % SVG.tspan.content
+ "( #PCDATA | %SVG.tspan.qname; | %SVG.tref.qname; | %SVG.altGlyph.qname;
+ | %SVG.animate.qname; | %SVG.set.qname; | %SVG.animateColor.qname;
+ | %SVG.Description.class; %SVG.Hyperlink.class;
+ %SVG.tspan.extra.content; )*"
+>
+<!ELEMENT %SVG.tspan.qname; %SVG.tspan.content; >
+<!-- end of SVG.tspan.element -->]]>
+
+<!ENTITY % SVG.tspan.attlist "INCLUDE" >
+<![%SVG.tspan.attlist;[
+<!ATTLIST %SVG.tspan.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.External.attrib;
+ x %Coordinates.datatype; #IMPLIED
+ y %Coordinates.datatype; #IMPLIED
+ dx %Lengths.datatype; #IMPLIED
+ dy %Lengths.datatype; #IMPLIED
+ rotate %Numbers.datatype; #IMPLIED
+ textLength %Length.datatype; #IMPLIED
+ lengthAdjust ( spacing | spacingAndGlyphs ) #IMPLIED
+>
+<!-- end of SVG.tspan.attlist -->]]>
+
+<!-- tref: Text Reference Element ...................... -->
+
+<!ENTITY % SVG.tref.extra.content "" >
+
+<!ENTITY % SVG.tref.element "INCLUDE" >
+<![%SVG.tref.element;[
+<!ENTITY % SVG.tref.content
+ "( %SVG.animate.qname; | %SVG.set.qname; | %SVG.animateColor.qname;
+ | %SVG.Description.class; %SVG.tref.extra.content; )*"
+>
+<!ELEMENT %SVG.tref.qname; %SVG.tref.content; >
+<!-- end of SVG.tref.element -->]]>
+
+<!ENTITY % SVG.tref.attlist "INCLUDE" >
+<![%SVG.tref.attlist;[
+<!ATTLIST %SVG.tref.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.XLinkRequired.attrib;
+ %SVG.External.attrib;
+ x %Coordinates.datatype; #IMPLIED
+ y %Coordinates.datatype; #IMPLIED
+ dx %Lengths.datatype; #IMPLIED
+ dy %Lengths.datatype; #IMPLIED
+ rotate %Numbers.datatype; #IMPLIED
+ textLength %Length.datatype; #IMPLIED
+ lengthAdjust ( spacing | spacingAndGlyphs ) #IMPLIED
+>
+<!-- end of SVG.tref.attlist -->]]>
+
+<!-- textPath: Text Path Element ....................... -->
+
+<!ENTITY % SVG.textPath.extra.content "" >
+
+<!ENTITY % SVG.textPath.element "INCLUDE" >
+<![%SVG.textPath.element;[
+<!ENTITY % SVG.textPath.content
+ "( #PCDATA | %SVG.tspan.qname; | %SVG.tref.qname; | %SVG.altGlyph.qname;
+ | %SVG.animate.qname; | %SVG.set.qname; | %SVG.animateColor.qname;
+ | %SVG.Description.class; %SVG.Hyperlink.class;
+ %SVG.textPath.extra.content; )*"
+>
+<!ELEMENT %SVG.textPath.qname; %SVG.textPath.content; >
+<!-- end of SVG.textPath.element -->]]>
+
+<!ENTITY % SVG.textPath.attlist "INCLUDE" >
+<![%SVG.textPath.attlist;[
+<!ATTLIST %SVG.textPath.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.XLinkRequired.attrib;
+ %SVG.External.attrib;
+ startOffset %Length.datatype; #IMPLIED
+ textLength %Length.datatype; #IMPLIED
+ lengthAdjust ( spacing | spacingAndGlyphs ) #IMPLIED
+ method ( align | stretch ) #IMPLIED
+ spacing ( auto | exact ) #IMPLIED
+>
+<!-- end of SVG.textPath.attlist -->]]>
+
+<!-- altGlyph: Alternate Glyph Element ................. -->
+
+<!ENTITY % SVG.altGlyph.extra.content "" >
+
+<!ENTITY % SVG.altGlyph.element "INCLUDE" >
+<![%SVG.altGlyph.element;[
+<!ENTITY % SVG.altGlyph.content
+ "( #PCDATA %SVG.altGlyph.extra.content; )*"
+>
+<!ELEMENT %SVG.altGlyph.qname; %SVG.altGlyph.content; >
+<!-- end of SVG.altGlyph.element -->]]>
+
+<!ENTITY % SVG.altGlyph.attlist "INCLUDE" >
+<![%SVG.altGlyph.attlist;[
+<!ATTLIST %SVG.altGlyph.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.XLink.attrib;
+ %SVG.External.attrib;
+ x %Coordinates.datatype; #IMPLIED
+ y %Coordinates.datatype; #IMPLIED
+ dx %Lengths.datatype; #IMPLIED
+ dy %Lengths.datatype; #IMPLIED
+ glyphRef CDATA #IMPLIED
+ format CDATA #IMPLIED
+ rotate %Numbers.datatype; #IMPLIED
+>
+<!-- end of SVG.altGlyph.attlist -->]]>
+
+<!-- altGlyphDef: Alternate Glyph Definition Element ... -->
+
+<!ENTITY % SVG.altGlyphDef.extra.content "" >
+
+<!ENTITY % SVG.altGlyphDef.element "INCLUDE" >
+<![%SVG.altGlyphDef.element;[
+<!ENTITY % SVG.altGlyphDef.content
+ "(( %SVG.glyphRef.qname;+ | %SVG.altGlyphItem.qname;+ )
+ %SVG.altGlyphDef.extra.content; )"
+>
+<!ELEMENT %SVG.altGlyphDef.qname; %SVG.altGlyphDef.content; >
+<!-- end of SVG.altGlyphDef.element -->]]>
+
+<!ENTITY % SVG.altGlyphDef.attlist "INCLUDE" >
+<![%SVG.altGlyphDef.attlist;[
+<!ATTLIST %SVG.altGlyphDef.qname;
+ %SVG.Core.attrib;
+>
+<!-- end of SVG.altGlyphDef.attlist -->]]>
+
+<!-- altGlyphItem: Alternate Glyph Item Element ........ -->
+
+<!ENTITY % SVG.altGlyphItem.extra.content "" >
+
+<!ENTITY % SVG.altGlyphItem.element "INCLUDE" >
+<![%SVG.altGlyphItem.element;[
+<!ENTITY % SVG.altGlyphItem.content
+ "( %SVG.glyphRef.qname;+ %SVG.altGlyphItem.extra.content; )"
+>
+<!ELEMENT %SVG.altGlyphItem.qname; %SVG.altGlyphItem.content; >
+<!-- end of SVG.altGlyphItem.element -->]]>
+
+<!ENTITY % SVG.altGlyphItem.attlist "INCLUDE" >
+<![%SVG.altGlyphItem.attlist;[
+<!ATTLIST %SVG.altGlyphItem.qname;
+ %SVG.Core.attrib;
+>
+<!-- end of SVG.altGlyphItem.attlist -->]]>
+
+<!-- glyphRef: Glyph Reference Element ................. -->
+
+<!ENTITY % SVG.glyphRef.element "INCLUDE" >
+<![%SVG.glyphRef.element;[
+<!ENTITY % SVG.glyphRef.content "EMPTY" >
+<!ELEMENT %SVG.glyphRef.qname; %SVG.glyphRef.content; >
+<!-- end of SVG.glyphRef.element -->]]>
+
+<!ENTITY % SVG.glyphRef.attlist "INCLUDE" >
+<![%SVG.glyphRef.attlist;[
+<!ATTLIST %SVG.glyphRef.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Font.attrib;
+ %SVG.XLink.attrib;
+ x %Number.datatype; #IMPLIED
+ y %Number.datatype; #IMPLIED
+ dx %Number.datatype; #IMPLIED
+ dy %Number.datatype; #IMPLIED
+ glyphRef CDATA #IMPLIED
+ format CDATA #IMPLIED
+>
+<!-- end of SVG.glyphRef.attlist -->]]>
+
+<!-- end of svg-text.mod -->
diff --git a/org/apache/batik/dom/svg/resources/svg-view.mod b/org/apache/batik/dom/svg/resources/svg-view.mod
new file mode 100644
index 0000000..0448817
--- /dev/null
+++ b/org/apache/batik/dom/svg/resources/svg-view.mod
@@ -0,0 +1,64 @@
+<!-- ....................................................................... -->
+<!-- SVG 1.1 View Module ................................................... -->
+<!-- file: svg-view.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg-view.mod 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 View//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-view.mod"
+
+ ....................................................................... -->
+
+<!-- View
+
+ view
+
+ This module declares markup to provide support for view.
+-->
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.view.qname "view" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.View.class .................................... -->
+
+<!ENTITY % SVG.View.extra.class "" >
+
+<!ENTITY % SVG.View.class
+ "| %SVG.view.qname; %SVG.View.extra.class;"
+>
+
+<!-- view: View Element ................................ -->
+
+<!ENTITY % SVG.view.extra.content "" >
+
+<!ENTITY % SVG.view.element "INCLUDE" >
+<![%SVG.view.element;[
+<!ENTITY % SVG.view.content
+ "( %SVG.Description.class; %SVG.view.extra.content; )*"
+>
+<!ELEMENT %SVG.view.qname; %SVG.view.content; >
+<!-- end of SVG.view.element -->]]>
+
+<!ENTITY % SVG.view.attlist "INCLUDE" >
+<![%SVG.view.attlist;[
+<!ATTLIST %SVG.view.qname;
+ %SVG.Core.attrib;
+ %SVG.External.attrib;
+ viewBox %ViewBoxSpec.datatype; #IMPLIED
+ preserveAspectRatio %PreserveAspectRatioSpec.datatype; 'xMidYMid meet'
+ zoomAndPan ( disable | magnify ) 'magnify'
+ viewTarget CDATA #IMPLIED
+>
+<!-- end of SVG.view.attlist -->]]>
+
+<!-- end of svg-view.mod -->
diff --git a/org/apache/batik/dom/svg/resources/svg-viewport-attrib.mod b/org/apache/batik/dom/svg/resources/svg-viewport-attrib.mod
new file mode 100644
index 0000000..6289ec6
--- /dev/null
+++ b/org/apache/batik/dom/svg/resources/svg-viewport-attrib.mod
@@ -0,0 +1,42 @@
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Viewport Attribute Module ..................................... -->
+<!-- file: svg-viewport-attrib.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg-viewport-attrib.mod 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Viewport Attribute//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-viewport-attrib.mod"
+
+ ....................................................................... -->
+
+<!-- Viewport Attribute
+
+ clip, overflow
+
+ This module defines the Viewport attribute set.
+-->
+
+<!-- 'clip' property/attribute value (e.g., 'auto', rect(...)) -->
+<!ENTITY % ClipValue.datatype "CDATA" >
+
+<!ENTITY % SVG.clip.attrib
+ "clip %ClipValue.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.overflow.attrib
+ "overflow ( visible | hidden | scroll | auto | inherit ) #IMPLIED"
+>
+
+<!ENTITY % SVG.Viewport.extra.attrib "" >
+
+<!ENTITY % SVG.Viewport.attrib
+ "%SVG.clip.attrib;
+ %SVG.overflow.attrib;
+ %SVG.Viewport.extra.attrib;"
+>
+
+<!-- end of svg-viewport-attrib.mod -->
diff --git a/org/apache/batik/dom/svg/resources/svg-xlink-attrib.mod b/org/apache/batik/dom/svg/resources/svg-xlink-attrib.mod
new file mode 100644
index 0000000..5845a65
--- /dev/null
+++ b/org/apache/batik/dom/svg/resources/svg-xlink-attrib.mod
@@ -0,0 +1,80 @@
+<!-- ....................................................................... -->
+<!-- SVG 1.1 XLink Attribute Module ........................................ -->
+<!-- file: svg-xlink-attrib.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg-xlink-attrib.mod 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 XLink Attribute//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-xlink-attrib.mod"
+
+ ....................................................................... -->
+
+<!-- XLink Attribute
+
+ type, href, role, arcrole, title, show, actuate
+
+ This module defines the XLink, XLinkRequired, XLinkEmbed, and
+ XLinkReplace attribute set.
+-->
+
+<!ENTITY % SVG.XLink.extra.attrib "" >
+
+<!ENTITY % SVG.XLink.attrib
+ "%XLINK.xmlns.attrib;
+ %XLINK.pfx;type ( simple ) #FIXED 'simple'
+ %XLINK.pfx;href %URI.datatype; #IMPLIED
+ %XLINK.pfx;role %URI.datatype; #IMPLIED
+ %XLINK.pfx;arcrole %URI.datatype; #IMPLIED
+ %XLINK.pfx;title CDATA #IMPLIED
+ %XLINK.pfx;show ( other ) 'other'
+ %XLINK.pfx;actuate ( onLoad ) #FIXED 'onLoad'
+ %SVG.XLink.extra.attrib;"
+>
+
+<!ENTITY % SVG.XLinkRequired.extra.attrib "" >
+
+<!ENTITY % SVG.XLinkRequired.attrib
+ "%XLINK.xmlns.attrib;
+ %XLINK.pfx;type ( simple ) #FIXED 'simple'
+ %XLINK.pfx;href %URI.datatype; #REQUIRED
+ %XLINK.pfx;role %URI.datatype; #IMPLIED
+ %XLINK.pfx;arcrole %URI.datatype; #IMPLIED
+ %XLINK.pfx;title CDATA #IMPLIED
+ %XLINK.pfx;show ( other ) 'other'
+ %XLINK.pfx;actuate ( onLoad ) #FIXED 'onLoad'
+ %SVG.XLinkRequired.extra.attrib;"
+>
+
+<!ENTITY % SVG.XLinkEmbed.extra.attrib "" >
+
+<!ENTITY % SVG.XLinkEmbed.attrib
+ "%XLINK.xmlns.attrib;
+ %XLINK.pfx;type ( simple ) #FIXED 'simple'
+ %XLINK.pfx;href %URI.datatype; #REQUIRED
+ %XLINK.pfx;role %URI.datatype; #IMPLIED
+ %XLINK.pfx;arcrole %URI.datatype; #IMPLIED
+ %XLINK.pfx;title CDATA #IMPLIED
+ %XLINK.pfx;show ( embed ) 'embed'
+ %XLINK.pfx;actuate ( onLoad ) #FIXED 'onLoad'
+ %SVG.XLinkEmbed.extra.attrib;"
+>
+
+<!ENTITY % SVG.XLinkReplace.extra.attrib "" >
+
+<!ENTITY % SVG.XLinkReplace.attrib
+ "%XLINK.xmlns.attrib;
+ %XLINK.pfx;type ( simple ) #FIXED 'simple'
+ %XLINK.pfx;href %URI.datatype; #REQUIRED
+ %XLINK.pfx;role %URI.datatype; #IMPLIED
+ %XLINK.pfx;arcrole %URI.datatype; #IMPLIED
+ %XLINK.pfx;title CDATA #IMPLIED
+ %XLINK.pfx;show ( new | replace ) 'replace'
+ %XLINK.pfx;actuate ( onRequest ) #FIXED 'onRequest'
+ %SVG.XLinkReplace.extra.attrib;"
+>
+
+<!-- end of svg-xlink-attrib.mod -->
diff --git a/org/apache/batik/dom/svg/resources/svg10.dtd b/org/apache/batik/dom/svg/resources/svg10.dtd
new file mode 100644
index 0000000..146290f
--- /dev/null
+++ b/org/apache/batik/dom/svg/resources/svg10.dtd
@@ -0,0 +1,1539 @@
+<!-- =====================================================================
+ This is the DTD for SVG 1.0.
+
+ The specification for SVG that corresponds to this DTD is available at:
+
+ http://www.w3.org/TR/2001/REC-SVG-20010904/
+
+ Copyright (c) 2000 W3C (MIT, INRIA, Keio), All Rights Reserved.
+
+ For SVG 1.0:
+
+ Namespace:
+ http://www.w3.org/2000/svg
+
+ Public identifier:
+ PUBLIC "-//W3C//DTD SVG 1.0//EN"
+
+ URI for the DTD:
+ http://www.w3.org/TR/2001/REC-SVG-20010904/DTD/svg10.dtd
+============================================================================= -->
+<!-- ==============================================================
+ ENTITY DECLARATIONS: Data types
+ ============================================================== -->
+<!ENTITY % BaselineShiftValue "CDATA">
+<!-- 'baseline-shift' property/attribute value (e.g., 'baseline', 'sub', etc.) -->
+<!ENTITY % Boolean "(false | true)">
+<!-- feature specification -->
+<!ENTITY % ClassList "CDATA">
+<!-- list of classes -->
+<!ENTITY % ClipValue "CDATA">
+<!-- 'clip' property/attribute value (e.g., 'auto', rect(...)) -->
+<!ENTITY % ClipPathValue "CDATA">
+<!-- 'clip-path' property/attribute value (e.g., 'none', %URI;) -->
+<!ENTITY % ClipFillRule "(nonzero | evenodd | inherit)">
+<!-- 'clip-rule' or fill-rule property/attribute value -->
+<!ENTITY % ContentType "CDATA">
+<!-- media type, as per [RFC2045] -->
+<!ENTITY % Coordinate "CDATA">
+<!-- a <coordinate> -->
+<!ENTITY % Coordinates "CDATA">
+<!-- a list of <coordinate>s -->
+<!ENTITY % Color "CDATA">
+<!-- a <color> value -->
+<!ENTITY % CursorValue "CDATA">
+<!-- 'cursor' property/attribute value (e.g., 'crosshair', %URI;) -->
+<!ENTITY % EnableBackgroundValue "CDATA">
+<!-- 'enable-background' property/attribute value (e.g., 'new', 'accumulate') -->
+<!ENTITY % ExtensionList "CDATA">
+<!-- extension list specification -->
+<!ENTITY % FeatureList "CDATA">
+<!-- feature list specification -->
+<!ENTITY % FilterValue "CDATA">
+<!-- 'filter' property/attribute value (e.g., 'none', %URI;) -->
+<!ENTITY % FontFamilyValue "CDATA">
+<!-- 'font-family' property/attribute value (i.e., list of fonts) -->
+<!ENTITY % FontSizeValue "CDATA">
+<!-- 'font-size' property/attribute value -->
+<!ENTITY % FontSizeAdjustValue "CDATA">
+<!-- 'font-size-adjust' property/attribute value -->
+<!ENTITY % GlyphOrientationHorizontalValue "CDATA">
+<!-- 'glyph-orientation-horizontal' property/attribute value (e.g., <angle>) -->
+<!ENTITY % GlyphOrientationVerticalValue "CDATA">
+<!-- 'glyph-orientation-vertical' property/attribute value (e.g., 'auto', <angle>) -->
+<!ENTITY % Integer "CDATA">
+<!-- a <integer> -->
+<!ENTITY % KerningValue "CDATA">
+<!-- 'kerning' property/attribute value (e.g., auto | <length>) -->
+<!ENTITY % LanguageCode "NMTOKEN">
+<!-- a language code, as per [RFC3066] -->
+<!ENTITY % LanguageCodes "CDATA">
+<!-- comma-separated list of language codes, as per [RFC3066] -->
+<!ENTITY % Length "CDATA">
+<!-- a <length> -->
+<!ENTITY % Lengths "CDATA">
+<!-- a list of <length>s -->
+<!ENTITY % LinkTarget "NMTOKEN">
+<!-- link to this target -->
+<!ENTITY % MarkerValue "CDATA">
+<!-- 'marker' property/attribute value (e.g., 'none', %URI;) -->
+<!ENTITY % MaskValue "CDATA">
+<!-- 'mask' property/attribute value (e.g., 'none', %URI;) -->
+<!ENTITY % MediaDesc "CDATA">
+<!-- comma-separated list of media descriptors. -->
+<!ENTITY % Number "CDATA">
+<!-- a <number> -->
+<!ENTITY % NumberOptionalNumber "CDATA">
+<!-- list of <number>s, but at least one and at most two -->
+<!ENTITY % NumberOrPercentage "CDATA">
+<!-- a <number> or a <percentage> -->
+<!ENTITY % Numbers "CDATA">
+<!-- a list of <number>s -->
+<!ENTITY % OpacityValue "CDATA">
+<!-- opacity value (e.g., <number>) -->
+<!ENTITY % Paint "CDATA">
+<!-- a 'fill' or 'stroke' property/attribute value: <paint> -->
+<!ENTITY % PathData "CDATA">
+<!-- a path data specification -->
+<!ENTITY % Points "CDATA">
+<!-- a list of points -->
+<!ENTITY % PreserveAspectRatioSpec "CDATA">
+<!-- 'preserveAspectRatio' attribute specification -->
+<!ENTITY % Script "CDATA">
+<!-- script expression -->
+<!ENTITY % SpacingValue "CDATA">
+<!-- 'letter-spacing' or 'word-spacing' property/attribute value (e.g., normal | <length>) -->
+<!ENTITY % StrokeDashArrayValue "CDATA">
+<!-- 'stroke-dasharray' property/attribute value (e.g., 'none', list of <number>s) -->
+<!ENTITY % StrokeDashOffsetValue "CDATA">
+<!-- 'stroke-dashoffset' property/attribute value (e.g., 'none', <legnth>) -->
+<!ENTITY % StrokeMiterLimitValue "CDATA">
+<!-- 'stroke-miterlimit' property/attribute value (e.g., <number>) -->
+<!ENTITY % StrokeWidthValue "CDATA">
+<!-- 'stroke-width' property/attribute value (e.g., <length>) -->
+<!ENTITY % StructuredText "content CDATA #FIXED 'structured text'">
+<!ENTITY % StyleSheet "CDATA">
+<!-- style sheet data -->
+<!ENTITY % SVGColor "CDATA">
+<!-- An SVG color value (RGB plus optional ICC) -->
+<!ENTITY % Text "CDATA">
+<!-- arbitrary text string -->
+<!ENTITY % TextDecorationValue "CDATA">
+<!-- 'text-decoration' property/attribute value (e.g., 'none', 'underline') -->
+<!ENTITY % TransformList "CDATA">
+<!-- list of transforms -->
+<!ENTITY % URI "CDATA">
+<!-- a Uniform Resource Identifier, see [URI] -->
+<!ENTITY % ViewBoxSpec "CDATA">
+<!-- 'viewBox' attribute specification -->
+<!-- ==============================================================
+ ENTITY DECLARATIONS: Collections of common attributes
+ ============================================================== -->
+<!-- All elements have an ID. -->
+<!ENTITY % stdAttrs "id ID #IMPLIED
+ xml:base %URI; #IMPLIED">
+<!-- Common attributes for elements that might contain character data content. -->
+<!ENTITY % langSpaceAttrs "xml:lang %LanguageCode; #IMPLIED
+ xml:space (default|preserve) #IMPLIED">
+<!-- Common attributes to check for system capabilities. -->
+<!ENTITY % testAttrs "requiredFeatures %FeatureList; #IMPLIED
+ requiredExtensions %ExtensionList; #IMPLIED
+ systemLanguage %LanguageCodes; #IMPLIED">
+<!-- For most uses of URI referencing:
+ standard XLink attributes other than xlink:href. -->
+<!ENTITY % xlinkRefAttrs "xmlns:xlink CDATA #FIXED 'http://www.w3.org/1999/xlink'
+ xlink:type (simple) #FIXED 'simple'
+ xlink:role %URI; #IMPLIED
+ xlink:arcrole %URI; #IMPLIED
+ xlink:title CDATA #IMPLIED
+ xlink:show (other) 'other'
+ xlink:actuate (onLoad) #FIXED 'onLoad'">
+<!-- Standard XLink attributes for uses of URI referencing where xlink:show is 'embed' -->
+<!ENTITY % xlinkRefAttrsEmbed "xmlns:xlink CDATA #FIXED 'http://www.w3.org/1999/xlink'
+ xlink:type (simple) #FIXED 'simple'
+ xlink:role %URI; #IMPLIED
+ xlink:arcrole %URI; #IMPLIED
+ xlink:title CDATA #IMPLIED
+ xlink:show (embed) 'embed'
+ xlink:actuate (onLoad) #FIXED 'onLoad'">
+<!ENTITY % graphicsElementEvents "onfocusin %Script; #IMPLIED
+ onfocusout %Script; #IMPLIED
+ onactivate %Script; #IMPLIED
+ onclick %Script; #IMPLIED
+ onmousedown %Script; #IMPLIED
+ onmouseup %Script; #IMPLIED
+ onmouseover %Script; #IMPLIED
+ onmousemove %Script; #IMPLIED
+ onmouseout %Script; #IMPLIED
+ onload %Script; #IMPLIED">
+<!ENTITY % documentEvents "onunload %Script; #IMPLIED
+ onabort %Script; #IMPLIED
+ onerror %Script; #IMPLIED
+ onresize %Script; #IMPLIED
+ onscroll %Script; #IMPLIED
+ onzoom %Script; #IMPLIED">
+<!ENTITY % animationEvents "onbegin %Script; #IMPLIED
+ onend %Script; #IMPLIED
+ onrepeat %Script; #IMPLIED">
+<!-- This entity allows for at most one of desc, title and metadata,
+ supplied in any order -->
+<!ENTITY % descTitleMetadata "(((desc,((title,metadata?)|(metadata,title?))?)|
+ (title,((desc,metadata?)|(metadata,desc?))?)|
+ (metadata,((desc,title?)|(title,desc?))?))?)">
+<!-- ==============================================================
+ ENTITY DECLARATIONS: Collections of presentation attributes
+ ============================================================== -->
+<!-- The following presentation attributes have to do with specifying color. -->
+<!ENTITY % PresentationAttributes-Color "color %Color; #IMPLIED
+ color-interpolation (auto | sRGB | linearRGB | inherit) #IMPLIED
+ color-rendering (auto | optimizeSpeed | optimizeQuality | inherit) #IMPLIED ">
+<!-- The following presentation attributes apply to container elements. -->
+<!ENTITY % PresentationAttributes-Containers "enable-background %EnableBackgroundValue; #IMPLIED ">
+<!-- The following presentation attributes apply to 'feFlood' elements. -->
+<!ENTITY % PresentationAttributes-feFlood "flood-color %SVGColor; #IMPLIED
+ flood-opacity %OpacityValue; #IMPLIED ">
+<!-- The following presentation attributes apply to filling and stroking operations. -->
+<!ENTITY % PresentationAttributes-FillStroke "fill %Paint; #IMPLIED
+ fill-opacity %OpacityValue; #IMPLIED
+ fill-rule %ClipFillRule; #IMPLIED
+ stroke %Paint; #IMPLIED
+ stroke-dasharray %StrokeDashArrayValue; #IMPLIED
+ stroke-dashoffset %StrokeDashOffsetValue; #IMPLIED
+ stroke-linecap (butt | round | square | inherit) #IMPLIED
+ stroke-linejoin (miter | round | bevel | inherit) #IMPLIED
+ stroke-miterlimit %StrokeMiterLimitValue; #IMPLIED
+ stroke-opacity %OpacityValue; #IMPLIED
+ stroke-width %StrokeWidthValue; #IMPLIED ">
+<!-- The following presentation attributes apply to filter primitives. -->
+<!ENTITY % PresentationAttributes-FilterPrimitives "color-interpolation-filters (auto | sRGB | linearRGB | inherit) #IMPLIED ">
+<!-- The following presentation attributes have to do with selecting a font to use. -->
+<!ENTITY % PresentationAttributes-FontSpecification "font-family %FontFamilyValue; #IMPLIED
+ font-size %FontSizeValue; #IMPLIED
+ font-size-adjust %FontSizeAdjustValue; #IMPLIED
+ font-stretch (normal | wider | narrower | ultra-condensed | extra-condensed |
+ condensed | semi-condensed | semi-expanded | expanded |
+ extra-expanded | ultra-expanded | inherit) #IMPLIED
+ font-style (normal | italic | oblique | inherit) #IMPLIED
+ font-variant (normal | small-caps | inherit) #IMPLIED
+ font-weight (normal | bold | bolder | lighter | 100 | 200 | 300 |
+ 400 | 500 | 600 | 700 | 800 | 900 | inherit) #IMPLIED ">
+<!-- The following presentation attributes apply to gradient 'stop' elements. -->
+<!ENTITY % PresentationAttributes-Gradients "stop-color %SVGColor; #IMPLIED
+ stop-opacity %OpacityValue; #IMPLIED ">
+<!-- The following presentation attributes apply to graphics elements. -->
+<!ENTITY % PresentationAttributes-Graphics "clip-path %ClipPathValue; #IMPLIED
+ clip-rule %ClipFillRule; #IMPLIED
+ cursor %CursorValue; #IMPLIED
+ display (inline | block | list-item | run-in | compact | marker |
+ table | inline-table | table-row-group | table-header-group |
+ table-footer-group | table-row | table-column-group | table-column |
+ table-cell | table-caption | none | inherit) #IMPLIED
+ filter %FilterValue; #IMPLIED
+ image-rendering (auto | optimizeSpeed | optimizeQuality | inherit) #IMPLIED
+ mask %MaskValue; #IMPLIED
+ opacity %OpacityValue; #IMPLIED
+ pointer-events (visiblePainted | visibleFill | visibleStroke | visible |
+ painted | fill | stroke | all | none | inherit) #IMPLIED
+ shape-rendering (auto | optimizeSpeed | crispEdges | geometricPrecision | inherit) #IMPLIED
+ text-rendering (auto | optimizeSpeed | optimizeLegibility | geometricPrecision | inherit) #IMPLIED
+ visibility (visible | hidden | inherit) #IMPLIED ">
+<!-- The following presentation attributes apply to 'image' elements. -->
+<!ENTITY % PresentationAttributes-Images "color-profile CDATA #IMPLIED ">
+<!--The following presentation attributes apply to 'feDiffuseLighting' and 'feSpecularLighting' elements. -->
+<!ENTITY % PresentationAttributes-LightingEffects "lighting-color %SVGColor; #IMPLIED ">
+<!-- The following presentation attributes apply to marker operations. -->
+<!ENTITY % PresentationAttributes-Markers "marker-start %MarkerValue; #IMPLIED
+ marker-mid %MarkerValue; #IMPLIED
+ marker-end %MarkerValue; #IMPLIED ">
+<!-- The following presentation attributes apply to text content elements. -->
+<!ENTITY % PresentationAttributes-TextContentElements "alignment-baseline (baseline | top | before-edge | text-top | text-before-edge |
+ middle | bottom | after-edge | text-bottom | text-after-edge |
+ ideographic | lower | hanging | mathematical | inherit) #IMPLIED
+ baseline-shift %BaselineShiftValue; #IMPLIED
+ direction (ltr | rtl | inherit) #IMPLIED
+ dominant-baseline (auto | autosense-script | no-change | reset|
+ ideographic | lower | hanging | mathematical | inherit ) #IMPLIED
+ glyph-orientation-horizontal %GlyphOrientationHorizontalValue; #IMPLIED
+ glyph-orientation-vertical %GlyphOrientationVerticalValue; #IMPLIED
+ kerning %KerningValue; #IMPLIED
+ letter-spacing %SpacingValue; #IMPLIED
+ text-anchor (start | middle | end | inherit) #IMPLIED
+ text-decoration %TextDecorationValue; #IMPLIED
+ unicode-bidi (normal | embed | bidi-override | inherit) #IMPLIED
+ word-spacing %SpacingValue; #IMPLIED ">
+<!-- The following presentation attributes apply to 'text' elements. -->
+<!ENTITY % PresentationAttributes-TextElements "writing-mode (lr-tb | rl-tb | tb-rl | lr | rl | tb | inherit) #IMPLIED ">
+<!-- The following presentation attributes apply to elements that establish viewports. -->
+<!ENTITY % PresentationAttributes-Viewports "clip %ClipValue; #IMPLIED
+ overflow (visible | hidden | scroll | auto | inherit) #IMPLIED ">
+<!--The following represents the complete list of presentation attributes. -->
+<!ENTITY % PresentationAttributes-All "%PresentationAttributes-Color;
+ %PresentationAttributes-Containers;
+ %PresentationAttributes-feFlood;
+ %PresentationAttributes-FillStroke;
+ %PresentationAttributes-FilterPrimitives;
+ %PresentationAttributes-FontSpecification;
+ %PresentationAttributes-Gradients;
+ %PresentationAttributes-Graphics;
+ %PresentationAttributes-Images;
+ %PresentationAttributes-LightingEffects;
+ %PresentationAttributes-Markers;
+ %PresentationAttributes-TextContentElements;
+ %PresentationAttributes-TextElements;
+ %PresentationAttributes-Viewports;">
+<!-- ==============================================================
+ ENTITY DECLARATIONS: DTD extensions
+ ============================================================== -->
+<!-- Allow for extending the DTD with internal subset for
+ container and graphics elements -->
+<!ENTITY % ceExt "">
+<!ENTITY % geExt "">
+<!-- ==============================================================
+ DECLARATIONS CORRESPONDING TO: Document Structure
+ ============================================================== -->
+<!ENTITY % svgExt "">
+<!ELEMENT svg (desc|title|metadata|defs|
+ path|text|rect|circle|ellipse|line|polyline|polygon|
+ use|image|svg|g|view|switch|a|altGlyphDef|
+ script|style|symbol|marker|clipPath|mask|
+ linearGradient|radialGradient|pattern|filter|cursor|font|
+ animate|set|animateMotion|animateColor|animateTransform|
+ color-profile|font-face
+ %ceExt;%svgExt;)* >
+<!ATTLIST svg
+ xmlns CDATA #FIXED "http://www.w3.org/2000/svg"
+ xmlns:xlink CDATA #FIXED "http://www.w3.org/1999/xlink"
+ %stdAttrs;
+ %testAttrs;
+ %langSpaceAttrs;
+ externalResourcesRequired %Boolean; #IMPLIED
+ class %ClassList; #IMPLIED
+ style %StyleSheet; #IMPLIED
+ %PresentationAttributes-All;
+ viewBox %ViewBoxSpec; #IMPLIED
+ preserveAspectRatio %PreserveAspectRatioSpec; "xMidYMid meet"
+ zoomAndPan (disable | magnify) "magnify"
+ %graphicsElementEvents;
+ %documentEvents;
+ version %Number; #FIXED "1.0"
+ x %Coordinate; #IMPLIED
+ y %Coordinate; #IMPLIED
+ width %Length; #IMPLIED
+ height %Length; #IMPLIED
+ contentScriptType %ContentType; "text/ecmascript"
+ contentStyleType %ContentType; "text/css"
+>
+<!ENTITY % gExt "">
+<!ELEMENT g (desc|title|metadata|defs|
+ path|text|rect|circle|ellipse|line|polyline|polygon|
+ use|image|svg|g|view|switch|a|altGlyphDef|
+ script|style|symbol|marker|clipPath|mask|
+ linearGradient|radialGradient|pattern|filter|cursor|font|
+ animate|set|animateMotion|animateColor|animateTransform|
+ color-profile|font-face
+ %ceExt;%gExt;)* >
+<!ATTLIST g
+ %stdAttrs;
+ %testAttrs;
+ %langSpaceAttrs;
+ externalResourcesRequired %Boolean; #IMPLIED
+ class %ClassList; #IMPLIED
+ style %StyleSheet; #IMPLIED
+ %PresentationAttributes-All;
+ transform %TransformList; #IMPLIED
+ %graphicsElementEvents;
+>
+<!ENTITY % defsExt "">
+<!ELEMENT defs (desc|title|metadata|defs|
+ path|text|rect|circle|ellipse|line|polyline|polygon|
+ use|image|svg|g|view|switch|a|altGlyphDef|
+ script|style|symbol|marker|clipPath|mask|
+ linearGradient|radialGradient|pattern|filter|cursor|font|
+ animate|set|animateMotion|animateColor|animateTransform|
+ color-profile|font-face
+ %ceExt;%defsExt;)* >
+<!ATTLIST defs
+ %stdAttrs;
+ %testAttrs;
+ %langSpaceAttrs;
+ externalResourcesRequired %Boolean; #IMPLIED
+ class %ClassList; #IMPLIED
+ style %StyleSheet; #IMPLIED
+ %PresentationAttributes-All;
+ transform %TransformList; #IMPLIED
+ %graphicsElementEvents;
+>
+<!ENTITY % descExt "">
+<!ELEMENT desc (#PCDATA %descExt;)* >
+<!ATTLIST desc
+ %stdAttrs;
+ %langSpaceAttrs;
+ class %ClassList; #IMPLIED
+ style %StyleSheet; #IMPLIED
+ %StructuredText;
+>
+<!ENTITY % titleExt "">
+<!ELEMENT title (#PCDATA %titleExt;)* >
+<!ATTLIST title
+ %stdAttrs;
+ %langSpaceAttrs;
+ class %ClassList; #IMPLIED
+ style %StyleSheet; #IMPLIED
+ %StructuredText;
+>
+<!ENTITY % symbolExt "">
+<!ELEMENT symbol (desc|title|metadata|defs|
+ path|text|rect|circle|ellipse|line|polyline|polygon|
+ use|image|svg|g|view|switch|a|altGlyphDef|
+ script|style|symbol|marker|clipPath|mask|
+ linearGradient|radialGradient|pattern|filter|cursor|font|
+ animate|set|animateMotion|animateColor|animateTransform|
+ color-profile|font-face
+ %ceExt;%symbolExt;)* >
+<!ATTLIST symbol
+ %stdAttrs;
+ %langSpaceAttrs;
+ externalResourcesRequired %Boolean; #IMPLIED
+ class %ClassList; #IMPLIED
+ style %StyleSheet; #IMPLIED
+ %PresentationAttributes-All;
+ viewBox %ViewBoxSpec; #IMPLIED
+ preserveAspectRatio %PreserveAspectRatioSpec; "xMidYMid meet"
+ %graphicsElementEvents;
+>
+<!ENTITY % useExt "">
+<!ELEMENT use (%descTitleMetadata;,(animate|set|animateMotion|animateColor|animateTransform
+ %geExt;%useExt;)*) >
+<!ATTLIST use
+ %stdAttrs;
+ %xlinkRefAttrsEmbed;
+ xlink:href %URI; #REQUIRED
+ %testAttrs;
+ %langSpaceAttrs;
+ externalResourcesRequired %Boolean; #IMPLIED
+ class %ClassList; #IMPLIED
+ style %StyleSheet; #IMPLIED
+ %PresentationAttributes-All;
+ transform %TransformList; #IMPLIED
+ %graphicsElementEvents;
+ x %Coordinate; #IMPLIED
+ y %Coordinate; #IMPLIED
+ width %Length; #IMPLIED
+ height %Length; #IMPLIED
+>
+<!ENTITY % imageExt "">
+<!ELEMENT image (%descTitleMetadata;,(animate|set|animateMotion|animateColor|animateTransform
+ %geExt;%imageExt;)*) >
+<!ATTLIST image
+ %stdAttrs;
+ %xlinkRefAttrsEmbed;
+ xlink:href %URI; #REQUIRED
+ %testAttrs;
+ %langSpaceAttrs;
+ externalResourcesRequired %Boolean; #IMPLIED
+ class %ClassList; #IMPLIED
+ style %StyleSheet; #IMPLIED
+ %PresentationAttributes-Color;
+ %PresentationAttributes-Graphics;
+ %PresentationAttributes-Images;
+ %PresentationAttributes-Viewports;
+ transform %TransformList; #IMPLIED
+ preserveAspectRatio %PreserveAspectRatioSpec; "xMidYMid meet"
+ %graphicsElementEvents;
+ x %Coordinate; #IMPLIED
+ y %Coordinate; #IMPLIED
+ width %Length; #REQUIRED
+ height %Length; #REQUIRED
+>
+<!ENTITY % switchExt "">
+<!ELEMENT switch (%descTitleMetadata;,
+ (path|text|rect|circle|ellipse|line|polyline|polygon|
+ use|image|svg|g|switch|a|foreignObject|
+ animate|set|animateMotion|animateColor|animateTransform
+ %ceExt;%switchExt;)*) >
+<!ATTLIST switch
+ %stdAttrs;
+ %testAttrs;
+ %langSpaceAttrs;
+ externalResourcesRequired %Boolean; #IMPLIED
+ class %ClassList; #IMPLIED
+ style %StyleSheet; #IMPLIED
+ %PresentationAttributes-All;
+ transform %TransformList; #IMPLIED
+ %graphicsElementEvents;
+>
+<!-- ==============================================================
+ DECLARATIONS CORRESPONDING TO: Styling
+ ============================================================== -->
+<!ELEMENT style (#PCDATA)>
+<!ATTLIST style
+ %stdAttrs;
+ xml:space (preserve) #FIXED "preserve"
+ type %ContentType; #REQUIRED
+ media %MediaDesc; #IMPLIED
+ title %Text; #IMPLIED
+>
+<!-- ==============================================================
+ DECLARATIONS CORRESPONDING TO: Paths
+ ============================================================== -->
+<!ENTITY % pathExt "">
+<!ELEMENT path (%descTitleMetadata;,(animate|set|animateMotion|animateColor|animateTransform
+ %geExt;%pathExt;)*) >
+<!ATTLIST path
+ %stdAttrs;
+ %testAttrs;
+ %langSpaceAttrs;
+ externalResourcesRequired %Boolean; #IMPLIED
+ class %ClassList; #IMPLIED
+ style %StyleSheet; #IMPLIED
+ %PresentationAttributes-Color;
+ %PresentationAttributes-FillStroke;
+ %PresentationAttributes-Graphics;
+ %PresentationAttributes-Markers;
+ transform %TransformList; #IMPLIED
+ %graphicsElementEvents;
+ d %PathData; #REQUIRED
+ pathLength %Number; #IMPLIED
+>
+<!-- ==============================================================
+ DECLARATIONS CORRESPONDING TO: Basic Shapes
+ ============================================================== -->
+<!ENTITY % rectExt "">
+<!ELEMENT rect (%descTitleMetadata;,(animate|set|animateMotion|animateColor|animateTransform
+ %geExt;%rectExt;)*) >
+<!ATTLIST rect
+ %stdAttrs;
+ %testAttrs;
+ %langSpaceAttrs;
+ externalResourcesRequired %Boolean; #IMPLIED
+ class %ClassList; #IMPLIED
+ style %StyleSheet; #IMPLIED
+ %PresentationAttributes-Color;
+ %PresentationAttributes-FillStroke;
+ %PresentationAttributes-Graphics;
+ transform %TransformList; #IMPLIED
+ %graphicsElementEvents;
+ x %Coordinate; #IMPLIED
+ y %Coordinate; #IMPLIED
+ width %Length; #REQUIRED
+ height %Length; #REQUIRED
+ rx %Length; #IMPLIED
+ ry %Length; #IMPLIED
+>
+<!ENTITY % circleExt "">
+<!ELEMENT circle (%descTitleMetadata;,(animate|set|animateMotion|animateColor|animateTransform
+ %geExt;%circleExt;)*) >
+<!ATTLIST circle
+ %stdAttrs;
+ %testAttrs;
+ %langSpaceAttrs;
+ externalResourcesRequired %Boolean; #IMPLIED
+ class %ClassList; #IMPLIED
+ style %StyleSheet; #IMPLIED
+ %PresentationAttributes-Color;
+ %PresentationAttributes-FillStroke;
+ %PresentationAttributes-Graphics;
+ transform %TransformList; #IMPLIED
+ %graphicsElementEvents;
+ cx %Coordinate; #IMPLIED
+ cy %Coordinate; #IMPLIED
+ r %Length; #REQUIRED
+>
+<!ENTITY % ellipseExt "">
+<!ELEMENT ellipse (%descTitleMetadata;,(animate|set|animateMotion|animateColor|animateTransform
+ %geExt;%ellipseExt;)*) >
+<!ATTLIST ellipse
+ %stdAttrs;
+ %testAttrs;
+ %langSpaceAttrs;
+ externalResourcesRequired %Boolean; #IMPLIED
+ class %ClassList; #IMPLIED
+ style %StyleSheet; #IMPLIED
+ %PresentationAttributes-Color;
+ %PresentationAttributes-FillStroke;
+ %PresentationAttributes-Graphics;
+ transform %TransformList; #IMPLIED
+ %graphicsElementEvents;
+ cx %Coordinate; #IMPLIED
+ cy %Coordinate; #IMPLIED
+ rx %Length; #REQUIRED
+ ry %Length; #REQUIRED
+>
+<!ENTITY % lineExt "">
+<!ELEMENT line (%descTitleMetadata;,(animate|set|animateMotion|animateColor|animateTransform
+ %geExt;%lineExt;)*) >
+<!ATTLIST line
+ %stdAttrs;
+ %testAttrs;
+ %langSpaceAttrs;
+ externalResourcesRequired %Boolean; #IMPLIED
+ class %ClassList; #IMPLIED
+ style %StyleSheet; #IMPLIED
+ %PresentationAttributes-Color;
+ %PresentationAttributes-FillStroke;
+ %PresentationAttributes-Graphics;
+ %PresentationAttributes-Markers;
+ transform %TransformList; #IMPLIED
+ %graphicsElementEvents;
+ x1 %Coordinate; #IMPLIED
+ y1 %Coordinate; #IMPLIED
+ x2 %Coordinate; #IMPLIED
+ y2 %Coordinate; #IMPLIED
+>
+<!ENTITY % polylineExt "">
+<!ELEMENT polyline (%descTitleMetadata;,(animate|set|animateMotion|animateColor|animateTransform
+ %geExt;%polylineExt;)*) >
+<!ATTLIST polyline
+ %stdAttrs;
+ %testAttrs;
+ %langSpaceAttrs;
+ externalResourcesRequired %Boolean; #IMPLIED
+ class %ClassList; #IMPLIED
+ style %StyleSheet; #IMPLIED
+ %PresentationAttributes-Color;
+ %PresentationAttributes-FillStroke;
+ %PresentationAttributes-Graphics;
+ %PresentationAttributes-Markers;
+ transform %TransformList; #IMPLIED
+ %graphicsElementEvents;
+ points %Points; #REQUIRED
+>
+<!ENTITY % polygonExt "">
+<!ELEMENT polygon (%descTitleMetadata;,(animate|set|animateMotion|animateColor|animateTransform
+ %geExt;%polygonExt;)*) >
+<!ATTLIST polygon
+ %stdAttrs;
+ %testAttrs;
+ %langSpaceAttrs;
+ externalResourcesRequired %Boolean; #IMPLIED
+ class %ClassList; #IMPLIED
+ style %StyleSheet; #IMPLIED
+ %PresentationAttributes-Color;
+ %PresentationAttributes-FillStroke;
+ %PresentationAttributes-Graphics;
+ %PresentationAttributes-Markers;
+ transform %TransformList; #IMPLIED
+ %graphicsElementEvents;
+ points %Points; #REQUIRED
+>
+<!-- ==============================================================
+ DECLARATIONS CORRESPONDING TO: Text
+ ============================================================== -->
+<!ENTITY % textExt "">
+<!ELEMENT text (#PCDATA|desc|title|metadata|
+ tspan|tref|textPath|altGlyph|a|animate|set|
+ animateMotion|animateColor|animateTransform
+ %geExt;%textExt;)* >
+<!ATTLIST text
+ %stdAttrs;
+ %testAttrs;
+ %langSpaceAttrs;
+ externalResourcesRequired %Boolean; #IMPLIED
+ class %ClassList; #IMPLIED
+ style %StyleSheet; #IMPLIED
+ %PresentationAttributes-Color;
+ %PresentationAttributes-FillStroke;
+ %PresentationAttributes-FontSpecification;
+ %PresentationAttributes-Graphics;
+ %PresentationAttributes-TextContentElements;
+ %PresentationAttributes-TextElements;
+ transform %TransformList; #IMPLIED
+ %graphicsElementEvents;
+ x %Coordinates; #IMPLIED
+ y %Coordinates; #IMPLIED
+ dx %Lengths; #IMPLIED
+ dy %Lengths; #IMPLIED
+ rotate %Numbers; #IMPLIED
+ textLength %Length; #IMPLIED
+ lengthAdjust (spacing | spacingAndGlyphs) #IMPLIED
+>
+<!ENTITY % tspanExt "">
+<!ELEMENT tspan (#PCDATA|desc|title|metadata|tspan|tref|altGlyph|a|animate|set|animateColor
+ %tspanExt;)* >
+<!ATTLIST tspan
+ %stdAttrs;
+ %testAttrs;
+ %langSpaceAttrs;
+ externalResourcesRequired %Boolean; #IMPLIED
+ class %ClassList; #IMPLIED
+ style %StyleSheet; #IMPLIED
+ %PresentationAttributes-Color;
+ %PresentationAttributes-FillStroke;
+ %PresentationAttributes-FontSpecification;
+ %PresentationAttributes-Graphics;
+ %PresentationAttributes-TextContentElements;
+ %graphicsElementEvents;
+ x %Coordinates; #IMPLIED
+ y %Coordinates; #IMPLIED
+ dx %Lengths; #IMPLIED
+ dy %Lengths; #IMPLIED
+ rotate %Numbers; #IMPLIED
+ textLength %Length; #IMPLIED
+ lengthAdjust (spacing | spacingAndGlyphs) #IMPLIED
+>
+<!ENTITY % trefExt "">
+<!ELEMENT tref (desc|title|metadata|animate|set|animateColor
+ %trefExt;)* >
+<!ATTLIST tref
+ %stdAttrs;
+ %xlinkRefAttrs;
+ xlink:href %URI; #REQUIRED
+ %testAttrs;
+ %langSpaceAttrs;
+ externalResourcesRequired %Boolean; #IMPLIED
+ class %ClassList; #IMPLIED
+ style %StyleSheet; #IMPLIED
+ %PresentationAttributes-Color;
+ %PresentationAttributes-FillStroke;
+ %PresentationAttributes-FontSpecification;
+ %PresentationAttributes-Graphics;
+ %PresentationAttributes-TextContentElements;
+ %graphicsElementEvents;
+ x %Coordinates; #IMPLIED
+ y %Coordinates; #IMPLIED
+ dx %Lengths; #IMPLIED
+ dy %Lengths; #IMPLIED
+ rotate %Numbers; #IMPLIED
+ textLength %Length; #IMPLIED
+ lengthAdjust (spacing | spacingAndGlyphs) #IMPLIED
+>
+<!ENTITY % textPathExt "">
+<!ELEMENT textPath (#PCDATA|desc|title|metadata|tspan|tref|altGlyph|a|animate|set|animateColor
+ %textPathExt;)* >
+<!ATTLIST textPath
+ %stdAttrs;
+ %xlinkRefAttrs;
+ xlink:href %URI; #REQUIRED
+ %langSpaceAttrs;
+ %testAttrs;
+ externalResourcesRequired %Boolean; #IMPLIED
+ class %ClassList; #IMPLIED
+ style %StyleSheet; #IMPLIED
+ %PresentationAttributes-Color;
+ %PresentationAttributes-FillStroke;
+ %PresentationAttributes-FontSpecification;
+ %PresentationAttributes-Graphics;
+ %PresentationAttributes-TextContentElements;
+ %graphicsElementEvents;
+ startOffset %Length; #IMPLIED
+ textLength %Length; #IMPLIED
+ lengthAdjust (spacing | spacingAndGlyphs) #IMPLIED
+ method (align | stretch) #IMPLIED
+ spacing (auto | exact) #IMPLIED
+>
+<!ENTITY % altGlyphExt "">
+<!ELEMENT altGlyph (#PCDATA %altGlyphExt;)* >
+<!ATTLIST altGlyph
+ %stdAttrs;
+ %xlinkRefAttrs;
+ xlink:href %URI; #IMPLIED
+ glyphRef CDATA #IMPLIED
+ format CDATA #IMPLIED
+ %testAttrs;
+ %langSpaceAttrs;
+ externalResourcesRequired %Boolean; #IMPLIED
+ class %ClassList; #IMPLIED
+ style %StyleSheet; #IMPLIED
+ %PresentationAttributes-Color;
+ %PresentationAttributes-FillStroke;
+ %PresentationAttributes-FontSpecification;
+ %PresentationAttributes-Graphics;
+ %PresentationAttributes-TextContentElements;
+ %graphicsElementEvents;
+ x %Coordinates; #IMPLIED
+ y %Coordinates; #IMPLIED
+ dx %Lengths; #IMPLIED
+ dy %Lengths; #IMPLIED
+ rotate %Numbers; #IMPLIED
+>
+<!ENTITY % altGlyphDefExt "">
+<!ELEMENT altGlyphDef ((glyphRef+|altGlyphItem+) %altGlyphDefExt;) >
+<!ATTLIST altGlyphDef
+ %stdAttrs;
+>
+<!ENTITY % altGlyphItemExt "">
+<!ELEMENT altGlyphItem (glyphRef+ %altGlyphItemExt;) >
+<!ATTLIST altGlyphItem
+ %stdAttrs;
+>
+<!ELEMENT glyphRef EMPTY>
+<!ATTLIST glyphRef
+ %stdAttrs;
+ %xlinkRefAttrs;
+ xlink:href %URI; #IMPLIED
+ class %ClassList; #IMPLIED
+ style %StyleSheet; #IMPLIED
+ %PresentationAttributes-FontSpecification;
+ glyphRef CDATA #IMPLIED
+ format CDATA #IMPLIED
+ x %Number; #IMPLIED
+ y %Number; #IMPLIED
+ dx %Number; #IMPLIED
+ dy %Number; #IMPLIED
+>
+<!-- ==============================================================
+ DECLARATIONS CORRESPONDING TO: Painting: Filling, Stroking and Marker Symbols
+ ============================================================== -->
+<!ENTITY % markerExt "">
+<!ELEMENT marker (desc|title|metadata|defs|
+ path|text|rect|circle|ellipse|line|polyline|polygon|
+ use|image|svg|g|view|switch|a|altGlyphDef|
+ script|style|symbol|marker|clipPath|mask|
+ linearGradient|radialGradient|pattern|filter|cursor|font|
+ animate|set|animateMotion|animateColor|animateTransform|
+ color-profile|font-face
+ %ceExt;%markerExt;)* >
+<!ATTLIST marker
+ %stdAttrs;
+ %langSpaceAttrs;
+ externalResourcesRequired %Boolean; #IMPLIED
+ class %ClassList; #IMPLIED
+ style %StyleSheet; #IMPLIED
+ %PresentationAttributes-All;
+ viewBox %ViewBoxSpec; #IMPLIED
+ preserveAspectRatio %PreserveAspectRatioSpec; "xMidYMid meet"
+ refX %Coordinate; #IMPLIED
+ refY %Coordinate; #IMPLIED
+ markerUnits (strokeWidth | userSpaceOnUse) #IMPLIED
+ markerWidth %Length; #IMPLIED
+ markerHeight %Length; #IMPLIED
+ orient CDATA #IMPLIED
+>
+<!-- ==============================================================
+ DECLARATIONS CORRESPONDING TO: Color
+ ============================================================== -->
+<!ELEMENT color-profile (%descTitleMetadata;)>
+<!ATTLIST color-profile
+ %stdAttrs;
+ %xlinkRefAttrs;
+ xlink:href %URI; #IMPLIED
+ local CDATA #IMPLIED
+ name CDATA #REQUIRED
+ rendering-intent (auto | perceptual | relative-colorimetric | saturation | absolute-colorimetric) "auto"
+>
+<!-- ==============================================================
+ DECLARATIONS CORRESPONDING TO: Gradients and Patterns
+ ============================================================== -->
+<!ENTITY % linearGradientExt "">
+<!ELEMENT linearGradient (%descTitleMetadata;,(stop|animate|set|animateTransform
+ %linearGradientExt;)*) >
+<!ATTLIST linearGradient
+ %stdAttrs;
+ %xlinkRefAttrs;
+ xlink:href %URI; #IMPLIED
+ externalResourcesRequired %Boolean; #IMPLIED
+ class %ClassList; #IMPLIED
+ style %StyleSheet; #IMPLIED
+ %PresentationAttributes-Color;
+ %PresentationAttributes-Gradients;
+ gradientUnits (userSpaceOnUse | objectBoundingBox) #IMPLIED
+ gradientTransform %TransformList; #IMPLIED
+ x1 %Coordinate; #IMPLIED
+ y1 %Coordinate; #IMPLIED
+ x2 %Coordinate; #IMPLIED
+ y2 %Coordinate; #IMPLIED
+ spreadMethod (pad | reflect | repeat) #IMPLIED
+>
+<!ENTITY % radialGradientExt "">
+<!ELEMENT radialGradient (%descTitleMetadata;,(stop|animate|set|animateTransform
+ %radialGradientExt;)*) >
+<!ATTLIST radialGradient
+ %stdAttrs;
+ %xlinkRefAttrs;
+ xlink:href %URI; #IMPLIED
+ externalResourcesRequired %Boolean; #IMPLIED
+ class %ClassList; #IMPLIED
+ style %StyleSheet; #IMPLIED
+ %PresentationAttributes-Color;
+ %PresentationAttributes-Gradients;
+ gradientUnits (userSpaceOnUse | objectBoundingBox) #IMPLIED
+ gradientTransform %TransformList; #IMPLIED
+ cx %Coordinate; #IMPLIED
+ cy %Coordinate; #IMPLIED
+ r %Length; #IMPLIED
+ fx %Coordinate; #IMPLIED
+ fy %Coordinate; #IMPLIED
+ spreadMethod (pad | reflect | repeat) #IMPLIED
+>
+<!ENTITY % stopExt "">
+<!ELEMENT stop (animate|set|animateColor
+ %stopExt;)* >
+<!ATTLIST stop
+ %stdAttrs;
+ class %ClassList; #IMPLIED
+ style %StyleSheet; #IMPLIED
+ %PresentationAttributes-Color;
+ %PresentationAttributes-Gradients;
+ offset %NumberOrPercentage; #REQUIRED
+>
+<!ENTITY % patternExt "">
+<!ELEMENT pattern (desc|title|metadata|defs|
+ path|text|rect|circle|ellipse|line|polyline|polygon|
+ use|image|svg|g|view|switch|a|altGlyphDef|
+ script|style|symbol|marker|clipPath|mask|
+ linearGradient|radialGradient|pattern|filter|cursor|font|
+ animate|set|animateMotion|animateColor|animateTransform|
+ color-profile|font-face
+ %ceExt;%patternExt;)* >
+<!ATTLIST pattern
+ %stdAttrs;
+ %xlinkRefAttrs;
+ xlink:href %URI; #IMPLIED
+ %testAttrs;
+ %langSpaceAttrs;
+ externalResourcesRequired %Boolean; #IMPLIED
+ class %ClassList; #IMPLIED
+ style %StyleSheet; #IMPLIED
+ %PresentationAttributes-All;
+ viewBox %ViewBoxSpec; #IMPLIED
+ preserveAspectRatio %PreserveAspectRatioSpec; "xMidYMid meet"
+ patternUnits (userSpaceOnUse | objectBoundingBox) #IMPLIED
+ patternContentUnits (userSpaceOnUse | objectBoundingBox) #IMPLIED
+ patternTransform %TransformList; #IMPLIED
+ x %Coordinate; #IMPLIED
+ y %Coordinate; #IMPLIED
+ width %Length; #IMPLIED
+ height %Length; #IMPLIED
+>
+<!-- ==============================================================
+ DECLARATIONS CORRESPONDING TO: Clipping, Masking and Compositing
+ ============================================================== -->
+<!ENTITY % clipPathExt "">
+<!ELEMENT clipPath (%descTitleMetadata;,
+ (path|text|rect|circle|ellipse|line|polyline|polygon|
+ use|animate|set|animateMotion|animateColor|animateTransform
+ %ceExt;%clipPathExt;)*) >
+<!ATTLIST clipPath
+ %stdAttrs;
+ %testAttrs;
+ %langSpaceAttrs;
+ externalResourcesRequired %Boolean; #IMPLIED
+ class %ClassList; #IMPLIED
+ style %StyleSheet; #IMPLIED
+ %PresentationAttributes-Color;
+ %PresentationAttributes-FillStroke;
+ %PresentationAttributes-FontSpecification;
+ %PresentationAttributes-Graphics;
+ %PresentationAttributes-TextContentElements;
+ %PresentationAttributes-TextElements;
+ transform %TransformList; #IMPLIED
+ clipPathUnits (userSpaceOnUse | objectBoundingBox) #IMPLIED
+>
+<!ENTITY % maskExt "">
+<!ELEMENT mask (desc|title|metadata|defs|
+ path|text|rect|circle|ellipse|line|polyline|polygon|
+ use|image|svg|g|view|switch|a|altGlyphDef|
+ script|style|symbol|marker|clipPath|mask|
+ linearGradient|radialGradient|pattern|filter|cursor|font|
+ animate|set|animateMotion|animateColor|animateTransform|
+ color-profile|font-face
+ %ceExt;%maskExt;)* >
+<!ATTLIST mask
+ %stdAttrs;
+ %testAttrs;
+ %langSpaceAttrs;
+ externalResourcesRequired %Boolean; #IMPLIED
+ class %ClassList; #IMPLIED
+ style %StyleSheet; #IMPLIED
+ %PresentationAttributes-All;
+ maskUnits (userSpaceOnUse | objectBoundingBox) #IMPLIED
+ maskContentUnits (userSpaceOnUse | objectBoundingBox) #IMPLIED
+ x %Coordinate; #IMPLIED
+ y %Coordinate; #IMPLIED
+ width %Length; #IMPLIED
+ height %Length; #IMPLIED
+>
+<!-- ==============================================================
+ DECLARATIONS CORRESPONDING TO: Filter Effects
+ ============================================================== -->
+<!ENTITY % filterExt "">
+<!ELEMENT filter (%descTitleMetadata;,(feBlend|feFlood|
+ feColorMatrix|feComponentTransfer|
+ feComposite|feConvolveMatrix|feDiffuseLighting|feDisplacementMap|
+ feGaussianBlur|feImage|feMerge|
+ feMorphology|feOffset|feSpecularLighting|
+ feTile|feTurbulence|
+ animate|set
+ %filterExt;)*) >
+<!ATTLIST filter
+ %stdAttrs;
+ %xlinkRefAttrs;
+ xlink:href %URI; #IMPLIED
+ %langSpaceAttrs;
+ externalResourcesRequired %Boolean; #IMPLIED
+ class %ClassList; #IMPLIED
+ style %StyleSheet; #IMPLIED
+ %PresentationAttributes-All;
+ filterUnits (userSpaceOnUse | objectBoundingBox) #IMPLIED
+ primitiveUnits (userSpaceOnUse | objectBoundingBox) #IMPLIED
+ x %Coordinate; #IMPLIED
+ y %Coordinate; #IMPLIED
+ width %Length; #IMPLIED
+ height %Length; #IMPLIED
+ filterRes %NumberOptionalNumber; #IMPLIED
+>
+<!ENTITY % filter_primitive_attributes "x %Coordinate; #IMPLIED
+ y %Coordinate; #IMPLIED
+ width %Length; #IMPLIED
+ height %Length; #IMPLIED
+ result CDATA #IMPLIED">
+<!ENTITY % filter_primitive_attributes_with_in "%filter_primitive_attributes;
+ in CDATA #IMPLIED">
+<!ELEMENT feDistantLight (animate | set)*>
+<!ATTLIST feDistantLight
+ %stdAttrs;
+ azimuth %Number; #IMPLIED
+ elevation %Number; #IMPLIED
+>
+<!ELEMENT fePointLight (animate | set)*>
+<!ATTLIST fePointLight
+ %stdAttrs;
+ x %Number; #IMPLIED
+ y %Number; #IMPLIED
+ z %Number; #IMPLIED
+>
+<!ELEMENT feSpotLight (animate | set)*>
+<!ATTLIST feSpotLight
+ %stdAttrs;
+ x %Number; #IMPLIED
+ y %Number; #IMPLIED
+ z %Number; #IMPLIED
+ pointsAtX %Number; #IMPLIED
+ pointsAtY %Number; #IMPLIED
+ pointsAtZ %Number; #IMPLIED
+ specularExponent %Number; #IMPLIED
+ limitingConeAngle %Number; #IMPLIED
+>
+<!ELEMENT feBlend (animate | set)*>
+<!ATTLIST feBlend
+ %stdAttrs;
+ %PresentationAttributes-FilterPrimitives;
+ %filter_primitive_attributes_with_in;
+ in2 CDATA #REQUIRED
+ mode (normal | multiply | screen | darken | lighten) "normal"
+>
+<!ELEMENT feColorMatrix (animate | set)*>
+<!ATTLIST feColorMatrix
+ %stdAttrs;
+ %PresentationAttributes-FilterPrimitives;
+ %filter_primitive_attributes_with_in;
+ type (matrix | saturate | hueRotate | luminanceToAlpha) "matrix"
+ values CDATA #IMPLIED
+>
+<!ELEMENT feComponentTransfer (feFuncR?, feFuncG?, feFuncB?, feFuncA?)>
+<!ATTLIST feComponentTransfer
+ %stdAttrs;
+ %PresentationAttributes-FilterPrimitives;
+ %filter_primitive_attributes_with_in;
+>
+<!ENTITY % component_transfer_function_attributes "type (identity | table | discrete | linear | gamma) #REQUIRED
+ tableValues CDATA #IMPLIED
+ slope %Number; #IMPLIED
+ intercept %Number; #IMPLIED
+ amplitude %Number; #IMPLIED
+ exponent %Number; #IMPLIED
+ offset %Number; #IMPLIED">
+<!ELEMENT feFuncR (animate | set)*>
+<!ATTLIST feFuncR
+ %stdAttrs;
+ %component_transfer_function_attributes;
+>
+<!ELEMENT feFuncG (animate | set)*>
+<!ATTLIST feFuncG
+ %stdAttrs;
+ %component_transfer_function_attributes;
+>
+<!ELEMENT feFuncB (animate | set)*>
+<!ATTLIST feFuncB
+ %stdAttrs;
+ %component_transfer_function_attributes;
+>
+<!ELEMENT feFuncA (animate | set)*>
+<!ATTLIST feFuncA
+ %stdAttrs;
+ %component_transfer_function_attributes;
+>
+<!ELEMENT feComposite (animate | set)*>
+<!ATTLIST feComposite
+ %stdAttrs;
+ %PresentationAttributes-FilterPrimitives;
+ %filter_primitive_attributes_with_in;
+ in2 CDATA #REQUIRED
+ operator (over | in | out | atop | xor | arithmetic) "over"
+ k1 %Number; #IMPLIED
+ k2 %Number; #IMPLIED
+ k3 %Number; #IMPLIED
+ k4 %Number; #IMPLIED
+>
+<!ELEMENT feConvolveMatrix (animate | set)*>
+<!ATTLIST feConvolveMatrix
+ %stdAttrs;
+ %PresentationAttributes-FilterPrimitives;
+ %filter_primitive_attributes_with_in;
+ order %NumberOptionalNumber; #REQUIRED
+ kernelMatrix CDATA #REQUIRED
+ divisor %Number; #IMPLIED
+ bias %Number; #IMPLIED
+ targetX %Integer; #IMPLIED
+ targetY %Integer; #IMPLIED
+ edgeMode (duplicate | wrap | none) "duplicate"
+ kernelUnitLength %NumberOptionalNumber; #IMPLIED
+ preserveAlpha %Boolean; #IMPLIED
+>
+<!ELEMENT feDiffuseLighting ((feDistantLight | fePointLight | feSpotLight), (animate | set | animateColor)*)>
+<!ATTLIST feDiffuseLighting
+ %stdAttrs;
+ class %ClassList; #IMPLIED
+ style %StyleSheet; #IMPLIED
+ %PresentationAttributes-Color;
+ %PresentationAttributes-FilterPrimitives;
+ %PresentationAttributes-LightingEffects;
+ %filter_primitive_attributes_with_in;
+ surfaceScale %Number; #IMPLIED
+ diffuseConstant %Number; #IMPLIED
+ kernelUnitLength %NumberOptionalNumber; #IMPLIED
+>
+<!ELEMENT feDisplacementMap (animate | set)*>
+<!ATTLIST feDisplacementMap
+ %stdAttrs;
+ %PresentationAttributes-FilterPrimitives;
+ %filter_primitive_attributes_with_in;
+ in2 CDATA #REQUIRED
+ scale %Number; #IMPLIED
+ xChannelSelector (R | G | B | A) "A"
+ yChannelSelector (R | G | B | A) "A"
+>
+<!ELEMENT feFlood (animate | set | animateColor)*>
+<!ATTLIST feFlood
+ %stdAttrs;
+ class %ClassList; #IMPLIED
+ style %StyleSheet; #IMPLIED
+ %PresentationAttributes-Color;
+ %PresentationAttributes-feFlood;
+ %PresentationAttributes-FilterPrimitives;
+ %filter_primitive_attributes_with_in;
+>
+<!ELEMENT feGaussianBlur (animate | set)*>
+<!ATTLIST feGaussianBlur
+ %stdAttrs;
+ %PresentationAttributes-FilterPrimitives;
+ %filter_primitive_attributes_with_in;
+ stdDeviation %NumberOptionalNumber; #IMPLIED
+>
+<!ELEMENT feImage (animate | set | animateTransform)*>
+<!ATTLIST feImage
+ %stdAttrs;
+ %xlinkRefAttrsEmbed;
+ xlink:href %URI; #REQUIRED
+ %langSpaceAttrs;
+ externalResourcesRequired %Boolean; #IMPLIED
+ class %ClassList; #IMPLIED
+ style %StyleSheet; #IMPLIED
+ %PresentationAttributes-All;
+ %filter_primitive_attributes;
+>
+<!ELEMENT feMerge (feMergeNode)*>
+<!ATTLIST feMerge
+ %stdAttrs;
+ %PresentationAttributes-FilterPrimitives;
+ %filter_primitive_attributes;
+>
+<!ELEMENT feMergeNode (animate | set)*>
+<!ATTLIST feMergeNode
+ %stdAttrs;
+ in CDATA #IMPLIED
+>
+<!ELEMENT feMorphology (animate | set)*>
+<!ATTLIST feMorphology
+ %stdAttrs;
+ %PresentationAttributes-FilterPrimitives;
+ %filter_primitive_attributes_with_in;
+ operator (erode | dilate) "erode"
+ radius %NumberOptionalNumber; #IMPLIED
+>
+<!ELEMENT feOffset (animate | set)*>
+<!ATTLIST feOffset
+ %stdAttrs;
+ %PresentationAttributes-FilterPrimitives;
+ %filter_primitive_attributes_with_in;
+ dx %Number; #IMPLIED
+ dy %Number; #IMPLIED
+>
+<!ELEMENT feSpecularLighting ((feDistantLight | fePointLight | feSpotLight), (animate | set | animateColor)*)>
+<!ATTLIST feSpecularLighting
+ %stdAttrs;
+ class %ClassList; #IMPLIED
+ style %StyleSheet; #IMPLIED
+ %PresentationAttributes-Color;
+ %PresentationAttributes-FilterPrimitives;
+ %PresentationAttributes-LightingEffects;
+ %filter_primitive_attributes_with_in;
+ surfaceScale %Number; #IMPLIED
+ specularConstant %Number; #IMPLIED
+ specularExponent %Number; #IMPLIED
+ kernelUnitLength %NumberOptionalNumber; #IMPLIED
+>
+<!ELEMENT feTile (animate | set)*>
+<!ATTLIST feTile
+ %stdAttrs;
+ %PresentationAttributes-FilterPrimitives;
+ %filter_primitive_attributes_with_in;
+>
+<!ELEMENT feTurbulence (animate | set)*>
+<!ATTLIST feTurbulence
+ %stdAttrs;
+ %PresentationAttributes-FilterPrimitives;
+ %filter_primitive_attributes;
+ baseFrequency %NumberOptionalNumber; #IMPLIED
+ numOctaves %Integer; #IMPLIED
+ seed %Number; #IMPLIED
+ stitchTiles (stitch | noStitch) "noStitch"
+ type (fractalNoise | turbulence) "turbulence"
+>
+<!-- ==============================================================
+ DECLARATIONS CORRESPONDING TO: Interactivity
+ ============================================================== -->
+<!ELEMENT cursor (%descTitleMetadata;)>
+<!ATTLIST cursor
+ %stdAttrs;
+ %xlinkRefAttrs;
+ xlink:href %URI; #REQUIRED
+ %testAttrs;
+ externalResourcesRequired %Boolean; #IMPLIED
+ x %Coordinate; #IMPLIED
+ y %Coordinate; #IMPLIED
+>
+<!-- ==============================================================
+ DECLARATIONS CORRESPONDING TO: Linking
+ ============================================================== -->
+<!ENTITY % aExt "">
+<!ELEMENT a (#PCDATA|desc|title|metadata|defs|
+ path|text|rect|circle|ellipse|line|polyline|polygon|
+ use|image|svg|g|view|switch|a|altGlyphDef|
+ script|style|symbol|marker|clipPath|mask|
+ linearGradient|radialGradient|pattern|filter|cursor|font|
+ animate|set|animateMotion|animateColor|animateTransform|
+ color-profile|font-face
+ %ceExt;%aExt;)* >
+<!ATTLIST a
+ %stdAttrs;
+ xmlns:xlink CDATA #FIXED "http://www.w3.org/1999/xlink"
+ xlink:type (simple) #FIXED "simple"
+ xlink:role %URI; #IMPLIED
+ xlink:arcrole %URI; #IMPLIED
+ xlink:title CDATA #IMPLIED
+ xlink:show (new | replace) "replace"
+ xlink:actuate (onRequest) #FIXED "onRequest"
+ xlink:href %URI; #REQUIRED
+ %testAttrs;
+ %langSpaceAttrs;
+ externalResourcesRequired %Boolean; #IMPLIED
+ class %ClassList; #IMPLIED
+ style %StyleSheet; #IMPLIED
+ %PresentationAttributes-All;
+ transform %TransformList; #IMPLIED
+ %graphicsElementEvents;
+ target %LinkTarget; #IMPLIED
+>
+<!ENTITY % viewExt "">
+<!ELEMENT view (%descTitleMetadata;%viewExt;) >
+<!ATTLIST view
+ %stdAttrs;
+ externalResourcesRequired %Boolean; #IMPLIED
+ viewBox %ViewBoxSpec; #IMPLIED
+ preserveAspectRatio %PreserveAspectRatioSpec; "xMidYMid meet"
+ zoomAndPan (disable | magnify) "magnify"
+ viewTarget CDATA #IMPLIED
+>
+<!-- ==============================================================
+ DECLARATIONS CORRESPONDING TO: Scripting
+ ============================================================== -->
+<!ELEMENT script (#PCDATA)>
+<!ATTLIST script
+ %stdAttrs;
+ %xlinkRefAttrs;
+ xlink:href %URI; #IMPLIED
+ externalResourcesRequired %Boolean; #IMPLIED
+ type %ContentType; #REQUIRED
+>
+<!-- ==============================================================
+ DECLARATIONS CORRESPONDING TO: Animation
+ ============================================================== -->
+<!ENTITY % animElementAttrs "%xlinkRefAttrs;
+ xlink:href %URI; #IMPLIED">
+<!ENTITY % animAttributeAttrs "attributeName CDATA #REQUIRED
+ attributeType CDATA #IMPLIED">
+<!ENTITY % animTimingAttrs "begin CDATA #IMPLIED
+ dur CDATA #IMPLIED
+ end CDATA #IMPLIED
+ min CDATA #IMPLIED
+ max CDATA #IMPLIED
+ restart (always | never | whenNotActive) 'always'
+ repeatCount CDATA #IMPLIED
+ repeatDur CDATA #IMPLIED
+ fill (remove | freeze) 'remove'">
+<!ENTITY % animValueAttrs "calcMode (discrete | linear | paced | spline) 'linear'
+ values CDATA #IMPLIED
+ keyTimes CDATA #IMPLIED
+ keySplines CDATA #IMPLIED
+ from CDATA #IMPLIED
+ to CDATA #IMPLIED
+ by CDATA #IMPLIED">
+<!ENTITY % animAdditionAttrs "additive (replace | sum) 'replace'
+ accumulate (none | sum) 'none'">
+<!ENTITY % animateExt "">
+<!ELEMENT animate (%descTitleMetadata;%animateExt;) >
+<!ATTLIST animate
+ %stdAttrs;
+ %testAttrs;
+ externalResourcesRequired %Boolean; #IMPLIED
+ %animationEvents;
+ %animElementAttrs;
+ %animAttributeAttrs;
+ %animTimingAttrs;
+ %animValueAttrs;
+ %animAdditionAttrs;
+>
+<!ENTITY % setExt "">
+<!ELEMENT set (%descTitleMetadata;%setExt;) >
+<!ATTLIST set
+ %stdAttrs;
+ %testAttrs;
+ externalResourcesRequired %Boolean; #IMPLIED
+ %animationEvents;
+ %animElementAttrs;
+ %animAttributeAttrs;
+ %animTimingAttrs;
+ to CDATA #IMPLIED
+>
+<!ENTITY % animateMotionExt "">
+<!ELEMENT animateMotion (%descTitleMetadata;,mpath? %animateMotionExt;) >
+<!ATTLIST animateMotion
+ %stdAttrs;
+ %testAttrs;
+ externalResourcesRequired %Boolean; #IMPLIED
+ %animationEvents;
+ %animElementAttrs;
+ %animTimingAttrs;
+ calcMode (discrete | linear | paced | spline) "paced"
+ values CDATA #IMPLIED
+ keyTimes CDATA #IMPLIED
+ keySplines CDATA #IMPLIED
+ from CDATA #IMPLIED
+ to CDATA #IMPLIED
+ by CDATA #IMPLIED
+ %animAdditionAttrs;
+ path CDATA #IMPLIED
+ keyPoints CDATA #IMPLIED
+ rotate CDATA #IMPLIED
+ origin CDATA #IMPLIED
+>
+<!ENTITY % mpathExt "">
+<!ELEMENT mpath (%descTitleMetadata;%mpathExt;) >
+<!ATTLIST mpath
+ %stdAttrs;
+ %xlinkRefAttrs;
+ xlink:href %URI; #REQUIRED
+ externalResourcesRequired %Boolean; #IMPLIED
+>
+<!ENTITY % animateColorExt "">
+<!ELEMENT animateColor (%descTitleMetadata;%animateColorExt;) >
+<!ATTLIST animateColor
+ %stdAttrs;
+ %testAttrs;
+ externalResourcesRequired %Boolean; #IMPLIED
+ %animationEvents;
+ %animElementAttrs;
+ %animAttributeAttrs;
+ %animTimingAttrs;
+ %animValueAttrs;
+ %animAdditionAttrs;
+>
+<!ENTITY % animateTransformExt "">
+<!ELEMENT animateTransform (%descTitleMetadata;%animateTransformExt;) >
+<!ATTLIST animateTransform
+ %stdAttrs;
+ %testAttrs;
+ externalResourcesRequired %Boolean; #IMPLIED
+ %animationEvents;
+ %animElementAttrs;
+ %animAttributeAttrs;
+ %animTimingAttrs;
+ %animValueAttrs;
+ %animAdditionAttrs;
+ type (translate | scale | rotate | skewX | skewY) "translate"
+>
+<!-- ==============================================================
+ DECLARATIONS CORRESPONDING TO: Fonts
+ ============================================================== -->
+<!ENTITY % fontExt "">
+<!ELEMENT font (%descTitleMetadata;,font-face,
+ missing-glyph,(glyph|hkern|vkern %fontExt;)*) >
+<!ATTLIST font
+ %stdAttrs;
+ externalResourcesRequired %Boolean; #IMPLIED
+ class %ClassList; #IMPLIED
+ style %StyleSheet; #IMPLIED
+ %PresentationAttributes-All;
+ horiz-origin-x %Number; #IMPLIED
+ horiz-origin-y %Number; #IMPLIED
+ horiz-adv-x %Number; #REQUIRED
+ vert-origin-x %Number; #IMPLIED
+ vert-origin-y %Number; #IMPLIED
+ vert-adv-y %Number; #IMPLIED
+>
+<!ENTITY % glyphExt "">
+<!ELEMENT glyph (desc|title|metadata|defs|
+ path|text|rect|circle|ellipse|line|polyline|polygon|
+ use|image|svg|g|view|switch|a|altGlyphDef|
+ script|style|symbol|marker|clipPath|mask|
+ linearGradient|radialGradient|pattern|filter|cursor|font|
+ animate|set|animateMotion|animateColor|animateTransform|
+ color-profile|font-face
+ %glyphExt;)* >
+<!ATTLIST glyph
+ %stdAttrs;
+ class %ClassList; #IMPLIED
+ style %StyleSheet; #IMPLIED
+ %PresentationAttributes-All;
+ unicode CDATA #IMPLIED
+ glyph-name CDATA #IMPLIED
+ d %PathData; #IMPLIED
+ orientation CDATA #IMPLIED
+ arabic-form CDATA #IMPLIED
+ lang %LanguageCodes; #IMPLIED
+ horiz-adv-x %Number; #IMPLIED
+ vert-origin-x %Number; #IMPLIED
+ vert-origin-y %Number; #IMPLIED
+ vert-adv-y %Number; #IMPLIED
+>
+<!ENTITY % missing-glyphExt "">
+<!ELEMENT missing-glyph (desc|title|metadata|defs|
+ path|text|rect|circle|ellipse|line|polyline|polygon|
+ use|image|svg|g|view|switch|a|altGlyphDef|
+ script|style|symbol|marker|clipPath|mask|
+ linearGradient|radialGradient|pattern|filter|cursor|font|
+ animate|set|animateMotion|animateColor|animateTransform|
+ color-profile|font-face
+ %missing-glyphExt;)* >
+<!ATTLIST missing-glyph
+ %stdAttrs;
+ class %ClassList; #IMPLIED
+ style %StyleSheet; #IMPLIED
+ %PresentationAttributes-All;
+ d %PathData; #IMPLIED
+ horiz-adv-x %Number; #IMPLIED
+ vert-origin-x %Number; #IMPLIED
+ vert-origin-y %Number; #IMPLIED
+ vert-adv-y %Number; #IMPLIED
+>
+<!ELEMENT hkern EMPTY>
+<!ATTLIST hkern
+ %stdAttrs;
+ u1 CDATA #IMPLIED
+ g1 CDATA #IMPLIED
+ u2 CDATA #IMPLIED
+ g2 CDATA #IMPLIED
+ k %Number; #REQUIRED
+>
+<!ELEMENT vkern EMPTY>
+<!ATTLIST vkern
+ %stdAttrs;
+ u1 CDATA #IMPLIED
+ g1 CDATA #IMPLIED
+ u2 CDATA #IMPLIED
+ g2 CDATA #IMPLIED
+ k %Number; #REQUIRED
+>
+<!ELEMENT font-face (%descTitleMetadata;, font-face-src?, definition-src?)>
+<!ATTLIST font-face
+ %stdAttrs;
+ font-family CDATA #IMPLIED
+ font-style CDATA #IMPLIED
+ font-variant CDATA #IMPLIED
+ font-weight CDATA #IMPLIED
+ font-stretch CDATA #IMPLIED
+ font-size CDATA #IMPLIED
+ unicode-range CDATA #IMPLIED
+ units-per-em %Number; #IMPLIED
+ panose-1 CDATA #IMPLIED
+ stemv %Number; #IMPLIED
+ stemh %Number; #IMPLIED
+ slope %Number; #IMPLIED
+ cap-height %Number; #IMPLIED
+ x-height %Number; #IMPLIED
+ accent-height %Number; #IMPLIED
+ ascent %Number; #IMPLIED
+ descent %Number; #IMPLIED
+ widths CDATA #IMPLIED
+ bbox CDATA #IMPLIED
+ ideographic %Number; #IMPLIED
+ alphabetic %Number; #IMPLIED
+ mathematical %Number; #IMPLIED
+ hanging %Number; #IMPLIED
+ v-ideographic %Number; #IMPLIED
+ v-alphabetic %Number; #IMPLIED
+ v-mathematical %Number; #IMPLIED
+ v-hanging %Number; #IMPLIED
+ underline-position %Number; #IMPLIED
+ underline-thickness %Number; #IMPLIED
+ strikethrough-position %Number; #IMPLIED
+ strikethrough-thickness %Number; #IMPLIED
+ overline-position %Number; #IMPLIED
+ overline-thickness %Number; #IMPLIED
+>
+<!ELEMENT font-face-src (font-face-uri | font-face-name)+>
+<!ATTLIST font-face-src
+ %stdAttrs;
+>
+<!ELEMENT font-face-uri (font-face-format*)>
+<!ATTLIST font-face-uri
+ %stdAttrs;
+ %xlinkRefAttrs;
+ xlink:href %URI; #REQUIRED
+>
+<!ELEMENT font-face-format EMPTY>
+<!ATTLIST font-face-format
+ %stdAttrs;
+ string CDATA #IMPLIED
+>
+<!ELEMENT font-face-name EMPTY>
+<!ATTLIST font-face-name
+ %stdAttrs;
+ name CDATA #IMPLIED
+>
+<!ELEMENT definition-src EMPTY>
+<!ATTLIST definition-src
+ %stdAttrs;
+ %xlinkRefAttrs;
+ xlink:href %URI; #REQUIRED
+>
+<!-- ==============================================================
+ DECLARATIONS CORRESPONDING TO: Metadata
+ ============================================================== -->
+<!ENTITY % metadataExt "">
+<!ELEMENT metadata (#PCDATA %metadataExt;)* >
+<!ATTLIST metadata
+ %stdAttrs;
+>
+<!-- ==============================================================
+ DECLARATIONS CORRESPONDING TO: Extensibility
+ ============================================================== -->
+<!ENTITY % foreignObjectExt "">
+<!ELEMENT foreignObject (#PCDATA %ceExt;%foreignObjectExt;)* >
+<!ATTLIST foreignObject
+ %stdAttrs;
+ %testAttrs;
+ %langSpaceAttrs;
+ externalResourcesRequired %Boolean; #IMPLIED
+ class %ClassList; #IMPLIED
+ style %StyleSheet; #IMPLIED
+ %PresentationAttributes-All;
+ transform %TransformList; #IMPLIED
+ %graphicsElementEvents;
+ x %Coordinate; #IMPLIED
+ y %Coordinate; #IMPLIED
+ width %Length; #REQUIRED
+ height %Length; #REQUIRED
+ %StructuredText;
+>
diff --git a/org/apache/batik/dom/svg/resources/svg11-attribs.mod b/org/apache/batik/dom/svg/resources/svg11-attribs.mod
new file mode 100644
index 0000000..dc31dc6
--- /dev/null
+++ b/org/apache/batik/dom/svg/resources/svg11-attribs.mod
@@ -0,0 +1,186 @@
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Attribute Collection Module ................................... -->
+<!-- file: svg11-attribs.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-attribs.mod 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Attribute Collection//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11-attribs.mod"
+
+ ....................................................................... -->
+
+<!-- SVG 1.1 Attribute Collection
+
+ This module defines the set of common attributes that can be present
+ on many SVG elements.
+-->
+
+<!-- module: svg-conditional.mod ....................... -->
+
+<!ENTITY % ExtensionList.datatype "CDATA" >
+<!ENTITY % FeatureList.datatype "CDATA" >
+
+<!ENTITY % SVG.Conditional.extra.attrib "" >
+<!ENTITY % SVG.Conditional.attrib
+ "requiredFeatures %FeatureList.datatype; #IMPLIED
+ requiredExtensions %ExtensionList.datatype; #IMPLIED
+ systemLanguage %LanguageCodes.datatype; #IMPLIED
+ %SVG.Conditional.extra.attrib;"
+>
+
+<!-- module: svg-style.mod ............................. -->
+
+<!ENTITY % ClassList.datatype "CDATA" >
+<!ENTITY % StyleSheet.datatype "CDATA" >
+
+<!ENTITY % SVG.Style.extra.attrib "" >
+<!ENTITY % SVG.Style.attrib
+ "style %StyleSheet.datatype; #IMPLIED
+ class %ClassList.datatype; #IMPLIED
+ %SVG.Style.extra.attrib;"
+>
+
+<!-- module: svg-text.mod .............................. -->
+
+<!ENTITY % BaselineShiftValue.datatype "CDATA" >
+<!ENTITY % FontFamilyValue.datatype "CDATA" >
+<!ENTITY % FontSizeValue.datatype "CDATA" >
+<!ENTITY % FontSizeAdjustValue.datatype "CDATA" >
+<!ENTITY % GlyphOrientationHorizontalValue.datatype "CDATA" >
+<!ENTITY % GlyphOrientationVerticalValue.datatype "CDATA" >
+<!ENTITY % KerningValue.datatype "CDATA" >
+<!ENTITY % SpacingValue.datatype "CDATA" >
+<!ENTITY % TextDecorationValue.datatype "CDATA" >
+
+<!ENTITY % SVG.Text.extra.attrib "" >
+<!ENTITY % SVG.Text.attrib
+ "writing-mode ( lr-tb | rl-tb | tb-rl | lr | rl | tb | inherit ) #IMPLIED
+ %SVG.Text.extra.attrib;"
+>
+
+<!ENTITY % SVG.TextContent.extra.attrib "" >
+<!ENTITY % SVG.TextContent.attrib
+ "alignment-baseline ( auto | baseline | before-edge | text-before-edge |
+ middle | central | after-edge | text-after-edge |
+ ideographic | alphabetic | hanging | mathematical |
+ inherit ) #IMPLIED
+ baseline-shift %BaselineShiftValue.datatype; #IMPLIED
+ direction ( ltr | rtl | inherit ) #IMPLIED
+ dominant-baseline ( auto | use-script | no-change | reset-size |
+ ideographic | alphabetic | hanging | mathematical |
+ central | middle | text-after-edge | text-before-edge |
+ inherit ) #IMPLIED
+ glyph-orientation-horizontal %GlyphOrientationHorizontalValue.datatype;
+ #IMPLIED
+ glyph-orientation-vertical %GlyphOrientationVerticalValue.datatype;
+ #IMPLIED
+ kerning %KerningValue.datatype; #IMPLIED
+ letter-spacing %SpacingValue.datatype; #IMPLIED
+ text-anchor ( start | middle | end | inherit ) #IMPLIED
+ text-decoration %TextDecorationValue.datatype; #IMPLIED
+ unicode-bidi ( normal | embed | bidi-override | inherit ) #IMPLIED
+ word-spacing %SpacingValue.datatype; #IMPLIED
+ %SVG.TextContent.extra.attrib;"
+>
+
+<!ENTITY % SVG.Font.extra.attrib "" >
+<!ENTITY % SVG.Font.attrib
+ "font-family %FontFamilyValue.datatype; #IMPLIED
+ font-size %FontSizeValue.datatype; #IMPLIED
+ font-size-adjust %FontSizeAdjustValue.datatype; #IMPLIED
+ font-stretch ( normal | wider | narrower | ultra-condensed |
+ extra-condensed | condensed | semi-condensed |
+ semi-expanded | expanded | extra-expanded |
+ ultra-expanded | inherit ) #IMPLIED
+ font-style ( normal | italic | oblique | inherit ) #IMPLIED
+ font-variant ( normal | small-caps | inherit ) #IMPLIED
+ font-weight ( normal | bold | bolder | lighter | 100 | 200 | 300 | 400 |
+ 500 | 600 | 700 | 800 | 900 | inherit ) #IMPLIED
+ %SVG.Font.extra.attrib;"
+>
+
+<!-- module: svg-marker.mod ............................ -->
+
+<!ENTITY % MarkerValue.datatype "CDATA" >
+
+<!ENTITY % SVG.Marker.extra.attrib "" >
+<!ENTITY % SVG.Marker.attrib
+ "marker-start %MarkerValue.datatype; #IMPLIED
+ marker-mid %MarkerValue.datatype; #IMPLIED
+ marker-end %MarkerValue.datatype; #IMPLIED
+ %SVG.Marker.extra.attrib;"
+>
+
+<!-- module: svg-profile.mod ........................... -->
+
+<!ENTITY % SVG.Profile.extra.attrib "" >
+<!ENTITY % SVG.Profile.attrib
+ "color-profile CDATA #IMPLIED
+ %SVG.Profile.extra.attrib;"
+>
+
+<!-- module: svg-gradient.mod .......................... -->
+
+<!ENTITY % NumberOrPercentage.datatype "CDATA" >
+
+<!ENTITY % SVG.Gradient.extra.attrib "" >
+<!ENTITY % SVG.Gradient.attrib
+ "stop-color %SVGColor.datatype; #IMPLIED
+ stop-opacity %OpacityValue.datatype; #IMPLIED
+ %SVG.Gradient.extra.attrib;"
+>
+
+<!-- module: svg-clip.mod .............................. -->
+
+<!ENTITY % ClipPathValue.datatype "CDATA" >
+
+<!ENTITY % SVG.Clip.extra.attrib "" >
+<!ENTITY % SVG.Clip.attrib
+ "clip-path %ClipPathValue.datatype; #IMPLIED
+ clip-rule %ClipFillRule.datatype; #IMPLIED
+ %SVG.Clip.extra.attrib;"
+>
+
+<!-- module: svg-mask.mod .............................. -->
+
+<!ENTITY % MaskValue.datatype "CDATA" >
+
+<!ENTITY % SVG.Mask.extra.attrib "" >
+<!ENTITY % SVG.Mask.attrib
+ "mask %MaskValue.datatype; #IMPLIED
+ %SVG.Mask.extra.attrib;"
+>
+
+<!-- module: svg-filter.mod ............................ -->
+
+<!ENTITY % FilterValue.datatype "CDATA" >
+<!ENTITY % NumberOptionalNumber.datatype "CDATA" >
+
+<!ENTITY % SVG.Filter.extra.attrib "" >
+<!ENTITY % SVG.Filter.attrib
+ "filter %FilterValue.datatype; #IMPLIED
+ %SVG.Filter.extra.attrib;"
+>
+
+<!ENTITY % SVG.FilterColor.extra.attrib "" >
+<!ENTITY % SVG.FilterColor.attrib
+ "color-interpolation-filters ( auto | sRGB | linearRGB | inherit )
+ #IMPLIED
+ %SVG.FilterColor.extra.attrib;"
+>
+
+<!-- module: svg-cursor.mod ............................ -->
+
+<!ENTITY % CursorValue.datatype "CDATA" >
+
+<!ENTITY % SVG.Cursor.extra.attrib "" >
+<!ENTITY % SVG.Cursor.attrib
+ "cursor %CursorValue.datatype; #IMPLIED
+ %SVG.Cursor.extra.attrib;"
+>
+
+<!-- end of svg11-attribs.mod -->
diff --git a/org/apache/batik/dom/svg/resources/svg11-basic-attribs.mod b/org/apache/batik/dom/svg/resources/svg11-basic-attribs.mod
new file mode 100644
index 0000000..9e28e42
--- /dev/null
+++ b/org/apache/batik/dom/svg/resources/svg11-basic-attribs.mod
@@ -0,0 +1,174 @@
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Basic Attribute Collection Module ............................. -->
+<!-- file: svg11-basic-attribs.mod
+
+ This is SVG Basic, a proper subset of SVG.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-basic-attribs.mod 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Basic Attribute Collection//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11-basic-attribs.mod"
+
+ ....................................................................... -->
+
+<!-- SVG 1.1 Basic Attribute Collection
+
+ This module defines the set of common attributes that can be present
+ on many SVG elements.
+-->
+
+<!-- module: svg-conditional.mod ....................... -->
+
+<!ENTITY % ExtensionList.datatype "CDATA" >
+<!ENTITY % FeatureList.datatype "CDATA" >
+
+<!ENTITY % SVG.Conditional.extra.attrib "" >
+<!ENTITY % SVG.Conditional.attrib
+ "requiredFeatures %FeatureList.datatype; #IMPLIED
+ requiredExtensions %ExtensionList.datatype; #IMPLIED
+ systemLanguage %LanguageCodes.datatype; #IMPLIED
+ %SVG.Conditional.extra.attrib;"
+>
+
+<!-- module: svg-style.mod ............................. -->
+
+<!ENTITY % ClassList.datatype "CDATA" >
+<!ENTITY % StyleSheet.datatype "CDATA" >
+
+<!ENTITY % SVG.Style.extra.attrib "" >
+<!ENTITY % SVG.Style.attrib
+ "style %StyleSheet.datatype; #IMPLIED
+ class %ClassList.datatype; #IMPLIED
+ %SVG.Style.extra.attrib;"
+>
+
+<!-- module: svg-text.mod .............................. -->
+
+<!ENTITY % BaselineShiftValue.datatype "CDATA" >
+<!ENTITY % FontFamilyValue.datatype "CDATA" >
+<!ENTITY % FontSizeValue.datatype "CDATA" >
+<!ENTITY % FontSizeAdjustValue.datatype "CDATA" >
+<!ENTITY % GlyphOrientationHorizontalValue.datatype "CDATA" >
+<!ENTITY % GlyphOrientationVerticalValue.datatype "CDATA" >
+<!ENTITY % KerningValue.datatype "CDATA" >
+<!ENTITY % SpacingValue.datatype "CDATA" >
+<!ENTITY % TextDecorationValue.datatype "CDATA" >
+
+<!ENTITY % SVG.Text.extra.attrib "" >
+<!ENTITY % SVG.Text.attrib
+ "writing-mode ( lr-tb | rl-tb | tb-rl | lr | rl | tb | inherit ) #IMPLIED
+ %SVG.Text.extra.attrib;"
+>
+
+<!ENTITY % SVG.TextContent.extra.attrib "" >
+<!ENTITY % SVG.TextContent.attrib
+ "alignment-baseline ( auto | baseline | before-edge | text-before-edge |
+ middle | central | after-edge | text-after-edge |
+ ideographic | alphabetic | hanging | mathematical |
+ inherit ) #IMPLIED
+ baseline-shift %BaselineShiftValue.datatype; #IMPLIED
+ direction ( ltr | rtl | inherit ) #IMPLIED
+ dominant-baseline ( auto | use-script | no-change | reset-size |
+ ideographic | alphabetic | hanging | mathematical |
+ central | middle | text-after-edge | text-before-edge |
+ inherit ) #IMPLIED
+ glyph-orientation-horizontal %GlyphOrientationHorizontalValue.datatype;
+ #IMPLIED
+ glyph-orientation-vertical %GlyphOrientationVerticalValue.datatype;
+ #IMPLIED
+ kerning %KerningValue.datatype; #IMPLIED
+ letter-spacing %SpacingValue.datatype; #IMPLIED
+ text-anchor ( start | middle | end | inherit ) #IMPLIED
+ text-decoration %TextDecorationValue.datatype; #IMPLIED
+ unicode-bidi ( normal | embed | bidi-override | inherit ) #IMPLIED
+ word-spacing %SpacingValue.datatype; #IMPLIED
+ %SVG.TextContent.extra.attrib;"
+>
+
+<!ENTITY % SVG.Font.extra.attrib "" >
+<!ENTITY % SVG.Font.attrib
+ "font-family %FontFamilyValue.datatype; #IMPLIED
+ font-size %FontSizeValue.datatype; #IMPLIED
+ font-size-adjust %FontSizeAdjustValue.datatype; #IMPLIED
+ font-stretch ( normal | wider | narrower | ultra-condensed |
+ extra-condensed | condensed | semi-condensed |
+ semi-expanded | expanded | extra-expanded |
+ ultra-expanded | inherit ) #IMPLIED
+ font-style ( normal | italic | oblique | inherit ) #IMPLIED
+ font-variant ( normal | small-caps | inherit ) #IMPLIED
+ font-weight ( normal | bold | bolder | lighter | 100 | 200 | 300 | 400 |
+ 500 | 600 | 700 | 800 | 900 | inherit ) #IMPLIED
+ %SVG.Font.extra.attrib;"
+>
+
+<!-- module: svg-profile.mod ........................... -->
+
+<!ENTITY % SVG.Profile.extra.attrib "" >
+<!ENTITY % SVG.Profile.attrib
+ "color-profile CDATA #IMPLIED
+ %SVG.Profile.extra.attrib;"
+>
+
+<!-- module: svg-gradient.mod .......................... -->
+
+<!ENTITY % NumberOrPercentage.datatype "CDATA" >
+
+<!ENTITY % SVG.Gradient.extra.attrib "" >
+<!ENTITY % SVG.Gradient.attrib
+ "stop-color %SVGColor.datatype; #IMPLIED
+ stop-opacity %OpacityValue.datatype; #IMPLIED
+ %SVG.Gradient.extra.attrib;"
+>
+
+<!-- module: svg-basic-clip.mod ........................ -->
+
+<!ENTITY % ClipPathValue.datatype "CDATA" >
+
+<!ENTITY % SVG.Clip.extra.attrib "" >
+<!ENTITY % SVG.Clip.attrib
+ "clip-path %ClipPathValue.datatype; #IMPLIED
+ clip-rule %ClipFillRule.datatype; #IMPLIED
+ %SVG.Clip.extra.attrib;"
+>
+
+<!-- module: svg-mask.mod .............................. -->
+
+<!ENTITY % MaskValue.datatype "CDATA" >
+
+<!ENTITY % SVG.Mask.extra.attrib "" >
+<!ENTITY % SVG.Mask.attrib
+ "mask %MaskValue.datatype; #IMPLIED
+ %SVG.Mask.extra.attrib;"
+>
+
+<!-- module: svg-basic-filter.mod ...................... -->
+
+<!ENTITY % FilterValue.datatype "CDATA" >
+<!ENTITY % NumberOptionalNumber.datatype "CDATA" >
+
+<!ENTITY % SVG.Filter.extra.attrib "" >
+<!ENTITY % SVG.Filter.attrib
+ "filter %FilterValue.datatype; #IMPLIED
+ %SVG.Filter.extra.attrib;"
+>
+
+<!ENTITY % SVG.FilterColor.extra.attrib "" >
+<!ENTITY % SVG.FilterColor.attrib
+ "color-interpolation-filters ( auto | sRGB | linearRGB | inherit )
+ #IMPLIED
+ %SVG.FilterColor.extra.attrib;"
+>
+
+<!-- module: svg-cursor.mod ............................ -->
+
+<!ENTITY % CursorValue.datatype "CDATA" >
+
+<!ENTITY % SVG.Cursor.extra.attrib "" >
+<!ENTITY % SVG.Cursor.attrib
+ "cursor %CursorValue.datatype; #IMPLIED
+ %SVG.Cursor.extra.attrib;"
+>
+
+<!-- end of svg11-basic-attribs.mod -->
diff --git a/org/apache/batik/dom/svg/resources/svg11-basic-flat.dtd b/org/apache/batik/dom/svg/resources/svg11-basic-flat.dtd
new file mode 100644
index 0000000..cdfc25f
--- /dev/null
+++ b/org/apache/batik/dom/svg/resources/svg11-basic-flat.dtd
@@ -0,0 +1,5329 @@
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Basic DTD ..................................................... -->
+<!-- file: svg11-basic.dtd
+-->
+
+<!-- SVG 1.1 Basic DTD
+
+ This is SVG Basic, a proper subset of SVG.
+
+ The Scalable Vector Graphics (SVG)
+ Copyright 2001, 2002 World Wide Web Consortium
+ (Massachusetts Institute of Technology, Institut National de
+ Recherche en Informatique et en Automatique, Keio University).
+ All Rights Reserved.
+
+ Permission to use, copy, modify and distribute the SVG DTD and its
+ accompanying documentation for any purpose and without fee is hereby
+ granted in perpetuity, provided that the above copyright notice and
+ this paragraph appear in all copies. The copyright holders make no
+ representation about the suitability of the DTD for any purpose.
+
+ It is provided "as is" without expressed or implied warranty.
+
+ Author: Jun Fujisawa <fujisawa.jun at canon.co.jp>
+ Revision: $Id: svg11-basic-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+-->
+<!-- This is the driver file for version 1.1 of the SVG Basic DTD.
+
+ This DTD is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//DTD SVG 1.1 Basic//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11-basic.dtd"
+-->
+<!ENTITY % SVG.version "-//W3C//DTD SVG 1.1 Basic//EN" >
+
+<!-- Use this URI to identify the default namespace:
+
+ "http://www.w3.org/2000/svg"
+
+ See the Qualified Names module for information
+ on the use of namespace prefixes in the DTD.
+-->
+<!ENTITY % NS.prefixed "IGNORE" >
+<!ENTITY % SVG.prefix "" >
+
+<!-- reserved for future use with document profiles -->
+<!ENTITY % SVG.profile "" >
+
+<!-- ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: -->
+
+<!-- Pre-Framework Redeclaration Placeholder ..................... -->
+<!ENTITY % svg-prefw-redecl.module "IGNORE" >
+<![%svg-prefw-redecl.module;[
+%svg-prefw-redecl.mod;]]>
+
+<!-- Document Model Module ....................................... -->
+<!ENTITY % svg-model.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Basic Document Model//EN"
+ "svg11-basic-model.mod" >
+
+<!-- Attribute Collection Module ................................. -->
+<!ENTITY % svg-attribs.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Basic Attribute Collection//EN"
+ "svg11-basic-attribs.mod" >
+
+<!-- Modular Framework Module .................................... -->
+<!ENTITY % svg-framework.module "INCLUDE" >
+<![%svg-framework.module;[
+<!ENTITY % svg-framework.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Modular Framework//EN"
+ "svg-framework.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Modular Framework Module ...................................... -->
+<!-- file: svg-framework.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-basic-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Modular Framework//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-framework.mod"
+
+ ....................................................................... -->
+
+<!-- Modular Framework
+
+ This module instantiates the modules needed o support the SVG
+ modularization model, including:
+
+ + Datatypes
+ + Qualified Name
+ + Document Model
+ + Attribute Collection
+-->
+
+<!ENTITY % svg-datatypes.module "INCLUDE" >
+<![%svg-datatypes.module;[
+<!ENTITY % svg-datatypes.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Datatypes//EN"
+ "svg-datatypes.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Datatypes Module .............................................. -->
+<!-- file: svg-datatypes.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-basic-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Datatypes//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-datatypes.mod"
+
+ ....................................................................... -->
+
+<!-- Datatypes
+
+ This module declares common data types for properties and attributes.
+-->
+
+<!-- feature specification -->
+<!ENTITY % Boolean.datatype "( false | true )" >
+
+<!-- 'clip-rule' or 'fill-rule' property/attribute value -->
+<!ENTITY % ClipFillRule.datatype "( nonzero | evenodd | inherit )" >
+
+<!-- media type, as per [RFC2045] -->
+<!ENTITY % ContentType.datatype "CDATA" >
+
+<!-- a <coordinate> -->
+<!ENTITY % Coordinate.datatype "CDATA" >
+
+<!-- a list of <coordinate>s -->
+<!ENTITY % Coordinates.datatype "CDATA" >
+
+<!-- a <color> value -->
+<!ENTITY % Color.datatype "CDATA" >
+
+<!-- a <integer> -->
+<!ENTITY % Integer.datatype "CDATA" >
+
+<!-- a language code, as per [RFC3066] -->
+<!ENTITY % LanguageCode.datatype "NMTOKEN" >
+
+<!-- comma-separated list of language codes, as per [RFC3066] -->
+<!ENTITY % LanguageCodes.datatype "CDATA" >
+
+<!-- a <length> -->
+<!ENTITY % Length.datatype "CDATA" >
+
+<!-- a list of <length>s -->
+<!ENTITY % Lengths.datatype "CDATA" >
+
+<!-- a <number> -->
+<!ENTITY % Number.datatype "CDATA" >
+
+<!-- a list of <number>s -->
+<!ENTITY % Numbers.datatype "CDATA" >
+
+<!-- opacity value (e.g., <number>) -->
+<!ENTITY % OpacityValue.datatype "CDATA" >
+
+<!-- a path data specification -->
+<!ENTITY % PathData.datatype "CDATA" >
+
+<!-- 'preserveAspectRatio' attribute specification -->
+<!ENTITY % PreserveAspectRatioSpec.datatype "CDATA" >
+
+<!-- script expression -->
+<!ENTITY % Script.datatype "CDATA" >
+
+<!-- An SVG color value (RGB plus optional ICC) -->
+<!ENTITY % SVGColor.datatype "CDATA" >
+
+<!-- arbitrary text string -->
+<!ENTITY % Text.datatype "CDATA" >
+
+<!-- list of transforms -->
+<!ENTITY % TransformList.datatype "CDATA" >
+
+<!-- a Uniform Resource Identifier, see [URI] -->
+<!ENTITY % URI.datatype "CDATA" >
+
+<!-- 'viewBox' attribute specification -->
+<!ENTITY % ViewBoxSpec.datatype "CDATA" >
+
+<!-- end of svg-datatypes.mod -->
+]]>
+
+<!ENTITY % svg-qname.module "INCLUDE" >
+<![%svg-qname.module;[
+<!ENTITY % svg-qname.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Qualified Name//EN"
+ "svg-qname.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Qualified Name Module ......................................... -->
+<!-- file: svg-qname.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-basic-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Qualified Name//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-qname.mod"
+
+ ....................................................................... -->
+
+<!-- Qualified Name
+
+ This module is contained in two parts, labeled Section 'A' and 'B':
+
+ Section A declares parameter entities to support namespace-
+ qualified names, namespace declarations, and name prefixing
+ for SVG and extensions.
+
+ Section B declares parameter entities used to provide
+ namespace-qualified names for all SVG element types:
+-->
+
+<!-- Section A: SVG XML Namespace Framework :::::::::::::::::::::: -->
+
+<!-- 1. Declare a %SVG.prefixed; conditional section keyword, used
+ to activate namespace prefixing. The default value should
+ inherit '%NS.prefixed;' from the DTD driver, so that unless
+ overridden, the default behaviour follows the overall DTD
+ prefixing scheme.
+-->
+<!ENTITY % NS.prefixed "IGNORE" >
+<!ENTITY % SVG.prefixed "%NS.prefixed;" >
+
+<!-- 2. Declare a parameter entity (eg., %SVG.xmlns;) containing
+ the URI reference used to identify the SVG namespace:
+-->
+<!ENTITY % SVG.xmlns "http://www.w3.org/2000/svg" >
+<!ENTITY % XLINK.xmlns "http://www.w3.org/1999/xlink" >
+
+<!-- 3. Declare parameter entities (eg., %SVG.prefix;) containing
+ the default namespace prefix string(s) to use when prefixing
+ is enabled. This may be overridden in the DTD driver or the
+ internal subset of an document instance. If no default prefix
+ is desired, this may be declared as an empty string.
+-->
+<!ENTITY % SVG.prefix "" >
+<!ENTITY % XLINK.prefix "xlink" >
+
+<!-- 4. Declare parameter entities (eg., %SVG.pfx;) containing the
+ colonized prefix(es) (eg., '%SVG.prefix;:') used when
+ prefixing is active, an empty string when it is not.
+-->
+<![%SVG.prefixed;[
+<!ENTITY % SVG.pfx "%SVG.prefix;:" >
+]]>
+<!ENTITY % SVG.pfx "" >
+<!ENTITY % XLINK.pfx "%XLINK.prefix;:" >
+
+<!-- 5. The parameter entity %SVG.xmlns.extra.attrib; may be
+ redeclared to contain any non-SVG namespace declaration
+ attributes for namespaces embedded in SVG. The default
+ is an empty string.
+-->
+<!ENTITY % SVG.xmlns.extra.attrib "" >
+
+<!-- Declare a parameter entity XLINK.xmlns.attrib containing
+ the XML Namespace declarations for XLink.
+-->
+<!ENTITY % XLINK.xmlns.attrib
+ "xmlns:%XLINK.prefix; %URI.datatype; #FIXED '%XLINK.xmlns;'"
+>
+
+<!-- Declare a parameter entity %NS.decl.attrib; containing
+ all XML Namespace declarations used in the DTD, plus the
+ xmlns declaration for SVG, its form dependent on whether
+ prefixing is active.
+-->
+<![%SVG.prefixed;[
+<!ENTITY % NS.decl.attrib
+ "xmlns:%SVG.prefix; %URI.datatype; #FIXED '%SVG.xmlns;'
+ %XLINK.xmlns.attrib;
+ %SVG.xmlns.extra.attrib;"
+>
+]]>
+<!ENTITY % NS.decl.attrib
+ "%XLINK.xmlns.attrib;
+ %SVG.xmlns.extra.attrib;"
+>
+
+<!-- Declare a parameter entity %SVG.xmlns.attrib; containing
+ all XML namespace declaration attributes used by SVG,
+ including a default xmlns attribute when prefixing is
+ inactive.
+-->
+<![%SVG.prefixed;[
+<!ENTITY % SVG.xmlns.attrib
+ "%NS.decl.attrib;"
+>
+]]>
+<!ENTITY % SVG.xmlns.attrib
+ "xmlns %URI.datatype; #FIXED '%SVG.xmlns;'
+ %XLINK.xmlns.attrib;"
+>
+
+<!-- Section B: SVG Qualified Names :::::::::::::::::::::::::::::: -->
+
+<!-- 6. This section declares parameter entities used to provide
+ namespace-qualified names for all SVG element types.
+-->
+
+<!-- module: svg-structure.mod ......................... -->
+
+<!ENTITY % SVG.svg.qname "%SVG.pfx;svg" >
+<!ENTITY % SVG.g.qname "%SVG.pfx;g" >
+<!ENTITY % SVG.defs.qname "%SVG.pfx;defs" >
+<!ENTITY % SVG.desc.qname "%SVG.pfx;desc" >
+<!ENTITY % SVG.title.qname "%SVG.pfx;title" >
+<!ENTITY % SVG.metadata.qname "%SVG.pfx;metadata" >
+<!ENTITY % SVG.symbol.qname "%SVG.pfx;symbol" >
+<!ENTITY % SVG.use.qname "%SVG.pfx;use" >
+
+<!-- module: svg-conditional.mod ....................... -->
+
+<!ENTITY % SVG.switch.qname "%SVG.pfx;switch" >
+
+<!-- module: svg-image.mod ............................. -->
+
+<!ENTITY % SVG.image.qname "%SVG.pfx;image" >
+
+<!-- module: svg-style.mod ............................. -->
+
+<!ENTITY % SVG.style.qname "%SVG.pfx;style" >
+
+<!-- module: svg-shape.mod ............................. -->
+
+<!ENTITY % SVG.path.qname "%SVG.pfx;path" >
+<!ENTITY % SVG.rect.qname "%SVG.pfx;rect" >
+<!ENTITY % SVG.circle.qname "%SVG.pfx;circle" >
+<!ENTITY % SVG.line.qname "%SVG.pfx;line" >
+<!ENTITY % SVG.ellipse.qname "%SVG.pfx;ellipse" >
+<!ENTITY % SVG.polyline.qname "%SVG.pfx;polyline" >
+<!ENTITY % SVG.polygon.qname "%SVG.pfx;polygon" >
+
+<!-- module: svg-text.mod .............................. -->
+
+<!ENTITY % SVG.text.qname "%SVG.pfx;text" >
+<!ENTITY % SVG.tspan.qname "%SVG.pfx;tspan" >
+<!ENTITY % SVG.tref.qname "%SVG.pfx;tref" >
+<!ENTITY % SVG.textPath.qname "%SVG.pfx;textPath" >
+<!ENTITY % SVG.altGlyph.qname "%SVG.pfx;altGlyph" >
+<!ENTITY % SVG.altGlyphDef.qname "%SVG.pfx;altGlyphDef" >
+<!ENTITY % SVG.altGlyphItem.qname "%SVG.pfx;altGlyphItem" >
+<!ENTITY % SVG.glyphRef.qname "%SVG.pfx;glyphRef" >
+
+<!-- module: svg-marker.mod ............................ -->
+
+<!ENTITY % SVG.marker.qname "%SVG.pfx;marker" >
+
+<!-- module: svg-profile.mod ........................... -->
+
+<!ENTITY % SVG.color-profile.qname "%SVG.pfx;color-profile" >
+
+<!-- module: svg-gradient.mod .......................... -->
+
+<!ENTITY % SVG.linearGradient.qname "%SVG.pfx;linearGradient" >
+<!ENTITY % SVG.radialGradient.qname "%SVG.pfx;radialGradient" >
+<!ENTITY % SVG.stop.qname "stop" >
+
+<!-- module: svg-pattern.mod ........................... -->
+
+<!ENTITY % SVG.pattern.qname "%SVG.pfx;pattern" >
+
+<!-- module: svg-clip.mod .............................. -->
+
+<!ENTITY % SVG.clipPath.qname "%SVG.pfx;clipPath" >
+
+<!-- module: svg-mask.mod .............................. -->
+
+<!ENTITY % SVG.mask.qname "%SVG.pfx;mask" >
+
+<!-- module: svg-filter.mod ............................ -->
+
+<!ENTITY % SVG.filter.qname "%SVG.pfx;filter" >
+<!ENTITY % SVG.feBlend.qname "%SVG.pfx;feBlend" >
+<!ENTITY % SVG.feColorMatrix.qname "%SVG.pfx;feColorMatrix" >
+<!ENTITY % SVG.feComponentTransfer.qname "%SVG.pfx;feComponentTransfer" >
+<!ENTITY % SVG.feComposite.qname "%SVG.pfx;feComposite" >
+<!ENTITY % SVG.feConvolveMatrix.qname "%SVG.pfx;feConvolveMatrix" >
+<!ENTITY % SVG.feDiffuseLighting.qname "%SVG.pfx;feDiffuseLighting" >
+<!ENTITY % SVG.feDisplacementMap.qname "%SVG.pfx;feDisplacementMap" >
+<!ENTITY % SVG.feFlood.qname "%SVG.pfx;feFlood" >
+<!ENTITY % SVG.feGaussianBlur.qname "%SVG.pfx;feGaussianBlur" >
+<!ENTITY % SVG.feImage.qname "%SVG.pfx;feImage" >
+<!ENTITY % SVG.feMerge.qname "%SVG.pfx;feMerge" >
+<!ENTITY % SVG.feMergeNode.qname "%SVG.pfx;feMergeNode" >
+<!ENTITY % SVG.feMorphology.qname "%SVG.pfx;feMorphology" >
+<!ENTITY % SVG.feOffset.qname "%SVG.pfx;feOffset" >
+<!ENTITY % SVG.feSpecularLighting.qname "%SVG.pfx;feSpecularLighting" >
+<!ENTITY % SVG.feTile.qname "%SVG.pfx;feTile" >
+<!ENTITY % SVG.feTurbulence.qname "%SVG.pfx;feTurbulence" >
+<!ENTITY % SVG.feDistantLight.qname "%SVG.pfx;feDistantLight" >
+<!ENTITY % SVG.fePointLight.qname "%SVG.pfx;fePointLight" >
+<!ENTITY % SVG.feSpotLight.qname "%SVG.pfx;feSpotLight" >
+<!ENTITY % SVG.feFuncR.qname "%SVG.pfx;feFuncR" >
+<!ENTITY % SVG.feFuncG.qname "%SVG.pfx;feFuncG" >
+<!ENTITY % SVG.feFuncB.qname "%SVG.pfx;feFuncB" >
+<!ENTITY % SVG.feFuncA.qname "%SVG.pfx;feFuncA" >
+
+<!-- module: svg-cursor.mod ............................ -->
+
+<!ENTITY % SVG.cursor.qname "%SVG.pfx;cursor" >
+
+<!-- module: svg-hyperlink.mod ......................... -->
+
+<!ENTITY % SVG.a.qname "%SVG.pfx;a" >
+
+<!-- module: svg-view.mod .............................. -->
+
+<!ENTITY % SVG.view.qname "%SVG.pfx;view" >
+
+<!-- module: svg-script.mod ............................ -->
+
+<!ENTITY % SVG.script.qname "%SVG.pfx;script" >
+
+<!-- module: svg-animation.mod ......................... -->
+
+<!ENTITY % SVG.animate.qname "%SVG.pfx;animate" >
+<!ENTITY % SVG.set.qname "%SVG.pfx;set" >
+<!ENTITY % SVG.animateMotion.qname "%SVG.pfx;animateMotion" >
+<!ENTITY % SVG.animateColor.qname "%SVG.pfx;animateColor" >
+<!ENTITY % SVG.animateTransform.qname "%SVG.pfx;animateTransform" >
+<!ENTITY % SVG.mpath.qname "%SVG.pfx;mpath" >
+
+<!-- module: svg-font.mod .............................. -->
+
+<!ENTITY % SVG.font.qname "%SVG.pfx;font" >
+<!ENTITY % SVG.font-face.qname "%SVG.pfx;font-face" >
+<!ENTITY % SVG.glyph.qname "%SVG.pfx;glyph" >
+<!ENTITY % SVG.missing-glyph.qname "%SVG.pfx;missing-glyph" >
+<!ENTITY % SVG.hkern.qname "%SVG.pfx;hkern" >
+<!ENTITY % SVG.vkern.qname "%SVG.pfx;vkern" >
+<!ENTITY % SVG.font-face-src.qname "%SVG.pfx;font-face-src" >
+<!ENTITY % SVG.font-face-uri.qname "%SVG.pfx;font-face-uri" >
+<!ENTITY % SVG.font-face-format.qname "%SVG.pfx;font-face-format" >
+<!ENTITY % SVG.font-face-name.qname "%SVG.pfx;font-face-name" >
+<!ENTITY % SVG.definition-src.qname "%SVG.pfx;definition-src" >
+
+<!-- module: svg-extensibility.mod ..................... -->
+
+<!ENTITY % SVG.foreignObject.qname "%SVG.pfx;foreignObject" >
+
+<!-- end of svg-qname.mod -->
+]]>
+
+<!ENTITY % svg-model.module "INCLUDE" >
+<![%svg-model.module;[
+<!-- instantiate the Document Model declared in the DTD driver -->
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Basic Document Model Module ................................... -->
+<!-- file: svg11-basic-model.mod
+
+ This is SVG Basic, a proper subset of SVG.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-basic-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Basic Document Model//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11-basic-model.mod"
+
+ ....................................................................... -->
+
+<!-- SVG 1.1 Basic Document Model
+
+ This module describes the groupings of elements that make up
+ common content models for SVG elements.
+-->
+
+<!-- Content Models (Default) .......................... -->
+
+<!ENTITY % SVG.Marker.class "" >
+
+<!-- module: svg-structure.mod ......................... -->
+
+<!ENTITY % SVG.Description.extra.class "" >
+<!ENTITY % SVG.Description.class
+ "%SVG.desc.qname; | %SVG.title.qname; | %SVG.metadata.qname;
+ %SVG.Description.extra.class;"
+>
+
+<!ENTITY % SVG.Use.extra.class "" >
+<!ENTITY % SVG.Use.class
+ "| %SVG.use.qname; %SVG.Use.extra.class;"
+>
+
+<!ENTITY % SVG.Structure.extra.class "" >
+<!ENTITY % SVG.Structure.class
+ "| %SVG.svg.qname; | %SVG.g.qname; | %SVG.defs.qname; | %SVG.symbol.qname;
+ %SVG.Use.class; %SVG.Structure.extra.class;"
+>
+
+<!-- module: svg-conditional.mod ....................... -->
+
+<!ENTITY % SVG.Conditional.extra.class "" >
+<!ENTITY % SVG.Conditional.class
+ "| %SVG.switch.qname; %SVG.Conditional.extra.class;"
+>
+
+<!-- module: svg-image.mod ............................. -->
+
+<!ENTITY % SVG.Image.extra.class "" >
+<!ENTITY % SVG.Image.class
+ "| %SVG.image.qname; %SVG.Image.extra.class;"
+>
+
+<!-- module: svg-style.mod ............................. -->
+
+<!ENTITY % SVG.Style.extra.class "" >
+<!ENTITY % SVG.Style.class
+ "| %SVG.style.qname; %SVG.Style.extra.class;"
+>
+
+<!-- module: svg-shape.mod ............................. -->
+
+<!ENTITY % SVG.Shape.extra.class "" >
+<!ENTITY % SVG.Shape.class
+ "| %SVG.path.qname; | %SVG.rect.qname; | %SVG.circle.qname;
+ | %SVG.line.qname; | %SVG.ellipse.qname; | %SVG.polyline.qname;
+ | %SVG.polygon.qname; %SVG.Shape.extra.class;"
+>
+
+<!-- module: svg-text.mod .............................. -->
+
+<!ENTITY % SVG.Text.extra.class "" >
+<!ENTITY % SVG.Text.class
+ "| %SVG.text.qname; %SVG.Text.extra.class;"
+>
+
+<!ENTITY % SVG.TextContent.extra.class "" >
+<!ENTITY % SVG.TextContent.class
+ "| %SVG.tspan.qname; | %SVG.tref.qname; | %SVG.textPath.qname;
+ %SVG.TextContent.extra.class;"
+>
+
+<!-- module: svg-profile.mod ........................... -->
+
+<!ENTITY % SVG.Profile.extra.class "" >
+<!ENTITY % SVG.Profile.class
+ "| %SVG.color-profile.qname; %SVG.Profile.extra.class;"
+>
+
+<!-- module: svg-gradient.mod .......................... -->
+
+<!ENTITY % SVG.Gradient.extra.class "" >
+<!ENTITY % SVG.Gradient.class
+ "| %SVG.linearGradient.qname; | %SVG.radialGradient.qname;
+ %SVG.Gradient.extra.class;"
+>
+
+<!-- module: svg-pattern.mod ........................... -->
+
+<!ENTITY % SVG.Pattern.extra.class "" >
+<!ENTITY % SVG.Pattern.class
+ "| %SVG.pattern.qname; %SVG.Pattern.extra.class;"
+>
+
+<!-- module: svg-basic-clip.mod ........................ -->
+
+<!ENTITY % SVG.Clip.extra.class "" >
+<!ENTITY % SVG.Clip.class
+ "| %SVG.clipPath.qname; %SVG.Clip.extra.class;"
+>
+
+<!-- module: svg-mask.mod .............................. -->
+
+<!ENTITY % SVG.Mask.extra.class "" >
+<!ENTITY % SVG.Mask.class
+ "| %SVG.mask.qname; %SVG.Mask.extra.class;"
+>
+
+<!-- module: svg-basic-filter.mod ...................... -->
+
+<!ENTITY % SVG.Filter.extra.class "" >
+<!ENTITY % SVG.Filter.class
+ "| %SVG.filter.qname; %SVG.Filter.extra.class;"
+>
+
+<!ENTITY % SVG.FilterPrimitive.extra.class "" >
+<!ENTITY % SVG.FilterPrimitive.class
+ "| %SVG.feBlend.qname; | %SVG.feColorMatrix.qname;
+ | %SVG.feComponentTransfer.qname; | %SVG.feComposite.qname;
+ | %SVG.feFlood.qname; | %SVG.feGaussianBlur.qname; | %SVG.feImage.qname;
+ | %SVG.feMerge.qname; | %SVG.feOffset.qname; | %SVG.feTile.qname;
+ %SVG.FilterPrimitive.extra.class;"
+>
+
+<!-- module: svg-cursor.mod ............................ -->
+
+<!ENTITY % SVG.Cursor.extra.class "" >
+<!ENTITY % SVG.Cursor.class
+ "| %SVG.cursor.qname; %SVG.Cursor.extra.class;"
+>
+
+<!-- module: svg-hyperlink.mod ......................... -->
+
+<!ENTITY % SVG.Hyperlink.extra.class "" >
+<!ENTITY % SVG.Hyperlink.class
+ "| %SVG.a.qname; %SVG.Hyperlink.extra.class;"
+>
+
+<!-- module: svg-view.mod .............................. -->
+
+<!ENTITY % SVG.View.extra.class "" >
+<!ENTITY % SVG.View.class
+ "| %SVG.view.qname; %SVG.View.extra.class;"
+>
+
+<!-- module: svg-script.mod ............................ -->
+
+<!ENTITY % SVG.Script.extra.class "" >
+<!ENTITY % SVG.Script.class
+ "| %SVG.script.qname; %SVG.Script.extra.class;"
+>
+
+<!-- module: svg-animation.mod ......................... -->
+
+<!ENTITY % SVG.Animation.extra.class "" >
+<!ENTITY % SVG.Animation.class
+ "%SVG.animate.qname; | %SVG.set.qname; | %SVG.animateMotion.qname; |
+ %SVG.animateColor.qname; | %SVG.animateTransform.qname;
+ %SVG.Animation.extra.class;"
+>
+
+<!-- module: svg-font.mod .............................. -->
+
+<!ENTITY % SVG.Font.extra.class "" >
+<!ENTITY % SVG.Font.class
+ "| %SVG.font.qname; | %SVG.font-face.qname; %SVG.Font.extra.class;"
+>
+
+<!-- module: svg-extensibility.mod ..................... -->
+
+<!ENTITY % SVG.Extensibility.extra.class "" >
+<!ENTITY % SVG.Extensibility.class
+ "| %SVG.foreignObject.qname; %SVG.Extensibility.extra.class;"
+>
+
+<!-- end of svg11-basic-model.mod -->
+]]>
+
+<!ENTITY % svg-attribs.module "INCLUDE" >
+<![%svg-attribs.module;[
+<!-- instantiate the Attribute Collection declared in the DTD driver -->
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Basic Attribute Collection Module ............................. -->
+<!-- file: svg11-basic-attribs.mod
+
+ This is SVG Basic, a proper subset of SVG.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-basic-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Basic Attribute Collection//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11-basic-attribs.mod"
+
+ ....................................................................... -->
+
+<!-- SVG 1.1 Basic Attribute Collection
+
+ This module defines the set of common attributes that can be present
+ on many SVG elements.
+-->
+
+<!-- module: svg-conditional.mod ....................... -->
+
+<!ENTITY % ExtensionList.datatype "CDATA" >
+<!ENTITY % FeatureList.datatype "CDATA" >
+
+<!ENTITY % SVG.Conditional.extra.attrib "" >
+<!ENTITY % SVG.Conditional.attrib
+ "requiredFeatures %FeatureList.datatype; #IMPLIED
+ requiredExtensions %ExtensionList.datatype; #IMPLIED
+ systemLanguage %LanguageCodes.datatype; #IMPLIED
+ %SVG.Conditional.extra.attrib;"
+>
+
+<!-- module: svg-style.mod ............................. -->
+
+<!ENTITY % ClassList.datatype "CDATA" >
+<!ENTITY % StyleSheet.datatype "CDATA" >
+
+<!ENTITY % SVG.Style.extra.attrib "" >
+<!ENTITY % SVG.Style.attrib
+ "style %StyleSheet.datatype; #IMPLIED
+ class %ClassList.datatype; #IMPLIED
+ %SVG.Style.extra.attrib;"
+>
+
+<!-- module: svg-text.mod .............................. -->
+
+<!ENTITY % BaselineShiftValue.datatype "CDATA" >
+<!ENTITY % FontFamilyValue.datatype "CDATA" >
+<!ENTITY % FontSizeValue.datatype "CDATA" >
+<!ENTITY % FontSizeAdjustValue.datatype "CDATA" >
+<!ENTITY % GlyphOrientationHorizontalValue.datatype "CDATA" >
+<!ENTITY % GlyphOrientationVerticalValue.datatype "CDATA" >
+<!ENTITY % KerningValue.datatype "CDATA" >
+<!ENTITY % SpacingValue.datatype "CDATA" >
+<!ENTITY % TextDecorationValue.datatype "CDATA" >
+
+<!ENTITY % SVG.Text.extra.attrib "" >
+<!ENTITY % SVG.Text.attrib
+ "writing-mode ( lr-tb | rl-tb | tb-rl | lr | rl | tb | inherit ) #IMPLIED
+ %SVG.Text.extra.attrib;"
+>
+
+<!ENTITY % SVG.TextContent.extra.attrib "" >
+<!ENTITY % SVG.TextContent.attrib
+ "alignment-baseline ( auto | baseline | before-edge | text-before-edge |
+ middle | central | after-edge | text-after-edge |
+ ideographic | alphabetic | hanging | mathematical |
+ inherit ) #IMPLIED
+ baseline-shift %BaselineShiftValue.datatype; #IMPLIED
+ direction ( ltr | rtl | inherit ) #IMPLIED
+ dominant-baseline ( auto | use-script | no-change | reset-size |
+ ideographic | alphabetic | hanging | mathematical |
+ central | middle | text-after-edge | text-before-edge |
+ inherit ) #IMPLIED
+ glyph-orientation-horizontal %GlyphOrientationHorizontalValue.datatype;
+ #IMPLIED
+ glyph-orientation-vertical %GlyphOrientationVerticalValue.datatype;
+ #IMPLIED
+ kerning %KerningValue.datatype; #IMPLIED
+ letter-spacing %SpacingValue.datatype; #IMPLIED
+ text-anchor ( start | middle | end | inherit ) #IMPLIED
+ text-decoration %TextDecorationValue.datatype; #IMPLIED
+ unicode-bidi ( normal | embed | bidi-override | inherit ) #IMPLIED
+ word-spacing %SpacingValue.datatype; #IMPLIED
+ %SVG.TextContent.extra.attrib;"
+>
+
+<!ENTITY % SVG.Font.extra.attrib "" >
+<!ENTITY % SVG.Font.attrib
+ "font-family %FontFamilyValue.datatype; #IMPLIED
+ font-size %FontSizeValue.datatype; #IMPLIED
+ font-size-adjust %FontSizeAdjustValue.datatype; #IMPLIED
+ font-stretch ( normal | wider | narrower | ultra-condensed |
+ extra-condensed | condensed | semi-condensed |
+ semi-expanded | expanded | extra-expanded |
+ ultra-expanded | inherit ) #IMPLIED
+ font-style ( normal | italic | oblique | inherit ) #IMPLIED
+ font-variant ( normal | small-caps | inherit ) #IMPLIED
+ font-weight ( normal | bold | bolder | lighter | 100 | 200 | 300 | 400 |
+ 500 | 600 | 700 | 800 | 900 | inherit ) #IMPLIED
+ %SVG.Font.extra.attrib;"
+>
+
+<!-- module: svg-profile.mod ........................... -->
+
+<!ENTITY % SVG.Profile.extra.attrib "" >
+<!ENTITY % SVG.Profile.attrib
+ "color-profile CDATA #IMPLIED
+ %SVG.Profile.extra.attrib;"
+>
+
+<!-- module: svg-gradient.mod .......................... -->
+
+<!ENTITY % NumberOrPercentage.datatype "CDATA" >
+
+<!ENTITY % SVG.Gradient.extra.attrib "" >
+<!ENTITY % SVG.Gradient.attrib
+ "stop-color %SVGColor.datatype; #IMPLIED
+ stop-opacity %OpacityValue.datatype; #IMPLIED
+ %SVG.Gradient.extra.attrib;"
+>
+
+<!-- module: svg-basic-clip.mod ........................ -->
+
+<!ENTITY % ClipPathValue.datatype "CDATA" >
+
+<!ENTITY % SVG.Clip.extra.attrib "" >
+<!ENTITY % SVG.Clip.attrib
+ "clip-path %ClipPathValue.datatype; #IMPLIED
+ clip-rule %ClipFillRule.datatype; #IMPLIED
+ %SVG.Clip.extra.attrib;"
+>
+
+<!-- module: svg-mask.mod .............................. -->
+
+<!ENTITY % MaskValue.datatype "CDATA" >
+
+<!ENTITY % SVG.Mask.extra.attrib "" >
+<!ENTITY % SVG.Mask.attrib
+ "mask %MaskValue.datatype; #IMPLIED
+ %SVG.Mask.extra.attrib;"
+>
+
+<!-- module: svg-basic-filter.mod ...................... -->
+
+<!ENTITY % FilterValue.datatype "CDATA" >
+<!ENTITY % NumberOptionalNumber.datatype "CDATA" >
+
+<!ENTITY % SVG.Filter.extra.attrib "" >
+<!ENTITY % SVG.Filter.attrib
+ "filter %FilterValue.datatype; #IMPLIED
+ %SVG.Filter.extra.attrib;"
+>
+
+<!ENTITY % SVG.FilterColor.extra.attrib "" >
+<!ENTITY % SVG.FilterColor.attrib
+ "color-interpolation-filters ( auto | sRGB | linearRGB | inherit )
+ #IMPLIED
+ %SVG.FilterColor.extra.attrib;"
+>
+
+<!-- module: svg-cursor.mod ............................ -->
+
+<!ENTITY % CursorValue.datatype "CDATA" >
+
+<!ENTITY % SVG.Cursor.extra.attrib "" >
+<!ENTITY % SVG.Cursor.attrib
+ "cursor %CursorValue.datatype; #IMPLIED
+ %SVG.Cursor.extra.attrib;"
+>
+
+<!-- end of svg11-basic-attribs.mod -->
+]]>
+
+<!-- end of svg-framework.mod -->
+]]>
+
+<!-- Post-Framework Redeclaration Placeholder .................... -->
+<!ENTITY % svg-postfw-redecl.module "IGNORE" >
+<![%svg-postfw-redecl.module;[
+%svg-postfw-redecl.mod;]]>
+
+<!-- ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: -->
+
+<!-- Core Attribute Module ....................................... -->
+<!ENTITY % svg-core-attrib.module "INCLUDE" >
+<![%svg-core-attrib.module;[
+<!ENTITY % svg-core-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Core Attribute//EN"
+ "svg-core-attrib.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Core Attribute Module ......................................... -->
+<!-- file: svg-core-attrib.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-basic-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Core Attribute//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-core-attrib.mod"
+
+ ....................................................................... -->
+
+<!-- Core Attribute
+
+ id, xml:base, xml:lang, xml:space
+
+ This module defines the core set of attributes that can be present on
+ any element.
+-->
+
+<!ENTITY % SVG.id.attrib
+ "id ID #IMPLIED"
+>
+
+<!ENTITY % SVG.base.attrib
+ "xml:base %URI.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.lang.attrib
+ "xml:lang %LanguageCode.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.space.attrib
+ "xml:space ( default | preserve ) #IMPLIED"
+>
+
+<!ENTITY % SVG.Core.extra.attrib "" >
+
+<!ENTITY % SVG.Core.attrib
+ "%SVG.id.attrib;
+ %SVG.base.attrib;
+ %SVG.lang.attrib;
+ %SVG.space.attrib;
+ %SVG.Core.extra.attrib;"
+>
+
+<!-- end of svg-core-attrib.mod -->
+]]>
+
+<!-- Viewport Attribute Module ................................... -->
+<!ENTITY % svg-viewport-attrib.module "INCLUDE" >
+<![%svg-viewport-attrib.module;[
+<!ENTITY % svg-viewport-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Viewport Attribute//EN"
+ "svg-viewport-attrib.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Viewport Attribute Module ..................................... -->
+<!-- file: svg-viewport-attrib.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-basic-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Viewport Attribute//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-viewport-attrib.mod"
+
+ ....................................................................... -->
+
+<!-- Viewport Attribute
+
+ clip, overflow
+
+ This module defines the Viewport attribute set.
+-->
+
+<!-- 'clip' property/attribute value (e.g., 'auto', rect(...)) -->
+<!ENTITY % ClipValue.datatype "CDATA" >
+
+<!ENTITY % SVG.clip.attrib
+ "clip %ClipValue.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.overflow.attrib
+ "overflow ( visible | hidden | scroll | auto | inherit ) #IMPLIED"
+>
+
+<!ENTITY % SVG.Viewport.extra.attrib "" >
+
+<!ENTITY % SVG.Viewport.attrib
+ "%SVG.clip.attrib;
+ %SVG.overflow.attrib;
+ %SVG.Viewport.extra.attrib;"
+>
+
+<!-- end of svg-viewport-attrib.mod -->
+]]>
+
+<!-- Paint Attribute Module ...................................... -->
+<!ENTITY % svg-paint-attrib.module "INCLUDE" >
+<![%svg-paint-attrib.module;[
+<!ENTITY % svg-paint-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Paint Attribute//EN"
+ "svg-paint-attrib.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Paint Attribute Module ........................................ -->
+<!-- file: svg-paint-attrib.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-basic-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Paint Attribute//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-paint-attrib.mod"
+
+ ....................................................................... -->
+
+<!-- Paint Attribute
+
+ fill, fill-rule, stroke, stroke-dasharray, stroke-dashoffset,
+ stroke-linecap, stroke-linejoin, stroke-miterlimit, stroke-width, color,
+ color-interpolation, color-rendering
+
+ This module defines the Paint and Color attribute sets.
+-->
+
+<!-- a 'fill' or 'stroke' property/attribute value: <paint> -->
+<!ENTITY % Paint.datatype "CDATA" >
+
+<!-- 'stroke-dasharray' property/attribute value (e.g., 'none', list of <number>s) -->
+<!ENTITY % StrokeDashArrayValue.datatype "CDATA" >
+
+<!-- 'stroke-dashoffset' property/attribute value (e.g., 'none', <legnth>) -->
+<!ENTITY % StrokeDashOffsetValue.datatype "CDATA" >
+
+<!-- 'stroke-miterlimit' property/attribute value (e.g., <number>) -->
+<!ENTITY % StrokeMiterLimitValue.datatype "CDATA" >
+
+<!-- 'stroke-width' property/attribute value (e.g., <length>) -->
+<!ENTITY % StrokeWidthValue.datatype "CDATA" >
+
+<!ENTITY % SVG.fill.attrib
+ "fill %Paint.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.fill-rule.attrib
+ "fill-rule %ClipFillRule.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.stroke.attrib
+ "stroke %Paint.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.stroke-dasharray.attrib
+ "stroke-dasharray %StrokeDashArrayValue.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.stroke-dashoffset.attrib
+ "stroke-dashoffset %StrokeDashOffsetValue.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.stroke-linecap.attrib
+ "stroke-linecap ( butt | round | square | inherit ) #IMPLIED"
+>
+
+<!ENTITY % SVG.stroke-linejoin.attrib
+ "stroke-linejoin ( miter | round | bevel | inherit ) #IMPLIED"
+>
+
+<!ENTITY % SVG.stroke-miterlimit.attrib
+ "stroke-miterlimit %StrokeMiterLimitValue.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.stroke-width.attrib
+ "stroke-width %StrokeWidthValue.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.Paint.extra.attrib "" >
+
+<!ENTITY % SVG.Paint.attrib
+ "%SVG.fill.attrib;
+ %SVG.fill-rule.attrib;
+ %SVG.stroke.attrib;
+ %SVG.stroke-dasharray.attrib;
+ %SVG.stroke-dashoffset.attrib;
+ %SVG.stroke-linecap.attrib;
+ %SVG.stroke-linejoin.attrib;
+ %SVG.stroke-miterlimit.attrib;
+ %SVG.stroke-width.attrib;
+ %SVG.Paint.extra.attrib;"
+>
+
+<!ENTITY % SVG.color.attrib
+ "color %Color.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.color-interpolation.attrib
+ "color-interpolation ( auto | sRGB | linearRGB | inherit ) #IMPLIED"
+>
+
+<!ENTITY % SVG.color-rendering.attrib
+ "color-rendering ( auto | optimizeSpeed | optimizeQuality | inherit )
+ #IMPLIED"
+>
+
+<!ENTITY % SVG.Color.extra.attrib "" >
+
+<!ENTITY % SVG.Color.attrib
+ "%SVG.color.attrib;
+ %SVG.color-interpolation.attrib;
+ %SVG.color-rendering.attrib;
+ %SVG.Color.extra.attrib;"
+>
+
+<!-- end of svg-paint-attrib.mod -->
+]]>
+
+<!-- Opacity Attribute Module .................................... -->
+<!ENTITY % svg-opacity-attrib.module "INCLUDE" >
+<![%svg-opacity-attrib.module;[
+<!ENTITY % svg-opacity-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Paint Opacity Attribute//EN"
+ "svg-opacity-attrib.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Paint Opacity Attribute Module ................................ -->
+<!-- file: svg-opacity-attrib.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-basic-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Paint Opacity Attribute//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-opacity-attrib.mod"
+
+ ....................................................................... -->
+
+<!-- Paint Opacity Attribute
+
+ opacity, fill-opacity, stroke-opacity
+
+ This module defines the Opacity attribute set.
+-->
+
+<!ENTITY % SVG.opacity.attrib
+ "opacity %OpacityValue.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.fill-opacity.attrib
+ "fill-opacity %OpacityValue.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.stroke-opacity.attrib
+ "stroke-opacity %OpacityValue.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.Opacity.extra.attrib "" >
+
+<!ENTITY % SVG.Opacity.attrib
+ "%SVG.opacity.attrib;
+ %SVG.fill-opacity.attrib;
+ %SVG.stroke-opacity.attrib;
+ %SVG.Opacity.extra.attrib;"
+>
+
+<!-- end of svg-opacity-attrib.mod -->
+]]>
+
+<!-- Graphics Attribute Module ................................... -->
+<!ENTITY % svg-graphics-attrib.module "INCLUDE" >
+<![%svg-graphics-attrib.module;[
+<!ENTITY % svg-graphics-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Graphics Attribute//EN"
+ "svg-graphics-attrib.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Graphics Attribute Module ..................................... -->
+<!-- file: svg-graphics-attrib.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-basic-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Graphics Attribute//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-graphics-attrib.mod"
+
+ ....................................................................... -->
+
+<!-- Graphics Attribute
+
+ display, image-rendering, pointer-events, shape-rendering,
+ text-rendering, visibility
+
+ This module defines the Graphics attribute set.
+-->
+
+<!ENTITY % SVG.display.attrib
+ "display ( inline | block | list-item | run-in | compact | marker |
+ table | inline-table | table-row-group | table-header-group |
+ table-footer-group | table-row | table-column-group |
+ table-column | table-cell | table-caption | none | inherit )
+ #IMPLIED"
+>
+
+<!ENTITY % SVG.image-rendering.attrib
+ "image-rendering ( auto | optimizeSpeed | optimizeQuality | inherit )
+ #IMPLIED"
+>
+
+<!ENTITY % SVG.pointer-events.attrib
+ "pointer-events ( visiblePainted | visibleFill | visibleStroke | visible |
+ painted | fill | stroke | all | none | inherit )
+ #IMPLIED"
+>
+
+<!ENTITY % SVG.shape-rendering.attrib
+ "shape-rendering ( auto | optimizeSpeed | crispEdges | geometricPrecision |
+ inherit ) #IMPLIED"
+>
+
+<!ENTITY % SVG.text-rendering.attrib
+ "text-rendering ( auto | optimizeSpeed | optimizeLegibility |
+ geometricPrecision | inherit ) #IMPLIED"
+>
+
+<!ENTITY % SVG.visibility.attrib
+ "visibility ( visible | hidden | inherit ) #IMPLIED"
+>
+
+<!ENTITY % SVG.Graphics.extra.attrib "" >
+
+<!ENTITY % SVG.Graphics.attrib
+ "%SVG.display.attrib;
+ %SVG.image-rendering.attrib;
+ %SVG.pointer-events.attrib;
+ %SVG.shape-rendering.attrib;
+ %SVG.text-rendering.attrib;
+ %SVG.visibility.attrib;
+ %SVG.Graphics.extra.attrib;"
+>
+
+<!-- end of svg-graphics-attrib.mod -->
+]]>
+
+<!-- Document Events Attribute Module ............................ -->
+<!ENTITY % svg-docevents-attrib.module "INCLUDE" >
+<![%svg-docevents-attrib.module;[
+<!ENTITY % svg-docevents-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Document Events Attribute//EN"
+ "svg-docevents-attrib.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Document Events Attribute Module .............................. -->
+<!-- file: svg-docevents-attrib.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-basic-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Document Events Attribute//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-docevents-attrib.mod"
+
+ ....................................................................... -->
+
+<!-- Document Events Attribute
+
+ onunload, onabort, onerror, onresize, onscroll, onzoom
+
+ This module defines the DocumentEvents attribute set.
+-->
+
+<!ENTITY % SVG.onunload.attrib
+ "onunload %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onabort.attrib
+ "onabort %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onerror.attrib
+ "onerror %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onresize.attrib
+ "onresize %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onscroll.attrib
+ "onscroll %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onzoom.attrib
+ "onzoom %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.DocumentEvents.extra.attrib "" >
+
+<!ENTITY % SVG.DocumentEvents.attrib
+ "%SVG.onunload.attrib;
+ %SVG.onabort.attrib;
+ %SVG.onerror.attrib;
+ %SVG.onresize.attrib;
+ %SVG.onscroll.attrib;
+ %SVG.onzoom.attrib;
+ %SVG.DocumentEvents.extra.attrib;"
+>
+
+<!-- end of svg-docevents-attrib.mod -->
+]]>
+
+<!-- Graphical Element Events Attribute Module ................... -->
+<!ENTITY % svg-graphevents-attrib.module "INCLUDE" >
+<![%svg-graphevents-attrib.module;[
+<!ENTITY % svg-graphevents-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Graphical Element Events Attribute//EN"
+ "svg-graphevents-attrib.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Graphical Element Events Attribute Module ..................... -->
+<!-- file: svg-graphevents-attrib.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-basic-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Graphical Element Events Attribute//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-graphevents-attrib.mod"
+
+ ....................................................................... -->
+
+<!-- Graphical Element Events Attribute
+
+ onfocusin, onfocusout, onactivate, onclick, onmousedown, onmouseup,
+ onmouseover, onmousemove, onmouseout, onload
+
+ This module defines the GraphicalEvents attribute set.
+-->
+
+<!ENTITY % SVG.onfocusin.attrib
+ "onfocusin %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onfocusout.attrib
+ "onfocusout %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onactivate.attrib
+ "onactivate %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onclick.attrib
+ "onclick %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onmousedown.attrib
+ "onmousedown %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onmouseup.attrib
+ "onmouseup %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onmouseover.attrib
+ "onmouseover %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onmousemove.attrib
+ "onmousemove %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onmouseout.attrib
+ "onmouseout %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onload.attrib
+ "onload %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.GraphicalEvents.extra.attrib "" >
+
+<!ENTITY % SVG.GraphicalEvents.attrib
+ "%SVG.onfocusin.attrib;
+ %SVG.onfocusout.attrib;
+ %SVG.onactivate.attrib;
+ %SVG.onclick.attrib;
+ %SVG.onmousedown.attrib;
+ %SVG.onmouseup.attrib;
+ %SVG.onmouseover.attrib;
+ %SVG.onmousemove.attrib;
+ %SVG.onmouseout.attrib;
+ %SVG.onload.attrib;
+ %SVG.GraphicalEvents.extra.attrib;"
+>
+
+<!-- end of svg-graphevents-attrib.mod -->
+]]>
+
+<!-- Animation Events Attribute Module ........................... -->
+<!ENTITY % svg-animevents-attrib.module "INCLUDE" >
+<![%svg-animevents-attrib.module;[
+<!ENTITY % svg-animevents-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Animation Events Attribute//EN"
+ "svg-animevents-attrib.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Animation Events Attribute Module ............................. -->
+<!-- file: svg-animevents-attrib.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-basic-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Animation Events Attribute//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-animevents-attrib.mod"
+
+ ....................................................................... -->
+
+<!-- Animation Events Attribute
+
+ onbegin, onend, onrepeat, onload
+
+ This module defines the AnimationEvents attribute set.
+-->
+
+<!ENTITY % SVG.onbegin.attrib
+ "onbegin %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onend.attrib
+ "onend %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onrepeat.attrib
+ "onrepeat %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onload.attrib
+ "onload %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.AnimationEvents.extra.attrib "" >
+
+<!ENTITY % SVG.AnimationEvents.attrib
+ "%SVG.onbegin.attrib;
+ %SVG.onend.attrib;
+ %SVG.onrepeat.attrib;
+ %SVG.onload.attrib;
+ %SVG.AnimationEvents.extra.attrib;"
+>
+
+<!-- end of svg-animevents-attrib.mod -->
+]]>
+
+<!-- XLink Attribute Module ...................................... -->
+<!ENTITY % svg-xlink-attrib.module "INCLUDE" >
+<![%svg-xlink-attrib.module;[
+<!ENTITY % svg-xlink-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 XLink Attribute//EN"
+ "svg-xlink-attrib.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 XLink Attribute Module ........................................ -->
+<!-- file: svg-xlink-attrib.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-basic-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 XLink Attribute//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-xlink-attrib.mod"
+
+ ....................................................................... -->
+
+<!-- XLink Attribute
+
+ type, href, role, arcrole, title, show, actuate
+
+ This module defines the XLink, XLinkRequired, XLinkEmbed, and
+ XLinkReplace attribute set.
+-->
+
+<!ENTITY % SVG.XLink.extra.attrib "" >
+
+<!ENTITY % SVG.XLink.attrib
+ "%XLINK.xmlns.attrib;
+ %XLINK.pfx;type ( simple ) #FIXED 'simple'
+ %XLINK.pfx;href %URI.datatype; #IMPLIED
+ %XLINK.pfx;role %URI.datatype; #IMPLIED
+ %XLINK.pfx;arcrole %URI.datatype; #IMPLIED
+ %XLINK.pfx;title CDATA #IMPLIED
+ %XLINK.pfx;show ( other ) 'other'
+ %XLINK.pfx;actuate ( onLoad ) #FIXED 'onLoad'
+ %SVG.XLink.extra.attrib;"
+>
+
+<!ENTITY % SVG.XLinkRequired.extra.attrib "" >
+
+<!ENTITY % SVG.XLinkRequired.attrib
+ "%XLINK.xmlns.attrib;
+ %XLINK.pfx;type ( simple ) #FIXED 'simple'
+ %XLINK.pfx;href %URI.datatype; #REQUIRED
+ %XLINK.pfx;role %URI.datatype; #IMPLIED
+ %XLINK.pfx;arcrole %URI.datatype; #IMPLIED
+ %XLINK.pfx;title CDATA #IMPLIED
+ %XLINK.pfx;show ( other ) 'other'
+ %XLINK.pfx;actuate ( onLoad ) #FIXED 'onLoad'
+ %SVG.XLinkRequired.extra.attrib;"
+>
+
+<!ENTITY % SVG.XLinkEmbed.extra.attrib "" >
+
+<!ENTITY % SVG.XLinkEmbed.attrib
+ "%XLINK.xmlns.attrib;
+ %XLINK.pfx;type ( simple ) #FIXED 'simple'
+ %XLINK.pfx;href %URI.datatype; #REQUIRED
+ %XLINK.pfx;role %URI.datatype; #IMPLIED
+ %XLINK.pfx;arcrole %URI.datatype; #IMPLIED
+ %XLINK.pfx;title CDATA #IMPLIED
+ %XLINK.pfx;show ( embed ) 'embed'
+ %XLINK.pfx;actuate ( onLoad ) #FIXED 'onLoad'
+ %SVG.XLinkEmbed.extra.attrib;"
+>
+
+<!ENTITY % SVG.XLinkReplace.extra.attrib "" >
+
+<!ENTITY % SVG.XLinkReplace.attrib
+ "%XLINK.xmlns.attrib;
+ %XLINK.pfx;type ( simple ) #FIXED 'simple'
+ %XLINK.pfx;href %URI.datatype; #REQUIRED
+ %XLINK.pfx;role %URI.datatype; #IMPLIED
+ %XLINK.pfx;arcrole %URI.datatype; #IMPLIED
+ %XLINK.pfx;title CDATA #IMPLIED
+ %XLINK.pfx;show ( new | replace ) 'replace'
+ %XLINK.pfx;actuate ( onRequest ) #FIXED 'onRequest'
+ %SVG.XLinkReplace.extra.attrib;"
+>
+
+<!-- end of svg-xlink-attrib.mod -->
+]]>
+
+<!-- External Resources Attribute Module ......................... -->
+<!ENTITY % svg-extresources-attrib.module "INCLUDE" >
+<![%svg-extresources-attrib.module;[
+<!ENTITY % svg-extresources-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 External Resources Attribute//EN"
+ "svg-extresources-attrib.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 External Resources Attribute Module ........................... -->
+<!-- file: svg-extresources-attrib.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-basic-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 External Resources Attribute//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-extresources-attrib.mod"
+
+ ....................................................................... -->
+
+<!-- External Resources Attribute
+
+ externalResourcesRequired
+
+ This module defines the External attribute set.
+-->
+
+<!ENTITY % SVG.externalResourcesRequired.attrib
+ "externalResourcesRequired %Boolean.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.External.extra.attrib "" >
+
+<!ENTITY % SVG.External.attrib
+ "%SVG.externalResourcesRequired.attrib;
+ %SVG.External.extra.attrib;"
+>
+
+<!-- end of svg-extresources-attrib.mod -->
+]]>
+
+<!-- ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: -->
+
+<!-- Structure Module ............................................ -->
+<!ENTITY % svg-structure.module "INCLUDE" >
+<![%svg-structure.module;[
+<!ENTITY % svg-structure.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Structure//EN"
+ "svg-structure.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Structure Module .............................................. -->
+<!-- file: svg-structure.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-basic-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Structure//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-structure.mod"
+
+ ....................................................................... -->
+
+<!-- Structure
+
+ svg, g, defs, desc, title, metadata, symbol, use
+
+ This module declares the major structural elements and their attributes.
+-->
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.svg.qname "svg" >
+<!ENTITY % SVG.g.qname "g" >
+<!ENTITY % SVG.defs.qname "defs" >
+<!ENTITY % SVG.desc.qname "desc" >
+<!ENTITY % SVG.title.qname "title" >
+<!ENTITY % SVG.metadata.qname "metadata" >
+<!ENTITY % SVG.symbol.qname "symbol" >
+<!ENTITY % SVG.use.qname "use" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Container.attrib "" >
+<!ENTITY % SVG.Conditional.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Viewport.attrib "" >
+<!ENTITY % SVG.Text.attrib "" >
+<!ENTITY % SVG.TextContent.attrib "" >
+<!ENTITY % SVG.Font.attrib "" >
+<!ENTITY % SVG.Paint.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Marker.attrib "" >
+<!ENTITY % SVG.Profile.attrib "" >
+<!ENTITY % SVG.Gradient.attrib "" >
+<!ENTITY % SVG.Clip.attrib "" >
+<!ENTITY % SVG.Mask.attrib "" >
+<!ENTITY % SVG.Filter.attrib "" >
+<!ENTITY % SVG.FilterColor.attrib "" >
+<!ENTITY % SVG.DocumentEvents.attrib "" >
+<!ENTITY % SVG.GraphicalEvents.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.XLinkEmbed.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Description.class ............................. -->
+
+<!ENTITY % SVG.Description.extra.class "" >
+
+<!ENTITY % SVG.Description.class
+ "%SVG.desc.qname; | %SVG.title.qname; | %SVG.metadata.qname;
+ %SVG.Description.extra.class;"
+>
+
+<!-- SVG.Use.class ..................................... -->
+
+<!ENTITY % SVG.Use.extra.class "" >
+
+<!ENTITY % SVG.Use.class
+ "| %SVG.use.qname; %SVG.Use.extra.class;"
+>
+
+<!-- SVG.Structure.class ............................... -->
+
+<!ENTITY % SVG.Structure.extra.class "" >
+
+<!ENTITY % SVG.Structure.class
+ "| %SVG.svg.qname; | %SVG.g.qname; | %SVG.defs.qname; | %SVG.symbol.qname;
+ %SVG.Use.class; %SVG.Structure.extra.class;"
+>
+
+<!-- SVG.Presentation.attrib ........................... -->
+
+<!ENTITY % SVG.Presentation.extra.attrib "" >
+
+<!ENTITY % SVG.Presentation.attrib
+ "%SVG.Container.attrib;
+ %SVG.Viewport.attrib;
+ %SVG.Text.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Profile.attrib;
+ %SVG.Gradient.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.Cursor.attrib;
+ flood-color %SVGColor.datatype; #IMPLIED
+ flood-opacity %OpacityValue.datatype; #IMPLIED
+ lighting-color %SVGColor.datatype; #IMPLIED
+ %SVG.Presentation.extra.attrib;"
+>
+
+<!-- svg: SVG Document Element ......................... -->
+
+<!ENTITY % SVG.svg.extra.content "" >
+
+<!ENTITY % SVG.svg.element "INCLUDE" >
+<![%SVG.svg.element;[
+<!ENTITY % SVG.svg.content
+ "( %SVG.Description.class; | %SVG.Animation.class; %SVG.Structure.class;
+ %SVG.Conditional.class; %SVG.Image.class; %SVG.Style.class;
+ %SVG.Shape.class; %SVG.Text.class; %SVG.Marker.class; %SVG.Profile.class;
+ %SVG.Gradient.class; %SVG.Pattern.class; %SVG.Clip.class;
+ %SVG.Mask.class; %SVG.Filter.class; %SVG.Cursor.class;
+ %SVG.Hyperlink.class; %SVG.View.class; %SVG.Script.class;
+ %SVG.Font.class; %SVG.svg.extra.content; )*"
+>
+<!ELEMENT %SVG.svg.qname; %SVG.svg.content; >
+<!-- end of SVG.svg.element -->]]>
+
+<!ENTITY % SVG.svg.attlist "INCLUDE" >
+<![%SVG.svg.attlist;[
+<!ATTLIST %SVG.svg.qname;
+ %SVG.xmlns.attrib;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.DocumentEvents.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.External.attrib;
+ x %Coordinate.datatype; #IMPLIED
+ y %Coordinate.datatype; #IMPLIED
+ width %Length.datatype; #IMPLIED
+ height %Length.datatype; #IMPLIED
+ viewBox %ViewBoxSpec.datatype; #IMPLIED
+ preserveAspectRatio %PreserveAspectRatioSpec.datatype; 'xMidYMid meet'
+ zoomAndPan ( disable | magnify ) 'magnify'
+ version %Number.datatype; #FIXED '1.1'
+ baseProfile %Text.datatype; #IMPLIED
+ contentScriptType %ContentType.datatype; 'text/ecmascript'
+ contentStyleType %ContentType.datatype; 'text/css'
+>
+<!-- end of SVG.svg.attlist -->]]>
+
+<!-- g: Group Element .................................. -->
+
+<!ENTITY % SVG.g.extra.content "" >
+
+<!ENTITY % SVG.g.element "INCLUDE" >
+<![%SVG.g.element;[
+<!ENTITY % SVG.g.content
+ "( %SVG.Description.class; | %SVG.Animation.class; %SVG.Structure.class;
+ %SVG.Conditional.class; %SVG.Image.class; %SVG.Style.class;
+ %SVG.Shape.class; %SVG.Text.class; %SVG.Marker.class; %SVG.Profile.class;
+ %SVG.Gradient.class; %SVG.Pattern.class; %SVG.Clip.class;
+ %SVG.Mask.class; %SVG.Filter.class; %SVG.Cursor.class;
+ %SVG.Hyperlink.class; %SVG.View.class; %SVG.Script.class;
+ %SVG.Font.class; %SVG.g.extra.content; )*"
+>
+<!ELEMENT %SVG.g.qname; %SVG.g.content; >
+<!-- end of SVG.g.element -->]]>
+
+<!ENTITY % SVG.g.attlist "INCLUDE" >
+<![%SVG.g.attlist;[
+<!ATTLIST %SVG.g.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.External.attrib;
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.g.attlist -->]]>
+
+<!-- defs: Definisions Element ......................... -->
+
+<!ENTITY % SVG.defs.extra.content "" >
+
+<!ENTITY % SVG.defs.element "INCLUDE" >
+<![%SVG.defs.element;[
+<!ENTITY % SVG.defs.content
+ "( %SVG.Description.class; | %SVG.Animation.class; %SVG.Structure.class;
+ %SVG.Conditional.class; %SVG.Image.class; %SVG.Style.class;
+ %SVG.Shape.class; %SVG.Text.class; %SVG.Marker.class; %SVG.Profile.class;
+ %SVG.Gradient.class; %SVG.Pattern.class; %SVG.Clip.class;
+ %SVG.Mask.class; %SVG.Filter.class; %SVG.Cursor.class;
+ %SVG.Hyperlink.class; %SVG.View.class; %SVG.Script.class;
+ %SVG.Font.class; %SVG.defs.extra.content; )*"
+>
+<!ELEMENT %SVG.defs.qname; %SVG.defs.content; >
+<!-- end of SVG.defs.element -->]]>
+
+<!ENTITY % SVG.defs.attlist "INCLUDE" >
+<![%SVG.defs.attlist;[
+<!ATTLIST %SVG.defs.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.External.attrib;
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.defs.attlist -->]]>
+
+<!-- desc: Description Element ......................... -->
+
+<!ENTITY % SVG.desc.extra.content "" >
+
+<!ENTITY % SVG.desc.element "INCLUDE" >
+<![%SVG.desc.element;[
+<!ENTITY % SVG.desc.content
+ "( #PCDATA %SVG.desc.extra.content; )*"
+>
+<!ELEMENT %SVG.desc.qname; %SVG.desc.content; >
+<!-- end of SVG.desc.element -->]]>
+
+<!ENTITY % SVG.desc.attlist "INCLUDE" >
+<![%SVG.desc.attlist;[
+<!ATTLIST %SVG.desc.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+>
+<!-- end of SVG.desc.attlist -->]]>
+
+<!-- title: Title Element .............................. -->
+
+<!ENTITY % SVG.title.extra.content "" >
+
+<!ENTITY % SVG.title.element "INCLUDE" >
+<![%SVG.title.element;[
+<!ENTITY % SVG.title.content
+ "( #PCDATA %SVG.title.extra.content; )*"
+>
+<!ELEMENT %SVG.title.qname; %SVG.title.content; >
+<!-- end of SVG.title.element -->]]>
+
+<!ENTITY % SVG.title.attlist "INCLUDE" >
+<![%SVG.title.attlist;[
+<!ATTLIST %SVG.title.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+>
+<!-- end of SVG.title.attlist -->]]>
+
+<!-- metadata: Metadata Element ........................ -->
+
+<!ENTITY % SVG.metadata.extra.content "" >
+
+<!ENTITY % SVG.metadata.element "INCLUDE" >
+<![%SVG.metadata.element;[
+<!ENTITY % SVG.metadata.content
+ "( #PCDATA %SVG.metadata.extra.content; )*"
+>
+<!ELEMENT %SVG.metadata.qname; %SVG.metadata.content; >
+<!-- end of SVG.metadata.element -->]]>
+
+<!ENTITY % SVG.metadata.attlist "INCLUDE" >
+<![%SVG.metadata.attlist;[
+<!ATTLIST %SVG.metadata.qname;
+ %SVG.Core.attrib;
+>
+<!-- end of SVG.metadata.attlist -->]]>
+
+<!-- symbol: Symbol Element ............................ -->
+
+<!ENTITY % SVG.symbol.extra.content "" >
+
+<!ENTITY % SVG.symbol.element "INCLUDE" >
+<![%SVG.symbol.element;[
+<!ENTITY % SVG.symbol.content
+ "( %SVG.Description.class; | %SVG.Animation.class; %SVG.Structure.class;
+ %SVG.Conditional.class; %SVG.Image.class; %SVG.Style.class;
+ %SVG.Shape.class; %SVG.Text.class; %SVG.Marker.class; %SVG.Profile.class;
+ %SVG.Gradient.class; %SVG.Pattern.class; %SVG.Clip.class;
+ %SVG.Mask.class; %SVG.Filter.class; %SVG.Cursor.class;
+ %SVG.Hyperlink.class; %SVG.View.class; %SVG.Script.class;
+ %SVG.Font.class; %SVG.symbol.extra.content; )*"
+>
+<!ELEMENT %SVG.symbol.qname; %SVG.symbol.content; >
+<!-- end of SVG.symbol.element -->]]>
+
+<!ENTITY % SVG.symbol.attlist "INCLUDE" >
+<![%SVG.symbol.attlist;[
+<!ATTLIST %SVG.symbol.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.External.attrib;
+ viewBox %ViewBoxSpec.datatype; #IMPLIED
+ preserveAspectRatio %PreserveAspectRatioSpec.datatype; 'xMidYMid meet'
+>
+<!-- end of SVG.symbol.attlist -->]]>
+
+<!-- use: Use Element .................................. -->
+
+<!ENTITY % SVG.use.extra.content "" >
+
+<!ENTITY % SVG.use.element "INCLUDE" >
+<![%SVG.use.element;[
+<!ENTITY % SVG.use.content
+ "(( %SVG.Description.class; )*, ( %SVG.Animation.class;
+ %SVG.use.extra.content; )*)"
+>
+<!ELEMENT %SVG.use.qname; %SVG.use.content; >
+<!-- end of SVG.use.element -->]]>
+
+<!ENTITY % SVG.use.attlist "INCLUDE" >
+<![%SVG.use.attlist;[
+<!ATTLIST %SVG.use.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.XLinkEmbed.attrib;
+ %SVG.External.attrib;
+ x %Coordinate.datatype; #IMPLIED
+ y %Coordinate.datatype; #IMPLIED
+ width %Length.datatype; #IMPLIED
+ height %Length.datatype; #IMPLIED
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.use.attlist -->]]>
+
+<!-- end of svg-structure.mod -->
+]]>
+
+<!-- Conditional Processing Module ............................... -->
+<!ENTITY % svg-conditional.module "INCLUDE" >
+<![%svg-conditional.module;[
+<!ENTITY % svg-conditional.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Conditional Processing//EN"
+ "svg-conditional.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Conditional Processing Module ................................. -->
+<!-- file: svg-conditional.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-basic-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Conditional Processing//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-conditional.mod"
+
+ ....................................................................... -->
+
+<!-- Conditional Processing
+
+ switch
+
+ This module declares markup to provide support for conditional processing.
+-->
+
+<!-- extension list specification -->
+<!ENTITY % ExtensionList.datatype "CDATA" >
+
+<!-- feature list specification -->
+<!ENTITY % FeatureList.datatype "CDATA" >
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.switch.qname "switch" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Container.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Viewport.attrib "" >
+<!ENTITY % SVG.Text.attrib "" >
+<!ENTITY % SVG.TextContent.attrib "" >
+<!ENTITY % SVG.Font.attrib "" >
+<!ENTITY % SVG.Paint.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Marker.attrib "" >
+<!ENTITY % SVG.Profile.attrib "" >
+<!ENTITY % SVG.Gradient.attrib "" >
+<!ENTITY % SVG.Clip.attrib "" >
+<!ENTITY % SVG.Mask.attrib "" >
+<!ENTITY % SVG.Filter.attrib "" >
+<!ENTITY % SVG.FilterColor.attrib "" >
+<!ENTITY % SVG.GraphicalEvents.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Conditional.class ............................. -->
+
+<!ENTITY % SVG.Conditional.extra.class "" >
+
+<!ENTITY % SVG.Conditional.class
+ "| %SVG.switch.qname; %SVG.Conditional.extra.class;"
+>
+
+<!-- SVG.Conditional.attrib ............................ -->
+
+<!ENTITY % SVG.Conditional.extra.attrib "" >
+
+<!ENTITY % SVG.Conditional.attrib
+ "requiredFeatures %FeatureList.datatype; #IMPLIED
+ requiredExtensions %ExtensionList.datatype; #IMPLIED
+ systemLanguage %LanguageCodes.datatype; #IMPLIED
+ %SVG.Conditional.extra.attrib;"
+>
+
+<!-- SVG.Presentation.attrib ........................... -->
+
+<!ENTITY % SVG.Presentation.extra.attrib "" >
+
+<!ENTITY % SVG.Presentation.attrib
+ "%SVG.Container.attrib;
+ %SVG.Viewport.attrib;
+ %SVG.Text.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Profile.attrib;
+ %SVG.Gradient.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.Cursor.attrib;
+ flood-color %SVGColor.datatype; #IMPLIED
+ flood-opacity %OpacityValue.datatype; #IMPLIED
+ lighting-color %SVGColor.datatype; #IMPLIED
+ %SVG.Presentation.extra.attrib;"
+>
+
+<!-- switch: Switch Element ............................ -->
+
+<!ENTITY % SVG.switch.extra.content "" >
+
+<!ENTITY % SVG.switch.element "INCLUDE" >
+<![%SVG.switch.element;[
+<!ENTITY % SVG.switch.content
+ "(( %SVG.Description.class; )*, ( %SVG.svg.qname; | %SVG.g.qname;
+ | %SVG.use.qname; | %SVG.text.qname; | %SVG.Animation.class;
+ %SVG.Conditional.class; %SVG.Image.class; %SVG.Shape.class;
+ %SVG.Hyperlink.class; %SVG.Extensibility.class;
+ %SVG.switch.extra.content; )*)"
+>
+<!ELEMENT %SVG.switch.qname; %SVG.switch.content; >
+<!-- end of SVG.switch.element -->]]>
+
+<!ENTITY % SVG.switch.attlist "INCLUDE" >
+<![%SVG.switch.attlist;[
+<!ATTLIST %SVG.switch.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.External.attrib;
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.switch.attlist -->]]>
+
+<!-- end of svg-conditional.mod -->
+]]>
+
+<!-- Image Module ................................................ -->
+<!ENTITY % svg-image.module "INCLUDE" >
+<![%svg-image.module;[
+<!ENTITY % svg-image.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Image//EN"
+ "svg-image.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Image Module .................................................. -->
+<!-- file: svg-image.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-basic-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Image//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-image.mod"
+
+ ....................................................................... -->
+
+<!-- Image
+
+ image
+
+ This module declares markup to provide support for image.
+-->
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.image.qname "image" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Conditional.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Viewport.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Profile.attrib "" >
+<!ENTITY % SVG.Clip.attrib "" >
+<!ENTITY % SVG.Mask.attrib "" >
+<!ENTITY % SVG.Filter.attrib "" >
+<!ENTITY % SVG.GraphicalEvents.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.XLinkEmbed.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Image.class ................................... -->
+
+<!ENTITY % SVG.Image.extra.class "" >
+
+<!ENTITY % SVG.Image.class
+ "| %SVG.image.qname; %SVG.Image.extra.class;"
+>
+
+<!-- image: Image Element .............................. -->
+
+<!ENTITY % SVG.image.extra.content "" >
+
+<!ENTITY % SVG.image.element "INCLUDE" >
+<![%SVG.image.element;[
+<!ENTITY % SVG.image.content
+ "(( %SVG.Description.class; )*, ( %SVG.Animation.class;
+ %SVG.image.extra.content; )*)"
+>
+<!ELEMENT %SVG.image.qname; %SVG.image.content; >
+<!-- end of SVG.image.element -->]]>
+
+<!ENTITY % SVG.image.attlist "INCLUDE" >
+<![%SVG.image.attlist;[
+<!ATTLIST %SVG.image.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Viewport.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Profile.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.XLinkEmbed.attrib;
+ %SVG.External.attrib;
+ x %Coordinate.datatype; #IMPLIED
+ y %Coordinate.datatype; #IMPLIED
+ width %Length.datatype; #REQUIRED
+ height %Length.datatype; #REQUIRED
+ preserveAspectRatio %PreserveAspectRatioSpec.datatype; 'xMidYMid meet'
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.image.attlist -->]]>
+
+<!-- end of svg-image.mod -->
+]]>
+
+<!-- Style Module ................................................ -->
+<!ENTITY % svg-style.module "INCLUDE" >
+<![%svg-style.module;[
+<!ENTITY % svg-style.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Style//EN"
+ "svg-style.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Style Module .................................................. -->
+<!-- file: svg-style.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-basic-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Style//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-style.mod"
+
+ ....................................................................... -->
+
+<!-- Style
+
+ style
+
+ This module declares markup to provide support for stylesheet.
+-->
+
+<!-- list of classes -->
+<!ENTITY % ClassList.datatype "CDATA" >
+
+<!-- comma-separated list of media descriptors. -->
+<!ENTITY % MediaDesc.datatype "CDATA" >
+
+<!-- style sheet data -->
+<!ENTITY % StyleSheet.datatype "CDATA" >
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.style.qname "style" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+
+<!-- SVG.Style.class ................................... -->
+
+<!ENTITY % SVG.Style.extra.class "" >
+
+<!ENTITY % SVG.Style.class
+ "| %SVG.style.qname; %SVG.Style.extra.class;"
+>
+
+<!-- SVG.Style.attrib .................................. -->
+
+<!ENTITY % SVG.Style.extra.attrib "" >
+
+<!ENTITY % SVG.Style.attrib
+ "style %StyleSheet.datatype; #IMPLIED
+ class %ClassList.datatype; #IMPLIED
+ %SVG.Style.extra.attrib;"
+>
+
+<!-- style: Style Element .............................. -->
+
+<!ENTITY % SVG.style.extra.content "" >
+
+<!ENTITY % SVG.style.element "INCLUDE" >
+<![%SVG.style.element;[
+<!ENTITY % SVG.style.content
+ "( #PCDATA %SVG.style.extra.content; )*"
+>
+<!ELEMENT %SVG.style.qname; %SVG.style.content; >
+<!-- end of SVG.style.element -->]]>
+
+<!ENTITY % SVG.style.attlist "INCLUDE" >
+<![%SVG.style.attlist;[
+<!ATTLIST %SVG.style.qname;
+ xml:space ( preserve ) #FIXED 'preserve'
+ %SVG.Core.attrib;
+ type %ContentType.datatype; #REQUIRED
+ media %MediaDesc.datatype; #IMPLIED
+ title %Text.datatype; #IMPLIED
+>
+<!-- end of SVG.style.attlist -->]]>
+
+<!-- end of svg-style.mod -->
+]]>
+
+<!-- Shape Module ................................................ -->
+<!ENTITY % svg-shape.module "INCLUDE" >
+<![%svg-shape.module;[
+<!ENTITY % svg-shape.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Shape//EN"
+ "svg-shape.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Shape Module .................................................. -->
+<!-- file: svg-shape.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-basic-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Shape//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-shape.mod"
+
+ ....................................................................... -->
+
+<!-- Shape
+
+ path, rect, circle, line, ellipse, polyline, polygon
+
+ This module declares markup to provide support for graphical shapes.
+-->
+
+<!-- a list of points -->
+<!ENTITY % Points.datatype "CDATA" >
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.path.qname "path" >
+<!ENTITY % SVG.rect.qname "rect" >
+<!ENTITY % SVG.circle.qname "circle" >
+<!ENTITY % SVG.line.qname "line" >
+<!ENTITY % SVG.ellipse.qname "ellipse" >
+<!ENTITY % SVG.polyline.qname "polyline" >
+<!ENTITY % SVG.polygon.qname "polygon" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Conditional.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Paint.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Marker.attrib "" >
+<!ENTITY % SVG.Clip.attrib "" >
+<!ENTITY % SVG.Mask.attrib "" >
+<!ENTITY % SVG.Filter.attrib "" >
+<!ENTITY % SVG.GraphicalEvents.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Shape.class ................................... -->
+
+<!ENTITY % SVG.Shape.extra.class "" >
+
+<!ENTITY % SVG.Shape.class
+ "| %SVG.path.qname; | %SVG.rect.qname; | %SVG.circle.qname;
+ | %SVG.line.qname; | %SVG.ellipse.qname; | %SVG.polyline.qname;
+ | %SVG.polygon.qname; %SVG.Shape.extra.class;"
+>
+
+<!-- path: Path Element ................................ -->
+
+<!ENTITY % SVG.path.extra.content "" >
+
+<!ENTITY % SVG.path.element "INCLUDE" >
+<![%SVG.path.element;[
+<!ENTITY % SVG.path.content
+ "(( %SVG.Description.class; )*, ( %SVG.Animation.class;
+ %SVG.path.extra.content; )*)"
+>
+<!ELEMENT %SVG.path.qname; %SVG.path.content; >
+<!-- end of SVG.path.element -->]]>
+
+<!ENTITY % SVG.path.attlist "INCLUDE" >
+<![%SVG.path.attlist;[
+<!ATTLIST %SVG.path.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.External.attrib;
+ d %PathData.datatype; #REQUIRED
+ pathLength %Number.datatype; #IMPLIED
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.path.attlist -->]]>
+
+<!-- rect: Rectangle Element ........................... -->
+
+<!ENTITY % SVG.rect.extra.content "" >
+
+<!ENTITY % SVG.rect.element "INCLUDE" >
+<![%SVG.rect.element;[
+<!ENTITY % SVG.rect.content
+ "(( %SVG.Description.class; )*, ( %SVG.Animation.class;
+ %SVG.rect.extra.content; )*)"
+>
+<!ELEMENT %SVG.rect.qname; %SVG.rect.content; >
+<!-- end of SVG.rect.element -->]]>
+
+<!ENTITY % SVG.rect.attlist "INCLUDE" >
+<![%SVG.rect.attlist;[
+<!ATTLIST %SVG.rect.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.External.attrib;
+ x %Coordinate.datatype; #IMPLIED
+ y %Coordinate.datatype; #IMPLIED
+ width %Length.datatype; #REQUIRED
+ height %Length.datatype; #REQUIRED
+ rx %Length.datatype; #IMPLIED
+ ry %Length.datatype; #IMPLIED
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.rect.attlist -->]]>
+
+<!-- circle: Circle Element ............................ -->
+
+<!ENTITY % SVG.circle.extra.content "" >
+
+<!ENTITY % SVG.circle.element "INCLUDE" >
+<![%SVG.circle.element;[
+<!ENTITY % SVG.circle.content
+ "(( %SVG.Description.class; )*, ( %SVG.Animation.class;
+ %SVG.circle.extra.content; )*)"
+>
+<!ELEMENT %SVG.circle.qname; %SVG.circle.content; >
+<!-- end of SVG.circle.element -->]]>
+
+<!ENTITY % SVG.circle.attlist "INCLUDE" >
+<![%SVG.circle.attlist;[
+<!ATTLIST %SVG.circle.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.External.attrib;
+ cx %Coordinate.datatype; #IMPLIED
+ cy %Coordinate.datatype; #IMPLIED
+ r %Length.datatype; #REQUIRED
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.circle.attlist -->]]>
+
+<!-- line: Line Element ................................ -->
+
+<!ENTITY % SVG.line.extra.content "" >
+
+<!ENTITY % SVG.line.element "INCLUDE" >
+<![%SVG.line.element;[
+<!ENTITY % SVG.line.content
+ "(( %SVG.Description.class; )*, ( %SVG.Animation.class;
+ %SVG.line.extra.content; )*)"
+>
+<!ELEMENT %SVG.line.qname; %SVG.line.content; >
+<!-- end of SVG.line.element -->]]>
+
+<!ENTITY % SVG.line.attlist "INCLUDE" >
+<![%SVG.line.attlist;[
+<!ATTLIST %SVG.line.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.External.attrib;
+ x1 %Coordinate.datatype; #IMPLIED
+ y1 %Coordinate.datatype; #IMPLIED
+ x2 %Coordinate.datatype; #IMPLIED
+ y2 %Coordinate.datatype; #IMPLIED
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.line.attlist -->]]>
+
+<!-- ellipse: Ellipse Element .......................... -->
+
+<!ENTITY % SVG.ellipse.extra.content "" >
+
+<!ENTITY % SVG.ellipse.element "INCLUDE" >
+<![%SVG.ellipse.element;[
+<!ENTITY % SVG.ellipse.content
+ "(( %SVG.Description.class; )*, ( %SVG.Animation.class;
+ %SVG.ellipse.extra.content; )*)"
+>
+<!ELEMENT %SVG.ellipse.qname; %SVG.ellipse.content; >
+<!-- end of SVG.ellipse.element -->]]>
+
+<!ENTITY % SVG.ellipse.attlist "INCLUDE" >
+<![%SVG.ellipse.attlist;[
+<!ATTLIST %SVG.ellipse.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.External.attrib;
+ cx %Coordinate.datatype; #IMPLIED
+ cy %Coordinate.datatype; #IMPLIED
+ rx %Length.datatype; #REQUIRED
+ ry %Length.datatype; #REQUIRED
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.ellipse.attlist -->]]>
+
+<!-- polyline: Polyline Element ........................ -->
+
+<!ENTITY % SVG.polyline.extra.content "" >
+
+<!ENTITY % SVG.polyline.element "INCLUDE" >
+<![%SVG.polyline.element;[
+<!ENTITY % SVG.polyline.content
+ "(( %SVG.Description.class; )*, ( %SVG.Animation.class;
+ %SVG.polyline.extra.content; )*)"
+>
+<!ELEMENT %SVG.polyline.qname; %SVG.polyline.content; >
+<!-- end of SVG.polyline.element -->]]>
+
+<!ENTITY % SVG.polyline.attlist "INCLUDE" >
+<![%SVG.polyline.attlist;[
+<!ATTLIST %SVG.polyline.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.External.attrib;
+ points %Points.datatype; #REQUIRED
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.polyline.attlist -->]]>
+
+<!-- polygon: Polygon Element .......................... -->
+
+<!ENTITY % SVG.polygon.extra.content "" >
+
+<!ENTITY % SVG.polygon.element "INCLUDE" >
+<![%SVG.polygon.element;[
+<!ENTITY % SVG.polygon.content
+ "(( %SVG.Description.class; )*, ( %SVG.Animation.class;
+ %SVG.polygon.extra.content; )*)"
+>
+<!ELEMENT %SVG.polygon.qname; %SVG.polygon.content; >
+<!-- end of SVG.polygon.element -->]]>
+
+<!ENTITY % SVG.polygon.attlist "INCLUDE" >
+<![%SVG.polygon.attlist;[
+<!ATTLIST %SVG.polygon.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.External.attrib;
+ points %Points.datatype; #REQUIRED
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.polygon.attlist -->]]>
+
+<!-- end of svg-shape.mod -->
+]]>
+
+<!-- Text Module ................................................. -->
+<!ENTITY % svg-text.module "INCLUDE" >
+<![%svg-text.module;[
+<!ENTITY % svg-text.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Text//EN"
+ "svg-text.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Text Module ................................................... -->
+<!-- file: svg-text.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-basic-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Text//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-text.mod"
+
+ ....................................................................... -->
+
+<!-- Text
+
+ text, tspan, tref, textPath, altGlyph, altGlyphDef, altGlyphItem,
+ glyphRef
+
+ This module declares markup to provide support for alternate glyph.
+-->
+
+<!-- 'baseline-shift' property/attribute value (e.g., 'baseline', 'sub', etc.) -->
+<!ENTITY % BaselineShiftValue.datatype "CDATA" >
+
+<!-- 'font-family' property/attribute value (i.e., list of fonts) -->
+<!ENTITY % FontFamilyValue.datatype "CDATA" >
+
+<!-- 'font-size' property/attribute value -->
+<!ENTITY % FontSizeValue.datatype "CDATA" >
+
+<!-- 'font-size-adjust' property/attribute value -->
+<!ENTITY % FontSizeAdjustValue.datatype "CDATA" >
+
+<!-- 'glyph-orientation-horizontal' property/attribute value (e.g., <angle>) -->
+<!ENTITY % GlyphOrientationHorizontalValue.datatype "CDATA" >
+
+<!-- 'glyph-orientation-vertical' property/attribute value (e.g., 'auto', <angle>) -->
+<!ENTITY % GlyphOrientationVerticalValue.datatype "CDATA" >
+
+<!-- 'kerning' property/attribute value (e.g., 'auto', <length>) -->
+<!ENTITY % KerningValue.datatype "CDATA" >
+
+<!-- 'letter-spacing' or 'word-spacing' property/attribute value (e.g., 'normal', <length>) -->
+<!ENTITY % SpacingValue.datatype "CDATA" >
+
+<!-- 'text-decoration' property/attribute value (e.g., 'none', 'underline') -->
+<!ENTITY % TextDecorationValue.datatype "CDATA" >
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.text.qname "text" >
+<!ENTITY % SVG.tspan.qname "tspan" >
+<!ENTITY % SVG.tref.qname "tref" >
+<!ENTITY % SVG.textPath.qname "textPath" >
+<!ENTITY % SVG.altGlyph.qname "altGlyph" >
+<!ENTITY % SVG.altGlyphDef.qname "altGlyphDef" >
+<!ENTITY % SVG.altGlyphItem.qname "altGlyphItem" >
+<!ENTITY % SVG.glyphRef.qname "glyphRef" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Conditional.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Paint.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Clip.attrib "" >
+<!ENTITY % SVG.Mask.attrib "" >
+<!ENTITY % SVG.Filter.attrib "" >
+<!ENTITY % SVG.GraphicalEvents.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.XLink.attrib "" >
+<!ENTITY % SVG.XLinkRequired.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Text.class .................................... -->
+
+<!ENTITY % SVG.Text.extra.class "" >
+
+<!ENTITY % SVG.Text.class
+ "| %SVG.text.qname; | %SVG.altGlyphDef.qname; %SVG.Text.extra.class;"
+>
+
+<!-- SVG.TextContent.class ............................. -->
+
+<!ENTITY % SVG.TextContent.extra.class "" >
+
+<!ENTITY % SVG.TextContent.class
+ "| %SVG.tspan.qname; | %SVG.tref.qname; | %SVG.textPath.qname;
+ | %SVG.altGlyph.qname; %SVG.TextContent.extra.class;"
+>
+
+<!-- SVG.Text.attrib ................................... -->
+
+<!ENTITY % SVG.Text.extra.attrib "" >
+
+<!ENTITY % SVG.Text.attrib
+ "writing-mode ( lr-tb | rl-tb | tb-rl | lr | rl | tb | inherit ) #IMPLIED
+ %SVG.Text.extra.attrib;"
+>
+
+<!-- SVG.TextContent.attrib ............................ -->
+
+<!ENTITY % SVG.TextContent.extra.attrib "" >
+
+<!ENTITY % SVG.TextContent.attrib
+ "alignment-baseline ( auto | baseline | before-edge | text-before-edge |
+ middle | central | after-edge | text-after-edge |
+ ideographic | alphabetic | hanging | mathematical |
+ inherit ) #IMPLIED
+ baseline-shift %BaselineShiftValue.datatype; #IMPLIED
+ direction ( ltr | rtl | inherit ) #IMPLIED
+ dominant-baseline ( auto | use-script | no-change | reset-size |
+ ideographic | alphabetic | hanging | mathematical |
+ central | middle | text-after-edge | text-before-edge |
+ inherit ) #IMPLIED
+ glyph-orientation-horizontal %GlyphOrientationHorizontalValue.datatype;
+ #IMPLIED
+ glyph-orientation-vertical %GlyphOrientationVerticalValue.datatype;
+ #IMPLIED
+ kerning %KerningValue.datatype; #IMPLIED
+ letter-spacing %SpacingValue.datatype; #IMPLIED
+ text-anchor ( start | middle | end | inherit ) #IMPLIED
+ text-decoration %TextDecorationValue.datatype; #IMPLIED
+ unicode-bidi ( normal | embed | bidi-override | inherit ) #IMPLIED
+ word-spacing %SpacingValue.datatype; #IMPLIED
+ %SVG.TextContent.extra.attrib;"
+>
+
+<!-- SVG.Font.attrib ................................... -->
+
+<!ENTITY % SVG.Font.extra.attrib "" >
+
+<!ENTITY % SVG.Font.attrib
+ "font-family %FontFamilyValue.datatype; #IMPLIED
+ font-size %FontSizeValue.datatype; #IMPLIED
+ font-size-adjust %FontSizeAdjustValue.datatype; #IMPLIED
+ font-stretch ( normal | wider | narrower | ultra-condensed |
+ extra-condensed | condensed | semi-condensed |
+ semi-expanded | expanded | extra-expanded |
+ ultra-expanded | inherit ) #IMPLIED
+ font-style ( normal | italic | oblique | inherit ) #IMPLIED
+ font-variant ( normal | small-caps | inherit ) #IMPLIED
+ font-weight ( normal | bold | bolder | lighter | 100 | 200 | 300 | 400 |
+ 500 | 600 | 700 | 800 | 900 | inherit ) #IMPLIED
+ %SVG.Font.extra.attrib;"
+>
+
+<!-- text: Text Element ................................ -->
+
+<!ENTITY % SVG.text.extra.content "" >
+
+<!ENTITY % SVG.text.element "INCLUDE" >
+<![%SVG.text.element;[
+<!ENTITY % SVG.text.content
+ "( #PCDATA | %SVG.Description.class; | %SVG.Animation.class;
+ %SVG.TextContent.class; %SVG.Hyperlink.class;
+ %SVG.text.extra.content; )*"
+>
+<!ELEMENT %SVG.text.qname; %SVG.text.content; >
+<!-- end of SVG.text.element -->]]>
+
+<!ENTITY % SVG.text.attlist "INCLUDE" >
+<![%SVG.text.attlist;[
+<!ATTLIST %SVG.text.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Text.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.External.attrib;
+ x %Coordinates.datatype; #IMPLIED
+ y %Coordinates.datatype; #IMPLIED
+ dx %Lengths.datatype; #IMPLIED
+ dy %Lengths.datatype; #IMPLIED
+ rotate %Numbers.datatype; #IMPLIED
+ textLength %Length.datatype; #IMPLIED
+ lengthAdjust ( spacing | spacingAndGlyphs ) #IMPLIED
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.text.attlist -->]]>
+
+<!-- tspan: Text Span Element .......................... -->
+
+<!ENTITY % SVG.tspan.extra.content "" >
+
+<!ENTITY % SVG.tspan.element "INCLUDE" >
+<![%SVG.tspan.element;[
+<!ENTITY % SVG.tspan.content
+ "( #PCDATA | %SVG.tspan.qname; | %SVG.tref.qname; | %SVG.altGlyph.qname;
+ | %SVG.animate.qname; | %SVG.set.qname; | %SVG.animateColor.qname;
+ | %SVG.Description.class; %SVG.Hyperlink.class;
+ %SVG.tspan.extra.content; )*"
+>
+<!ELEMENT %SVG.tspan.qname; %SVG.tspan.content; >
+<!-- end of SVG.tspan.element -->]]>
+
+<!ENTITY % SVG.tspan.attlist "INCLUDE" >
+<![%SVG.tspan.attlist;[
+<!ATTLIST %SVG.tspan.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.External.attrib;
+ x %Coordinates.datatype; #IMPLIED
+ y %Coordinates.datatype; #IMPLIED
+ dx %Lengths.datatype; #IMPLIED
+ dy %Lengths.datatype; #IMPLIED
+ rotate %Numbers.datatype; #IMPLIED
+ textLength %Length.datatype; #IMPLIED
+ lengthAdjust ( spacing | spacingAndGlyphs ) #IMPLIED
+>
+<!-- end of SVG.tspan.attlist -->]]>
+
+<!-- tref: Text Reference Element ...................... -->
+
+<!ENTITY % SVG.tref.extra.content "" >
+
+<!ENTITY % SVG.tref.element "INCLUDE" >
+<![%SVG.tref.element;[
+<!ENTITY % SVG.tref.content
+ "( %SVG.animate.qname; | %SVG.set.qname; | %SVG.animateColor.qname;
+ | %SVG.Description.class; %SVG.tref.extra.content; )*"
+>
+<!ELEMENT %SVG.tref.qname; %SVG.tref.content; >
+<!-- end of SVG.tref.element -->]]>
+
+<!ENTITY % SVG.tref.attlist "INCLUDE" >
+<![%SVG.tref.attlist;[
+<!ATTLIST %SVG.tref.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.XLinkRequired.attrib;
+ %SVG.External.attrib;
+ x %Coordinates.datatype; #IMPLIED
+ y %Coordinates.datatype; #IMPLIED
+ dx %Lengths.datatype; #IMPLIED
+ dy %Lengths.datatype; #IMPLIED
+ rotate %Numbers.datatype; #IMPLIED
+ textLength %Length.datatype; #IMPLIED
+ lengthAdjust ( spacing | spacingAndGlyphs ) #IMPLIED
+>
+<!-- end of SVG.tref.attlist -->]]>
+
+<!-- textPath: Text Path Element ....................... -->
+
+<!ENTITY % SVG.textPath.extra.content "" >
+
+<!ENTITY % SVG.textPath.element "INCLUDE" >
+<![%SVG.textPath.element;[
+<!ENTITY % SVG.textPath.content
+ "( #PCDATA | %SVG.tspan.qname; | %SVG.tref.qname; | %SVG.altGlyph.qname;
+ | %SVG.animate.qname; | %SVG.set.qname; | %SVG.animateColor.qname;
+ | %SVG.Description.class; %SVG.Hyperlink.class;
+ %SVG.textPath.extra.content; )*"
+>
+<!ELEMENT %SVG.textPath.qname; %SVG.textPath.content; >
+<!-- end of SVG.textPath.element -->]]>
+
+<!ENTITY % SVG.textPath.attlist "INCLUDE" >
+<![%SVG.textPath.attlist;[
+<!ATTLIST %SVG.textPath.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.XLinkRequired.attrib;
+ %SVG.External.attrib;
+ startOffset %Length.datatype; #IMPLIED
+ textLength %Length.datatype; #IMPLIED
+ lengthAdjust ( spacing | spacingAndGlyphs ) #IMPLIED
+ method ( align | stretch ) #IMPLIED
+ spacing ( auto | exact ) #IMPLIED
+>
+<!-- end of SVG.textPath.attlist -->]]>
+
+<!-- altGlyph: Alternate Glyph Element ................. -->
+
+<!ENTITY % SVG.altGlyph.extra.content "" >
+
+<!ENTITY % SVG.altGlyph.element "INCLUDE" >
+<![%SVG.altGlyph.element;[
+<!ENTITY % SVG.altGlyph.content
+ "( #PCDATA %SVG.altGlyph.extra.content; )*"
+>
+<!ELEMENT %SVG.altGlyph.qname; %SVG.altGlyph.content; >
+<!-- end of SVG.altGlyph.element -->]]>
+
+<!ENTITY % SVG.altGlyph.attlist "INCLUDE" >
+<![%SVG.altGlyph.attlist;[
+<!ATTLIST %SVG.altGlyph.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.XLink.attrib;
+ %SVG.External.attrib;
+ x %Coordinates.datatype; #IMPLIED
+ y %Coordinates.datatype; #IMPLIED
+ dx %Lengths.datatype; #IMPLIED
+ dy %Lengths.datatype; #IMPLIED
+ glyphRef CDATA #IMPLIED
+ format CDATA #IMPLIED
+ rotate %Numbers.datatype; #IMPLIED
+>
+<!-- end of SVG.altGlyph.attlist -->]]>
+
+<!-- altGlyphDef: Alternate Glyph Definition Element ... -->
+
+<!ENTITY % SVG.altGlyphDef.extra.content "" >
+
+<!ENTITY % SVG.altGlyphDef.element "INCLUDE" >
+<![%SVG.altGlyphDef.element;[
+<!ENTITY % SVG.altGlyphDef.content
+ "(( %SVG.glyphRef.qname;+ | %SVG.altGlyphItem.qname;+ )
+ %SVG.altGlyphDef.extra.content; )"
+>
+<!ELEMENT %SVG.altGlyphDef.qname; %SVG.altGlyphDef.content; >
+<!-- end of SVG.altGlyphDef.element -->]]>
+
+<!ENTITY % SVG.altGlyphDef.attlist "INCLUDE" >
+<![%SVG.altGlyphDef.attlist;[
+<!ATTLIST %SVG.altGlyphDef.qname;
+ %SVG.Core.attrib;
+>
+<!-- end of SVG.altGlyphDef.attlist -->]]>
+
+<!-- altGlyphItem: Alternate Glyph Item Element ........ -->
+
+<!ENTITY % SVG.altGlyphItem.extra.content "" >
+
+<!ENTITY % SVG.altGlyphItem.element "INCLUDE" >
+<![%SVG.altGlyphItem.element;[
+<!ENTITY % SVG.altGlyphItem.content
+ "( %SVG.glyphRef.qname;+ %SVG.altGlyphItem.extra.content; )"
+>
+<!ELEMENT %SVG.altGlyphItem.qname; %SVG.altGlyphItem.content; >
+<!-- end of SVG.altGlyphItem.element -->]]>
+
+<!ENTITY % SVG.altGlyphItem.attlist "INCLUDE" >
+<![%SVG.altGlyphItem.attlist;[
+<!ATTLIST %SVG.altGlyphItem.qname;
+ %SVG.Core.attrib;
+>
+<!-- end of SVG.altGlyphItem.attlist -->]]>
+
+<!-- glyphRef: Glyph Reference Element ................. -->
+
+<!ENTITY % SVG.glyphRef.element "INCLUDE" >
+<![%SVG.glyphRef.element;[
+<!ENTITY % SVG.glyphRef.content "EMPTY" >
+<!ELEMENT %SVG.glyphRef.qname; %SVG.glyphRef.content; >
+<!-- end of SVG.glyphRef.element -->]]>
+
+<!ENTITY % SVG.glyphRef.attlist "INCLUDE" >
+<![%SVG.glyphRef.attlist;[
+<!ATTLIST %SVG.glyphRef.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Font.attrib;
+ %SVG.XLink.attrib;
+ x %Number.datatype; #IMPLIED
+ y %Number.datatype; #IMPLIED
+ dx %Number.datatype; #IMPLIED
+ dy %Number.datatype; #IMPLIED
+ glyphRef CDATA #IMPLIED
+ format CDATA #IMPLIED
+>
+<!-- end of SVG.glyphRef.attlist -->]]>
+
+<!-- end of svg-text.mod -->
+]]>
+
+<!-- Color Profile Module ........................................ -->
+<!ENTITY % svg-profile.module "INCLUDE" >
+<![%svg-profile.module;[
+<!ENTITY % svg-profile.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Color Profile//EN"
+ "svg-profile.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Color Profile Module .......................................... -->
+<!-- file: svg-profile.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-basic-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Color Profile//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-profile.mod"
+
+ ....................................................................... -->
+
+<!-- Color Profile
+
+ color-profile
+
+ This module declares markup to provide support for color profile.
+-->
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.color-profile.qname "color-profile" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.XLink.attrib "" >
+
+<!-- SVG.Profile.class ................................. -->
+
+<!ENTITY % SVG.Profile.extra.class "" >
+
+<!ENTITY % SVG.Profile.class
+ "| %SVG.color-profile.qname; %SVG.Profile.extra.class;"
+>
+
+<!-- SVG.Profile.attrib ................................ -->
+
+<!ENTITY % SVG.Profile.extra.attrib "" >
+
+<!ENTITY % SVG.Profile.attrib
+ "color-profile CDATA #IMPLIED
+ %SVG.Profile.extra.attrib;"
+>
+
+<!-- color-profile: Color Profile Element .............. -->
+
+<!ENTITY % SVG.color-profile.extra.content "" >
+
+<!ENTITY % SVG.color-profile.element "INCLUDE" >
+<![%SVG.color-profile.element;[
+<!ENTITY % SVG.color-profile.content
+ "( %SVG.Description.class; %SVG.color-profile.extra.content; )*"
+>
+<!ELEMENT %SVG.color-profile.qname; %SVG.color-profile.content; >
+<!-- end of SVG.color-profile.element -->]]>
+
+<!ENTITY % SVG.color-profile.attlist "INCLUDE" >
+<![%SVG.color-profile.attlist;[
+<!ATTLIST %SVG.color-profile.qname;
+ %SVG.Core.attrib;
+ %SVG.XLink.attrib;
+ local CDATA #IMPLIED
+ name CDATA #REQUIRED
+ rendering-intent ( auto | perceptual | relative-colorimetric | saturation |
+ absolute-colorimetric ) 'auto'
+>
+<!-- end of SVG.color-profile.attlist -->]]>
+
+<!-- end of svg-profile.mod -->
+]]>
+
+<!-- Gradient Module ............................................. -->
+<!ENTITY % svg-gradient.module "INCLUDE" >
+<![%svg-gradient.module;[
+<!ENTITY % svg-gradient.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Gradient//EN"
+ "svg-gradient.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Gradient Module ............................................... -->
+<!-- file: svg-gradient.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-basic-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Gradient//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-gradient.mod"
+
+ ....................................................................... -->
+
+<!-- Gradient
+
+ linearGradient, radialGradient, stop
+
+ This module declares markup to provide support for gradient fill.
+-->
+
+<!-- a <number> or a <percentage> -->
+<!ENTITY % NumberOrPercentage.datatype "CDATA" >
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.linearGradient.qname "linearGradient" >
+<!ENTITY % SVG.radialGradient.qname "radialGradient" >
+<!ENTITY % SVG.stop.qname "stop" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.XLink.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Gradient.class ................................ -->
+
+<!ENTITY % SVG.Gradient.extra.class "" >
+
+<!ENTITY % SVG.Gradient.class
+ "| %SVG.linearGradient.qname; | %SVG.radialGradient.qname;
+ %SVG.Gradient.extra.class;"
+>
+
+<!-- SVG.Gradient.attrib ............................... -->
+
+<!ENTITY % SVG.Gradient.extra.attrib "" >
+
+<!ENTITY % SVG.Gradient.attrib
+ "stop-color %SVGColor.datatype; #IMPLIED
+ stop-opacity %OpacityValue.datatype; #IMPLIED
+ %SVG.Gradient.extra.attrib;"
+>
+
+<!-- linearGradient: Linear Gradient Element ........... -->
+
+<!ENTITY % SVG.linearGradient.extra.content "" >
+
+<!ENTITY % SVG.linearGradient.element "INCLUDE" >
+<![%SVG.linearGradient.element;[
+<!ENTITY % SVG.linearGradient.content
+ "(( %SVG.Description.class; )*, ( %SVG.stop.qname; | %SVG.animate.qname;
+ | %SVG.set.qname; | %SVG.animateTransform.qname;
+ %SVG.linearGradient.extra.content; )*)"
+>
+<!ELEMENT %SVG.linearGradient.qname; %SVG.linearGradient.content; >
+<!-- end of SVG.linearGradient.element -->]]>
+
+<!ENTITY % SVG.linearGradient.attlist "INCLUDE" >
+<![%SVG.linearGradient.attlist;[
+<!ATTLIST %SVG.linearGradient.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Color.attrib;
+ %SVG.Gradient.attrib;
+ %SVG.XLink.attrib;
+ %SVG.External.attrib;
+ x1 %Coordinate.datatype; #IMPLIED
+ y1 %Coordinate.datatype; #IMPLIED
+ x2 %Coordinate.datatype; #IMPLIED
+ y2 %Coordinate.datatype; #IMPLIED
+ gradientUnits ( userSpaceOnUse | objectBoundingBox ) #IMPLIED
+ gradientTransform %TransformList.datatype; #IMPLIED
+ spreadMethod ( pad | reflect | repeat ) #IMPLIED
+>
+<!-- end of SVG.linearGradient.attlist -->]]>
+
+<!-- radialGradient: Radial Gradient Element ........... -->
+
+<!ENTITY % SVG.radialGradient.extra.content "" >
+
+<!ENTITY % SVG.radialGradient.element "INCLUDE" >
+<![%SVG.radialGradient.element;[
+<!ENTITY % SVG.radialGradient.content
+ "(( %SVG.Description.class; )*, ( %SVG.stop.qname; | %SVG.animate.qname;
+ | %SVG.set.qname; | %SVG.animateTransform.qname;
+ %SVG.radialGradient.extra.content; )*)"
+>
+<!ELEMENT %SVG.radialGradient.qname; %SVG.radialGradient.content; >
+<!-- end of SVG.radialGradient.element -->]]>
+
+<!ENTITY % SVG.radialGradient.attlist "INCLUDE" >
+<![%SVG.radialGradient.attlist;[
+<!ATTLIST %SVG.radialGradient.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Color.attrib;
+ %SVG.Gradient.attrib;
+ %SVG.XLink.attrib;
+ %SVG.External.attrib;
+ cx %Coordinate.datatype; #IMPLIED
+ cy %Coordinate.datatype; #IMPLIED
+ r %Length.datatype; #IMPLIED
+ fx %Coordinate.datatype; #IMPLIED
+ fy %Coordinate.datatype; #IMPLIED
+ gradientUnits ( userSpaceOnUse | objectBoundingBox ) #IMPLIED
+ gradientTransform %TransformList.datatype; #IMPLIED
+ spreadMethod ( pad | reflect | repeat ) #IMPLIED
+>
+<!-- end of SVG.radialGradient.attlist -->]]>
+
+<!-- stop: Stop Element ................................ -->
+
+<!ENTITY % SVG.stop.extra.content "" >
+
+<!ENTITY % SVG.stop.element "INCLUDE" >
+<![%SVG.stop.element;[
+<!ENTITY % SVG.stop.content
+ "( %SVG.animate.qname; | %SVG.set.qname; | %SVG.animateColor.qname;
+ %SVG.stop.extra.content; )*"
+>
+<!ELEMENT %SVG.stop.qname; %SVG.stop.content; >
+<!-- end of SVG.stop.element -->]]>
+
+<!ENTITY % SVG.stop.attlist "INCLUDE" >
+<![%SVG.stop.attlist;[
+<!ATTLIST %SVG.stop.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Color.attrib;
+ %SVG.Gradient.attrib;
+ offset %NumberOrPercentage.datatype; #REQUIRED
+>
+<!-- end of SVG.stop.attlist -->]]>
+
+<!-- end of svg-gradient.mod -->
+]]>
+
+<!-- Pattern Module .............................................. -->
+<!ENTITY % svg-pattern.module "INCLUDE" >
+<![%svg-pattern.module;[
+<!ENTITY % svg-pattern.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Pattern//EN"
+ "svg-pattern.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Pattern Module ................................................ -->
+<!-- file: svg-pattern.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-basic-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Pattern//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-pattern.mod"
+
+ ....................................................................... -->
+
+<!-- Pattern
+
+ pattern
+
+ This module declares markup to provide support for pattern fill.
+-->
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.pattern.qname "pattern" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Container.attrib "" >
+<!ENTITY % SVG.Conditional.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Viewport.attrib "" >
+<!ENTITY % SVG.Text.attrib "" >
+<!ENTITY % SVG.TextContent.attrib "" >
+<!ENTITY % SVG.Font.attrib "" >
+<!ENTITY % SVG.Paint.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Marker.attrib "" >
+<!ENTITY % SVG.Profile.attrib "" >
+<!ENTITY % SVG.Gradient.attrib "" >
+<!ENTITY % SVG.Clip.attrib "" >
+<!ENTITY % SVG.Mask.attrib "" >
+<!ENTITY % SVG.Filter.attrib "" >
+<!ENTITY % SVG.FilterColor.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.XLink.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Pattern.class ................................. -->
+
+<!ENTITY % SVG.Pattern.extra.class "" >
+
+<!ENTITY % SVG.Pattern.class
+ "| %SVG.pattern.qname; %SVG.Pattern.extra.class;"
+>
+
+<!-- SVG.Presentation.attrib ........................... -->
+
+<!ENTITY % SVG.Presentation.extra.attrib "" >
+
+<!ENTITY % SVG.Presentation.attrib
+ "%SVG.Container.attrib;
+ %SVG.Viewport.attrib;
+ %SVG.Text.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Profile.attrib;
+ %SVG.Gradient.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.Cursor.attrib;
+ flood-color %SVGColor.datatype; #IMPLIED
+ flood-opacity %OpacityValue.datatype; #IMPLIED
+ lighting-color %SVGColor.datatype; #IMPLIED
+ %SVG.Presentation.extra.attrib;"
+>
+
+<!-- pattern: Pattern Element .......................... -->
+
+<!ENTITY % SVG.pattern.extra.content "" >
+
+<!ENTITY % SVG.pattern.element "INCLUDE" >
+<![%SVG.pattern.element;[
+<!ENTITY % SVG.pattern.content
+ "( %SVG.Description.class; | %SVG.Animation.class; %SVG.Structure.class;
+ %SVG.Conditional.class; %SVG.Image.class; %SVG.Style.class;
+ %SVG.Shape.class; %SVG.Text.class; %SVG.Marker.class; %SVG.Profile.class;
+ %SVG.Gradient.class; %SVG.Pattern.class; %SVG.Clip.class;
+ %SVG.Mask.class; %SVG.Filter.class; %SVG.Cursor.class;
+ %SVG.Hyperlink.class; %SVG.View.class; %SVG.Script.class;
+ %SVG.Font.class; %SVG.pattern.extra.content; )*"
+>
+<!ELEMENT %SVG.pattern.qname; %SVG.pattern.content; >
+<!-- end of SVG.pattern.element -->]]>
+
+<!ENTITY % SVG.pattern.attlist "INCLUDE" >
+<![%SVG.pattern.attlist;[
+<!ATTLIST %SVG.pattern.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.XLink.attrib;
+ %SVG.External.attrib;
+ x %Coordinate.datatype; #IMPLIED
+ y %Coordinate.datatype; #IMPLIED
+ width %Length.datatype; #IMPLIED
+ height %Length.datatype; #IMPLIED
+ patternUnits ( userSpaceOnUse | objectBoundingBox ) #IMPLIED
+ patternContentUnits ( userSpaceOnUse | objectBoundingBox ) #IMPLIED
+ patternTransform %TransformList.datatype; #IMPLIED
+ viewBox %ViewBoxSpec.datatype; #IMPLIED
+ preserveAspectRatio %PreserveAspectRatioSpec.datatype; 'xMidYMid meet'
+>
+<!-- end of SVG.pattern.attlist -->]]>
+
+<!-- end of svg-pattern.mod -->
+]]>
+
+<!-- Basic Clip Module ........................................... -->
+<!ENTITY % svg-clip.module "INCLUDE" >
+<![%svg-clip.module;[
+<!ENTITY % svg-clip.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Basic Clip//EN"
+ "svg-basic-clip.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Basic Clip Module ............................................. -->
+<!-- file: svg-basic-clip.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-basic-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Basic Clip//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-basic-clip.mod"
+
+ ....................................................................... -->
+
+<!-- Basic Clip
+
+ clipPath
+
+ This module declares markup to provide support for clipping.
+-->
+
+<!-- 'clip-path' property/attribute value (e.g., 'none', <uri>) -->
+<!ENTITY % ClipPathValue.datatype "CDATA" >
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.clipPath.qname "clipPath" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Conditional.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Text.attrib "" >
+<!ENTITY % SVG.TextContent.attrib "" >
+<!ENTITY % SVG.Font.attrib "" >
+<!ENTITY % SVG.Paint.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Mask.attrib "" >
+<!ENTITY % SVG.Filter.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Clip.class .................................... -->
+
+<!ENTITY % SVG.Clip.extra.class "" >
+
+<!ENTITY % SVG.Clip.class
+ "| %SVG.clipPath.qname; %SVG.Clip.extra.class;"
+>
+
+<!-- SVG.Clip.attrib ................................... -->
+
+<!ENTITY % SVG.Clip.extra.attrib "" >
+
+<!ENTITY % SVG.Clip.attrib
+ "clip-path %ClipPathValue.datatype; #IMPLIED
+ clip-rule %ClipFillRule.datatype; #IMPLIED
+ %SVG.Clip.extra.attrib;"
+>
+
+<!-- clipPath: Clip Path Element ....................... -->
+
+<!ENTITY % SVG.clipPath.extra.content "" >
+
+<!ENTITY % SVG.clipPath.element "INCLUDE" >
+<![%SVG.clipPath.element;[
+<!ENTITY % SVG.clipPath.content
+ "(( %SVG.Description.class; )*, ( %SVG.rect.qname; | %SVG.Animation.class;
+ %SVG.Use.class; %SVG.clipPath.extra.content; )*)"
+>
+<!ELEMENT %SVG.clipPath.qname; %SVG.clipPath.content; >
+<!-- end of SVG.clipPath.element -->]]>
+
+<!ENTITY % SVG.clipPath.attlist "INCLUDE" >
+<![%SVG.clipPath.attlist;[
+<!ATTLIST %SVG.clipPath.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Text.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.External.attrib;
+ transform %TransformList.datatype; #IMPLIED
+ clipPathUnits ( userSpaceOnUse | objectBoundingBox ) #IMPLIED
+>
+<!-- end of SVG.clipPath.attlist -->]]>
+
+<!-- end of svg-basic-clip.mod -->
+]]>
+
+<!-- Mask Module ................................................. -->
+<!ENTITY % svg-mask.module "INCLUDE" >
+<![%svg-mask.module;[
+<!ENTITY % svg-mask.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Mask//EN"
+ "svg-mask.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Mask Module ................................................... -->
+<!-- file: svg-mask.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-basic-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Mask//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-mask.mod"
+
+ ....................................................................... -->
+
+<!-- Mask
+
+ mask
+
+ This module declares markup to provide support for masking.
+-->
+
+<!-- 'mask' property/attribute value (e.g., 'none', <uri>) -->
+<!ENTITY % MaskValue.datatype "CDATA" >
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.mask.qname "mask" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Container.attrib "" >
+<!ENTITY % SVG.Conditional.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Viewport.attrib "" >
+<!ENTITY % SVG.Text.attrib "" >
+<!ENTITY % SVG.TextContent.attrib "" >
+<!ENTITY % SVG.Font.attrib "" >
+<!ENTITY % SVG.Paint.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Marker.attrib "" >
+<!ENTITY % SVG.Profile.attrib "" >
+<!ENTITY % SVG.Gradient.attrib "" >
+<!ENTITY % SVG.Clip.attrib "" >
+<!ENTITY % SVG.Filter.attrib "" >
+<!ENTITY % SVG.FilterColor.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Mask.class .................................... -->
+
+<!ENTITY % SVG.Mask.extra.class "" >
+
+<!ENTITY % SVG.Mask.class
+ "| %SVG.mask.qname; %SVG.Mask.extra.class;"
+>
+
+<!-- SVG.Mask.attrib ................................... -->
+
+<!ENTITY % SVG.Mask.extra.attrib "" >
+
+<!ENTITY % SVG.Mask.attrib
+ "mask %MaskValue.datatype; #IMPLIED
+ %SVG.Mask.extra.attrib;"
+>
+
+<!-- SVG.Presentation.attrib ........................... -->
+
+<!ENTITY % SVG.Presentation.extra.attrib "" >
+
+<!ENTITY % SVG.Presentation.attrib
+ "%SVG.Container.attrib;
+ %SVG.Viewport.attrib;
+ %SVG.Text.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Profile.attrib;
+ %SVG.Gradient.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.Cursor.attrib;
+ flood-color %SVGColor.datatype; #IMPLIED
+ flood-opacity %OpacityValue.datatype; #IMPLIED
+ lighting-color %SVGColor.datatype; #IMPLIED
+ %SVG.Presentation.extra.attrib;"
+>
+
+<!-- mask: Mask Element ................................ -->
+
+<!ENTITY % SVG.mask.extra.content "" >
+
+<!ENTITY % SVG.mask.element "INCLUDE" >
+<![%SVG.mask.element;[
+<!ENTITY % SVG.mask.content
+ "( %SVG.Description.class; | %SVG.Animation.class; %SVG.Structure.class;
+ %SVG.Conditional.class; %SVG.Image.class; %SVG.Style.class;
+ %SVG.Shape.class; %SVG.Text.class; %SVG.Marker.class; %SVG.Profile.class;
+ %SVG.Gradient.class; %SVG.Pattern.class; %SVG.Clip.class;
+ %SVG.Mask.class; %SVG.Filter.class; %SVG.Cursor.class;
+ %SVG.Hyperlink.class; %SVG.View.class; %SVG.Script.class;
+ %SVG.Font.class; %SVG.mask.extra.content; )*"
+>
+<!ELEMENT %SVG.mask.qname; %SVG.mask.content; >
+<!-- end of SVG.mask.element -->]]>
+
+<!ENTITY % SVG.mask.attlist "INCLUDE" >
+<![%SVG.mask.attlist;[
+<!ATTLIST %SVG.mask.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.External.attrib;
+ x %Coordinate.datatype; #IMPLIED
+ y %Coordinate.datatype; #IMPLIED
+ width %Length.datatype; #IMPLIED
+ height %Length.datatype; #IMPLIED
+ maskUnits ( userSpaceOnUse | objectBoundingBox ) #IMPLIED
+ maskContentUnits ( userSpaceOnUse | objectBoundingBox ) #IMPLIED
+>
+<!-- end of SVG.mask.attlist -->]]>
+
+<!-- end of svg-mask.mod -->
+]]>
+
+<!-- Basic Filter Module ......................................... -->
+<!ENTITY % svg-filter.module "INCLUDE" >
+<![%svg-filter.module;[
+<!ENTITY % svg-filter.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Basic Filter//EN"
+ "svg-basic-filter.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Basic Filter Module ........................................... -->
+<!-- file: svg-basic-filter.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-basic-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Basic Filter//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-basic-filter.mod"
+
+ ....................................................................... -->
+
+<!-- Basic Filter
+
+ filter, feBlend, feColorMatrix, feComponentTransfer, feComposite,
+ feFlood, feGaussianBlur, feImage, feMerge, feMergeNode, feOffset,
+ feTile, feFuncR, feFuncG, feFuncB, feFuncA
+
+ This module declares markup to provide support for filter effect.
+-->
+
+<!-- 'filter' property/attribute value (e.g., 'none', <uri>) -->
+<!ENTITY % FilterValue.datatype "CDATA" >
+
+<!-- list of <number>s, but at least one and at most two -->
+<!ENTITY % NumberOptionalNumber.datatype "CDATA" >
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.filter.qname "filter" >
+<!ENTITY % SVG.feBlend.qname "feBlend" >
+<!ENTITY % SVG.feColorMatrix.qname "feColorMatrix" >
+<!ENTITY % SVG.feComponentTransfer.qname "feComponentTransfer" >
+<!ENTITY % SVG.feComposite.qname "feComposite" >
+<!ENTITY % SVG.feFlood.qname "feFlood" >
+<!ENTITY % SVG.feGaussianBlur.qname "feGaussianBlur" >
+<!ENTITY % SVG.feImage.qname "feImage" >
+<!ENTITY % SVG.feMerge.qname "feMerge" >
+<!ENTITY % SVG.feMergeNode.qname "feMergeNode" >
+<!ENTITY % SVG.feOffset.qname "feOffset" >
+<!ENTITY % SVG.feTile.qname "feTile" >
+<!ENTITY % SVG.feFuncR.qname "feFuncR" >
+<!ENTITY % SVG.feFuncG.qname "feFuncG" >
+<!ENTITY % SVG.feFuncB.qname "feFuncB" >
+<!ENTITY % SVG.feFuncA.qname "feFuncA" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Container.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Viewport.attrib "" >
+<!ENTITY % SVG.Text.attrib "" >
+<!ENTITY % SVG.TextContent.attrib "" >
+<!ENTITY % SVG.Font.attrib "" >
+<!ENTITY % SVG.Paint.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Marker.attrib "" >
+<!ENTITY % SVG.Profile.attrib "" >
+<!ENTITY % SVG.Gradient.attrib "" >
+<!ENTITY % SVG.Clip.attrib "" >
+<!ENTITY % SVG.Mask.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.XLink.attrib "" >
+<!ENTITY % SVG.XLinkEmbed.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Filter.class .................................. -->
+
+<!ENTITY % SVG.Filter.extra.class "" >
+
+<!ENTITY % SVG.Filter.class
+ "| %SVG.filter.qname; %SVG.Filter.extra.class;"
+>
+
+<!-- SVG.FilterPrimitive.class ......................... -->
+
+<!ENTITY % SVG.FilterPrimitive.extra.class "" >
+
+<!ENTITY % SVG.FilterPrimitive.class
+ "| %SVG.feBlend.qname; | %SVG.feColorMatrix.qname;
+ | %SVG.feComponentTransfer.qname; | %SVG.feComposite.qname;
+ | %SVG.feFlood.qname; | %SVG.feGaussianBlur.qname; | %SVG.feImage.qname;
+ | %SVG.feMerge.qname; | %SVG.feOffset.qname; | %SVG.feTile.qname;
+ %SVG.FilterPrimitive.extra.class;"
+>
+
+<!-- SVG.Filter.attrib ................................. -->
+
+<!ENTITY % SVG.Filter.extra.attrib "" >
+
+<!ENTITY % SVG.Filter.attrib
+ "filter %FilterValue.datatype; #IMPLIED
+ %SVG.Filter.extra.attrib;"
+>
+
+<!-- SVG.FilterColor.attrib ............................ -->
+
+<!ENTITY % SVG.FilterColor.extra.attrib "" >
+
+<!ENTITY % SVG.FilterColor.attrib
+ "color-interpolation-filters ( auto | sRGB | linearRGB | inherit )
+ #IMPLIED
+ %SVG.FilterColor.extra.attrib;"
+>
+
+<!-- SVG.FilterPrimitive.attrib ........................ -->
+
+<!ENTITY % SVG.FilterPrimitive.extra.attrib "" >
+
+<!ENTITY % SVG.FilterPrimitive.attrib
+ "x %Coordinate.datatype; #IMPLIED
+ y %Coordinate.datatype; #IMPLIED
+ width %Length.datatype; #IMPLIED
+ height %Length.datatype; #IMPLIED
+ result CDATA #IMPLIED
+ %SVG.FilterPrimitive.extra.attrib;"
+>
+
+<!-- SVG.FilterPrimitiveWithIn.attrib .................. -->
+
+<!ENTITY % SVG.FilterPrimitiveWithIn.extra.attrib "" >
+
+<!ENTITY % SVG.FilterPrimitiveWithIn.attrib
+ "%SVG.FilterPrimitive.attrib;
+ in CDATA #IMPLIED
+ %SVG.FilterPrimitiveWithIn.extra.attrib;"
+>
+
+<!-- SVG.Presentation.attrib ........................... -->
+
+<!ENTITY % SVG.Presentation.extra.attrib "" >
+
+<!ENTITY % SVG.Presentation.attrib
+ "%SVG.Container.attrib;
+ %SVG.Viewport.attrib;
+ %SVG.Text.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Profile.attrib;
+ %SVG.Gradient.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.Cursor.attrib;
+ flood-color %SVGColor.datatype; #IMPLIED
+ flood-opacity %OpacityValue.datatype; #IMPLIED
+ lighting-color %SVGColor.datatype; #IMPLIED
+ %SVG.Presentation.extra.attrib;"
+>
+
+<!-- filter: Filter Element ............................ -->
+
+<!ENTITY % SVG.filter.extra.content "" >
+
+<!ENTITY % SVG.filter.element "INCLUDE" >
+<![%SVG.filter.element;[
+<!ENTITY % SVG.filter.content
+ "(( %SVG.Description.class; )*, ( %SVG.animate.qname; | %SVG.set.qname;
+ %SVG.FilterPrimitive.class; %SVG.filter.extra.content; )*)"
+>
+<!ELEMENT %SVG.filter.qname; %SVG.filter.content; >
+<!-- end of SVG.filter.element -->]]>
+
+<!ENTITY % SVG.filter.attlist "INCLUDE" >
+<![%SVG.filter.attlist;[
+<!ATTLIST %SVG.filter.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.XLink.attrib;
+ %SVG.External.attrib;
+ x %Coordinate.datatype; #IMPLIED
+ y %Coordinate.datatype; #IMPLIED
+ width %Length.datatype; #IMPLIED
+ height %Length.datatype; #IMPLIED
+ filterRes %NumberOptionalNumber.datatype; #IMPLIED
+ filterUnits ( userSpaceOnUse | objectBoundingBox ) #IMPLIED
+ primitiveUnits ( userSpaceOnUse | objectBoundingBox ) #IMPLIED
+>
+<!-- end of SVG.filter.attlist -->]]>
+
+<!-- feBlend: Filter Effect Blend Element .............. -->
+
+<!ENTITY % SVG.feBlend.extra.content "" >
+
+<!ENTITY % SVG.feBlend.element "INCLUDE" >
+<![%SVG.feBlend.element;[
+<!ENTITY % SVG.feBlend.content
+ "( %SVG.animate.qname; | %SVG.set.qname; %SVG.feBlend.extra.content; )*"
+>
+<!ELEMENT %SVG.feBlend.qname; %SVG.feBlend.content; >
+<!-- end of SVG.feBlend.element -->]]>
+
+<!ENTITY % SVG.feBlend.attlist "INCLUDE" >
+<![%SVG.feBlend.attlist;[
+<!ATTLIST %SVG.feBlend.qname;
+ %SVG.Core.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitiveWithIn.attrib;
+ in2 CDATA #REQUIRED
+ mode ( normal | multiply | screen | darken | lighten ) 'normal'
+>
+<!-- end of SVG.feBlend.attlist -->]]>
+
+<!-- feColorMatrix: Filter Effect Color Matrix Element . -->
+
+<!ENTITY % SVG.feColorMatrix.extra.content "" >
+
+<!ENTITY % SVG.feColorMatrix.element "INCLUDE" >
+<![%SVG.feColorMatrix.element;[
+<!ENTITY % SVG.feColorMatrix.content
+ "( %SVG.animate.qname; | %SVG.set.qname;
+ %SVG.feColorMatrix.extra.content; )*"
+>
+<!ELEMENT %SVG.feColorMatrix.qname; %SVG.feColorMatrix.content; >
+<!-- end of SVG.feColorMatrix.element -->]]>
+
+<!ENTITY % SVG.feColorMatrix.attlist "INCLUDE" >
+<![%SVG.feColorMatrix.attlist;[
+<!ATTLIST %SVG.feColorMatrix.qname;
+ %SVG.Core.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitiveWithIn.attrib;
+ type ( matrix | saturate | hueRotate | luminanceToAlpha ) 'matrix'
+ values CDATA #IMPLIED
+>
+<!-- end of SVG.feColorMatrix.attlist -->]]>
+
+<!-- feComponentTransfer: Filter Effect Component Transfer Element -->
+
+<!ENTITY % SVG.feComponentTransfer.extra.content "" >
+
+<!ENTITY % SVG.feComponentTransfer.element "INCLUDE" >
+<![%SVG.feComponentTransfer.element;[
+<!ENTITY % SVG.feComponentTransfer.content
+ "( %SVG.feFuncR.qname;?, %SVG.feFuncG.qname;?, %SVG.feFuncB.qname;?,
+ %SVG.feFuncA.qname;? %SVG.feComponentTransfer.extra.content; )"
+>
+<!ELEMENT %SVG.feComponentTransfer.qname; %SVG.feComponentTransfer.content; >
+<!-- end of SVG.feComponentTransfer.element -->]]>
+
+<!ENTITY % SVG.feComponentTransfer.attlist "INCLUDE" >
+<![%SVG.feComponentTransfer.attlist;[
+<!ATTLIST %SVG.feComponentTransfer.qname;
+ %SVG.Core.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitiveWithIn.attrib;
+>
+<!-- end of SVG.feComponentTransfer.attlist -->]]>
+
+<!-- feComposite: Filter Effect Composite Element ...... -->
+
+<!ENTITY % SVG.feComposite.extra.content "" >
+
+<!ENTITY % SVG.feComposite.element "INCLUDE" >
+<![%SVG.feComposite.element;[
+<!ENTITY % SVG.feComposite.content
+ "( %SVG.animate.qname; | %SVG.set.qname; %SVG.feComposite.extra.content; )*"
+>
+<!ELEMENT %SVG.feComposite.qname; %SVG.feComposite.content; >
+<!-- end of SVG.feComposite.element -->]]>
+
+<!ENTITY % SVG.feComposite.attlist "INCLUDE" >
+<![%SVG.feComposite.attlist;[
+<!ATTLIST %SVG.feComposite.qname;
+ %SVG.Core.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitiveWithIn.attrib;
+ in2 CDATA #REQUIRED
+ operator ( over | in | out | atop | xor | arithmetic ) 'over'
+ k1 %Number.datatype; #IMPLIED
+ k2 %Number.datatype; #IMPLIED
+ k3 %Number.datatype; #IMPLIED
+ k4 %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.feComposite.attlist -->]]>
+
+<!-- feFlood: Filter Effect Flood Element .............. -->
+
+<!ENTITY % SVG.feFlood.extra.content "" >
+
+<!ENTITY % SVG.feFlood.element "INCLUDE" >
+<![%SVG.feFlood.element;[
+<!ENTITY % SVG.feFlood.content
+ "( %SVG.animate.qname; | %SVG.set.qname; | %SVG.animateColor.qname;
+ %SVG.feFlood.extra.content; )*"
+>
+<!ELEMENT %SVG.feFlood.qname; %SVG.feFlood.content; >
+<!-- end of SVG.feFlood.element -->]]>
+
+<!ENTITY % SVG.feFlood.attlist "INCLUDE" >
+<![%SVG.feFlood.attlist;[
+<!ATTLIST %SVG.feFlood.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Color.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitiveWithIn.attrib;
+ flood-color %SVGColor.datatype; #IMPLIED
+ flood-opacity %OpacityValue.datatype; #IMPLIED
+>
+<!-- end of SVG.feFlood.attlist -->]]>
+
+<!-- feGaussianBlur: Filter Effect Gaussian Blur Element -->
+
+<!ENTITY % SVG.feGaussianBlur.extra.content "" >
+
+<!ENTITY % SVG.feGaussianBlur.element "INCLUDE" >
+<![%SVG.feGaussianBlur.element;[
+<!ENTITY % SVG.feGaussianBlur.content
+ "( %SVG.animate.qname; | %SVG.set.qname;
+ %SVG.feGaussianBlur.extra.content; )*"
+>
+<!ELEMENT %SVG.feGaussianBlur.qname; %SVG.feGaussianBlur.content; >
+<!-- end of SVG.feGaussianBlur.element -->]]>
+
+<!ENTITY % SVG.feGaussianBlur.attlist "INCLUDE" >
+<![%SVG.feGaussianBlur.attlist;[
+<!ATTLIST %SVG.feGaussianBlur.qname;
+ %SVG.Core.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitiveWithIn.attrib;
+ stdDeviation %NumberOptionalNumber.datatype; #IMPLIED
+>
+<!-- end of SVG.feGaussianBlur.attlist -->]]>
+
+<!-- feImage: Filter Effect Image Element .............. -->
+
+<!ENTITY % SVG.feImage.extra.content "" >
+
+<!ENTITY % SVG.feImage.element "INCLUDE" >
+<![%SVG.feImage.element;[
+<!ENTITY % SVG.feImage.content
+ "( %SVG.animate.qname; | %SVG.set.qname; | %SVG.animateTransform.qname;
+ %SVG.feImage.extra.content; )*"
+>
+<!ELEMENT %SVG.feImage.qname; %SVG.feImage.content; >
+<!-- end of SVG.feImage.element -->]]>
+
+<!ENTITY % SVG.feImage.attlist "INCLUDE" >
+<![%SVG.feImage.attlist;[
+<!ATTLIST %SVG.feImage.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.FilterPrimitive.attrib;
+ %SVG.XLinkEmbed.attrib;
+ %SVG.External.attrib;
+ preserveAspectRatio %PreserveAspectRatioSpec.datatype; 'xMidYMid meet'
+>
+<!-- end of SVG.feImage.attlist -->]]>
+
+<!-- feMerge: Filter Effect Merge Element .............. -->
+
+<!ENTITY % SVG.feMerge.extra.content "" >
+
+<!ENTITY % SVG.feMerge.element "INCLUDE" >
+<![%SVG.feMerge.element;[
+<!ENTITY % SVG.feMerge.content
+ "( %SVG.feMergeNode.qname; %SVG.feMerge.extra.content; )*"
+>
+<!ELEMENT %SVG.feMerge.qname; %SVG.feMerge.content; >
+<!-- end of SVG.feMerge.element -->]]>
+
+<!ENTITY % SVG.feMerge.attlist "INCLUDE" >
+<![%SVG.feMerge.attlist;[
+<!ATTLIST %SVG.feMerge.qname;
+ %SVG.Core.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitive.attrib;
+>
+<!-- end of SVG.feMerge.attlist -->]]>
+
+<!-- feMergeNode: Filter Effect Merge Node Element ..... -->
+
+<!ENTITY % SVG.feMergeNode.extra.content "" >
+
+<!ENTITY % SVG.feMergeNode.element "INCLUDE" >
+<![%SVG.feMergeNode.element;[
+<!ENTITY % SVG.feMergeNode.content
+ "( %SVG.animate.qname; | %SVG.set.qname; %SVG.feMergeNode.extra.content; )*"
+>
+<!ELEMENT %SVG.feMergeNode.qname; %SVG.feMergeNode.content; >
+<!-- end of SVG.feMergeNode.element -->]]>
+
+<!ENTITY % SVG.feMergeNode.attlist "INCLUDE" >
+<![%SVG.feMergeNode.attlist;[
+<!ATTLIST %SVG.feMergeNode.qname;
+ %SVG.Core.attrib;
+ in CDATA #IMPLIED
+>
+<!-- end of SVG.feMergeNode.attlist -->]]>
+
+<!-- feOffset: Filter Effect Offset Element ............ -->
+
+<!ENTITY % SVG.feOffset.extra.content "" >
+
+<!ENTITY % SVG.feOffset.element "INCLUDE" >
+<![%SVG.feOffset.element;[
+<!ENTITY % SVG.feOffset.content
+ "( %SVG.animate.qname; | %SVG.set.qname; %SVG.feOffset.extra.content; )*"
+>
+<!ELEMENT %SVG.feOffset.qname; %SVG.feOffset.content; >
+<!-- end of SVG.feOffset.element -->]]>
+
+<!ENTITY % SVG.feOffset.attlist "INCLUDE" >
+<![%SVG.feOffset.attlist;[
+<!ATTLIST %SVG.feOffset.qname;
+ %SVG.Core.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitiveWithIn.attrib;
+ dx %Number.datatype; #IMPLIED
+ dy %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.feOffset.attlist -->]]>
+
+<!-- feTile: Filter Effect Tile Element ................ -->
+
+<!ENTITY % SVG.feTile.extra.content "" >
+
+<!ENTITY % SVG.feTile.element "INCLUDE" >
+<![%SVG.feTile.element;[
+<!ENTITY % SVG.feTile.content
+ "( %SVG.animate.qname; | %SVG.set.qname; %SVG.feTile.extra.content; )*"
+>
+<!ELEMENT %SVG.feTile.qname; %SVG.feTile.content; >
+<!-- end of SVG.feTile.element -->]]>
+
+<!ENTITY % SVG.feTile.attlist "INCLUDE" >
+<![%SVG.feTile.attlist;[
+<!ATTLIST %SVG.feTile.qname;
+ %SVG.Core.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitiveWithIn.attrib;
+>
+<!-- end of SVG.feTile.attlist -->]]>
+
+<!-- feFuncR: Filter Effect Function Red Element ....... -->
+
+<!ENTITY % SVG.feFuncR.extra.content "" >
+
+<!ENTITY % SVG.feFuncR.element "INCLUDE" >
+<![%SVG.feFuncR.element;[
+<!ENTITY % SVG.feFuncR.content
+ "( %SVG.animate.qname; | %SVG.set.qname; %SVG.feFuncR.extra.content; )*"
+>
+<!ELEMENT %SVG.feFuncR.qname; %SVG.feFuncR.content; >
+<!-- end of SVG.feFuncR.element -->]]>
+
+<!ENTITY % SVG.feFuncR.attlist "INCLUDE" >
+<![%SVG.feFuncR.attlist;[
+<!ATTLIST %SVG.feFuncR.qname;
+ %SVG.Core.attrib;
+ type ( identity | table | discrete | linear | gamma ) #REQUIRED
+ tableValues CDATA #IMPLIED
+ slope %Number.datatype; #IMPLIED
+ intercept %Number.datatype; #IMPLIED
+ amplitude %Number.datatype; #IMPLIED
+ exponent %Number.datatype; #IMPLIED
+ offset %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.feFuncR.attlist -->]]>
+
+<!-- feFuncG: Filter Effect Function Green Element ..... -->
+
+<!ENTITY % SVG.feFuncG.extra.content "" >
+
+<!ENTITY % SVG.feFuncG.element "INCLUDE" >
+<![%SVG.feFuncG.element;[
+<!ENTITY % SVG.feFuncG.content
+ "( %SVG.animate.qname; | %SVG.set.qname; %SVG.feFuncG.extra.content; )*"
+>
+<!ELEMENT %SVG.feFuncG.qname; %SVG.feFuncG.content; >
+<!-- end of SVG.feFuncG.element -->]]>
+
+<!ENTITY % SVG.feFuncG.attlist "INCLUDE" >
+<![%SVG.feFuncG.attlist;[
+<!ATTLIST %SVG.feFuncG.qname;
+ %SVG.Core.attrib;
+ type ( identity | table | discrete | linear | gamma ) #REQUIRED
+ tableValues CDATA #IMPLIED
+ slope %Number.datatype; #IMPLIED
+ intercept %Number.datatype; #IMPLIED
+ amplitude %Number.datatype; #IMPLIED
+ exponent %Number.datatype; #IMPLIED
+ offset %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.feFuncG.attlist -->]]>
+
+<!-- feFuncB: Filter Effect Function Blue Element ...... -->
+
+<!ENTITY % SVG.feFuncB.extra.content "" >
+
+<!ENTITY % SVG.feFuncB.element "INCLUDE" >
+<![%SVG.feFuncB.element;[
+<!ENTITY % SVG.feFuncB.content
+ "( %SVG.animate.qname; | %SVG.set.qname; %SVG.feFuncB.extra.content; )*"
+>
+<!ELEMENT %SVG.feFuncB.qname; %SVG.feFuncB.content; >
+<!-- end of SVG.feFuncB.element -->]]>
+
+<!ENTITY % SVG.feFuncB.attlist "INCLUDE" >
+<![%SVG.feFuncB.attlist;[
+<!ATTLIST %SVG.feFuncB.qname;
+ %SVG.Core.attrib;
+ type ( identity | table | discrete | linear | gamma ) #REQUIRED
+ tableValues CDATA #IMPLIED
+ slope %Number.datatype; #IMPLIED
+ intercept %Number.datatype; #IMPLIED
+ amplitude %Number.datatype; #IMPLIED
+ exponent %Number.datatype; #IMPLIED
+ offset %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.feFuncB.attlist -->]]>
+
+<!-- feFuncA: Filter Effect Function Alpha Element ..... -->
+
+<!ENTITY % SVG.feFuncA.extra.content "" >
+
+<!ENTITY % SVG.feFuncA.element "INCLUDE" >
+<![%SVG.feFuncA.element;[
+<!ENTITY % SVG.feFuncA.content
+ "( %SVG.animate.qname; | %SVG.set.qname; %SVG.feFuncA.extra.content; )*"
+>
+<!ELEMENT %SVG.feFuncA.qname; %SVG.feFuncA.content; >
+<!-- end of SVG.feFuncA.element -->]]>
+
+<!ENTITY % SVG.feFuncA.attlist "INCLUDE" >
+<![%SVG.feFuncA.attlist;[
+<!ATTLIST %SVG.feFuncA.qname;
+ %SVG.Core.attrib;
+ type ( identity | table | discrete | linear | gamma ) #REQUIRED
+ tableValues CDATA #IMPLIED
+ slope %Number.datatype; #IMPLIED
+ intercept %Number.datatype; #IMPLIED
+ amplitude %Number.datatype; #IMPLIED
+ exponent %Number.datatype; #IMPLIED
+ offset %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.feFuncA.attlist -->]]>
+
+<!-- end of svg-basic-filter.mod -->
+]]>
+
+<!-- Cursor Module ............................................... -->
+<!ENTITY % svg-cursor.module "INCLUDE" >
+<![%svg-cursor.module;[
+<!ENTITY % svg-cursor.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Cursor//EN"
+ "svg-cursor.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Cursor Module ................................................. -->
+<!-- file: svg-cursor.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-basic-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Cursor//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-cursor.mod"
+
+ ....................................................................... -->
+
+<!-- Cursor
+
+ cursor
+
+ This module declares markup to provide support for cursor.
+-->
+
+<!-- 'cursor' property/attribute value (e.g., 'crosshair', <uri>) -->
+<!ENTITY % CursorValue.datatype "CDATA" >
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.cursor.qname "cursor" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Conditional.attrib "" >
+<!ENTITY % SVG.XLinkRequired.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Cursor.class .................................. -->
+
+<!ENTITY % SVG.Cursor.extra.class "" >
+
+<!ENTITY % SVG.Cursor.class
+ "| %SVG.cursor.qname; %SVG.Cursor.extra.class;"
+>
+
+<!-- SVG.Cursor.attrib ................................. -->
+
+<!ENTITY % SVG.Cursor.extra.attrib "" >
+
+<!ENTITY % SVG.Cursor.attrib
+ "cursor %CursorValue.datatype; #IMPLIED
+ %SVG.Cursor.extra.attrib;"
+>
+
+<!-- cursor: Cursor Element ............................ -->
+
+<!ENTITY % SVG.cursor.extra.content "" >
+
+<!ENTITY % SVG.cursor.element "INCLUDE" >
+<![%SVG.cursor.element;[
+<!ENTITY % SVG.cursor.content
+ "( %SVG.Description.class; %SVG.cursor.extra.content; )*"
+>
+<!ELEMENT %SVG.cursor.qname; %SVG.cursor.content; >
+<!-- end of SVG.cursor.element -->]]>
+
+<!ENTITY % SVG.cursor.attlist "INCLUDE" >
+<![%SVG.cursor.attlist;[
+<!ATTLIST %SVG.cursor.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.XLinkRequired.attrib;
+ %SVG.External.attrib;
+ x %Coordinate.datatype; #IMPLIED
+ y %Coordinate.datatype; #IMPLIED
+>
+<!-- end of SVG.cursor.attlist -->]]>
+
+<!-- end of svg-cursor.mod -->
+]]>
+
+<!-- Hyperlinking Module ......................................... -->
+<!ENTITY % svg-hyperlink.module "INCLUDE" >
+<![%svg-hyperlink.module;[
+<!ENTITY % svg-hyperlink.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Hyperlinking//EN"
+ "svg-hyperlink.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Hyperlinking Module ........................................... -->
+<!-- file: svg-hyperlink.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-basic-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Hyperlinking//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-hyperlink.mod"
+
+ ....................................................................... -->
+
+<!-- Hyperlinking
+
+ a
+
+ This module declares markup to provide support for hyper linking.
+-->
+
+<!-- link to this target -->
+<!ENTITY % LinkTarget.datatype "NMTOKEN" >
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.a.qname "a" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Conditional.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Viewport.attrib "" >
+<!ENTITY % SVG.Text.attrib "" >
+<!ENTITY % SVG.TextContent.attrib "" >
+<!ENTITY % SVG.Font.attrib "" >
+<!ENTITY % SVG.Paint.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Marker.attrib "" >
+<!ENTITY % SVG.Gradient.attrib "" >
+<!ENTITY % SVG.Clip.attrib "" >
+<!ENTITY % SVG.Mask.attrib "" >
+<!ENTITY % SVG.Filter.attrib "" >
+<!ENTITY % SVG.FilterColor.attrib "" >
+<!ENTITY % SVG.GraphicalEvents.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.XLinkReplace.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Hyperlink.class ............................... -->
+
+<!ENTITY % SVG.Hyperlink.extra.class "" >
+
+<!ENTITY % SVG.Hyperlink.class
+ "| %SVG.a.qname; %SVG.Hyperlink.extra.class;"
+>
+
+<!-- SVG.Presentation.attrib ........................... -->
+
+<!ENTITY % SVG.Presentation.extra.attrib "" >
+
+<!ENTITY % SVG.Presentation.attrib
+ "%SVG.Container.attrib;
+ %SVG.Viewport.attrib;
+ %SVG.Text.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Profile.attrib;
+ %SVG.Gradient.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.Cursor.attrib;
+ flood-color %SVGColor.datatype; #IMPLIED
+ flood-opacity %OpacityValue.datatype; #IMPLIED
+ lighting-color %SVGColor.datatype; #IMPLIED
+ %SVG.Presentation.extra.attrib;"
+>
+
+<!-- a: Anchor Element ................................. -->
+
+<!ENTITY % SVG.a.extra.content "" >
+
+<!ENTITY % SVG.a.element "INCLUDE" >
+<![%SVG.a.element;[
+<!ENTITY % SVG.a.content
+ "( #PCDATA | %SVG.Description.class; | %SVG.Animation.class;
+ %SVG.Structure.class; %SVG.Conditional.class; %SVG.Image.class;
+ %SVG.Style.class; %SVG.Shape.class; %SVG.Text.class; %SVG.Marker.class;
+ %SVG.Profile.class; %SVG.Gradient.class; %SVG.Pattern.class;
+ %SVG.Clip.class; %SVG.Mask.class; %SVG.Filter.class; %SVG.Cursor.class;
+ %SVG.Hyperlink.class; %SVG.View.class; %SVG.Script.class;
+ %SVG.Font.class; %SVG.a.extra.content; )*"
+>
+<!ELEMENT %SVG.a.qname; %SVG.a.content; >
+<!-- end of SVG.a.element -->]]>
+
+<!ENTITY % SVG.a.attlist "INCLUDE" >
+<![%SVG.a.attlist;[
+<!ATTLIST %SVG.a.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.XLinkReplace.attrib;
+ %SVG.External.attrib;
+ transform %TransformList.datatype; #IMPLIED
+ target %LinkTarget.datatype; #IMPLIED
+>
+<!-- end of SVG.a.attlist -->]]>
+
+<!-- end of svg-hyperlink.mod -->
+]]>
+
+<!-- View Module ................................................. -->
+<!ENTITY % svg-view.module "INCLUDE" >
+<![%svg-view.module;[
+<!ENTITY % svg-view.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 View//EN"
+ "svg-view.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 View Module ................................................... -->
+<!-- file: svg-view.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-basic-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 View//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-view.mod"
+
+ ....................................................................... -->
+
+<!-- View
+
+ view
+
+ This module declares markup to provide support for view.
+-->
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.view.qname "view" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.View.class .................................... -->
+
+<!ENTITY % SVG.View.extra.class "" >
+
+<!ENTITY % SVG.View.class
+ "| %SVG.view.qname; %SVG.View.extra.class;"
+>
+
+<!-- view: View Element ................................ -->
+
+<!ENTITY % SVG.view.extra.content "" >
+
+<!ENTITY % SVG.view.element "INCLUDE" >
+<![%SVG.view.element;[
+<!ENTITY % SVG.view.content
+ "( %SVG.Description.class; %SVG.view.extra.content; )*"
+>
+<!ELEMENT %SVG.view.qname; %SVG.view.content; >
+<!-- end of SVG.view.element -->]]>
+
+<!ENTITY % SVG.view.attlist "INCLUDE" >
+<![%SVG.view.attlist;[
+<!ATTLIST %SVG.view.qname;
+ %SVG.Core.attrib;
+ %SVG.External.attrib;
+ viewBox %ViewBoxSpec.datatype; #IMPLIED
+ preserveAspectRatio %PreserveAspectRatioSpec.datatype; 'xMidYMid meet'
+ zoomAndPan ( disable | magnify ) 'magnify'
+ viewTarget CDATA #IMPLIED
+>
+<!-- end of SVG.view.attlist -->]]>
+
+<!-- end of svg-view.mod -->
+]]>
+
+<!-- Scripting Module ............................................ -->
+<!ENTITY % svg-script.module "INCLUDE" >
+<![%svg-script.module;[
+<!ENTITY % svg-script.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Scripting//EN"
+ "svg-script.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Scripting Module .............................................. -->
+<!-- file: svg-script.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-basic-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Scripting//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-script.mod"
+
+ ....................................................................... -->
+
+<!-- Scripting
+
+ script
+
+ This module declares markup to provide support for scripting.
+-->
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.script.qname "script" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.XLink.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Script.class .................................. -->
+
+<!ENTITY % SVG.Script.extra.class "" >
+
+<!ENTITY % SVG.Script.class
+ "| %SVG.script.qname; %SVG.Script.extra.class;"
+>
+
+<!-- script: Script Element ............................ -->
+
+<!ENTITY % SVG.script.extra.content "" >
+
+<!ENTITY % SVG.script.element "INCLUDE" >
+<![%SVG.script.element;[
+<!ENTITY % SVG.script.content
+ "( #PCDATA %SVG.script.extra.content; )*"
+>
+<!ELEMENT %SVG.script.qname; %SVG.script.content; >
+<!-- end of SVG.script.element -->]]>
+
+<!ENTITY % SVG.script.attlist "INCLUDE" >
+<![%SVG.script.attlist;[
+<!ATTLIST %SVG.script.qname;
+ %SVG.Core.attrib;
+ %SVG.XLink.attrib;
+ %SVG.External.attrib;
+ type %ContentType.datatype; #REQUIRED
+>
+<!-- end of SVG.script.attlist -->]]>
+
+<!-- end of svg-script.mod -->
+]]>
+
+<!-- Animation Module ............................................ -->
+<!ENTITY % svg-animation.module "INCLUDE" >
+<![%svg-animation.module;[
+<!ENTITY % svg-animation.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Animation//EN"
+ "svg-animation.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Animation Module .............................................. -->
+<!-- file: svg-animation.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-basic-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Animation//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-animation.mod"
+
+ ....................................................................... -->
+
+<!-- Animation
+
+ animate, set, animateMotion, animateColor, animateTransform, mpath
+
+ This module declares markup to provide support for animation.
+-->
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.animate.qname "animate" >
+<!ENTITY % SVG.set.qname "set" >
+<!ENTITY % SVG.animateMotion.qname "animateMotion" >
+<!ENTITY % SVG.animateColor.qname "animateColor" >
+<!ENTITY % SVG.animateTransform.qname "animateTransform" >
+<!ENTITY % SVG.mpath.qname "mpath" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Conditional.attrib "" >
+<!ENTITY % SVG.AnimationEvents.attrib "" >
+<!ENTITY % SVG.XLink.attrib "" >
+<!ENTITY % SVG.XLinkRequired.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Animation.class ............................... -->
+
+<!ENTITY % SVG.Animation.extra.class "" >
+
+<!ENTITY % SVG.Animation.class
+ "%SVG.animate.qname; | %SVG.set.qname; | %SVG.animateMotion.qname; |
+ %SVG.animateColor.qname; | %SVG.animateTransform.qname;
+ %SVG.Animation.extra.class;"
+>
+
+<!-- SVG.Animation.attrib .............................. -->
+
+<!ENTITY % SVG.Animation.extra.attrib "" >
+
+<!ENTITY % SVG.Animation.attrib
+ "%SVG.XLink.attrib;
+ %SVG.Animation.extra.attrib;"
+>
+
+<!-- SVG.AnimationAttribute.attrib ..................... -->
+
+<!ENTITY % SVG.AnimationAttribute.extra.attrib "" >
+
+<!ENTITY % SVG.AnimationAttribute.attrib
+ "attributeName CDATA #REQUIRED
+ attributeType CDATA #IMPLIED
+ %SVG.AnimationAttribute.extra.attrib;"
+>
+
+<!-- SVG.AnimationTiming.attrib ........................ -->
+
+<!ENTITY % SVG.AnimationTiming.extra.attrib "" >
+
+<!ENTITY % SVG.AnimationTiming.attrib
+ "begin CDATA #IMPLIED
+ dur CDATA #IMPLIED
+ end CDATA #IMPLIED
+ min CDATA #IMPLIED
+ max CDATA #IMPLIED
+ restart ( always | never | whenNotActive ) 'always'
+ repeatCount CDATA #IMPLIED
+ repeatDur CDATA #IMPLIED
+ fill ( remove | freeze ) 'remove'
+ %SVG.AnimationTiming.extra.attrib;"
+>
+
+<!-- SVG.AnimationValue.attrib ......................... -->
+
+<!ENTITY % SVG.AnimationValue.extra.attrib "" >
+
+<!ENTITY % SVG.AnimationValue.attrib
+ "calcMode ( discrete | linear | paced | spline ) 'linear'
+ values CDATA #IMPLIED
+ keyTimes CDATA #IMPLIED
+ keySplines CDATA #IMPLIED
+ from CDATA #IMPLIED
+ to CDATA #IMPLIED
+ by CDATA #IMPLIED
+ %SVG.AnimationValue.extra.attrib;"
+>
+
+<!-- SVG.AnimationAddtion.attrib ....................... -->
+
+<!ENTITY % SVG.AnimationAddtion.extra.attrib "" >
+
+<!ENTITY % SVG.AnimationAddtion.attrib
+ "additive ( replace | sum ) 'replace'
+ accumulate ( none | sum ) 'none'
+ %SVG.AnimationAddtion.extra.attrib;"
+>
+
+<!-- animate: Animate Element .......................... -->
+
+<!ENTITY % SVG.animate.extra.content "" >
+
+<!ENTITY % SVG.animate.element "INCLUDE" >
+<![%SVG.animate.element;[
+<!ENTITY % SVG.animate.content
+ "( %SVG.Description.class; %SVG.animate.extra.content; )*"
+>
+<!ELEMENT %SVG.animate.qname; %SVG.animate.content; >
+<!-- end of SVG.animate.element -->]]>
+
+<!ENTITY % SVG.animate.attlist "INCLUDE" >
+<![%SVG.animate.attlist;[
+<!ATTLIST %SVG.animate.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.AnimationEvents.attrib;
+ %SVG.External.attrib;
+ %SVG.Animation.attrib;
+ %SVG.AnimationAttribute.attrib;
+ %SVG.AnimationTiming.attrib;
+ %SVG.AnimationValue.attrib;
+ %SVG.AnimationAddtion.attrib;
+>
+<!-- end of SVG.animate.attlist -->]]>
+
+<!-- set: Set Element .................................. -->
+
+<!ENTITY % SVG.set.extra.content "" >
+
+<!ENTITY % SVG.set.element "INCLUDE" >
+<![%SVG.set.element;[
+<!ENTITY % SVG.set.content
+ "( %SVG.Description.class; %SVG.set.extra.content; )*"
+>
+<!ELEMENT %SVG.set.qname; %SVG.set.content; >
+<!-- end of SVG.set.element -->]]>
+
+<!ENTITY % SVG.set.attlist "INCLUDE" >
+<![%SVG.set.attlist;[
+<!ATTLIST %SVG.set.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.AnimationEvents.attrib;
+ %SVG.External.attrib;
+ %SVG.Animation.attrib;
+ %SVG.AnimationAttribute.attrib;
+ %SVG.AnimationTiming.attrib;
+ to CDATA #IMPLIED
+>
+<!-- end of SVG.set.attlist -->]]>
+
+<!-- animateMotion: Animate Motion Element ............. -->
+
+<!ENTITY % SVG.animateMotion.extra.content "" >
+
+<!ENTITY % SVG.animateMotion.element "INCLUDE" >
+<![%SVG.animateMotion.element;[
+<!ENTITY % SVG.animateMotion.content
+ "(( %SVG.Description.class; )*, %SVG.mpath.qname;?
+ %SVG.animateMotion.extra.content; )"
+>
+<!ELEMENT %SVG.animateMotion.qname; %SVG.animateMotion.content; >
+<!-- end of SVG.animateMotion.element -->]]>
+
+<!ENTITY % SVG.animateMotion.attlist "INCLUDE" >
+<![%SVG.animateMotion.attlist;[
+<!ATTLIST %SVG.animateMotion.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.AnimationEvents.attrib;
+ %SVG.External.attrib;
+ %SVG.Animation.attrib;
+ %SVG.AnimationTiming.attrib;
+ %SVG.AnimationAddtion.attrib;
+ calcMode ( discrete | linear | paced | spline ) 'paced'
+ values CDATA #IMPLIED
+ keyTimes CDATA #IMPLIED
+ keySplines CDATA #IMPLIED
+ from CDATA #IMPLIED
+ to CDATA #IMPLIED
+ by CDATA #IMPLIED
+ path CDATA #IMPLIED
+ keyPoints CDATA #IMPLIED
+ rotate CDATA #IMPLIED
+ origin CDATA #IMPLIED
+>
+<!-- end of SVG.animateMotion.attlist -->]]>
+
+<!-- animateColor: Animate Color Element ............... -->
+
+<!ENTITY % SVG.animateColor.extra.content "" >
+
+<!ENTITY % SVG.animateColor.element "INCLUDE" >
+<![%SVG.animateColor.element;[
+<!ENTITY % SVG.animateColor.content
+ "( %SVG.Description.class; %SVG.animateColor.extra.content; )*"
+>
+<!ELEMENT %SVG.animateColor.qname; %SVG.animateColor.content; >
+<!-- end of SVG.animateColor.element -->]]>
+
+<!ENTITY % SVG.animateColor.attlist "INCLUDE" >
+<![%SVG.animateColor.attlist;[
+<!ATTLIST %SVG.animateColor.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.AnimationEvents.attrib;
+ %SVG.External.attrib;
+ %SVG.Animation.attrib;
+ %SVG.AnimationAttribute.attrib;
+ %SVG.AnimationTiming.attrib;
+ %SVG.AnimationValue.attrib;
+ %SVG.AnimationAddtion.attrib;
+>
+<!-- end of SVG.animateColor.attlist -->]]>
+
+<!-- animateTransform: Animate Transform Element ....... -->
+
+<!ENTITY % SVG.animateTransform.extra.content "" >
+
+<!ENTITY % SVG.animateTransform.element "INCLUDE" >
+<![%SVG.animateTransform.element;[
+<!ENTITY % SVG.animateTransform.content
+ "( %SVG.Description.class; %SVG.animateTransform.extra.content; )*"
+>
+<!ELEMENT %SVG.animateTransform.qname; %SVG.animateTransform.content; >
+<!-- end of SVG.animateTransform.element -->]]>
+
+<!ENTITY % SVG.animateTransform.attlist "INCLUDE" >
+<![%SVG.animateTransform.attlist;[
+<!ATTLIST %SVG.animateTransform.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.AnimationEvents.attrib;
+ %SVG.External.attrib;
+ %SVG.Animation.attrib;
+ %SVG.AnimationAttribute.attrib;
+ %SVG.AnimationTiming.attrib;
+ %SVG.AnimationValue.attrib;
+ %SVG.AnimationAddtion.attrib;
+ type ( translate | scale | rotate | skewX | skewY ) 'translate'
+>
+<!-- end of SVG.animateTransform.attlist -->]]>
+
+<!-- mpath: Motion Path Element ........................ -->
+
+<!ENTITY % SVG.mpath.extra.content "" >
+
+<!ENTITY % SVG.mpath.element "INCLUDE" >
+<![%SVG.mpath.element;[
+<!ENTITY % SVG.mpath.content
+ "( %SVG.Description.class; %SVG.mpath.extra.content; )*"
+>
+<!ELEMENT %SVG.mpath.qname; %SVG.mpath.content; >
+<!-- end of SVG.mpath.element -->]]>
+
+<!ENTITY % SVG.mpath.attlist "INCLUDE" >
+<![%SVG.mpath.attlist;[
+<!ATTLIST %SVG.mpath.qname;
+ %SVG.Core.attrib;
+ %SVG.XLinkRequired.attrib;
+ %SVG.External.attrib;
+>
+<!-- end of SVG.mpath.attlist -->]]>
+
+<!-- end of svg-animation.mod -->
+]]>
+
+<!-- Font Module ................................................. -->
+<!ENTITY % svg-font.module "INCLUDE" >
+<![%svg-font.module;[
+<!ENTITY % svg-font.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Font//EN"
+ "svg-font.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Font Module ................................................... -->
+<!-- file: svg-font.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-basic-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Font//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-font.mod"
+
+ ....................................................................... -->
+
+<!-- Font
+
+ font, font-face, glyph, missing-glyph, hkern, vkern, font-face-src,
+ font-face-uri, font-face-format, font-face-name, definition-src
+
+ This module declares markup to provide support for template.
+-->
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.font.qname "font" >
+<!ENTITY % SVG.font-face.qname "font-face" >
+<!ENTITY % SVG.glyph.qname "glyph" >
+<!ENTITY % SVG.missing-glyph.qname "missing-glyph" >
+<!ENTITY % SVG.hkern.qname "hkern" >
+<!ENTITY % SVG.vkern.qname "vkern" >
+<!ENTITY % SVG.font-face-src.qname "font-face-src" >
+<!ENTITY % SVG.font-face-uri.qname "font-face-uri" >
+<!ENTITY % SVG.font-face-format.qname "font-face-format" >
+<!ENTITY % SVG.font-face-name.qname "font-face-name" >
+<!ENTITY % SVG.definition-src.qname "definition-src" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Container.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Viewport.attrib "" >
+<!ENTITY % SVG.Text.attrib "" >
+<!ENTITY % SVG.TextContent.attrib "" >
+<!ENTITY % SVG.Font.attrib "" >
+<!ENTITY % SVG.Paint.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Marker.attrib "" >
+<!ENTITY % SVG.Profile.attrib "" >
+<!ENTITY % SVG.Gradient.attrib "" >
+<!ENTITY % SVG.Clip.attrib "" >
+<!ENTITY % SVG.Mask.attrib "" >
+<!ENTITY % SVG.Filter.attrib "" >
+<!ENTITY % SVG.FilterColor.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.XLinkRequired.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Font.class .................................... -->
+
+<!ENTITY % SVG.Font.extra.class "" >
+
+<!ENTITY % SVG.Font.class
+ "| %SVG.font.qname; | %SVG.font-face.qname; %SVG.Font.extra.class;"
+>
+
+<!-- SVG.Presentation.attrib ........................... -->
+
+<!ENTITY % SVG.Presentation.extra.attrib "" >
+
+<!ENTITY % SVG.Presentation.attrib
+ "%SVG.Container.attrib;
+ %SVG.Viewport.attrib;
+ %SVG.Text.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Profile.attrib;
+ %SVG.Gradient.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.Cursor.attrib;
+ flood-color %SVGColor.datatype; #IMPLIED
+ flood-opacity %OpacityValue.datatype; #IMPLIED
+ lighting-color %SVGColor.datatype; #IMPLIED
+ %SVG.Presentation.extra.attrib;"
+>
+
+<!-- font: Font Element ................................ -->
+
+<!ENTITY % SVG.font.extra.content "" >
+
+<!ENTITY % SVG.font.element "INCLUDE" >
+<![%SVG.font.element;[
+<!ENTITY % SVG.font.content
+ "(( %SVG.Description.class; )*, %SVG.font-face.qname;,
+ %SVG.missing-glyph.qname;, ( %SVG.glyph.qname; | %SVG.hkern.qname;
+ | %SVG.vkern.qname; %SVG.font.extra.content; )*)"
+>
+<!ELEMENT %SVG.font.qname; %SVG.font.content; >
+<!-- end of SVG.font.element -->]]>
+
+<!ENTITY % SVG.font.attlist "INCLUDE" >
+<![%SVG.font.attlist;[
+<!ATTLIST %SVG.font.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.External.attrib;
+ horiz-origin-x %Number.datatype; #IMPLIED
+ horiz-origin-y %Number.datatype; #IMPLIED
+ horiz-adv-x %Number.datatype; #REQUIRED
+ vert-origin-x %Number.datatype; #IMPLIED
+ vert-origin-y %Number.datatype; #IMPLIED
+ vert-adv-y %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.font.attlist -->]]>
+
+<!-- font-face: Font Face Element ...................... -->
+
+<!ENTITY % SVG.font-face.extra.content "" >
+
+<!ENTITY % SVG.font-face.element "INCLUDE" >
+<![%SVG.font-face.element;[
+<!ENTITY % SVG.font-face.content
+ "(( %SVG.Description.class; )*, %SVG.font-face-src.qname;?,
+ %SVG.definition-src.qname;? %SVG.font-face.extra.content; )"
+>
+<!ELEMENT %SVG.font-face.qname; %SVG.font-face.content; >
+<!-- end of SVG.font-face.element -->]]>
+
+<!ENTITY % SVG.font-face.attlist "INCLUDE" >
+<![%SVG.font-face.attlist;[
+<!ATTLIST %SVG.font-face.qname;
+ %SVG.Core.attrib;
+ font-family CDATA #IMPLIED
+ font-style CDATA #IMPLIED
+ font-variant CDATA #IMPLIED
+ font-weight CDATA #IMPLIED
+ font-stretch CDATA #IMPLIED
+ font-size CDATA #IMPLIED
+ unicode-range CDATA #IMPLIED
+ units-per-em %Number.datatype; #IMPLIED
+ panose-1 CDATA #IMPLIED
+ stemv %Number.datatype; #IMPLIED
+ stemh %Number.datatype; #IMPLIED
+ slope %Number.datatype; #IMPLIED
+ cap-height %Number.datatype; #IMPLIED
+ x-height %Number.datatype; #IMPLIED
+ accent-height %Number.datatype; #IMPLIED
+ ascent %Number.datatype; #IMPLIED
+ descent %Number.datatype; #IMPLIED
+ widths CDATA #IMPLIED
+ bbox CDATA #IMPLIED
+ ideographic %Number.datatype; #IMPLIED
+ alphabetic %Number.datatype; #IMPLIED
+ mathematical %Number.datatype; #IMPLIED
+ hanging %Number.datatype; #IMPLIED
+ v-ideographic %Number.datatype; #IMPLIED
+ v-alphabetic %Number.datatype; #IMPLIED
+ v-mathematical %Number.datatype; #IMPLIED
+ v-hanging %Number.datatype; #IMPLIED
+ underline-position %Number.datatype; #IMPLIED
+ underline-thickness %Number.datatype; #IMPLIED
+ strikethrough-position %Number.datatype; #IMPLIED
+ strikethrough-thickness %Number.datatype; #IMPLIED
+ overline-position %Number.datatype; #IMPLIED
+ overline-thickness %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.font-face.attlist -->]]>
+
+<!-- glyph: Glyph Element .............................. -->
+
+<!ENTITY % SVG.glyph.extra.content "" >
+
+<!ENTITY % SVG.glyph.element "INCLUDE" >
+<![%SVG.glyph.element;[
+<!ENTITY % SVG.glyph.content
+ "( %SVG.Description.class; | %SVG.Animation.class; %SVG.Structure.class;
+ %SVG.Conditional.class; %SVG.Image.class; %SVG.Style.class;
+ %SVG.Shape.class; %SVG.Text.class; %SVG.Marker.class; %SVG.Profile.class;
+ %SVG.Gradient.class; %SVG.Pattern.class; %SVG.Clip.class;
+ %SVG.Mask.class; %SVG.Filter.class; %SVG.Cursor.class;
+ %SVG.Hyperlink.class; %SVG.View.class; %SVG.Script.class;
+ %SVG.Font.class; %SVG.glyph.extra.content; )*"
+>
+<!ELEMENT %SVG.glyph.qname; %SVG.glyph.content; >
+<!-- end of SVG.glyph.element -->]]>
+
+<!ENTITY % SVG.glyph.attlist "INCLUDE" >
+<![%SVG.glyph.attlist;[
+<!ATTLIST %SVG.glyph.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ unicode CDATA #IMPLIED
+ glyph-name CDATA #IMPLIED
+ d %PathData.datatype; #IMPLIED
+ orientation CDATA #IMPLIED
+ arabic-form CDATA #IMPLIED
+ lang %LanguageCodes.datatype; #IMPLIED
+ horiz-adv-x %Number.datatype; #IMPLIED
+ vert-origin-x %Number.datatype; #IMPLIED
+ vert-origin-y %Number.datatype; #IMPLIED
+ vert-adv-y %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.glyph.attlist -->]]>
+
+<!-- missing-glyph: Missing Glyph Element .............. -->
+
+<!ENTITY % SVG.missing-glyph.extra.content "" >
+
+<!ENTITY % SVG.missing-glyph.element "INCLUDE" >
+<![%SVG.missing-glyph.element;[
+<!ENTITY % SVG.missing-glyph.content
+ "( %SVG.Description.class; | %SVG.Animation.class; %SVG.Structure.class;
+ %SVG.Conditional.class; %SVG.Image.class; %SVG.Style.class;
+ %SVG.Shape.class; %SVG.Text.class; %SVG.Marker.class; %SVG.Profile.class;
+ %SVG.Gradient.class; %SVG.Pattern.class; %SVG.Clip.class;
+ %SVG.Mask.class; %SVG.Filter.class; %SVG.Cursor.class;
+ %SVG.Hyperlink.class; %SVG.View.class; %SVG.Script.class;
+ %SVG.Font.class; %SVG.missing-glyph.extra.content; )*"
+>
+<!ELEMENT %SVG.missing-glyph.qname; %SVG.missing-glyph.content; >
+<!-- end of SVG.missing-glyph.element -->]]>
+
+<!ENTITY % SVG.missing-glyph.attlist "INCLUDE" >
+<![%SVG.missing-glyph.attlist;[
+<!ATTLIST %SVG.missing-glyph.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ d %PathData.datatype; #IMPLIED
+ horiz-adv-x %Number.datatype; #IMPLIED
+ vert-origin-x %Number.datatype; #IMPLIED
+ vert-origin-y %Number.datatype; #IMPLIED
+ vert-adv-y %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.missing-glyph.attlist -->]]>
+
+<!-- hkern: Horizontal Kerning Element ................. -->
+
+<!ENTITY % SVG.hkern.element "INCLUDE" >
+<![%SVG.hkern.element;[
+<!ENTITY % SVG.hkern.content "EMPTY" >
+<!ELEMENT %SVG.hkern.qname; %SVG.hkern.content; >
+<!-- end of SVG.hkern.element -->]]>
+
+<!ENTITY % SVG.hkern.attlist "INCLUDE" >
+<![%SVG.hkern.attlist;[
+<!ATTLIST %SVG.hkern.qname;
+ %SVG.Core.attrib;
+ u1 CDATA #IMPLIED
+ g1 CDATA #IMPLIED
+ u2 CDATA #IMPLIED
+ g2 CDATA #IMPLIED
+ k %Number.datatype; #REQUIRED
+>
+<!-- end of SVG.hkern.attlist -->]]>
+
+<!-- vkern: Vertical Kerning Element ................... -->
+
+<!ENTITY % SVG.vkern.element "INCLUDE" >
+<![%SVG.vkern.element;[
+<!ENTITY % SVG.vkern.content "EMPTY" >
+<!ELEMENT %SVG.vkern.qname; %SVG.vkern.content; >
+<!-- end of SVG.vkern.element -->]]>
+
+<!ENTITY % SVG.vkern.attlist "INCLUDE" >
+<![%SVG.vkern.attlist;[
+<!ATTLIST %SVG.vkern.qname;
+ %SVG.Core.attrib;
+ u1 CDATA #IMPLIED
+ g1 CDATA #IMPLIED
+ u2 CDATA #IMPLIED
+ g2 CDATA #IMPLIED
+ k %Number.datatype; #REQUIRED
+>
+<!-- end of SVG.vkern.attlist -->]]>
+
+<!-- font-face-src: Font Face Source Element ........... -->
+
+<!ENTITY % SVG.font-face-src.extra.content "" >
+
+<!ENTITY % SVG.font-face-src.element "INCLUDE" >
+<![%SVG.font-face-src.element;[
+<!ENTITY % SVG.font-face-src.content
+ "( %SVG.font-face-uri.qname; | %SVG.font-face-name.qname;
+ %SVG.font-face-src.extra.content; )+"
+>
+<!ELEMENT %SVG.font-face-src.qname; %SVG.font-face-src.content; >
+<!-- end of SVG.font-face-src.element -->]]>
+
+<!ENTITY % SVG.font-face-src.attlist "INCLUDE" >
+<![%SVG.font-face-src.attlist;[
+<!ATTLIST %SVG.font-face-src.qname;
+ %SVG.Core.attrib;
+>
+<!-- end of SVG.font-face-src.attlist -->]]>
+
+<!-- font-face-uri: Font Face URI Element .............. -->
+
+<!ENTITY % SVG.font-face-uri.extra.content "" >
+
+<!ENTITY % SVG.font-face-uri.element "INCLUDE" >
+<![%SVG.font-face-uri.element;[
+<!ENTITY % SVG.font-face-uri.content
+ "( %SVG.font-face-format.qname; %SVG.font-face-uri.extra.content; )*"
+>
+<!ELEMENT %SVG.font-face-uri.qname; %SVG.font-face-uri.content; >
+<!-- end of SVG.font-face-uri.element -->]]>
+
+<!ENTITY % SVG.font-face-uri.attlist "INCLUDE" >
+<![%SVG.font-face-uri.attlist;[
+<!ATTLIST %SVG.font-face-uri.qname;
+ %SVG.Core.attrib;
+ %SVG.XLinkRequired.attrib;
+>
+<!-- end of SVG.font-face-uri.attlist -->]]>
+
+<!-- font-face-format: Font Face Format Element ........ -->
+
+<!ENTITY % SVG.font-face-format.element "INCLUDE" >
+<![%SVG.font-face-format.element;[
+<!ENTITY % SVG.font-face-format.content "EMPTY" >
+<!ELEMENT %SVG.font-face-format.qname; %SVG.font-face-format.content; >
+<!-- end of SVG.font-face-format.element -->]]>
+
+<!ENTITY % SVG.font-face-format.attlist "INCLUDE" >
+<![%SVG.font-face-format.attlist;[
+<!ATTLIST %SVG.font-face-format.qname;
+ %SVG.Core.attrib;
+ string CDATA #IMPLIED
+>
+<!-- end of SVG.font-face-format.attlist -->]]>
+
+<!-- font-face-name: Font Face Name Element ............ -->
+
+<!ENTITY % SVG.font-face-name.element "INCLUDE" >
+<![%SVG.font-face-name.element;[
+<!ENTITY % SVG.font-face-name.content "EMPTY" >
+<!ELEMENT %SVG.font-face-name.qname; %SVG.font-face-name.content; >
+<!-- end of SVG.font-face-name.element -->]]>
+
+<!ENTITY % SVG.font-face-name.attlist "INCLUDE" >
+<![%SVG.font-face-name.attlist;[
+<!ATTLIST %SVG.font-face-name.qname;
+ %SVG.Core.attrib;
+ name CDATA #IMPLIED
+>
+<!-- end of SVG.font-face-name.attlist -->]]>
+
+<!-- definition-src: Definition Source Element ......... -->
+
+<!ENTITY % SVG.definition-src.element "INCLUDE" >
+<![%SVG.definition-src.element;[
+<!ENTITY % SVG.definition-src.content "EMPTY" >
+<!ELEMENT %SVG.definition-src.qname; %SVG.definition-src.content; >
+<!-- end of SVG.definition-src.element -->]]>
+
+<!ENTITY % SVG.definition-src.attlist "INCLUDE" >
+<![%SVG.definition-src.attlist;[
+<!ATTLIST %SVG.definition-src.qname;
+ %SVG.Core.attrib;
+ %SVG.XLinkRequired.attrib;
+>
+<!-- end of SVG.definition-src.attlist -->]]>
+
+<!-- end of svg-font.mod -->
+]]>
+
+<!-- Extensibility Module ........................................ -->
+<!ENTITY % svg-extensibility.module "INCLUDE" >
+<![%svg-extensibility.module;[
+<!ENTITY % svg-extensibility.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Extensibility//EN"
+ "svg-extensibility.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Extensibility Module .......................................... -->
+<!-- file: svg-extensibility.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-basic-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Extensibility//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-extensibility.mod"
+
+ ....................................................................... -->
+
+<!-- Extensibility
+
+ foreignObject
+
+ This module declares markup to provide support for extensibility.
+-->
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.foreignObject.qname "foreignObject" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Conditional.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Viewport.attrib "" >
+<!ENTITY % SVG.Text.attrib "" >
+<!ENTITY % SVG.TextContent.attrib "" >
+<!ENTITY % SVG.Font.attrib "" >
+<!ENTITY % SVG.Paint.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Marker.attrib "" >
+<!ENTITY % SVG.Gradient.attrib "" >
+<!ENTITY % SVG.Clip.attrib "" >
+<!ENTITY % SVG.Mask.attrib "" >
+<!ENTITY % SVG.Filter.attrib "" >
+<!ENTITY % SVG.FilterColor.attrib "" >
+<!ENTITY % SVG.GraphicalEvents.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Extensibility.class ........................... -->
+
+<!ENTITY % SVG.Extensibility.extra.class "" >
+
+<!ENTITY % SVG.Extensibility.class
+ "| %SVG.foreignObject.qname; %SVG.Extensibility.extra.class;"
+>
+
+<!-- SVG.Presentation.attrib ........................... -->
+
+<!ENTITY % SVG.Presentation.extra.attrib "" >
+
+<!ENTITY % SVG.Presentation.attrib
+ "%SVG.Container.attrib;
+ %SVG.Viewport.attrib;
+ %SVG.Text.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Profile.attrib;
+ %SVG.Gradient.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.Cursor.attrib;
+ flood-color %SVGColor.datatype; #IMPLIED
+ flood-opacity %OpacityValue.datatype; #IMPLIED
+ lighting-color %SVGColor.datatype; #IMPLIED
+ %SVG.Presentation.extra.attrib;"
+>
+
+<!-- foreignObject: Foreign Object Element ............. -->
+
+<!ENTITY % SVG.foreignObject.extra.content "" >
+
+<!ENTITY % SVG.foreignObject.element "INCLUDE" >
+<![%SVG.foreignObject.element;[
+<!ENTITY % SVG.foreignObject.content
+ "( #PCDATA %SVG.foreignObject.extra.content; )*"
+>
+<!ELEMENT %SVG.foreignObject.qname; %SVG.foreignObject.content; >
+<!-- end of SVG.foreignObject.element -->]]>
+
+<!ENTITY % SVG.foreignObject.attlist "INCLUDE" >
+<![%SVG.foreignObject.attlist;[
+<!ATTLIST %SVG.foreignObject.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.External.attrib;
+ x %Coordinate.datatype; #IMPLIED
+ y %Coordinate.datatype; #IMPLIED
+ width %Length.datatype; #REQUIRED
+ height %Length.datatype; #REQUIRED
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.foreignObject.attlist -->]]>
+
+<!-- end of svg-extensibility.mod -->
+]]>
+
+<!-- end of SVG 1.1 Basic DTD .............................................. -->
+<!-- ....................................................................... -->
diff --git a/org/apache/batik/dom/svg/resources/svg11-basic-model.mod b/org/apache/batik/dom/svg/resources/svg11-basic-model.mod
new file mode 100644
index 0000000..46e0479
--- /dev/null
+++ b/org/apache/batik/dom/svg/resources/svg11-basic-model.mod
@@ -0,0 +1,191 @@
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Basic Document Model Module ................................... -->
+<!-- file: svg11-basic-model.mod
+
+ This is SVG Basic, a proper subset of SVG.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-basic-model.mod 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Basic Document Model//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11-basic-model.mod"
+
+ ....................................................................... -->
+
+<!-- SVG 1.1 Basic Document Model
+
+ This module describes the groupings of elements that make up
+ common content models for SVG elements.
+-->
+
+<!-- Content Models (Default) .......................... -->
+
+<!ENTITY % SVG.Marker.class "" >
+
+<!-- module: svg-structure.mod ......................... -->
+
+<!ENTITY % SVG.Description.extra.class "" >
+<!ENTITY % SVG.Description.class
+ "%SVG.desc.qname; | %SVG.title.qname; | %SVG.metadata.qname;
+ %SVG.Description.extra.class;"
+>
+
+<!ENTITY % SVG.Use.extra.class "" >
+<!ENTITY % SVG.Use.class
+ "| %SVG.use.qname; %SVG.Use.extra.class;"
+>
+
+<!ENTITY % SVG.Structure.extra.class "" >
+<!ENTITY % SVG.Structure.class
+ "| %SVG.svg.qname; | %SVG.g.qname; | %SVG.defs.qname; | %SVG.symbol.qname;
+ %SVG.Use.class; %SVG.Structure.extra.class;"
+>
+
+<!-- module: svg-conditional.mod ....................... -->
+
+<!ENTITY % SVG.Conditional.extra.class "" >
+<!ENTITY % SVG.Conditional.class
+ "| %SVG.switch.qname; %SVG.Conditional.extra.class;"
+>
+
+<!-- module: svg-image.mod ............................. -->
+
+<!ENTITY % SVG.Image.extra.class "" >
+<!ENTITY % SVG.Image.class
+ "| %SVG.image.qname; %SVG.Image.extra.class;"
+>
+
+<!-- module: svg-style.mod ............................. -->
+
+<!ENTITY % SVG.Style.extra.class "" >
+<!ENTITY % SVG.Style.class
+ "| %SVG.style.qname; %SVG.Style.extra.class;"
+>
+
+<!-- module: svg-shape.mod ............................. -->
+
+<!ENTITY % SVG.Shape.extra.class "" >
+<!ENTITY % SVG.Shape.class
+ "| %SVG.path.qname; | %SVG.rect.qname; | %SVG.circle.qname;
+ | %SVG.line.qname; | %SVG.ellipse.qname; | %SVG.polyline.qname;
+ | %SVG.polygon.qname; %SVG.Shape.extra.class;"
+>
+
+<!-- module: svg-text.mod .............................. -->
+
+<!ENTITY % SVG.Text.extra.class "" >
+<!ENTITY % SVG.Text.class
+ "| %SVG.text.qname; %SVG.Text.extra.class;"
+>
+
+<!ENTITY % SVG.TextContent.extra.class "" >
+<!ENTITY % SVG.TextContent.class
+ "| %SVG.tspan.qname; | %SVG.tref.qname; | %SVG.textPath.qname;
+ %SVG.TextContent.extra.class;"
+>
+
+<!-- module: svg-profile.mod ........................... -->
+
+<!ENTITY % SVG.Profile.extra.class "" >
+<!ENTITY % SVG.Profile.class
+ "| %SVG.color-profile.qname; %SVG.Profile.extra.class;"
+>
+
+<!-- module: svg-gradient.mod .......................... -->
+
+<!ENTITY % SVG.Gradient.extra.class "" >
+<!ENTITY % SVG.Gradient.class
+ "| %SVG.linearGradient.qname; | %SVG.radialGradient.qname;
+ %SVG.Gradient.extra.class;"
+>
+
+<!-- module: svg-pattern.mod ........................... -->
+
+<!ENTITY % SVG.Pattern.extra.class "" >
+<!ENTITY % SVG.Pattern.class
+ "| %SVG.pattern.qname; %SVG.Pattern.extra.class;"
+>
+
+<!-- module: svg-basic-clip.mod ........................ -->
+
+<!ENTITY % SVG.Clip.extra.class "" >
+<!ENTITY % SVG.Clip.class
+ "| %SVG.clipPath.qname; %SVG.Clip.extra.class;"
+>
+
+<!-- module: svg-mask.mod .............................. -->
+
+<!ENTITY % SVG.Mask.extra.class "" >
+<!ENTITY % SVG.Mask.class
+ "| %SVG.mask.qname; %SVG.Mask.extra.class;"
+>
+
+<!-- module: svg-basic-filter.mod ...................... -->
+
+<!ENTITY % SVG.Filter.extra.class "" >
+<!ENTITY % SVG.Filter.class
+ "| %SVG.filter.qname; %SVG.Filter.extra.class;"
+>
+
+<!ENTITY % SVG.FilterPrimitive.extra.class "" >
+<!ENTITY % SVG.FilterPrimitive.class
+ "| %SVG.feBlend.qname; | %SVG.feColorMatrix.qname;
+ | %SVG.feComponentTransfer.qname; | %SVG.feComposite.qname;
+ | %SVG.feFlood.qname; | %SVG.feGaussianBlur.qname; | %SVG.feImage.qname;
+ | %SVG.feMerge.qname; | %SVG.feOffset.qname; | %SVG.feTile.qname;
+ %SVG.FilterPrimitive.extra.class;"
+>
+
+<!-- module: svg-cursor.mod ............................ -->
+
+<!ENTITY % SVG.Cursor.extra.class "" >
+<!ENTITY % SVG.Cursor.class
+ "| %SVG.cursor.qname; %SVG.Cursor.extra.class;"
+>
+
+<!-- module: svg-hyperlink.mod ......................... -->
+
+<!ENTITY % SVG.Hyperlink.extra.class "" >
+<!ENTITY % SVG.Hyperlink.class
+ "| %SVG.a.qname; %SVG.Hyperlink.extra.class;"
+>
+
+<!-- module: svg-view.mod .............................. -->
+
+<!ENTITY % SVG.View.extra.class "" >
+<!ENTITY % SVG.View.class
+ "| %SVG.view.qname; %SVG.View.extra.class;"
+>
+
+<!-- module: svg-script.mod ............................ -->
+
+<!ENTITY % SVG.Script.extra.class "" >
+<!ENTITY % SVG.Script.class
+ "| %SVG.script.qname; %SVG.Script.extra.class;"
+>
+
+<!-- module: svg-animation.mod ......................... -->
+
+<!ENTITY % SVG.Animation.extra.class "" >
+<!ENTITY % SVG.Animation.class
+ "%SVG.animate.qname; | %SVG.set.qname; | %SVG.animateMotion.qname; |
+ %SVG.animateColor.qname; | %SVG.animateTransform.qname;
+ %SVG.Animation.extra.class;"
+>
+
+<!-- module: svg-font.mod .............................. -->
+
+<!ENTITY % SVG.Font.extra.class "" >
+<!ENTITY % SVG.Font.class
+ "| %SVG.font.qname; | %SVG.font-face.qname; %SVG.Font.extra.class;"
+>
+
+<!-- module: svg-extensibility.mod ..................... -->
+
+<!ENTITY % SVG.Extensibility.extra.class "" >
+<!ENTITY % SVG.Extensibility.class
+ "| %SVG.foreignObject.qname; %SVG.Extensibility.extra.class;"
+>
+
+<!-- end of svg11-basic-model.mod -->
diff --git a/org/apache/batik/dom/svg/resources/svg11-basic.dtd b/org/apache/batik/dom/svg/resources/svg11-basic.dtd
new file mode 100644
index 0000000..7a824b2
--- /dev/null
+++ b/org/apache/batik/dom/svg/resources/svg11-basic.dtd
@@ -0,0 +1,317 @@
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Basic DTD ..................................................... -->
+<!-- file: svg11-basic.dtd
+-->
+
+<!-- SVG 1.1 Basic DTD
+
+ This is SVG Basic, a proper subset of SVG.
+
+ The Scalable Vector Graphics (SVG)
+ Copyright 2001, 2002 World Wide Web Consortium
+ (Massachusetts Institute of Technology, Institut National de
+ Recherche en Informatique et en Automatique, Keio University).
+ All Rights Reserved.
+
+ Permission to use, copy, modify and distribute the SVG DTD and its
+ accompanying documentation for any purpose and without fee is hereby
+ granted in perpetuity, provided that the above copyright notice and
+ this paragraph appear in all copies. The copyright holders make no
+ representation about the suitability of the DTD for any purpose.
+
+ It is provided "as is" without expressed or implied warranty.
+
+ Author: Jun Fujisawa <fujisawa.jun at canon.co.jp>
+ Revision: $Id: svg11-basic.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+-->
+<!-- This is the driver file for version 1.1 of the SVG Basic DTD.
+
+ This DTD is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//DTD SVG 1.1 Basic//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11-basic.dtd"
+-->
+<!ENTITY % SVG.version "-//W3C//DTD SVG 1.1 Basic//EN" >
+
+<!-- Use this URI to identify the default namespace:
+
+ "http://www.w3.org/2000/svg"
+
+ See the Qualified Names module for information
+ on the use of namespace prefixes in the DTD.
+-->
+<!ENTITY % NS.prefixed "IGNORE" >
+<!ENTITY % SVG.prefix "" >
+
+<!-- reserved for future use with document profiles -->
+<!ENTITY % SVG.profile "" >
+
+<!-- ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: -->
+
+<!-- Pre-Framework Redeclaration Placeholder ..................... -->
+<!ENTITY % svg-prefw-redecl.module "IGNORE" >
+<![%svg-prefw-redecl.module;[
+%svg-prefw-redecl.mod;]]>
+
+<!-- Document Model Module ....................................... -->
+<!ENTITY % svg-model.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Basic Document Model//EN"
+ "svg11-basic-model.mod" >
+
+<!-- Attribute Collection Module ................................. -->
+<!ENTITY % svg-attribs.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Basic Attribute Collection//EN"
+ "svg11-basic-attribs.mod" >
+
+<!-- Modular Framework Module .................................... -->
+<!ENTITY % svg-framework.module "INCLUDE" >
+<![%svg-framework.module;[
+<!ENTITY % svg-framework.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Modular Framework//EN"
+ "svg-framework.mod" >
+%svg-framework.mod;]]>
+
+<!-- Post-Framework Redeclaration Placeholder .................... -->
+<!ENTITY % svg-postfw-redecl.module "IGNORE" >
+<![%svg-postfw-redecl.module;[
+%svg-postfw-redecl.mod;]]>
+
+<!-- ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: -->
+
+<!-- Core Attribute Module ....................................... -->
+<!ENTITY % svg-core-attrib.module "INCLUDE" >
+<![%svg-core-attrib.module;[
+<!ENTITY % svg-core-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Core Attribute//EN"
+ "svg-core-attrib.mod" >
+%svg-core-attrib.mod;]]>
+
+<!-- Viewport Attribute Module ................................... -->
+<!ENTITY % svg-viewport-attrib.module "INCLUDE" >
+<![%svg-viewport-attrib.module;[
+<!ENTITY % svg-viewport-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Viewport Attribute//EN"
+ "svg-viewport-attrib.mod" >
+%svg-viewport-attrib.mod;]]>
+
+<!-- Paint Attribute Module ...................................... -->
+<!ENTITY % svg-paint-attrib.module "INCLUDE" >
+<![%svg-paint-attrib.module;[
+<!ENTITY % svg-paint-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Paint Attribute//EN"
+ "svg-paint-attrib.mod" >
+%svg-paint-attrib.mod;]]>
+
+<!-- Opacity Attribute Module .................................... -->
+<!ENTITY % svg-opacity-attrib.module "INCLUDE" >
+<![%svg-opacity-attrib.module;[
+<!ENTITY % svg-opacity-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Paint Opacity Attribute//EN"
+ "svg-opacity-attrib.mod" >
+%svg-opacity-attrib.mod;]]>
+
+<!-- Graphics Attribute Module ................................... -->
+<!ENTITY % svg-graphics-attrib.module "INCLUDE" >
+<![%svg-graphics-attrib.module;[
+<!ENTITY % svg-graphics-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Graphics Attribute//EN"
+ "svg-graphics-attrib.mod" >
+%svg-graphics-attrib.mod;]]>
+
+<!-- Document Events Attribute Module ............................ -->
+<!ENTITY % svg-docevents-attrib.module "INCLUDE" >
+<![%svg-docevents-attrib.module;[
+<!ENTITY % svg-docevents-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Document Events Attribute//EN"
+ "svg-docevents-attrib.mod" >
+%svg-docevents-attrib.mod;]]>
+
+<!-- Graphical Element Events Attribute Module ................... -->
+<!ENTITY % svg-graphevents-attrib.module "INCLUDE" >
+<![%svg-graphevents-attrib.module;[
+<!ENTITY % svg-graphevents-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Graphical Element Events Attribute//EN"
+ "svg-graphevents-attrib.mod" >
+%svg-graphevents-attrib.mod;]]>
+
+<!-- Animation Events Attribute Module ........................... -->
+<!ENTITY % svg-animevents-attrib.module "INCLUDE" >
+<![%svg-animevents-attrib.module;[
+<!ENTITY % svg-animevents-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Animation Events Attribute//EN"
+ "svg-animevents-attrib.mod" >
+%svg-animevents-attrib.mod;]]>
+
+<!-- XLink Attribute Module ...................................... -->
+<!ENTITY % svg-xlink-attrib.module "INCLUDE" >
+<![%svg-xlink-attrib.module;[
+<!ENTITY % svg-xlink-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 XLink Attribute//EN"
+ "svg-xlink-attrib.mod" >
+%svg-xlink-attrib.mod;]]>
+
+<!-- External Resources Attribute Module ......................... -->
+<!ENTITY % svg-extresources-attrib.module "INCLUDE" >
+<![%svg-extresources-attrib.module;[
+<!ENTITY % svg-extresources-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 External Resources Attribute//EN"
+ "svg-extresources-attrib.mod" >
+%svg-extresources-attrib.mod;]]>
+
+<!-- ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: -->
+
+<!-- Structure Module ............................................ -->
+<!ENTITY % svg-structure.module "INCLUDE" >
+<![%svg-structure.module;[
+<!ENTITY % svg-structure.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Structure//EN"
+ "svg-structure.mod" >
+%svg-structure.mod;]]>
+
+<!-- Conditional Processing Module ............................... -->
+<!ENTITY % svg-conditional.module "INCLUDE" >
+<![%svg-conditional.module;[
+<!ENTITY % svg-conditional.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Conditional Processing//EN"
+ "svg-conditional.mod" >
+%svg-conditional.mod;]]>
+
+<!-- Image Module ................................................ -->
+<!ENTITY % svg-image.module "INCLUDE" >
+<![%svg-image.module;[
+<!ENTITY % svg-image.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Image//EN"
+ "svg-image.mod" >
+%svg-image.mod;]]>
+
+<!-- Style Module ................................................ -->
+<!ENTITY % svg-style.module "INCLUDE" >
+<![%svg-style.module;[
+<!ENTITY % svg-style.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Style//EN"
+ "svg-style.mod" >
+%svg-style.mod;]]>
+
+<!-- Shape Module ................................................ -->
+<!ENTITY % svg-shape.module "INCLUDE" >
+<![%svg-shape.module;[
+<!ENTITY % svg-shape.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Shape//EN"
+ "svg-shape.mod" >
+%svg-shape.mod;]]>
+
+<!-- Text Module ................................................. -->
+<!ENTITY % svg-text.module "INCLUDE" >
+<![%svg-text.module;[
+<!ENTITY % svg-text.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Text//EN"
+ "svg-text.mod" >
+%svg-text.mod;]]>
+
+<!-- Color Profile Module ........................................ -->
+<!ENTITY % svg-profile.module "INCLUDE" >
+<![%svg-profile.module;[
+<!ENTITY % svg-profile.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Color Profile//EN"
+ "svg-profile.mod" >
+%svg-profile.mod;]]>
+
+<!-- Gradient Module ............................................. -->
+<!ENTITY % svg-gradient.module "INCLUDE" >
+<![%svg-gradient.module;[
+<!ENTITY % svg-gradient.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Gradient//EN"
+ "svg-gradient.mod" >
+%svg-gradient.mod;]]>
+
+<!-- Pattern Module .............................................. -->
+<!ENTITY % svg-pattern.module "INCLUDE" >
+<![%svg-pattern.module;[
+<!ENTITY % svg-pattern.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Pattern//EN"
+ "svg-pattern.mod" >
+%svg-pattern.mod;]]>
+
+<!-- Basic Clip Module ........................................... -->
+<!ENTITY % svg-clip.module "INCLUDE" >
+<![%svg-clip.module;[
+<!ENTITY % svg-clip.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Basic Clip//EN"
+ "svg-basic-clip.mod" >
+%svg-clip.mod;]]>
+
+<!-- Mask Module ................................................. -->
+<!ENTITY % svg-mask.module "INCLUDE" >
+<![%svg-mask.module;[
+<!ENTITY % svg-mask.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Mask//EN"
+ "svg-mask.mod" >
+%svg-mask.mod;]]>
+
+<!-- Basic Filter Module ......................................... -->
+<!ENTITY % svg-filter.module "INCLUDE" >
+<![%svg-filter.module;[
+<!ENTITY % svg-filter.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Basic Filter//EN"
+ "svg-basic-filter.mod" >
+%svg-filter.mod;]]>
+
+<!-- Cursor Module ............................................... -->
+<!ENTITY % svg-cursor.module "INCLUDE" >
+<![%svg-cursor.module;[
+<!ENTITY % svg-cursor.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Cursor//EN"
+ "svg-cursor.mod" >
+%svg-cursor.mod;]]>
+
+<!-- Hyperlinking Module ......................................... -->
+<!ENTITY % svg-hyperlink.module "INCLUDE" >
+<![%svg-hyperlink.module;[
+<!ENTITY % svg-hyperlink.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Hyperlinking//EN"
+ "svg-hyperlink.mod" >
+%svg-hyperlink.mod;]]>
+
+<!-- View Module ................................................. -->
+<!ENTITY % svg-view.module "INCLUDE" >
+<![%svg-view.module;[
+<!ENTITY % svg-view.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 View//EN"
+ "svg-view.mod" >
+%svg-view.mod;]]>
+
+<!-- Scripting Module ............................................ -->
+<!ENTITY % svg-script.module "INCLUDE" >
+<![%svg-script.module;[
+<!ENTITY % svg-script.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Scripting//EN"
+ "svg-script.mod" >
+%svg-script.mod;]]>
+
+<!-- Animation Module ............................................ -->
+<!ENTITY % svg-animation.module "INCLUDE" >
+<![%svg-animation.module;[
+<!ENTITY % svg-animation.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Animation//EN"
+ "svg-animation.mod" >
+%svg-animation.mod;]]>
+
+<!-- Font Module ................................................. -->
+<!ENTITY % svg-font.module "INCLUDE" >
+<![%svg-font.module;[
+<!ENTITY % svg-font.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Font//EN"
+ "svg-font.mod" >
+%svg-font.mod;]]>
+
+<!-- Extensibility Module ........................................ -->
+<!ENTITY % svg-extensibility.module "INCLUDE" >
+<![%svg-extensibility.module;[
+<!ENTITY % svg-extensibility.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Extensibility//EN"
+ "svg-extensibility.mod" >
+%svg-extensibility.mod;]]>
+
+<!-- end of SVG 1.1 Basic DTD .............................................. -->
+<!-- ....................................................................... -->
diff --git a/org/apache/batik/dom/svg/resources/svg11-flat.dtd b/org/apache/batik/dom/svg/resources/svg11-flat.dtd
new file mode 100644
index 0000000..2e99adb
--- /dev/null
+++ b/org/apache/batik/dom/svg/resources/svg11-flat.dtd
@@ -0,0 +1,5788 @@
+<!-- ....................................................................... -->
+<!-- SVG 1.1 DTD ........................................................... -->
+<!-- file: svg11.dtd
+-->
+
+<!-- SVG 1.1 DTD
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+
+ The Scalable Vector Graphics (SVG)
+ Copyright 2001, 2002 World Wide Web Consortium
+ (Massachusetts Institute of Technology, Institut National de
+ Recherche en Informatique et en Automatique, Keio University).
+ All Rights Reserved.
+
+ Permission to use, copy, modify and distribute the SVG DTD and its
+ accompanying documentation for any purpose and without fee is hereby
+ granted in perpetuity, provided that the above copyright notice and
+ this paragraph appear in all copies. The copyright holders make no
+ representation about the suitability of the DTD for any purpose.
+
+ It is provided "as is" without expressed or implied warranty.
+
+ Author: Jun Fujisawa <fujisawa.jun at canon.co.jp>
+ Revision: $Id: svg11-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+-->
+<!-- This is the driver file for version 1.1 of the SVG DTD.
+
+ This DTD is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//DTD SVG 1.1//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd"
+-->
+<!ENTITY % SVG.version "-//W3C//DTD SVG 1.1//EN" >
+
+<!-- Use this URI to identify the default namespace:
+
+ "http://www.w3.org/2000/svg"
+
+ See the Qualified Names module for information
+ on the use of namespace prefixes in the DTD.
+-->
+<!ENTITY % NS.prefixed "IGNORE" >
+<!ENTITY % SVG.prefix "" >
+
+<!-- reserved for future use with document profiles -->
+<!ENTITY % SVG.profile "" >
+
+<!-- ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: -->
+
+<!-- Pre-Framework Redeclaration Placeholder ..................... -->
+<!ENTITY % svg-prefw-redecl.module "IGNORE" >
+<![%svg-prefw-redecl.module;[
+%svg-prefw-redecl.mod;]]>
+
+<!-- Document Model Module ....................................... -->
+<!ENTITY % svg-model.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Document Model//EN"
+ "svg11-model.mod" >
+
+<!-- Attribute Collection Module ................................. -->
+<!ENTITY % svg-attribs.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Attribute Collection//EN"
+ "svg11-attribs.mod" >
+
+<!-- Modular Framework Module .................................... -->
+<!ENTITY % svg-framework.module "INCLUDE" >
+<![%svg-framework.module;[
+<!ENTITY % svg-framework.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Modular Framework//EN"
+ "svg-framework.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Modular Framework Module ...................................... -->
+<!-- file: svg-framework.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Modular Framework//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-framework.mod"
+
+ ....................................................................... -->
+
+<!-- Modular Framework
+
+ This module instantiates the modules needed o support the SVG
+ modularization model, including:
+
+ + Datatypes
+ + Qualified Name
+ + Document Model
+ + Attribute Collection
+-->
+
+<!ENTITY % svg-datatypes.module "INCLUDE" >
+<![%svg-datatypes.module;[
+<!ENTITY % svg-datatypes.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Datatypes//EN"
+ "svg-datatypes.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Datatypes Module .............................................. -->
+<!-- file: svg-datatypes.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Datatypes//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-datatypes.mod"
+
+ ....................................................................... -->
+
+<!-- Datatypes
+
+ This module declares common data types for properties and attributes.
+-->
+
+<!-- feature specification -->
+<!ENTITY % Boolean.datatype "( false | true )" >
+
+<!-- 'clip-rule' or 'fill-rule' property/attribute value -->
+<!ENTITY % ClipFillRule.datatype "( nonzero | evenodd | inherit )" >
+
+<!-- media type, as per [RFC2045] -->
+<!ENTITY % ContentType.datatype "CDATA" >
+
+<!-- a <coordinate> -->
+<!ENTITY % Coordinate.datatype "CDATA" >
+
+<!-- a list of <coordinate>s -->
+<!ENTITY % Coordinates.datatype "CDATA" >
+
+<!-- a <color> value -->
+<!ENTITY % Color.datatype "CDATA" >
+
+<!-- a <integer> -->
+<!ENTITY % Integer.datatype "CDATA" >
+
+<!-- a language code, as per [RFC3066] -->
+<!ENTITY % LanguageCode.datatype "NMTOKEN" >
+
+<!-- comma-separated list of language codes, as per [RFC3066] -->
+<!ENTITY % LanguageCodes.datatype "CDATA" >
+
+<!-- a <length> -->
+<!ENTITY % Length.datatype "CDATA" >
+
+<!-- a list of <length>s -->
+<!ENTITY % Lengths.datatype "CDATA" >
+
+<!-- a <number> -->
+<!ENTITY % Number.datatype "CDATA" >
+
+<!-- a list of <number>s -->
+<!ENTITY % Numbers.datatype "CDATA" >
+
+<!-- opacity value (e.g., <number>) -->
+<!ENTITY % OpacityValue.datatype "CDATA" >
+
+<!-- a path data specification -->
+<!ENTITY % PathData.datatype "CDATA" >
+
+<!-- 'preserveAspectRatio' attribute specification -->
+<!ENTITY % PreserveAspectRatioSpec.datatype "CDATA" >
+
+<!-- script expression -->
+<!ENTITY % Script.datatype "CDATA" >
+
+<!-- An SVG color value (RGB plus optional ICC) -->
+<!ENTITY % SVGColor.datatype "CDATA" >
+
+<!-- arbitrary text string -->
+<!ENTITY % Text.datatype "CDATA" >
+
+<!-- list of transforms -->
+<!ENTITY % TransformList.datatype "CDATA" >
+
+<!-- a Uniform Resource Identifier, see [URI] -->
+<!ENTITY % URI.datatype "CDATA" >
+
+<!-- 'viewBox' attribute specification -->
+<!ENTITY % ViewBoxSpec.datatype "CDATA" >
+
+<!-- end of svg-datatypes.mod -->
+]]>
+
+<!ENTITY % svg-qname.module "INCLUDE" >
+<![%svg-qname.module;[
+<!ENTITY % svg-qname.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Qualified Name//EN"
+ "svg-qname.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Qualified Name Module ......................................... -->
+<!-- file: svg-qname.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Qualified Name//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-qname.mod"
+
+ ....................................................................... -->
+
+<!-- Qualified Name
+
+ This module is contained in two parts, labeled Section 'A' and 'B':
+
+ Section A declares parameter entities to support namespace-
+ qualified names, namespace declarations, and name prefixing
+ for SVG and extensions.
+
+ Section B declares parameter entities used to provide
+ namespace-qualified names for all SVG element types:
+-->
+
+<!-- Section A: SVG XML Namespace Framework :::::::::::::::::::::: -->
+
+<!-- 1. Declare a %SVG.prefixed; conditional section keyword, used
+ to activate namespace prefixing. The default value should
+ inherit '%NS.prefixed;' from the DTD driver, so that unless
+ overridden, the default behaviour follows the overall DTD
+ prefixing scheme.
+-->
+<!ENTITY % NS.prefixed "IGNORE" >
+<!ENTITY % SVG.prefixed "%NS.prefixed;" >
+
+<!-- 2. Declare a parameter entity (eg., %SVG.xmlns;) containing
+ the URI reference used to identify the SVG namespace:
+-->
+<!ENTITY % SVG.xmlns "http://www.w3.org/2000/svg" >
+<!ENTITY % XLINK.xmlns "http://www.w3.org/1999/xlink" >
+
+<!-- 3. Declare parameter entities (eg., %SVG.prefix;) containing
+ the default namespace prefix string(s) to use when prefixing
+ is enabled. This may be overridden in the DTD driver or the
+ internal subset of an document instance. If no default prefix
+ is desired, this may be declared as an empty string.
+-->
+<!ENTITY % SVG.prefix "" >
+<!ENTITY % XLINK.prefix "xlink" >
+
+<!-- 4. Declare parameter entities (eg., %SVG.pfx;) containing the
+ colonized prefix(es) (eg., '%SVG.prefix;:') used when
+ prefixing is active, an empty string when it is not.
+-->
+<![%SVG.prefixed;[
+<!ENTITY % SVG.pfx "%SVG.prefix;:" >
+]]>
+<!ENTITY % SVG.pfx "" >
+<!ENTITY % XLINK.pfx "%XLINK.prefix;:" >
+
+<!-- 5. The parameter entity %SVG.xmlns.extra.attrib; may be
+ redeclared to contain any non-SVG namespace declaration
+ attributes for namespaces embedded in SVG. The default
+ is an empty string.
+-->
+<!ENTITY % SVG.xmlns.extra.attrib "" >
+
+<!-- Declare a parameter entity XLINK.xmlns.attrib containing
+ the XML Namespace declarations for XLink.
+-->
+<!ENTITY % XLINK.xmlns.attrib
+ "xmlns:%XLINK.prefix; %URI.datatype; #FIXED '%XLINK.xmlns;'"
+>
+
+<!-- Declare a parameter entity %NS.decl.attrib; containing
+ all XML Namespace declarations used in the DTD, plus the
+ xmlns declaration for SVG, its form dependent on whether
+ prefixing is active.
+-->
+<![%SVG.prefixed;[
+<!ENTITY % NS.decl.attrib
+ "xmlns:%SVG.prefix; %URI.datatype; #FIXED '%SVG.xmlns;'
+ %XLINK.xmlns.attrib;
+ %SVG.xmlns.extra.attrib;"
+>
+]]>
+<!ENTITY % NS.decl.attrib
+ "%XLINK.xmlns.attrib;
+ %SVG.xmlns.extra.attrib;"
+>
+
+<!-- Declare a parameter entity %SVG.xmlns.attrib; containing
+ all XML namespace declaration attributes used by SVG,
+ including a default xmlns attribute when prefixing is
+ inactive.
+-->
+<![%SVG.prefixed;[
+<!ENTITY % SVG.xmlns.attrib
+ "%NS.decl.attrib;"
+>
+]]>
+<!ENTITY % SVG.xmlns.attrib
+ "xmlns %URI.datatype; #FIXED '%SVG.xmlns;'
+ %XLINK.xmlns.attrib;"
+>
+
+<!-- Section B: SVG Qualified Names :::::::::::::::::::::::::::::: -->
+
+<!-- 6. This section declares parameter entities used to provide
+ namespace-qualified names for all SVG element types.
+-->
+
+<!-- module: svg-structure.mod ......................... -->
+
+<!ENTITY % SVG.svg.qname "%SVG.pfx;svg" >
+<!ENTITY % SVG.g.qname "%SVG.pfx;g" >
+<!ENTITY % SVG.defs.qname "%SVG.pfx;defs" >
+<!ENTITY % SVG.desc.qname "%SVG.pfx;desc" >
+<!ENTITY % SVG.title.qname "%SVG.pfx;title" >
+<!ENTITY % SVG.metadata.qname "%SVG.pfx;metadata" >
+<!ENTITY % SVG.symbol.qname "%SVG.pfx;symbol" >
+<!ENTITY % SVG.use.qname "%SVG.pfx;use" >
+
+<!-- module: svg-conditional.mod ....................... -->
+
+<!ENTITY % SVG.switch.qname "%SVG.pfx;switch" >
+
+<!-- module: svg-image.mod ............................. -->
+
+<!ENTITY % SVG.image.qname "%SVG.pfx;image" >
+
+<!-- module: svg-style.mod ............................. -->
+
+<!ENTITY % SVG.style.qname "%SVG.pfx;style" >
+
+<!-- module: svg-shape.mod ............................. -->
+
+<!ENTITY % SVG.path.qname "%SVG.pfx;path" >
+<!ENTITY % SVG.rect.qname "%SVG.pfx;rect" >
+<!ENTITY % SVG.circle.qname "%SVG.pfx;circle" >
+<!ENTITY % SVG.line.qname "%SVG.pfx;line" >
+<!ENTITY % SVG.ellipse.qname "%SVG.pfx;ellipse" >
+<!ENTITY % SVG.polyline.qname "%SVG.pfx;polyline" >
+<!ENTITY % SVG.polygon.qname "%SVG.pfx;polygon" >
+
+<!-- module: svg-text.mod .............................. -->
+
+<!ENTITY % SVG.text.qname "%SVG.pfx;text" >
+<!ENTITY % SVG.tspan.qname "%SVG.pfx;tspan" >
+<!ENTITY % SVG.tref.qname "%SVG.pfx;tref" >
+<!ENTITY % SVG.textPath.qname "%SVG.pfx;textPath" >
+<!ENTITY % SVG.altGlyph.qname "%SVG.pfx;altGlyph" >
+<!ENTITY % SVG.altGlyphDef.qname "%SVG.pfx;altGlyphDef" >
+<!ENTITY % SVG.altGlyphItem.qname "%SVG.pfx;altGlyphItem" >
+<!ENTITY % SVG.glyphRef.qname "%SVG.pfx;glyphRef" >
+
+<!-- module: svg-marker.mod ............................ -->
+
+<!ENTITY % SVG.marker.qname "%SVG.pfx;marker" >
+
+<!-- module: svg-profile.mod ........................... -->
+
+<!ENTITY % SVG.color-profile.qname "%SVG.pfx;color-profile" >
+
+<!-- module: svg-gradient.mod .......................... -->
+
+<!ENTITY % SVG.linearGradient.qname "%SVG.pfx;linearGradient" >
+<!ENTITY % SVG.radialGradient.qname "%SVG.pfx;radialGradient" >
+<!ENTITY % SVG.stop.qname "stop" >
+
+<!-- module: svg-pattern.mod ........................... -->
+
+<!ENTITY % SVG.pattern.qname "%SVG.pfx;pattern" >
+
+<!-- module: svg-clip.mod .............................. -->
+
+<!ENTITY % SVG.clipPath.qname "%SVG.pfx;clipPath" >
+
+<!-- module: svg-mask.mod .............................. -->
+
+<!ENTITY % SVG.mask.qname "%SVG.pfx;mask" >
+
+<!-- module: svg-filter.mod ............................ -->
+
+<!ENTITY % SVG.filter.qname "%SVG.pfx;filter" >
+<!ENTITY % SVG.feBlend.qname "%SVG.pfx;feBlend" >
+<!ENTITY % SVG.feColorMatrix.qname "%SVG.pfx;feColorMatrix" >
+<!ENTITY % SVG.feComponentTransfer.qname "%SVG.pfx;feComponentTransfer" >
+<!ENTITY % SVG.feComposite.qname "%SVG.pfx;feComposite" >
+<!ENTITY % SVG.feConvolveMatrix.qname "%SVG.pfx;feConvolveMatrix" >
+<!ENTITY % SVG.feDiffuseLighting.qname "%SVG.pfx;feDiffuseLighting" >
+<!ENTITY % SVG.feDisplacementMap.qname "%SVG.pfx;feDisplacementMap" >
+<!ENTITY % SVG.feFlood.qname "%SVG.pfx;feFlood" >
+<!ENTITY % SVG.feGaussianBlur.qname "%SVG.pfx;feGaussianBlur" >
+<!ENTITY % SVG.feImage.qname "%SVG.pfx;feImage" >
+<!ENTITY % SVG.feMerge.qname "%SVG.pfx;feMerge" >
+<!ENTITY % SVG.feMergeNode.qname "%SVG.pfx;feMergeNode" >
+<!ENTITY % SVG.feMorphology.qname "%SVG.pfx;feMorphology" >
+<!ENTITY % SVG.feOffset.qname "%SVG.pfx;feOffset" >
+<!ENTITY % SVG.feSpecularLighting.qname "%SVG.pfx;feSpecularLighting" >
+<!ENTITY % SVG.feTile.qname "%SVG.pfx;feTile" >
+<!ENTITY % SVG.feTurbulence.qname "%SVG.pfx;feTurbulence" >
+<!ENTITY % SVG.feDistantLight.qname "%SVG.pfx;feDistantLight" >
+<!ENTITY % SVG.fePointLight.qname "%SVG.pfx;fePointLight" >
+<!ENTITY % SVG.feSpotLight.qname "%SVG.pfx;feSpotLight" >
+<!ENTITY % SVG.feFuncR.qname "%SVG.pfx;feFuncR" >
+<!ENTITY % SVG.feFuncG.qname "%SVG.pfx;feFuncG" >
+<!ENTITY % SVG.feFuncB.qname "%SVG.pfx;feFuncB" >
+<!ENTITY % SVG.feFuncA.qname "%SVG.pfx;feFuncA" >
+
+<!-- module: svg-cursor.mod ............................ -->
+
+<!ENTITY % SVG.cursor.qname "%SVG.pfx;cursor" >
+
+<!-- module: svg-hyperlink.mod ......................... -->
+
+<!ENTITY % SVG.a.qname "%SVG.pfx;a" >
+
+<!-- module: svg-view.mod .............................. -->
+
+<!ENTITY % SVG.view.qname "%SVG.pfx;view" >
+
+<!-- module: svg-script.mod ............................ -->
+
+<!ENTITY % SVG.script.qname "%SVG.pfx;script" >
+
+<!-- module: svg-animation.mod ......................... -->
+
+<!ENTITY % SVG.animate.qname "%SVG.pfx;animate" >
+<!ENTITY % SVG.set.qname "%SVG.pfx;set" >
+<!ENTITY % SVG.animateMotion.qname "%SVG.pfx;animateMotion" >
+<!ENTITY % SVG.animateColor.qname "%SVG.pfx;animateColor" >
+<!ENTITY % SVG.animateTransform.qname "%SVG.pfx;animateTransform" >
+<!ENTITY % SVG.mpath.qname "%SVG.pfx;mpath" >
+
+<!-- module: svg-font.mod .............................. -->
+
+<!ENTITY % SVG.font.qname "%SVG.pfx;font" >
+<!ENTITY % SVG.font-face.qname "%SVG.pfx;font-face" >
+<!ENTITY % SVG.glyph.qname "%SVG.pfx;glyph" >
+<!ENTITY % SVG.missing-glyph.qname "%SVG.pfx;missing-glyph" >
+<!ENTITY % SVG.hkern.qname "%SVG.pfx;hkern" >
+<!ENTITY % SVG.vkern.qname "%SVG.pfx;vkern" >
+<!ENTITY % SVG.font-face-src.qname "%SVG.pfx;font-face-src" >
+<!ENTITY % SVG.font-face-uri.qname "%SVG.pfx;font-face-uri" >
+<!ENTITY % SVG.font-face-format.qname "%SVG.pfx;font-face-format" >
+<!ENTITY % SVG.font-face-name.qname "%SVG.pfx;font-face-name" >
+<!ENTITY % SVG.definition-src.qname "%SVG.pfx;definition-src" >
+
+<!-- module: svg-extensibility.mod ..................... -->
+
+<!ENTITY % SVG.foreignObject.qname "%SVG.pfx;foreignObject" >
+
+<!-- end of svg-qname.mod -->
+]]>
+
+<!ENTITY % svg-model.module "INCLUDE" >
+<![%svg-model.module;[
+<!-- instantiate the Document Model declared in the DTD driver -->
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Document Model Module ......................................... -->
+<!-- file: svg11-model.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Document Model//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11-model.mod"
+
+ ....................................................................... -->
+
+<!-- SVG 1.1 Document Model
+
+ This module describes the groupings of elements that make up
+ common content models for SVG elements.
+-->
+
+<!-- module: svg-structure.mod ......................... -->
+
+<!ENTITY % SVG.Description.extra.class "" >
+<!ENTITY % SVG.Description.class
+ "%SVG.desc.qname; | %SVG.title.qname; | %SVG.metadata.qname;
+ %SVG.Description.extra.class;"
+>
+
+<!ENTITY % SVG.Use.extra.class "" >
+<!ENTITY % SVG.Use.class
+ "| %SVG.use.qname; %SVG.Use.extra.class;"
+>
+
+<!ENTITY % SVG.Structure.extra.class "" >
+<!ENTITY % SVG.Structure.class
+ "| %SVG.svg.qname; | %SVG.g.qname; | %SVG.defs.qname; | %SVG.symbol.qname;
+ %SVG.Use.class; %SVG.Structure.extra.class;"
+>
+
+<!-- module: svg-conditional.mod ....................... -->
+
+<!ENTITY % SVG.Conditional.extra.class "" >
+<!ENTITY % SVG.Conditional.class
+ "| %SVG.switch.qname; %SVG.Conditional.extra.class;"
+>
+
+<!-- module: svg-image.mod ............................. -->
+
+<!ENTITY % SVG.Image.extra.class "" >
+<!ENTITY % SVG.Image.class
+ "| %SVG.image.qname; %SVG.Image.extra.class;"
+>
+
+<!-- module: svg-style.mod ............................. -->
+
+<!ENTITY % SVG.Style.extra.class "" >
+<!ENTITY % SVG.Style.class
+ "| %SVG.style.qname; %SVG.Style.extra.class;"
+>
+
+<!-- module: svg-shape.mod ............................. -->
+
+<!ENTITY % SVG.Shape.extra.class "" >
+<!ENTITY % SVG.Shape.class
+ "| %SVG.path.qname; | %SVG.rect.qname; | %SVG.circle.qname;
+ | %SVG.line.qname; | %SVG.ellipse.qname; | %SVG.polyline.qname;
+ | %SVG.polygon.qname; %SVG.Shape.extra.class;"
+>
+
+<!-- module: svg-text.mod .............................. -->
+
+<!ENTITY % SVG.Text.extra.class "" >
+<!ENTITY % SVG.Text.class
+ "| %SVG.text.qname; | %SVG.altGlyphDef.qname; %SVG.Text.extra.class;"
+>
+
+<!ENTITY % SVG.TextContent.extra.class "" >
+<!ENTITY % SVG.TextContent.class
+ "| %SVG.tspan.qname; | %SVG.tref.qname; | %SVG.textPath.qname;
+ | %SVG.altGlyph.qname; %SVG.TextContent.extra.class;"
+>
+
+<!-- module: svg-marker.mod ............................ -->
+
+<!ENTITY % SVG.Marker.extra.class "" >
+<!ENTITY % SVG.Marker.class
+ "| %SVG.marker.qname; %SVG.Marker.extra.class;"
+>
+
+<!-- module: svg-profile.mod ........................... -->
+
+<!ENTITY % SVG.Profile.extra.class "" >
+<!ENTITY % SVG.Profile.class
+ "| %SVG.color-profile.qname; %SVG.Profile.extra.class;"
+>
+
+<!-- module: svg-gradient.mod .......................... -->
+
+<!ENTITY % SVG.Gradient.extra.class "" >
+<!ENTITY % SVG.Gradient.class
+ "| %SVG.linearGradient.qname; | %SVG.radialGradient.qname;
+ %SVG.Gradient.extra.class;"
+>
+
+<!-- module: svg-pattern.mod ........................... -->
+
+<!ENTITY % SVG.Pattern.extra.class "" >
+<!ENTITY % SVG.Pattern.class
+ "| %SVG.pattern.qname; %SVG.Pattern.extra.class;"
+>
+
+<!-- module: svg-clip.mod .............................. -->
+
+<!ENTITY % SVG.Clip.extra.class "" >
+<!ENTITY % SVG.Clip.class
+ "| %SVG.clipPath.qname; %SVG.Clip.extra.class;"
+>
+
+<!-- module: svg-mask.mod .............................. -->
+
+<!ENTITY % SVG.Mask.extra.class "" >
+<!ENTITY % SVG.Mask.class
+ "| %SVG.mask.qname; %SVG.Mask.extra.class;"
+>
+
+<!-- module: svg-filter.mod ............................ -->
+
+<!ENTITY % SVG.Filter.extra.class "" >
+<!ENTITY % SVG.Filter.class
+ "| %SVG.filter.qname; %SVG.Filter.extra.class;"
+>
+
+<!ENTITY % SVG.FilterPrimitive.extra.class "" >
+<!ENTITY % SVG.FilterPrimitive.class
+ "| %SVG.feBlend.qname; | %SVG.feColorMatrix.qname;
+ | %SVG.feComponentTransfer.qname; | %SVG.feComposite.qname;
+ | %SVG.feConvolveMatrix.qname; | %SVG.feDiffuseLighting.qname;
+ | %SVG.feDisplacementMap.qname; | %SVG.feFlood.qname;
+ | %SVG.feGaussianBlur.qname; | %SVG.feImage.qname; | %SVG.feMerge.qname;
+ | %SVG.feMorphology.qname; | %SVG.feOffset.qname;
+ | %SVG.feSpecularLighting.qname; | %SVG.feTile.qname;
+ | %SVG.feTurbulence.qname; %SVG.FilterPrimitive.extra.class;"
+>
+
+<!-- module: svg-cursor.mod ............................ -->
+
+<!ENTITY % SVG.Cursor.extra.class "" >
+<!ENTITY % SVG.Cursor.class
+ "| %SVG.cursor.qname; %SVG.Cursor.extra.class;"
+>
+
+<!-- module: svg-hyperlink.mod ......................... -->
+
+<!ENTITY % SVG.Hyperlink.extra.class "" >
+<!ENTITY % SVG.Hyperlink.class
+ "| %SVG.a.qname; %SVG.Hyperlink.extra.class;"
+>
+
+<!-- module: svg-view.mod .............................. -->
+
+<!ENTITY % SVG.View.extra.class "" >
+<!ENTITY % SVG.View.class
+ "| %SVG.view.qname; %SVG.View.extra.class;"
+>
+
+<!-- module: svg-script.mod ............................ -->
+
+<!ENTITY % SVG.Script.extra.class "" >
+<!ENTITY % SVG.Script.class
+ "| %SVG.script.qname; %SVG.Script.extra.class;"
+>
+
+<!-- module: svg-animation.mod ......................... -->
+
+<!ENTITY % SVG.Animation.extra.class "" >
+<!ENTITY % SVG.Animation.class
+ "%SVG.animate.qname; | %SVG.set.qname; | %SVG.animateMotion.qname; |
+ %SVG.animateColor.qname; | %SVG.animateTransform.qname;
+ %SVG.Animation.extra.class;"
+>
+
+<!-- module: svg-font.mod .............................. -->
+
+<!ENTITY % SVG.Font.extra.class "" >
+<!ENTITY % SVG.Font.class
+ "| %SVG.font.qname; | %SVG.font-face.qname; %SVG.Font.extra.class;"
+>
+
+<!-- module: svg-extensibility.mod ..................... -->
+
+<!ENTITY % SVG.Extensibility.extra.class "" >
+<!ENTITY % SVG.Extensibility.class
+ "| %SVG.foreignObject.qname; %SVG.Extensibility.extra.class;"
+>
+
+<!-- end of svg11-model.mod -->
+]]>
+
+<!ENTITY % svg-attribs.module "INCLUDE" >
+<![%svg-attribs.module;[
+<!-- instantiate the Attribute Collection declared in the DTD driver -->
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Attribute Collection Module ................................... -->
+<!-- file: svg11-attribs.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Attribute Collection//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11-attribs.mod"
+
+ ....................................................................... -->
+
+<!-- SVG 1.1 Attribute Collection
+
+ This module defines the set of common attributes that can be present
+ on many SVG elements.
+-->
+
+<!-- module: svg-conditional.mod ....................... -->
+
+<!ENTITY % ExtensionList.datatype "CDATA" >
+<!ENTITY % FeatureList.datatype "CDATA" >
+
+<!ENTITY % SVG.Conditional.extra.attrib "" >
+<!ENTITY % SVG.Conditional.attrib
+ "requiredFeatures %FeatureList.datatype; #IMPLIED
+ requiredExtensions %ExtensionList.datatype; #IMPLIED
+ systemLanguage %LanguageCodes.datatype; #IMPLIED
+ %SVG.Conditional.extra.attrib;"
+>
+
+<!-- module: svg-style.mod ............................. -->
+
+<!ENTITY % ClassList.datatype "CDATA" >
+<!ENTITY % StyleSheet.datatype "CDATA" >
+
+<!ENTITY % SVG.Style.extra.attrib "" >
+<!ENTITY % SVG.Style.attrib
+ "style %StyleSheet.datatype; #IMPLIED
+ class %ClassList.datatype; #IMPLIED
+ %SVG.Style.extra.attrib;"
+>
+
+<!-- module: svg-text.mod .............................. -->
+
+<!ENTITY % BaselineShiftValue.datatype "CDATA" >
+<!ENTITY % FontFamilyValue.datatype "CDATA" >
+<!ENTITY % FontSizeValue.datatype "CDATA" >
+<!ENTITY % FontSizeAdjustValue.datatype "CDATA" >
+<!ENTITY % GlyphOrientationHorizontalValue.datatype "CDATA" >
+<!ENTITY % GlyphOrientationVerticalValue.datatype "CDATA" >
+<!ENTITY % KerningValue.datatype "CDATA" >
+<!ENTITY % SpacingValue.datatype "CDATA" >
+<!ENTITY % TextDecorationValue.datatype "CDATA" >
+
+<!ENTITY % SVG.Text.extra.attrib "" >
+<!ENTITY % SVG.Text.attrib
+ "writing-mode ( lr-tb | rl-tb | tb-rl | lr | rl | tb | inherit ) #IMPLIED
+ %SVG.Text.extra.attrib;"
+>
+
+<!ENTITY % SVG.TextContent.extra.attrib "" >
+<!ENTITY % SVG.TextContent.attrib
+ "alignment-baseline ( auto | baseline | before-edge | text-before-edge |
+ middle | central | after-edge | text-after-edge |
+ ideographic | alphabetic | hanging | mathematical |
+ inherit ) #IMPLIED
+ baseline-shift %BaselineShiftValue.datatype; #IMPLIED
+ direction ( ltr | rtl | inherit ) #IMPLIED
+ dominant-baseline ( auto | use-script | no-change | reset-size |
+ ideographic | alphabetic | hanging | mathematical |
+ central | middle | text-after-edge | text-before-edge |
+ inherit ) #IMPLIED
+ glyph-orientation-horizontal %GlyphOrientationHorizontalValue.datatype;
+ #IMPLIED
+ glyph-orientation-vertical %GlyphOrientationVerticalValue.datatype;
+ #IMPLIED
+ kerning %KerningValue.datatype; #IMPLIED
+ letter-spacing %SpacingValue.datatype; #IMPLIED
+ text-anchor ( start | middle | end | inherit ) #IMPLIED
+ text-decoration %TextDecorationValue.datatype; #IMPLIED
+ unicode-bidi ( normal | embed | bidi-override | inherit ) #IMPLIED
+ word-spacing %SpacingValue.datatype; #IMPLIED
+ %SVG.TextContent.extra.attrib;"
+>
+
+<!ENTITY % SVG.Font.extra.attrib "" >
+<!ENTITY % SVG.Font.attrib
+ "font-family %FontFamilyValue.datatype; #IMPLIED
+ font-size %FontSizeValue.datatype; #IMPLIED
+ font-size-adjust %FontSizeAdjustValue.datatype; #IMPLIED
+ font-stretch ( normal | wider | narrower | ultra-condensed |
+ extra-condensed | condensed | semi-condensed |
+ semi-expanded | expanded | extra-expanded |
+ ultra-expanded | inherit ) #IMPLIED
+ font-style ( normal | italic | oblique | inherit ) #IMPLIED
+ font-variant ( normal | small-caps | inherit ) #IMPLIED
+ font-weight ( normal | bold | bolder | lighter | 100 | 200 | 300 | 400 |
+ 500 | 600 | 700 | 800 | 900 | inherit ) #IMPLIED
+ %SVG.Font.extra.attrib;"
+>
+
+<!-- module: svg-marker.mod ............................ -->
+
+<!ENTITY % MarkerValue.datatype "CDATA" >
+
+<!ENTITY % SVG.Marker.extra.attrib "" >
+<!ENTITY % SVG.Marker.attrib
+ "marker-start %MarkerValue.datatype; #IMPLIED
+ marker-mid %MarkerValue.datatype; #IMPLIED
+ marker-end %MarkerValue.datatype; #IMPLIED
+ %SVG.Marker.extra.attrib;"
+>
+
+<!-- module: svg-profile.mod ........................... -->
+
+<!ENTITY % SVG.Profile.extra.attrib "" >
+<!ENTITY % SVG.Profile.attrib
+ "color-profile CDATA #IMPLIED
+ %SVG.Profile.extra.attrib;"
+>
+
+<!-- module: svg-gradient.mod .......................... -->
+
+<!ENTITY % NumberOrPercentage.datatype "CDATA" >
+
+<!ENTITY % SVG.Gradient.extra.attrib "" >
+<!ENTITY % SVG.Gradient.attrib
+ "stop-color %SVGColor.datatype; #IMPLIED
+ stop-opacity %OpacityValue.datatype; #IMPLIED
+ %SVG.Gradient.extra.attrib;"
+>
+
+<!-- module: svg-clip.mod .............................. -->
+
+<!ENTITY % ClipPathValue.datatype "CDATA" >
+
+<!ENTITY % SVG.Clip.extra.attrib "" >
+<!ENTITY % SVG.Clip.attrib
+ "clip-path %ClipPathValue.datatype; #IMPLIED
+ clip-rule %ClipFillRule.datatype; #IMPLIED
+ %SVG.Clip.extra.attrib;"
+>
+
+<!-- module: svg-mask.mod .............................. -->
+
+<!ENTITY % MaskValue.datatype "CDATA" >
+
+<!ENTITY % SVG.Mask.extra.attrib "" >
+<!ENTITY % SVG.Mask.attrib
+ "mask %MaskValue.datatype; #IMPLIED
+ %SVG.Mask.extra.attrib;"
+>
+
+<!-- module: svg-filter.mod ............................ -->
+
+<!ENTITY % FilterValue.datatype "CDATA" >
+<!ENTITY % NumberOptionalNumber.datatype "CDATA" >
+
+<!ENTITY % SVG.Filter.extra.attrib "" >
+<!ENTITY % SVG.Filter.attrib
+ "filter %FilterValue.datatype; #IMPLIED
+ %SVG.Filter.extra.attrib;"
+>
+
+<!ENTITY % SVG.FilterColor.extra.attrib "" >
+<!ENTITY % SVG.FilterColor.attrib
+ "color-interpolation-filters ( auto | sRGB | linearRGB | inherit )
+ #IMPLIED
+ %SVG.FilterColor.extra.attrib;"
+>
+
+<!-- module: svg-cursor.mod ............................ -->
+
+<!ENTITY % CursorValue.datatype "CDATA" >
+
+<!ENTITY % SVG.Cursor.extra.attrib "" >
+<!ENTITY % SVG.Cursor.attrib
+ "cursor %CursorValue.datatype; #IMPLIED
+ %SVG.Cursor.extra.attrib;"
+>
+
+<!-- end of svg11-attribs.mod -->
+]]>
+
+<!-- end of svg-framework.mod -->
+]]>
+
+<!-- Post-Framework Redeclaration Placeholder .................... -->
+<!ENTITY % svg-postfw-redecl.module "IGNORE" >
+<![%svg-postfw-redecl.module;[
+%svg-postfw-redecl.mod;]]>
+
+<!-- ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: -->
+
+<!-- Core Attribute Module ....................................... -->
+<!ENTITY % svg-core-attrib.module "INCLUDE" >
+<![%svg-core-attrib.module;[
+<!ENTITY % svg-core-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Core Attribute//EN"
+ "svg-core-attrib.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Core Attribute Module ......................................... -->
+<!-- file: svg-core-attrib.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Core Attribute//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-core-attrib.mod"
+
+ ....................................................................... -->
+
+<!-- Core Attribute
+
+ id, xml:base, xml:lang, xml:space
+
+ This module defines the core set of attributes that can be present on
+ any element.
+-->
+
+<!ENTITY % SVG.id.attrib
+ "id ID #IMPLIED"
+>
+
+<!ENTITY % SVG.base.attrib
+ "xml:base %URI.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.lang.attrib
+ "xml:lang %LanguageCode.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.space.attrib
+ "xml:space ( default | preserve ) #IMPLIED"
+>
+
+<!ENTITY % SVG.Core.extra.attrib "" >
+
+<!ENTITY % SVG.Core.attrib
+ "%SVG.id.attrib;
+ %SVG.base.attrib;
+ %SVG.lang.attrib;
+ %SVG.space.attrib;
+ %SVG.Core.extra.attrib;"
+>
+
+<!-- end of svg-core-attrib.mod -->
+]]>
+
+<!-- Container Attribute Module .................................. -->
+<!ENTITY % svg-container-attrib.module "INCLUDE" >
+<![%svg-container-attrib.module;[
+<!ENTITY % svg-container-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Container Attribute//EN"
+ "svg-container-attrib.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Container Attribute Module .................................... -->
+<!-- file: svg-container-attrib.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Container Attribute//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-container-attrib.mod"
+
+ ....................................................................... -->
+
+<!-- Container Attribute
+
+ enable-background
+
+ This module defines the Container attribute set.
+-->
+
+<!-- 'enable-background' property/attribute value (e.g., 'new', 'accumulate') -->
+<!ENTITY % EnableBackgroundValue.datatype "CDATA" >
+
+<!ENTITY % SVG.enable-background.attrib
+ "enable-background %EnableBackgroundValue.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.Container.extra.attrib "" >
+
+<!ENTITY % SVG.Container.attrib
+ "%SVG.enable-background.attrib;
+ %SVG.Container.extra.attrib;"
+>
+
+<!-- end of svg-container-attrib.mod -->
+]]>
+
+<!-- Viewport Attribute Module ................................... -->
+<!ENTITY % svg-viewport-attrib.module "INCLUDE" >
+<![%svg-viewport-attrib.module;[
+<!ENTITY % svg-viewport-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Viewport Attribute//EN"
+ "svg-viewport-attrib.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Viewport Attribute Module ..................................... -->
+<!-- file: svg-viewport-attrib.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Viewport Attribute//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-viewport-attrib.mod"
+
+ ....................................................................... -->
+
+<!-- Viewport Attribute
+
+ clip, overflow
+
+ This module defines the Viewport attribute set.
+-->
+
+<!-- 'clip' property/attribute value (e.g., 'auto', rect(...)) -->
+<!ENTITY % ClipValue.datatype "CDATA" >
+
+<!ENTITY % SVG.clip.attrib
+ "clip %ClipValue.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.overflow.attrib
+ "overflow ( visible | hidden | scroll | auto | inherit ) #IMPLIED"
+>
+
+<!ENTITY % SVG.Viewport.extra.attrib "" >
+
+<!ENTITY % SVG.Viewport.attrib
+ "%SVG.clip.attrib;
+ %SVG.overflow.attrib;
+ %SVG.Viewport.extra.attrib;"
+>
+
+<!-- end of svg-viewport-attrib.mod -->
+]]>
+
+<!-- Paint Attribute Module ...................................... -->
+<!ENTITY % svg-paint-attrib.module "INCLUDE" >
+<![%svg-paint-attrib.module;[
+<!ENTITY % svg-paint-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Paint Attribute//EN"
+ "svg-paint-attrib.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Paint Attribute Module ........................................ -->
+<!-- file: svg-paint-attrib.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Paint Attribute//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-paint-attrib.mod"
+
+ ....................................................................... -->
+
+<!-- Paint Attribute
+
+ fill, fill-rule, stroke, stroke-dasharray, stroke-dashoffset,
+ stroke-linecap, stroke-linejoin, stroke-miterlimit, stroke-width, color,
+ color-interpolation, color-rendering
+
+ This module defines the Paint and Color attribute sets.
+-->
+
+<!-- a 'fill' or 'stroke' property/attribute value: <paint> -->
+<!ENTITY % Paint.datatype "CDATA" >
+
+<!-- 'stroke-dasharray' property/attribute value (e.g., 'none', list of <number>s) -->
+<!ENTITY % StrokeDashArrayValue.datatype "CDATA" >
+
+<!-- 'stroke-dashoffset' property/attribute value (e.g., 'none', <legnth>) -->
+<!ENTITY % StrokeDashOffsetValue.datatype "CDATA" >
+
+<!-- 'stroke-miterlimit' property/attribute value (e.g., <number>) -->
+<!ENTITY % StrokeMiterLimitValue.datatype "CDATA" >
+
+<!-- 'stroke-width' property/attribute value (e.g., <length>) -->
+<!ENTITY % StrokeWidthValue.datatype "CDATA" >
+
+<!ENTITY % SVG.fill.attrib
+ "fill %Paint.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.fill-rule.attrib
+ "fill-rule %ClipFillRule.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.stroke.attrib
+ "stroke %Paint.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.stroke-dasharray.attrib
+ "stroke-dasharray %StrokeDashArrayValue.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.stroke-dashoffset.attrib
+ "stroke-dashoffset %StrokeDashOffsetValue.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.stroke-linecap.attrib
+ "stroke-linecap ( butt | round | square | inherit ) #IMPLIED"
+>
+
+<!ENTITY % SVG.stroke-linejoin.attrib
+ "stroke-linejoin ( miter | round | bevel | inherit ) #IMPLIED"
+>
+
+<!ENTITY % SVG.stroke-miterlimit.attrib
+ "stroke-miterlimit %StrokeMiterLimitValue.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.stroke-width.attrib
+ "stroke-width %StrokeWidthValue.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.Paint.extra.attrib "" >
+
+<!ENTITY % SVG.Paint.attrib
+ "%SVG.fill.attrib;
+ %SVG.fill-rule.attrib;
+ %SVG.stroke.attrib;
+ %SVG.stroke-dasharray.attrib;
+ %SVG.stroke-dashoffset.attrib;
+ %SVG.stroke-linecap.attrib;
+ %SVG.stroke-linejoin.attrib;
+ %SVG.stroke-miterlimit.attrib;
+ %SVG.stroke-width.attrib;
+ %SVG.Paint.extra.attrib;"
+>
+
+<!ENTITY % SVG.color.attrib
+ "color %Color.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.color-interpolation.attrib
+ "color-interpolation ( auto | sRGB | linearRGB | inherit ) #IMPLIED"
+>
+
+<!ENTITY % SVG.color-rendering.attrib
+ "color-rendering ( auto | optimizeSpeed | optimizeQuality | inherit )
+ #IMPLIED"
+>
+
+<!ENTITY % SVG.Color.extra.attrib "" >
+
+<!ENTITY % SVG.Color.attrib
+ "%SVG.color.attrib;
+ %SVG.color-interpolation.attrib;
+ %SVG.color-rendering.attrib;
+ %SVG.Color.extra.attrib;"
+>
+
+<!-- end of svg-paint-attrib.mod -->
+]]>
+
+<!-- Paint Opacity Attribute Module .............................. -->
+<!ENTITY % svg-opacity-attrib.module "INCLUDE" >
+<![%svg-opacity-attrib.module;[
+<!ENTITY % svg-opacity-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Paint Opacity Attribute//EN"
+ "svg-opacity-attrib.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Paint Opacity Attribute Module ................................ -->
+<!-- file: svg-opacity-attrib.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Paint Opacity Attribute//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-opacity-attrib.mod"
+
+ ....................................................................... -->
+
+<!-- Paint Opacity Attribute
+
+ opacity, fill-opacity, stroke-opacity
+
+ This module defines the Opacity attribute set.
+-->
+
+<!ENTITY % SVG.opacity.attrib
+ "opacity %OpacityValue.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.fill-opacity.attrib
+ "fill-opacity %OpacityValue.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.stroke-opacity.attrib
+ "stroke-opacity %OpacityValue.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.Opacity.extra.attrib "" >
+
+<!ENTITY % SVG.Opacity.attrib
+ "%SVG.opacity.attrib;
+ %SVG.fill-opacity.attrib;
+ %SVG.stroke-opacity.attrib;
+ %SVG.Opacity.extra.attrib;"
+>
+
+<!-- end of svg-opacity-attrib.mod -->
+]]>
+
+<!-- Graphics Attribute Module ................................... -->
+<!ENTITY % svg-graphics-attrib.module "INCLUDE" >
+<![%svg-graphics-attrib.module;[
+<!ENTITY % svg-graphics-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Graphics Attribute//EN"
+ "svg-graphics-attrib.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Graphics Attribute Module ..................................... -->
+<!-- file: svg-graphics-attrib.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Graphics Attribute//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-graphics-attrib.mod"
+
+ ....................................................................... -->
+
+<!-- Graphics Attribute
+
+ display, image-rendering, pointer-events, shape-rendering,
+ text-rendering, visibility
+
+ This module defines the Graphics attribute set.
+-->
+
+<!ENTITY % SVG.display.attrib
+ "display ( inline | block | list-item | run-in | compact | marker |
+ table | inline-table | table-row-group | table-header-group |
+ table-footer-group | table-row | table-column-group |
+ table-column | table-cell | table-caption | none | inherit )
+ #IMPLIED"
+>
+
+<!ENTITY % SVG.image-rendering.attrib
+ "image-rendering ( auto | optimizeSpeed | optimizeQuality | inherit )
+ #IMPLIED"
+>
+
+<!ENTITY % SVG.pointer-events.attrib
+ "pointer-events ( visiblePainted | visibleFill | visibleStroke | visible |
+ painted | fill | stroke | all | none | inherit )
+ #IMPLIED"
+>
+
+<!ENTITY % SVG.shape-rendering.attrib
+ "shape-rendering ( auto | optimizeSpeed | crispEdges | geometricPrecision |
+ inherit ) #IMPLIED"
+>
+
+<!ENTITY % SVG.text-rendering.attrib
+ "text-rendering ( auto | optimizeSpeed | optimizeLegibility |
+ geometricPrecision | inherit ) #IMPLIED"
+>
+
+<!ENTITY % SVG.visibility.attrib
+ "visibility ( visible | hidden | inherit ) #IMPLIED"
+>
+
+<!ENTITY % SVG.Graphics.extra.attrib "" >
+
+<!ENTITY % SVG.Graphics.attrib
+ "%SVG.display.attrib;
+ %SVG.image-rendering.attrib;
+ %SVG.pointer-events.attrib;
+ %SVG.shape-rendering.attrib;
+ %SVG.text-rendering.attrib;
+ %SVG.visibility.attrib;
+ %SVG.Graphics.extra.attrib;"
+>
+
+<!-- end of svg-graphics-attrib.mod -->
+]]>
+
+<!-- Document Events Attribute Module ............................ -->
+<!ENTITY % svg-docevents-attrib.module "INCLUDE" >
+<![%svg-docevents-attrib.module;[
+<!ENTITY % svg-docevents-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Document Events Attribute//EN"
+ "svg-docevents-attrib.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Document Events Attribute Module .............................. -->
+<!-- file: svg-docevents-attrib.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Document Events Attribute//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-docevents-attrib.mod"
+
+ ....................................................................... -->
+
+<!-- Document Events Attribute
+
+ onunload, onabort, onerror, onresize, onscroll, onzoom
+
+ This module defines the DocumentEvents attribute set.
+-->
+
+<!ENTITY % SVG.onunload.attrib
+ "onunload %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onabort.attrib
+ "onabort %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onerror.attrib
+ "onerror %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onresize.attrib
+ "onresize %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onscroll.attrib
+ "onscroll %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onzoom.attrib
+ "onzoom %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.DocumentEvents.extra.attrib "" >
+
+<!ENTITY % SVG.DocumentEvents.attrib
+ "%SVG.onunload.attrib;
+ %SVG.onabort.attrib;
+ %SVG.onerror.attrib;
+ %SVG.onresize.attrib;
+ %SVG.onscroll.attrib;
+ %SVG.onzoom.attrib;
+ %SVG.DocumentEvents.extra.attrib;"
+>
+
+<!-- end of svg-docevents-attrib.mod -->
+]]>
+
+<!-- Graphical Element Events Attribute Module ................... -->
+<!ENTITY % svg-graphevents-attrib.module "INCLUDE" >
+<![%svg-graphevents-attrib.module;[
+<!ENTITY % svg-graphevents-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Graphical Element Events Attribute//EN"
+ "svg-graphevents-attrib.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Graphical Element Events Attribute Module ..................... -->
+<!-- file: svg-graphevents-attrib.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Graphical Element Events Attribute//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-graphevents-attrib.mod"
+
+ ....................................................................... -->
+
+<!-- Graphical Element Events Attribute
+
+ onfocusin, onfocusout, onactivate, onclick, onmousedown, onmouseup,
+ onmouseover, onmousemove, onmouseout, onload
+
+ This module defines the GraphicalEvents attribute set.
+-->
+
+<!ENTITY % SVG.onfocusin.attrib
+ "onfocusin %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onfocusout.attrib
+ "onfocusout %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onactivate.attrib
+ "onactivate %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onclick.attrib
+ "onclick %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onmousedown.attrib
+ "onmousedown %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onmouseup.attrib
+ "onmouseup %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onmouseover.attrib
+ "onmouseover %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onmousemove.attrib
+ "onmousemove %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onmouseout.attrib
+ "onmouseout %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onload.attrib
+ "onload %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.GraphicalEvents.extra.attrib "" >
+
+<!ENTITY % SVG.GraphicalEvents.attrib
+ "%SVG.onfocusin.attrib;
+ %SVG.onfocusout.attrib;
+ %SVG.onactivate.attrib;
+ %SVG.onclick.attrib;
+ %SVG.onmousedown.attrib;
+ %SVG.onmouseup.attrib;
+ %SVG.onmouseover.attrib;
+ %SVG.onmousemove.attrib;
+ %SVG.onmouseout.attrib;
+ %SVG.onload.attrib;
+ %SVG.GraphicalEvents.extra.attrib;"
+>
+
+<!-- end of svg-graphevents-attrib.mod -->
+]]>
+
+<!-- Animation Events Attribute Module ........................... -->
+<!ENTITY % svg-animevents-attrib.module "INCLUDE" >
+<![%svg-animevents-attrib.module;[
+<!ENTITY % svg-animevents-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Animation Events Attribute//EN"
+ "svg-animevents-attrib.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Animation Events Attribute Module ............................. -->
+<!-- file: svg-animevents-attrib.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Animation Events Attribute//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-animevents-attrib.mod"
+
+ ....................................................................... -->
+
+<!-- Animation Events Attribute
+
+ onbegin, onend, onrepeat, onload
+
+ This module defines the AnimationEvents attribute set.
+-->
+
+<!ENTITY % SVG.onbegin.attrib
+ "onbegin %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onend.attrib
+ "onend %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onrepeat.attrib
+ "onrepeat %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onload.attrib
+ "onload %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.AnimationEvents.extra.attrib "" >
+
+<!ENTITY % SVG.AnimationEvents.attrib
+ "%SVG.onbegin.attrib;
+ %SVG.onend.attrib;
+ %SVG.onrepeat.attrib;
+ %SVG.onload.attrib;
+ %SVG.AnimationEvents.extra.attrib;"
+>
+
+<!-- end of svg-animevents-attrib.mod -->
+]]>
+
+<!-- XLink Attribute Module ...................................... -->
+<!ENTITY % svg-xlink-attrib.module "INCLUDE" >
+<![%svg-xlink-attrib.module;[
+<!ENTITY % svg-xlink-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 XLink Attribute//EN"
+ "svg-xlink-attrib.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 XLink Attribute Module ........................................ -->
+<!-- file: svg-xlink-attrib.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 XLink Attribute//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-xlink-attrib.mod"
+
+ ....................................................................... -->
+
+<!-- XLink Attribute
+
+ type, href, role, arcrole, title, show, actuate
+
+ This module defines the XLink, XLinkRequired, XLinkEmbed, and
+ XLinkReplace attribute set.
+-->
+
+<!ENTITY % SVG.XLink.extra.attrib "" >
+
+<!ENTITY % SVG.XLink.attrib
+ "%XLINK.xmlns.attrib;
+ %XLINK.pfx;type ( simple ) #FIXED 'simple'
+ %XLINK.pfx;href %URI.datatype; #IMPLIED
+ %XLINK.pfx;role %URI.datatype; #IMPLIED
+ %XLINK.pfx;arcrole %URI.datatype; #IMPLIED
+ %XLINK.pfx;title CDATA #IMPLIED
+ %XLINK.pfx;show ( other ) 'other'
+ %XLINK.pfx;actuate ( onLoad ) #FIXED 'onLoad'
+ %SVG.XLink.extra.attrib;"
+>
+
+<!ENTITY % SVG.XLinkRequired.extra.attrib "" >
+
+<!ENTITY % SVG.XLinkRequired.attrib
+ "%XLINK.xmlns.attrib;
+ %XLINK.pfx;type ( simple ) #FIXED 'simple'
+ %XLINK.pfx;href %URI.datatype; #REQUIRED
+ %XLINK.pfx;role %URI.datatype; #IMPLIED
+ %XLINK.pfx;arcrole %URI.datatype; #IMPLIED
+ %XLINK.pfx;title CDATA #IMPLIED
+ %XLINK.pfx;show ( other ) 'other'
+ %XLINK.pfx;actuate ( onLoad ) #FIXED 'onLoad'
+ %SVG.XLinkRequired.extra.attrib;"
+>
+
+<!ENTITY % SVG.XLinkEmbed.extra.attrib "" >
+
+<!ENTITY % SVG.XLinkEmbed.attrib
+ "%XLINK.xmlns.attrib;
+ %XLINK.pfx;type ( simple ) #FIXED 'simple'
+ %XLINK.pfx;href %URI.datatype; #REQUIRED
+ %XLINK.pfx;role %URI.datatype; #IMPLIED
+ %XLINK.pfx;arcrole %URI.datatype; #IMPLIED
+ %XLINK.pfx;title CDATA #IMPLIED
+ %XLINK.pfx;show ( embed ) 'embed'
+ %XLINK.pfx;actuate ( onLoad ) #FIXED 'onLoad'
+ %SVG.XLinkEmbed.extra.attrib;"
+>
+
+<!ENTITY % SVG.XLinkReplace.extra.attrib "" >
+
+<!ENTITY % SVG.XLinkReplace.attrib
+ "%XLINK.xmlns.attrib;
+ %XLINK.pfx;type ( simple ) #FIXED 'simple'
+ %XLINK.pfx;href %URI.datatype; #REQUIRED
+ %XLINK.pfx;role %URI.datatype; #IMPLIED
+ %XLINK.pfx;arcrole %URI.datatype; #IMPLIED
+ %XLINK.pfx;title CDATA #IMPLIED
+ %XLINK.pfx;show ( new | replace ) 'replace'
+ %XLINK.pfx;actuate ( onRequest ) #FIXED 'onRequest'
+ %SVG.XLinkReplace.extra.attrib;"
+>
+
+<!-- end of svg-xlink-attrib.mod -->
+]]>
+
+<!-- External Resources Attribute Module ......................... -->
+<!ENTITY % svg-extresources-attrib.module "INCLUDE" >
+<![%svg-extresources-attrib.module;[
+<!ENTITY % svg-extresources-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 External Resources Attribute//EN"
+ "svg-extresources-attrib.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 External Resources Attribute Module ........................... -->
+<!-- file: svg-extresources-attrib.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 External Resources Attribute//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-extresources-attrib.mod"
+
+ ....................................................................... -->
+
+<!-- External Resources Attribute
+
+ externalResourcesRequired
+
+ This module defines the External attribute set.
+-->
+
+<!ENTITY % SVG.externalResourcesRequired.attrib
+ "externalResourcesRequired %Boolean.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.External.extra.attrib "" >
+
+<!ENTITY % SVG.External.attrib
+ "%SVG.externalResourcesRequired.attrib;
+ %SVG.External.extra.attrib;"
+>
+
+<!-- end of svg-extresources-attrib.mod -->
+]]>
+
+<!-- ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: -->
+
+<!-- Structure Module ............................................ -->
+<!ENTITY % svg-structure.module "INCLUDE" >
+<![%svg-structure.module;[
+<!ENTITY % svg-structure.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Structure//EN"
+ "svg-structure.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Structure Module .............................................. -->
+<!-- file: svg-structure.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Structure//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-structure.mod"
+
+ ....................................................................... -->
+
+<!-- Structure
+
+ svg, g, defs, desc, title, metadata, symbol, use
+
+ This module declares the major structural elements and their attributes.
+-->
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.svg.qname "svg" >
+<!ENTITY % SVG.g.qname "g" >
+<!ENTITY % SVG.defs.qname "defs" >
+<!ENTITY % SVG.desc.qname "desc" >
+<!ENTITY % SVG.title.qname "title" >
+<!ENTITY % SVG.metadata.qname "metadata" >
+<!ENTITY % SVG.symbol.qname "symbol" >
+<!ENTITY % SVG.use.qname "use" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Container.attrib "" >
+<!ENTITY % SVG.Conditional.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Viewport.attrib "" >
+<!ENTITY % SVG.Text.attrib "" >
+<!ENTITY % SVG.TextContent.attrib "" >
+<!ENTITY % SVG.Font.attrib "" >
+<!ENTITY % SVG.Paint.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Marker.attrib "" >
+<!ENTITY % SVG.Profile.attrib "" >
+<!ENTITY % SVG.Gradient.attrib "" >
+<!ENTITY % SVG.Clip.attrib "" >
+<!ENTITY % SVG.Mask.attrib "" >
+<!ENTITY % SVG.Filter.attrib "" >
+<!ENTITY % SVG.FilterColor.attrib "" >
+<!ENTITY % SVG.DocumentEvents.attrib "" >
+<!ENTITY % SVG.GraphicalEvents.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.XLinkEmbed.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Description.class ............................. -->
+
+<!ENTITY % SVG.Description.extra.class "" >
+
+<!ENTITY % SVG.Description.class
+ "%SVG.desc.qname; | %SVG.title.qname; | %SVG.metadata.qname;
+ %SVG.Description.extra.class;"
+>
+
+<!-- SVG.Use.class ..................................... -->
+
+<!ENTITY % SVG.Use.extra.class "" >
+
+<!ENTITY % SVG.Use.class
+ "| %SVG.use.qname; %SVG.Use.extra.class;"
+>
+
+<!-- SVG.Structure.class ............................... -->
+
+<!ENTITY % SVG.Structure.extra.class "" >
+
+<!ENTITY % SVG.Structure.class
+ "| %SVG.svg.qname; | %SVG.g.qname; | %SVG.defs.qname; | %SVG.symbol.qname;
+ %SVG.Use.class; %SVG.Structure.extra.class;"
+>
+
+<!-- SVG.Presentation.attrib ........................... -->
+
+<!ENTITY % SVG.Presentation.extra.attrib "" >
+
+<!ENTITY % SVG.Presentation.attrib
+ "%SVG.Container.attrib;
+ %SVG.Viewport.attrib;
+ %SVG.Text.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Profile.attrib;
+ %SVG.Gradient.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.Cursor.attrib;
+ flood-color %SVGColor.datatype; #IMPLIED
+ flood-opacity %OpacityValue.datatype; #IMPLIED
+ lighting-color %SVGColor.datatype; #IMPLIED
+ %SVG.Presentation.extra.attrib;"
+>
+
+<!-- svg: SVG Document Element ......................... -->
+
+<!ENTITY % SVG.svg.extra.content "" >
+
+<!ENTITY % SVG.svg.element "INCLUDE" >
+<![%SVG.svg.element;[
+<!ENTITY % SVG.svg.content
+ "( %SVG.Description.class; | %SVG.Animation.class; %SVG.Structure.class;
+ %SVG.Conditional.class; %SVG.Image.class; %SVG.Style.class;
+ %SVG.Shape.class; %SVG.Text.class; %SVG.Marker.class; %SVG.Profile.class;
+ %SVG.Gradient.class; %SVG.Pattern.class; %SVG.Clip.class;
+ %SVG.Mask.class; %SVG.Filter.class; %SVG.Cursor.class;
+ %SVG.Hyperlink.class; %SVG.View.class; %SVG.Script.class;
+ %SVG.Font.class; %SVG.svg.extra.content; )*"
+>
+<!ELEMENT %SVG.svg.qname; %SVG.svg.content; >
+<!-- end of SVG.svg.element -->]]>
+
+<!ENTITY % SVG.svg.attlist "INCLUDE" >
+<![%SVG.svg.attlist;[
+<!ATTLIST %SVG.svg.qname;
+ %SVG.xmlns.attrib;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.DocumentEvents.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.External.attrib;
+ x %Coordinate.datatype; #IMPLIED
+ y %Coordinate.datatype; #IMPLIED
+ width %Length.datatype; #IMPLIED
+ height %Length.datatype; #IMPLIED
+ viewBox %ViewBoxSpec.datatype; #IMPLIED
+ preserveAspectRatio %PreserveAspectRatioSpec.datatype; 'xMidYMid meet'
+ zoomAndPan ( disable | magnify ) 'magnify'
+ version %Number.datatype; #FIXED '1.1'
+ baseProfile %Text.datatype; #IMPLIED
+ contentScriptType %ContentType.datatype; 'text/ecmascript'
+ contentStyleType %ContentType.datatype; 'text/css'
+>
+<!-- end of SVG.svg.attlist -->]]>
+
+<!-- g: Group Element .................................. -->
+
+<!ENTITY % SVG.g.extra.content "" >
+
+<!ENTITY % SVG.g.element "INCLUDE" >
+<![%SVG.g.element;[
+<!ENTITY % SVG.g.content
+ "( %SVG.Description.class; | %SVG.Animation.class; %SVG.Structure.class;
+ %SVG.Conditional.class; %SVG.Image.class; %SVG.Style.class;
+ %SVG.Shape.class; %SVG.Text.class; %SVG.Marker.class; %SVG.Profile.class;
+ %SVG.Gradient.class; %SVG.Pattern.class; %SVG.Clip.class;
+ %SVG.Mask.class; %SVG.Filter.class; %SVG.Cursor.class;
+ %SVG.Hyperlink.class; %SVG.View.class; %SVG.Script.class;
+ %SVG.Font.class; %SVG.g.extra.content; )*"
+>
+<!ELEMENT %SVG.g.qname; %SVG.g.content; >
+<!-- end of SVG.g.element -->]]>
+
+<!ENTITY % SVG.g.attlist "INCLUDE" >
+<![%SVG.g.attlist;[
+<!ATTLIST %SVG.g.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.External.attrib;
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.g.attlist -->]]>
+
+<!-- defs: Definisions Element ......................... -->
+
+<!ENTITY % SVG.defs.extra.content "" >
+
+<!ENTITY % SVG.defs.element "INCLUDE" >
+<![%SVG.defs.element;[
+<!ENTITY % SVG.defs.content
+ "( %SVG.Description.class; | %SVG.Animation.class; %SVG.Structure.class;
+ %SVG.Conditional.class; %SVG.Image.class; %SVG.Style.class;
+ %SVG.Shape.class; %SVG.Text.class; %SVG.Marker.class; %SVG.Profile.class;
+ %SVG.Gradient.class; %SVG.Pattern.class; %SVG.Clip.class;
+ %SVG.Mask.class; %SVG.Filter.class; %SVG.Cursor.class;
+ %SVG.Hyperlink.class; %SVG.View.class; %SVG.Script.class;
+ %SVG.Font.class; %SVG.defs.extra.content; )*"
+>
+<!ELEMENT %SVG.defs.qname; %SVG.defs.content; >
+<!-- end of SVG.defs.element -->]]>
+
+<!ENTITY % SVG.defs.attlist "INCLUDE" >
+<![%SVG.defs.attlist;[
+<!ATTLIST %SVG.defs.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.External.attrib;
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.defs.attlist -->]]>
+
+<!-- desc: Description Element ......................... -->
+
+<!ENTITY % SVG.desc.extra.content "" >
+
+<!ENTITY % SVG.desc.element "INCLUDE" >
+<![%SVG.desc.element;[
+<!ENTITY % SVG.desc.content
+ "( #PCDATA %SVG.desc.extra.content; )*"
+>
+<!ELEMENT %SVG.desc.qname; %SVG.desc.content; >
+<!-- end of SVG.desc.element -->]]>
+
+<!ENTITY % SVG.desc.attlist "INCLUDE" >
+<![%SVG.desc.attlist;[
+<!ATTLIST %SVG.desc.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+>
+<!-- end of SVG.desc.attlist -->]]>
+
+<!-- title: Title Element .............................. -->
+
+<!ENTITY % SVG.title.extra.content "" >
+
+<!ENTITY % SVG.title.element "INCLUDE" >
+<![%SVG.title.element;[
+<!ENTITY % SVG.title.content
+ "( #PCDATA %SVG.title.extra.content; )*"
+>
+<!ELEMENT %SVG.title.qname; %SVG.title.content; >
+<!-- end of SVG.title.element -->]]>
+
+<!ENTITY % SVG.title.attlist "INCLUDE" >
+<![%SVG.title.attlist;[
+<!ATTLIST %SVG.title.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+>
+<!-- end of SVG.title.attlist -->]]>
+
+<!-- metadata: Metadata Element ........................ -->
+
+<!ENTITY % SVG.metadata.extra.content "" >
+
+<!ENTITY % SVG.metadata.element "INCLUDE" >
+<![%SVG.metadata.element;[
+<!ENTITY % SVG.metadata.content
+ "( #PCDATA %SVG.metadata.extra.content; )*"
+>
+<!ELEMENT %SVG.metadata.qname; %SVG.metadata.content; >
+<!-- end of SVG.metadata.element -->]]>
+
+<!ENTITY % SVG.metadata.attlist "INCLUDE" >
+<![%SVG.metadata.attlist;[
+<!ATTLIST %SVG.metadata.qname;
+ %SVG.Core.attrib;
+>
+<!-- end of SVG.metadata.attlist -->]]>
+
+<!-- symbol: Symbol Element ............................ -->
+
+<!ENTITY % SVG.symbol.extra.content "" >
+
+<!ENTITY % SVG.symbol.element "INCLUDE" >
+<![%SVG.symbol.element;[
+<!ENTITY % SVG.symbol.content
+ "( %SVG.Description.class; | %SVG.Animation.class; %SVG.Structure.class;
+ %SVG.Conditional.class; %SVG.Image.class; %SVG.Style.class;
+ %SVG.Shape.class; %SVG.Text.class; %SVG.Marker.class; %SVG.Profile.class;
+ %SVG.Gradient.class; %SVG.Pattern.class; %SVG.Clip.class;
+ %SVG.Mask.class; %SVG.Filter.class; %SVG.Cursor.class;
+ %SVG.Hyperlink.class; %SVG.View.class; %SVG.Script.class;
+ %SVG.Font.class; %SVG.symbol.extra.content; )*"
+>
+<!ELEMENT %SVG.symbol.qname; %SVG.symbol.content; >
+<!-- end of SVG.symbol.element -->]]>
+
+<!ENTITY % SVG.symbol.attlist "INCLUDE" >
+<![%SVG.symbol.attlist;[
+<!ATTLIST %SVG.symbol.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.External.attrib;
+ viewBox %ViewBoxSpec.datatype; #IMPLIED
+ preserveAspectRatio %PreserveAspectRatioSpec.datatype; 'xMidYMid meet'
+>
+<!-- end of SVG.symbol.attlist -->]]>
+
+<!-- use: Use Element .................................. -->
+
+<!ENTITY % SVG.use.extra.content "" >
+
+<!ENTITY % SVG.use.element "INCLUDE" >
+<![%SVG.use.element;[
+<!ENTITY % SVG.use.content
+ "(( %SVG.Description.class; )*, ( %SVG.Animation.class;
+ %SVG.use.extra.content; )*)"
+>
+<!ELEMENT %SVG.use.qname; %SVG.use.content; >
+<!-- end of SVG.use.element -->]]>
+
+<!ENTITY % SVG.use.attlist "INCLUDE" >
+<![%SVG.use.attlist;[
+<!ATTLIST %SVG.use.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.XLinkEmbed.attrib;
+ %SVG.External.attrib;
+ x %Coordinate.datatype; #IMPLIED
+ y %Coordinate.datatype; #IMPLIED
+ width %Length.datatype; #IMPLIED
+ height %Length.datatype; #IMPLIED
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.use.attlist -->]]>
+
+<!-- end of svg-structure.mod -->
+]]>
+
+<!-- Conditional Processing Module ............................... -->
+<!ENTITY % svg-conditional.module "INCLUDE" >
+<![%svg-conditional.module;[
+<!ENTITY % svg-conditional.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Conditional Processing//EN"
+ "svg-conditional.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Conditional Processing Module ................................. -->
+<!-- file: svg-conditional.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Conditional Processing//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-conditional.mod"
+
+ ....................................................................... -->
+
+<!-- Conditional Processing
+
+ switch
+
+ This module declares markup to provide support for conditional processing.
+-->
+
+<!-- extension list specification -->
+<!ENTITY % ExtensionList.datatype "CDATA" >
+
+<!-- feature list specification -->
+<!ENTITY % FeatureList.datatype "CDATA" >
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.switch.qname "switch" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Container.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Viewport.attrib "" >
+<!ENTITY % SVG.Text.attrib "" >
+<!ENTITY % SVG.TextContent.attrib "" >
+<!ENTITY % SVG.Font.attrib "" >
+<!ENTITY % SVG.Paint.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Marker.attrib "" >
+<!ENTITY % SVG.Profile.attrib "" >
+<!ENTITY % SVG.Gradient.attrib "" >
+<!ENTITY % SVG.Clip.attrib "" >
+<!ENTITY % SVG.Mask.attrib "" >
+<!ENTITY % SVG.Filter.attrib "" >
+<!ENTITY % SVG.FilterColor.attrib "" >
+<!ENTITY % SVG.GraphicalEvents.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Conditional.class ............................. -->
+
+<!ENTITY % SVG.Conditional.extra.class "" >
+
+<!ENTITY % SVG.Conditional.class
+ "| %SVG.switch.qname; %SVG.Conditional.extra.class;"
+>
+
+<!-- SVG.Conditional.attrib ............................ -->
+
+<!ENTITY % SVG.Conditional.extra.attrib "" >
+
+<!ENTITY % SVG.Conditional.attrib
+ "requiredFeatures %FeatureList.datatype; #IMPLIED
+ requiredExtensions %ExtensionList.datatype; #IMPLIED
+ systemLanguage %LanguageCodes.datatype; #IMPLIED
+ %SVG.Conditional.extra.attrib;"
+>
+
+<!-- SVG.Presentation.attrib ........................... -->
+
+<!ENTITY % SVG.Presentation.extra.attrib "" >
+
+<!ENTITY % SVG.Presentation.attrib
+ "%SVG.Container.attrib;
+ %SVG.Viewport.attrib;
+ %SVG.Text.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Profile.attrib;
+ %SVG.Gradient.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.Cursor.attrib;
+ flood-color %SVGColor.datatype; #IMPLIED
+ flood-opacity %OpacityValue.datatype; #IMPLIED
+ lighting-color %SVGColor.datatype; #IMPLIED
+ %SVG.Presentation.extra.attrib;"
+>
+
+<!-- switch: Switch Element ............................ -->
+
+<!ENTITY % SVG.switch.extra.content "" >
+
+<!ENTITY % SVG.switch.element "INCLUDE" >
+<![%SVG.switch.element;[
+<!ENTITY % SVG.switch.content
+ "(( %SVG.Description.class; )*, ( %SVG.svg.qname; | %SVG.g.qname;
+ | %SVG.use.qname; | %SVG.text.qname; | %SVG.Animation.class;
+ %SVG.Conditional.class; %SVG.Image.class; %SVG.Shape.class;
+ %SVG.Hyperlink.class; %SVG.Extensibility.class;
+ %SVG.switch.extra.content; )*)"
+>
+<!ELEMENT %SVG.switch.qname; %SVG.switch.content; >
+<!-- end of SVG.switch.element -->]]>
+
+<!ENTITY % SVG.switch.attlist "INCLUDE" >
+<![%SVG.switch.attlist;[
+<!ATTLIST %SVG.switch.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.External.attrib;
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.switch.attlist -->]]>
+
+<!-- end of svg-conditional.mod -->
+]]>
+
+<!-- Image Module ................................................ -->
+<!ENTITY % svg-image.module "INCLUDE" >
+<![%svg-image.module;[
+<!ENTITY % svg-image.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Image//EN"
+ "svg-image.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Image Module .................................................. -->
+<!-- file: svg-image.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Image//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-image.mod"
+
+ ....................................................................... -->
+
+<!-- Image
+
+ image
+
+ This module declares markup to provide support for image.
+-->
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.image.qname "image" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Conditional.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Viewport.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Profile.attrib "" >
+<!ENTITY % SVG.Clip.attrib "" >
+<!ENTITY % SVG.Mask.attrib "" >
+<!ENTITY % SVG.Filter.attrib "" >
+<!ENTITY % SVG.GraphicalEvents.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.XLinkEmbed.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Image.class ................................... -->
+
+<!ENTITY % SVG.Image.extra.class "" >
+
+<!ENTITY % SVG.Image.class
+ "| %SVG.image.qname; %SVG.Image.extra.class;"
+>
+
+<!-- image: Image Element .............................. -->
+
+<!ENTITY % SVG.image.extra.content "" >
+
+<!ENTITY % SVG.image.element "INCLUDE" >
+<![%SVG.image.element;[
+<!ENTITY % SVG.image.content
+ "(( %SVG.Description.class; )*, ( %SVG.Animation.class;
+ %SVG.image.extra.content; )*)"
+>
+<!ELEMENT %SVG.image.qname; %SVG.image.content; >
+<!-- end of SVG.image.element -->]]>
+
+<!ENTITY % SVG.image.attlist "INCLUDE" >
+<![%SVG.image.attlist;[
+<!ATTLIST %SVG.image.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Viewport.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Profile.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.XLinkEmbed.attrib;
+ %SVG.External.attrib;
+ x %Coordinate.datatype; #IMPLIED
+ y %Coordinate.datatype; #IMPLIED
+ width %Length.datatype; #REQUIRED
+ height %Length.datatype; #REQUIRED
+ preserveAspectRatio %PreserveAspectRatioSpec.datatype; 'xMidYMid meet'
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.image.attlist -->]]>
+
+<!-- end of svg-image.mod -->
+]]>
+
+<!-- Style Module ................................................ -->
+<!ENTITY % svg-style.module "INCLUDE" >
+<![%svg-style.module;[
+<!ENTITY % svg-style.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Style//EN"
+ "svg-style.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Style Module .................................................. -->
+<!-- file: svg-style.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Style//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-style.mod"
+
+ ....................................................................... -->
+
+<!-- Style
+
+ style
+
+ This module declares markup to provide support for stylesheet.
+-->
+
+<!-- list of classes -->
+<!ENTITY % ClassList.datatype "CDATA" >
+
+<!-- comma-separated list of media descriptors. -->
+<!ENTITY % MediaDesc.datatype "CDATA" >
+
+<!-- style sheet data -->
+<!ENTITY % StyleSheet.datatype "CDATA" >
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.style.qname "style" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+
+<!-- SVG.Style.class ................................... -->
+
+<!ENTITY % SVG.Style.extra.class "" >
+
+<!ENTITY % SVG.Style.class
+ "| %SVG.style.qname; %SVG.Style.extra.class;"
+>
+
+<!-- SVG.Style.attrib .................................. -->
+
+<!ENTITY % SVG.Style.extra.attrib "" >
+
+<!ENTITY % SVG.Style.attrib
+ "style %StyleSheet.datatype; #IMPLIED
+ class %ClassList.datatype; #IMPLIED
+ %SVG.Style.extra.attrib;"
+>
+
+<!-- style: Style Element .............................. -->
+
+<!ENTITY % SVG.style.extra.content "" >
+
+<!ENTITY % SVG.style.element "INCLUDE" >
+<![%SVG.style.element;[
+<!ENTITY % SVG.style.content
+ "( #PCDATA %SVG.style.extra.content; )*"
+>
+<!ELEMENT %SVG.style.qname; %SVG.style.content; >
+<!-- end of SVG.style.element -->]]>
+
+<!ENTITY % SVG.style.attlist "INCLUDE" >
+<![%SVG.style.attlist;[
+<!ATTLIST %SVG.style.qname;
+ xml:space ( preserve ) #FIXED 'preserve'
+ %SVG.Core.attrib;
+ type %ContentType.datatype; #REQUIRED
+ media %MediaDesc.datatype; #IMPLIED
+ title %Text.datatype; #IMPLIED
+>
+<!-- end of SVG.style.attlist -->]]>
+
+<!-- end of svg-style.mod -->
+]]>
+
+<!-- Shape Module ................................................ -->
+<!ENTITY % svg-shape.module "INCLUDE" >
+<![%svg-shape.module;[
+<!ENTITY % svg-shape.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Shape//EN"
+ "svg-shape.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Shape Module .................................................. -->
+<!-- file: svg-shape.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Shape//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-shape.mod"
+
+ ....................................................................... -->
+
+<!-- Shape
+
+ path, rect, circle, line, ellipse, polyline, polygon
+
+ This module declares markup to provide support for graphical shapes.
+-->
+
+<!-- a list of points -->
+<!ENTITY % Points.datatype "CDATA" >
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.path.qname "path" >
+<!ENTITY % SVG.rect.qname "rect" >
+<!ENTITY % SVG.circle.qname "circle" >
+<!ENTITY % SVG.line.qname "line" >
+<!ENTITY % SVG.ellipse.qname "ellipse" >
+<!ENTITY % SVG.polyline.qname "polyline" >
+<!ENTITY % SVG.polygon.qname "polygon" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Conditional.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Paint.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Marker.attrib "" >
+<!ENTITY % SVG.Clip.attrib "" >
+<!ENTITY % SVG.Mask.attrib "" >
+<!ENTITY % SVG.Filter.attrib "" >
+<!ENTITY % SVG.GraphicalEvents.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Shape.class ................................... -->
+
+<!ENTITY % SVG.Shape.extra.class "" >
+
+<!ENTITY % SVG.Shape.class
+ "| %SVG.path.qname; | %SVG.rect.qname; | %SVG.circle.qname;
+ | %SVG.line.qname; | %SVG.ellipse.qname; | %SVG.polyline.qname;
+ | %SVG.polygon.qname; %SVG.Shape.extra.class;"
+>
+
+<!-- path: Path Element ................................ -->
+
+<!ENTITY % SVG.path.extra.content "" >
+
+<!ENTITY % SVG.path.element "INCLUDE" >
+<![%SVG.path.element;[
+<!ENTITY % SVG.path.content
+ "(( %SVG.Description.class; )*, ( %SVG.Animation.class;
+ %SVG.path.extra.content; )*)"
+>
+<!ELEMENT %SVG.path.qname; %SVG.path.content; >
+<!-- end of SVG.path.element -->]]>
+
+<!ENTITY % SVG.path.attlist "INCLUDE" >
+<![%SVG.path.attlist;[
+<!ATTLIST %SVG.path.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.External.attrib;
+ d %PathData.datatype; #REQUIRED
+ pathLength %Number.datatype; #IMPLIED
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.path.attlist -->]]>
+
+<!-- rect: Rectangle Element ........................... -->
+
+<!ENTITY % SVG.rect.extra.content "" >
+
+<!ENTITY % SVG.rect.element "INCLUDE" >
+<![%SVG.rect.element;[
+<!ENTITY % SVG.rect.content
+ "(( %SVG.Description.class; )*, ( %SVG.Animation.class;
+ %SVG.rect.extra.content; )*)"
+>
+<!ELEMENT %SVG.rect.qname; %SVG.rect.content; >
+<!-- end of SVG.rect.element -->]]>
+
+<!ENTITY % SVG.rect.attlist "INCLUDE" >
+<![%SVG.rect.attlist;[
+<!ATTLIST %SVG.rect.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.External.attrib;
+ x %Coordinate.datatype; #IMPLIED
+ y %Coordinate.datatype; #IMPLIED
+ width %Length.datatype; #REQUIRED
+ height %Length.datatype; #REQUIRED
+ rx %Length.datatype; #IMPLIED
+ ry %Length.datatype; #IMPLIED
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.rect.attlist -->]]>
+
+<!-- circle: Circle Element ............................ -->
+
+<!ENTITY % SVG.circle.extra.content "" >
+
+<!ENTITY % SVG.circle.element "INCLUDE" >
+<![%SVG.circle.element;[
+<!ENTITY % SVG.circle.content
+ "(( %SVG.Description.class; )*, ( %SVG.Animation.class;
+ %SVG.circle.extra.content; )*)"
+>
+<!ELEMENT %SVG.circle.qname; %SVG.circle.content; >
+<!-- end of SVG.circle.element -->]]>
+
+<!ENTITY % SVG.circle.attlist "INCLUDE" >
+<![%SVG.circle.attlist;[
+<!ATTLIST %SVG.circle.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.External.attrib;
+ cx %Coordinate.datatype; #IMPLIED
+ cy %Coordinate.datatype; #IMPLIED
+ r %Length.datatype; #REQUIRED
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.circle.attlist -->]]>
+
+<!-- line: Line Element ................................ -->
+
+<!ENTITY % SVG.line.extra.content "" >
+
+<!ENTITY % SVG.line.element "INCLUDE" >
+<![%SVG.line.element;[
+<!ENTITY % SVG.line.content
+ "(( %SVG.Description.class; )*, ( %SVG.Animation.class;
+ %SVG.line.extra.content; )*)"
+>
+<!ELEMENT %SVG.line.qname; %SVG.line.content; >
+<!-- end of SVG.line.element -->]]>
+
+<!ENTITY % SVG.line.attlist "INCLUDE" >
+<![%SVG.line.attlist;[
+<!ATTLIST %SVG.line.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.External.attrib;
+ x1 %Coordinate.datatype; #IMPLIED
+ y1 %Coordinate.datatype; #IMPLIED
+ x2 %Coordinate.datatype; #IMPLIED
+ y2 %Coordinate.datatype; #IMPLIED
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.line.attlist -->]]>
+
+<!-- ellipse: Ellipse Element .......................... -->
+
+<!ENTITY % SVG.ellipse.extra.content "" >
+
+<!ENTITY % SVG.ellipse.element "INCLUDE" >
+<![%SVG.ellipse.element;[
+<!ENTITY % SVG.ellipse.content
+ "(( %SVG.Description.class; )*, ( %SVG.Animation.class;
+ %SVG.ellipse.extra.content; )*)"
+>
+<!ELEMENT %SVG.ellipse.qname; %SVG.ellipse.content; >
+<!-- end of SVG.ellipse.element -->]]>
+
+<!ENTITY % SVG.ellipse.attlist "INCLUDE" >
+<![%SVG.ellipse.attlist;[
+<!ATTLIST %SVG.ellipse.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.External.attrib;
+ cx %Coordinate.datatype; #IMPLIED
+ cy %Coordinate.datatype; #IMPLIED
+ rx %Length.datatype; #REQUIRED
+ ry %Length.datatype; #REQUIRED
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.ellipse.attlist -->]]>
+
+<!-- polyline: Polyline Element ........................ -->
+
+<!ENTITY % SVG.polyline.extra.content "" >
+
+<!ENTITY % SVG.polyline.element "INCLUDE" >
+<![%SVG.polyline.element;[
+<!ENTITY % SVG.polyline.content
+ "(( %SVG.Description.class; )*, ( %SVG.Animation.class;
+ %SVG.polyline.extra.content; )*)"
+>
+<!ELEMENT %SVG.polyline.qname; %SVG.polyline.content; >
+<!-- end of SVG.polyline.element -->]]>
+
+<!ENTITY % SVG.polyline.attlist "INCLUDE" >
+<![%SVG.polyline.attlist;[
+<!ATTLIST %SVG.polyline.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.External.attrib;
+ points %Points.datatype; #REQUIRED
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.polyline.attlist -->]]>
+
+<!-- polygon: Polygon Element .......................... -->
+
+<!ENTITY % SVG.polygon.extra.content "" >
+
+<!ENTITY % SVG.polygon.element "INCLUDE" >
+<![%SVG.polygon.element;[
+<!ENTITY % SVG.polygon.content
+ "(( %SVG.Description.class; )*, ( %SVG.Animation.class;
+ %SVG.polygon.extra.content; )*)"
+>
+<!ELEMENT %SVG.polygon.qname; %SVG.polygon.content; >
+<!-- end of SVG.polygon.element -->]]>
+
+<!ENTITY % SVG.polygon.attlist "INCLUDE" >
+<![%SVG.polygon.attlist;[
+<!ATTLIST %SVG.polygon.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.External.attrib;
+ points %Points.datatype; #REQUIRED
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.polygon.attlist -->]]>
+
+<!-- end of svg-shape.mod -->
+]]>
+
+<!-- Text Module ................................................. -->
+<!ENTITY % svg-text.module "INCLUDE" >
+<![%svg-text.module;[
+<!ENTITY % svg-text.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Text//EN"
+ "svg-text.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Text Module ................................................... -->
+<!-- file: svg-text.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Text//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-text.mod"
+
+ ....................................................................... -->
+
+<!-- Text
+
+ text, tspan, tref, textPath, altGlyph, altGlyphDef, altGlyphItem,
+ glyphRef
+
+ This module declares markup to provide support for alternate glyph.
+-->
+
+<!-- 'baseline-shift' property/attribute value (e.g., 'baseline', 'sub', etc.) -->
+<!ENTITY % BaselineShiftValue.datatype "CDATA" >
+
+<!-- 'font-family' property/attribute value (i.e., list of fonts) -->
+<!ENTITY % FontFamilyValue.datatype "CDATA" >
+
+<!-- 'font-size' property/attribute value -->
+<!ENTITY % FontSizeValue.datatype "CDATA" >
+
+<!-- 'font-size-adjust' property/attribute value -->
+<!ENTITY % FontSizeAdjustValue.datatype "CDATA" >
+
+<!-- 'glyph-orientation-horizontal' property/attribute value (e.g., <angle>) -->
+<!ENTITY % GlyphOrientationHorizontalValue.datatype "CDATA" >
+
+<!-- 'glyph-orientation-vertical' property/attribute value (e.g., 'auto', <angle>) -->
+<!ENTITY % GlyphOrientationVerticalValue.datatype "CDATA" >
+
+<!-- 'kerning' property/attribute value (e.g., 'auto', <length>) -->
+<!ENTITY % KerningValue.datatype "CDATA" >
+
+<!-- 'letter-spacing' or 'word-spacing' property/attribute value (e.g., 'normal', <length>) -->
+<!ENTITY % SpacingValue.datatype "CDATA" >
+
+<!-- 'text-decoration' property/attribute value (e.g., 'none', 'underline') -->
+<!ENTITY % TextDecorationValue.datatype "CDATA" >
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.text.qname "text" >
+<!ENTITY % SVG.tspan.qname "tspan" >
+<!ENTITY % SVG.tref.qname "tref" >
+<!ENTITY % SVG.textPath.qname "textPath" >
+<!ENTITY % SVG.altGlyph.qname "altGlyph" >
+<!ENTITY % SVG.altGlyphDef.qname "altGlyphDef" >
+<!ENTITY % SVG.altGlyphItem.qname "altGlyphItem" >
+<!ENTITY % SVG.glyphRef.qname "glyphRef" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Conditional.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Paint.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Clip.attrib "" >
+<!ENTITY % SVG.Mask.attrib "" >
+<!ENTITY % SVG.Filter.attrib "" >
+<!ENTITY % SVG.GraphicalEvents.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.XLink.attrib "" >
+<!ENTITY % SVG.XLinkRequired.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Text.class .................................... -->
+
+<!ENTITY % SVG.Text.extra.class "" >
+
+<!ENTITY % SVG.Text.class
+ "| %SVG.text.qname; | %SVG.altGlyphDef.qname; %SVG.Text.extra.class;"
+>
+
+<!-- SVG.TextContent.class ............................. -->
+
+<!ENTITY % SVG.TextContent.extra.class "" >
+
+<!ENTITY % SVG.TextContent.class
+ "| %SVG.tspan.qname; | %SVG.tref.qname; | %SVG.textPath.qname;
+ | %SVG.altGlyph.qname; %SVG.TextContent.extra.class;"
+>
+
+<!-- SVG.Text.attrib ................................... -->
+
+<!ENTITY % SVG.Text.extra.attrib "" >
+
+<!ENTITY % SVG.Text.attrib
+ "writing-mode ( lr-tb | rl-tb | tb-rl | lr | rl | tb | inherit ) #IMPLIED
+ %SVG.Text.extra.attrib;"
+>
+
+<!-- SVG.TextContent.attrib ............................ -->
+
+<!ENTITY % SVG.TextContent.extra.attrib "" >
+
+<!ENTITY % SVG.TextContent.attrib
+ "alignment-baseline ( auto | baseline | before-edge | text-before-edge |
+ middle | central | after-edge | text-after-edge |
+ ideographic | alphabetic | hanging | mathematical |
+ inherit ) #IMPLIED
+ baseline-shift %BaselineShiftValue.datatype; #IMPLIED
+ direction ( ltr | rtl | inherit ) #IMPLIED
+ dominant-baseline ( auto | use-script | no-change | reset-size |
+ ideographic | alphabetic | hanging | mathematical |
+ central | middle | text-after-edge | text-before-edge |
+ inherit ) #IMPLIED
+ glyph-orientation-horizontal %GlyphOrientationHorizontalValue.datatype;
+ #IMPLIED
+ glyph-orientation-vertical %GlyphOrientationVerticalValue.datatype;
+ #IMPLIED
+ kerning %KerningValue.datatype; #IMPLIED
+ letter-spacing %SpacingValue.datatype; #IMPLIED
+ text-anchor ( start | middle | end | inherit ) #IMPLIED
+ text-decoration %TextDecorationValue.datatype; #IMPLIED
+ unicode-bidi ( normal | embed | bidi-override | inherit ) #IMPLIED
+ word-spacing %SpacingValue.datatype; #IMPLIED
+ %SVG.TextContent.extra.attrib;"
+>
+
+<!-- SVG.Font.attrib ................................... -->
+
+<!ENTITY % SVG.Font.extra.attrib "" >
+
+<!ENTITY % SVG.Font.attrib
+ "font-family %FontFamilyValue.datatype; #IMPLIED
+ font-size %FontSizeValue.datatype; #IMPLIED
+ font-size-adjust %FontSizeAdjustValue.datatype; #IMPLIED
+ font-stretch ( normal | wider | narrower | ultra-condensed |
+ extra-condensed | condensed | semi-condensed |
+ semi-expanded | expanded | extra-expanded |
+ ultra-expanded | inherit ) #IMPLIED
+ font-style ( normal | italic | oblique | inherit ) #IMPLIED
+ font-variant ( normal | small-caps | inherit ) #IMPLIED
+ font-weight ( normal | bold | bolder | lighter | 100 | 200 | 300 | 400 |
+ 500 | 600 | 700 | 800 | 900 | inherit ) #IMPLIED
+ %SVG.Font.extra.attrib;"
+>
+
+<!-- text: Text Element ................................ -->
+
+<!ENTITY % SVG.text.extra.content "" >
+
+<!ENTITY % SVG.text.element "INCLUDE" >
+<![%SVG.text.element;[
+<!ENTITY % SVG.text.content
+ "( #PCDATA | %SVG.Description.class; | %SVG.Animation.class;
+ %SVG.TextContent.class; %SVG.Hyperlink.class;
+ %SVG.text.extra.content; )*"
+>
+<!ELEMENT %SVG.text.qname; %SVG.text.content; >
+<!-- end of SVG.text.element -->]]>
+
+<!ENTITY % SVG.text.attlist "INCLUDE" >
+<![%SVG.text.attlist;[
+<!ATTLIST %SVG.text.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Text.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.External.attrib;
+ x %Coordinates.datatype; #IMPLIED
+ y %Coordinates.datatype; #IMPLIED
+ dx %Lengths.datatype; #IMPLIED
+ dy %Lengths.datatype; #IMPLIED
+ rotate %Numbers.datatype; #IMPLIED
+ textLength %Length.datatype; #IMPLIED
+ lengthAdjust ( spacing | spacingAndGlyphs ) #IMPLIED
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.text.attlist -->]]>
+
+<!-- tspan: Text Span Element .......................... -->
+
+<!ENTITY % SVG.tspan.extra.content "" >
+
+<!ENTITY % SVG.tspan.element "INCLUDE" >
+<![%SVG.tspan.element;[
+<!ENTITY % SVG.tspan.content
+ "( #PCDATA | %SVG.tspan.qname; | %SVG.tref.qname; | %SVG.altGlyph.qname;
+ | %SVG.animate.qname; | %SVG.set.qname; | %SVG.animateColor.qname;
+ | %SVG.Description.class; %SVG.Hyperlink.class;
+ %SVG.tspan.extra.content; )*"
+>
+<!ELEMENT %SVG.tspan.qname; %SVG.tspan.content; >
+<!-- end of SVG.tspan.element -->]]>
+
+<!ENTITY % SVG.tspan.attlist "INCLUDE" >
+<![%SVG.tspan.attlist;[
+<!ATTLIST %SVG.tspan.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.External.attrib;
+ x %Coordinates.datatype; #IMPLIED
+ y %Coordinates.datatype; #IMPLIED
+ dx %Lengths.datatype; #IMPLIED
+ dy %Lengths.datatype; #IMPLIED
+ rotate %Numbers.datatype; #IMPLIED
+ textLength %Length.datatype; #IMPLIED
+ lengthAdjust ( spacing | spacingAndGlyphs ) #IMPLIED
+>
+<!-- end of SVG.tspan.attlist -->]]>
+
+<!-- tref: Text Reference Element ...................... -->
+
+<!ENTITY % SVG.tref.extra.content "" >
+
+<!ENTITY % SVG.tref.element "INCLUDE" >
+<![%SVG.tref.element;[
+<!ENTITY % SVG.tref.content
+ "( %SVG.animate.qname; | %SVG.set.qname; | %SVG.animateColor.qname;
+ | %SVG.Description.class; %SVG.tref.extra.content; )*"
+>
+<!ELEMENT %SVG.tref.qname; %SVG.tref.content; >
+<!-- end of SVG.tref.element -->]]>
+
+<!ENTITY % SVG.tref.attlist "INCLUDE" >
+<![%SVG.tref.attlist;[
+<!ATTLIST %SVG.tref.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.XLinkRequired.attrib;
+ %SVG.External.attrib;
+ x %Coordinates.datatype; #IMPLIED
+ y %Coordinates.datatype; #IMPLIED
+ dx %Lengths.datatype; #IMPLIED
+ dy %Lengths.datatype; #IMPLIED
+ rotate %Numbers.datatype; #IMPLIED
+ textLength %Length.datatype; #IMPLIED
+ lengthAdjust ( spacing | spacingAndGlyphs ) #IMPLIED
+>
+<!-- end of SVG.tref.attlist -->]]>
+
+<!-- textPath: Text Path Element ....................... -->
+
+<!ENTITY % SVG.textPath.extra.content "" >
+
+<!ENTITY % SVG.textPath.element "INCLUDE" >
+<![%SVG.textPath.element;[
+<!ENTITY % SVG.textPath.content
+ "( #PCDATA | %SVG.tspan.qname; | %SVG.tref.qname; | %SVG.altGlyph.qname;
+ | %SVG.animate.qname; | %SVG.set.qname; | %SVG.animateColor.qname;
+ | %SVG.Description.class; %SVG.Hyperlink.class;
+ %SVG.textPath.extra.content; )*"
+>
+<!ELEMENT %SVG.textPath.qname; %SVG.textPath.content; >
+<!-- end of SVG.textPath.element -->]]>
+
+<!ENTITY % SVG.textPath.attlist "INCLUDE" >
+<![%SVG.textPath.attlist;[
+<!ATTLIST %SVG.textPath.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.XLinkRequired.attrib;
+ %SVG.External.attrib;
+ startOffset %Length.datatype; #IMPLIED
+ textLength %Length.datatype; #IMPLIED
+ lengthAdjust ( spacing | spacingAndGlyphs ) #IMPLIED
+ method ( align | stretch ) #IMPLIED
+ spacing ( auto | exact ) #IMPLIED
+>
+<!-- end of SVG.textPath.attlist -->]]>
+
+<!-- altGlyph: Alternate Glyph Element ................. -->
+
+<!ENTITY % SVG.altGlyph.extra.content "" >
+
+<!ENTITY % SVG.altGlyph.element "INCLUDE" >
+<![%SVG.altGlyph.element;[
+<!ENTITY % SVG.altGlyph.content
+ "( #PCDATA %SVG.altGlyph.extra.content; )*"
+>
+<!ELEMENT %SVG.altGlyph.qname; %SVG.altGlyph.content; >
+<!-- end of SVG.altGlyph.element -->]]>
+
+<!ENTITY % SVG.altGlyph.attlist "INCLUDE" >
+<![%SVG.altGlyph.attlist;[
+<!ATTLIST %SVG.altGlyph.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.XLink.attrib;
+ %SVG.External.attrib;
+ x %Coordinates.datatype; #IMPLIED
+ y %Coordinates.datatype; #IMPLIED
+ dx %Lengths.datatype; #IMPLIED
+ dy %Lengths.datatype; #IMPLIED
+ glyphRef CDATA #IMPLIED
+ format CDATA #IMPLIED
+ rotate %Numbers.datatype; #IMPLIED
+>
+<!-- end of SVG.altGlyph.attlist -->]]>
+
+<!-- altGlyphDef: Alternate Glyph Definition Element ... -->
+
+<!ENTITY % SVG.altGlyphDef.extra.content "" >
+
+<!ENTITY % SVG.altGlyphDef.element "INCLUDE" >
+<![%SVG.altGlyphDef.element;[
+<!ENTITY % SVG.altGlyphDef.content
+ "(( %SVG.glyphRef.qname;+ | %SVG.altGlyphItem.qname;+ )
+ %SVG.altGlyphDef.extra.content; )"
+>
+<!ELEMENT %SVG.altGlyphDef.qname; %SVG.altGlyphDef.content; >
+<!-- end of SVG.altGlyphDef.element -->]]>
+
+<!ENTITY % SVG.altGlyphDef.attlist "INCLUDE" >
+<![%SVG.altGlyphDef.attlist;[
+<!ATTLIST %SVG.altGlyphDef.qname;
+ %SVG.Core.attrib;
+>
+<!-- end of SVG.altGlyphDef.attlist -->]]>
+
+<!-- altGlyphItem: Alternate Glyph Item Element ........ -->
+
+<!ENTITY % SVG.altGlyphItem.extra.content "" >
+
+<!ENTITY % SVG.altGlyphItem.element "INCLUDE" >
+<![%SVG.altGlyphItem.element;[
+<!ENTITY % SVG.altGlyphItem.content
+ "( %SVG.glyphRef.qname;+ %SVG.altGlyphItem.extra.content; )"
+>
+<!ELEMENT %SVG.altGlyphItem.qname; %SVG.altGlyphItem.content; >
+<!-- end of SVG.altGlyphItem.element -->]]>
+
+<!ENTITY % SVG.altGlyphItem.attlist "INCLUDE" >
+<![%SVG.altGlyphItem.attlist;[
+<!ATTLIST %SVG.altGlyphItem.qname;
+ %SVG.Core.attrib;
+>
+<!-- end of SVG.altGlyphItem.attlist -->]]>
+
+<!-- glyphRef: Glyph Reference Element ................. -->
+
+<!ENTITY % SVG.glyphRef.element "INCLUDE" >
+<![%SVG.glyphRef.element;[
+<!ENTITY % SVG.glyphRef.content "EMPTY" >
+<!ELEMENT %SVG.glyphRef.qname; %SVG.glyphRef.content; >
+<!-- end of SVG.glyphRef.element -->]]>
+
+<!ENTITY % SVG.glyphRef.attlist "INCLUDE" >
+<![%SVG.glyphRef.attlist;[
+<!ATTLIST %SVG.glyphRef.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Font.attrib;
+ %SVG.XLink.attrib;
+ x %Number.datatype; #IMPLIED
+ y %Number.datatype; #IMPLIED
+ dx %Number.datatype; #IMPLIED
+ dy %Number.datatype; #IMPLIED
+ glyphRef CDATA #IMPLIED
+ format CDATA #IMPLIED
+>
+<!-- end of SVG.glyphRef.attlist -->]]>
+
+<!-- end of svg-text.mod -->
+]]>
+
+<!-- Marker Module ............................................... -->
+<!ENTITY % svg-marker.module "INCLUDE" >
+<![%svg-marker.module;[
+<!ENTITY % svg-marker.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Marker//EN"
+ "svg-marker.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Marker Module ................................................. -->
+<!-- file: svg-marker.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Marker//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-marker.mod"
+
+ ....................................................................... -->
+
+<!-- Marker
+
+ marker
+
+ This module declares markup to provide support for marker.
+-->
+
+<!-- 'marker' property/attribute value (e.g., 'none', <uri>) -->
+<!ENTITY % MarkerValue.datatype "CDATA" >
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.marker.qname "marker" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Container.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Viewport.attrib "" >
+<!ENTITY % SVG.Text.attrib "" >
+<!ENTITY % SVG.TextContent.attrib "" >
+<!ENTITY % SVG.Font.attrib "" >
+<!ENTITY % SVG.Paint.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Profile.attrib "" >
+<!ENTITY % SVG.Gradient.attrib "" >
+<!ENTITY % SVG.Clip.attrib "" >
+<!ENTITY % SVG.Mask.attrib "" >
+<!ENTITY % SVG.Filter.attrib "" >
+<!ENTITY % SVG.FilterColor.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Marker.class .................................. -->
+
+<!ENTITY % SVG.Marker.extra.class "" >
+
+<!ENTITY % SVG.Marker.class
+ "| %SVG.marker.qname; %SVG.Marker.extra.class;"
+>
+
+<!-- SVG.Marker.attrib ................................. -->
+
+<!ENTITY % SVG.Marker.extra.attrib "" >
+
+<!ENTITY % SVG.Marker.attrib
+ "marker-start %MarkerValue.datatype; #IMPLIED
+ marker-mid %MarkerValue.datatype; #IMPLIED
+ marker-end %MarkerValue.datatype; #IMPLIED
+ %SVG.Marker.extra.attrib;"
+>
+
+<!-- SVG.Presentation.attrib ........................... -->
+
+<!ENTITY % SVG.Presentation.extra.attrib "" >
+
+<!ENTITY % SVG.Presentation.attrib
+ "%SVG.Container.attrib;
+ %SVG.Viewport.attrib;
+ %SVG.Text.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Profile.attrib;
+ %SVG.Gradient.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.Cursor.attrib;
+ flood-color %SVGColor.datatype; #IMPLIED
+ flood-opacity %OpacityValue.datatype; #IMPLIED
+ lighting-color %SVGColor.datatype; #IMPLIED
+ %SVG.Presentation.extra.attrib;"
+>
+
+<!-- marker: Marker Element ............................ -->
+
+<!ENTITY % SVG.marker.extra.content "" >
+
+<!ENTITY % SVG.marker.element "INCLUDE" >
+<![%SVG.marker.element;[
+<!ENTITY % SVG.marker.content
+ "( %SVG.Description.class; | %SVG.Animation.class; %SVG.Structure.class;
+ %SVG.Conditional.class; %SVG.Image.class; %SVG.Style.class;
+ %SVG.Shape.class; %SVG.Text.class; %SVG.Marker.class; %SVG.Profile.class;
+ %SVG.Gradient.class; %SVG.Pattern.class; %SVG.Clip.class;
+ %SVG.Mask.class; %SVG.Filter.class; %SVG.Cursor.class;
+ %SVG.Hyperlink.class; %SVG.View.class; %SVG.Script.class;
+ %SVG.Font.class; %SVG.marker.extra.content; )*"
+>
+<!ELEMENT %SVG.marker.qname; %SVG.marker.content; >
+<!-- end of SVG.marker.element -->]]>
+
+<!ENTITY % SVG.marker.attlist "INCLUDE" >
+<![%SVG.marker.attlist;[
+<!ATTLIST %SVG.marker.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.External.attrib;
+ refX %Coordinate.datatype; #IMPLIED
+ refY %Coordinate.datatype; #IMPLIED
+ markerUnits ( strokeWidth | userSpaceOnUse ) #IMPLIED
+ markerWidth %Length.datatype; #IMPLIED
+ markerHeight %Length.datatype; #IMPLIED
+ orient CDATA #IMPLIED
+ viewBox %ViewBoxSpec.datatype; #IMPLIED
+ preserveAspectRatio %PreserveAspectRatioSpec.datatype; 'xMidYMid meet'
+>
+<!-- end of SVG.marker.attlist -->]]>
+
+<!-- end of svg-marker.mod -->
+]]>
+
+<!-- Color Profile Module ........................................ -->
+<!ENTITY % svg-profile.module "INCLUDE" >
+<![%svg-profile.module;[
+<!ENTITY % svg-profile.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Color Profile//EN"
+ "svg-profile.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Color Profile Module .......................................... -->
+<!-- file: svg-profile.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Color Profile//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-profile.mod"
+
+ ....................................................................... -->
+
+<!-- Color Profile
+
+ color-profile
+
+ This module declares markup to provide support for color profile.
+-->
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.color-profile.qname "color-profile" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.XLink.attrib "" >
+
+<!-- SVG.Profile.class ................................. -->
+
+<!ENTITY % SVG.Profile.extra.class "" >
+
+<!ENTITY % SVG.Profile.class
+ "| %SVG.color-profile.qname; %SVG.Profile.extra.class;"
+>
+
+<!-- SVG.Profile.attrib ................................ -->
+
+<!ENTITY % SVG.Profile.extra.attrib "" >
+
+<!ENTITY % SVG.Profile.attrib
+ "color-profile CDATA #IMPLIED
+ %SVG.Profile.extra.attrib;"
+>
+
+<!-- color-profile: Color Profile Element .............. -->
+
+<!ENTITY % SVG.color-profile.extra.content "" >
+
+<!ENTITY % SVG.color-profile.element "INCLUDE" >
+<![%SVG.color-profile.element;[
+<!ENTITY % SVG.color-profile.content
+ "( %SVG.Description.class; %SVG.color-profile.extra.content; )*"
+>
+<!ELEMENT %SVG.color-profile.qname; %SVG.color-profile.content; >
+<!-- end of SVG.color-profile.element -->]]>
+
+<!ENTITY % SVG.color-profile.attlist "INCLUDE" >
+<![%SVG.color-profile.attlist;[
+<!ATTLIST %SVG.color-profile.qname;
+ %SVG.Core.attrib;
+ %SVG.XLink.attrib;
+ local CDATA #IMPLIED
+ name CDATA #REQUIRED
+ rendering-intent ( auto | perceptual | relative-colorimetric | saturation |
+ absolute-colorimetric ) 'auto'
+>
+<!-- end of SVG.color-profile.attlist -->]]>
+
+<!-- end of svg-profile.mod -->
+]]>
+
+<!-- Gradient Module ............................................. -->
+<!ENTITY % svg-gradient.module "INCLUDE" >
+<![%svg-gradient.module;[
+<!ENTITY % svg-gradient.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Gradient//EN"
+ "svg-gradient.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Gradient Module ............................................... -->
+<!-- file: svg-gradient.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Gradient//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-gradient.mod"
+
+ ....................................................................... -->
+
+<!-- Gradient
+
+ linearGradient, radialGradient, stop
+
+ This module declares markup to provide support for gradient fill.
+-->
+
+<!-- a <number> or a <percentage> -->
+<!ENTITY % NumberOrPercentage.datatype "CDATA" >
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.linearGradient.qname "linearGradient" >
+<!ENTITY % SVG.radialGradient.qname "radialGradient" >
+<!ENTITY % SVG.stop.qname "stop" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.XLink.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Gradient.class ................................ -->
+
+<!ENTITY % SVG.Gradient.extra.class "" >
+
+<!ENTITY % SVG.Gradient.class
+ "| %SVG.linearGradient.qname; | %SVG.radialGradient.qname;
+ %SVG.Gradient.extra.class;"
+>
+
+<!-- SVG.Gradient.attrib ............................... -->
+
+<!ENTITY % SVG.Gradient.extra.attrib "" >
+
+<!ENTITY % SVG.Gradient.attrib
+ "stop-color %SVGColor.datatype; #IMPLIED
+ stop-opacity %OpacityValue.datatype; #IMPLIED
+ %SVG.Gradient.extra.attrib;"
+>
+
+<!-- linearGradient: Linear Gradient Element ........... -->
+
+<!ENTITY % SVG.linearGradient.extra.content "" >
+
+<!ENTITY % SVG.linearGradient.element "INCLUDE" >
+<![%SVG.linearGradient.element;[
+<!ENTITY % SVG.linearGradient.content
+ "(( %SVG.Description.class; )*, ( %SVG.stop.qname; | %SVG.animate.qname;
+ | %SVG.set.qname; | %SVG.animateTransform.qname;
+ %SVG.linearGradient.extra.content; )*)"
+>
+<!ELEMENT %SVG.linearGradient.qname; %SVG.linearGradient.content; >
+<!-- end of SVG.linearGradient.element -->]]>
+
+<!ENTITY % SVG.linearGradient.attlist "INCLUDE" >
+<![%SVG.linearGradient.attlist;[
+<!ATTLIST %SVG.linearGradient.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Color.attrib;
+ %SVG.Gradient.attrib;
+ %SVG.XLink.attrib;
+ %SVG.External.attrib;
+ x1 %Coordinate.datatype; #IMPLIED
+ y1 %Coordinate.datatype; #IMPLIED
+ x2 %Coordinate.datatype; #IMPLIED
+ y2 %Coordinate.datatype; #IMPLIED
+ gradientUnits ( userSpaceOnUse | objectBoundingBox ) #IMPLIED
+ gradientTransform %TransformList.datatype; #IMPLIED
+ spreadMethod ( pad | reflect | repeat ) #IMPLIED
+>
+<!-- end of SVG.linearGradient.attlist -->]]>
+
+<!-- radialGradient: Radial Gradient Element ........... -->
+
+<!ENTITY % SVG.radialGradient.extra.content "" >
+
+<!ENTITY % SVG.radialGradient.element "INCLUDE" >
+<![%SVG.radialGradient.element;[
+<!ENTITY % SVG.radialGradient.content
+ "(( %SVG.Description.class; )*, ( %SVG.stop.qname; | %SVG.animate.qname;
+ | %SVG.set.qname; | %SVG.animateTransform.qname;
+ %SVG.radialGradient.extra.content; )*)"
+>
+<!ELEMENT %SVG.radialGradient.qname; %SVG.radialGradient.content; >
+<!-- end of SVG.radialGradient.element -->]]>
+
+<!ENTITY % SVG.radialGradient.attlist "INCLUDE" >
+<![%SVG.radialGradient.attlist;[
+<!ATTLIST %SVG.radialGradient.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Color.attrib;
+ %SVG.Gradient.attrib;
+ %SVG.XLink.attrib;
+ %SVG.External.attrib;
+ cx %Coordinate.datatype; #IMPLIED
+ cy %Coordinate.datatype; #IMPLIED
+ r %Length.datatype; #IMPLIED
+ fx %Coordinate.datatype; #IMPLIED
+ fy %Coordinate.datatype; #IMPLIED
+ gradientUnits ( userSpaceOnUse | objectBoundingBox ) #IMPLIED
+ gradientTransform %TransformList.datatype; #IMPLIED
+ spreadMethod ( pad | reflect | repeat ) #IMPLIED
+>
+<!-- end of SVG.radialGradient.attlist -->]]>
+
+<!-- stop: Stop Element ................................ -->
+
+<!ENTITY % SVG.stop.extra.content "" >
+
+<!ENTITY % SVG.stop.element "INCLUDE" >
+<![%SVG.stop.element;[
+<!ENTITY % SVG.stop.content
+ "( %SVG.animate.qname; | %SVG.set.qname; | %SVG.animateColor.qname;
+ %SVG.stop.extra.content; )*"
+>
+<!ELEMENT %SVG.stop.qname; %SVG.stop.content; >
+<!-- end of SVG.stop.element -->]]>
+
+<!ENTITY % SVG.stop.attlist "INCLUDE" >
+<![%SVG.stop.attlist;[
+<!ATTLIST %SVG.stop.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Color.attrib;
+ %SVG.Gradient.attrib;
+ offset %NumberOrPercentage.datatype; #REQUIRED
+>
+<!-- end of SVG.stop.attlist -->]]>
+
+<!-- end of svg-gradient.mod -->
+]]>
+
+<!-- Pattern Module .............................................. -->
+<!ENTITY % svg-pattern.module "INCLUDE" >
+<![%svg-pattern.module;[
+<!ENTITY % svg-pattern.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Pattern//EN"
+ "svg-pattern.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Pattern Module ................................................ -->
+<!-- file: svg-pattern.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Pattern//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-pattern.mod"
+
+ ....................................................................... -->
+
+<!-- Pattern
+
+ pattern
+
+ This module declares markup to provide support for pattern fill.
+-->
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.pattern.qname "pattern" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Container.attrib "" >
+<!ENTITY % SVG.Conditional.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Viewport.attrib "" >
+<!ENTITY % SVG.Text.attrib "" >
+<!ENTITY % SVG.TextContent.attrib "" >
+<!ENTITY % SVG.Font.attrib "" >
+<!ENTITY % SVG.Paint.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Marker.attrib "" >
+<!ENTITY % SVG.Profile.attrib "" >
+<!ENTITY % SVG.Gradient.attrib "" >
+<!ENTITY % SVG.Clip.attrib "" >
+<!ENTITY % SVG.Mask.attrib "" >
+<!ENTITY % SVG.Filter.attrib "" >
+<!ENTITY % SVG.FilterColor.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.XLink.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Pattern.class ................................. -->
+
+<!ENTITY % SVG.Pattern.extra.class "" >
+
+<!ENTITY % SVG.Pattern.class
+ "| %SVG.pattern.qname; %SVG.Pattern.extra.class;"
+>
+
+<!-- SVG.Presentation.attrib ........................... -->
+
+<!ENTITY % SVG.Presentation.extra.attrib "" >
+
+<!ENTITY % SVG.Presentation.attrib
+ "%SVG.Container.attrib;
+ %SVG.Viewport.attrib;
+ %SVG.Text.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Profile.attrib;
+ %SVG.Gradient.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.Cursor.attrib;
+ flood-color %SVGColor.datatype; #IMPLIED
+ flood-opacity %OpacityValue.datatype; #IMPLIED
+ lighting-color %SVGColor.datatype; #IMPLIED
+ %SVG.Presentation.extra.attrib;"
+>
+
+<!-- pattern: Pattern Element .......................... -->
+
+<!ENTITY % SVG.pattern.extra.content "" >
+
+<!ENTITY % SVG.pattern.element "INCLUDE" >
+<![%SVG.pattern.element;[
+<!ENTITY % SVG.pattern.content
+ "( %SVG.Description.class; | %SVG.Animation.class; %SVG.Structure.class;
+ %SVG.Conditional.class; %SVG.Image.class; %SVG.Style.class;
+ %SVG.Shape.class; %SVG.Text.class; %SVG.Marker.class; %SVG.Profile.class;
+ %SVG.Gradient.class; %SVG.Pattern.class; %SVG.Clip.class;
+ %SVG.Mask.class; %SVG.Filter.class; %SVG.Cursor.class;
+ %SVG.Hyperlink.class; %SVG.View.class; %SVG.Script.class;
+ %SVG.Font.class; %SVG.pattern.extra.content; )*"
+>
+<!ELEMENT %SVG.pattern.qname; %SVG.pattern.content; >
+<!-- end of SVG.pattern.element -->]]>
+
+<!ENTITY % SVG.pattern.attlist "INCLUDE" >
+<![%SVG.pattern.attlist;[
+<!ATTLIST %SVG.pattern.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.XLink.attrib;
+ %SVG.External.attrib;
+ x %Coordinate.datatype; #IMPLIED
+ y %Coordinate.datatype; #IMPLIED
+ width %Length.datatype; #IMPLIED
+ height %Length.datatype; #IMPLIED
+ patternUnits ( userSpaceOnUse | objectBoundingBox ) #IMPLIED
+ patternContentUnits ( userSpaceOnUse | objectBoundingBox ) #IMPLIED
+ patternTransform %TransformList.datatype; #IMPLIED
+ viewBox %ViewBoxSpec.datatype; #IMPLIED
+ preserveAspectRatio %PreserveAspectRatioSpec.datatype; 'xMidYMid meet'
+>
+<!-- end of SVG.pattern.attlist -->]]>
+
+<!-- end of svg-pattern.mod -->
+]]>
+
+<!-- Clip Module ................................................. -->
+<!ENTITY % svg-clip.module "INCLUDE" >
+<![%svg-clip.module;[
+<!ENTITY % svg-clip.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Clip//EN"
+ "svg-clip.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Clip Module ................................................... -->
+<!-- file: svg-clip.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Clip//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-clip.mod"
+
+ ....................................................................... -->
+
+<!-- Clip
+
+ clipPath
+
+ This module declares markup to provide support for clipping.
+-->
+
+<!-- 'clip-path' property/attribute value (e.g., 'none', <uri>) -->
+<!ENTITY % ClipPathValue.datatype "CDATA" >
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.clipPath.qname "clipPath" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Conditional.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Text.attrib "" >
+<!ENTITY % SVG.TextContent.attrib "" >
+<!ENTITY % SVG.Font.attrib "" >
+<!ENTITY % SVG.Paint.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Mask.attrib "" >
+<!ENTITY % SVG.Filter.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Clip.class .................................... -->
+
+<!ENTITY % SVG.Clip.extra.class "" >
+
+<!ENTITY % SVG.Clip.class
+ "| %SVG.clipPath.qname; %SVG.Clip.extra.class;"
+>
+
+<!-- SVG.Clip.attrib ................................... -->
+
+<!ENTITY % SVG.Clip.extra.attrib "" >
+
+<!ENTITY % SVG.Clip.attrib
+ "clip-path %ClipPathValue.datatype; #IMPLIED
+ clip-rule %ClipFillRule.datatype; #IMPLIED
+ %SVG.Clip.extra.attrib;"
+>
+
+<!-- clipPath: Clip Path Element ....................... -->
+
+<!ENTITY % SVG.clipPath.extra.content "" >
+
+<!ENTITY % SVG.clipPath.element "INCLUDE" >
+<![%SVG.clipPath.element;[
+<!ENTITY % SVG.clipPath.content
+ "(( %SVG.Description.class; )*, ( %SVG.Animation.class; %SVG.Use.class;
+ %SVG.Shape.class; %SVG.Text.class; %SVG.clipPath.extra.content; )*)"
+>
+<!ELEMENT %SVG.clipPath.qname; %SVG.clipPath.content; >
+<!-- end of SVG.clipPath.element -->]]>
+
+<!ENTITY % SVG.clipPath.attlist "INCLUDE" >
+<![%SVG.clipPath.attlist;[
+<!ATTLIST %SVG.clipPath.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Text.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.External.attrib;
+ transform %TransformList.datatype; #IMPLIED
+ clipPathUnits ( userSpaceOnUse | objectBoundingBox ) #IMPLIED
+>
+<!-- end of SVG.clipPath.attlist -->]]>
+
+<!-- end of svg-clip.mod -->
+]]>
+
+<!-- Mask Module ................................................. -->
+<!ENTITY % svg-mask.module "INCLUDE" >
+<![%svg-mask.module;[
+<!ENTITY % svg-mask.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Mask//EN"
+ "svg-mask.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Mask Module ................................................... -->
+<!-- file: svg-mask.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Mask//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-mask.mod"
+
+ ....................................................................... -->
+
+<!-- Mask
+
+ mask
+
+ This module declares markup to provide support for masking.
+-->
+
+<!-- 'mask' property/attribute value (e.g., 'none', <uri>) -->
+<!ENTITY % MaskValue.datatype "CDATA" >
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.mask.qname "mask" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Container.attrib "" >
+<!ENTITY % SVG.Conditional.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Viewport.attrib "" >
+<!ENTITY % SVG.Text.attrib "" >
+<!ENTITY % SVG.TextContent.attrib "" >
+<!ENTITY % SVG.Font.attrib "" >
+<!ENTITY % SVG.Paint.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Marker.attrib "" >
+<!ENTITY % SVG.Profile.attrib "" >
+<!ENTITY % SVG.Gradient.attrib "" >
+<!ENTITY % SVG.Clip.attrib "" >
+<!ENTITY % SVG.Filter.attrib "" >
+<!ENTITY % SVG.FilterColor.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Mask.class .................................... -->
+
+<!ENTITY % SVG.Mask.extra.class "" >
+
+<!ENTITY % SVG.Mask.class
+ "| %SVG.mask.qname; %SVG.Mask.extra.class;"
+>
+
+<!-- SVG.Mask.attrib ................................... -->
+
+<!ENTITY % SVG.Mask.extra.attrib "" >
+
+<!ENTITY % SVG.Mask.attrib
+ "mask %MaskValue.datatype; #IMPLIED
+ %SVG.Mask.extra.attrib;"
+>
+
+<!-- SVG.Presentation.attrib ........................... -->
+
+<!ENTITY % SVG.Presentation.extra.attrib "" >
+
+<!ENTITY % SVG.Presentation.attrib
+ "%SVG.Container.attrib;
+ %SVG.Viewport.attrib;
+ %SVG.Text.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Profile.attrib;
+ %SVG.Gradient.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.Cursor.attrib;
+ flood-color %SVGColor.datatype; #IMPLIED
+ flood-opacity %OpacityValue.datatype; #IMPLIED
+ lighting-color %SVGColor.datatype; #IMPLIED
+ %SVG.Presentation.extra.attrib;"
+>
+
+<!-- mask: Mask Element ................................ -->
+
+<!ENTITY % SVG.mask.extra.content "" >
+
+<!ENTITY % SVG.mask.element "INCLUDE" >
+<![%SVG.mask.element;[
+<!ENTITY % SVG.mask.content
+ "( %SVG.Description.class; | %SVG.Animation.class; %SVG.Structure.class;
+ %SVG.Conditional.class; %SVG.Image.class; %SVG.Style.class;
+ %SVG.Shape.class; %SVG.Text.class; %SVG.Marker.class; %SVG.Profile.class;
+ %SVG.Gradient.class; %SVG.Pattern.class; %SVG.Clip.class;
+ %SVG.Mask.class; %SVG.Filter.class; %SVG.Cursor.class;
+ %SVG.Hyperlink.class; %SVG.View.class; %SVG.Script.class;
+ %SVG.Font.class; %SVG.mask.extra.content; )*"
+>
+<!ELEMENT %SVG.mask.qname; %SVG.mask.content; >
+<!-- end of SVG.mask.element -->]]>
+
+<!ENTITY % SVG.mask.attlist "INCLUDE" >
+<![%SVG.mask.attlist;[
+<!ATTLIST %SVG.mask.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.External.attrib;
+ x %Coordinate.datatype; #IMPLIED
+ y %Coordinate.datatype; #IMPLIED
+ width %Length.datatype; #IMPLIED
+ height %Length.datatype; #IMPLIED
+ maskUnits ( userSpaceOnUse | objectBoundingBox ) #IMPLIED
+ maskContentUnits ( userSpaceOnUse | objectBoundingBox ) #IMPLIED
+>
+<!-- end of SVG.mask.attlist -->]]>
+
+<!-- end of svg-mask.mod -->
+]]>
+
+<!-- Filter Module ............................................... -->
+<!ENTITY % svg-filter.module "INCLUDE" >
+<![%svg-filter.module;[
+<!ENTITY % svg-filter.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Filter//EN"
+ "svg-filter.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Filter Module ................................................. -->
+<!-- file: svg-filter.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Filter//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-filter.mod"
+
+ ....................................................................... -->
+
+<!-- Filter
+
+ filter, feBlend, feColorMatrix, feComponentTransfer, feComposite,
+ feConvolveMatrix, feDiffuseLighting, feDisplacementMap, feFlood,
+ feGaussianBlur, feImage, feMerge, feMergeNode, feMorphology, feOffset,
+ feSpecularLighting, feTile, feTurbulence, feDistantLight, fePointLight,
+ feSpotLight, feFuncR, feFuncG, feFuncB, feFuncA
+
+ This module declares markup to provide support for filter effect.
+-->
+
+<!-- 'filter' property/attribute value (e.g., 'none', <uri>) -->
+<!ENTITY % FilterValue.datatype "CDATA" >
+
+<!-- list of <number>s, but at least one and at most two -->
+<!ENTITY % NumberOptionalNumber.datatype "CDATA" >
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.filter.qname "filter" >
+<!ENTITY % SVG.feBlend.qname "feBlend" >
+<!ENTITY % SVG.feColorMatrix.qname "feColorMatrix" >
+<!ENTITY % SVG.feComponentTransfer.qname "feComponentTransfer" >
+<!ENTITY % SVG.feComposite.qname "feComposite" >
+<!ENTITY % SVG.feConvolveMatrix.qname "feConvolveMatrix" >
+<!ENTITY % SVG.feDiffuseLighting.qname "feDiffuseLighting" >
+<!ENTITY % SVG.feDisplacementMap.qname "feDisplacementMap" >
+<!ENTITY % SVG.feFlood.qname "feFlood" >
+<!ENTITY % SVG.feGaussianBlur.qname "feGaussianBlur" >
+<!ENTITY % SVG.feImage.qname "feImage" >
+<!ENTITY % SVG.feMerge.qname "feMerge" >
+<!ENTITY % SVG.feMergeNode.qname "feMergeNode" >
+<!ENTITY % SVG.feMorphology.qname "feMorphology" >
+<!ENTITY % SVG.feOffset.qname "feOffset" >
+<!ENTITY % SVG.feSpecularLighting.qname "feSpecularLighting" >
+<!ENTITY % SVG.feTile.qname "feTile" >
+<!ENTITY % SVG.feTurbulence.qname "feTurbulence" >
+<!ENTITY % SVG.feDistantLight.qname "feDistantLight" >
+<!ENTITY % SVG.fePointLight.qname "fePointLight" >
+<!ENTITY % SVG.feSpotLight.qname "feSpotLight" >
+<!ENTITY % SVG.feFuncR.qname "feFuncR" >
+<!ENTITY % SVG.feFuncG.qname "feFuncG" >
+<!ENTITY % SVG.feFuncB.qname "feFuncB" >
+<!ENTITY % SVG.feFuncA.qname "feFuncA" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Container.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Viewport.attrib "" >
+<!ENTITY % SVG.Text.attrib "" >
+<!ENTITY % SVG.TextContent.attrib "" >
+<!ENTITY % SVG.Font.attrib "" >
+<!ENTITY % SVG.Paint.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Marker.attrib "" >
+<!ENTITY % SVG.Profile.attrib "" >
+<!ENTITY % SVG.Gradient.attrib "" >
+<!ENTITY % SVG.Clip.attrib "" >
+<!ENTITY % SVG.Mask.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.XLink.attrib "" >
+<!ENTITY % SVG.XLinkEmbed.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Filter.class .................................. -->
+
+<!ENTITY % SVG.Filter.extra.class "" >
+
+<!ENTITY % SVG.Filter.class
+ "| %SVG.filter.qname; %SVG.Filter.extra.class;"
+>
+
+<!-- SVG.FilterPrimitive.class ......................... -->
+
+<!ENTITY % SVG.FilterPrimitive.extra.class "" >
+
+<!ENTITY % SVG.FilterPrimitive.class
+ "| %SVG.feBlend.qname; | %SVG.feColorMatrix.qname;
+ | %SVG.feComponentTransfer.qname; | %SVG.feComposite.qname;
+ | %SVG.feConvolveMatrix.qname; | %SVG.feDiffuseLighting.qname;
+ | %SVG.feDisplacementMap.qname; | %SVG.feFlood.qname;
+ | %SVG.feGaussianBlur.qname; | %SVG.feImage.qname; | %SVG.feMerge.qname;
+ | %SVG.feMorphology.qname; | %SVG.feOffset.qname;
+ | %SVG.feSpecularLighting.qname; | %SVG.feTile.qname;
+ | %SVG.feTurbulence.qname; %SVG.FilterPrimitive.extra.class;"
+>
+
+<!-- SVG.Filter.attrib ................................. -->
+
+<!ENTITY % SVG.Filter.extra.attrib "" >
+
+<!ENTITY % SVG.Filter.attrib
+ "filter %FilterValue.datatype; #IMPLIED
+ %SVG.Filter.extra.attrib;"
+>
+
+<!-- SVG.FilterColor.attrib ............................ -->
+
+<!ENTITY % SVG.FilterColor.extra.attrib "" >
+
+<!ENTITY % SVG.FilterColor.attrib
+ "color-interpolation-filters ( auto | sRGB | linearRGB | inherit )
+ #IMPLIED
+ %SVG.FilterColor.extra.attrib;"
+>
+
+<!-- SVG.FilterPrimitive.attrib ........................ -->
+
+<!ENTITY % SVG.FilterPrimitive.extra.attrib "" >
+
+<!ENTITY % SVG.FilterPrimitive.attrib
+ "x %Coordinate.datatype; #IMPLIED
+ y %Coordinate.datatype; #IMPLIED
+ width %Length.datatype; #IMPLIED
+ height %Length.datatype; #IMPLIED
+ result CDATA #IMPLIED
+ %SVG.FilterPrimitive.extra.attrib;"
+>
+
+<!-- SVG.FilterPrimitiveWithIn.attrib .................. -->
+
+<!ENTITY % SVG.FilterPrimitiveWithIn.extra.attrib "" >
+
+<!ENTITY % SVG.FilterPrimitiveWithIn.attrib
+ "%SVG.FilterPrimitive.attrib;
+ in CDATA #IMPLIED
+ %SVG.FilterPrimitiveWithIn.extra.attrib;"
+>
+
+<!-- SVG.Presentation.attrib ........................... -->
+
+<!ENTITY % SVG.Presentation.extra.attrib "" >
+
+<!ENTITY % SVG.Presentation.attrib
+ "%SVG.Container.attrib;
+ %SVG.Viewport.attrib;
+ %SVG.Text.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Profile.attrib;
+ %SVG.Gradient.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.Cursor.attrib;
+ flood-color %SVGColor.datatype; #IMPLIED
+ flood-opacity %OpacityValue.datatype; #IMPLIED
+ lighting-color %SVGColor.datatype; #IMPLIED
+ %SVG.Presentation.extra.attrib;"
+>
+
+<!-- filter: Filter Element ............................ -->
+
+<!ENTITY % SVG.filter.extra.content "" >
+
+<!ENTITY % SVG.filter.element "INCLUDE" >
+<![%SVG.filter.element;[
+<!ENTITY % SVG.filter.content
+ "(( %SVG.Description.class; )*, ( %SVG.animate.qname; | %SVG.set.qname;
+ %SVG.FilterPrimitive.class; %SVG.filter.extra.content; )*)"
+>
+<!ELEMENT %SVG.filter.qname; %SVG.filter.content; >
+<!-- end of SVG.filter.element -->]]>
+
+<!ENTITY % SVG.filter.attlist "INCLUDE" >
+<![%SVG.filter.attlist;[
+<!ATTLIST %SVG.filter.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.XLink.attrib;
+ %SVG.External.attrib;
+ x %Coordinate.datatype; #IMPLIED
+ y %Coordinate.datatype; #IMPLIED
+ width %Length.datatype; #IMPLIED
+ height %Length.datatype; #IMPLIED
+ filterRes %NumberOptionalNumber.datatype; #IMPLIED
+ filterUnits ( userSpaceOnUse | objectBoundingBox ) #IMPLIED
+ primitiveUnits ( userSpaceOnUse | objectBoundingBox ) #IMPLIED
+>
+<!-- end of SVG.filter.attlist -->]]>
+
+<!-- feBlend: Filter Effect Blend Element .............. -->
+
+<!ENTITY % SVG.feBlend.extra.content "" >
+
+<!ENTITY % SVG.feBlend.element "INCLUDE" >
+<![%SVG.feBlend.element;[
+<!ENTITY % SVG.feBlend.content
+ "( %SVG.animate.qname; | %SVG.set.qname; %SVG.feBlend.extra.content; )*"
+>
+<!ELEMENT %SVG.feBlend.qname; %SVG.feBlend.content; >
+<!-- end of SVG.feBlend.element -->]]>
+
+<!ENTITY % SVG.feBlend.attlist "INCLUDE" >
+<![%SVG.feBlend.attlist;[
+<!ATTLIST %SVG.feBlend.qname;
+ %SVG.Core.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitiveWithIn.attrib;
+ in2 CDATA #REQUIRED
+ mode ( normal | multiply | screen | darken | lighten ) 'normal'
+>
+<!-- end of SVG.feBlend.attlist -->]]>
+
+<!-- feColorMatrix: Filter Effect Color Matrix Element . -->
+
+<!ENTITY % SVG.feColorMatrix.extra.content "" >
+
+<!ENTITY % SVG.feColorMatrix.element "INCLUDE" >
+<![%SVG.feColorMatrix.element;[
+<!ENTITY % SVG.feColorMatrix.content
+ "( %SVG.animate.qname; | %SVG.set.qname;
+ %SVG.feColorMatrix.extra.content; )*"
+>
+<!ELEMENT %SVG.feColorMatrix.qname; %SVG.feColorMatrix.content; >
+<!-- end of SVG.feColorMatrix.element -->]]>
+
+<!ENTITY % SVG.feColorMatrix.attlist "INCLUDE" >
+<![%SVG.feColorMatrix.attlist;[
+<!ATTLIST %SVG.feColorMatrix.qname;
+ %SVG.Core.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitiveWithIn.attrib;
+ type ( matrix | saturate | hueRotate | luminanceToAlpha ) 'matrix'
+ values CDATA #IMPLIED
+>
+<!-- end of SVG.feColorMatrix.attlist -->]]>
+
+<!-- feComponentTransfer: Filter Effect Component Transfer Element -->
+
+<!ENTITY % SVG.feComponentTransfer.extra.content "" >
+
+<!ENTITY % SVG.feComponentTransfer.element "INCLUDE" >
+<![%SVG.feComponentTransfer.element;[
+<!ENTITY % SVG.feComponentTransfer.content
+ "( %SVG.feFuncR.qname;?, %SVG.feFuncG.qname;?, %SVG.feFuncB.qname;?,
+ %SVG.feFuncA.qname;? %SVG.feComponentTransfer.extra.content; )"
+>
+<!ELEMENT %SVG.feComponentTransfer.qname; %SVG.feComponentTransfer.content; >
+<!-- end of SVG.feComponentTransfer.element -->]]>
+
+<!ENTITY % SVG.feComponentTransfer.attlist "INCLUDE" >
+<![%SVG.feComponentTransfer.attlist;[
+<!ATTLIST %SVG.feComponentTransfer.qname;
+ %SVG.Core.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitiveWithIn.attrib;
+>
+<!-- end of SVG.feComponentTransfer.attlist -->]]>
+
+<!-- feComposite: Filter Effect Composite Element ...... -->
+
+<!ENTITY % SVG.feComposite.extra.content "" >
+
+<!ENTITY % SVG.feComposite.element "INCLUDE" >
+<![%SVG.feComposite.element;[
+<!ENTITY % SVG.feComposite.content
+ "( %SVG.animate.qname; | %SVG.set.qname; %SVG.feComposite.extra.content; )*"
+>
+<!ELEMENT %SVG.feComposite.qname; %SVG.feComposite.content; >
+<!-- end of SVG.feComposite.element -->]]>
+
+<!ENTITY % SVG.feComposite.attlist "INCLUDE" >
+<![%SVG.feComposite.attlist;[
+<!ATTLIST %SVG.feComposite.qname;
+ %SVG.Core.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitiveWithIn.attrib;
+ in2 CDATA #REQUIRED
+ operator ( over | in | out | atop | xor | arithmetic ) 'over'
+ k1 %Number.datatype; #IMPLIED
+ k2 %Number.datatype; #IMPLIED
+ k3 %Number.datatype; #IMPLIED
+ k4 %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.feComposite.attlist -->]]>
+
+<!-- feConvolveMatrix: Filter Effect Convolve Matrix Element -->
+
+<!ENTITY % SVG.feConvolveMatrix.extra.content "" >
+
+<!ENTITY % SVG.feConvolveMatrix.element "INCLUDE" >
+<![%SVG.feConvolveMatrix.element;[
+<!ENTITY % SVG.feConvolveMatrix.content
+ "( %SVG.animate.qname; | %SVG.set.qname;
+ %SVG.feConvolveMatrix.extra.content; )*"
+>
+<!ELEMENT %SVG.feConvolveMatrix.qname; %SVG.feConvolveMatrix.content; >
+<!-- end of SVG.feConvolveMatrix.element -->]]>
+
+<!ENTITY % SVG.feConvolveMatrix.attlist "INCLUDE" >
+<![%SVG.feConvolveMatrix.attlist;[
+<!ATTLIST %SVG.feConvolveMatrix.qname;
+ %SVG.Core.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitiveWithIn.attrib;
+ order %NumberOptionalNumber.datatype; #REQUIRED
+ kernelMatrix CDATA #REQUIRED
+ divisor %Number.datatype; #IMPLIED
+ bias %Number.datatype; #IMPLIED
+ targetX %Integer.datatype; #IMPLIED
+ targetY %Integer.datatype; #IMPLIED
+ edgeMode ( duplicate | wrap | none ) 'duplicate'
+ kernelUnitLength %NumberOptionalNumber.datatype; #IMPLIED
+ preserveAlpha %Boolean.datatype; #IMPLIED
+>
+<!-- end of SVG.feConvolveMatrix.attlist -->]]>
+
+<!-- feDiffuseLighting: Filter Effect Diffuse Lighting Element -->
+
+<!ENTITY % SVG.feDiffuseLighting.extra.content "" >
+
+<!ENTITY % SVG.feDiffuseLighting.element "INCLUDE" >
+<![%SVG.feDiffuseLighting.element;[
+<!ENTITY % SVG.feDiffuseLighting.content
+ "(( %SVG.feDistantLight.qname; | %SVG.fePointLight.qname;
+ | %SVG.feSpotLight.qname; ), ( %SVG.animate.qname; | %SVG.set.qname;
+ | %SVG.animateColor.qname; %SVG.feDiffuseLighting.extra.content; )*)"
+>
+<!ELEMENT %SVG.feDiffuseLighting.qname; %SVG.feDiffuseLighting.content; >
+<!-- end of SVG.feDiffuseLighting.element -->]]>
+
+<!ENTITY % SVG.feDiffuseLighting.attlist "INCLUDE" >
+<![%SVG.feDiffuseLighting.attlist;[
+<!ATTLIST %SVG.feDiffuseLighting.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Color.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitiveWithIn.attrib;
+ lighting-color %SVGColor.datatype; #IMPLIED
+ surfaceScale %Number.datatype; #IMPLIED
+ diffuseConstant %Number.datatype; #IMPLIED
+ kernelUnitLength %NumberOptionalNumber.datatype; #IMPLIED
+>
+<!-- end of SVG.feDiffuseLighting.attlist -->]]>
+
+<!-- feDisplacementMap: Filter Effect Displacement Map Element -->
+
+<!ENTITY % SVG.feDisplacementMap.extra.content "" >
+
+<!ENTITY % SVG.feDisplacementMap.element "INCLUDE" >
+<![%SVG.feDisplacementMap.element;[
+<!ENTITY % SVG.feDisplacementMap.content
+ "( %SVG.animate.qname; | %SVG.set.qname;
+ %SVG.feDisplacementMap.extra.content; )*"
+>
+<!ELEMENT %SVG.feDisplacementMap.qname; %SVG.feDisplacementMap.content; >
+<!-- end of SVG.feDisplacementMap.element -->]]>
+
+<!ENTITY % SVG.feDisplacementMap.attlist "INCLUDE" >
+<![%SVG.feDisplacementMap.attlist;[
+<!ATTLIST %SVG.feDisplacementMap.qname;
+ %SVG.Core.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitiveWithIn.attrib;
+ in2 CDATA #REQUIRED
+ scale %Number.datatype; #IMPLIED
+ xChannelSelector ( R | G | B | A ) 'A'
+ yChannelSelector ( R | G | B | A ) 'A'
+>
+<!-- end of SVG.feDisplacementMap.attlist -->]]>
+
+<!-- feFlood: Filter Effect Flood Element .............. -->
+
+<!ENTITY % SVG.feFlood.extra.content "" >
+
+<!ENTITY % SVG.feFlood.element "INCLUDE" >
+<![%SVG.feFlood.element;[
+<!ENTITY % SVG.feFlood.content
+ "( %SVG.animate.qname; | %SVG.set.qname; | %SVG.animateColor.qname;
+ %SVG.feFlood.extra.content; )*"
+>
+<!ELEMENT %SVG.feFlood.qname; %SVG.feFlood.content; >
+<!-- end of SVG.feFlood.element -->]]>
+
+<!ENTITY % SVG.feFlood.attlist "INCLUDE" >
+<![%SVG.feFlood.attlist;[
+<!ATTLIST %SVG.feFlood.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Color.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitiveWithIn.attrib;
+ flood-color %SVGColor.datatype; #IMPLIED
+ flood-opacity %OpacityValue.datatype; #IMPLIED
+>
+<!-- end of SVG.feFlood.attlist -->]]>
+
+<!-- feGaussianBlur: Filter Effect Gaussian Blur Element -->
+
+<!ENTITY % SVG.feGaussianBlur.extra.content "" >
+
+<!ENTITY % SVG.feGaussianBlur.element "INCLUDE" >
+<![%SVG.feGaussianBlur.element;[
+<!ENTITY % SVG.feGaussianBlur.content
+ "( %SVG.animate.qname; | %SVG.set.qname;
+ %SVG.feGaussianBlur.extra.content; )*"
+>
+<!ELEMENT %SVG.feGaussianBlur.qname; %SVG.feGaussianBlur.content; >
+<!-- end of SVG.feGaussianBlur.element -->]]>
+
+<!ENTITY % SVG.feGaussianBlur.attlist "INCLUDE" >
+<![%SVG.feGaussianBlur.attlist;[
+<!ATTLIST %SVG.feGaussianBlur.qname;
+ %SVG.Core.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitiveWithIn.attrib;
+ stdDeviation %NumberOptionalNumber.datatype; #IMPLIED
+>
+<!-- end of SVG.feGaussianBlur.attlist -->]]>
+
+<!-- feImage: Filter Effect Image Element .............. -->
+
+<!ENTITY % SVG.feImage.extra.content "" >
+
+<!ENTITY % SVG.feImage.element "INCLUDE" >
+<![%SVG.feImage.element;[
+<!ENTITY % SVG.feImage.content
+ "( %SVG.animate.qname; | %SVG.set.qname; | %SVG.animateTransform.qname;
+ %SVG.feImage.extra.content; )*"
+>
+<!ELEMENT %SVG.feImage.qname; %SVG.feImage.content; >
+<!-- end of SVG.feImage.element -->]]>
+
+<!ENTITY % SVG.feImage.attlist "INCLUDE" >
+<![%SVG.feImage.attlist;[
+<!ATTLIST %SVG.feImage.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.FilterPrimitive.attrib;
+ %SVG.XLinkEmbed.attrib;
+ %SVG.External.attrib;
+ preserveAspectRatio %PreserveAspectRatioSpec.datatype; 'xMidYMid meet'
+>
+<!-- end of SVG.feImage.attlist -->]]>
+
+<!-- feMerge: Filter Effect Merge Element .............. -->
+
+<!ENTITY % SVG.feMerge.extra.content "" >
+
+<!ENTITY % SVG.feMerge.element "INCLUDE" >
+<![%SVG.feMerge.element;[
+<!ENTITY % SVG.feMerge.content
+ "( %SVG.feMergeNode.qname; %SVG.feMerge.extra.content; )*"
+>
+<!ELEMENT %SVG.feMerge.qname; %SVG.feMerge.content; >
+<!-- end of SVG.feMerge.element -->]]>
+
+<!ENTITY % SVG.feMerge.attlist "INCLUDE" >
+<![%SVG.feMerge.attlist;[
+<!ATTLIST %SVG.feMerge.qname;
+ %SVG.Core.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitive.attrib;
+>
+<!-- end of SVG.feMerge.attlist -->]]>
+
+<!-- feMergeNode: Filter Effect Merge Node Element ..... -->
+
+<!ENTITY % SVG.feMergeNode.extra.content "" >
+
+<!ENTITY % SVG.feMergeNode.element "INCLUDE" >
+<![%SVG.feMergeNode.element;[
+<!ENTITY % SVG.feMergeNode.content
+ "( %SVG.animate.qname; | %SVG.set.qname; %SVG.feMergeNode.extra.content; )*"
+>
+<!ELEMENT %SVG.feMergeNode.qname; %SVG.feMergeNode.content; >
+<!-- end of SVG.feMergeNode.element -->]]>
+
+<!ENTITY % SVG.feMergeNode.attlist "INCLUDE" >
+<![%SVG.feMergeNode.attlist;[
+<!ATTLIST %SVG.feMergeNode.qname;
+ %SVG.Core.attrib;
+ in CDATA #IMPLIED
+>
+<!-- end of SVG.feMergeNode.attlist -->]]>
+
+<!-- feMorphology: Filter Effect Morphology Element .... -->
+
+<!ENTITY % SVG.feMorphology.extra.content "" >
+
+<!ENTITY % SVG.feMorphology.element "INCLUDE" >
+<![%SVG.feMorphology.element;[
+<!ENTITY % SVG.feMorphology.content
+ "( %SVG.animate.qname; | %SVG.set.qname;
+ %SVG.feMorphology.extra.content; )*"
+>
+<!ELEMENT %SVG.feMorphology.qname; %SVG.feMorphology.content; >
+<!-- end of SVG.feMorphology.element -->]]>
+
+<!ENTITY % SVG.feMorphology.attlist "INCLUDE" >
+<![%SVG.feMorphology.attlist;[
+<!ATTLIST %SVG.feMorphology.qname;
+ %SVG.Core.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitiveWithIn.attrib;
+ operator ( erode | dilate ) 'erode'
+ radius %NumberOptionalNumber.datatype; #IMPLIED
+>
+<!-- end of SVG.feMorphology.attlist -->]]>
+
+<!-- feOffset: Filter Effect Offset Element ............ -->
+
+<!ENTITY % SVG.feOffset.extra.content "" >
+
+<!ENTITY % SVG.feOffset.element "INCLUDE" >
+<![%SVG.feOffset.element;[
+<!ENTITY % SVG.feOffset.content
+ "( %SVG.animate.qname; | %SVG.set.qname; %SVG.feOffset.extra.content; )*"
+>
+<!ELEMENT %SVG.feOffset.qname; %SVG.feOffset.content; >
+<!-- end of SVG.feOffset.element -->]]>
+
+<!ENTITY % SVG.feOffset.attlist "INCLUDE" >
+<![%SVG.feOffset.attlist;[
+<!ATTLIST %SVG.feOffset.qname;
+ %SVG.Core.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitiveWithIn.attrib;
+ dx %Number.datatype; #IMPLIED
+ dy %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.feOffset.attlist -->]]>
+
+<!-- feSpecularLighting: Filter Effect Specular Lighting Element -->
+
+<!ENTITY % SVG.feSpecularLighting.extra.content "" >
+
+<!ENTITY % SVG.feSpecularLighting.element "INCLUDE" >
+<![%SVG.feSpecularLighting.element;[
+<!ENTITY % SVG.feSpecularLighting.content
+ "(( %SVG.feDistantLight.qname; | %SVG.fePointLight.qname;
+ | %SVG.feSpotLight.qname; ), ( %SVG.animate.qname; | %SVG.set.qname;
+ | %SVG.animateColor.qname; %SVG.feSpecularLighting.extra.content; )*)"
+>
+<!ELEMENT %SVG.feSpecularLighting.qname; %SVG.feSpecularLighting.content; >
+<!-- end of SVG.feSpecularLighting.element -->]]>
+
+<!ENTITY % SVG.feSpecularLighting.attlist "INCLUDE" >
+<![%SVG.feSpecularLighting.attlist;[
+<!ATTLIST %SVG.feSpecularLighting.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Color.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitiveWithIn.attrib;
+ lighting-color %SVGColor.datatype; #IMPLIED
+ surfaceScale %Number.datatype; #IMPLIED
+ specularConstant %Number.datatype; #IMPLIED
+ specularExponent %Number.datatype; #IMPLIED
+ kernelUnitLength %NumberOptionalNumber.datatype; #IMPLIED
+>
+<!-- end of SVG.feSpecularLighting.attlist -->]]>
+
+<!-- feTile: Filter Effect Tile Element ................ -->
+
+<!ENTITY % SVG.feTile.extra.content "" >
+
+<!ENTITY % SVG.feTile.element "INCLUDE" >
+<![%SVG.feTile.element;[
+<!ENTITY % SVG.feTile.content
+ "( %SVG.animate.qname; | %SVG.set.qname; %SVG.feTile.extra.content; )*"
+>
+<!ELEMENT %SVG.feTile.qname; %SVG.feTile.content; >
+<!-- end of SVG.feTile.element -->]]>
+
+<!ENTITY % SVG.feTile.attlist "INCLUDE" >
+<![%SVG.feTile.attlist;[
+<!ATTLIST %SVG.feTile.qname;
+ %SVG.Core.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitiveWithIn.attrib;
+>
+<!-- end of SVG.feTile.attlist -->]]>
+
+<!-- feTurbulence: Filter Effect Turbulence Element .... -->
+
+<!ENTITY % SVG.feTurbulence.extra.content "" >
+
+<!ENTITY % SVG.feTurbulence.element "INCLUDE" >
+<![%SVG.feTurbulence.element;[
+<!ENTITY % SVG.feTurbulence.content
+ "( %SVG.animate.qname; | %SVG.set.qname;
+ %SVG.feTurbulence.extra.content; )*"
+>
+<!ELEMENT %SVG.feTurbulence.qname; %SVG.feTurbulence.content; >
+<!-- end of SVG.feTurbulence.element -->]]>
+
+<!ENTITY % SVG.feTurbulence.attlist "INCLUDE" >
+<![%SVG.feTurbulence.attlist;[
+<!ATTLIST %SVG.feTurbulence.qname;
+ %SVG.Core.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitive.attrib;
+ baseFrequency %NumberOptionalNumber.datatype; #IMPLIED
+ numOctaves %Integer.datatype; #IMPLIED
+ seed %Number.datatype; #IMPLIED
+ stitchTiles ( stitch | noStitch ) 'noStitch'
+ type ( fractalNoise | turbulence ) 'turbulence'
+>
+<!-- end of SVG.feTurbulence.attlist -->]]>
+
+<!-- feDistantLight: Filter Effect Distant Light Element -->
+
+<!ENTITY % SVG.feDistantLight.extra.content "" >
+
+<!ENTITY % SVG.feDistantLight.element "INCLUDE" >
+<![%SVG.feDistantLight.element;[
+<!ENTITY % SVG.feDistantLight.content
+ "( %SVG.animate.qname; | %SVG.set.qname;
+ %SVG.feDistantLight.extra.content; )*"
+>
+<!ELEMENT %SVG.feDistantLight.qname; %SVG.feDistantLight.content; >
+<!-- end of SVG.feDistantLight.element -->]]>
+
+<!ENTITY % SVG.feDistantLight.attlist "INCLUDE" >
+<![%SVG.feDistantLight.attlist;[
+<!ATTLIST %SVG.feDistantLight.qname;
+ %SVG.Core.attrib;
+ azimuth %Number.datatype; #IMPLIED
+ elevation %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.feDistantLight.attlist -->]]>
+
+<!-- fePointLight: Filter Effect Point Light Element ... -->
+
+<!ENTITY % SVG.fePointLight.extra.content "" >
+
+<!ENTITY % SVG.fePointLight.element "INCLUDE" >
+<![%SVG.fePointLight.element;[
+<!ENTITY % SVG.fePointLight.content
+ "( %SVG.animate.qname; | %SVG.set.qname;
+ %SVG.fePointLight.extra.content; )*"
+>
+<!ELEMENT %SVG.fePointLight.qname; %SVG.fePointLight.content; >
+<!-- end of SVG.fePointLight.element -->]]>
+
+<!ENTITY % SVG.fePointLight.attlist "INCLUDE" >
+<![%SVG.fePointLight.attlist;[
+<!ATTLIST %SVG.fePointLight.qname;
+ %SVG.Core.attrib;
+ x %Number.datatype; #IMPLIED
+ y %Number.datatype; #IMPLIED
+ z %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.fePointLight.attlist -->]]>
+
+<!-- feSpotLight: Filter Effect Spot Light Element ..... -->
+
+<!ENTITY % SVG.feSpotLight.extra.content "" >
+
+<!ENTITY % SVG.feSpotLight.element "INCLUDE" >
+<![%SVG.feSpotLight.element;[
+<!ENTITY % SVG.feSpotLight.content
+ "( %SVG.animate.qname; | %SVG.set.qname; %SVG.feSpotLight.extra.content; )*"
+>
+<!ELEMENT %SVG.feSpotLight.qname; %SVG.feSpotLight.content; >
+<!-- end of SVG.feSpotLight.element -->]]>
+
+<!ENTITY % SVG.feSpotLight.attlist "INCLUDE" >
+<![%SVG.feSpotLight.attlist;[
+<!ATTLIST %SVG.feSpotLight.qname;
+ %SVG.Core.attrib;
+ x %Number.datatype; #IMPLIED
+ y %Number.datatype; #IMPLIED
+ z %Number.datatype; #IMPLIED
+ pointsAtX %Number.datatype; #IMPLIED
+ pointsAtY %Number.datatype; #IMPLIED
+ pointsAtZ %Number.datatype; #IMPLIED
+ specularExponent %Number.datatype; #IMPLIED
+ limitingConeAngle %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.feSpotLight.attlist -->]]>
+
+<!-- feFuncR: Filter Effect Function Red Element ....... -->
+
+<!ENTITY % SVG.feFuncR.extra.content "" >
+
+<!ENTITY % SVG.feFuncR.element "INCLUDE" >
+<![%SVG.feFuncR.element;[
+<!ENTITY % SVG.feFuncR.content
+ "( %SVG.animate.qname; | %SVG.set.qname; %SVG.feFuncR.extra.content; )*"
+>
+<!ELEMENT %SVG.feFuncR.qname; %SVG.feFuncR.content; >
+<!-- end of SVG.feFuncR.element -->]]>
+
+<!ENTITY % SVG.feFuncR.attlist "INCLUDE" >
+<![%SVG.feFuncR.attlist;[
+<!ATTLIST %SVG.feFuncR.qname;
+ %SVG.Core.attrib;
+ type ( identity | table | discrete | linear | gamma ) #REQUIRED
+ tableValues CDATA #IMPLIED
+ slope %Number.datatype; #IMPLIED
+ intercept %Number.datatype; #IMPLIED
+ amplitude %Number.datatype; #IMPLIED
+ exponent %Number.datatype; #IMPLIED
+ offset %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.feFuncR.attlist -->]]>
+
+<!-- feFuncG: Filter Effect Function Green Element ..... -->
+
+<!ENTITY % SVG.feFuncG.extra.content "" >
+
+<!ENTITY % SVG.feFuncG.element "INCLUDE" >
+<![%SVG.feFuncG.element;[
+<!ENTITY % SVG.feFuncG.content
+ "( %SVG.animate.qname; | %SVG.set.qname; %SVG.feFuncG.extra.content; )*"
+>
+<!ELEMENT %SVG.feFuncG.qname; %SVG.feFuncG.content; >
+<!-- end of SVG.feFuncG.element -->]]>
+
+<!ENTITY % SVG.feFuncG.attlist "INCLUDE" >
+<![%SVG.feFuncG.attlist;[
+<!ATTLIST %SVG.feFuncG.qname;
+ %SVG.Core.attrib;
+ type ( identity | table | discrete | linear | gamma ) #REQUIRED
+ tableValues CDATA #IMPLIED
+ slope %Number.datatype; #IMPLIED
+ intercept %Number.datatype; #IMPLIED
+ amplitude %Number.datatype; #IMPLIED
+ exponent %Number.datatype; #IMPLIED
+ offset %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.feFuncG.attlist -->]]>
+
+<!-- feFuncB: Filter Effect Function Blue Element ...... -->
+
+<!ENTITY % SVG.feFuncB.extra.content "" >
+
+<!ENTITY % SVG.feFuncB.element "INCLUDE" >
+<![%SVG.feFuncB.element;[
+<!ENTITY % SVG.feFuncB.content
+ "( %SVG.animate.qname; | %SVG.set.qname; %SVG.feFuncB.extra.content; )*"
+>
+<!ELEMENT %SVG.feFuncB.qname; %SVG.feFuncB.content; >
+<!-- end of SVG.feFuncB.element -->]]>
+
+<!ENTITY % SVG.feFuncB.attlist "INCLUDE" >
+<![%SVG.feFuncB.attlist;[
+<!ATTLIST %SVG.feFuncB.qname;
+ %SVG.Core.attrib;
+ type ( identity | table | discrete | linear | gamma ) #REQUIRED
+ tableValues CDATA #IMPLIED
+ slope %Number.datatype; #IMPLIED
+ intercept %Number.datatype; #IMPLIED
+ amplitude %Number.datatype; #IMPLIED
+ exponent %Number.datatype; #IMPLIED
+ offset %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.feFuncB.attlist -->]]>
+
+<!-- feFuncA: Filter Effect Function Alpha Element ..... -->
+
+<!ENTITY % SVG.feFuncA.extra.content "" >
+
+<!ENTITY % SVG.feFuncA.element "INCLUDE" >
+<![%SVG.feFuncA.element;[
+<!ENTITY % SVG.feFuncA.content
+ "( %SVG.animate.qname; | %SVG.set.qname; %SVG.feFuncA.extra.content; )*"
+>
+<!ELEMENT %SVG.feFuncA.qname; %SVG.feFuncA.content; >
+<!-- end of SVG.feFuncA.element -->]]>
+
+<!ENTITY % SVG.feFuncA.attlist "INCLUDE" >
+<![%SVG.feFuncA.attlist;[
+<!ATTLIST %SVG.feFuncA.qname;
+ %SVG.Core.attrib;
+ type ( identity | table | discrete | linear | gamma ) #REQUIRED
+ tableValues CDATA #IMPLIED
+ slope %Number.datatype; #IMPLIED
+ intercept %Number.datatype; #IMPLIED
+ amplitude %Number.datatype; #IMPLIED
+ exponent %Number.datatype; #IMPLIED
+ offset %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.feFuncA.attlist -->]]>
+
+<!-- end of svg-filter.mod -->
+]]>
+
+<!-- Cursor Module ............................................... -->
+<!ENTITY % svg-cursor.module "INCLUDE" >
+<![%svg-cursor.module;[
+<!ENTITY % svg-cursor.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Cursor//EN"
+ "svg-cursor.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Cursor Module ................................................. -->
+<!-- file: svg-cursor.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Cursor//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-cursor.mod"
+
+ ....................................................................... -->
+
+<!-- Cursor
+
+ cursor
+
+ This module declares markup to provide support for cursor.
+-->
+
+<!-- 'cursor' property/attribute value (e.g., 'crosshair', <uri>) -->
+<!ENTITY % CursorValue.datatype "CDATA" >
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.cursor.qname "cursor" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Conditional.attrib "" >
+<!ENTITY % SVG.XLinkRequired.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Cursor.class .................................. -->
+
+<!ENTITY % SVG.Cursor.extra.class "" >
+
+<!ENTITY % SVG.Cursor.class
+ "| %SVG.cursor.qname; %SVG.Cursor.extra.class;"
+>
+
+<!-- SVG.Cursor.attrib ................................. -->
+
+<!ENTITY % SVG.Cursor.extra.attrib "" >
+
+<!ENTITY % SVG.Cursor.attrib
+ "cursor %CursorValue.datatype; #IMPLIED
+ %SVG.Cursor.extra.attrib;"
+>
+
+<!-- cursor: Cursor Element ............................ -->
+
+<!ENTITY % SVG.cursor.extra.content "" >
+
+<!ENTITY % SVG.cursor.element "INCLUDE" >
+<![%SVG.cursor.element;[
+<!ENTITY % SVG.cursor.content
+ "( %SVG.Description.class; %SVG.cursor.extra.content; )*"
+>
+<!ELEMENT %SVG.cursor.qname; %SVG.cursor.content; >
+<!-- end of SVG.cursor.element -->]]>
+
+<!ENTITY % SVG.cursor.attlist "INCLUDE" >
+<![%SVG.cursor.attlist;[
+<!ATTLIST %SVG.cursor.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.XLinkRequired.attrib;
+ %SVG.External.attrib;
+ x %Coordinate.datatype; #IMPLIED
+ y %Coordinate.datatype; #IMPLIED
+>
+<!-- end of SVG.cursor.attlist -->]]>
+
+<!-- end of svg-cursor.mod -->
+]]>
+
+<!-- Hyperlinking Module ......................................... -->
+<!ENTITY % svg-hyperlink.module "INCLUDE" >
+<![%svg-hyperlink.module;[
+<!ENTITY % svg-hyperlink.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Hyperlinking//EN"
+ "svg-hyperlink.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Hyperlinking Module ........................................... -->
+<!-- file: svg-hyperlink.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Hyperlinking//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-hyperlink.mod"
+
+ ....................................................................... -->
+
+<!-- Hyperlinking
+
+ a
+
+ This module declares markup to provide support for hyper linking.
+-->
+
+<!-- link to this target -->
+<!ENTITY % LinkTarget.datatype "NMTOKEN" >
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.a.qname "a" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Conditional.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Viewport.attrib "" >
+<!ENTITY % SVG.Text.attrib "" >
+<!ENTITY % SVG.TextContent.attrib "" >
+<!ENTITY % SVG.Font.attrib "" >
+<!ENTITY % SVG.Paint.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Marker.attrib "" >
+<!ENTITY % SVG.Gradient.attrib "" >
+<!ENTITY % SVG.Clip.attrib "" >
+<!ENTITY % SVG.Mask.attrib "" >
+<!ENTITY % SVG.Filter.attrib "" >
+<!ENTITY % SVG.FilterColor.attrib "" >
+<!ENTITY % SVG.GraphicalEvents.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.XLinkReplace.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Hyperlink.class ............................... -->
+
+<!ENTITY % SVG.Hyperlink.extra.class "" >
+
+<!ENTITY % SVG.Hyperlink.class
+ "| %SVG.a.qname; %SVG.Hyperlink.extra.class;"
+>
+
+<!-- SVG.Presentation.attrib ........................... -->
+
+<!ENTITY % SVG.Presentation.extra.attrib "" >
+
+<!ENTITY % SVG.Presentation.attrib
+ "%SVG.Container.attrib;
+ %SVG.Viewport.attrib;
+ %SVG.Text.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Profile.attrib;
+ %SVG.Gradient.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.Cursor.attrib;
+ flood-color %SVGColor.datatype; #IMPLIED
+ flood-opacity %OpacityValue.datatype; #IMPLIED
+ lighting-color %SVGColor.datatype; #IMPLIED
+ %SVG.Presentation.extra.attrib;"
+>
+
+<!-- a: Anchor Element ................................. -->
+
+<!ENTITY % SVG.a.extra.content "" >
+
+<!ENTITY % SVG.a.element "INCLUDE" >
+<![%SVG.a.element;[
+<!ENTITY % SVG.a.content
+ "( #PCDATA | %SVG.Description.class; | %SVG.Animation.class;
+ %SVG.Structure.class; %SVG.Conditional.class; %SVG.Image.class;
+ %SVG.Style.class; %SVG.Shape.class; %SVG.Text.class; %SVG.Marker.class;
+ %SVG.Profile.class; %SVG.Gradient.class; %SVG.Pattern.class;
+ %SVG.Clip.class; %SVG.Mask.class; %SVG.Filter.class; %SVG.Cursor.class;
+ %SVG.Hyperlink.class; %SVG.View.class; %SVG.Script.class;
+ %SVG.Font.class; %SVG.a.extra.content; )*"
+>
+<!ELEMENT %SVG.a.qname; %SVG.a.content; >
+<!-- end of SVG.a.element -->]]>
+
+<!ENTITY % SVG.a.attlist "INCLUDE" >
+<![%SVG.a.attlist;[
+<!ATTLIST %SVG.a.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.XLinkReplace.attrib;
+ %SVG.External.attrib;
+ transform %TransformList.datatype; #IMPLIED
+ target %LinkTarget.datatype; #IMPLIED
+>
+<!-- end of SVG.a.attlist -->]]>
+
+<!-- end of svg-hyperlink.mod -->
+]]>
+
+<!-- View Module ................................................. -->
+<!ENTITY % svg-view.module "INCLUDE" >
+<![%svg-view.module;[
+<!ENTITY % svg-view.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 View//EN"
+ "svg-view.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 View Module ................................................... -->
+<!-- file: svg-view.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 View//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-view.mod"
+
+ ....................................................................... -->
+
+<!-- View
+
+ view
+
+ This module declares markup to provide support for view.
+-->
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.view.qname "view" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.View.class .................................... -->
+
+<!ENTITY % SVG.View.extra.class "" >
+
+<!ENTITY % SVG.View.class
+ "| %SVG.view.qname; %SVG.View.extra.class;"
+>
+
+<!-- view: View Element ................................ -->
+
+<!ENTITY % SVG.view.extra.content "" >
+
+<!ENTITY % SVG.view.element "INCLUDE" >
+<![%SVG.view.element;[
+<!ENTITY % SVG.view.content
+ "( %SVG.Description.class; %SVG.view.extra.content; )*"
+>
+<!ELEMENT %SVG.view.qname; %SVG.view.content; >
+<!-- end of SVG.view.element -->]]>
+
+<!ENTITY % SVG.view.attlist "INCLUDE" >
+<![%SVG.view.attlist;[
+<!ATTLIST %SVG.view.qname;
+ %SVG.Core.attrib;
+ %SVG.External.attrib;
+ viewBox %ViewBoxSpec.datatype; #IMPLIED
+ preserveAspectRatio %PreserveAspectRatioSpec.datatype; 'xMidYMid meet'
+ zoomAndPan ( disable | magnify ) 'magnify'
+ viewTarget CDATA #IMPLIED
+>
+<!-- end of SVG.view.attlist -->]]>
+
+<!-- end of svg-view.mod -->
+]]>
+
+<!-- Scripting Module ............................................ -->
+<!ENTITY % svg-script.module "INCLUDE" >
+<![%svg-script.module;[
+<!ENTITY % svg-script.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Scripting//EN"
+ "svg-script.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Scripting Module .............................................. -->
+<!-- file: svg-script.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Scripting//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-script.mod"
+
+ ....................................................................... -->
+
+<!-- Scripting
+
+ script
+
+ This module declares markup to provide support for scripting.
+-->
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.script.qname "script" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.XLink.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Script.class .................................. -->
+
+<!ENTITY % SVG.Script.extra.class "" >
+
+<!ENTITY % SVG.Script.class
+ "| %SVG.script.qname; %SVG.Script.extra.class;"
+>
+
+<!-- script: Script Element ............................ -->
+
+<!ENTITY % SVG.script.extra.content "" >
+
+<!ENTITY % SVG.script.element "INCLUDE" >
+<![%SVG.script.element;[
+<!ENTITY % SVG.script.content
+ "( #PCDATA %SVG.script.extra.content; )*"
+>
+<!ELEMENT %SVG.script.qname; %SVG.script.content; >
+<!-- end of SVG.script.element -->]]>
+
+<!ENTITY % SVG.script.attlist "INCLUDE" >
+<![%SVG.script.attlist;[
+<!ATTLIST %SVG.script.qname;
+ %SVG.Core.attrib;
+ %SVG.XLink.attrib;
+ %SVG.External.attrib;
+ type %ContentType.datatype; #REQUIRED
+>
+<!-- end of SVG.script.attlist -->]]>
+
+<!-- end of svg-script.mod -->
+]]>
+
+<!-- Animation Module ............................................ -->
+<!ENTITY % svg-animation.module "INCLUDE" >
+<![%svg-animation.module;[
+<!ENTITY % svg-animation.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Animation//EN"
+ "svg-animation.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Animation Module .............................................. -->
+<!-- file: svg-animation.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Animation//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-animation.mod"
+
+ ....................................................................... -->
+
+<!-- Animation
+
+ animate, set, animateMotion, animateColor, animateTransform, mpath
+
+ This module declares markup to provide support for animation.
+-->
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.animate.qname "animate" >
+<!ENTITY % SVG.set.qname "set" >
+<!ENTITY % SVG.animateMotion.qname "animateMotion" >
+<!ENTITY % SVG.animateColor.qname "animateColor" >
+<!ENTITY % SVG.animateTransform.qname "animateTransform" >
+<!ENTITY % SVG.mpath.qname "mpath" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Conditional.attrib "" >
+<!ENTITY % SVG.AnimationEvents.attrib "" >
+<!ENTITY % SVG.XLink.attrib "" >
+<!ENTITY % SVG.XLinkRequired.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Animation.class ............................... -->
+
+<!ENTITY % SVG.Animation.extra.class "" >
+
+<!ENTITY % SVG.Animation.class
+ "%SVG.animate.qname; | %SVG.set.qname; | %SVG.animateMotion.qname; |
+ %SVG.animateColor.qname; | %SVG.animateTransform.qname;
+ %SVG.Animation.extra.class;"
+>
+
+<!-- SVG.Animation.attrib .............................. -->
+
+<!ENTITY % SVG.Animation.extra.attrib "" >
+
+<!ENTITY % SVG.Animation.attrib
+ "%SVG.XLink.attrib;
+ %SVG.Animation.extra.attrib;"
+>
+
+<!-- SVG.AnimationAttribute.attrib ..................... -->
+
+<!ENTITY % SVG.AnimationAttribute.extra.attrib "" >
+
+<!ENTITY % SVG.AnimationAttribute.attrib
+ "attributeName CDATA #REQUIRED
+ attributeType CDATA #IMPLIED
+ %SVG.AnimationAttribute.extra.attrib;"
+>
+
+<!-- SVG.AnimationTiming.attrib ........................ -->
+
+<!ENTITY % SVG.AnimationTiming.extra.attrib "" >
+
+<!ENTITY % SVG.AnimationTiming.attrib
+ "begin CDATA #IMPLIED
+ dur CDATA #IMPLIED
+ end CDATA #IMPLIED
+ min CDATA #IMPLIED
+ max CDATA #IMPLIED
+ restart ( always | never | whenNotActive ) 'always'
+ repeatCount CDATA #IMPLIED
+ repeatDur CDATA #IMPLIED
+ fill ( remove | freeze ) 'remove'
+ %SVG.AnimationTiming.extra.attrib;"
+>
+
+<!-- SVG.AnimationValue.attrib ......................... -->
+
+<!ENTITY % SVG.AnimationValue.extra.attrib "" >
+
+<!ENTITY % SVG.AnimationValue.attrib
+ "calcMode ( discrete | linear | paced | spline ) 'linear'
+ values CDATA #IMPLIED
+ keyTimes CDATA #IMPLIED
+ keySplines CDATA #IMPLIED
+ from CDATA #IMPLIED
+ to CDATA #IMPLIED
+ by CDATA #IMPLIED
+ %SVG.AnimationValue.extra.attrib;"
+>
+
+<!-- SVG.AnimationAddtion.attrib ....................... -->
+
+<!ENTITY % SVG.AnimationAddtion.extra.attrib "" >
+
+<!ENTITY % SVG.AnimationAddtion.attrib
+ "additive ( replace | sum ) 'replace'
+ accumulate ( none | sum ) 'none'
+ %SVG.AnimationAddtion.extra.attrib;"
+>
+
+<!-- animate: Animate Element .......................... -->
+
+<!ENTITY % SVG.animate.extra.content "" >
+
+<!ENTITY % SVG.animate.element "INCLUDE" >
+<![%SVG.animate.element;[
+<!ENTITY % SVG.animate.content
+ "( %SVG.Description.class; %SVG.animate.extra.content; )*"
+>
+<!ELEMENT %SVG.animate.qname; %SVG.animate.content; >
+<!-- end of SVG.animate.element -->]]>
+
+<!ENTITY % SVG.animate.attlist "INCLUDE" >
+<![%SVG.animate.attlist;[
+<!ATTLIST %SVG.animate.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.AnimationEvents.attrib;
+ %SVG.External.attrib;
+ %SVG.Animation.attrib;
+ %SVG.AnimationAttribute.attrib;
+ %SVG.AnimationTiming.attrib;
+ %SVG.AnimationValue.attrib;
+ %SVG.AnimationAddtion.attrib;
+>
+<!-- end of SVG.animate.attlist -->]]>
+
+<!-- set: Set Element .................................. -->
+
+<!ENTITY % SVG.set.extra.content "" >
+
+<!ENTITY % SVG.set.element "INCLUDE" >
+<![%SVG.set.element;[
+<!ENTITY % SVG.set.content
+ "( %SVG.Description.class; %SVG.set.extra.content; )*"
+>
+<!ELEMENT %SVG.set.qname; %SVG.set.content; >
+<!-- end of SVG.set.element -->]]>
+
+<!ENTITY % SVG.set.attlist "INCLUDE" >
+<![%SVG.set.attlist;[
+<!ATTLIST %SVG.set.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.AnimationEvents.attrib;
+ %SVG.External.attrib;
+ %SVG.Animation.attrib;
+ %SVG.AnimationAttribute.attrib;
+ %SVG.AnimationTiming.attrib;
+ to CDATA #IMPLIED
+>
+<!-- end of SVG.set.attlist -->]]>
+
+<!-- animateMotion: Animate Motion Element ............. -->
+
+<!ENTITY % SVG.animateMotion.extra.content "" >
+
+<!ENTITY % SVG.animateMotion.element "INCLUDE" >
+<![%SVG.animateMotion.element;[
+<!ENTITY % SVG.animateMotion.content
+ "(( %SVG.Description.class; )*, %SVG.mpath.qname;?
+ %SVG.animateMotion.extra.content; )"
+>
+<!ELEMENT %SVG.animateMotion.qname; %SVG.animateMotion.content; >
+<!-- end of SVG.animateMotion.element -->]]>
+
+<!ENTITY % SVG.animateMotion.attlist "INCLUDE" >
+<![%SVG.animateMotion.attlist;[
+<!ATTLIST %SVG.animateMotion.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.AnimationEvents.attrib;
+ %SVG.External.attrib;
+ %SVG.Animation.attrib;
+ %SVG.AnimationTiming.attrib;
+ %SVG.AnimationAddtion.attrib;
+ calcMode ( discrete | linear | paced | spline ) 'paced'
+ values CDATA #IMPLIED
+ keyTimes CDATA #IMPLIED
+ keySplines CDATA #IMPLIED
+ from CDATA #IMPLIED
+ to CDATA #IMPLIED
+ by CDATA #IMPLIED
+ path CDATA #IMPLIED
+ keyPoints CDATA #IMPLIED
+ rotate CDATA #IMPLIED
+ origin CDATA #IMPLIED
+>
+<!-- end of SVG.animateMotion.attlist -->]]>
+
+<!-- animateColor: Animate Color Element ............... -->
+
+<!ENTITY % SVG.animateColor.extra.content "" >
+
+<!ENTITY % SVG.animateColor.element "INCLUDE" >
+<![%SVG.animateColor.element;[
+<!ENTITY % SVG.animateColor.content
+ "( %SVG.Description.class; %SVG.animateColor.extra.content; )*"
+>
+<!ELEMENT %SVG.animateColor.qname; %SVG.animateColor.content; >
+<!-- end of SVG.animateColor.element -->]]>
+
+<!ENTITY % SVG.animateColor.attlist "INCLUDE" >
+<![%SVG.animateColor.attlist;[
+<!ATTLIST %SVG.animateColor.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.AnimationEvents.attrib;
+ %SVG.External.attrib;
+ %SVG.Animation.attrib;
+ %SVG.AnimationAttribute.attrib;
+ %SVG.AnimationTiming.attrib;
+ %SVG.AnimationValue.attrib;
+ %SVG.AnimationAddtion.attrib;
+>
+<!-- end of SVG.animateColor.attlist -->]]>
+
+<!-- animateTransform: Animate Transform Element ....... -->
+
+<!ENTITY % SVG.animateTransform.extra.content "" >
+
+<!ENTITY % SVG.animateTransform.element "INCLUDE" >
+<![%SVG.animateTransform.element;[
+<!ENTITY % SVG.animateTransform.content
+ "( %SVG.Description.class; %SVG.animateTransform.extra.content; )*"
+>
+<!ELEMENT %SVG.animateTransform.qname; %SVG.animateTransform.content; >
+<!-- end of SVG.animateTransform.element -->]]>
+
+<!ENTITY % SVG.animateTransform.attlist "INCLUDE" >
+<![%SVG.animateTransform.attlist;[
+<!ATTLIST %SVG.animateTransform.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.AnimationEvents.attrib;
+ %SVG.External.attrib;
+ %SVG.Animation.attrib;
+ %SVG.AnimationAttribute.attrib;
+ %SVG.AnimationTiming.attrib;
+ %SVG.AnimationValue.attrib;
+ %SVG.AnimationAddtion.attrib;
+ type ( translate | scale | rotate | skewX | skewY ) 'translate'
+>
+<!-- end of SVG.animateTransform.attlist -->]]>
+
+<!-- mpath: Motion Path Element ........................ -->
+
+<!ENTITY % SVG.mpath.extra.content "" >
+
+<!ENTITY % SVG.mpath.element "INCLUDE" >
+<![%SVG.mpath.element;[
+<!ENTITY % SVG.mpath.content
+ "( %SVG.Description.class; %SVG.mpath.extra.content; )*"
+>
+<!ELEMENT %SVG.mpath.qname; %SVG.mpath.content; >
+<!-- end of SVG.mpath.element -->]]>
+
+<!ENTITY % SVG.mpath.attlist "INCLUDE" >
+<![%SVG.mpath.attlist;[
+<!ATTLIST %SVG.mpath.qname;
+ %SVG.Core.attrib;
+ %SVG.XLinkRequired.attrib;
+ %SVG.External.attrib;
+>
+<!-- end of SVG.mpath.attlist -->]]>
+
+<!-- end of svg-animation.mod -->
+]]>
+
+<!-- Font Module ................................................. -->
+<!ENTITY % svg-font.module "INCLUDE" >
+<![%svg-font.module;[
+<!ENTITY % svg-font.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Font//EN"
+ "svg-font.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Font Module ................................................... -->
+<!-- file: svg-font.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Font//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-font.mod"
+
+ ....................................................................... -->
+
+<!-- Font
+
+ font, font-face, glyph, missing-glyph, hkern, vkern, font-face-src,
+ font-face-uri, font-face-format, font-face-name, definition-src
+
+ This module declares markup to provide support for template.
+-->
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.font.qname "font" >
+<!ENTITY % SVG.font-face.qname "font-face" >
+<!ENTITY % SVG.glyph.qname "glyph" >
+<!ENTITY % SVG.missing-glyph.qname "missing-glyph" >
+<!ENTITY % SVG.hkern.qname "hkern" >
+<!ENTITY % SVG.vkern.qname "vkern" >
+<!ENTITY % SVG.font-face-src.qname "font-face-src" >
+<!ENTITY % SVG.font-face-uri.qname "font-face-uri" >
+<!ENTITY % SVG.font-face-format.qname "font-face-format" >
+<!ENTITY % SVG.font-face-name.qname "font-face-name" >
+<!ENTITY % SVG.definition-src.qname "definition-src" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Container.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Viewport.attrib "" >
+<!ENTITY % SVG.Text.attrib "" >
+<!ENTITY % SVG.TextContent.attrib "" >
+<!ENTITY % SVG.Font.attrib "" >
+<!ENTITY % SVG.Paint.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Marker.attrib "" >
+<!ENTITY % SVG.Profile.attrib "" >
+<!ENTITY % SVG.Gradient.attrib "" >
+<!ENTITY % SVG.Clip.attrib "" >
+<!ENTITY % SVG.Mask.attrib "" >
+<!ENTITY % SVG.Filter.attrib "" >
+<!ENTITY % SVG.FilterColor.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.XLinkRequired.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Font.class .................................... -->
+
+<!ENTITY % SVG.Font.extra.class "" >
+
+<!ENTITY % SVG.Font.class
+ "| %SVG.font.qname; | %SVG.font-face.qname; %SVG.Font.extra.class;"
+>
+
+<!-- SVG.Presentation.attrib ........................... -->
+
+<!ENTITY % SVG.Presentation.extra.attrib "" >
+
+<!ENTITY % SVG.Presentation.attrib
+ "%SVG.Container.attrib;
+ %SVG.Viewport.attrib;
+ %SVG.Text.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Profile.attrib;
+ %SVG.Gradient.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.Cursor.attrib;
+ flood-color %SVGColor.datatype; #IMPLIED
+ flood-opacity %OpacityValue.datatype; #IMPLIED
+ lighting-color %SVGColor.datatype; #IMPLIED
+ %SVG.Presentation.extra.attrib;"
+>
+
+<!-- font: Font Element ................................ -->
+
+<!ENTITY % SVG.font.extra.content "" >
+
+<!ENTITY % SVG.font.element "INCLUDE" >
+<![%SVG.font.element;[
+<!ENTITY % SVG.font.content
+ "(( %SVG.Description.class; )*, %SVG.font-face.qname;,
+ %SVG.missing-glyph.qname;, ( %SVG.glyph.qname; | %SVG.hkern.qname;
+ | %SVG.vkern.qname; %SVG.font.extra.content; )*)"
+>
+<!ELEMENT %SVG.font.qname; %SVG.font.content; >
+<!-- end of SVG.font.element -->]]>
+
+<!ENTITY % SVG.font.attlist "INCLUDE" >
+<![%SVG.font.attlist;[
+<!ATTLIST %SVG.font.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.External.attrib;
+ horiz-origin-x %Number.datatype; #IMPLIED
+ horiz-origin-y %Number.datatype; #IMPLIED
+ horiz-adv-x %Number.datatype; #REQUIRED
+ vert-origin-x %Number.datatype; #IMPLIED
+ vert-origin-y %Number.datatype; #IMPLIED
+ vert-adv-y %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.font.attlist -->]]>
+
+<!-- font-face: Font Face Element ...................... -->
+
+<!ENTITY % SVG.font-face.extra.content "" >
+
+<!ENTITY % SVG.font-face.element "INCLUDE" >
+<![%SVG.font-face.element;[
+<!ENTITY % SVG.font-face.content
+ "(( %SVG.Description.class; )*, %SVG.font-face-src.qname;?,
+ %SVG.definition-src.qname;? %SVG.font-face.extra.content; )"
+>
+<!ELEMENT %SVG.font-face.qname; %SVG.font-face.content; >
+<!-- end of SVG.font-face.element -->]]>
+
+<!ENTITY % SVG.font-face.attlist "INCLUDE" >
+<![%SVG.font-face.attlist;[
+<!ATTLIST %SVG.font-face.qname;
+ %SVG.Core.attrib;
+ font-family CDATA #IMPLIED
+ font-style CDATA #IMPLIED
+ font-variant CDATA #IMPLIED
+ font-weight CDATA #IMPLIED
+ font-stretch CDATA #IMPLIED
+ font-size CDATA #IMPLIED
+ unicode-range CDATA #IMPLIED
+ units-per-em %Number.datatype; #IMPLIED
+ panose-1 CDATA #IMPLIED
+ stemv %Number.datatype; #IMPLIED
+ stemh %Number.datatype; #IMPLIED
+ slope %Number.datatype; #IMPLIED
+ cap-height %Number.datatype; #IMPLIED
+ x-height %Number.datatype; #IMPLIED
+ accent-height %Number.datatype; #IMPLIED
+ ascent %Number.datatype; #IMPLIED
+ descent %Number.datatype; #IMPLIED
+ widths CDATA #IMPLIED
+ bbox CDATA #IMPLIED
+ ideographic %Number.datatype; #IMPLIED
+ alphabetic %Number.datatype; #IMPLIED
+ mathematical %Number.datatype; #IMPLIED
+ hanging %Number.datatype; #IMPLIED
+ v-ideographic %Number.datatype; #IMPLIED
+ v-alphabetic %Number.datatype; #IMPLIED
+ v-mathematical %Number.datatype; #IMPLIED
+ v-hanging %Number.datatype; #IMPLIED
+ underline-position %Number.datatype; #IMPLIED
+ underline-thickness %Number.datatype; #IMPLIED
+ strikethrough-position %Number.datatype; #IMPLIED
+ strikethrough-thickness %Number.datatype; #IMPLIED
+ overline-position %Number.datatype; #IMPLIED
+ overline-thickness %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.font-face.attlist -->]]>
+
+<!-- glyph: Glyph Element .............................. -->
+
+<!ENTITY % SVG.glyph.extra.content "" >
+
+<!ENTITY % SVG.glyph.element "INCLUDE" >
+<![%SVG.glyph.element;[
+<!ENTITY % SVG.glyph.content
+ "( %SVG.Description.class; | %SVG.Animation.class; %SVG.Structure.class;
+ %SVG.Conditional.class; %SVG.Image.class; %SVG.Style.class;
+ %SVG.Shape.class; %SVG.Text.class; %SVG.Marker.class; %SVG.Profile.class;
+ %SVG.Gradient.class; %SVG.Pattern.class; %SVG.Clip.class;
+ %SVG.Mask.class; %SVG.Filter.class; %SVG.Cursor.class;
+ %SVG.Hyperlink.class; %SVG.View.class; %SVG.Script.class;
+ %SVG.Font.class; %SVG.glyph.extra.content; )*"
+>
+<!ELEMENT %SVG.glyph.qname; %SVG.glyph.content; >
+<!-- end of SVG.glyph.element -->]]>
+
+<!ENTITY % SVG.glyph.attlist "INCLUDE" >
+<![%SVG.glyph.attlist;[
+<!ATTLIST %SVG.glyph.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ unicode CDATA #IMPLIED
+ glyph-name CDATA #IMPLIED
+ d %PathData.datatype; #IMPLIED
+ orientation CDATA #IMPLIED
+ arabic-form CDATA #IMPLIED
+ lang %LanguageCodes.datatype; #IMPLIED
+ horiz-adv-x %Number.datatype; #IMPLIED
+ vert-origin-x %Number.datatype; #IMPLIED
+ vert-origin-y %Number.datatype; #IMPLIED
+ vert-adv-y %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.glyph.attlist -->]]>
+
+<!-- missing-glyph: Missing Glyph Element .............. -->
+
+<!ENTITY % SVG.missing-glyph.extra.content "" >
+
+<!ENTITY % SVG.missing-glyph.element "INCLUDE" >
+<![%SVG.missing-glyph.element;[
+<!ENTITY % SVG.missing-glyph.content
+ "( %SVG.Description.class; | %SVG.Animation.class; %SVG.Structure.class;
+ %SVG.Conditional.class; %SVG.Image.class; %SVG.Style.class;
+ %SVG.Shape.class; %SVG.Text.class; %SVG.Marker.class; %SVG.Profile.class;
+ %SVG.Gradient.class; %SVG.Pattern.class; %SVG.Clip.class;
+ %SVG.Mask.class; %SVG.Filter.class; %SVG.Cursor.class;
+ %SVG.Hyperlink.class; %SVG.View.class; %SVG.Script.class;
+ %SVG.Font.class; %SVG.missing-glyph.extra.content; )*"
+>
+<!ELEMENT %SVG.missing-glyph.qname; %SVG.missing-glyph.content; >
+<!-- end of SVG.missing-glyph.element -->]]>
+
+<!ENTITY % SVG.missing-glyph.attlist "INCLUDE" >
+<![%SVG.missing-glyph.attlist;[
+<!ATTLIST %SVG.missing-glyph.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ d %PathData.datatype; #IMPLIED
+ horiz-adv-x %Number.datatype; #IMPLIED
+ vert-origin-x %Number.datatype; #IMPLIED
+ vert-origin-y %Number.datatype; #IMPLIED
+ vert-adv-y %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.missing-glyph.attlist -->]]>
+
+<!-- hkern: Horizontal Kerning Element ................. -->
+
+<!ENTITY % SVG.hkern.element "INCLUDE" >
+<![%SVG.hkern.element;[
+<!ENTITY % SVG.hkern.content "EMPTY" >
+<!ELEMENT %SVG.hkern.qname; %SVG.hkern.content; >
+<!-- end of SVG.hkern.element -->]]>
+
+<!ENTITY % SVG.hkern.attlist "INCLUDE" >
+<![%SVG.hkern.attlist;[
+<!ATTLIST %SVG.hkern.qname;
+ %SVG.Core.attrib;
+ u1 CDATA #IMPLIED
+ g1 CDATA #IMPLIED
+ u2 CDATA #IMPLIED
+ g2 CDATA #IMPLIED
+ k %Number.datatype; #REQUIRED
+>
+<!-- end of SVG.hkern.attlist -->]]>
+
+<!-- vkern: Vertical Kerning Element ................... -->
+
+<!ENTITY % SVG.vkern.element "INCLUDE" >
+<![%SVG.vkern.element;[
+<!ENTITY % SVG.vkern.content "EMPTY" >
+<!ELEMENT %SVG.vkern.qname; %SVG.vkern.content; >
+<!-- end of SVG.vkern.element -->]]>
+
+<!ENTITY % SVG.vkern.attlist "INCLUDE" >
+<![%SVG.vkern.attlist;[
+<!ATTLIST %SVG.vkern.qname;
+ %SVG.Core.attrib;
+ u1 CDATA #IMPLIED
+ g1 CDATA #IMPLIED
+ u2 CDATA #IMPLIED
+ g2 CDATA #IMPLIED
+ k %Number.datatype; #REQUIRED
+>
+<!-- end of SVG.vkern.attlist -->]]>
+
+<!-- font-face-src: Font Face Source Element ........... -->
+
+<!ENTITY % SVG.font-face-src.extra.content "" >
+
+<!ENTITY % SVG.font-face-src.element "INCLUDE" >
+<![%SVG.font-face-src.element;[
+<!ENTITY % SVG.font-face-src.content
+ "( %SVG.font-face-uri.qname; | %SVG.font-face-name.qname;
+ %SVG.font-face-src.extra.content; )+"
+>
+<!ELEMENT %SVG.font-face-src.qname; %SVG.font-face-src.content; >
+<!-- end of SVG.font-face-src.element -->]]>
+
+<!ENTITY % SVG.font-face-src.attlist "INCLUDE" >
+<![%SVG.font-face-src.attlist;[
+<!ATTLIST %SVG.font-face-src.qname;
+ %SVG.Core.attrib;
+>
+<!-- end of SVG.font-face-src.attlist -->]]>
+
+<!-- font-face-uri: Font Face URI Element .............. -->
+
+<!ENTITY % SVG.font-face-uri.extra.content "" >
+
+<!ENTITY % SVG.font-face-uri.element "INCLUDE" >
+<![%SVG.font-face-uri.element;[
+<!ENTITY % SVG.font-face-uri.content
+ "( %SVG.font-face-format.qname; %SVG.font-face-uri.extra.content; )*"
+>
+<!ELEMENT %SVG.font-face-uri.qname; %SVG.font-face-uri.content; >
+<!-- end of SVG.font-face-uri.element -->]]>
+
+<!ENTITY % SVG.font-face-uri.attlist "INCLUDE" >
+<![%SVG.font-face-uri.attlist;[
+<!ATTLIST %SVG.font-face-uri.qname;
+ %SVG.Core.attrib;
+ %SVG.XLinkRequired.attrib;
+>
+<!-- end of SVG.font-face-uri.attlist -->]]>
+
+<!-- font-face-format: Font Face Format Element ........ -->
+
+<!ENTITY % SVG.font-face-format.element "INCLUDE" >
+<![%SVG.font-face-format.element;[
+<!ENTITY % SVG.font-face-format.content "EMPTY" >
+<!ELEMENT %SVG.font-face-format.qname; %SVG.font-face-format.content; >
+<!-- end of SVG.font-face-format.element -->]]>
+
+<!ENTITY % SVG.font-face-format.attlist "INCLUDE" >
+<![%SVG.font-face-format.attlist;[
+<!ATTLIST %SVG.font-face-format.qname;
+ %SVG.Core.attrib;
+ string CDATA #IMPLIED
+>
+<!-- end of SVG.font-face-format.attlist -->]]>
+
+<!-- font-face-name: Font Face Name Element ............ -->
+
+<!ENTITY % SVG.font-face-name.element "INCLUDE" >
+<![%SVG.font-face-name.element;[
+<!ENTITY % SVG.font-face-name.content "EMPTY" >
+<!ELEMENT %SVG.font-face-name.qname; %SVG.font-face-name.content; >
+<!-- end of SVG.font-face-name.element -->]]>
+
+<!ENTITY % SVG.font-face-name.attlist "INCLUDE" >
+<![%SVG.font-face-name.attlist;[
+<!ATTLIST %SVG.font-face-name.qname;
+ %SVG.Core.attrib;
+ name CDATA #IMPLIED
+>
+<!-- end of SVG.font-face-name.attlist -->]]>
+
+<!-- definition-src: Definition Source Element ......... -->
+
+<!ENTITY % SVG.definition-src.element "INCLUDE" >
+<![%SVG.definition-src.element;[
+<!ENTITY % SVG.definition-src.content "EMPTY" >
+<!ELEMENT %SVG.definition-src.qname; %SVG.definition-src.content; >
+<!-- end of SVG.definition-src.element -->]]>
+
+<!ENTITY % SVG.definition-src.attlist "INCLUDE" >
+<![%SVG.definition-src.attlist;[
+<!ATTLIST %SVG.definition-src.qname;
+ %SVG.Core.attrib;
+ %SVG.XLinkRequired.attrib;
+>
+<!-- end of SVG.definition-src.attlist -->]]>
+
+<!-- end of svg-font.mod -->
+]]>
+
+<!-- Extensibility Module ........................................ -->
+<!ENTITY % svg-extensibility.module "INCLUDE" >
+<![%svg-extensibility.module;[
+<!ENTITY % svg-extensibility.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Extensibility//EN"
+ "svg-extensibility.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Extensibility Module .......................................... -->
+<!-- file: svg-extensibility.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Extensibility//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-extensibility.mod"
+
+ ....................................................................... -->
+
+<!-- Extensibility
+
+ foreignObject
+
+ This module declares markup to provide support for extensibility.
+-->
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.foreignObject.qname "foreignObject" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Conditional.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Viewport.attrib "" >
+<!ENTITY % SVG.Text.attrib "" >
+<!ENTITY % SVG.TextContent.attrib "" >
+<!ENTITY % SVG.Font.attrib "" >
+<!ENTITY % SVG.Paint.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Marker.attrib "" >
+<!ENTITY % SVG.Gradient.attrib "" >
+<!ENTITY % SVG.Clip.attrib "" >
+<!ENTITY % SVG.Mask.attrib "" >
+<!ENTITY % SVG.Filter.attrib "" >
+<!ENTITY % SVG.FilterColor.attrib "" >
+<!ENTITY % SVG.GraphicalEvents.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Extensibility.class ........................... -->
+
+<!ENTITY % SVG.Extensibility.extra.class "" >
+
+<!ENTITY % SVG.Extensibility.class
+ "| %SVG.foreignObject.qname; %SVG.Extensibility.extra.class;"
+>
+
+<!-- SVG.Presentation.attrib ........................... -->
+
+<!ENTITY % SVG.Presentation.extra.attrib "" >
+
+<!ENTITY % SVG.Presentation.attrib
+ "%SVG.Container.attrib;
+ %SVG.Viewport.attrib;
+ %SVG.Text.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Profile.attrib;
+ %SVG.Gradient.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.Cursor.attrib;
+ flood-color %SVGColor.datatype; #IMPLIED
+ flood-opacity %OpacityValue.datatype; #IMPLIED
+ lighting-color %SVGColor.datatype; #IMPLIED
+ %SVG.Presentation.extra.attrib;"
+>
+
+<!-- foreignObject: Foreign Object Element ............. -->
+
+<!ENTITY % SVG.foreignObject.extra.content "" >
+
+<!ENTITY % SVG.foreignObject.element "INCLUDE" >
+<![%SVG.foreignObject.element;[
+<!ENTITY % SVG.foreignObject.content
+ "( #PCDATA %SVG.foreignObject.extra.content; )*"
+>
+<!ELEMENT %SVG.foreignObject.qname; %SVG.foreignObject.content; >
+<!-- end of SVG.foreignObject.element -->]]>
+
+<!ENTITY % SVG.foreignObject.attlist "INCLUDE" >
+<![%SVG.foreignObject.attlist;[
+<!ATTLIST %SVG.foreignObject.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.External.attrib;
+ x %Coordinate.datatype; #IMPLIED
+ y %Coordinate.datatype; #IMPLIED
+ width %Length.datatype; #REQUIRED
+ height %Length.datatype; #REQUIRED
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.foreignObject.attlist -->]]>
+
+<!-- end of svg-extensibility.mod -->
+]]>
+
+<!-- end of SVG 1.1 DTD .................................................... -->
+<!-- ....................................................................... -->
diff --git a/org/apache/batik/dom/svg/resources/svg11-model.mod b/org/apache/batik/dom/svg/resources/svg11-model.mod
new file mode 100644
index 0000000..4732fd9
--- /dev/null
+++ b/org/apache/batik/dom/svg/resources/svg11-model.mod
@@ -0,0 +1,197 @@
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Document Model Module ......................................... -->
+<!-- file: svg11-model.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-model.mod 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Document Model//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11-model.mod"
+
+ ....................................................................... -->
+
+<!-- SVG 1.1 Document Model
+
+ This module describes the groupings of elements that make up
+ common content models for SVG elements.
+-->
+
+<!-- module: svg-structure.mod ......................... -->
+
+<!ENTITY % SVG.Description.extra.class "" >
+<!ENTITY % SVG.Description.class
+ "%SVG.desc.qname; | %SVG.title.qname; | %SVG.metadata.qname;
+ %SVG.Description.extra.class;"
+>
+
+<!ENTITY % SVG.Use.extra.class "" >
+<!ENTITY % SVG.Use.class
+ "| %SVG.use.qname; %SVG.Use.extra.class;"
+>
+
+<!ENTITY % SVG.Structure.extra.class "" >
+<!ENTITY % SVG.Structure.class
+ "| %SVG.svg.qname; | %SVG.g.qname; | %SVG.defs.qname; | %SVG.symbol.qname;
+ %SVG.Use.class; %SVG.Structure.extra.class;"
+>
+
+<!-- module: svg-conditional.mod ....................... -->
+
+<!ENTITY % SVG.Conditional.extra.class "" >
+<!ENTITY % SVG.Conditional.class
+ "| %SVG.switch.qname; %SVG.Conditional.extra.class;"
+>
+
+<!-- module: svg-image.mod ............................. -->
+
+<!ENTITY % SVG.Image.extra.class "" >
+<!ENTITY % SVG.Image.class
+ "| %SVG.image.qname; %SVG.Image.extra.class;"
+>
+
+<!-- module: svg-style.mod ............................. -->
+
+<!ENTITY % SVG.Style.extra.class "" >
+<!ENTITY % SVG.Style.class
+ "| %SVG.style.qname; %SVG.Style.extra.class;"
+>
+
+<!-- module: svg-shape.mod ............................. -->
+
+<!ENTITY % SVG.Shape.extra.class "" >
+<!ENTITY % SVG.Shape.class
+ "| %SVG.path.qname; | %SVG.rect.qname; | %SVG.circle.qname;
+ | %SVG.line.qname; | %SVG.ellipse.qname; | %SVG.polyline.qname;
+ | %SVG.polygon.qname; %SVG.Shape.extra.class;"
+>
+
+<!-- module: svg-text.mod .............................. -->
+
+<!ENTITY % SVG.Text.extra.class "" >
+<!ENTITY % SVG.Text.class
+ "| %SVG.text.qname; | %SVG.altGlyphDef.qname; %SVG.Text.extra.class;"
+>
+
+<!ENTITY % SVG.TextContent.extra.class "" >
+<!ENTITY % SVG.TextContent.class
+ "| %SVG.tspan.qname; | %SVG.tref.qname; | %SVG.textPath.qname;
+ | %SVG.altGlyph.qname; %SVG.TextContent.extra.class;"
+>
+
+<!-- module: svg-marker.mod ............................ -->
+
+<!ENTITY % SVG.Marker.extra.class "" >
+<!ENTITY % SVG.Marker.class
+ "| %SVG.marker.qname; %SVG.Marker.extra.class;"
+>
+
+<!-- module: svg-profile.mod ........................... -->
+
+<!ENTITY % SVG.Profile.extra.class "" >
+<!ENTITY % SVG.Profile.class
+ "| %SVG.color-profile.qname; %SVG.Profile.extra.class;"
+>
+
+<!-- module: svg-gradient.mod .......................... -->
+
+<!ENTITY % SVG.Gradient.extra.class "" >
+<!ENTITY % SVG.Gradient.class
+ "| %SVG.linearGradient.qname; | %SVG.radialGradient.qname;
+ %SVG.Gradient.extra.class;"
+>
+
+<!-- module: svg-pattern.mod ........................... -->
+
+<!ENTITY % SVG.Pattern.extra.class "" >
+<!ENTITY % SVG.Pattern.class
+ "| %SVG.pattern.qname; %SVG.Pattern.extra.class;"
+>
+
+<!-- module: svg-clip.mod .............................. -->
+
+<!ENTITY % SVG.Clip.extra.class "" >
+<!ENTITY % SVG.Clip.class
+ "| %SVG.clipPath.qname; %SVG.Clip.extra.class;"
+>
+
+<!-- module: svg-mask.mod .............................. -->
+
+<!ENTITY % SVG.Mask.extra.class "" >
+<!ENTITY % SVG.Mask.class
+ "| %SVG.mask.qname; %SVG.Mask.extra.class;"
+>
+
+<!-- module: svg-filter.mod ............................ -->
+
+<!ENTITY % SVG.Filter.extra.class "" >
+<!ENTITY % SVG.Filter.class
+ "| %SVG.filter.qname; %SVG.Filter.extra.class;"
+>
+
+<!ENTITY % SVG.FilterPrimitive.extra.class "" >
+<!ENTITY % SVG.FilterPrimitive.class
+ "| %SVG.feBlend.qname; | %SVG.feColorMatrix.qname;
+ | %SVG.feComponentTransfer.qname; | %SVG.feComposite.qname;
+ | %SVG.feConvolveMatrix.qname; | %SVG.feDiffuseLighting.qname;
+ | %SVG.feDisplacementMap.qname; | %SVG.feFlood.qname;
+ | %SVG.feGaussianBlur.qname; | %SVG.feImage.qname; | %SVG.feMerge.qname;
+ | %SVG.feMorphology.qname; | %SVG.feOffset.qname;
+ | %SVG.feSpecularLighting.qname; | %SVG.feTile.qname;
+ | %SVG.feTurbulence.qname; %SVG.FilterPrimitive.extra.class;"
+>
+
+<!-- module: svg-cursor.mod ............................ -->
+
+<!ENTITY % SVG.Cursor.extra.class "" >
+<!ENTITY % SVG.Cursor.class
+ "| %SVG.cursor.qname; %SVG.Cursor.extra.class;"
+>
+
+<!-- module: svg-hyperlink.mod ......................... -->
+
+<!ENTITY % SVG.Hyperlink.extra.class "" >
+<!ENTITY % SVG.Hyperlink.class
+ "| %SVG.a.qname; %SVG.Hyperlink.extra.class;"
+>
+
+<!-- module: svg-view.mod .............................. -->
+
+<!ENTITY % SVG.View.extra.class "" >
+<!ENTITY % SVG.View.class
+ "| %SVG.view.qname; %SVG.View.extra.class;"
+>
+
+<!-- module: svg-script.mod ............................ -->
+
+<!ENTITY % SVG.Script.extra.class "" >
+<!ENTITY % SVG.Script.class
+ "| %SVG.script.qname; %SVG.Script.extra.class;"
+>
+
+<!-- module: svg-animation.mod ......................... -->
+
+<!ENTITY % SVG.Animation.extra.class "" >
+<!ENTITY % SVG.Animation.class
+ "%SVG.animate.qname; | %SVG.set.qname; | %SVG.animateMotion.qname; |
+ %SVG.animateColor.qname; | %SVG.animateTransform.qname;
+ %SVG.Animation.extra.class;"
+>
+
+<!-- module: svg-font.mod .............................. -->
+
+<!ENTITY % SVG.Font.extra.class "" >
+<!ENTITY % SVG.Font.class
+ "| %SVG.font.qname; | %SVG.font-face.qname; %SVG.Font.extra.class;"
+>
+
+<!-- module: svg-extensibility.mod ..................... -->
+
+<!ENTITY % SVG.Extensibility.extra.class "" >
+<!ENTITY % SVG.Extensibility.class
+ "| %SVG.foreignObject.qname; %SVG.Extensibility.extra.class;"
+>
+
+<!-- end of svg11-model.mod -->
diff --git a/org/apache/batik/dom/svg/resources/svg11-tiny-attribs.mod b/org/apache/batik/dom/svg/resources/svg11-tiny-attribs.mod
new file mode 100644
index 0000000..46e42fa
--- /dev/null
+++ b/org/apache/batik/dom/svg/resources/svg11-tiny-attribs.mod
@@ -0,0 +1,62 @@
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Tiny Attribute Collection Module .............................. -->
+<!-- file: svg11-tiny-attribs.mod
+
+ This is SVG Tiny, a proper subset of SVG.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-tiny-attribs.mod 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Tiny Attribute Collection//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11-tiny-attribs.mod"
+
+ ....................................................................... -->
+
+<!-- SVG 1.1 Tiny Attribute Collection
+
+ This module defines the set of common attributes that can be present
+ on many SVG elements.
+-->
+
+<!-- module: svg-conditional.mod ....................... -->
+
+<!ENTITY % ExtensionList.datatype "CDATA" >
+<!ENTITY % FeatureList.datatype "CDATA" >
+
+<!ENTITY % SVG.Conditional.extra.attrib "" >
+<!ENTITY % SVG.Conditional.attrib
+ "requiredFeatures %FeatureList.datatype; #IMPLIED
+ requiredExtensions %ExtensionList.datatype; #IMPLIED
+ systemLanguage %LanguageCodes.datatype; #IMPLIED
+ %SVG.Conditional.extra.attrib;"
+>
+
+<!-- module: svg-style.mod ............................. -->
+
+<!ENTITY % ClassList.datatype "CDATA" >
+<!ENTITY % StyleSheet.datatype "CDATA" >
+
+<!ENTITY % SVG.Style.extra.attrib "" >
+<!ENTITY % SVG.Style.attrib
+ "style %StyleSheet.datatype; #IMPLIED
+ class %ClassList.datatype; #IMPLIED
+ %SVG.Style.extra.attrib;"
+>
+
+<!-- module: svg-basic-text.mod ........................ -->
+
+<!ENTITY % FontFamilyValue.datatype "CDATA" >
+<!ENTITY % FontSizeValue.datatype "CDATA" >
+
+<!ENTITY % SVG.Font.extra.attrib "" >
+<!ENTITY % SVG.Font.attrib
+ "font-family %FontFamilyValue.datatype; #IMPLIED
+ font-size %FontSizeValue.datatype; #IMPLIED
+ font-style ( normal | italic | oblique | inherit ) #IMPLIED
+ font-weight ( normal | bold | bolder | lighter | 100 | 200 | 300 | 400 |
+ 500 | 600 | 700 | 800 | 900 | inherit ) #IMPLIED
+ %SVG.Font.extra.attrib;"
+>
+
+<!-- end of svg11-tiny-attribs.mod -->
diff --git a/org/apache/batik/dom/svg/resources/svg11-tiny-flat.dtd b/org/apache/batik/dom/svg/resources/svg11-tiny-flat.dtd
new file mode 100644
index 0000000..1027f41
--- /dev/null
+++ b/org/apache/batik/dom/svg/resources/svg11-tiny-flat.dtd
@@ -0,0 +1,3449 @@
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Tiny DTD ...................................................... -->
+<!-- file: svg11-tiny.dtd
+-->
+
+<!-- SVG 1.1 Tiny DTD
+
+ This is SVG Tiny, a proper subset of SVG.
+
+ The Scalable Vector Graphics (SVG)
+ Copyright 2001, 2002 World Wide Web Consortium
+ (Massachusetts Institute of Technology, Institut National de
+ Recherche en Informatique et en Automatique, Keio University).
+ All Rights Reserved.
+
+ Permission to use, copy, modify and distribute the SVG DTD and its
+ accompanying documentation for any purpose and without fee is hereby
+ granted in perpetuity, provided that the above copyright notice and
+ this paragraph appear in all copies. The copyright holders make no
+ representation about the suitability of the DTD for any purpose.
+
+ It is provided "as is" without expressed or implied warranty.
+
+ Author: Jun Fujisawa <fujisawa.jun at canon.co.jp>
+ Revision: $Id: svg11-tiny-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+-->
+<!-- This is the driver file for version 1.1 of the SVG Tiny DTD.
+
+ This DTD is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//DTD SVG 1.1 Tiny//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11-tiny.dtd"
+-->
+<!ENTITY % SVG.version "-//W3C//DTD SVG 1.1 Tiny//EN" >
+
+<!-- Use this URI to identify the default namespace:
+
+ "http://www.w3.org/2000/svg"
+
+ See the Qualified Names module for information
+ on the use of namespace prefixes in the DTD.
+-->
+<!ENTITY % NS.prefixed "IGNORE" >
+<!ENTITY % SVG.prefix "" >
+
+<!-- reserved for future use with document profiles -->
+<!ENTITY % SVG.profile "" >
+
+<!-- ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: -->
+
+<!-- Pre-Framework Redeclaration Placeholder ..................... -->
+<!ENTITY % svg-prefw-redecl.module "IGNORE" >
+<![%svg-prefw-redecl.module;[
+%svg-prefw-redecl.mod;]]>
+
+<!-- Document Model Module ....................................... -->
+<!ENTITY % svg-model.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Tiny Document Model//EN"
+ "svg11-tiny-model.mod" >
+
+<!-- Attribute Collection Module ................................. -->
+<!ENTITY % svg-attribs.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Tiny Attribute Collection//EN"
+ "svg11-tiny-attribs.mod" >
+
+<!-- Modular Framework Module .................................... -->
+<!ENTITY % svg-framework.module "INCLUDE" >
+<![%svg-framework.module;[
+<!ENTITY % svg-framework.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Modular Framework//EN"
+ "svg-framework.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Modular Framework Module ...................................... -->
+<!-- file: svg-framework.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-tiny-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Modular Framework//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-framework.mod"
+
+ ....................................................................... -->
+
+<!-- Modular Framework
+
+ This module instantiates the modules needed o support the SVG
+ modularization model, including:
+
+ + Datatypes
+ + Qualified Name
+ + Document Model
+ + Attribute Collection
+-->
+
+<!ENTITY % svg-datatypes.module "INCLUDE" >
+<![%svg-datatypes.module;[
+<!ENTITY % svg-datatypes.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Datatypes//EN"
+ "svg-datatypes.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Datatypes Module .............................................. -->
+<!-- file: svg-datatypes.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-tiny-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Datatypes//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-datatypes.mod"
+
+ ....................................................................... -->
+
+<!-- Datatypes
+
+ This module declares common data types for properties and attributes.
+-->
+
+<!-- feature specification -->
+<!ENTITY % Boolean.datatype "( false | true )" >
+
+<!-- 'clip-rule' or 'fill-rule' property/attribute value -->
+<!ENTITY % ClipFillRule.datatype "( nonzero | evenodd | inherit )" >
+
+<!-- media type, as per [RFC2045] -->
+<!ENTITY % ContentType.datatype "CDATA" >
+
+<!-- a <coordinate> -->
+<!ENTITY % Coordinate.datatype "CDATA" >
+
+<!-- a list of <coordinate>s -->
+<!ENTITY % Coordinates.datatype "CDATA" >
+
+<!-- a <color> value -->
+<!ENTITY % Color.datatype "CDATA" >
+
+<!-- a <integer> -->
+<!ENTITY % Integer.datatype "CDATA" >
+
+<!-- a language code, as per [RFC3066] -->
+<!ENTITY % LanguageCode.datatype "NMTOKEN" >
+
+<!-- comma-separated list of language codes, as per [RFC3066] -->
+<!ENTITY % LanguageCodes.datatype "CDATA" >
+
+<!-- a <length> -->
+<!ENTITY % Length.datatype "CDATA" >
+
+<!-- a list of <length>s -->
+<!ENTITY % Lengths.datatype "CDATA" >
+
+<!-- a <number> -->
+<!ENTITY % Number.datatype "CDATA" >
+
+<!-- a list of <number>s -->
+<!ENTITY % Numbers.datatype "CDATA" >
+
+<!-- opacity value (e.g., <number>) -->
+<!ENTITY % OpacityValue.datatype "CDATA" >
+
+<!-- a path data specification -->
+<!ENTITY % PathData.datatype "CDATA" >
+
+<!-- 'preserveAspectRatio' attribute specification -->
+<!ENTITY % PreserveAspectRatioSpec.datatype "CDATA" >
+
+<!-- script expression -->
+<!ENTITY % Script.datatype "CDATA" >
+
+<!-- An SVG color value (RGB plus optional ICC) -->
+<!ENTITY % SVGColor.datatype "CDATA" >
+
+<!-- arbitrary text string -->
+<!ENTITY % Text.datatype "CDATA" >
+
+<!-- list of transforms -->
+<!ENTITY % TransformList.datatype "CDATA" >
+
+<!-- a Uniform Resource Identifier, see [URI] -->
+<!ENTITY % URI.datatype "CDATA" >
+
+<!-- 'viewBox' attribute specification -->
+<!ENTITY % ViewBoxSpec.datatype "CDATA" >
+
+<!-- end of svg-datatypes.mod -->
+]]>
+
+<!ENTITY % svg-qname.module "INCLUDE" >
+<![%svg-qname.module;[
+<!ENTITY % svg-qname.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Qualified Name//EN"
+ "svg-qname.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Qualified Name Module ......................................... -->
+<!-- file: svg-qname.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-tiny-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Qualified Name//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-qname.mod"
+
+ ....................................................................... -->
+
+<!-- Qualified Name
+
+ This module is contained in two parts, labeled Section 'A' and 'B':
+
+ Section A declares parameter entities to support namespace-
+ qualified names, namespace declarations, and name prefixing
+ for SVG and extensions.
+
+ Section B declares parameter entities used to provide
+ namespace-qualified names for all SVG element types:
+-->
+
+<!-- Section A: SVG XML Namespace Framework :::::::::::::::::::::: -->
+
+<!-- 1. Declare a %SVG.prefixed; conditional section keyword, used
+ to activate namespace prefixing. The default value should
+ inherit '%NS.prefixed;' from the DTD driver, so that unless
+ overridden, the default behaviour follows the overall DTD
+ prefixing scheme.
+-->
+<!ENTITY % NS.prefixed "IGNORE" >
+<!ENTITY % SVG.prefixed "%NS.prefixed;" >
+
+<!-- 2. Declare a parameter entity (eg., %SVG.xmlns;) containing
+ the URI reference used to identify the SVG namespace:
+-->
+<!ENTITY % SVG.xmlns "http://www.w3.org/2000/svg" >
+<!ENTITY % XLINK.xmlns "http://www.w3.org/1999/xlink" >
+
+<!-- 3. Declare parameter entities (eg., %SVG.prefix;) containing
+ the default namespace prefix string(s) to use when prefixing
+ is enabled. This may be overridden in the DTD driver or the
+ internal subset of an document instance. If no default prefix
+ is desired, this may be declared as an empty string.
+-->
+<!ENTITY % SVG.prefix "" >
+<!ENTITY % XLINK.prefix "xlink" >
+
+<!-- 4. Declare parameter entities (eg., %SVG.pfx;) containing the
+ colonized prefix(es) (eg., '%SVG.prefix;:') used when
+ prefixing is active, an empty string when it is not.
+-->
+<![%SVG.prefixed;[
+<!ENTITY % SVG.pfx "%SVG.prefix;:" >
+]]>
+<!ENTITY % SVG.pfx "" >
+<!ENTITY % XLINK.pfx "%XLINK.prefix;:" >
+
+<!-- 5. The parameter entity %SVG.xmlns.extra.attrib; may be
+ redeclared to contain any non-SVG namespace declaration
+ attributes for namespaces embedded in SVG. The default
+ is an empty string.
+-->
+<!ENTITY % SVG.xmlns.extra.attrib "" >
+
+<!-- Declare a parameter entity XLINK.xmlns.attrib containing
+ the XML Namespace declarations for XLink.
+-->
+<!ENTITY % XLINK.xmlns.attrib
+ "xmlns:%XLINK.prefix; %URI.datatype; #FIXED '%XLINK.xmlns;'"
+>
+
+<!-- Declare a parameter entity %NS.decl.attrib; containing
+ all XML Namespace declarations used in the DTD, plus the
+ xmlns declaration for SVG, its form dependent on whether
+ prefixing is active.
+-->
+<![%SVG.prefixed;[
+<!ENTITY % NS.decl.attrib
+ "xmlns:%SVG.prefix; %URI.datatype; #FIXED '%SVG.xmlns;'
+ %XLINK.xmlns.attrib;
+ %SVG.xmlns.extra.attrib;"
+>
+]]>
+<!ENTITY % NS.decl.attrib
+ "%XLINK.xmlns.attrib;
+ %SVG.xmlns.extra.attrib;"
+>
+
+<!-- Declare a parameter entity %SVG.xmlns.attrib; containing
+ all XML namespace declaration attributes used by SVG,
+ including a default xmlns attribute when prefixing is
+ inactive.
+-->
+<![%SVG.prefixed;[
+<!ENTITY % SVG.xmlns.attrib
+ "%NS.decl.attrib;"
+>
+]]>
+<!ENTITY % SVG.xmlns.attrib
+ "xmlns %URI.datatype; #FIXED '%SVG.xmlns;'
+ %XLINK.xmlns.attrib;"
+>
+
+<!-- Section B: SVG Qualified Names :::::::::::::::::::::::::::::: -->
+
+<!-- 6. This section declares parameter entities used to provide
+ namespace-qualified names for all SVG element types.
+-->
+
+<!-- module: svg-structure.mod ......................... -->
+
+<!ENTITY % SVG.svg.qname "%SVG.pfx;svg" >
+<!ENTITY % SVG.g.qname "%SVG.pfx;g" >
+<!ENTITY % SVG.defs.qname "%SVG.pfx;defs" >
+<!ENTITY % SVG.desc.qname "%SVG.pfx;desc" >
+<!ENTITY % SVG.title.qname "%SVG.pfx;title" >
+<!ENTITY % SVG.metadata.qname "%SVG.pfx;metadata" >
+<!ENTITY % SVG.symbol.qname "%SVG.pfx;symbol" >
+<!ENTITY % SVG.use.qname "%SVG.pfx;use" >
+
+<!-- module: svg-conditional.mod ....................... -->
+
+<!ENTITY % SVG.switch.qname "%SVG.pfx;switch" >
+
+<!-- module: svg-image.mod ............................. -->
+
+<!ENTITY % SVG.image.qname "%SVG.pfx;image" >
+
+<!-- module: svg-style.mod ............................. -->
+
+<!ENTITY % SVG.style.qname "%SVG.pfx;style" >
+
+<!-- module: svg-shape.mod ............................. -->
+
+<!ENTITY % SVG.path.qname "%SVG.pfx;path" >
+<!ENTITY % SVG.rect.qname "%SVG.pfx;rect" >
+<!ENTITY % SVG.circle.qname "%SVG.pfx;circle" >
+<!ENTITY % SVG.line.qname "%SVG.pfx;line" >
+<!ENTITY % SVG.ellipse.qname "%SVG.pfx;ellipse" >
+<!ENTITY % SVG.polyline.qname "%SVG.pfx;polyline" >
+<!ENTITY % SVG.polygon.qname "%SVG.pfx;polygon" >
+
+<!-- module: svg-text.mod .............................. -->
+
+<!ENTITY % SVG.text.qname "%SVG.pfx;text" >
+<!ENTITY % SVG.tspan.qname "%SVG.pfx;tspan" >
+<!ENTITY % SVG.tref.qname "%SVG.pfx;tref" >
+<!ENTITY % SVG.textPath.qname "%SVG.pfx;textPath" >
+<!ENTITY % SVG.altGlyph.qname "%SVG.pfx;altGlyph" >
+<!ENTITY % SVG.altGlyphDef.qname "%SVG.pfx;altGlyphDef" >
+<!ENTITY % SVG.altGlyphItem.qname "%SVG.pfx;altGlyphItem" >
+<!ENTITY % SVG.glyphRef.qname "%SVG.pfx;glyphRef" >
+
+<!-- module: svg-marker.mod ............................ -->
+
+<!ENTITY % SVG.marker.qname "%SVG.pfx;marker" >
+
+<!-- module: svg-profile.mod ........................... -->
+
+<!ENTITY % SVG.color-profile.qname "%SVG.pfx;color-profile" >
+
+<!-- module: svg-gradient.mod .......................... -->
+
+<!ENTITY % SVG.linearGradient.qname "%SVG.pfx;linearGradient" >
+<!ENTITY % SVG.radialGradient.qname "%SVG.pfx;radialGradient" >
+<!ENTITY % SVG.stop.qname "stop" >
+
+<!-- module: svg-pattern.mod ........................... -->
+
+<!ENTITY % SVG.pattern.qname "%SVG.pfx;pattern" >
+
+<!-- module: svg-clip.mod .............................. -->
+
+<!ENTITY % SVG.clipPath.qname "%SVG.pfx;clipPath" >
+
+<!-- module: svg-mask.mod .............................. -->
+
+<!ENTITY % SVG.mask.qname "%SVG.pfx;mask" >
+
+<!-- module: svg-filter.mod ............................ -->
+
+<!ENTITY % SVG.filter.qname "%SVG.pfx;filter" >
+<!ENTITY % SVG.feBlend.qname "%SVG.pfx;feBlend" >
+<!ENTITY % SVG.feColorMatrix.qname "%SVG.pfx;feColorMatrix" >
+<!ENTITY % SVG.feComponentTransfer.qname "%SVG.pfx;feComponentTransfer" >
+<!ENTITY % SVG.feComposite.qname "%SVG.pfx;feComposite" >
+<!ENTITY % SVG.feConvolveMatrix.qname "%SVG.pfx;feConvolveMatrix" >
+<!ENTITY % SVG.feDiffuseLighting.qname "%SVG.pfx;feDiffuseLighting" >
+<!ENTITY % SVG.feDisplacementMap.qname "%SVG.pfx;feDisplacementMap" >
+<!ENTITY % SVG.feFlood.qname "%SVG.pfx;feFlood" >
+<!ENTITY % SVG.feGaussianBlur.qname "%SVG.pfx;feGaussianBlur" >
+<!ENTITY % SVG.feImage.qname "%SVG.pfx;feImage" >
+<!ENTITY % SVG.feMerge.qname "%SVG.pfx;feMerge" >
+<!ENTITY % SVG.feMergeNode.qname "%SVG.pfx;feMergeNode" >
+<!ENTITY % SVG.feMorphology.qname "%SVG.pfx;feMorphology" >
+<!ENTITY % SVG.feOffset.qname "%SVG.pfx;feOffset" >
+<!ENTITY % SVG.feSpecularLighting.qname "%SVG.pfx;feSpecularLighting" >
+<!ENTITY % SVG.feTile.qname "%SVG.pfx;feTile" >
+<!ENTITY % SVG.feTurbulence.qname "%SVG.pfx;feTurbulence" >
+<!ENTITY % SVG.feDistantLight.qname "%SVG.pfx;feDistantLight" >
+<!ENTITY % SVG.fePointLight.qname "%SVG.pfx;fePointLight" >
+<!ENTITY % SVG.feSpotLight.qname "%SVG.pfx;feSpotLight" >
+<!ENTITY % SVG.feFuncR.qname "%SVG.pfx;feFuncR" >
+<!ENTITY % SVG.feFuncG.qname "%SVG.pfx;feFuncG" >
+<!ENTITY % SVG.feFuncB.qname "%SVG.pfx;feFuncB" >
+<!ENTITY % SVG.feFuncA.qname "%SVG.pfx;feFuncA" >
+
+<!-- module: svg-cursor.mod ............................ -->
+
+<!ENTITY % SVG.cursor.qname "%SVG.pfx;cursor" >
+
+<!-- module: svg-hyperlink.mod ......................... -->
+
+<!ENTITY % SVG.a.qname "%SVG.pfx;a" >
+
+<!-- module: svg-view.mod .............................. -->
+
+<!ENTITY % SVG.view.qname "%SVG.pfx;view" >
+
+<!-- module: svg-script.mod ............................ -->
+
+<!ENTITY % SVG.script.qname "%SVG.pfx;script" >
+
+<!-- module: svg-animation.mod ......................... -->
+
+<!ENTITY % SVG.animate.qname "%SVG.pfx;animate" >
+<!ENTITY % SVG.set.qname "%SVG.pfx;set" >
+<!ENTITY % SVG.animateMotion.qname "%SVG.pfx;animateMotion" >
+<!ENTITY % SVG.animateColor.qname "%SVG.pfx;animateColor" >
+<!ENTITY % SVG.animateTransform.qname "%SVG.pfx;animateTransform" >
+<!ENTITY % SVG.mpath.qname "%SVG.pfx;mpath" >
+
+<!-- module: svg-font.mod .............................. -->
+
+<!ENTITY % SVG.font.qname "%SVG.pfx;font" >
+<!ENTITY % SVG.font-face.qname "%SVG.pfx;font-face" >
+<!ENTITY % SVG.glyph.qname "%SVG.pfx;glyph" >
+<!ENTITY % SVG.missing-glyph.qname "%SVG.pfx;missing-glyph" >
+<!ENTITY % SVG.hkern.qname "%SVG.pfx;hkern" >
+<!ENTITY % SVG.vkern.qname "%SVG.pfx;vkern" >
+<!ENTITY % SVG.font-face-src.qname "%SVG.pfx;font-face-src" >
+<!ENTITY % SVG.font-face-uri.qname "%SVG.pfx;font-face-uri" >
+<!ENTITY % SVG.font-face-format.qname "%SVG.pfx;font-face-format" >
+<!ENTITY % SVG.font-face-name.qname "%SVG.pfx;font-face-name" >
+<!ENTITY % SVG.definition-src.qname "%SVG.pfx;definition-src" >
+
+<!-- module: svg-extensibility.mod ..................... -->
+
+<!ENTITY % SVG.foreignObject.qname "%SVG.pfx;foreignObject" >
+
+<!-- end of svg-qname.mod -->
+]]>
+
+<!ENTITY % svg-model.module "INCLUDE" >
+<![%svg-model.module;[
+<!-- instantiate the Document Model declared in the DTD driver -->
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Tiny Document Model Module .................................... -->
+<!-- file: svg11-tiny-model.mod
+
+ This is SVG Tiny, a proper subset of SVG.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-tiny-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Tiny Document Model//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11-tiny-model.mod"
+
+ ....................................................................... -->
+
+<!-- SVG 1.1 Tiny Document Model
+
+ This module describes the groupings of elements that make up
+ common content models for SVG elements.
+-->
+
+<!-- Content Models (Default) .......................... -->
+
+<!ENTITY % SVG.Marker.class "" >
+<!ENTITY % SVG.Profile.class "" >
+<!ENTITY % SVG.Gradient.class "" >
+<!ENTITY % SVG.Pattern.class "" >
+<!ENTITY % SVG.Clip.class "" >
+<!ENTITY % SVG.Mask.class "" >
+<!ENTITY % SVG.Filter.class "" >
+<!ENTITY % SVG.FilterPrimitive.class "" >
+<!ENTITY % SVG.Cursor.class "" >
+
+<!-- module: svg-basic-structure.mod ................... -->
+
+<!ENTITY % SVG.Description.extra.class "" >
+<!ENTITY % SVG.Description.class
+ "%SVG.desc.qname; | %SVG.title.qname; | %SVG.metadata.qname;
+ %SVG.Description.extra.class;"
+>
+
+<!ENTITY % SVG.Use.extra.class "" >
+<!ENTITY % SVG.Use.class
+ "| %SVG.use.qname; %SVG.Use.extra.class;"
+>
+
+<!ENTITY % SVG.Structure.extra.class "" >
+<!ENTITY % SVG.Structure.class
+ "| %SVG.svg.qname; | %SVG.g.qname; | %SVG.defs.qname; %SVG.Use.class;
+ %SVG.Structure.extra.class;"
+>
+
+<!-- module: svg-conditional.mod ....................... -->
+
+<!ENTITY % SVG.Conditional.extra.class "" >
+<!ENTITY % SVG.Conditional.class
+ "| %SVG.switch.qname; %SVG.Conditional.extra.class;"
+>
+
+<!-- module: svg-image.mod ............................. -->
+
+<!ENTITY % SVG.Image.extra.class "" >
+<!ENTITY % SVG.Image.class
+ "| %SVG.image.qname; %SVG.Image.extra.class;"
+>
+
+<!-- module: svg-style.mod ............................. -->
+
+<!ENTITY % SVG.Style.extra.class "" >
+<!ENTITY % SVG.Style.class
+ "| %SVG.style.qname; %SVG.Style.extra.class;"
+>
+
+<!-- module: svg-shape.mod ............................. -->
+
+<!ENTITY % SVG.Shape.extra.class "" >
+<!ENTITY % SVG.Shape.class
+ "| %SVG.path.qname; | %SVG.rect.qname; | %SVG.circle.qname;
+ | %SVG.line.qname; | %SVG.ellipse.qname; | %SVG.polyline.qname;
+ | %SVG.polygon.qname; %SVG.Shape.extra.class;"
+>
+
+<!-- module: svg-basic-text.mod ........................ -->
+
+<!ENTITY % SVG.Text.extra.class "" >
+<!ENTITY % SVG.Text.class
+ "| %SVG.text.qname; %SVG.Text.extra.class;"
+>
+
+<!ENTITY % SVG.TextContent.extra.class "" >
+<!ENTITY % SVG.TextContent.class
+ "%SVG.TextContent.extra.class;"
+>
+
+<!-- module: svg-hyperlink.mod ......................... -->
+
+<!ENTITY % SVG.Hyperlink.extra.class "" >
+<!ENTITY % SVG.Hyperlink.class
+ "| %SVG.a.qname; %SVG.Hyperlink.extra.class;"
+>
+
+<!-- module: svg-view.mod .............................. -->
+
+<!ENTITY % SVG.View.extra.class "" >
+<!ENTITY % SVG.View.class
+ "| %SVG.view.qname; %SVG.View.extra.class;"
+>
+
+<!-- module: svg-script.mod ............................ -->
+
+<!ENTITY % SVG.Script.extra.class "" >
+<!ENTITY % SVG.Script.class
+ "| %SVG.script.qname; %SVG.Script.extra.class;"
+>
+
+<!-- module: svg-animation.mod ......................... -->
+
+<!ENTITY % SVG.Animation.extra.class "" >
+<!ENTITY % SVG.Animation.class
+ "%SVG.animate.qname; | %SVG.set.qname; | %SVG.animateMotion.qname; |
+ %SVG.animateColor.qname; | %SVG.animateTransform.qname;
+ %SVG.Animation.extra.class;"
+>
+
+<!-- module: svg-basic-font.mod ........................ -->
+
+<!ENTITY % SVG.Font.extra.class "" >
+<!ENTITY % SVG.Font.class
+ "| %SVG.font.qname; | %SVG.font-face.qname; %SVG.Font.extra.class;"
+>
+
+<!-- module: svg-extensibility.mod ..................... -->
+
+<!ENTITY % SVG.Extensibility.extra.class "" >
+<!ENTITY % SVG.Extensibility.class
+ "| %SVG.foreignObject.qname; %SVG.Extensibility.extra.class;"
+>
+
+<!-- end of svg11-tiny-model.mod -->
+]]>
+
+<!ENTITY % svg-attribs.module "INCLUDE" >
+<![%svg-attribs.module;[
+<!-- instantiate the Attribute Collection declared in the DTD driver -->
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Tiny Attribute Collection Module .............................. -->
+<!-- file: svg11-tiny-attribs.mod
+
+ This is SVG Tiny, a proper subset of SVG.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-tiny-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Tiny Attribute Collection//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11-tiny-attribs.mod"
+
+ ....................................................................... -->
+
+<!-- SVG 1.1 Tiny Attribute Collection
+
+ This module defines the set of common attributes that can be present
+ on many SVG elements.
+-->
+
+<!-- module: svg-conditional.mod ....................... -->
+
+<!ENTITY % ExtensionList.datatype "CDATA" >
+<!ENTITY % FeatureList.datatype "CDATA" >
+
+<!ENTITY % SVG.Conditional.extra.attrib "" >
+<!ENTITY % SVG.Conditional.attrib
+ "requiredFeatures %FeatureList.datatype; #IMPLIED
+ requiredExtensions %ExtensionList.datatype; #IMPLIED
+ systemLanguage %LanguageCodes.datatype; #IMPLIED
+ %SVG.Conditional.extra.attrib;"
+>
+
+<!-- module: svg-style.mod ............................. -->
+
+<!ENTITY % ClassList.datatype "CDATA" >
+<!ENTITY % StyleSheet.datatype "CDATA" >
+
+<!ENTITY % SVG.Style.extra.attrib "" >
+<!ENTITY % SVG.Style.attrib
+ "style %StyleSheet.datatype; #IMPLIED
+ class %ClassList.datatype; #IMPLIED
+ %SVG.Style.extra.attrib;"
+>
+
+<!-- module: svg-basic-text.mod ........................ -->
+
+<!ENTITY % FontFamilyValue.datatype "CDATA" >
+<!ENTITY % FontSizeValue.datatype "CDATA" >
+
+<!ENTITY % SVG.Font.extra.attrib "" >
+<!ENTITY % SVG.Font.attrib
+ "font-family %FontFamilyValue.datatype; #IMPLIED
+ font-size %FontSizeValue.datatype; #IMPLIED
+ font-style ( normal | italic | oblique | inherit ) #IMPLIED
+ font-weight ( normal | bold | bolder | lighter | 100 | 200 | 300 | 400 |
+ 500 | 600 | 700 | 800 | 900 | inherit ) #IMPLIED
+ %SVG.Font.extra.attrib;"
+>
+
+<!-- end of svg11-tiny-attribs.mod -->
+]]>
+
+<!-- end of svg-framework.mod -->
+]]>
+
+<!-- Post-Framework Redeclaration Placeholder .................... -->
+<!ENTITY % svg-postfw-redecl.module "IGNORE" >
+<![%svg-postfw-redecl.module;[
+%svg-postfw-redecl.mod;]]>
+
+<!-- ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: -->
+
+<!-- Core Attribute Module ....................................... -->
+<!ENTITY % svg-core-attrib.module "INCLUDE" >
+<![%svg-core-attrib.module;[
+<!ENTITY % svg-core-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Core Attribute//EN"
+ "svg-core-attrib.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Core Attribute Module ......................................... -->
+<!-- file: svg-core-attrib.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-tiny-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Core Attribute//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-core-attrib.mod"
+
+ ....................................................................... -->
+
+<!-- Core Attribute
+
+ id, xml:base, xml:lang, xml:space
+
+ This module defines the core set of attributes that can be present on
+ any element.
+-->
+
+<!ENTITY % SVG.id.attrib
+ "id ID #IMPLIED"
+>
+
+<!ENTITY % SVG.base.attrib
+ "xml:base %URI.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.lang.attrib
+ "xml:lang %LanguageCode.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.space.attrib
+ "xml:space ( default | preserve ) #IMPLIED"
+>
+
+<!ENTITY % SVG.Core.extra.attrib "" >
+
+<!ENTITY % SVG.Core.attrib
+ "%SVG.id.attrib;
+ %SVG.base.attrib;
+ %SVG.lang.attrib;
+ %SVG.space.attrib;
+ %SVG.Core.extra.attrib;"
+>
+
+<!-- end of svg-core-attrib.mod -->
+]]>
+
+<!-- Paint Attribute Module ...................................... -->
+<!ENTITY % svg-paint-attrib.module "INCLUDE" >
+<![%svg-paint-attrib.module;[
+<!ENTITY % svg-paint-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Paint Attribute//EN"
+ "svg-paint-attrib.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Paint Attribute Module ........................................ -->
+<!-- file: svg-paint-attrib.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-tiny-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Paint Attribute//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-paint-attrib.mod"
+
+ ....................................................................... -->
+
+<!-- Paint Attribute
+
+ fill, fill-rule, stroke, stroke-dasharray, stroke-dashoffset,
+ stroke-linecap, stroke-linejoin, stroke-miterlimit, stroke-width, color,
+ color-interpolation, color-rendering
+
+ This module defines the Paint and Color attribute sets.
+-->
+
+<!-- a 'fill' or 'stroke' property/attribute value: <paint> -->
+<!ENTITY % Paint.datatype "CDATA" >
+
+<!-- 'stroke-dasharray' property/attribute value (e.g., 'none', list of <number>s) -->
+<!ENTITY % StrokeDashArrayValue.datatype "CDATA" >
+
+<!-- 'stroke-dashoffset' property/attribute value (e.g., 'none', <legnth>) -->
+<!ENTITY % StrokeDashOffsetValue.datatype "CDATA" >
+
+<!-- 'stroke-miterlimit' property/attribute value (e.g., <number>) -->
+<!ENTITY % StrokeMiterLimitValue.datatype "CDATA" >
+
+<!-- 'stroke-width' property/attribute value (e.g., <length>) -->
+<!ENTITY % StrokeWidthValue.datatype "CDATA" >
+
+<!ENTITY % SVG.fill.attrib
+ "fill %Paint.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.fill-rule.attrib
+ "fill-rule %ClipFillRule.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.stroke.attrib
+ "stroke %Paint.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.stroke-dasharray.attrib
+ "stroke-dasharray %StrokeDashArrayValue.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.stroke-dashoffset.attrib
+ "stroke-dashoffset %StrokeDashOffsetValue.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.stroke-linecap.attrib
+ "stroke-linecap ( butt | round | square | inherit ) #IMPLIED"
+>
+
+<!ENTITY % SVG.stroke-linejoin.attrib
+ "stroke-linejoin ( miter | round | bevel | inherit ) #IMPLIED"
+>
+
+<!ENTITY % SVG.stroke-miterlimit.attrib
+ "stroke-miterlimit %StrokeMiterLimitValue.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.stroke-width.attrib
+ "stroke-width %StrokeWidthValue.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.Paint.extra.attrib "" >
+
+<!ENTITY % SVG.Paint.attrib
+ "%SVG.fill.attrib;
+ %SVG.fill-rule.attrib;
+ %SVG.stroke.attrib;
+ %SVG.stroke-dasharray.attrib;
+ %SVG.stroke-dashoffset.attrib;
+ %SVG.stroke-linecap.attrib;
+ %SVG.stroke-linejoin.attrib;
+ %SVG.stroke-miterlimit.attrib;
+ %SVG.stroke-width.attrib;
+ %SVG.Paint.extra.attrib;"
+>
+
+<!ENTITY % SVG.color.attrib
+ "color %Color.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.color-interpolation.attrib
+ "color-interpolation ( auto | sRGB | linearRGB | inherit ) #IMPLIED"
+>
+
+<!ENTITY % SVG.color-rendering.attrib
+ "color-rendering ( auto | optimizeSpeed | optimizeQuality | inherit )
+ #IMPLIED"
+>
+
+<!ENTITY % SVG.Color.extra.attrib "" >
+
+<!ENTITY % SVG.Color.attrib
+ "%SVG.color.attrib;
+ %SVG.color-interpolation.attrib;
+ %SVG.color-rendering.attrib;
+ %SVG.Color.extra.attrib;"
+>
+
+<!-- end of svg-paint-attrib.mod -->
+]]>
+
+<!-- Basic Graphics Attribute Module .............................. -->
+<!ENTITY % svg-graphics-attrib.module "INCLUDE" >
+<![%svg-graphics-attrib.module;[
+<!ENTITY % svg-graphics-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Basic Graphics Attribute//EN"
+ "svg-basic-graphics-attrib.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Basic Graphics Attribute Module ............................... -->
+<!-- file: svg-basic-graphics-attrib.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-tiny-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Basic Graphics Attribute//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-basic-graphics-attrib.mod"
+
+ ....................................................................... -->
+
+<!-- Basic Graphics Attribute
+
+ display, visibility
+
+ This module defines the Graphics attribute set.
+-->
+
+<!ENTITY % SVG.display.attrib
+ "display ( inline | block | list-item | run-in | compact | marker |
+ table | inline-table | table-row-group | table-header-group |
+ table-footer-group | table-row | table-column-group |
+ table-column | table-cell | table-caption | none | inherit )
+ #IMPLIED"
+>
+
+<!ENTITY % SVG.visibility.attrib
+ "visibility ( visible | hidden | inherit ) #IMPLIED"
+>
+
+<!ENTITY % SVG.Graphics.extra.attrib "" >
+
+<!ENTITY % SVG.Graphics.attrib
+ "%SVG.display.attrib;
+ %SVG.visibility.attrib;
+ %SVG.Graphics.extra.attrib;"
+>
+
+<!-- end of svg-basic-graphics-attrib.mod -->
+]]>
+
+<!-- Document Events Attribute Module ............................ -->
+<!ENTITY % svg-docevents-attrib.module "INCLUDE" >
+<![%svg-docevents-attrib.module;[
+<!ENTITY % svg-docevents-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Document Events Attribute//EN"
+ "svg-docevents-attrib.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Document Events Attribute Module .............................. -->
+<!-- file: svg-docevents-attrib.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-tiny-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Document Events Attribute//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-docevents-attrib.mod"
+
+ ....................................................................... -->
+
+<!-- Document Events Attribute
+
+ onunload, onabort, onerror, onresize, onscroll, onzoom
+
+ This module defines the DocumentEvents attribute set.
+-->
+
+<!ENTITY % SVG.onunload.attrib
+ "onunload %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onabort.attrib
+ "onabort %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onerror.attrib
+ "onerror %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onresize.attrib
+ "onresize %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onscroll.attrib
+ "onscroll %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onzoom.attrib
+ "onzoom %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.DocumentEvents.extra.attrib "" >
+
+<!ENTITY % SVG.DocumentEvents.attrib
+ "%SVG.onunload.attrib;
+ %SVG.onabort.attrib;
+ %SVG.onerror.attrib;
+ %SVG.onresize.attrib;
+ %SVG.onscroll.attrib;
+ %SVG.onzoom.attrib;
+ %SVG.DocumentEvents.extra.attrib;"
+>
+
+<!-- end of svg-docevents-attrib.mod -->
+]]>
+
+<!-- Graphical Element Events Attribute Module ................... -->
+<!ENTITY % svg-graphevents-attrib.module "INCLUDE" >
+<![%svg-graphevents-attrib.module;[
+<!ENTITY % svg-graphevents-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Graphical Element Events Attribute//EN"
+ "svg-graphevents-attrib.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Graphical Element Events Attribute Module ..................... -->
+<!-- file: svg-graphevents-attrib.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-tiny-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Graphical Element Events Attribute//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-graphevents-attrib.mod"
+
+ ....................................................................... -->
+
+<!-- Graphical Element Events Attribute
+
+ onfocusin, onfocusout, onactivate, onclick, onmousedown, onmouseup,
+ onmouseover, onmousemove, onmouseout, onload
+
+ This module defines the GraphicalEvents attribute set.
+-->
+
+<!ENTITY % SVG.onfocusin.attrib
+ "onfocusin %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onfocusout.attrib
+ "onfocusout %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onactivate.attrib
+ "onactivate %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onclick.attrib
+ "onclick %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onmousedown.attrib
+ "onmousedown %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onmouseup.attrib
+ "onmouseup %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onmouseover.attrib
+ "onmouseover %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onmousemove.attrib
+ "onmousemove %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onmouseout.attrib
+ "onmouseout %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onload.attrib
+ "onload %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.GraphicalEvents.extra.attrib "" >
+
+<!ENTITY % SVG.GraphicalEvents.attrib
+ "%SVG.onfocusin.attrib;
+ %SVG.onfocusout.attrib;
+ %SVG.onactivate.attrib;
+ %SVG.onclick.attrib;
+ %SVG.onmousedown.attrib;
+ %SVG.onmouseup.attrib;
+ %SVG.onmouseover.attrib;
+ %SVG.onmousemove.attrib;
+ %SVG.onmouseout.attrib;
+ %SVG.onload.attrib;
+ %SVG.GraphicalEvents.extra.attrib;"
+>
+
+<!-- end of svg-graphevents-attrib.mod -->
+]]>
+
+<!-- Animation Events Attribute Module ........................... -->
+<!ENTITY % svg-animevents-attrib.module "INCLUDE" >
+<![%svg-animevents-attrib.module;[
+<!ENTITY % svg-animevents-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Animation Events Attribute//EN"
+ "svg-animevents-attrib.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Animation Events Attribute Module ............................. -->
+<!-- file: svg-animevents-attrib.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-tiny-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Animation Events Attribute//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-animevents-attrib.mod"
+
+ ....................................................................... -->
+
+<!-- Animation Events Attribute
+
+ onbegin, onend, onrepeat, onload
+
+ This module defines the AnimationEvents attribute set.
+-->
+
+<!ENTITY % SVG.onbegin.attrib
+ "onbegin %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onend.attrib
+ "onend %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onrepeat.attrib
+ "onrepeat %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onload.attrib
+ "onload %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.AnimationEvents.extra.attrib "" >
+
+<!ENTITY % SVG.AnimationEvents.attrib
+ "%SVG.onbegin.attrib;
+ %SVG.onend.attrib;
+ %SVG.onrepeat.attrib;
+ %SVG.onload.attrib;
+ %SVG.AnimationEvents.extra.attrib;"
+>
+
+<!-- end of svg-animevents-attrib.mod -->
+]]>
+
+<!-- XLink Attribute Module ...................................... -->
+<!ENTITY % svg-xlink-attrib.module "INCLUDE" >
+<![%svg-xlink-attrib.module;[
+<!ENTITY % svg-xlink-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 XLink Attribute//EN"
+ "svg-xlink-attrib.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 XLink Attribute Module ........................................ -->
+<!-- file: svg-xlink-attrib.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-tiny-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 XLink Attribute//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-xlink-attrib.mod"
+
+ ....................................................................... -->
+
+<!-- XLink Attribute
+
+ type, href, role, arcrole, title, show, actuate
+
+ This module defines the XLink, XLinkRequired, XLinkEmbed, and
+ XLinkReplace attribute set.
+-->
+
+<!ENTITY % SVG.XLink.extra.attrib "" >
+
+<!ENTITY % SVG.XLink.attrib
+ "%XLINK.xmlns.attrib;
+ %XLINK.pfx;type ( simple ) #FIXED 'simple'
+ %XLINK.pfx;href %URI.datatype; #IMPLIED
+ %XLINK.pfx;role %URI.datatype; #IMPLIED
+ %XLINK.pfx;arcrole %URI.datatype; #IMPLIED
+ %XLINK.pfx;title CDATA #IMPLIED
+ %XLINK.pfx;show ( other ) 'other'
+ %XLINK.pfx;actuate ( onLoad ) #FIXED 'onLoad'
+ %SVG.XLink.extra.attrib;"
+>
+
+<!ENTITY % SVG.XLinkRequired.extra.attrib "" >
+
+<!ENTITY % SVG.XLinkRequired.attrib
+ "%XLINK.xmlns.attrib;
+ %XLINK.pfx;type ( simple ) #FIXED 'simple'
+ %XLINK.pfx;href %URI.datatype; #REQUIRED
+ %XLINK.pfx;role %URI.datatype; #IMPLIED
+ %XLINK.pfx;arcrole %URI.datatype; #IMPLIED
+ %XLINK.pfx;title CDATA #IMPLIED
+ %XLINK.pfx;show ( other ) 'other'
+ %XLINK.pfx;actuate ( onLoad ) #FIXED 'onLoad'
+ %SVG.XLinkRequired.extra.attrib;"
+>
+
+<!ENTITY % SVG.XLinkEmbed.extra.attrib "" >
+
+<!ENTITY % SVG.XLinkEmbed.attrib
+ "%XLINK.xmlns.attrib;
+ %XLINK.pfx;type ( simple ) #FIXED 'simple'
+ %XLINK.pfx;href %URI.datatype; #REQUIRED
+ %XLINK.pfx;role %URI.datatype; #IMPLIED
+ %XLINK.pfx;arcrole %URI.datatype; #IMPLIED
+ %XLINK.pfx;title CDATA #IMPLIED
+ %XLINK.pfx;show ( embed ) 'embed'
+ %XLINK.pfx;actuate ( onLoad ) #FIXED 'onLoad'
+ %SVG.XLinkEmbed.extra.attrib;"
+>
+
+<!ENTITY % SVG.XLinkReplace.extra.attrib "" >
+
+<!ENTITY % SVG.XLinkReplace.attrib
+ "%XLINK.xmlns.attrib;
+ %XLINK.pfx;type ( simple ) #FIXED 'simple'
+ %XLINK.pfx;href %URI.datatype; #REQUIRED
+ %XLINK.pfx;role %URI.datatype; #IMPLIED
+ %XLINK.pfx;arcrole %URI.datatype; #IMPLIED
+ %XLINK.pfx;title CDATA #IMPLIED
+ %XLINK.pfx;show ( new | replace ) 'replace'
+ %XLINK.pfx;actuate ( onRequest ) #FIXED 'onRequest'
+ %SVG.XLinkReplace.extra.attrib;"
+>
+
+<!-- end of svg-xlink-attrib.mod -->
+]]>
+
+<!-- External Resources Attribute Module ......................... -->
+<!ENTITY % svg-extresources-attrib.module "INCLUDE" >
+<![%svg-extresources-attrib.module;[
+<!ENTITY % svg-extresources-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 External Resources Attribute//EN"
+ "svg-extresources-attrib.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 External Resources Attribute Module ........................... -->
+<!-- file: svg-extresources-attrib.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-tiny-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 External Resources Attribute//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-extresources-attrib.mod"
+
+ ....................................................................... -->
+
+<!-- External Resources Attribute
+
+ externalResourcesRequired
+
+ This module defines the External attribute set.
+-->
+
+<!ENTITY % SVG.externalResourcesRequired.attrib
+ "externalResourcesRequired %Boolean.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.External.extra.attrib "" >
+
+<!ENTITY % SVG.External.attrib
+ "%SVG.externalResourcesRequired.attrib;
+ %SVG.External.extra.attrib;"
+>
+
+<!-- end of svg-extresources-attrib.mod -->
+]]>
+
+<!-- ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: -->
+
+<!-- Basic Structure Module ...................................... -->
+<!ENTITY % svg-structure.module "INCLUDE" >
+<![%svg-structure.module;[
+<!ENTITY % svg-structure.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Basic Structure//EN"
+ "svg-basic-structure.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Basic Structure Module ........................................ -->
+<!-- file: svg-basic-structure.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-tiny-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Basic Structure//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-basic-structure.mod"
+
+ ....................................................................... -->
+
+<!-- Basic Structure
+
+ svg, g, defs, desc, title, metadata, use
+
+ This module declares the major structural elements and their attributes.
+-->
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.svg.qname "svg" >
+<!ENTITY % SVG.g.qname "g" >
+<!ENTITY % SVG.defs.qname "defs" >
+<!ENTITY % SVG.desc.qname "desc" >
+<!ENTITY % SVG.title.qname "title" >
+<!ENTITY % SVG.metadata.qname "metadata" >
+<!ENTITY % SVG.use.qname "use" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Container.attrib "" >
+<!ENTITY % SVG.Conditional.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Viewport.attrib "" >
+<!ENTITY % SVG.Text.attrib "" >
+<!ENTITY % SVG.TextContent.attrib "" >
+<!ENTITY % SVG.Font.attrib "" >
+<!ENTITY % SVG.Paint.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Marker.attrib "" >
+<!ENTITY % SVG.Profile.attrib "" >
+<!ENTITY % SVG.Gradient.attrib "" >
+<!ENTITY % SVG.Clip.attrib "" >
+<!ENTITY % SVG.Mask.attrib "" >
+<!ENTITY % SVG.Filter.attrib "" >
+<!ENTITY % SVG.FilterColor.attrib "" >
+<!ENTITY % SVG.DocumentEvents.attrib "" >
+<!ENTITY % SVG.GraphicalEvents.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.XLinkEmbed.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Description.class ............................. -->
+
+<!ENTITY % SVG.Description.extra.class "" >
+
+<!ENTITY % SVG.Description.class
+ "%SVG.desc.qname; | %SVG.title.qname; | %SVG.metadata.qname;
+ %SVG.Description.extra.class;"
+>
+
+<!-- SVG.Use.class ..................................... -->
+
+<!ENTITY % SVG.Use.extra.class "" >
+
+<!ENTITY % SVG.Use.class
+ "| %SVG.use.qname; %SVG.Use.extra.class;"
+>
+
+<!-- SVG.Structure.class ............................... -->
+
+<!ENTITY % SVG.Structure.extra.class "" >
+
+<!ENTITY % SVG.Structure.class
+ "| %SVG.svg.qname; | %SVG.g.qname; | %SVG.defs.qname; %SVG.Use.class;
+ %SVG.Structure.extra.class;"
+>
+
+<!-- SVG.Presentation.attrib ........................... -->
+
+<!ENTITY % SVG.Presentation.extra.attrib "" >
+
+<!ENTITY % SVG.Presentation.attrib
+ "%SVG.Container.attrib;
+ %SVG.Viewport.attrib;
+ %SVG.Text.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Profile.attrib;
+ %SVG.Gradient.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.Cursor.attrib;
+ flood-color %SVGColor.datatype; #IMPLIED
+ flood-opacity %OpacityValue.datatype; #IMPLIED
+ lighting-color %SVGColor.datatype; #IMPLIED
+ %SVG.Presentation.extra.attrib;"
+>
+
+<!-- svg: SVG Document Element ......................... -->
+
+<!ENTITY % SVG.svg.extra.content "" >
+
+<!ENTITY % SVG.svg.element "INCLUDE" >
+<![%SVG.svg.element;[
+<!ENTITY % SVG.svg.content
+ "( %SVG.Description.class; | %SVG.Animation.class; %SVG.Structure.class;
+ %SVG.Conditional.class; %SVG.Image.class; %SVG.Style.class;
+ %SVG.Shape.class; %SVG.Text.class; %SVG.Marker.class; %SVG.Profile.class;
+ %SVG.Gradient.class; %SVG.Pattern.class; %SVG.Clip.class;
+ %SVG.Mask.class; %SVG.Filter.class; %SVG.Cursor.class;
+ %SVG.Hyperlink.class; %SVG.View.class; %SVG.Script.class;
+ %SVG.Font.class; %SVG.svg.extra.content; )*"
+>
+<!ELEMENT %SVG.svg.qname; %SVG.svg.content; >
+<!-- end of SVG.svg.element -->]]>
+
+<!ENTITY % SVG.svg.attlist "INCLUDE" >
+<![%SVG.svg.attlist;[
+<!ATTLIST %SVG.svg.qname;
+ %SVG.xmlns.attrib;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.DocumentEvents.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.External.attrib;
+ x %Coordinate.datatype; #IMPLIED
+ y %Coordinate.datatype; #IMPLIED
+ width %Length.datatype; #IMPLIED
+ height %Length.datatype; #IMPLIED
+ viewBox %ViewBoxSpec.datatype; #IMPLIED
+ preserveAspectRatio %PreserveAspectRatioSpec.datatype; 'xMidYMid meet'
+ zoomAndPan ( disable | magnify ) 'magnify'
+ version %Number.datatype; #FIXED '1.1'
+ baseProfile %Text.datatype; #IMPLIED
+ contentScriptType %ContentType.datatype; 'text/ecmascript'
+ contentStyleType %ContentType.datatype; 'text/css'
+>
+<!-- end of SVG.svg.attlist -->]]>
+
+<!-- g: Group Element .................................. -->
+
+<!ENTITY % SVG.g.extra.content "" >
+
+<!ENTITY % SVG.g.element "INCLUDE" >
+<![%SVG.g.element;[
+<!ENTITY % SVG.g.content
+ "( %SVG.Description.class; | %SVG.Animation.class; %SVG.Structure.class;
+ %SVG.Conditional.class; %SVG.Image.class; %SVG.Style.class;
+ %SVG.Shape.class; %SVG.Text.class; %SVG.Marker.class; %SVG.Profile.class;
+ %SVG.Gradient.class; %SVG.Pattern.class; %SVG.Clip.class;
+ %SVG.Mask.class; %SVG.Filter.class; %SVG.Cursor.class;
+ %SVG.Hyperlink.class; %SVG.View.class; %SVG.Script.class;
+ %SVG.Font.class; %SVG.g.extra.content; )*"
+>
+<!ELEMENT %SVG.g.qname; %SVG.g.content; >
+<!-- end of SVG.g.element -->]]>
+
+<!ENTITY % SVG.g.attlist "INCLUDE" >
+<![%SVG.g.attlist;[
+<!ATTLIST %SVG.g.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.External.attrib;
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.g.attlist -->]]>
+
+<!-- defs: Definisions Element ......................... -->
+
+<!ENTITY % SVG.defs.extra.content "" >
+
+<!ENTITY % SVG.defs.element "INCLUDE" >
+<![%SVG.defs.element;[
+<!ENTITY % SVG.defs.content
+ "( %SVG.Description.class; | %SVG.Animation.class; %SVG.Structure.class;
+ %SVG.Conditional.class; %SVG.Image.class; %SVG.Style.class;
+ %SVG.Shape.class; %SVG.Text.class; %SVG.Marker.class; %SVG.Profile.class;
+ %SVG.Gradient.class; %SVG.Pattern.class; %SVG.Clip.class;
+ %SVG.Mask.class; %SVG.Filter.class; %SVG.Cursor.class;
+ %SVG.Hyperlink.class; %SVG.View.class; %SVG.Script.class;
+ %SVG.Font.class; %SVG.defs.extra.content; )*"
+>
+<!ELEMENT %SVG.defs.qname; %SVG.defs.content; >
+<!-- end of SVG.defs.element -->]]>
+
+<!ENTITY % SVG.defs.attlist "INCLUDE" >
+<![%SVG.defs.attlist;[
+<!ATTLIST %SVG.defs.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.External.attrib;
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.defs.attlist -->]]>
+
+<!-- desc: Description Element ......................... -->
+
+<!ENTITY % SVG.desc.extra.content "" >
+
+<!ENTITY % SVG.desc.element "INCLUDE" >
+<![%SVG.desc.element;[
+<!ENTITY % SVG.desc.content
+ "( #PCDATA %SVG.desc.extra.content; )*"
+>
+<!ELEMENT %SVG.desc.qname; %SVG.desc.content; >
+<!-- end of SVG.desc.element -->]]>
+
+<!ENTITY % SVG.desc.attlist "INCLUDE" >
+<![%SVG.desc.attlist;[
+<!ATTLIST %SVG.desc.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+>
+<!-- end of SVG.desc.attlist -->]]>
+
+<!-- title: Title Element .............................. -->
+
+<!ENTITY % SVG.title.extra.content "" >
+
+<!ENTITY % SVG.title.element "INCLUDE" >
+<![%SVG.title.element;[
+<!ENTITY % SVG.title.content
+ "( #PCDATA %SVG.title.extra.content; )*"
+>
+<!ELEMENT %SVG.title.qname; %SVG.title.content; >
+<!-- end of SVG.title.element -->]]>
+
+<!ENTITY % SVG.title.attlist "INCLUDE" >
+<![%SVG.title.attlist;[
+<!ATTLIST %SVG.title.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+>
+<!-- end of SVG.title.attlist -->]]>
+
+<!-- metadata: Metadata Element ........................ -->
+
+<!ENTITY % SVG.metadata.extra.content "" >
+
+<!ENTITY % SVG.metadata.element "INCLUDE" >
+<![%SVG.metadata.element;[
+<!ENTITY % SVG.metadata.content
+ "( #PCDATA %SVG.metadata.extra.content; )*"
+>
+<!ELEMENT %SVG.metadata.qname; %SVG.metadata.content; >
+<!-- end of SVG.metadata.element -->]]>
+
+<!ENTITY % SVG.metadata.attlist "INCLUDE" >
+<![%SVG.metadata.attlist;[
+<!ATTLIST %SVG.metadata.qname;
+ %SVG.Core.attrib;
+>
+<!-- end of SVG.metadata.attlist -->]]>
+
+<!-- use: Use Element .................................. -->
+
+<!ENTITY % SVG.use.extra.content "" >
+
+<!ENTITY % SVG.use.element "INCLUDE" >
+<![%SVG.use.element;[
+<!ENTITY % SVG.use.content
+ "(( %SVG.Description.class; )*, ( %SVG.Animation.class;
+ %SVG.use.extra.content; )*)"
+>
+<!ELEMENT %SVG.use.qname; %SVG.use.content; >
+<!-- end of SVG.use.element -->]]>
+
+<!ENTITY % SVG.use.attlist "INCLUDE" >
+<![%SVG.use.attlist;[
+<!ATTLIST %SVG.use.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.XLinkEmbed.attrib;
+ %SVG.External.attrib;
+ x %Coordinate.datatype; #IMPLIED
+ y %Coordinate.datatype; #IMPLIED
+ width %Length.datatype; #IMPLIED
+ height %Length.datatype; #IMPLIED
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.use.attlist -->]]>
+
+<!-- end of svg-basic-structure.mod -->
+]]>
+
+<!-- Conditional Processing Module ............................... -->
+<!ENTITY % svg-conditional.module "INCLUDE" >
+<![%svg-conditional.module;[
+<!ENTITY % svg-conditional.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Conditional Processing//EN"
+ "svg-conditional.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Conditional Processing Module ................................. -->
+<!-- file: svg-conditional.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-tiny-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Conditional Processing//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-conditional.mod"
+
+ ....................................................................... -->
+
+<!-- Conditional Processing
+
+ switch
+
+ This module declares markup to provide support for conditional processing.
+-->
+
+<!-- extension list specification -->
+<!ENTITY % ExtensionList.datatype "CDATA" >
+
+<!-- feature list specification -->
+<!ENTITY % FeatureList.datatype "CDATA" >
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.switch.qname "switch" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Container.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Viewport.attrib "" >
+<!ENTITY % SVG.Text.attrib "" >
+<!ENTITY % SVG.TextContent.attrib "" >
+<!ENTITY % SVG.Font.attrib "" >
+<!ENTITY % SVG.Paint.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Marker.attrib "" >
+<!ENTITY % SVG.Profile.attrib "" >
+<!ENTITY % SVG.Gradient.attrib "" >
+<!ENTITY % SVG.Clip.attrib "" >
+<!ENTITY % SVG.Mask.attrib "" >
+<!ENTITY % SVG.Filter.attrib "" >
+<!ENTITY % SVG.FilterColor.attrib "" >
+<!ENTITY % SVG.GraphicalEvents.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Conditional.class ............................. -->
+
+<!ENTITY % SVG.Conditional.extra.class "" >
+
+<!ENTITY % SVG.Conditional.class
+ "| %SVG.switch.qname; %SVG.Conditional.extra.class;"
+>
+
+<!-- SVG.Conditional.attrib ............................ -->
+
+<!ENTITY % SVG.Conditional.extra.attrib "" >
+
+<!ENTITY % SVG.Conditional.attrib
+ "requiredFeatures %FeatureList.datatype; #IMPLIED
+ requiredExtensions %ExtensionList.datatype; #IMPLIED
+ systemLanguage %LanguageCodes.datatype; #IMPLIED
+ %SVG.Conditional.extra.attrib;"
+>
+
+<!-- SVG.Presentation.attrib ........................... -->
+
+<!ENTITY % SVG.Presentation.extra.attrib "" >
+
+<!ENTITY % SVG.Presentation.attrib
+ "%SVG.Container.attrib;
+ %SVG.Viewport.attrib;
+ %SVG.Text.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Profile.attrib;
+ %SVG.Gradient.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.Cursor.attrib;
+ flood-color %SVGColor.datatype; #IMPLIED
+ flood-opacity %OpacityValue.datatype; #IMPLIED
+ lighting-color %SVGColor.datatype; #IMPLIED
+ %SVG.Presentation.extra.attrib;"
+>
+
+<!-- switch: Switch Element ............................ -->
+
+<!ENTITY % SVG.switch.extra.content "" >
+
+<!ENTITY % SVG.switch.element "INCLUDE" >
+<![%SVG.switch.element;[
+<!ENTITY % SVG.switch.content
+ "(( %SVG.Description.class; )*, ( %SVG.svg.qname; | %SVG.g.qname;
+ | %SVG.use.qname; | %SVG.text.qname; | %SVG.Animation.class;
+ %SVG.Conditional.class; %SVG.Image.class; %SVG.Shape.class;
+ %SVG.Hyperlink.class; %SVG.Extensibility.class;
+ %SVG.switch.extra.content; )*)"
+>
+<!ELEMENT %SVG.switch.qname; %SVG.switch.content; >
+<!-- end of SVG.switch.element -->]]>
+
+<!ENTITY % SVG.switch.attlist "INCLUDE" >
+<![%SVG.switch.attlist;[
+<!ATTLIST %SVG.switch.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.External.attrib;
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.switch.attlist -->]]>
+
+<!-- end of svg-conditional.mod -->
+]]>
+
+<!-- Image Module ................................................ -->
+<!ENTITY % svg-image.module "INCLUDE" >
+<![%svg-image.module;[
+<!ENTITY % svg-image.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Image//EN"
+ "svg-image.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Image Module .................................................. -->
+<!-- file: svg-image.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-tiny-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Image//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-image.mod"
+
+ ....................................................................... -->
+
+<!-- Image
+
+ image
+
+ This module declares markup to provide support for image.
+-->
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.image.qname "image" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Conditional.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Viewport.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Profile.attrib "" >
+<!ENTITY % SVG.Clip.attrib "" >
+<!ENTITY % SVG.Mask.attrib "" >
+<!ENTITY % SVG.Filter.attrib "" >
+<!ENTITY % SVG.GraphicalEvents.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.XLinkEmbed.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Image.class ................................... -->
+
+<!ENTITY % SVG.Image.extra.class "" >
+
+<!ENTITY % SVG.Image.class
+ "| %SVG.image.qname; %SVG.Image.extra.class;"
+>
+
+<!-- image: Image Element .............................. -->
+
+<!ENTITY % SVG.image.extra.content "" >
+
+<!ENTITY % SVG.image.element "INCLUDE" >
+<![%SVG.image.element;[
+<!ENTITY % SVG.image.content
+ "(( %SVG.Description.class; )*, ( %SVG.Animation.class;
+ %SVG.image.extra.content; )*)"
+>
+<!ELEMENT %SVG.image.qname; %SVG.image.content; >
+<!-- end of SVG.image.element -->]]>
+
+<!ENTITY % SVG.image.attlist "INCLUDE" >
+<![%SVG.image.attlist;[
+<!ATTLIST %SVG.image.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Viewport.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Profile.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.XLinkEmbed.attrib;
+ %SVG.External.attrib;
+ x %Coordinate.datatype; #IMPLIED
+ y %Coordinate.datatype; #IMPLIED
+ width %Length.datatype; #REQUIRED
+ height %Length.datatype; #REQUIRED
+ preserveAspectRatio %PreserveAspectRatioSpec.datatype; 'xMidYMid meet'
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.image.attlist -->]]>
+
+<!-- end of svg-image.mod -->
+]]>
+
+<!-- Style Module ................................................ -->
+<!ENTITY % svg-style.module "INCLUDE" >
+<![%svg-style.module;[
+<!ENTITY % svg-style.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Style//EN"
+ "svg-style.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Style Module .................................................. -->
+<!-- file: svg-style.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-tiny-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Style//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-style.mod"
+
+ ....................................................................... -->
+
+<!-- Style
+
+ style
+
+ This module declares markup to provide support for stylesheet.
+-->
+
+<!-- list of classes -->
+<!ENTITY % ClassList.datatype "CDATA" >
+
+<!-- comma-separated list of media descriptors. -->
+<!ENTITY % MediaDesc.datatype "CDATA" >
+
+<!-- style sheet data -->
+<!ENTITY % StyleSheet.datatype "CDATA" >
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.style.qname "style" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+
+<!-- SVG.Style.class ................................... -->
+
+<!ENTITY % SVG.Style.extra.class "" >
+
+<!ENTITY % SVG.Style.class
+ "| %SVG.style.qname; %SVG.Style.extra.class;"
+>
+
+<!-- SVG.Style.attrib .................................. -->
+
+<!ENTITY % SVG.Style.extra.attrib "" >
+
+<!ENTITY % SVG.Style.attrib
+ "style %StyleSheet.datatype; #IMPLIED
+ class %ClassList.datatype; #IMPLIED
+ %SVG.Style.extra.attrib;"
+>
+
+<!-- style: Style Element .............................. -->
+
+<!ENTITY % SVG.style.extra.content "" >
+
+<!ENTITY % SVG.style.element "INCLUDE" >
+<![%SVG.style.element;[
+<!ENTITY % SVG.style.content
+ "( #PCDATA %SVG.style.extra.content; )*"
+>
+<!ELEMENT %SVG.style.qname; %SVG.style.content; >
+<!-- end of SVG.style.element -->]]>
+
+<!ENTITY % SVG.style.attlist "INCLUDE" >
+<![%SVG.style.attlist;[
+<!ATTLIST %SVG.style.qname;
+ xml:space ( preserve ) #FIXED 'preserve'
+ %SVG.Core.attrib;
+ type %ContentType.datatype; #REQUIRED
+ media %MediaDesc.datatype; #IMPLIED
+ title %Text.datatype; #IMPLIED
+>
+<!-- end of SVG.style.attlist -->]]>
+
+<!-- end of svg-style.mod -->
+]]>
+
+<!-- Shape Module ................................................ -->
+<!ENTITY % svg-shape.module "INCLUDE" >
+<![%svg-shape.module;[
+<!ENTITY % svg-shape.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Shape//EN"
+ "svg-shape.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Shape Module .................................................. -->
+<!-- file: svg-shape.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-tiny-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Shape//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-shape.mod"
+
+ ....................................................................... -->
+
+<!-- Shape
+
+ path, rect, circle, line, ellipse, polyline, polygon
+
+ This module declares markup to provide support for graphical shapes.
+-->
+
+<!-- a list of points -->
+<!ENTITY % Points.datatype "CDATA" >
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.path.qname "path" >
+<!ENTITY % SVG.rect.qname "rect" >
+<!ENTITY % SVG.circle.qname "circle" >
+<!ENTITY % SVG.line.qname "line" >
+<!ENTITY % SVG.ellipse.qname "ellipse" >
+<!ENTITY % SVG.polyline.qname "polyline" >
+<!ENTITY % SVG.polygon.qname "polygon" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Conditional.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Paint.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Marker.attrib "" >
+<!ENTITY % SVG.Clip.attrib "" >
+<!ENTITY % SVG.Mask.attrib "" >
+<!ENTITY % SVG.Filter.attrib "" >
+<!ENTITY % SVG.GraphicalEvents.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Shape.class ................................... -->
+
+<!ENTITY % SVG.Shape.extra.class "" >
+
+<!ENTITY % SVG.Shape.class
+ "| %SVG.path.qname; | %SVG.rect.qname; | %SVG.circle.qname;
+ | %SVG.line.qname; | %SVG.ellipse.qname; | %SVG.polyline.qname;
+ | %SVG.polygon.qname; %SVG.Shape.extra.class;"
+>
+
+<!-- path: Path Element ................................ -->
+
+<!ENTITY % SVG.path.extra.content "" >
+
+<!ENTITY % SVG.path.element "INCLUDE" >
+<![%SVG.path.element;[
+<!ENTITY % SVG.path.content
+ "(( %SVG.Description.class; )*, ( %SVG.Animation.class;
+ %SVG.path.extra.content; )*)"
+>
+<!ELEMENT %SVG.path.qname; %SVG.path.content; >
+<!-- end of SVG.path.element -->]]>
+
+<!ENTITY % SVG.path.attlist "INCLUDE" >
+<![%SVG.path.attlist;[
+<!ATTLIST %SVG.path.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.External.attrib;
+ d %PathData.datatype; #REQUIRED
+ pathLength %Number.datatype; #IMPLIED
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.path.attlist -->]]>
+
+<!-- rect: Rectangle Element ........................... -->
+
+<!ENTITY % SVG.rect.extra.content "" >
+
+<!ENTITY % SVG.rect.element "INCLUDE" >
+<![%SVG.rect.element;[
+<!ENTITY % SVG.rect.content
+ "(( %SVG.Description.class; )*, ( %SVG.Animation.class;
+ %SVG.rect.extra.content; )*)"
+>
+<!ELEMENT %SVG.rect.qname; %SVG.rect.content; >
+<!-- end of SVG.rect.element -->]]>
+
+<!ENTITY % SVG.rect.attlist "INCLUDE" >
+<![%SVG.rect.attlist;[
+<!ATTLIST %SVG.rect.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.External.attrib;
+ x %Coordinate.datatype; #IMPLIED
+ y %Coordinate.datatype; #IMPLIED
+ width %Length.datatype; #REQUIRED
+ height %Length.datatype; #REQUIRED
+ rx %Length.datatype; #IMPLIED
+ ry %Length.datatype; #IMPLIED
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.rect.attlist -->]]>
+
+<!-- circle: Circle Element ............................ -->
+
+<!ENTITY % SVG.circle.extra.content "" >
+
+<!ENTITY % SVG.circle.element "INCLUDE" >
+<![%SVG.circle.element;[
+<!ENTITY % SVG.circle.content
+ "(( %SVG.Description.class; )*, ( %SVG.Animation.class;
+ %SVG.circle.extra.content; )*)"
+>
+<!ELEMENT %SVG.circle.qname; %SVG.circle.content; >
+<!-- end of SVG.circle.element -->]]>
+
+<!ENTITY % SVG.circle.attlist "INCLUDE" >
+<![%SVG.circle.attlist;[
+<!ATTLIST %SVG.circle.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.External.attrib;
+ cx %Coordinate.datatype; #IMPLIED
+ cy %Coordinate.datatype; #IMPLIED
+ r %Length.datatype; #REQUIRED
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.circle.attlist -->]]>
+
+<!-- line: Line Element ................................ -->
+
+<!ENTITY % SVG.line.extra.content "" >
+
+<!ENTITY % SVG.line.element "INCLUDE" >
+<![%SVG.line.element;[
+<!ENTITY % SVG.line.content
+ "(( %SVG.Description.class; )*, ( %SVG.Animation.class;
+ %SVG.line.extra.content; )*)"
+>
+<!ELEMENT %SVG.line.qname; %SVG.line.content; >
+<!-- end of SVG.line.element -->]]>
+
+<!ENTITY % SVG.line.attlist "INCLUDE" >
+<![%SVG.line.attlist;[
+<!ATTLIST %SVG.line.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.External.attrib;
+ x1 %Coordinate.datatype; #IMPLIED
+ y1 %Coordinate.datatype; #IMPLIED
+ x2 %Coordinate.datatype; #IMPLIED
+ y2 %Coordinate.datatype; #IMPLIED
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.line.attlist -->]]>
+
+<!-- ellipse: Ellipse Element .......................... -->
+
+<!ENTITY % SVG.ellipse.extra.content "" >
+
+<!ENTITY % SVG.ellipse.element "INCLUDE" >
+<![%SVG.ellipse.element;[
+<!ENTITY % SVG.ellipse.content
+ "(( %SVG.Description.class; )*, ( %SVG.Animation.class;
+ %SVG.ellipse.extra.content; )*)"
+>
+<!ELEMENT %SVG.ellipse.qname; %SVG.ellipse.content; >
+<!-- end of SVG.ellipse.element -->]]>
+
+<!ENTITY % SVG.ellipse.attlist "INCLUDE" >
+<![%SVG.ellipse.attlist;[
+<!ATTLIST %SVG.ellipse.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.External.attrib;
+ cx %Coordinate.datatype; #IMPLIED
+ cy %Coordinate.datatype; #IMPLIED
+ rx %Length.datatype; #REQUIRED
+ ry %Length.datatype; #REQUIRED
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.ellipse.attlist -->]]>
+
+<!-- polyline: Polyline Element ........................ -->
+
+<!ENTITY % SVG.polyline.extra.content "" >
+
+<!ENTITY % SVG.polyline.element "INCLUDE" >
+<![%SVG.polyline.element;[
+<!ENTITY % SVG.polyline.content
+ "(( %SVG.Description.class; )*, ( %SVG.Animation.class;
+ %SVG.polyline.extra.content; )*)"
+>
+<!ELEMENT %SVG.polyline.qname; %SVG.polyline.content; >
+<!-- end of SVG.polyline.element -->]]>
+
+<!ENTITY % SVG.polyline.attlist "INCLUDE" >
+<![%SVG.polyline.attlist;[
+<!ATTLIST %SVG.polyline.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.External.attrib;
+ points %Points.datatype; #REQUIRED
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.polyline.attlist -->]]>
+
+<!-- polygon: Polygon Element .......................... -->
+
+<!ENTITY % SVG.polygon.extra.content "" >
+
+<!ENTITY % SVG.polygon.element "INCLUDE" >
+<![%SVG.polygon.element;[
+<!ENTITY % SVG.polygon.content
+ "(( %SVG.Description.class; )*, ( %SVG.Animation.class;
+ %SVG.polygon.extra.content; )*)"
+>
+<!ELEMENT %SVG.polygon.qname; %SVG.polygon.content; >
+<!-- end of SVG.polygon.element -->]]>
+
+<!ENTITY % SVG.polygon.attlist "INCLUDE" >
+<![%SVG.polygon.attlist;[
+<!ATTLIST %SVG.polygon.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.External.attrib;
+ points %Points.datatype; #REQUIRED
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.polygon.attlist -->]]>
+
+<!-- end of svg-shape.mod -->
+]]>
+
+<!-- Basic Text Module ........................................... -->
+<!ENTITY % svg-text.module "INCLUDE" >
+<![%svg-text.module;[
+<!ENTITY % svg-text.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Basic Text//EN"
+ "svg-basic-text.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Basic Text Module ............................................. -->
+<!-- file: svg-basic-text.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-tiny-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Basic Text//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-basic-text.mod"
+
+ ....................................................................... -->
+
+<!-- Basic Text
+
+ text, altGlyph, altGlyphDef, glyphRef
+
+ This module declares markup to provide support for text.
+-->
+
+<!-- 'font-family' property/attribute value (i.e., list of fonts) -->
+<!ENTITY % FontFamilyValue.datatype "CDATA" >
+
+<!-- 'font-size' property/attribute value -->
+<!ENTITY % FontSizeValue.datatype "CDATA" >
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.text.qname "text" >
+<!ENTITY % SVG.altGlyph.qname "altGlyph" >
+<!ENTITY % SVG.altGlyphDef.qname "altGlyphDef" >
+<!ENTITY % SVG.glyphRef.qname "glyphRef" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Conditional.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Paint.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Clip.attrib "" >
+<!ENTITY % SVG.Mask.attrib "" >
+<!ENTITY % SVG.Filter.attrib "" >
+<!ENTITY % SVG.GraphicalEvents.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.XLink.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Text.class .................................... -->
+
+<!ENTITY % SVG.Text.extra.class "" >
+
+<!ENTITY % SVG.Text.class
+ "| %SVG.text.qname; | %SVG.altGlyphDef.qname; %SVG.Text.extra.class;"
+>
+
+<!-- SVG.TextContent.class ............................. -->
+
+<!ENTITY % SVG.TextContent.extra.class "" >
+
+<!ENTITY % SVG.TextContent.class
+ "| %SVG.altGlyph.qname; %SVG.TextContent.extra.class;"
+>
+
+<!-- SVG.Font.attrib ................................... -->
+
+<!ENTITY % SVG.Font.extra.attrib "" >
+
+<!ENTITY % SVG.Font.attrib
+ "font-family %FontFamilyValue.datatype; #IMPLIED
+ font-size %FontSizeValue.datatype; #IMPLIED
+ font-style ( normal | italic | oblique | inherit ) #IMPLIED
+ font-weight ( normal | bold | bolder | lighter | 100 | 200 | 300 | 400 |
+ 500 | 600 | 700 | 800 | 900 | inherit ) #IMPLIED
+ %SVG.Font.extra.attrib;"
+>
+
+<!-- text: Text Element ................................ -->
+
+<!ENTITY % SVG.text.extra.content "" >
+
+<!ENTITY % SVG.text.element "INCLUDE" >
+<![%SVG.text.element;[
+<!ENTITY % SVG.text.content
+ "( #PCDATA | %SVG.Description.class; | %SVG.Animation.class;
+ %SVG.TextContent.class; %SVG.Hyperlink.class;
+ %SVG.text.extra.content; )*"
+>
+<!ELEMENT %SVG.text.qname; %SVG.text.content; >
+<!-- end of SVG.text.element -->]]>
+
+<!ENTITY % SVG.text.attlist "INCLUDE" >
+<![%SVG.text.attlist;[
+<!ATTLIST %SVG.text.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.External.attrib;
+ x %Coordinates.datatype; #IMPLIED
+ y %Coordinates.datatype; #IMPLIED
+ rotate %Numbers.datatype; #IMPLIED
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.text.attlist -->]]>
+
+<!-- altGlyph: Alternate Glyph Element ................. -->
+
+<!ENTITY % SVG.altGlyph.extra.content "" >
+
+<!ENTITY % SVG.altGlyph.element "INCLUDE" >
+<![%SVG.altGlyph.element;[
+<!ENTITY % SVG.altGlyph.content
+ "( #PCDATA %SVG.altGlyph.extra.content; )*"
+>
+<!ELEMENT %SVG.altGlyph.qname; %SVG.altGlyph.content; >
+<!-- end of SVG.altGlyph.element -->]]>
+
+<!ENTITY % SVG.altGlyph.attlist "INCLUDE" >
+<![%SVG.altGlyph.attlist;[
+<!ATTLIST %SVG.altGlyph.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.XLink.attrib;
+ %SVG.External.attrib;
+ glyphRef CDATA #IMPLIED
+ format CDATA #IMPLIED
+>
+<!-- end of SVG.altGlyph.attlist -->]]>
+
+<!-- altGlyphDef: Alternate Glyph Definition Element ... -->
+
+<!ENTITY % SVG.altGlyphDef.extra.content "" >
+
+<!ENTITY % SVG.altGlyphDef.element "INCLUDE" >
+<![%SVG.altGlyphDef.element;[
+<!ENTITY % SVG.altGlyphDef.content
+ "( %SVG.glyphRef.qname;+ %SVG.altGlyphDef.extra.content; )"
+>
+<!ELEMENT %SVG.altGlyphDef.qname; %SVG.altGlyphDef.content; >
+<!-- end of SVG.altGlyphDef.element -->]]>
+
+<!ENTITY % SVG.altGlyphDef.attlist "INCLUDE" >
+<![%SVG.altGlyphDef.attlist;[
+<!ATTLIST %SVG.altGlyphDef.qname;
+ %SVG.Core.attrib;
+>
+<!-- end of SVG.altGlyphDef.attlist -->]]>
+
+<!-- glyphRef: Glyph Reference Element ................. -->
+
+<!ENTITY % SVG.glyphRef.element "INCLUDE" >
+<![%SVG.glyphRef.element;[
+<!ENTITY % SVG.glyphRef.content "EMPTY" >
+<!ELEMENT %SVG.glyphRef.qname; %SVG.glyphRef.content; >
+<!-- end of SVG.glyphRef.element -->]]>
+
+<!ENTITY % SVG.glyphRef.attlist "INCLUDE" >
+<![%SVG.glyphRef.attlist;[
+<!ATTLIST %SVG.glyphRef.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Font.attrib;
+ %SVG.XLink.attrib;
+ glyphRef CDATA #IMPLIED
+ format CDATA #IMPLIED
+>
+<!-- end of SVG.glyphRef.attlist -->]]>
+
+<!-- end of svg-basic-text.mod -->
+]]>
+
+<!-- Hyperlinking Module ......................................... -->
+<!ENTITY % svg-hyperlink.module "INCLUDE" >
+<![%svg-hyperlink.module;[
+<!ENTITY % svg-hyperlink.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Hyperlinking//EN"
+ "svg-hyperlink.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Hyperlinking Module ........................................... -->
+<!-- file: svg-hyperlink.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-tiny-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Hyperlinking//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-hyperlink.mod"
+
+ ....................................................................... -->
+
+<!-- Hyperlinking
+
+ a
+
+ This module declares markup to provide support for hyper linking.
+-->
+
+<!-- link to this target -->
+<!ENTITY % LinkTarget.datatype "NMTOKEN" >
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.a.qname "a" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Conditional.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Viewport.attrib "" >
+<!ENTITY % SVG.Text.attrib "" >
+<!ENTITY % SVG.TextContent.attrib "" >
+<!ENTITY % SVG.Font.attrib "" >
+<!ENTITY % SVG.Paint.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Marker.attrib "" >
+<!ENTITY % SVG.Gradient.attrib "" >
+<!ENTITY % SVG.Clip.attrib "" >
+<!ENTITY % SVG.Mask.attrib "" >
+<!ENTITY % SVG.Filter.attrib "" >
+<!ENTITY % SVG.FilterColor.attrib "" >
+<!ENTITY % SVG.GraphicalEvents.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.XLinkReplace.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Hyperlink.class ............................... -->
+
+<!ENTITY % SVG.Hyperlink.extra.class "" >
+
+<!ENTITY % SVG.Hyperlink.class
+ "| %SVG.a.qname; %SVG.Hyperlink.extra.class;"
+>
+
+<!-- SVG.Presentation.attrib ........................... -->
+
+<!ENTITY % SVG.Presentation.extra.attrib "" >
+
+<!ENTITY % SVG.Presentation.attrib
+ "%SVG.Container.attrib;
+ %SVG.Viewport.attrib;
+ %SVG.Text.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Profile.attrib;
+ %SVG.Gradient.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.Cursor.attrib;
+ flood-color %SVGColor.datatype; #IMPLIED
+ flood-opacity %OpacityValue.datatype; #IMPLIED
+ lighting-color %SVGColor.datatype; #IMPLIED
+ %SVG.Presentation.extra.attrib;"
+>
+
+<!-- a: Anchor Element ................................. -->
+
+<!ENTITY % SVG.a.extra.content "" >
+
+<!ENTITY % SVG.a.element "INCLUDE" >
+<![%SVG.a.element;[
+<!ENTITY % SVG.a.content
+ "( #PCDATA | %SVG.Description.class; | %SVG.Animation.class;
+ %SVG.Structure.class; %SVG.Conditional.class; %SVG.Image.class;
+ %SVG.Style.class; %SVG.Shape.class; %SVG.Text.class; %SVG.Marker.class;
+ %SVG.Profile.class; %SVG.Gradient.class; %SVG.Pattern.class;
+ %SVG.Clip.class; %SVG.Mask.class; %SVG.Filter.class; %SVG.Cursor.class;
+ %SVG.Hyperlink.class; %SVG.View.class; %SVG.Script.class;
+ %SVG.Font.class; %SVG.a.extra.content; )*"
+>
+<!ELEMENT %SVG.a.qname; %SVG.a.content; >
+<!-- end of SVG.a.element -->]]>
+
+<!ENTITY % SVG.a.attlist "INCLUDE" >
+<![%SVG.a.attlist;[
+<!ATTLIST %SVG.a.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.XLinkReplace.attrib;
+ %SVG.External.attrib;
+ transform %TransformList.datatype; #IMPLIED
+ target %LinkTarget.datatype; #IMPLIED
+>
+<!-- end of SVG.a.attlist -->]]>
+
+<!-- end of svg-hyperlink.mod -->
+]]>
+
+<!-- View Module ................................................. -->
+<!ENTITY % svg-view.module "INCLUDE" >
+<![%svg-view.module;[
+<!ENTITY % svg-view.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 View//EN"
+ "svg-view.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 View Module ................................................... -->
+<!-- file: svg-view.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-tiny-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 View//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-view.mod"
+
+ ....................................................................... -->
+
+<!-- View
+
+ view
+
+ This module declares markup to provide support for view.
+-->
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.view.qname "view" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.View.class .................................... -->
+
+<!ENTITY % SVG.View.extra.class "" >
+
+<!ENTITY % SVG.View.class
+ "| %SVG.view.qname; %SVG.View.extra.class;"
+>
+
+<!-- view: View Element ................................ -->
+
+<!ENTITY % SVG.view.extra.content "" >
+
+<!ENTITY % SVG.view.element "INCLUDE" >
+<![%SVG.view.element;[
+<!ENTITY % SVG.view.content
+ "( %SVG.Description.class; %SVG.view.extra.content; )*"
+>
+<!ELEMENT %SVG.view.qname; %SVG.view.content; >
+<!-- end of SVG.view.element -->]]>
+
+<!ENTITY % SVG.view.attlist "INCLUDE" >
+<![%SVG.view.attlist;[
+<!ATTLIST %SVG.view.qname;
+ %SVG.Core.attrib;
+ %SVG.External.attrib;
+ viewBox %ViewBoxSpec.datatype; #IMPLIED
+ preserveAspectRatio %PreserveAspectRatioSpec.datatype; 'xMidYMid meet'
+ zoomAndPan ( disable | magnify ) 'magnify'
+ viewTarget CDATA #IMPLIED
+>
+<!-- end of SVG.view.attlist -->]]>
+
+<!-- end of svg-view.mod -->
+]]>
+
+<!-- Scripting Module ............................................ -->
+<!ENTITY % svg-script.module "INCLUDE" >
+<![%svg-script.module;[
+<!ENTITY % svg-script.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Scripting//EN"
+ "svg-script.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Scripting Module .............................................. -->
+<!-- file: svg-script.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-tiny-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Scripting//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-script.mod"
+
+ ....................................................................... -->
+
+<!-- Scripting
+
+ script
+
+ This module declares markup to provide support for scripting.
+-->
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.script.qname "script" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.XLink.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Script.class .................................. -->
+
+<!ENTITY % SVG.Script.extra.class "" >
+
+<!ENTITY % SVG.Script.class
+ "| %SVG.script.qname; %SVG.Script.extra.class;"
+>
+
+<!-- script: Script Element ............................ -->
+
+<!ENTITY % SVG.script.extra.content "" >
+
+<!ENTITY % SVG.script.element "INCLUDE" >
+<![%SVG.script.element;[
+<!ENTITY % SVG.script.content
+ "( #PCDATA %SVG.script.extra.content; )*"
+>
+<!ELEMENT %SVG.script.qname; %SVG.script.content; >
+<!-- end of SVG.script.element -->]]>
+
+<!ENTITY % SVG.script.attlist "INCLUDE" >
+<![%SVG.script.attlist;[
+<!ATTLIST %SVG.script.qname;
+ %SVG.Core.attrib;
+ %SVG.XLink.attrib;
+ %SVG.External.attrib;
+ type %ContentType.datatype; #REQUIRED
+>
+<!-- end of SVG.script.attlist -->]]>
+
+<!-- end of svg-script.mod -->
+]]>
+
+<!-- Animation Module ............................................ -->
+<!ENTITY % svg-animation.module "INCLUDE" >
+<![%svg-animation.module;[
+<!ENTITY % svg-animation.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Animation//EN"
+ "svg-animation.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Animation Module .............................................. -->
+<!-- file: svg-animation.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-tiny-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Animation//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-animation.mod"
+
+ ....................................................................... -->
+
+<!-- Animation
+
+ animate, set, animateMotion, animateColor, animateTransform, mpath
+
+ This module declares markup to provide support for animation.
+-->
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.animate.qname "animate" >
+<!ENTITY % SVG.set.qname "set" >
+<!ENTITY % SVG.animateMotion.qname "animateMotion" >
+<!ENTITY % SVG.animateColor.qname "animateColor" >
+<!ENTITY % SVG.animateTransform.qname "animateTransform" >
+<!ENTITY % SVG.mpath.qname "mpath" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Conditional.attrib "" >
+<!ENTITY % SVG.AnimationEvents.attrib "" >
+<!ENTITY % SVG.XLink.attrib "" >
+<!ENTITY % SVG.XLinkRequired.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Animation.class ............................... -->
+
+<!ENTITY % SVG.Animation.extra.class "" >
+
+<!ENTITY % SVG.Animation.class
+ "%SVG.animate.qname; | %SVG.set.qname; | %SVG.animateMotion.qname; |
+ %SVG.animateColor.qname; | %SVG.animateTransform.qname;
+ %SVG.Animation.extra.class;"
+>
+
+<!-- SVG.Animation.attrib .............................. -->
+
+<!ENTITY % SVG.Animation.extra.attrib "" >
+
+<!ENTITY % SVG.Animation.attrib
+ "%SVG.XLink.attrib;
+ %SVG.Animation.extra.attrib;"
+>
+
+<!-- SVG.AnimationAttribute.attrib ..................... -->
+
+<!ENTITY % SVG.AnimationAttribute.extra.attrib "" >
+
+<!ENTITY % SVG.AnimationAttribute.attrib
+ "attributeName CDATA #REQUIRED
+ attributeType CDATA #IMPLIED
+ %SVG.AnimationAttribute.extra.attrib;"
+>
+
+<!-- SVG.AnimationTiming.attrib ........................ -->
+
+<!ENTITY % SVG.AnimationTiming.extra.attrib "" >
+
+<!ENTITY % SVG.AnimationTiming.attrib
+ "begin CDATA #IMPLIED
+ dur CDATA #IMPLIED
+ end CDATA #IMPLIED
+ min CDATA #IMPLIED
+ max CDATA #IMPLIED
+ restart ( always | never | whenNotActive ) 'always'
+ repeatCount CDATA #IMPLIED
+ repeatDur CDATA #IMPLIED
+ fill ( remove | freeze ) 'remove'
+ %SVG.AnimationTiming.extra.attrib;"
+>
+
+<!-- SVG.AnimationValue.attrib ......................... -->
+
+<!ENTITY % SVG.AnimationValue.extra.attrib "" >
+
+<!ENTITY % SVG.AnimationValue.attrib
+ "calcMode ( discrete | linear | paced | spline ) 'linear'
+ values CDATA #IMPLIED
+ keyTimes CDATA #IMPLIED
+ keySplines CDATA #IMPLIED
+ from CDATA #IMPLIED
+ to CDATA #IMPLIED
+ by CDATA #IMPLIED
+ %SVG.AnimationValue.extra.attrib;"
+>
+
+<!-- SVG.AnimationAddtion.attrib ....................... -->
+
+<!ENTITY % SVG.AnimationAddtion.extra.attrib "" >
+
+<!ENTITY % SVG.AnimationAddtion.attrib
+ "additive ( replace | sum ) 'replace'
+ accumulate ( none | sum ) 'none'
+ %SVG.AnimationAddtion.extra.attrib;"
+>
+
+<!-- animate: Animate Element .......................... -->
+
+<!ENTITY % SVG.animate.extra.content "" >
+
+<!ENTITY % SVG.animate.element "INCLUDE" >
+<![%SVG.animate.element;[
+<!ENTITY % SVG.animate.content
+ "( %SVG.Description.class; %SVG.animate.extra.content; )*"
+>
+<!ELEMENT %SVG.animate.qname; %SVG.animate.content; >
+<!-- end of SVG.animate.element -->]]>
+
+<!ENTITY % SVG.animate.attlist "INCLUDE" >
+<![%SVG.animate.attlist;[
+<!ATTLIST %SVG.animate.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.AnimationEvents.attrib;
+ %SVG.External.attrib;
+ %SVG.Animation.attrib;
+ %SVG.AnimationAttribute.attrib;
+ %SVG.AnimationTiming.attrib;
+ %SVG.AnimationValue.attrib;
+ %SVG.AnimationAddtion.attrib;
+>
+<!-- end of SVG.animate.attlist -->]]>
+
+<!-- set: Set Element .................................. -->
+
+<!ENTITY % SVG.set.extra.content "" >
+
+<!ENTITY % SVG.set.element "INCLUDE" >
+<![%SVG.set.element;[
+<!ENTITY % SVG.set.content
+ "( %SVG.Description.class; %SVG.set.extra.content; )*"
+>
+<!ELEMENT %SVG.set.qname; %SVG.set.content; >
+<!-- end of SVG.set.element -->]]>
+
+<!ENTITY % SVG.set.attlist "INCLUDE" >
+<![%SVG.set.attlist;[
+<!ATTLIST %SVG.set.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.AnimationEvents.attrib;
+ %SVG.External.attrib;
+ %SVG.Animation.attrib;
+ %SVG.AnimationAttribute.attrib;
+ %SVG.AnimationTiming.attrib;
+ to CDATA #IMPLIED
+>
+<!-- end of SVG.set.attlist -->]]>
+
+<!-- animateMotion: Animate Motion Element ............. -->
+
+<!ENTITY % SVG.animateMotion.extra.content "" >
+
+<!ENTITY % SVG.animateMotion.element "INCLUDE" >
+<![%SVG.animateMotion.element;[
+<!ENTITY % SVG.animateMotion.content
+ "(( %SVG.Description.class; )*, %SVG.mpath.qname;?
+ %SVG.animateMotion.extra.content; )"
+>
+<!ELEMENT %SVG.animateMotion.qname; %SVG.animateMotion.content; >
+<!-- end of SVG.animateMotion.element -->]]>
+
+<!ENTITY % SVG.animateMotion.attlist "INCLUDE" >
+<![%SVG.animateMotion.attlist;[
+<!ATTLIST %SVG.animateMotion.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.AnimationEvents.attrib;
+ %SVG.External.attrib;
+ %SVG.Animation.attrib;
+ %SVG.AnimationTiming.attrib;
+ %SVG.AnimationAddtion.attrib;
+ calcMode ( discrete | linear | paced | spline ) 'paced'
+ values CDATA #IMPLIED
+ keyTimes CDATA #IMPLIED
+ keySplines CDATA #IMPLIED
+ from CDATA #IMPLIED
+ to CDATA #IMPLIED
+ by CDATA #IMPLIED
+ path CDATA #IMPLIED
+ keyPoints CDATA #IMPLIED
+ rotate CDATA #IMPLIED
+ origin CDATA #IMPLIED
+>
+<!-- end of SVG.animateMotion.attlist -->]]>
+
+<!-- animateColor: Animate Color Element ............... -->
+
+<!ENTITY % SVG.animateColor.extra.content "" >
+
+<!ENTITY % SVG.animateColor.element "INCLUDE" >
+<![%SVG.animateColor.element;[
+<!ENTITY % SVG.animateColor.content
+ "( %SVG.Description.class; %SVG.animateColor.extra.content; )*"
+>
+<!ELEMENT %SVG.animateColor.qname; %SVG.animateColor.content; >
+<!-- end of SVG.animateColor.element -->]]>
+
+<!ENTITY % SVG.animateColor.attlist "INCLUDE" >
+<![%SVG.animateColor.attlist;[
+<!ATTLIST %SVG.animateColor.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.AnimationEvents.attrib;
+ %SVG.External.attrib;
+ %SVG.Animation.attrib;
+ %SVG.AnimationAttribute.attrib;
+ %SVG.AnimationTiming.attrib;
+ %SVG.AnimationValue.attrib;
+ %SVG.AnimationAddtion.attrib;
+>
+<!-- end of SVG.animateColor.attlist -->]]>
+
+<!-- animateTransform: Animate Transform Element ....... -->
+
+<!ENTITY % SVG.animateTransform.extra.content "" >
+
+<!ENTITY % SVG.animateTransform.element "INCLUDE" >
+<![%SVG.animateTransform.element;[
+<!ENTITY % SVG.animateTransform.content
+ "( %SVG.Description.class; %SVG.animateTransform.extra.content; )*"
+>
+<!ELEMENT %SVG.animateTransform.qname; %SVG.animateTransform.content; >
+<!-- end of SVG.animateTransform.element -->]]>
+
+<!ENTITY % SVG.animateTransform.attlist "INCLUDE" >
+<![%SVG.animateTransform.attlist;[
+<!ATTLIST %SVG.animateTransform.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.AnimationEvents.attrib;
+ %SVG.External.attrib;
+ %SVG.Animation.attrib;
+ %SVG.AnimationAttribute.attrib;
+ %SVG.AnimationTiming.attrib;
+ %SVG.AnimationValue.attrib;
+ %SVG.AnimationAddtion.attrib;
+ type ( translate | scale | rotate | skewX | skewY ) 'translate'
+>
+<!-- end of SVG.animateTransform.attlist -->]]>
+
+<!-- mpath: Motion Path Element ........................ -->
+
+<!ENTITY % SVG.mpath.extra.content "" >
+
+<!ENTITY % SVG.mpath.element "INCLUDE" >
+<![%SVG.mpath.element;[
+<!ENTITY % SVG.mpath.content
+ "( %SVG.Description.class; %SVG.mpath.extra.content; )*"
+>
+<!ELEMENT %SVG.mpath.qname; %SVG.mpath.content; >
+<!-- end of SVG.mpath.element -->]]>
+
+<!ENTITY % SVG.mpath.attlist "INCLUDE" >
+<![%SVG.mpath.attlist;[
+<!ATTLIST %SVG.mpath.qname;
+ %SVG.Core.attrib;
+ %SVG.XLinkRequired.attrib;
+ %SVG.External.attrib;
+>
+<!-- end of SVG.mpath.attlist -->]]>
+
+<!-- end of svg-animation.mod -->
+]]>
+
+<!-- Basic Font Module ........................................... -->
+<!ENTITY % svg-font.module "INCLUDE" >
+<![%svg-font.module;[
+<!ENTITY % svg-font.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Basic Font//EN"
+ "svg-basic-font.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Basic Font Module ............................................. -->
+<!-- file: svg-basic-font.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-tiny-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Basic Font//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-basic-font.mod"
+
+ ....................................................................... -->
+
+<!-- Basic Font
+
+ font, font-face, glyph, missing-glyph, hkern, vkern, font-face-src,
+ font-face-uri, font-face-name
+
+ This module declares markup to provide support for template.
+-->
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.font.qname "font" >
+<!ENTITY % SVG.font-face.qname "font-face" >
+<!ENTITY % SVG.glyph.qname "glyph" >
+<!ENTITY % SVG.missing-glyph.qname "missing-glyph" >
+<!ENTITY % SVG.hkern.qname "hkern" >
+<!ENTITY % SVG.vkern.qname "vkern" >
+<!ENTITY % SVG.font-face-src.qname "font-face-src" >
+<!ENTITY % SVG.font-face-uri.qname "font-face-uri" >
+<!ENTITY % SVG.font-face-name.qname "font-face-name" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Container.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Viewport.attrib "" >
+<!ENTITY % SVG.Text.attrib "" >
+<!ENTITY % SVG.TextContent.attrib "" >
+<!ENTITY % SVG.Font.attrib "" >
+<!ENTITY % SVG.Paint.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Marker.attrib "" >
+<!ENTITY % SVG.Profile.attrib "" >
+<!ENTITY % SVG.Gradient.attrib "" >
+<!ENTITY % SVG.Clip.attrib "" >
+<!ENTITY % SVG.Mask.attrib "" >
+<!ENTITY % SVG.Filter.attrib "" >
+<!ENTITY % SVG.FilterColor.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.XLinkRequired.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Font.class .................................... -->
+
+<!ENTITY % SVG.Font.extra.class "" >
+
+<!ENTITY % SVG.Font.class
+ "| %SVG.font.qname; | %SVG.font-face.qname; %SVG.Font.extra.class;"
+>
+
+<!-- SVG.Presentation.attrib ........................... -->
+
+<!ENTITY % SVG.Presentation.extra.attrib "" >
+
+<!ENTITY % SVG.Presentation.attrib
+ "%SVG.Container.attrib;
+ %SVG.Viewport.attrib;
+ %SVG.Text.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Profile.attrib;
+ %SVG.Gradient.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.Cursor.attrib;
+ flood-color %SVGColor.datatype; #IMPLIED
+ flood-opacity %OpacityValue.datatype; #IMPLIED
+ lighting-color %SVGColor.datatype; #IMPLIED
+ %SVG.Presentation.extra.attrib;"
+>
+
+<!-- font: Font Element ................................ -->
+
+<!ENTITY % SVG.font.extra.content "" >
+
+<!ENTITY % SVG.font.element "INCLUDE" >
+<![%SVG.font.element;[
+<!ENTITY % SVG.font.content
+ "(( %SVG.Description.class; )*, %SVG.font-face.qname;,
+ %SVG.missing-glyph.qname;, ( %SVG.glyph.qname; | %SVG.hkern.qname;
+ | %SVG.vkern.qname; %SVG.font.extra.content; )*)"
+>
+<!ELEMENT %SVG.font.qname; %SVG.font.content; >
+<!-- end of SVG.font.element -->]]>
+
+<!ENTITY % SVG.font.attlist "INCLUDE" >
+<![%SVG.font.attlist;[
+<!ATTLIST %SVG.font.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.External.attrib;
+ horiz-origin-x %Number.datatype; #IMPLIED
+ horiz-origin-y %Number.datatype; #IMPLIED
+ horiz-adv-x %Number.datatype; #REQUIRED
+ vert-origin-x %Number.datatype; #IMPLIED
+ vert-origin-y %Number.datatype; #IMPLIED
+ vert-adv-y %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.font.attlist -->]]>
+
+<!-- font-face: Font Face Element ...................... -->
+
+<!ENTITY % SVG.font-face.extra.content "" >
+
+<!ENTITY % SVG.font-face.element "INCLUDE" >
+<![%SVG.font-face.element;[
+<!ENTITY % SVG.font-face.content
+ "(( %SVG.Description.class; )*, %SVG.font-face-src.qname;?
+ %SVG.font-face.extra.content; )"
+>
+<!ELEMENT %SVG.font-face.qname; %SVG.font-face.content; >
+<!-- end of SVG.font-face.element -->]]>
+
+<!ENTITY % SVG.font-face.attlist "INCLUDE" >
+<![%SVG.font-face.attlist;[
+<!ATTLIST %SVG.font-face.qname;
+ %SVG.Core.attrib;
+ font-family CDATA #IMPLIED
+ font-style CDATA #IMPLIED
+ font-variant CDATA #IMPLIED
+ font-weight CDATA #IMPLIED
+ font-stretch CDATA #IMPLIED
+ font-size CDATA #IMPLIED
+ unicode-range CDATA #IMPLIED
+ units-per-em %Number.datatype; #IMPLIED
+ panose-1 CDATA #IMPLIED
+ stemv %Number.datatype; #IMPLIED
+ stemh %Number.datatype; #IMPLIED
+ slope %Number.datatype; #IMPLIED
+ cap-height %Number.datatype; #IMPLIED
+ x-height %Number.datatype; #IMPLIED
+ accent-height %Number.datatype; #IMPLIED
+ ascent %Number.datatype; #IMPLIED
+ descent %Number.datatype; #IMPLIED
+ widths CDATA #IMPLIED
+ bbox CDATA #IMPLIED
+ ideographic %Number.datatype; #IMPLIED
+ alphabetic %Number.datatype; #IMPLIED
+ mathematical %Number.datatype; #IMPLIED
+ hanging %Number.datatype; #IMPLIED
+ v-ideographic %Number.datatype; #IMPLIED
+ v-alphabetic %Number.datatype; #IMPLIED
+ v-mathematical %Number.datatype; #IMPLIED
+ v-hanging %Number.datatype; #IMPLIED
+ underline-position %Number.datatype; #IMPLIED
+ underline-thickness %Number.datatype; #IMPLIED
+ strikethrough-position %Number.datatype; #IMPLIED
+ strikethrough-thickness %Number.datatype; #IMPLIED
+ overline-position %Number.datatype; #IMPLIED
+ overline-thickness %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.font-face.attlist -->]]>
+
+<!-- glyph: Glyph Element .............................. -->
+
+<!ENTITY % SVG.glyph.extra.content "" >
+
+<!ENTITY % SVG.glyph.element "INCLUDE" >
+<![%SVG.glyph.element;[
+<!ENTITY % SVG.glyph.content
+ "( %SVG.Description.class; %SVG.glyph.extra.content; )*"
+>
+<!ELEMENT %SVG.glyph.qname; %SVG.glyph.content; >
+<!-- end of SVG.glyph.element -->]]>
+
+<!ENTITY % SVG.glyph.attlist "INCLUDE" >
+<![%SVG.glyph.attlist;[
+<!ATTLIST %SVG.glyph.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ unicode CDATA #IMPLIED
+ glyph-name CDATA #IMPLIED
+ d %PathData.datatype; #IMPLIED
+ orientation CDATA #IMPLIED
+ arabic-form CDATA #IMPLIED
+ lang %LanguageCodes.datatype; #IMPLIED
+ horiz-adv-x %Number.datatype; #IMPLIED
+ vert-origin-x %Number.datatype; #IMPLIED
+ vert-origin-y %Number.datatype; #IMPLIED
+ vert-adv-y %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.glyph.attlist -->]]>
+
+<!-- missing-glyph: Missing Glyph Element .............. -->
+
+<!ENTITY % SVG.missing-glyph.extra.content "" >
+
+<!ENTITY % SVG.missing-glyph.element "INCLUDE" >
+<![%SVG.missing-glyph.element;[
+<!ENTITY % SVG.missing-glyph.content
+ "( %SVG.Description.class; %SVG.missing-glyph.extra.content; )*"
+>
+<!ELEMENT %SVG.missing-glyph.qname; %SVG.missing-glyph.content; >
+<!-- end of SVG.missing-glyph.element -->]]>
+
+<!ENTITY % SVG.missing-glyph.attlist "INCLUDE" >
+<![%SVG.missing-glyph.attlist;[
+<!ATTLIST %SVG.missing-glyph.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ d %PathData.datatype; #IMPLIED
+ horiz-adv-x %Number.datatype; #IMPLIED
+ vert-origin-x %Number.datatype; #IMPLIED
+ vert-origin-y %Number.datatype; #IMPLIED
+ vert-adv-y %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.missing-glyph.attlist -->]]>
+
+<!-- hkern: Horizontal Kerning Element ................. -->
+
+<!ENTITY % SVG.hkern.element "INCLUDE" >
+<![%SVG.hkern.element;[
+<!ENTITY % SVG.hkern.content "EMPTY" >
+<!ELEMENT %SVG.hkern.qname; %SVG.hkern.content; >
+<!-- end of SVG.hkern.element -->]]>
+
+<!ENTITY % SVG.hkern.attlist "INCLUDE" >
+<![%SVG.hkern.attlist;[
+<!ATTLIST %SVG.hkern.qname;
+ %SVG.Core.attrib;
+ u1 CDATA #IMPLIED
+ g1 CDATA #IMPLIED
+ u2 CDATA #IMPLIED
+ g2 CDATA #IMPLIED
+ k %Number.datatype; #REQUIRED
+>
+<!-- end of SVG.hkern.attlist -->]]>
+
+<!-- vkern: Vertical Kerning Element ................... -->
+
+<!ENTITY % SVG.vkern.element "INCLUDE" >
+<![%SVG.vkern.element;[
+<!ENTITY % SVG.vkern.content "EMPTY" >
+<!ELEMENT %SVG.vkern.qname; %SVG.vkern.content; >
+<!-- end of SVG.vkern.element -->]]>
+
+<!ENTITY % SVG.vkern.attlist "INCLUDE" >
+<![%SVG.vkern.attlist;[
+<!ATTLIST %SVG.vkern.qname;
+ %SVG.Core.attrib;
+ u1 CDATA #IMPLIED
+ g1 CDATA #IMPLIED
+ u2 CDATA #IMPLIED
+ g2 CDATA #IMPLIED
+ k %Number.datatype; #REQUIRED
+>
+<!-- end of SVG.vkern.attlist -->]]>
+
+<!-- font-face-src: Font Face Source Element ........... -->
+
+<!ENTITY % SVG.font-face-src.extra.content "" >
+
+<!ENTITY % SVG.font-face-src.element "INCLUDE" >
+<![%SVG.font-face-src.element;[
+<!ENTITY % SVG.font-face-src.content
+ "( %SVG.font-face-uri.qname; | %SVG.font-face-name.qname;
+ %SVG.font-face-src.extra.content; )+"
+>
+<!ELEMENT %SVG.font-face-src.qname; %SVG.font-face-src.content; >
+<!-- end of SVG.font-face-src.element -->]]>
+
+<!ENTITY % SVG.font-face-src.attlist "INCLUDE" >
+<![%SVG.font-face-src.attlist;[
+<!ATTLIST %SVG.font-face-src.qname;
+ %SVG.Core.attrib;
+>
+<!-- end of SVG.font-face-src.attlist -->]]>
+
+<!-- font-face-uri: Font Face URI Element .............. -->
+
+<!ENTITY % SVG.font-face-uri.element "INCLUDE" >
+<![%SVG.font-face-uri.element;[
+<!ENTITY % SVG.font-face-uri.content "EMPTY" >
+<!ELEMENT %SVG.font-face-uri.qname; %SVG.font-face-uri.content; >
+<!-- end of SVG.font-face-uri.element -->]]>
+
+<!ENTITY % SVG.font-face-uri.attlist "INCLUDE" >
+<![%SVG.font-face-uri.attlist;[
+<!ATTLIST %SVG.font-face-uri.qname;
+ %SVG.Core.attrib;
+ %SVG.XLinkRequired.attrib;
+>
+<!-- end of SVG.font-face-uri.attlist -->]]>
+
+<!-- font-face-name: Font Face Name Element ............ -->
+
+<!ENTITY % SVG.font-face-name.element "INCLUDE" >
+<![%SVG.font-face-name.element;[
+<!ENTITY % SVG.font-face-name.content "EMPTY" >
+<!ELEMENT %SVG.font-face-name.qname; %SVG.font-face-name.content; >
+<!-- end of SVG.font-face-name.element -->]]>
+
+<!ENTITY % SVG.font-face-name.attlist "INCLUDE" >
+<![%SVG.font-face-name.attlist;[
+<!ATTLIST %SVG.font-face-name.qname;
+ %SVG.Core.attrib;
+ name CDATA #IMPLIED
+>
+<!-- end of SVG.font-face-name.attlist -->]]>
+
+<!-- end of svg-basic-font.mod -->
+]]>
+
+<!-- Extensibility Module ........................................ -->
+<!ENTITY % svg-extensibility.module "INCLUDE" >
+<![%svg-extensibility.module;[
+<!ENTITY % svg-extensibility.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Extensibility//EN"
+ "svg-extensibility.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Extensibility Module .......................................... -->
+<!-- file: svg-extensibility.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-tiny-flat.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Extensibility//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-extensibility.mod"
+
+ ....................................................................... -->
+
+<!-- Extensibility
+
+ foreignObject
+
+ This module declares markup to provide support for extensibility.
+-->
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.foreignObject.qname "foreignObject" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Conditional.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Viewport.attrib "" >
+<!ENTITY % SVG.Text.attrib "" >
+<!ENTITY % SVG.TextContent.attrib "" >
+<!ENTITY % SVG.Font.attrib "" >
+<!ENTITY % SVG.Paint.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Marker.attrib "" >
+<!ENTITY % SVG.Gradient.attrib "" >
+<!ENTITY % SVG.Clip.attrib "" >
+<!ENTITY % SVG.Mask.attrib "" >
+<!ENTITY % SVG.Filter.attrib "" >
+<!ENTITY % SVG.FilterColor.attrib "" >
+<!ENTITY % SVG.GraphicalEvents.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Extensibility.class ........................... -->
+
+<!ENTITY % SVG.Extensibility.extra.class "" >
+
+<!ENTITY % SVG.Extensibility.class
+ "| %SVG.foreignObject.qname; %SVG.Extensibility.extra.class;"
+>
+
+<!-- SVG.Presentation.attrib ........................... -->
+
+<!ENTITY % SVG.Presentation.extra.attrib "" >
+
+<!ENTITY % SVG.Presentation.attrib
+ "%SVG.Container.attrib;
+ %SVG.Viewport.attrib;
+ %SVG.Text.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Profile.attrib;
+ %SVG.Gradient.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.Cursor.attrib;
+ flood-color %SVGColor.datatype; #IMPLIED
+ flood-opacity %OpacityValue.datatype; #IMPLIED
+ lighting-color %SVGColor.datatype; #IMPLIED
+ %SVG.Presentation.extra.attrib;"
+>
+
+<!-- foreignObject: Foreign Object Element ............. -->
+
+<!ENTITY % SVG.foreignObject.extra.content "" >
+
+<!ENTITY % SVG.foreignObject.element "INCLUDE" >
+<![%SVG.foreignObject.element;[
+<!ENTITY % SVG.foreignObject.content
+ "( #PCDATA %SVG.foreignObject.extra.content; )*"
+>
+<!ELEMENT %SVG.foreignObject.qname; %SVG.foreignObject.content; >
+<!-- end of SVG.foreignObject.element -->]]>
+
+<!ENTITY % SVG.foreignObject.attlist "INCLUDE" >
+<![%SVG.foreignObject.attlist;[
+<!ATTLIST %SVG.foreignObject.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.External.attrib;
+ x %Coordinate.datatype; #IMPLIED
+ y %Coordinate.datatype; #IMPLIED
+ width %Length.datatype; #REQUIRED
+ height %Length.datatype; #REQUIRED
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.foreignObject.attlist -->]]>
+
+<!-- end of svg-extensibility.mod -->
+]]>
+
+<!-- end of SVG 1.1 Tiny DTD ............................................... -->
+<!-- ....................................................................... -->
diff --git a/org/apache/batik/dom/svg/resources/svg11-tiny-model.mod b/org/apache/batik/dom/svg/resources/svg11-tiny-model.mod
new file mode 100644
index 0000000..cb04a59
--- /dev/null
+++ b/org/apache/batik/dom/svg/resources/svg11-tiny-model.mod
@@ -0,0 +1,139 @@
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Tiny Document Model Module .................................... -->
+<!-- file: svg11-tiny-model.mod
+
+ This is SVG Tiny, a proper subset of SVG.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg11-tiny-model.mod 201058 2002-11-13 09:51:12Z vhardy $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Tiny Document Model//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11-tiny-model.mod"
+
+ ....................................................................... -->
+
+<!-- SVG 1.1 Tiny Document Model
+
+ This module describes the groupings of elements that make up
+ common content models for SVG elements.
+-->
+
+<!-- Content Models (Default) .......................... -->
+
+<!ENTITY % SVG.Marker.class "" >
+<!ENTITY % SVG.Profile.class "" >
+<!ENTITY % SVG.Gradient.class "" >
+<!ENTITY % SVG.Pattern.class "" >
+<!ENTITY % SVG.Clip.class "" >
+<!ENTITY % SVG.Mask.class "" >
+<!ENTITY % SVG.Filter.class "" >
+<!ENTITY % SVG.FilterPrimitive.class "" >
+<!ENTITY % SVG.Cursor.class "" >
+
+<!-- module: svg-basic-structure.mod ................... -->
+
+<!ENTITY % SVG.Description.extra.class "" >
+<!ENTITY % SVG.Description.class
+ "%SVG.desc.qname; | %SVG.title.qname; | %SVG.metadata.qname;
+ %SVG.Description.extra.class;"
+>
+
+<!ENTITY % SVG.Use.extra.class "" >
+<!ENTITY % SVG.Use.class
+ "| %SVG.use.qname; %SVG.Use.extra.class;"
+>
+
+<!ENTITY % SVG.Structure.extra.class "" >
+<!ENTITY % SVG.Structure.class
+ "| %SVG.svg.qname; | %SVG.g.qname; | %SVG.defs.qname; %SVG.Use.class;
+ %SVG.Structure.extra.class;"
+>
+
+<!-- module: svg-conditional.mod ....................... -->
+
+<!ENTITY % SVG.Conditional.extra.class "" >
+<!ENTITY % SVG.Conditional.class
+ "| %SVG.switch.qname; %SVG.Conditional.extra.class;"
+>
+
+<!-- module: svg-image.mod ............................. -->
+
+<!ENTITY % SVG.Image.extra.class "" >
+<!ENTITY % SVG.Image.class
+ "| %SVG.image.qname; %SVG.Image.extra.class;"
+>
+
+<!-- module: svg-style.mod ............................. -->
+
+<!ENTITY % SVG.Style.extra.class "" >
+<!ENTITY % SVG.Style.class
+ "| %SVG.style.qname; %SVG.Style.extra.class;"
+>
+
+<!-- module: svg-shape.mod ............................. -->
+
+<!ENTITY % SVG.Shape.extra.class "" >
+<!ENTITY % SVG.Shape.class
+ "| %SVG.path.qname; | %SVG.rect.qname; | %SVG.circle.qname;
+ | %SVG.line.qname; | %SVG.ellipse.qname; | %SVG.polyline.qname;
+ | %SVG.polygon.qname; %SVG.Shape.extra.class;"
+>
+
+<!-- module: svg-basic-text.mod ........................ -->
+
+<!ENTITY % SVG.Text.extra.class "" >
+<!ENTITY % SVG.Text.class
+ "| %SVG.text.qname; %SVG.Text.extra.class;"
+>
+
+<!ENTITY % SVG.TextContent.extra.class "" >
+<!ENTITY % SVG.TextContent.class
+ "%SVG.TextContent.extra.class;"
+>
+
+<!-- module: svg-hyperlink.mod ......................... -->
+
+<!ENTITY % SVG.Hyperlink.extra.class "" >
+<!ENTITY % SVG.Hyperlink.class
+ "| %SVG.a.qname; %SVG.Hyperlink.extra.class;"
+>
+
+<!-- module: svg-view.mod .............................. -->
+
+<!ENTITY % SVG.View.extra.class "" >
+<!ENTITY % SVG.View.class
+ "| %SVG.view.qname; %SVG.View.extra.class;"
+>
+
+<!-- module: svg-script.mod ............................ -->
+
+<!ENTITY % SVG.Script.extra.class "" >
+<!ENTITY % SVG.Script.class
+ "| %SVG.script.qname; %SVG.Script.extra.class;"
+>
+
+<!-- module: svg-animation.mod ......................... -->
+
+<!ENTITY % SVG.Animation.extra.class "" >
+<!ENTITY % SVG.Animation.class
+ "%SVG.animate.qname; | %SVG.set.qname; | %SVG.animateMotion.qname; |
+ %SVG.animateColor.qname; | %SVG.animateTransform.qname;
+ %SVG.Animation.extra.class;"
+>
+
+<!-- module: svg-basic-font.mod ........................ -->
+
+<!ENTITY % SVG.Font.extra.class "" >
+<!ENTITY % SVG.Font.class
+ "| %SVG.font.qname; | %SVG.font-face.qname; %SVG.Font.extra.class;"
+>
+
+<!-- module: svg-extensibility.mod ..................... -->
+
+<!ENTITY % SVG.Extensibility.extra.class "" >
+<!ENTITY % SVG.Extensibility.class
+ "| %SVG.foreignObject.qname; %SVG.Extensibility.extra.class;"
+>
+
+<!-- end of svg11-tiny-model.mod -->
diff --git a/org/apache/batik/dom/svg/resources/svg11-tiny.dtd b/org/apache/batik/dom/svg/resources/svg11-tiny.dtd
new file mode 100644
index 0000000..abe5e67
--- /dev/null
+++ b/org/apache/batik/dom/svg/resources/svg11-tiny.dtd
@@ -0,0 +1,245 @@
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Tiny DTD ...................................................... -->
+<!-- file: svg11-tiny.dtd
+-->
+
+<!-- SVG 1.1 Tiny DTD
+
+ This is SVG Tiny, a proper subset of SVG.
+
+ The Scalable Vector Graphics (SVG)
+ Copyright 2001, 2002 World Wide Web Consortium
+ (Massachusetts Institute of Technology, Institut National de
+ Recherche en Informatique et en Automatique, Keio University).
+ All Rights Reserved.
+
+ Permission to use, copy, modify and distribute the SVG DTD and its
+ accompanying documentation for any purpose and without fee is hereby
+ granted in perpetuity, provided that the above copyright notice and
+ this paragraph appear in all copies. The copyright holders make no
+ representation about the suitability of the DTD for any purpose.
+
+ It is provided "as is" without expressed or implied warranty.
+
+ Author: Jun Fujisawa <fujisawa.jun at canon.co.jp>
+ Revision: $Id: svg11-tiny.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+-->
+<!-- This is the driver file for version 1.1 of the SVG Tiny DTD.
+
+ This DTD is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//DTD SVG 1.1 Tiny//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11-tiny.dtd"
+-->
+<!ENTITY % SVG.version "-//W3C//DTD SVG 1.1 Tiny//EN" >
+
+<!-- Use this URI to identify the default namespace:
+
+ "http://www.w3.org/2000/svg"
+
+ See the Qualified Names module for information
+ on the use of namespace prefixes in the DTD.
+-->
+<!ENTITY % NS.prefixed "IGNORE" >
+<!ENTITY % SVG.prefix "" >
+
+<!-- reserved for future use with document profiles -->
+<!ENTITY % SVG.profile "" >
+
+<!-- ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: -->
+
+<!-- Pre-Framework Redeclaration Placeholder ..................... -->
+<!ENTITY % svg-prefw-redecl.module "IGNORE" >
+<![%svg-prefw-redecl.module;[
+%svg-prefw-redecl.mod;]]>
+
+<!-- Document Model Module ....................................... -->
+<!ENTITY % svg-model.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Tiny Document Model//EN"
+ "svg11-tiny-model.mod" >
+
+<!-- Attribute Collection Module ................................. -->
+<!ENTITY % svg-attribs.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Tiny Attribute Collection//EN"
+ "svg11-tiny-attribs.mod" >
+
+<!-- Modular Framework Module .................................... -->
+<!ENTITY % svg-framework.module "INCLUDE" >
+<![%svg-framework.module;[
+<!ENTITY % svg-framework.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Modular Framework//EN"
+ "svg-framework.mod" >
+%svg-framework.mod;]]>
+
+<!-- Post-Framework Redeclaration Placeholder .................... -->
+<!ENTITY % svg-postfw-redecl.module "IGNORE" >
+<![%svg-postfw-redecl.module;[
+%svg-postfw-redecl.mod;]]>
+
+<!-- ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: -->
+
+<!-- Core Attribute Module ....................................... -->
+<!ENTITY % svg-core-attrib.module "INCLUDE" >
+<![%svg-core-attrib.module;[
+<!ENTITY % svg-core-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Core Attribute//EN"
+ "svg-core-attrib.mod" >
+%svg-core-attrib.mod;]]>
+
+<!-- Paint Attribute Module ...................................... -->
+<!ENTITY % svg-paint-attrib.module "INCLUDE" >
+<![%svg-paint-attrib.module;[
+<!ENTITY % svg-paint-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Paint Attribute//EN"
+ "svg-paint-attrib.mod" >
+%svg-paint-attrib.mod;]]>
+
+<!-- Basic Graphics Attribute Module .............................. -->
+<!ENTITY % svg-graphics-attrib.module "INCLUDE" >
+<![%svg-graphics-attrib.module;[
+<!ENTITY % svg-graphics-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Basic Graphics Attribute//EN"
+ "svg-basic-graphics-attrib.mod" >
+%svg-graphics-attrib.mod;]]>
+
+<!-- Document Events Attribute Module ............................ -->
+<!ENTITY % svg-docevents-attrib.module "INCLUDE" >
+<![%svg-docevents-attrib.module;[
+<!ENTITY % svg-docevents-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Document Events Attribute//EN"
+ "svg-docevents-attrib.mod" >
+%svg-docevents-attrib.mod;]]>
+
+<!-- Graphical Element Events Attribute Module ................... -->
+<!ENTITY % svg-graphevents-attrib.module "INCLUDE" >
+<![%svg-graphevents-attrib.module;[
+<!ENTITY % svg-graphevents-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Graphical Element Events Attribute//EN"
+ "svg-graphevents-attrib.mod" >
+%svg-graphevents-attrib.mod;]]>
+
+<!-- Animation Events Attribute Module ........................... -->
+<!ENTITY % svg-animevents-attrib.module "INCLUDE" >
+<![%svg-animevents-attrib.module;[
+<!ENTITY % svg-animevents-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Animation Events Attribute//EN"
+ "svg-animevents-attrib.mod" >
+%svg-animevents-attrib.mod;]]>
+
+<!-- XLink Attribute Module ...................................... -->
+<!ENTITY % svg-xlink-attrib.module "INCLUDE" >
+<![%svg-xlink-attrib.module;[
+<!ENTITY % svg-xlink-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 XLink Attribute//EN"
+ "svg-xlink-attrib.mod" >
+%svg-xlink-attrib.mod;]]>
+
+<!-- External Resources Attribute Module ......................... -->
+<!ENTITY % svg-extresources-attrib.module "INCLUDE" >
+<![%svg-extresources-attrib.module;[
+<!ENTITY % svg-extresources-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 External Resources Attribute//EN"
+ "svg-extresources-attrib.mod" >
+%svg-extresources-attrib.mod;]]>
+
+<!-- ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: -->
+
+<!-- Basic Structure Module ...................................... -->
+<!ENTITY % svg-structure.module "INCLUDE" >
+<![%svg-structure.module;[
+<!ENTITY % svg-structure.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Basic Structure//EN"
+ "svg-basic-structure.mod" >
+%svg-structure.mod;]]>
+
+<!-- Conditional Processing Module ............................... -->
+<!ENTITY % svg-conditional.module "INCLUDE" >
+<![%svg-conditional.module;[
+<!ENTITY % svg-conditional.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Conditional Processing//EN"
+ "svg-conditional.mod" >
+%svg-conditional.mod;]]>
+
+<!-- Image Module ................................................ -->
+<!ENTITY % svg-image.module "INCLUDE" >
+<![%svg-image.module;[
+<!ENTITY % svg-image.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Image//EN"
+ "svg-image.mod" >
+%svg-image.mod;]]>
+
+<!-- Style Module ................................................ -->
+<!ENTITY % svg-style.module "INCLUDE" >
+<![%svg-style.module;[
+<!ENTITY % svg-style.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Style//EN"
+ "svg-style.mod" >
+%svg-style.mod;]]>
+
+<!-- Shape Module ................................................ -->
+<!ENTITY % svg-shape.module "INCLUDE" >
+<![%svg-shape.module;[
+<!ENTITY % svg-shape.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Shape//EN"
+ "svg-shape.mod" >
+%svg-shape.mod;]]>
+
+<!-- Basic Text Module ........................................... -->
+<!ENTITY % svg-text.module "INCLUDE" >
+<![%svg-text.module;[
+<!ENTITY % svg-text.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Basic Text//EN"
+ "svg-basic-text.mod" >
+%svg-text.mod;]]>
+
+<!-- Hyperlinking Module ......................................... -->
+<!ENTITY % svg-hyperlink.module "INCLUDE" >
+<![%svg-hyperlink.module;[
+<!ENTITY % svg-hyperlink.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Hyperlinking//EN"
+ "svg-hyperlink.mod" >
+%svg-hyperlink.mod;]]>
+
+<!-- View Module ................................................. -->
+<!ENTITY % svg-view.module "INCLUDE" >
+<![%svg-view.module;[
+<!ENTITY % svg-view.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 View//EN"
+ "svg-view.mod" >
+%svg-view.mod;]]>
+
+<!-- Scripting Module ............................................ -->
+<!ENTITY % svg-script.module "INCLUDE" >
+<![%svg-script.module;[
+<!ENTITY % svg-script.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Scripting//EN"
+ "svg-script.mod" >
+%svg-script.mod;]]>
+
+<!-- Animation Module ............................................ -->
+<!ENTITY % svg-animation.module "INCLUDE" >
+<![%svg-animation.module;[
+<!ENTITY % svg-animation.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Animation//EN"
+ "svg-animation.mod" >
+%svg-animation.mod;]]>
+
+<!-- Basic Font Module ........................................... -->
+<!ENTITY % svg-font.module "INCLUDE" >
+<![%svg-font.module;[
+<!ENTITY % svg-font.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Basic Font//EN"
+ "svg-basic-font.mod" >
+%svg-font.mod;]]>
+
+<!-- Extensibility Module ........................................ -->
+<!ENTITY % svg-extensibility.module "INCLUDE" >
+<![%svg-extensibility.module;[
+<!ENTITY % svg-extensibility.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Extensibility//EN"
+ "svg-extensibility.mod" >
+%svg-extensibility.mod;]]>
+
+<!-- end of SVG 1.1 Tiny DTD ............................................... -->
+<!-- ....................................................................... -->
diff --git a/org/apache/batik/dom/svg/resources/svg11.dtd b/org/apache/batik/dom/svg/resources/svg11.dtd
new file mode 100644
index 0000000..f13da82
--- /dev/null
+++ b/org/apache/batik/dom/svg/resources/svg11.dtd
@@ -0,0 +1,333 @@
+<!-- ....................................................................... -->
+<!-- SVG 1.1 DTD ........................................................... -->
+<!-- file: svg11.dtd
+-->
+
+<!-- SVG 1.1 DTD
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+
+ The Scalable Vector Graphics (SVG)
+ Copyright 2001, 2002 World Wide Web Consortium
+ (Massachusetts Institute of Technology, Institut National de
+ Recherche en Informatique et en Automatique, Keio University).
+ All Rights Reserved.
+
+ Permission to use, copy, modify and distribute the SVG DTD and its
+ accompanying documentation for any purpose and without fee is hereby
+ granted in perpetuity, provided that the above copyright notice and
+ this paragraph appear in all copies. The copyright holders make no
+ representation about the suitability of the DTD for any purpose.
+
+ It is provided "as is" without expressed or implied warranty.
+
+ Author: Jun Fujisawa <fujisawa.jun at canon.co.jp>
+ Revision: $Id: svg11.dtd 201058 2002-11-13 09:51:12Z vhardy $
+
+-->
+<!-- This is the driver file for version 1.1 of the SVG DTD.
+
+ This DTD is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//DTD SVG 1.1//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd"
+-->
+<!ENTITY % SVG.version "-//W3C//DTD SVG 1.1//EN" >
+
+<!-- Use this URI to identify the default namespace:
+
+ "http://www.w3.org/2000/svg"
+
+ See the Qualified Names module for information
+ on the use of namespace prefixes in the DTD.
+-->
+<!ENTITY % NS.prefixed "IGNORE" >
+<!ENTITY % SVG.prefix "" >
+
+<!-- reserved for future use with document profiles -->
+<!ENTITY % SVG.profile "" >
+
+<!-- ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: -->
+
+<!-- Pre-Framework Redeclaration Placeholder ..................... -->
+<!ENTITY % svg-prefw-redecl.module "IGNORE" >
+<![%svg-prefw-redecl.module;[
+%svg-prefw-redecl.mod;]]>
+
+<!-- Document Model Module ....................................... -->
+<!ENTITY % svg-model.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Document Model//EN"
+ "svg11-model.mod" >
+
+<!-- Attribute Collection Module ................................. -->
+<!ENTITY % svg-attribs.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Attribute Collection//EN"
+ "svg11-attribs.mod" >
+
+<!-- Modular Framework Module .................................... -->
+<!ENTITY % svg-framework.module "INCLUDE" >
+<![%svg-framework.module;[
+<!ENTITY % svg-framework.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Modular Framework//EN"
+ "svg-framework.mod" >
+%svg-framework.mod;]]>
+
+<!-- Post-Framework Redeclaration Placeholder .................... -->
+<!ENTITY % svg-postfw-redecl.module "IGNORE" >
+<![%svg-postfw-redecl.module;[
+%svg-postfw-redecl.mod;]]>
+
+<!-- ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: -->
+
+<!-- Core Attribute Module ....................................... -->
+<!ENTITY % svg-core-attrib.module "INCLUDE" >
+<![%svg-core-attrib.module;[
+<!ENTITY % svg-core-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Core Attribute//EN"
+ "svg-core-attrib.mod" >
+%svg-core-attrib.mod;]]>
+
+<!-- Container Attribute Module .................................. -->
+<!ENTITY % svg-container-attrib.module "INCLUDE" >
+<![%svg-container-attrib.module;[
+<!ENTITY % svg-container-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Container Attribute//EN"
+ "svg-container-attrib.mod" >
+%svg-container-attrib.mod;]]>
+
+<!-- Viewport Attribute Module ................................... -->
+<!ENTITY % svg-viewport-attrib.module "INCLUDE" >
+<![%svg-viewport-attrib.module;[
+<!ENTITY % svg-viewport-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Viewport Attribute//EN"
+ "svg-viewport-attrib.mod" >
+%svg-viewport-attrib.mod;]]>
+
+<!-- Paint Attribute Module ...................................... -->
+<!ENTITY % svg-paint-attrib.module "INCLUDE" >
+<![%svg-paint-attrib.module;[
+<!ENTITY % svg-paint-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Paint Attribute//EN"
+ "svg-paint-attrib.mod" >
+%svg-paint-attrib.mod;]]>
+
+<!-- Paint Opacity Attribute Module .............................. -->
+<!ENTITY % svg-opacity-attrib.module "INCLUDE" >
+<![%svg-opacity-attrib.module;[
+<!ENTITY % svg-opacity-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Paint Opacity Attribute//EN"
+ "svg-opacity-attrib.mod" >
+%svg-opacity-attrib.mod;]]>
+
+<!-- Graphics Attribute Module ................................... -->
+<!ENTITY % svg-graphics-attrib.module "INCLUDE" >
+<![%svg-graphics-attrib.module;[
+<!ENTITY % svg-graphics-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Graphics Attribute//EN"
+ "svg-graphics-attrib.mod" >
+%svg-graphics-attrib.mod;]]>
+
+<!-- Document Events Attribute Module ............................ -->
+<!ENTITY % svg-docevents-attrib.module "INCLUDE" >
+<![%svg-docevents-attrib.module;[
+<!ENTITY % svg-docevents-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Document Events Attribute//EN"
+ "svg-docevents-attrib.mod" >
+%svg-docevents-attrib.mod;]]>
+
+<!-- Graphical Element Events Attribute Module ................... -->
+<!ENTITY % svg-graphevents-attrib.module "INCLUDE" >
+<![%svg-graphevents-attrib.module;[
+<!ENTITY % svg-graphevents-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Graphical Element Events Attribute//EN"
+ "svg-graphevents-attrib.mod" >
+%svg-graphevents-attrib.mod;]]>
+
+<!-- Animation Events Attribute Module ........................... -->
+<!ENTITY % svg-animevents-attrib.module "INCLUDE" >
+<![%svg-animevents-attrib.module;[
+<!ENTITY % svg-animevents-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Animation Events Attribute//EN"
+ "svg-animevents-attrib.mod" >
+%svg-animevents-attrib.mod;]]>
+
+<!-- XLink Attribute Module ...................................... -->
+<!ENTITY % svg-xlink-attrib.module "INCLUDE" >
+<![%svg-xlink-attrib.module;[
+<!ENTITY % svg-xlink-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 XLink Attribute//EN"
+ "svg-xlink-attrib.mod" >
+%svg-xlink-attrib.mod;]]>
+
+<!-- External Resources Attribute Module ......................... -->
+<!ENTITY % svg-extresources-attrib.module "INCLUDE" >
+<![%svg-extresources-attrib.module;[
+<!ENTITY % svg-extresources-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 External Resources Attribute//EN"
+ "svg-extresources-attrib.mod" >
+%svg-extresources-attrib.mod;]]>
+
+<!-- ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: -->
+
+<!-- Structure Module ............................................ -->
+<!ENTITY % svg-structure.module "INCLUDE" >
+<![%svg-structure.module;[
+<!ENTITY % svg-structure.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Structure//EN"
+ "svg-structure.mod" >
+%svg-structure.mod;]]>
+
+<!-- Conditional Processing Module ............................... -->
+<!ENTITY % svg-conditional.module "INCLUDE" >
+<![%svg-conditional.module;[
+<!ENTITY % svg-conditional.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Conditional Processing//EN"
+ "svg-conditional.mod" >
+%svg-conditional.mod;]]>
+
+<!-- Image Module ................................................ -->
+<!ENTITY % svg-image.module "INCLUDE" >
+<![%svg-image.module;[
+<!ENTITY % svg-image.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Image//EN"
+ "svg-image.mod" >
+%svg-image.mod;]]>
+
+<!-- Style Module ................................................ -->
+<!ENTITY % svg-style.module "INCLUDE" >
+<![%svg-style.module;[
+<!ENTITY % svg-style.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Style//EN"
+ "svg-style.mod" >
+%svg-style.mod;]]>
+
+<!-- Shape Module ................................................ -->
+<!ENTITY % svg-shape.module "INCLUDE" >
+<![%svg-shape.module;[
+<!ENTITY % svg-shape.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Shape//EN"
+ "svg-shape.mod" >
+%svg-shape.mod;]]>
+
+<!-- Text Module ................................................. -->
+<!ENTITY % svg-text.module "INCLUDE" >
+<![%svg-text.module;[
+<!ENTITY % svg-text.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Text//EN"
+ "svg-text.mod" >
+%svg-text.mod;]]>
+
+<!-- Marker Module ............................................... -->
+<!ENTITY % svg-marker.module "INCLUDE" >
+<![%svg-marker.module;[
+<!ENTITY % svg-marker.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Marker//EN"
+ "svg-marker.mod" >
+%svg-marker.mod;]]>
+
+<!-- Color Profile Module ........................................ -->
+<!ENTITY % svg-profile.module "INCLUDE" >
+<![%svg-profile.module;[
+<!ENTITY % svg-profile.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Color Profile//EN"
+ "svg-profile.mod" >
+%svg-profile.mod;]]>
+
+<!-- Gradient Module ............................................. -->
+<!ENTITY % svg-gradient.module "INCLUDE" >
+<![%svg-gradient.module;[
+<!ENTITY % svg-gradient.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Gradient//EN"
+ "svg-gradient.mod" >
+%svg-gradient.mod;]]>
+
+<!-- Pattern Module .............................................. -->
+<!ENTITY % svg-pattern.module "INCLUDE" >
+<![%svg-pattern.module;[
+<!ENTITY % svg-pattern.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Pattern//EN"
+ "svg-pattern.mod" >
+%svg-pattern.mod;]]>
+
+<!-- Clip Module ................................................. -->
+<!ENTITY % svg-clip.module "INCLUDE" >
+<![%svg-clip.module;[
+<!ENTITY % svg-clip.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Clip//EN"
+ "svg-clip.mod" >
+%svg-clip.mod;]]>
+
+<!-- Mask Module ................................................. -->
+<!ENTITY % svg-mask.module "INCLUDE" >
+<![%svg-mask.module;[
+<!ENTITY % svg-mask.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Mask//EN"
+ "svg-mask.mod" >
+%svg-mask.mod;]]>
+
+<!-- Filter Module ............................................... -->
+<!ENTITY % svg-filter.module "INCLUDE" >
+<![%svg-filter.module;[
+<!ENTITY % svg-filter.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Filter//EN"
+ "svg-filter.mod" >
+%svg-filter.mod;]]>
+
+<!-- Cursor Module ............................................... -->
+<!ENTITY % svg-cursor.module "INCLUDE" >
+<![%svg-cursor.module;[
+<!ENTITY % svg-cursor.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Cursor//EN"
+ "svg-cursor.mod" >
+%svg-cursor.mod;]]>
+
+<!-- Hyperlinking Module ......................................... -->
+<!ENTITY % svg-hyperlink.module "INCLUDE" >
+<![%svg-hyperlink.module;[
+<!ENTITY % svg-hyperlink.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Hyperlinking//EN"
+ "svg-hyperlink.mod" >
+%svg-hyperlink.mod;]]>
+
+<!-- View Module ................................................. -->
+<!ENTITY % svg-view.module "INCLUDE" >
+<![%svg-view.module;[
+<!ENTITY % svg-view.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 View//EN"
+ "svg-view.mod" >
+%svg-view.mod;]]>
+
+<!-- Scripting Module ............................................ -->
+<!ENTITY % svg-script.module "INCLUDE" >
+<![%svg-script.module;[
+<!ENTITY % svg-script.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Scripting//EN"
+ "svg-script.mod" >
+%svg-script.mod;]]>
+
+<!-- Animation Module ............................................ -->
+<!ENTITY % svg-animation.module "INCLUDE" >
+<![%svg-animation.module;[
+<!ENTITY % svg-animation.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Animation//EN"
+ "svg-animation.mod" >
+%svg-animation.mod;]]>
+
+<!-- Font Module ................................................. -->
+<!ENTITY % svg-font.module "INCLUDE" >
+<![%svg-font.module;[
+<!ENTITY % svg-font.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Font//EN"
+ "svg-font.mod" >
+%svg-font.mod;]]>
+
+<!-- Extensibility Module ........................................ -->
+<!ENTITY % svg-extensibility.module "INCLUDE" >
+<![%svg-extensibility.module;[
+<!ENTITY % svg-extensibility.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Extensibility//EN"
+ "svg-extensibility.mod" >
+%svg-extensibility.mod;]]>
+
+<!-- end of SVG 1.1 DTD .................................................... -->
+<!-- ....................................................................... -->
diff --git a/org/apache/batik/dom/svg/resources/svg12-flat.dtd b/org/apache/batik/dom/svg/resources/svg12-flat.dtd
new file mode 100644
index 0000000..c5290f3
--- /dev/null
+++ b/org/apache/batik/dom/svg/resources/svg12-flat.dtd
@@ -0,0 +1,5788 @@
+<!-- ....................................................................... -->
+<!-- SVG 1.1 DTD ........................................................... -->
+<!-- file: svg11.dtd
+-->
+
+<!-- SVG 1.1 DTD
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+
+ The Scalable Vector Graphics (SVG)
+ Copyright 2001, 2002 World Wide Web Consortium
+ (Massachusetts Institute of Technology, Institut National de
+ Recherche en Informatique et en Automatique, Keio University).
+ All Rights Reserved.
+
+ Permission to use, copy, modify and distribute the SVG DTD and its
+ accompanying documentation for any purpose and without fee is hereby
+ granted in perpetuity, provided that the above copyright notice and
+ this paragraph appear in all copies. The copyright holders make no
+ representation about the suitability of the DTD for any purpose.
+
+ It is provided "as is" without expressed or implied warranty.
+
+ Author: Jun Fujisawa <fujisawa.jun at canon.co.jp>
+ Revision: $Id: svg12-flat.dtd 201394 2004-11-18 01:47:06Z deweese $
+
+-->
+<!-- This is the driver file for version 1.1 of the SVG DTD.
+
+ This DTD is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//DTD SVG 1.1//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd"
+-->
+<!ENTITY % SVG.version "-//W3C//DTD SVG 1.1//EN" >
+
+<!-- Use this URI to identify the default namespace:
+
+ "http://www.w3.org/2000/svg"
+
+ See the Qualified Names module for information
+ on the use of namespace prefixes in the DTD.
+-->
+<!ENTITY % NS.prefixed "IGNORE" >
+<!ENTITY % SVG.prefix "" >
+
+<!-- reserved for future use with document profiles -->
+<!ENTITY % SVG.profile "" >
+
+<!-- ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: -->
+
+<!-- Pre-Framework Redeclaration Placeholder ..................... -->
+<!ENTITY % svg-prefw-redecl.module "IGNORE" >
+<![%svg-prefw-redecl.module;[
+%svg-prefw-redecl.mod;]]>
+
+<!-- Document Model Module ....................................... -->
+<!ENTITY % svg-model.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Document Model//EN"
+ "svg11-model.mod" >
+
+<!-- Attribute Collection Module ................................. -->
+<!ENTITY % svg-attribs.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Attribute Collection//EN"
+ "svg11-attribs.mod" >
+
+<!-- Modular Framework Module .................................... -->
+<!ENTITY % svg-framework.module "INCLUDE" >
+<![%svg-framework.module;[
+<!ENTITY % svg-framework.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Modular Framework//EN"
+ "svg-framework.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Modular Framework Module ...................................... -->
+<!-- file: svg-framework.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg12-flat.dtd 201394 2004-11-18 01:47:06Z deweese $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Modular Framework//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-framework.mod"
+
+ ....................................................................... -->
+
+<!-- Modular Framework
+
+ This module instantiates the modules needed o support the SVG
+ modularization model, including:
+
+ + Datatypes
+ + Qualified Name
+ + Document Model
+ + Attribute Collection
+-->
+
+<!ENTITY % svg-datatypes.module "INCLUDE" >
+<![%svg-datatypes.module;[
+<!ENTITY % svg-datatypes.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Datatypes//EN"
+ "svg-datatypes.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Datatypes Module .............................................. -->
+<!-- file: svg-datatypes.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg12-flat.dtd 201394 2004-11-18 01:47:06Z deweese $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Datatypes//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-datatypes.mod"
+
+ ....................................................................... -->
+
+<!-- Datatypes
+
+ This module declares common data types for properties and attributes.
+-->
+
+<!-- feature specification -->
+<!ENTITY % Boolean.datatype "( false | true )" >
+
+<!-- 'clip-rule' or 'fill-rule' property/attribute value -->
+<!ENTITY % ClipFillRule.datatype "( nonzero | evenodd | inherit )" >
+
+<!-- media type, as per [RFC2045] -->
+<!ENTITY % ContentType.datatype "CDATA" >
+
+<!-- a <coordinate> -->
+<!ENTITY % Coordinate.datatype "CDATA" >
+
+<!-- a list of <coordinate>s -->
+<!ENTITY % Coordinates.datatype "CDATA" >
+
+<!-- a <color> value -->
+<!ENTITY % Color.datatype "CDATA" >
+
+<!-- a <integer> -->
+<!ENTITY % Integer.datatype "CDATA" >
+
+<!-- a language code, as per [RFC3066] -->
+<!ENTITY % LanguageCode.datatype "NMTOKEN" >
+
+<!-- comma-separated list of language codes, as per [RFC3066] -->
+<!ENTITY % LanguageCodes.datatype "CDATA" >
+
+<!-- a <length> -->
+<!ENTITY % Length.datatype "CDATA" >
+
+<!-- a list of <length>s -->
+<!ENTITY % Lengths.datatype "CDATA" >
+
+<!-- a <number> -->
+<!ENTITY % Number.datatype "CDATA" >
+
+<!-- a list of <number>s -->
+<!ENTITY % Numbers.datatype "CDATA" >
+
+<!-- opacity value (e.g., <number>) -->
+<!ENTITY % OpacityValue.datatype "CDATA" >
+
+<!-- a path data specification -->
+<!ENTITY % PathData.datatype "CDATA" >
+
+<!-- 'preserveAspectRatio' attribute specification -->
+<!ENTITY % PreserveAspectRatioSpec.datatype "CDATA" >
+
+<!-- script expression -->
+<!ENTITY % Script.datatype "CDATA" >
+
+<!-- An SVG color value (RGB plus optional ICC) -->
+<!ENTITY % SVGColor.datatype "CDATA" >
+
+<!-- arbitrary text string -->
+<!ENTITY % Text.datatype "CDATA" >
+
+<!-- list of transforms -->
+<!ENTITY % TransformList.datatype "CDATA" >
+
+<!-- a Uniform Resource Identifier, see [URI] -->
+<!ENTITY % URI.datatype "CDATA" >
+
+<!-- 'viewBox' attribute specification -->
+<!ENTITY % ViewBoxSpec.datatype "CDATA" >
+
+<!-- end of svg-datatypes.mod -->
+]]>
+
+<!ENTITY % svg-qname.module "INCLUDE" >
+<![%svg-qname.module;[
+<!ENTITY % svg-qname.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Qualified Name//EN"
+ "svg-qname.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Qualified Name Module ......................................... -->
+<!-- file: svg-qname.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg12-flat.dtd 201394 2004-11-18 01:47:06Z deweese $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Qualified Name//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-qname.mod"
+
+ ....................................................................... -->
+
+<!-- Qualified Name
+
+ This module is contained in two parts, labeled Section 'A' and 'B':
+
+ Section A declares parameter entities to support namespace-
+ qualified names, namespace declarations, and name prefixing
+ for SVG and extensions.
+
+ Section B declares parameter entities used to provide
+ namespace-qualified names for all SVG element types:
+-->
+
+<!-- Section A: SVG XML Namespace Framework :::::::::::::::::::::: -->
+
+<!-- 1. Declare a %SVG.prefixed; conditional section keyword, used
+ to activate namespace prefixing. The default value should
+ inherit '%NS.prefixed;' from the DTD driver, so that unless
+ overridden, the default behaviour follows the overall DTD
+ prefixing scheme.
+-->
+<!ENTITY % NS.prefixed "IGNORE" >
+<!ENTITY % SVG.prefixed "%NS.prefixed;" >
+
+<!-- 2. Declare a parameter entity (eg., %SVG.xmlns;) containing
+ the URI reference used to identify the SVG namespace:
+-->
+<!ENTITY % SVG.xmlns "http://www.w3.org/2000/svg" >
+<!ENTITY % XLINK.xmlns "http://www.w3.org/1999/xlink" >
+
+<!-- 3. Declare parameter entities (eg., %SVG.prefix;) containing
+ the default namespace prefix string(s) to use when prefixing
+ is enabled. This may be overridden in the DTD driver or the
+ internal subset of an document instance. If no default prefix
+ is desired, this may be declared as an empty string.
+-->
+<!ENTITY % SVG.prefix "" >
+<!ENTITY % XLINK.prefix "xlink" >
+
+<!-- 4. Declare parameter entities (eg., %SVG.pfx;) containing the
+ colonized prefix(es) (eg., '%SVG.prefix;:') used when
+ prefixing is active, an empty string when it is not.
+-->
+<![%SVG.prefixed;[
+<!ENTITY % SVG.pfx "%SVG.prefix;:" >
+]]>
+<!ENTITY % SVG.pfx "" >
+<!ENTITY % XLINK.pfx "%XLINK.prefix;:" >
+
+<!-- 5. The parameter entity %SVG.xmlns.extra.attrib; may be
+ redeclared to contain any non-SVG namespace declaration
+ attributes for namespaces embedded in SVG. The default
+ is an empty string.
+-->
+<!ENTITY % SVG.xmlns.extra.attrib "" >
+
+<!-- Declare a parameter entity XLINK.xmlns.attrib containing
+ the XML Namespace declarations for XLink.
+-->
+<!ENTITY % XLINK.xmlns.attrib
+ "xmlns:%XLINK.prefix; %URI.datatype; #FIXED '%XLINK.xmlns;'"
+>
+
+<!-- Declare a parameter entity %NS.decl.attrib; containing
+ all XML Namespace declarations used in the DTD, plus the
+ xmlns declaration for SVG, its form dependent on whether
+ prefixing is active.
+-->
+<![%SVG.prefixed;[
+<!ENTITY % NS.decl.attrib
+ "xmlns:%SVG.prefix; %URI.datatype; #FIXED '%SVG.xmlns;'
+ %XLINK.xmlns.attrib;
+ %SVG.xmlns.extra.attrib;"
+>
+]]>
+<!ENTITY % NS.decl.attrib
+ "%XLINK.xmlns.attrib;
+ %SVG.xmlns.extra.attrib;"
+>
+
+<!-- Declare a parameter entity %SVG.xmlns.attrib; containing
+ all XML namespace declaration attributes used by SVG,
+ including a default xmlns attribute when prefixing is
+ inactive.
+-->
+<![%SVG.prefixed;[
+<!ENTITY % SVG.xmlns.attrib
+ "%NS.decl.attrib;"
+>
+]]>
+<!ENTITY % SVG.xmlns.attrib
+ "xmlns %URI.datatype; #FIXED '%SVG.xmlns;'
+ %XLINK.xmlns.attrib;"
+>
+
+<!-- Section B: SVG Qualified Names :::::::::::::::::::::::::::::: -->
+
+<!-- 6. This section declares parameter entities used to provide
+ namespace-qualified names for all SVG element types.
+-->
+
+<!-- module: svg-structure.mod ......................... -->
+
+<!ENTITY % SVG.svg.qname "%SVG.pfx;svg" >
+<!ENTITY % SVG.g.qname "%SVG.pfx;g" >
+<!ENTITY % SVG.defs.qname "%SVG.pfx;defs" >
+<!ENTITY % SVG.desc.qname "%SVG.pfx;desc" >
+<!ENTITY % SVG.title.qname "%SVG.pfx;title" >
+<!ENTITY % SVG.metadata.qname "%SVG.pfx;metadata" >
+<!ENTITY % SVG.symbol.qname "%SVG.pfx;symbol" >
+<!ENTITY % SVG.use.qname "%SVG.pfx;use" >
+
+<!-- module: svg-conditional.mod ....................... -->
+
+<!ENTITY % SVG.switch.qname "%SVG.pfx;switch" >
+
+<!-- module: svg-image.mod ............................. -->
+
+<!ENTITY % SVG.image.qname "%SVG.pfx;image" >
+
+<!-- module: svg-style.mod ............................. -->
+
+<!ENTITY % SVG.style.qname "%SVG.pfx;style" >
+
+<!-- module: svg-shape.mod ............................. -->
+
+<!ENTITY % SVG.path.qname "%SVG.pfx;path" >
+<!ENTITY % SVG.rect.qname "%SVG.pfx;rect" >
+<!ENTITY % SVG.circle.qname "%SVG.pfx;circle" >
+<!ENTITY % SVG.line.qname "%SVG.pfx;line" >
+<!ENTITY % SVG.ellipse.qname "%SVG.pfx;ellipse" >
+<!ENTITY % SVG.polyline.qname "%SVG.pfx;polyline" >
+<!ENTITY % SVG.polygon.qname "%SVG.pfx;polygon" >
+
+<!-- module: svg-text.mod .............................. -->
+
+<!ENTITY % SVG.text.qname "%SVG.pfx;text" >
+<!ENTITY % SVG.tspan.qname "%SVG.pfx;tspan" >
+<!ENTITY % SVG.tref.qname "%SVG.pfx;tref" >
+<!ENTITY % SVG.textPath.qname "%SVG.pfx;textPath" >
+<!ENTITY % SVG.altGlyph.qname "%SVG.pfx;altGlyph" >
+<!ENTITY % SVG.altGlyphDef.qname "%SVG.pfx;altGlyphDef" >
+<!ENTITY % SVG.altGlyphItem.qname "%SVG.pfx;altGlyphItem" >
+<!ENTITY % SVG.glyphRef.qname "%SVG.pfx;glyphRef" >
+
+<!-- module: svg-marker.mod ............................ -->
+
+<!ENTITY % SVG.marker.qname "%SVG.pfx;marker" >
+
+<!-- module: svg-profile.mod ........................... -->
+
+<!ENTITY % SVG.color-profile.qname "%SVG.pfx;color-profile" >
+
+<!-- module: svg-gradient.mod .......................... -->
+
+<!ENTITY % SVG.linearGradient.qname "%SVG.pfx;linearGradient" >
+<!ENTITY % SVG.radialGradient.qname "%SVG.pfx;radialGradient" >
+<!ENTITY % SVG.stop.qname "stop" >
+
+<!-- module: svg-pattern.mod ........................... -->
+
+<!ENTITY % SVG.pattern.qname "%SVG.pfx;pattern" >
+
+<!-- module: svg-clip.mod .............................. -->
+
+<!ENTITY % SVG.clipPath.qname "%SVG.pfx;clipPath" >
+
+<!-- module: svg-mask.mod .............................. -->
+
+<!ENTITY % SVG.mask.qname "%SVG.pfx;mask" >
+
+<!-- module: svg-filter.mod ............................ -->
+
+<!ENTITY % SVG.filter.qname "%SVG.pfx;filter" >
+<!ENTITY % SVG.feBlend.qname "%SVG.pfx;feBlend" >
+<!ENTITY % SVG.feColorMatrix.qname "%SVG.pfx;feColorMatrix" >
+<!ENTITY % SVG.feComponentTransfer.qname "%SVG.pfx;feComponentTransfer" >
+<!ENTITY % SVG.feComposite.qname "%SVG.pfx;feComposite" >
+<!ENTITY % SVG.feConvolveMatrix.qname "%SVG.pfx;feConvolveMatrix" >
+<!ENTITY % SVG.feDiffuseLighting.qname "%SVG.pfx;feDiffuseLighting" >
+<!ENTITY % SVG.feDisplacementMap.qname "%SVG.pfx;feDisplacementMap" >
+<!ENTITY % SVG.feFlood.qname "%SVG.pfx;feFlood" >
+<!ENTITY % SVG.feGaussianBlur.qname "%SVG.pfx;feGaussianBlur" >
+<!ENTITY % SVG.feImage.qname "%SVG.pfx;feImage" >
+<!ENTITY % SVG.feMerge.qname "%SVG.pfx;feMerge" >
+<!ENTITY % SVG.feMergeNode.qname "%SVG.pfx;feMergeNode" >
+<!ENTITY % SVG.feMorphology.qname "%SVG.pfx;feMorphology" >
+<!ENTITY % SVG.feOffset.qname "%SVG.pfx;feOffset" >
+<!ENTITY % SVG.feSpecularLighting.qname "%SVG.pfx;feSpecularLighting" >
+<!ENTITY % SVG.feTile.qname "%SVG.pfx;feTile" >
+<!ENTITY % SVG.feTurbulence.qname "%SVG.pfx;feTurbulence" >
+<!ENTITY % SVG.feDistantLight.qname "%SVG.pfx;feDistantLight" >
+<!ENTITY % SVG.fePointLight.qname "%SVG.pfx;fePointLight" >
+<!ENTITY % SVG.feSpotLight.qname "%SVG.pfx;feSpotLight" >
+<!ENTITY % SVG.feFuncR.qname "%SVG.pfx;feFuncR" >
+<!ENTITY % SVG.feFuncG.qname "%SVG.pfx;feFuncG" >
+<!ENTITY % SVG.feFuncB.qname "%SVG.pfx;feFuncB" >
+<!ENTITY % SVG.feFuncA.qname "%SVG.pfx;feFuncA" >
+
+<!-- module: svg-cursor.mod ............................ -->
+
+<!ENTITY % SVG.cursor.qname "%SVG.pfx;cursor" >
+
+<!-- module: svg-hyperlink.mod ......................... -->
+
+<!ENTITY % SVG.a.qname "%SVG.pfx;a" >
+
+<!-- module: svg-view.mod .............................. -->
+
+<!ENTITY % SVG.view.qname "%SVG.pfx;view" >
+
+<!-- module: svg-script.mod ............................ -->
+
+<!ENTITY % SVG.script.qname "%SVG.pfx;script" >
+
+<!-- module: svg-animation.mod ......................... -->
+
+<!ENTITY % SVG.animate.qname "%SVG.pfx;animate" >
+<!ENTITY % SVG.set.qname "%SVG.pfx;set" >
+<!ENTITY % SVG.animateMotion.qname "%SVG.pfx;animateMotion" >
+<!ENTITY % SVG.animateColor.qname "%SVG.pfx;animateColor" >
+<!ENTITY % SVG.animateTransform.qname "%SVG.pfx;animateTransform" >
+<!ENTITY % SVG.mpath.qname "%SVG.pfx;mpath" >
+
+<!-- module: svg-font.mod .............................. -->
+
+<!ENTITY % SVG.font.qname "%SVG.pfx;font" >
+<!ENTITY % SVG.font-face.qname "%SVG.pfx;font-face" >
+<!ENTITY % SVG.glyph.qname "%SVG.pfx;glyph" >
+<!ENTITY % SVG.missing-glyph.qname "%SVG.pfx;missing-glyph" >
+<!ENTITY % SVG.hkern.qname "%SVG.pfx;hkern" >
+<!ENTITY % SVG.vkern.qname "%SVG.pfx;vkern" >
+<!ENTITY % SVG.font-face-src.qname "%SVG.pfx;font-face-src" >
+<!ENTITY % SVG.font-face-uri.qname "%SVG.pfx;font-face-uri" >
+<!ENTITY % SVG.font-face-format.qname "%SVG.pfx;font-face-format" >
+<!ENTITY % SVG.font-face-name.qname "%SVG.pfx;font-face-name" >
+<!ENTITY % SVG.definition-src.qname "%SVG.pfx;definition-src" >
+
+<!-- module: svg-extensibility.mod ..................... -->
+
+<!ENTITY % SVG.foreignObject.qname "%SVG.pfx;foreignObject" >
+
+<!-- end of svg-qname.mod -->
+]]>
+
+<!ENTITY % svg-model.module "INCLUDE" >
+<![%svg-model.module;[
+<!-- instantiate the Document Model declared in the DTD driver -->
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Document Model Module ......................................... -->
+<!-- file: svg11-model.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg12-flat.dtd 201394 2004-11-18 01:47:06Z deweese $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Document Model//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11-model.mod"
+
+ ....................................................................... -->
+
+<!-- SVG 1.1 Document Model
+
+ This module describes the groupings of elements that make up
+ common content models for SVG elements.
+-->
+
+<!-- module: svg-structure.mod ......................... -->
+
+<!ENTITY % SVG.Description.extra.class "" >
+<!ENTITY % SVG.Description.class
+ "%SVG.desc.qname; | %SVG.title.qname; | %SVG.metadata.qname;
+ %SVG.Description.extra.class;"
+>
+
+<!ENTITY % SVG.Use.extra.class "" >
+<!ENTITY % SVG.Use.class
+ "| %SVG.use.qname; %SVG.Use.extra.class;"
+>
+
+<!ENTITY % SVG.Structure.extra.class "" >
+<!ENTITY % SVG.Structure.class
+ "| %SVG.svg.qname; | %SVG.g.qname; | %SVG.defs.qname; | %SVG.symbol.qname;
+ %SVG.Use.class; %SVG.Structure.extra.class;"
+>
+
+<!-- module: svg-conditional.mod ....................... -->
+
+<!ENTITY % SVG.Conditional.extra.class "" >
+<!ENTITY % SVG.Conditional.class
+ "| %SVG.switch.qname; %SVG.Conditional.extra.class;"
+>
+
+<!-- module: svg-image.mod ............................. -->
+
+<!ENTITY % SVG.Image.extra.class "" >
+<!ENTITY % SVG.Image.class
+ "| %SVG.image.qname; %SVG.Image.extra.class;"
+>
+
+<!-- module: svg-style.mod ............................. -->
+
+<!ENTITY % SVG.Style.extra.class "" >
+<!ENTITY % SVG.Style.class
+ "| %SVG.style.qname; %SVG.Style.extra.class;"
+>
+
+<!-- module: svg-shape.mod ............................. -->
+
+<!ENTITY % SVG.Shape.extra.class "" >
+<!ENTITY % SVG.Shape.class
+ "| %SVG.path.qname; | %SVG.rect.qname; | %SVG.circle.qname;
+ | %SVG.line.qname; | %SVG.ellipse.qname; | %SVG.polyline.qname;
+ | %SVG.polygon.qname; %SVG.Shape.extra.class;"
+>
+
+<!-- module: svg-text.mod .............................. -->
+
+<!ENTITY % SVG.Text.extra.class "" >
+<!ENTITY % SVG.Text.class
+ "| %SVG.text.qname; | %SVG.altGlyphDef.qname; %SVG.Text.extra.class;"
+>
+
+<!ENTITY % SVG.TextContent.extra.class "" >
+<!ENTITY % SVG.TextContent.class
+ "| %SVG.tspan.qname; | %SVG.tref.qname; | %SVG.textPath.qname;
+ | %SVG.altGlyph.qname; %SVG.TextContent.extra.class;"
+>
+
+<!-- module: svg-marker.mod ............................ -->
+
+<!ENTITY % SVG.Marker.extra.class "" >
+<!ENTITY % SVG.Marker.class
+ "| %SVG.marker.qname; %SVG.Marker.extra.class;"
+>
+
+<!-- module: svg-profile.mod ........................... -->
+
+<!ENTITY % SVG.Profile.extra.class "" >
+<!ENTITY % SVG.Profile.class
+ "| %SVG.color-profile.qname; %SVG.Profile.extra.class;"
+>
+
+<!-- module: svg-gradient.mod .......................... -->
+
+<!ENTITY % SVG.Gradient.extra.class "" >
+<!ENTITY % SVG.Gradient.class
+ "| %SVG.linearGradient.qname; | %SVG.radialGradient.qname;
+ %SVG.Gradient.extra.class;"
+>
+
+<!-- module: svg-pattern.mod ........................... -->
+
+<!ENTITY % SVG.Pattern.extra.class "" >
+<!ENTITY % SVG.Pattern.class
+ "| %SVG.pattern.qname; %SVG.Pattern.extra.class;"
+>
+
+<!-- module: svg-clip.mod .............................. -->
+
+<!ENTITY % SVG.Clip.extra.class "" >
+<!ENTITY % SVG.Clip.class
+ "| %SVG.clipPath.qname; %SVG.Clip.extra.class;"
+>
+
+<!-- module: svg-mask.mod .............................. -->
+
+<!ENTITY % SVG.Mask.extra.class "" >
+<!ENTITY % SVG.Mask.class
+ "| %SVG.mask.qname; %SVG.Mask.extra.class;"
+>
+
+<!-- module: svg-filter.mod ............................ -->
+
+<!ENTITY % SVG.Filter.extra.class "" >
+<!ENTITY % SVG.Filter.class
+ "| %SVG.filter.qname; %SVG.Filter.extra.class;"
+>
+
+<!ENTITY % SVG.FilterPrimitive.extra.class "" >
+<!ENTITY % SVG.FilterPrimitive.class
+ "| %SVG.feBlend.qname; | %SVG.feColorMatrix.qname;
+ | %SVG.feComponentTransfer.qname; | %SVG.feComposite.qname;
+ | %SVG.feConvolveMatrix.qname; | %SVG.feDiffuseLighting.qname;
+ | %SVG.feDisplacementMap.qname; | %SVG.feFlood.qname;
+ | %SVG.feGaussianBlur.qname; | %SVG.feImage.qname; | %SVG.feMerge.qname;
+ | %SVG.feMorphology.qname; | %SVG.feOffset.qname;
+ | %SVG.feSpecularLighting.qname; | %SVG.feTile.qname;
+ | %SVG.feTurbulence.qname; %SVG.FilterPrimitive.extra.class;"
+>
+
+<!-- module: svg-cursor.mod ............................ -->
+
+<!ENTITY % SVG.Cursor.extra.class "" >
+<!ENTITY % SVG.Cursor.class
+ "| %SVG.cursor.qname; %SVG.Cursor.extra.class;"
+>
+
+<!-- module: svg-hyperlink.mod ......................... -->
+
+<!ENTITY % SVG.Hyperlink.extra.class "" >
+<!ENTITY % SVG.Hyperlink.class
+ "| %SVG.a.qname; %SVG.Hyperlink.extra.class;"
+>
+
+<!-- module: svg-view.mod .............................. -->
+
+<!ENTITY % SVG.View.extra.class "" >
+<!ENTITY % SVG.View.class
+ "| %SVG.view.qname; %SVG.View.extra.class;"
+>
+
+<!-- module: svg-script.mod ............................ -->
+
+<!ENTITY % SVG.Script.extra.class "" >
+<!ENTITY % SVG.Script.class
+ "| %SVG.script.qname; %SVG.Script.extra.class;"
+>
+
+<!-- module: svg-animation.mod ......................... -->
+
+<!ENTITY % SVG.Animation.extra.class "" >
+<!ENTITY % SVG.Animation.class
+ "%SVG.animate.qname; | %SVG.set.qname; | %SVG.animateMotion.qname; |
+ %SVG.animateColor.qname; | %SVG.animateTransform.qname;
+ %SVG.Animation.extra.class;"
+>
+
+<!-- module: svg-font.mod .............................. -->
+
+<!ENTITY % SVG.Font.extra.class "" >
+<!ENTITY % SVG.Font.class
+ "| %SVG.font.qname; | %SVG.font-face.qname; %SVG.Font.extra.class;"
+>
+
+<!-- module: svg-extensibility.mod ..................... -->
+
+<!ENTITY % SVG.Extensibility.extra.class "" >
+<!ENTITY % SVG.Extensibility.class
+ "| %SVG.foreignObject.qname; %SVG.Extensibility.extra.class;"
+>
+
+<!-- end of svg11-model.mod -->
+]]>
+
+<!ENTITY % svg-attribs.module "INCLUDE" >
+<![%svg-attribs.module;[
+<!-- instantiate the Attribute Collection declared in the DTD driver -->
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Attribute Collection Module ................................... -->
+<!-- file: svg11-attribs.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg12-flat.dtd 201394 2004-11-18 01:47:06Z deweese $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Attribute Collection//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11-attribs.mod"
+
+ ....................................................................... -->
+
+<!-- SVG 1.1 Attribute Collection
+
+ This module defines the set of common attributes that can be present
+ on many SVG elements.
+-->
+
+<!-- module: svg-conditional.mod ....................... -->
+
+<!ENTITY % ExtensionList.datatype "CDATA" >
+<!ENTITY % FeatureList.datatype "CDATA" >
+
+<!ENTITY % SVG.Conditional.extra.attrib "" >
+<!ENTITY % SVG.Conditional.attrib
+ "requiredFeatures %FeatureList.datatype; #IMPLIED
+ requiredExtensions %ExtensionList.datatype; #IMPLIED
+ systemLanguage %LanguageCodes.datatype; #IMPLIED
+ %SVG.Conditional.extra.attrib;"
+>
+
+<!-- module: svg-style.mod ............................. -->
+
+<!ENTITY % ClassList.datatype "CDATA" >
+<!ENTITY % StyleSheet.datatype "CDATA" >
+
+<!ENTITY % SVG.Style.extra.attrib "" >
+<!ENTITY % SVG.Style.attrib
+ "style %StyleSheet.datatype; #IMPLIED
+ class %ClassList.datatype; #IMPLIED
+ %SVG.Style.extra.attrib;"
+>
+
+<!-- module: svg-text.mod .............................. -->
+
+<!ENTITY % BaselineShiftValue.datatype "CDATA" >
+<!ENTITY % FontFamilyValue.datatype "CDATA" >
+<!ENTITY % FontSizeValue.datatype "CDATA" >
+<!ENTITY % FontSizeAdjustValue.datatype "CDATA" >
+<!ENTITY % GlyphOrientationHorizontalValue.datatype "CDATA" >
+<!ENTITY % GlyphOrientationVerticalValue.datatype "CDATA" >
+<!ENTITY % KerningValue.datatype "CDATA" >
+<!ENTITY % SpacingValue.datatype "CDATA" >
+<!ENTITY % TextDecorationValue.datatype "CDATA" >
+
+<!ENTITY % SVG.Text.extra.attrib "" >
+<!ENTITY % SVG.Text.attrib
+ "writing-mode ( lr-tb | rl-tb | tb-rl | lr | rl | tb | inherit ) #IMPLIED
+ %SVG.Text.extra.attrib;"
+>
+
+<!ENTITY % SVG.TextContent.extra.attrib "" >
+<!ENTITY % SVG.TextContent.attrib
+ "alignment-baseline ( auto | baseline | before-edge | text-before-edge |
+ middle | central | after-edge | text-after-edge |
+ ideographic | alphabetic | hanging | mathematical |
+ inherit ) #IMPLIED
+ baseline-shift %BaselineShiftValue.datatype; #IMPLIED
+ direction ( ltr | rtl | inherit ) #IMPLIED
+ dominant-baseline ( auto | use-script | no-change | reset-size |
+ ideographic | alphabetic | hanging | mathematical |
+ central | middle | text-after-edge | text-before-edge |
+ inherit ) #IMPLIED
+ glyph-orientation-horizontal %GlyphOrientationHorizontalValue.datatype;
+ #IMPLIED
+ glyph-orientation-vertical %GlyphOrientationVerticalValue.datatype;
+ #IMPLIED
+ kerning %KerningValue.datatype; #IMPLIED
+ letter-spacing %SpacingValue.datatype; #IMPLIED
+ text-anchor ( start | middle | end | inherit ) #IMPLIED
+ text-decoration %TextDecorationValue.datatype; #IMPLIED
+ unicode-bidi ( normal | embed | bidi-override | inherit ) #IMPLIED
+ word-spacing %SpacingValue.datatype; #IMPLIED
+ %SVG.TextContent.extra.attrib;"
+>
+
+<!ENTITY % SVG.Font.extra.attrib "" >
+<!ENTITY % SVG.Font.attrib
+ "font-family %FontFamilyValue.datatype; #IMPLIED
+ font-size %FontSizeValue.datatype; #IMPLIED
+ font-size-adjust %FontSizeAdjustValue.datatype; #IMPLIED
+ font-stretch ( normal | wider | narrower | ultra-condensed |
+ extra-condensed | condensed | semi-condensed |
+ semi-expanded | expanded | extra-expanded |
+ ultra-expanded | inherit ) #IMPLIED
+ font-style ( normal | italic | oblique | inherit ) #IMPLIED
+ font-variant ( normal | small-caps | inherit ) #IMPLIED
+ font-weight ( normal | bold | bolder | lighter | 100 | 200 | 300 | 400 |
+ 500 | 600 | 700 | 800 | 900 | inherit ) #IMPLIED
+ %SVG.Font.extra.attrib;"
+>
+
+<!-- module: svg-marker.mod ............................ -->
+
+<!ENTITY % MarkerValue.datatype "CDATA" >
+
+<!ENTITY % SVG.Marker.extra.attrib "" >
+<!ENTITY % SVG.Marker.attrib
+ "marker-start %MarkerValue.datatype; #IMPLIED
+ marker-mid %MarkerValue.datatype; #IMPLIED
+ marker-end %MarkerValue.datatype; #IMPLIED
+ %SVG.Marker.extra.attrib;"
+>
+
+<!-- module: svg-profile.mod ........................... -->
+
+<!ENTITY % SVG.Profile.extra.attrib "" >
+<!ENTITY % SVG.Profile.attrib
+ "color-profile CDATA #IMPLIED
+ %SVG.Profile.extra.attrib;"
+>
+
+<!-- module: svg-gradient.mod .......................... -->
+
+<!ENTITY % NumberOrPercentage.datatype "CDATA" >
+
+<!ENTITY % SVG.Gradient.extra.attrib "" >
+<!ENTITY % SVG.Gradient.attrib
+ "stop-color %SVGColor.datatype; #IMPLIED
+ stop-opacity %OpacityValue.datatype; #IMPLIED
+ %SVG.Gradient.extra.attrib;"
+>
+
+<!-- module: svg-clip.mod .............................. -->
+
+<!ENTITY % ClipPathValue.datatype "CDATA" >
+
+<!ENTITY % SVG.Clip.extra.attrib "" >
+<!ENTITY % SVG.Clip.attrib
+ "clip-path %ClipPathValue.datatype; #IMPLIED
+ clip-rule %ClipFillRule.datatype; #IMPLIED
+ %SVG.Clip.extra.attrib;"
+>
+
+<!-- module: svg-mask.mod .............................. -->
+
+<!ENTITY % MaskValue.datatype "CDATA" >
+
+<!ENTITY % SVG.Mask.extra.attrib "" >
+<!ENTITY % SVG.Mask.attrib
+ "mask %MaskValue.datatype; #IMPLIED
+ %SVG.Mask.extra.attrib;"
+>
+
+<!-- module: svg-filter.mod ............................ -->
+
+<!ENTITY % FilterValue.datatype "CDATA" >
+<!ENTITY % NumberOptionalNumber.datatype "CDATA" >
+
+<!ENTITY % SVG.Filter.extra.attrib "" >
+<!ENTITY % SVG.Filter.attrib
+ "filter %FilterValue.datatype; #IMPLIED
+ %SVG.Filter.extra.attrib;"
+>
+
+<!ENTITY % SVG.FilterColor.extra.attrib "" >
+<!ENTITY % SVG.FilterColor.attrib
+ "color-interpolation-filters ( auto | sRGB | linearRGB | inherit )
+ #IMPLIED
+ %SVG.FilterColor.extra.attrib;"
+>
+
+<!-- module: svg-cursor.mod ............................ -->
+
+<!ENTITY % CursorValue.datatype "CDATA" >
+
+<!ENTITY % SVG.Cursor.extra.attrib "" >
+<!ENTITY % SVG.Cursor.attrib
+ "cursor %CursorValue.datatype; #IMPLIED
+ %SVG.Cursor.extra.attrib;"
+>
+
+<!-- end of svg11-attribs.mod -->
+]]>
+
+<!-- end of svg-framework.mod -->
+]]>
+
+<!-- Post-Framework Redeclaration Placeholder .................... -->
+<!ENTITY % svg-postfw-redecl.module "IGNORE" >
+<![%svg-postfw-redecl.module;[
+%svg-postfw-redecl.mod;]]>
+
+<!-- ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: -->
+
+<!-- Core Attribute Module ....................................... -->
+<!ENTITY % svg-core-attrib.module "INCLUDE" >
+<![%svg-core-attrib.module;[
+<!ENTITY % svg-core-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Core Attribute//EN"
+ "svg-core-attrib.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Core Attribute Module ......................................... -->
+<!-- file: svg-core-attrib.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg12-flat.dtd 201394 2004-11-18 01:47:06Z deweese $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Core Attribute//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-core-attrib.mod"
+
+ ....................................................................... -->
+
+<!-- Core Attribute
+
+ id, xml:base, xml:lang, xml:space
+
+ This module defines the core set of attributes that can be present on
+ any element.
+-->
+
+<!ENTITY % SVG.id.attrib
+ "id ID #IMPLIED"
+>
+
+<!ENTITY % SVG.base.attrib
+ "xml:base %URI.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.lang.attrib
+ "xml:lang %LanguageCode.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.space.attrib
+ "xml:space ( default | preserve ) #IMPLIED"
+>
+
+<!ENTITY % SVG.Core.extra.attrib "" >
+
+<!ENTITY % SVG.Core.attrib
+ "%SVG.id.attrib;
+ %SVG.base.attrib;
+ %SVG.lang.attrib;
+ %SVG.space.attrib;
+ %SVG.Core.extra.attrib;"
+>
+
+<!-- end of svg-core-attrib.mod -->
+]]>
+
+<!-- Container Attribute Module .................................. -->
+<!ENTITY % svg-container-attrib.module "INCLUDE" >
+<![%svg-container-attrib.module;[
+<!ENTITY % svg-container-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Container Attribute//EN"
+ "svg-container-attrib.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Container Attribute Module .................................... -->
+<!-- file: svg-container-attrib.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg12-flat.dtd 201394 2004-11-18 01:47:06Z deweese $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Container Attribute//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-container-attrib.mod"
+
+ ....................................................................... -->
+
+<!-- Container Attribute
+
+ enable-background
+
+ This module defines the Container attribute set.
+-->
+
+<!-- 'enable-background' property/attribute value (e.g., 'new', 'accumulate') -->
+<!ENTITY % EnableBackgroundValue.datatype "CDATA" >
+
+<!ENTITY % SVG.enable-background.attrib
+ "enable-background %EnableBackgroundValue.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.Container.extra.attrib "" >
+
+<!ENTITY % SVG.Container.attrib
+ "%SVG.enable-background.attrib;
+ %SVG.Container.extra.attrib;"
+>
+
+<!-- end of svg-container-attrib.mod -->
+]]>
+
+<!-- Viewport Attribute Module ................................... -->
+<!ENTITY % svg-viewport-attrib.module "INCLUDE" >
+<![%svg-viewport-attrib.module;[
+<!ENTITY % svg-viewport-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Viewport Attribute//EN"
+ "svg-viewport-attrib.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Viewport Attribute Module ..................................... -->
+<!-- file: svg-viewport-attrib.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg12-flat.dtd 201394 2004-11-18 01:47:06Z deweese $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Viewport Attribute//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-viewport-attrib.mod"
+
+ ....................................................................... -->
+
+<!-- Viewport Attribute
+
+ clip, overflow
+
+ This module defines the Viewport attribute set.
+-->
+
+<!-- 'clip' property/attribute value (e.g., 'auto', rect(...)) -->
+<!ENTITY % ClipValue.datatype "CDATA" >
+
+<!ENTITY % SVG.clip.attrib
+ "clip %ClipValue.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.overflow.attrib
+ "overflow ( visible | hidden | scroll | auto | inherit ) #IMPLIED"
+>
+
+<!ENTITY % SVG.Viewport.extra.attrib "" >
+
+<!ENTITY % SVG.Viewport.attrib
+ "%SVG.clip.attrib;
+ %SVG.overflow.attrib;
+ %SVG.Viewport.extra.attrib;"
+>
+
+<!-- end of svg-viewport-attrib.mod -->
+]]>
+
+<!-- Paint Attribute Module ...................................... -->
+<!ENTITY % svg-paint-attrib.module "INCLUDE" >
+<![%svg-paint-attrib.module;[
+<!ENTITY % svg-paint-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Paint Attribute//EN"
+ "svg-paint-attrib.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Paint Attribute Module ........................................ -->
+<!-- file: svg-paint-attrib.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg12-flat.dtd 201394 2004-11-18 01:47:06Z deweese $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Paint Attribute//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-paint-attrib.mod"
+
+ ....................................................................... -->
+
+<!-- Paint Attribute
+
+ fill, fill-rule, stroke, stroke-dasharray, stroke-dashoffset,
+ stroke-linecap, stroke-linejoin, stroke-miterlimit, stroke-width, color,
+ color-interpolation, color-rendering
+
+ This module defines the Paint and Color attribute sets.
+-->
+
+<!-- a 'fill' or 'stroke' property/attribute value: <paint> -->
+<!ENTITY % Paint.datatype "CDATA" >
+
+<!-- 'stroke-dasharray' property/attribute value (e.g., 'none', list of <number>s) -->
+<!ENTITY % StrokeDashArrayValue.datatype "CDATA" >
+
+<!-- 'stroke-dashoffset' property/attribute value (e.g., 'none', <legnth>) -->
+<!ENTITY % StrokeDashOffsetValue.datatype "CDATA" >
+
+<!-- 'stroke-miterlimit' property/attribute value (e.g., <number>) -->
+<!ENTITY % StrokeMiterLimitValue.datatype "CDATA" >
+
+<!-- 'stroke-width' property/attribute value (e.g., <length>) -->
+<!ENTITY % StrokeWidthValue.datatype "CDATA" >
+
+<!ENTITY % SVG.fill.attrib
+ "fill %Paint.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.fill-rule.attrib
+ "fill-rule %ClipFillRule.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.stroke.attrib
+ "stroke %Paint.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.stroke-dasharray.attrib
+ "stroke-dasharray %StrokeDashArrayValue.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.stroke-dashoffset.attrib
+ "stroke-dashoffset %StrokeDashOffsetValue.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.stroke-linecap.attrib
+ "stroke-linecap ( butt | round | square | inherit ) #IMPLIED"
+>
+
+<!ENTITY % SVG.stroke-linejoin.attrib
+ "stroke-linejoin ( miter | round | bevel | inherit ) #IMPLIED"
+>
+
+<!ENTITY % SVG.stroke-miterlimit.attrib
+ "stroke-miterlimit %StrokeMiterLimitValue.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.stroke-width.attrib
+ "stroke-width %StrokeWidthValue.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.Paint.extra.attrib "" >
+
+<!ENTITY % SVG.Paint.attrib
+ "%SVG.fill.attrib;
+ %SVG.fill-rule.attrib;
+ %SVG.stroke.attrib;
+ %SVG.stroke-dasharray.attrib;
+ %SVG.stroke-dashoffset.attrib;
+ %SVG.stroke-linecap.attrib;
+ %SVG.stroke-linejoin.attrib;
+ %SVG.stroke-miterlimit.attrib;
+ %SVG.stroke-width.attrib;
+ %SVG.Paint.extra.attrib;"
+>
+
+<!ENTITY % SVG.color.attrib
+ "color %Color.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.color-interpolation.attrib
+ "color-interpolation ( auto | sRGB | linearRGB | inherit ) #IMPLIED"
+>
+
+<!ENTITY % SVG.color-rendering.attrib
+ "color-rendering ( auto | optimizeSpeed | optimizeQuality | inherit )
+ #IMPLIED"
+>
+
+<!ENTITY % SVG.Color.extra.attrib "" >
+
+<!ENTITY % SVG.Color.attrib
+ "%SVG.color.attrib;
+ %SVG.color-interpolation.attrib;
+ %SVG.color-rendering.attrib;
+ %SVG.Color.extra.attrib;"
+>
+
+<!-- end of svg-paint-attrib.mod -->
+]]>
+
+<!-- Paint Opacity Attribute Module .............................. -->
+<!ENTITY % svg-opacity-attrib.module "INCLUDE" >
+<![%svg-opacity-attrib.module;[
+<!ENTITY % svg-opacity-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Paint Opacity Attribute//EN"
+ "svg-opacity-attrib.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Paint Opacity Attribute Module ................................ -->
+<!-- file: svg-opacity-attrib.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg12-flat.dtd 201394 2004-11-18 01:47:06Z deweese $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Paint Opacity Attribute//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-opacity-attrib.mod"
+
+ ....................................................................... -->
+
+<!-- Paint Opacity Attribute
+
+ opacity, fill-opacity, stroke-opacity
+
+ This module defines the Opacity attribute set.
+-->
+
+<!ENTITY % SVG.opacity.attrib
+ "opacity %OpacityValue.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.fill-opacity.attrib
+ "fill-opacity %OpacityValue.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.stroke-opacity.attrib
+ "stroke-opacity %OpacityValue.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.Opacity.extra.attrib "" >
+
+<!ENTITY % SVG.Opacity.attrib
+ "%SVG.opacity.attrib;
+ %SVG.fill-opacity.attrib;
+ %SVG.stroke-opacity.attrib;
+ %SVG.Opacity.extra.attrib;"
+>
+
+<!-- end of svg-opacity-attrib.mod -->
+]]>
+
+<!-- Graphics Attribute Module ................................... -->
+<!ENTITY % svg-graphics-attrib.module "INCLUDE" >
+<![%svg-graphics-attrib.module;[
+<!ENTITY % svg-graphics-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Graphics Attribute//EN"
+ "svg-graphics-attrib.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Graphics Attribute Module ..................................... -->
+<!-- file: svg-graphics-attrib.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg12-flat.dtd 201394 2004-11-18 01:47:06Z deweese $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Graphics Attribute//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-graphics-attrib.mod"
+
+ ....................................................................... -->
+
+<!-- Graphics Attribute
+
+ display, image-rendering, pointer-events, shape-rendering,
+ text-rendering, visibility
+
+ This module defines the Graphics attribute set.
+-->
+
+<!ENTITY % SVG.display.attrib
+ "display ( inline | block | list-item | run-in | compact | marker |
+ table | inline-table | table-row-group | table-header-group |
+ table-footer-group | table-row | table-column-group |
+ table-column | table-cell | table-caption | none | inherit )
+ #IMPLIED"
+>
+
+<!ENTITY % SVG.image-rendering.attrib
+ "image-rendering ( auto | optimizeSpeed | optimizeQuality | inherit )
+ #IMPLIED"
+>
+
+<!ENTITY % SVG.pointer-events.attrib
+ "pointer-events ( visiblePainted | visibleFill | visibleStroke | visible |
+ painted | fill | stroke | all | none | inherit )
+ #IMPLIED"
+>
+
+<!ENTITY % SVG.shape-rendering.attrib
+ "shape-rendering ( auto | optimizeSpeed | crispEdges | geometricPrecision |
+ inherit ) #IMPLIED"
+>
+
+<!ENTITY % SVG.text-rendering.attrib
+ "text-rendering ( auto | optimizeSpeed | optimizeLegibility |
+ geometricPrecision | inherit ) #IMPLIED"
+>
+
+<!ENTITY % SVG.visibility.attrib
+ "visibility ( visible | hidden | inherit ) #IMPLIED"
+>
+
+<!ENTITY % SVG.Graphics.extra.attrib "" >
+
+<!ENTITY % SVG.Graphics.attrib
+ "%SVG.display.attrib;
+ %SVG.image-rendering.attrib;
+ %SVG.pointer-events.attrib;
+ %SVG.shape-rendering.attrib;
+ %SVG.text-rendering.attrib;
+ %SVG.visibility.attrib;
+ %SVG.Graphics.extra.attrib;"
+>
+
+<!-- end of svg-graphics-attrib.mod -->
+]]>
+
+<!-- Document Events Attribute Module ............................ -->
+<!ENTITY % svg-docevents-attrib.module "INCLUDE" >
+<![%svg-docevents-attrib.module;[
+<!ENTITY % svg-docevents-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Document Events Attribute//EN"
+ "svg-docevents-attrib.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Document Events Attribute Module .............................. -->
+<!-- file: svg-docevents-attrib.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg12-flat.dtd 201394 2004-11-18 01:47:06Z deweese $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Document Events Attribute//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-docevents-attrib.mod"
+
+ ....................................................................... -->
+
+<!-- Document Events Attribute
+
+ onunload, onabort, onerror, onresize, onscroll, onzoom
+
+ This module defines the DocumentEvents attribute set.
+-->
+
+<!ENTITY % SVG.onunload.attrib
+ "onunload %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onabort.attrib
+ "onabort %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onerror.attrib
+ "onerror %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onresize.attrib
+ "onresize %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onscroll.attrib
+ "onscroll %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onzoom.attrib
+ "onzoom %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.DocumentEvents.extra.attrib "" >
+
+<!ENTITY % SVG.DocumentEvents.attrib
+ "%SVG.onunload.attrib;
+ %SVG.onabort.attrib;
+ %SVG.onerror.attrib;
+ %SVG.onresize.attrib;
+ %SVG.onscroll.attrib;
+ %SVG.onzoom.attrib;
+ %SVG.DocumentEvents.extra.attrib;"
+>
+
+<!-- end of svg-docevents-attrib.mod -->
+]]>
+
+<!-- Graphical Element Events Attribute Module ................... -->
+<!ENTITY % svg-graphevents-attrib.module "INCLUDE" >
+<![%svg-graphevents-attrib.module;[
+<!ENTITY % svg-graphevents-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Graphical Element Events Attribute//EN"
+ "svg-graphevents-attrib.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Graphical Element Events Attribute Module ..................... -->
+<!-- file: svg-graphevents-attrib.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg12-flat.dtd 201394 2004-11-18 01:47:06Z deweese $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Graphical Element Events Attribute//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-graphevents-attrib.mod"
+
+ ....................................................................... -->
+
+<!-- Graphical Element Events Attribute
+
+ onfocusin, onfocusout, onactivate, onclick, onmousedown, onmouseup,
+ onmouseover, onmousemove, onmouseout, onload
+
+ This module defines the GraphicalEvents attribute set.
+-->
+
+<!ENTITY % SVG.onfocusin.attrib
+ "onfocusin %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onfocusout.attrib
+ "onfocusout %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onactivate.attrib
+ "onactivate %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onclick.attrib
+ "onclick %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onmousedown.attrib
+ "onmousedown %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onmouseup.attrib
+ "onmouseup %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onmouseover.attrib
+ "onmouseover %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onmousemove.attrib
+ "onmousemove %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onmouseout.attrib
+ "onmouseout %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onload.attrib
+ "onload %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.GraphicalEvents.extra.attrib "" >
+
+<!ENTITY % SVG.GraphicalEvents.attrib
+ "%SVG.onfocusin.attrib;
+ %SVG.onfocusout.attrib;
+ %SVG.onactivate.attrib;
+ %SVG.onclick.attrib;
+ %SVG.onmousedown.attrib;
+ %SVG.onmouseup.attrib;
+ %SVG.onmouseover.attrib;
+ %SVG.onmousemove.attrib;
+ %SVG.onmouseout.attrib;
+ %SVG.onload.attrib;
+ %SVG.GraphicalEvents.extra.attrib;"
+>
+
+<!-- end of svg-graphevents-attrib.mod -->
+]]>
+
+<!-- Animation Events Attribute Module ........................... -->
+<!ENTITY % svg-animevents-attrib.module "INCLUDE" >
+<![%svg-animevents-attrib.module;[
+<!ENTITY % svg-animevents-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Animation Events Attribute//EN"
+ "svg-animevents-attrib.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Animation Events Attribute Module ............................. -->
+<!-- file: svg-animevents-attrib.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg12-flat.dtd 201394 2004-11-18 01:47:06Z deweese $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 Animation Events Attribute//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-animevents-attrib.mod"
+
+ ....................................................................... -->
+
+<!-- Animation Events Attribute
+
+ onbegin, onend, onrepeat, onload
+
+ This module defines the AnimationEvents attribute set.
+-->
+
+<!ENTITY % SVG.onbegin.attrib
+ "onbegin %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onend.attrib
+ "onend %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onrepeat.attrib
+ "onrepeat %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.onload.attrib
+ "onload %Script.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.AnimationEvents.extra.attrib "" >
+
+<!ENTITY % SVG.AnimationEvents.attrib
+ "%SVG.onbegin.attrib;
+ %SVG.onend.attrib;
+ %SVG.onrepeat.attrib;
+ %SVG.onload.attrib;
+ %SVG.AnimationEvents.extra.attrib;"
+>
+
+<!-- end of svg-animevents-attrib.mod -->
+]]>
+
+<!-- XLink Attribute Module ...................................... -->
+<!ENTITY % svg-xlink-attrib.module "INCLUDE" >
+<![%svg-xlink-attrib.module;[
+<!ENTITY % svg-xlink-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 XLink Attribute//EN"
+ "svg-xlink-attrib.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 XLink Attribute Module ........................................ -->
+<!-- file: svg-xlink-attrib.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg12-flat.dtd 201394 2004-11-18 01:47:06Z deweese $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 XLink Attribute//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-xlink-attrib.mod"
+
+ ....................................................................... -->
+
+<!-- XLink Attribute
+
+ type, href, role, arcrole, title, show, actuate
+
+ This module defines the XLink, XLinkRequired, XLinkEmbed, and
+ XLinkReplace attribute set.
+-->
+
+<!ENTITY % SVG.XLink.extra.attrib "" >
+
+<!ENTITY % SVG.XLink.attrib
+ "%XLINK.xmlns.attrib;
+ %XLINK.pfx;type ( simple ) #FIXED 'simple'
+ %XLINK.pfx;href %URI.datatype; #IMPLIED
+ %XLINK.pfx;role %URI.datatype; #IMPLIED
+ %XLINK.pfx;arcrole %URI.datatype; #IMPLIED
+ %XLINK.pfx;title CDATA #IMPLIED
+ %XLINK.pfx;show ( other ) 'other'
+ %XLINK.pfx;actuate ( onLoad ) #FIXED 'onLoad'
+ %SVG.XLink.extra.attrib;"
+>
+
+<!ENTITY % SVG.XLinkRequired.extra.attrib "" >
+
+<!ENTITY % SVG.XLinkRequired.attrib
+ "%XLINK.xmlns.attrib;
+ %XLINK.pfx;type ( simple ) #FIXED 'simple'
+ %XLINK.pfx;href %URI.datatype; #REQUIRED
+ %XLINK.pfx;role %URI.datatype; #IMPLIED
+ %XLINK.pfx;arcrole %URI.datatype; #IMPLIED
+ %XLINK.pfx;title CDATA #IMPLIED
+ %XLINK.pfx;show ( other ) 'other'
+ %XLINK.pfx;actuate ( onLoad ) #FIXED 'onLoad'
+ %SVG.XLinkRequired.extra.attrib;"
+>
+
+<!ENTITY % SVG.XLinkEmbed.extra.attrib "" >
+
+<!ENTITY % SVG.XLinkEmbed.attrib
+ "%XLINK.xmlns.attrib;
+ %XLINK.pfx;type ( simple ) #FIXED 'simple'
+ %XLINK.pfx;href %URI.datatype; #REQUIRED
+ %XLINK.pfx;role %URI.datatype; #IMPLIED
+ %XLINK.pfx;arcrole %URI.datatype; #IMPLIED
+ %XLINK.pfx;title CDATA #IMPLIED
+ %XLINK.pfx;show ( embed ) 'embed'
+ %XLINK.pfx;actuate ( onLoad ) #FIXED 'onLoad'
+ %SVG.XLinkEmbed.extra.attrib;"
+>
+
+<!ENTITY % SVG.XLinkReplace.extra.attrib "" >
+
+<!ENTITY % SVG.XLinkReplace.attrib
+ "%XLINK.xmlns.attrib;
+ %XLINK.pfx;type ( simple ) #FIXED 'simple'
+ %XLINK.pfx;href %URI.datatype; #REQUIRED
+ %XLINK.pfx;role %URI.datatype; #IMPLIED
+ %XLINK.pfx;arcrole %URI.datatype; #IMPLIED
+ %XLINK.pfx;title CDATA #IMPLIED
+ %XLINK.pfx;show ( new | replace ) 'replace'
+ %XLINK.pfx;actuate ( onRequest ) #FIXED 'onRequest'
+ %SVG.XLinkReplace.extra.attrib;"
+>
+
+<!-- end of svg-xlink-attrib.mod -->
+]]>
+
+<!-- External Resources Attribute Module ......................... -->
+<!ENTITY % svg-extresources-attrib.module "INCLUDE" >
+<![%svg-extresources-attrib.module;[
+<!ENTITY % svg-extresources-attrib.mod
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 External Resources Attribute//EN"
+ "svg-extresources-attrib.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 External Resources Attribute Module ........................... -->
+<!-- file: svg-extresources-attrib.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg12-flat.dtd 201394 2004-11-18 01:47:06Z deweese $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ENTITIES SVG 1.1 External Resources Attribute//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-extresources-attrib.mod"
+
+ ....................................................................... -->
+
+<!-- External Resources Attribute
+
+ externalResourcesRequired
+
+ This module defines the External attribute set.
+-->
+
+<!ENTITY % SVG.externalResourcesRequired.attrib
+ "externalResourcesRequired %Boolean.datatype; #IMPLIED"
+>
+
+<!ENTITY % SVG.External.extra.attrib "" >
+
+<!ENTITY % SVG.External.attrib
+ "%SVG.externalResourcesRequired.attrib;
+ %SVG.External.extra.attrib;"
+>
+
+<!-- end of svg-extresources-attrib.mod -->
+]]>
+
+<!-- ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: -->
+
+<!-- Structure Module ............................................ -->
+<!ENTITY % svg-structure.module "INCLUDE" >
+<![%svg-structure.module;[
+<!ENTITY % svg-structure.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Structure//EN"
+ "svg-structure.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Structure Module .............................................. -->
+<!-- file: svg-structure.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg12-flat.dtd 201394 2004-11-18 01:47:06Z deweese $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Structure//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-structure.mod"
+
+ ....................................................................... -->
+
+<!-- Structure
+
+ svg, g, defs, desc, title, metadata, symbol, use
+
+ This module declares the major structural elements and their attributes.
+-->
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.svg.qname "svg" >
+<!ENTITY % SVG.g.qname "g" >
+<!ENTITY % SVG.defs.qname "defs" >
+<!ENTITY % SVG.desc.qname "desc" >
+<!ENTITY % SVG.title.qname "title" >
+<!ENTITY % SVG.metadata.qname "metadata" >
+<!ENTITY % SVG.symbol.qname "symbol" >
+<!ENTITY % SVG.use.qname "use" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Container.attrib "" >
+<!ENTITY % SVG.Conditional.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Viewport.attrib "" >
+<!ENTITY % SVG.Text.attrib "" >
+<!ENTITY % SVG.TextContent.attrib "" >
+<!ENTITY % SVG.Font.attrib "" >
+<!ENTITY % SVG.Paint.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Marker.attrib "" >
+<!ENTITY % SVG.Profile.attrib "" >
+<!ENTITY % SVG.Gradient.attrib "" >
+<!ENTITY % SVG.Clip.attrib "" >
+<!ENTITY % SVG.Mask.attrib "" >
+<!ENTITY % SVG.Filter.attrib "" >
+<!ENTITY % SVG.FilterColor.attrib "" >
+<!ENTITY % SVG.DocumentEvents.attrib "" >
+<!ENTITY % SVG.GraphicalEvents.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.XLinkEmbed.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Description.class ............................. -->
+
+<!ENTITY % SVG.Description.extra.class "" >
+
+<!ENTITY % SVG.Description.class
+ "%SVG.desc.qname; | %SVG.title.qname; | %SVG.metadata.qname;
+ %SVG.Description.extra.class;"
+>
+
+<!-- SVG.Use.class ..................................... -->
+
+<!ENTITY % SVG.Use.extra.class "" >
+
+<!ENTITY % SVG.Use.class
+ "| %SVG.use.qname; %SVG.Use.extra.class;"
+>
+
+<!-- SVG.Structure.class ............................... -->
+
+<!ENTITY % SVG.Structure.extra.class "" >
+
+<!ENTITY % SVG.Structure.class
+ "| %SVG.svg.qname; | %SVG.g.qname; | %SVG.defs.qname; | %SVG.symbol.qname;
+ %SVG.Use.class; %SVG.Structure.extra.class;"
+>
+
+<!-- SVG.Presentation.attrib ........................... -->
+
+<!ENTITY % SVG.Presentation.extra.attrib "" >
+
+<!ENTITY % SVG.Presentation.attrib
+ "%SVG.Container.attrib;
+ %SVG.Viewport.attrib;
+ %SVG.Text.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Profile.attrib;
+ %SVG.Gradient.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.Cursor.attrib;
+ flood-color %SVGColor.datatype; #IMPLIED
+ flood-opacity %OpacityValue.datatype; #IMPLIED
+ lighting-color %SVGColor.datatype; #IMPLIED
+ %SVG.Presentation.extra.attrib;"
+>
+
+<!-- svg: SVG Document Element ......................... -->
+
+<!ENTITY % SVG.svg.extra.content "" >
+
+<!ENTITY % SVG.svg.element "INCLUDE" >
+<![%SVG.svg.element;[
+<!ENTITY % SVG.svg.content
+ "( %SVG.Description.class; | %SVG.Animation.class; %SVG.Structure.class;
+ %SVG.Conditional.class; %SVG.Image.class; %SVG.Style.class;
+ %SVG.Shape.class; %SVG.Text.class; %SVG.Marker.class; %SVG.Profile.class;
+ %SVG.Gradient.class; %SVG.Pattern.class; %SVG.Clip.class;
+ %SVG.Mask.class; %SVG.Filter.class; %SVG.Cursor.class;
+ %SVG.Hyperlink.class; %SVG.View.class; %SVG.Script.class;
+ %SVG.Font.class; %SVG.svg.extra.content; )*"
+>
+<!ELEMENT %SVG.svg.qname; %SVG.svg.content; >
+<!-- end of SVG.svg.element -->]]>
+
+<!ENTITY % SVG.svg.attlist "INCLUDE" >
+<![%SVG.svg.attlist;[
+<!ATTLIST %SVG.svg.qname;
+ %SVG.xmlns.attrib;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.DocumentEvents.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.External.attrib;
+ x %Coordinate.datatype; #IMPLIED
+ y %Coordinate.datatype; #IMPLIED
+ width %Length.datatype; #IMPLIED
+ height %Length.datatype; #IMPLIED
+ viewBox %ViewBoxSpec.datatype; #IMPLIED
+ preserveAspectRatio %PreserveAspectRatioSpec.datatype; 'xMidYMid meet'
+ zoomAndPan ( disable | magnify ) 'magnify'
+ version %Number.datatype; #FIXED '1.1'
+ baseProfile %Text.datatype; #IMPLIED
+ contentScriptType %ContentType.datatype; 'text/ecmascript'
+ contentStyleType %ContentType.datatype; 'text/css'
+>
+<!-- end of SVG.svg.attlist -->]]>
+
+<!-- g: Group Element .................................. -->
+
+<!ENTITY % SVG.g.extra.content "" >
+
+<!ENTITY % SVG.g.element "INCLUDE" >
+<![%SVG.g.element;[
+<!ENTITY % SVG.g.content
+ "( %SVG.Description.class; | %SVG.Animation.class; %SVG.Structure.class;
+ %SVG.Conditional.class; %SVG.Image.class; %SVG.Style.class;
+ %SVG.Shape.class; %SVG.Text.class; %SVG.Marker.class; %SVG.Profile.class;
+ %SVG.Gradient.class; %SVG.Pattern.class; %SVG.Clip.class;
+ %SVG.Mask.class; %SVG.Filter.class; %SVG.Cursor.class;
+ %SVG.Hyperlink.class; %SVG.View.class; %SVG.Script.class;
+ %SVG.Font.class; %SVG.g.extra.content; )*"
+>
+<!ELEMENT %SVG.g.qname; %SVG.g.content; >
+<!-- end of SVG.g.element -->]]>
+
+<!ENTITY % SVG.g.attlist "INCLUDE" >
+<![%SVG.g.attlist;[
+<!ATTLIST %SVG.g.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.External.attrib;
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.g.attlist -->]]>
+
+<!-- defs: Definisions Element ......................... -->
+
+<!ENTITY % SVG.defs.extra.content "" >
+
+<!ENTITY % SVG.defs.element "INCLUDE" >
+<![%SVG.defs.element;[
+<!ENTITY % SVG.defs.content
+ "( %SVG.Description.class; | %SVG.Animation.class; %SVG.Structure.class;
+ %SVG.Conditional.class; %SVG.Image.class; %SVG.Style.class;
+ %SVG.Shape.class; %SVG.Text.class; %SVG.Marker.class; %SVG.Profile.class;
+ %SVG.Gradient.class; %SVG.Pattern.class; %SVG.Clip.class;
+ %SVG.Mask.class; %SVG.Filter.class; %SVG.Cursor.class;
+ %SVG.Hyperlink.class; %SVG.View.class; %SVG.Script.class;
+ %SVG.Font.class; %SVG.defs.extra.content; )*"
+>
+<!ELEMENT %SVG.defs.qname; %SVG.defs.content; >
+<!-- end of SVG.defs.element -->]]>
+
+<!ENTITY % SVG.defs.attlist "INCLUDE" >
+<![%SVG.defs.attlist;[
+<!ATTLIST %SVG.defs.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.External.attrib;
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.defs.attlist -->]]>
+
+<!-- desc: Description Element ......................... -->
+
+<!ENTITY % SVG.desc.extra.content "" >
+
+<!ENTITY % SVG.desc.element "INCLUDE" >
+<![%SVG.desc.element;[
+<!ENTITY % SVG.desc.content
+ "( #PCDATA %SVG.desc.extra.content; )*"
+>
+<!ELEMENT %SVG.desc.qname; %SVG.desc.content; >
+<!-- end of SVG.desc.element -->]]>
+
+<!ENTITY % SVG.desc.attlist "INCLUDE" >
+<![%SVG.desc.attlist;[
+<!ATTLIST %SVG.desc.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+>
+<!-- end of SVG.desc.attlist -->]]>
+
+<!-- title: Title Element .............................. -->
+
+<!ENTITY % SVG.title.extra.content "" >
+
+<!ENTITY % SVG.title.element "INCLUDE" >
+<![%SVG.title.element;[
+<!ENTITY % SVG.title.content
+ "( #PCDATA %SVG.title.extra.content; )*"
+>
+<!ELEMENT %SVG.title.qname; %SVG.title.content; >
+<!-- end of SVG.title.element -->]]>
+
+<!ENTITY % SVG.title.attlist "INCLUDE" >
+<![%SVG.title.attlist;[
+<!ATTLIST %SVG.title.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+>
+<!-- end of SVG.title.attlist -->]]>
+
+<!-- metadata: Metadata Element ........................ -->
+
+<!ENTITY % SVG.metadata.extra.content "" >
+
+<!ENTITY % SVG.metadata.element "INCLUDE" >
+<![%SVG.metadata.element;[
+<!ENTITY % SVG.metadata.content
+ "( #PCDATA %SVG.metadata.extra.content; )*"
+>
+<!ELEMENT %SVG.metadata.qname; %SVG.metadata.content; >
+<!-- end of SVG.metadata.element -->]]>
+
+<!ENTITY % SVG.metadata.attlist "INCLUDE" >
+<![%SVG.metadata.attlist;[
+<!ATTLIST %SVG.metadata.qname;
+ %SVG.Core.attrib;
+>
+<!-- end of SVG.metadata.attlist -->]]>
+
+<!-- symbol: Symbol Element ............................ -->
+
+<!ENTITY % SVG.symbol.extra.content "" >
+
+<!ENTITY % SVG.symbol.element "INCLUDE" >
+<![%SVG.symbol.element;[
+<!ENTITY % SVG.symbol.content
+ "( %SVG.Description.class; | %SVG.Animation.class; %SVG.Structure.class;
+ %SVG.Conditional.class; %SVG.Image.class; %SVG.Style.class;
+ %SVG.Shape.class; %SVG.Text.class; %SVG.Marker.class; %SVG.Profile.class;
+ %SVG.Gradient.class; %SVG.Pattern.class; %SVG.Clip.class;
+ %SVG.Mask.class; %SVG.Filter.class; %SVG.Cursor.class;
+ %SVG.Hyperlink.class; %SVG.View.class; %SVG.Script.class;
+ %SVG.Font.class; %SVG.symbol.extra.content; )*"
+>
+<!ELEMENT %SVG.symbol.qname; %SVG.symbol.content; >
+<!-- end of SVG.symbol.element -->]]>
+
+<!ENTITY % SVG.symbol.attlist "INCLUDE" >
+<![%SVG.symbol.attlist;[
+<!ATTLIST %SVG.symbol.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.External.attrib;
+ viewBox %ViewBoxSpec.datatype; #IMPLIED
+ preserveAspectRatio %PreserveAspectRatioSpec.datatype; 'xMidYMid meet'
+>
+<!-- end of SVG.symbol.attlist -->]]>
+
+<!-- use: Use Element .................................. -->
+
+<!ENTITY % SVG.use.extra.content "" >
+
+<!ENTITY % SVG.use.element "INCLUDE" >
+<![%SVG.use.element;[
+<!ENTITY % SVG.use.content
+ "(( %SVG.Description.class; )*, ( %SVG.Animation.class;
+ %SVG.use.extra.content; )*)"
+>
+<!ELEMENT %SVG.use.qname; %SVG.use.content; >
+<!-- end of SVG.use.element -->]]>
+
+<!ENTITY % SVG.use.attlist "INCLUDE" >
+<![%SVG.use.attlist;[
+<!ATTLIST %SVG.use.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.XLinkEmbed.attrib;
+ %SVG.External.attrib;
+ x %Coordinate.datatype; #IMPLIED
+ y %Coordinate.datatype; #IMPLIED
+ width %Length.datatype; #IMPLIED
+ height %Length.datatype; #IMPLIED
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.use.attlist -->]]>
+
+<!-- end of svg-structure.mod -->
+]]>
+
+<!-- Conditional Processing Module ............................... -->
+<!ENTITY % svg-conditional.module "INCLUDE" >
+<![%svg-conditional.module;[
+<!ENTITY % svg-conditional.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Conditional Processing//EN"
+ "svg-conditional.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Conditional Processing Module ................................. -->
+<!-- file: svg-conditional.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg12-flat.dtd 201394 2004-11-18 01:47:06Z deweese $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Conditional Processing//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-conditional.mod"
+
+ ....................................................................... -->
+
+<!-- Conditional Processing
+
+ switch
+
+ This module declares markup to provide support for conditional processing.
+-->
+
+<!-- extension list specification -->
+<!ENTITY % ExtensionList.datatype "CDATA" >
+
+<!-- feature list specification -->
+<!ENTITY % FeatureList.datatype "CDATA" >
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.switch.qname "switch" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Container.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Viewport.attrib "" >
+<!ENTITY % SVG.Text.attrib "" >
+<!ENTITY % SVG.TextContent.attrib "" >
+<!ENTITY % SVG.Font.attrib "" >
+<!ENTITY % SVG.Paint.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Marker.attrib "" >
+<!ENTITY % SVG.Profile.attrib "" >
+<!ENTITY % SVG.Gradient.attrib "" >
+<!ENTITY % SVG.Clip.attrib "" >
+<!ENTITY % SVG.Mask.attrib "" >
+<!ENTITY % SVG.Filter.attrib "" >
+<!ENTITY % SVG.FilterColor.attrib "" >
+<!ENTITY % SVG.GraphicalEvents.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Conditional.class ............................. -->
+
+<!ENTITY % SVG.Conditional.extra.class "" >
+
+<!ENTITY % SVG.Conditional.class
+ "| %SVG.switch.qname; %SVG.Conditional.extra.class;"
+>
+
+<!-- SVG.Conditional.attrib ............................ -->
+
+<!ENTITY % SVG.Conditional.extra.attrib "" >
+
+<!ENTITY % SVG.Conditional.attrib
+ "requiredFeatures %FeatureList.datatype; #IMPLIED
+ requiredExtensions %ExtensionList.datatype; #IMPLIED
+ systemLanguage %LanguageCodes.datatype; #IMPLIED
+ %SVG.Conditional.extra.attrib;"
+>
+
+<!-- SVG.Presentation.attrib ........................... -->
+
+<!ENTITY % SVG.Presentation.extra.attrib "" >
+
+<!ENTITY % SVG.Presentation.attrib
+ "%SVG.Container.attrib;
+ %SVG.Viewport.attrib;
+ %SVG.Text.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Profile.attrib;
+ %SVG.Gradient.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.Cursor.attrib;
+ flood-color %SVGColor.datatype; #IMPLIED
+ flood-opacity %OpacityValue.datatype; #IMPLIED
+ lighting-color %SVGColor.datatype; #IMPLIED
+ %SVG.Presentation.extra.attrib;"
+>
+
+<!-- switch: Switch Element ............................ -->
+
+<!ENTITY % SVG.switch.extra.content "" >
+
+<!ENTITY % SVG.switch.element "INCLUDE" >
+<![%SVG.switch.element;[
+<!ENTITY % SVG.switch.content
+ "(( %SVG.Description.class; )*, ( %SVG.svg.qname; | %SVG.g.qname;
+ | %SVG.use.qname; | %SVG.text.qname; | %SVG.Animation.class;
+ %SVG.Conditional.class; %SVG.Image.class; %SVG.Shape.class;
+ %SVG.Hyperlink.class; %SVG.Extensibility.class;
+ %SVG.switch.extra.content; )*)"
+>
+<!ELEMENT %SVG.switch.qname; %SVG.switch.content; >
+<!-- end of SVG.switch.element -->]]>
+
+<!ENTITY % SVG.switch.attlist "INCLUDE" >
+<![%SVG.switch.attlist;[
+<!ATTLIST %SVG.switch.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.External.attrib;
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.switch.attlist -->]]>
+
+<!-- end of svg-conditional.mod -->
+]]>
+
+<!-- Image Module ................................................ -->
+<!ENTITY % svg-image.module "INCLUDE" >
+<![%svg-image.module;[
+<!ENTITY % svg-image.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Image//EN"
+ "svg-image.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Image Module .................................................. -->
+<!-- file: svg-image.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg12-flat.dtd 201394 2004-11-18 01:47:06Z deweese $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Image//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-image.mod"
+
+ ....................................................................... -->
+
+<!-- Image
+
+ image
+
+ This module declares markup to provide support for image.
+-->
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.image.qname "image" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Conditional.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Viewport.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Profile.attrib "" >
+<!ENTITY % SVG.Clip.attrib "" >
+<!ENTITY % SVG.Mask.attrib "" >
+<!ENTITY % SVG.Filter.attrib "" >
+<!ENTITY % SVG.GraphicalEvents.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.XLinkEmbed.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Image.class ................................... -->
+
+<!ENTITY % SVG.Image.extra.class "" >
+
+<!ENTITY % SVG.Image.class
+ "| %SVG.image.qname; %SVG.Image.extra.class;"
+>
+
+<!-- image: Image Element .............................. -->
+
+<!ENTITY % SVG.image.extra.content "" >
+
+<!ENTITY % SVG.image.element "INCLUDE" >
+<![%SVG.image.element;[
+<!ENTITY % SVG.image.content
+ "(( %SVG.Description.class; )*, ( %SVG.Animation.class;
+ %SVG.image.extra.content; )*)"
+>
+<!ELEMENT %SVG.image.qname; %SVG.image.content; >
+<!-- end of SVG.image.element -->]]>
+
+<!ENTITY % SVG.image.attlist "INCLUDE" >
+<![%SVG.image.attlist;[
+<!ATTLIST %SVG.image.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Viewport.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Profile.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.XLinkEmbed.attrib;
+ %SVG.External.attrib;
+ x %Coordinate.datatype; #IMPLIED
+ y %Coordinate.datatype; #IMPLIED
+ width %Length.datatype; #REQUIRED
+ height %Length.datatype; #REQUIRED
+ preserveAspectRatio %PreserveAspectRatioSpec.datatype; 'xMidYMid meet'
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.image.attlist -->]]>
+
+<!-- end of svg-image.mod -->
+]]>
+
+<!-- Style Module ................................................ -->
+<!ENTITY % svg-style.module "INCLUDE" >
+<![%svg-style.module;[
+<!ENTITY % svg-style.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Style//EN"
+ "svg-style.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Style Module .................................................. -->
+<!-- file: svg-style.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg12-flat.dtd 201394 2004-11-18 01:47:06Z deweese $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Style//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-style.mod"
+
+ ....................................................................... -->
+
+<!-- Style
+
+ style
+
+ This module declares markup to provide support for stylesheet.
+-->
+
+<!-- list of classes -->
+<!ENTITY % ClassList.datatype "CDATA" >
+
+<!-- comma-separated list of media descriptors. -->
+<!ENTITY % MediaDesc.datatype "CDATA" >
+
+<!-- style sheet data -->
+<!ENTITY % StyleSheet.datatype "CDATA" >
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.style.qname "style" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+
+<!-- SVG.Style.class ................................... -->
+
+<!ENTITY % SVG.Style.extra.class "" >
+
+<!ENTITY % SVG.Style.class
+ "| %SVG.style.qname; %SVG.Style.extra.class;"
+>
+
+<!-- SVG.Style.attrib .................................. -->
+
+<!ENTITY % SVG.Style.extra.attrib "" >
+
+<!ENTITY % SVG.Style.attrib
+ "style %StyleSheet.datatype; #IMPLIED
+ class %ClassList.datatype; #IMPLIED
+ %SVG.Style.extra.attrib;"
+>
+
+<!-- style: Style Element .............................. -->
+
+<!ENTITY % SVG.style.extra.content "" >
+
+<!ENTITY % SVG.style.element "INCLUDE" >
+<![%SVG.style.element;[
+<!ENTITY % SVG.style.content
+ "( #PCDATA %SVG.style.extra.content; )*"
+>
+<!ELEMENT %SVG.style.qname; %SVG.style.content; >
+<!-- end of SVG.style.element -->]]>
+
+<!ENTITY % SVG.style.attlist "INCLUDE" >
+<![%SVG.style.attlist;[
+<!ATTLIST %SVG.style.qname;
+ xml:space ( preserve ) #FIXED 'preserve'
+ %SVG.Core.attrib;
+ type %ContentType.datatype; #REQUIRED
+ media %MediaDesc.datatype; #IMPLIED
+ title %Text.datatype; #IMPLIED
+>
+<!-- end of SVG.style.attlist -->]]>
+
+<!-- end of svg-style.mod -->
+]]>
+
+<!-- Shape Module ................................................ -->
+<!ENTITY % svg-shape.module "INCLUDE" >
+<![%svg-shape.module;[
+<!ENTITY % svg-shape.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Shape//EN"
+ "svg-shape.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Shape Module .................................................. -->
+<!-- file: svg-shape.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg12-flat.dtd 201394 2004-11-18 01:47:06Z deweese $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Shape//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-shape.mod"
+
+ ....................................................................... -->
+
+<!-- Shape
+
+ path, rect, circle, line, ellipse, polyline, polygon
+
+ This module declares markup to provide support for graphical shapes.
+-->
+
+<!-- a list of points -->
+<!ENTITY % Points.datatype "CDATA" >
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.path.qname "path" >
+<!ENTITY % SVG.rect.qname "rect" >
+<!ENTITY % SVG.circle.qname "circle" >
+<!ENTITY % SVG.line.qname "line" >
+<!ENTITY % SVG.ellipse.qname "ellipse" >
+<!ENTITY % SVG.polyline.qname "polyline" >
+<!ENTITY % SVG.polygon.qname "polygon" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Conditional.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Paint.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Marker.attrib "" >
+<!ENTITY % SVG.Clip.attrib "" >
+<!ENTITY % SVG.Mask.attrib "" >
+<!ENTITY % SVG.Filter.attrib "" >
+<!ENTITY % SVG.GraphicalEvents.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Shape.class ................................... -->
+
+<!ENTITY % SVG.Shape.extra.class "" >
+
+<!ENTITY % SVG.Shape.class
+ "| %SVG.path.qname; | %SVG.rect.qname; | %SVG.circle.qname;
+ | %SVG.line.qname; | %SVG.ellipse.qname; | %SVG.polyline.qname;
+ | %SVG.polygon.qname; %SVG.Shape.extra.class;"
+>
+
+<!-- path: Path Element ................................ -->
+
+<!ENTITY % SVG.path.extra.content "" >
+
+<!ENTITY % SVG.path.element "INCLUDE" >
+<![%SVG.path.element;[
+<!ENTITY % SVG.path.content
+ "(( %SVG.Description.class; )*, ( %SVG.Animation.class;
+ %SVG.path.extra.content; )*)"
+>
+<!ELEMENT %SVG.path.qname; %SVG.path.content; >
+<!-- end of SVG.path.element -->]]>
+
+<!ENTITY % SVG.path.attlist "INCLUDE" >
+<![%SVG.path.attlist;[
+<!ATTLIST %SVG.path.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.External.attrib;
+ d %PathData.datatype; #REQUIRED
+ pathLength %Number.datatype; #IMPLIED
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.path.attlist -->]]>
+
+<!-- rect: Rectangle Element ........................... -->
+
+<!ENTITY % SVG.rect.extra.content "" >
+
+<!ENTITY % SVG.rect.element "INCLUDE" >
+<![%SVG.rect.element;[
+<!ENTITY % SVG.rect.content
+ "(( %SVG.Description.class; )*, ( %SVG.Animation.class;
+ %SVG.rect.extra.content; )*)"
+>
+<!ELEMENT %SVG.rect.qname; %SVG.rect.content; >
+<!-- end of SVG.rect.element -->]]>
+
+<!ENTITY % SVG.rect.attlist "INCLUDE" >
+<![%SVG.rect.attlist;[
+<!ATTLIST %SVG.rect.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.External.attrib;
+ x %Coordinate.datatype; #IMPLIED
+ y %Coordinate.datatype; #IMPLIED
+ width %Length.datatype; #REQUIRED
+ height %Length.datatype; #REQUIRED
+ rx %Length.datatype; #IMPLIED
+ ry %Length.datatype; #IMPLIED
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.rect.attlist -->]]>
+
+<!-- circle: Circle Element ............................ -->
+
+<!ENTITY % SVG.circle.extra.content "" >
+
+<!ENTITY % SVG.circle.element "INCLUDE" >
+<![%SVG.circle.element;[
+<!ENTITY % SVG.circle.content
+ "(( %SVG.Description.class; )*, ( %SVG.Animation.class;
+ %SVG.circle.extra.content; )*)"
+>
+<!ELEMENT %SVG.circle.qname; %SVG.circle.content; >
+<!-- end of SVG.circle.element -->]]>
+
+<!ENTITY % SVG.circle.attlist "INCLUDE" >
+<![%SVG.circle.attlist;[
+<!ATTLIST %SVG.circle.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.External.attrib;
+ cx %Coordinate.datatype; #IMPLIED
+ cy %Coordinate.datatype; #IMPLIED
+ r %Length.datatype; #REQUIRED
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.circle.attlist -->]]>
+
+<!-- line: Line Element ................................ -->
+
+<!ENTITY % SVG.line.extra.content "" >
+
+<!ENTITY % SVG.line.element "INCLUDE" >
+<![%SVG.line.element;[
+<!ENTITY % SVG.line.content
+ "(( %SVG.Description.class; )*, ( %SVG.Animation.class;
+ %SVG.line.extra.content; )*)"
+>
+<!ELEMENT %SVG.line.qname; %SVG.line.content; >
+<!-- end of SVG.line.element -->]]>
+
+<!ENTITY % SVG.line.attlist "INCLUDE" >
+<![%SVG.line.attlist;[
+<!ATTLIST %SVG.line.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.External.attrib;
+ x1 %Coordinate.datatype; #IMPLIED
+ y1 %Coordinate.datatype; #IMPLIED
+ x2 %Coordinate.datatype; #IMPLIED
+ y2 %Coordinate.datatype; #IMPLIED
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.line.attlist -->]]>
+
+<!-- ellipse: Ellipse Element .......................... -->
+
+<!ENTITY % SVG.ellipse.extra.content "" >
+
+<!ENTITY % SVG.ellipse.element "INCLUDE" >
+<![%SVG.ellipse.element;[
+<!ENTITY % SVG.ellipse.content
+ "(( %SVG.Description.class; )*, ( %SVG.Animation.class;
+ %SVG.ellipse.extra.content; )*)"
+>
+<!ELEMENT %SVG.ellipse.qname; %SVG.ellipse.content; >
+<!-- end of SVG.ellipse.element -->]]>
+
+<!ENTITY % SVG.ellipse.attlist "INCLUDE" >
+<![%SVG.ellipse.attlist;[
+<!ATTLIST %SVG.ellipse.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.External.attrib;
+ cx %Coordinate.datatype; #IMPLIED
+ cy %Coordinate.datatype; #IMPLIED
+ rx %Length.datatype; #REQUIRED
+ ry %Length.datatype; #REQUIRED
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.ellipse.attlist -->]]>
+
+<!-- polyline: Polyline Element ........................ -->
+
+<!ENTITY % SVG.polyline.extra.content "" >
+
+<!ENTITY % SVG.polyline.element "INCLUDE" >
+<![%SVG.polyline.element;[
+<!ENTITY % SVG.polyline.content
+ "(( %SVG.Description.class; )*, ( %SVG.Animation.class;
+ %SVG.polyline.extra.content; )*)"
+>
+<!ELEMENT %SVG.polyline.qname; %SVG.polyline.content; >
+<!-- end of SVG.polyline.element -->]]>
+
+<!ENTITY % SVG.polyline.attlist "INCLUDE" >
+<![%SVG.polyline.attlist;[
+<!ATTLIST %SVG.polyline.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.External.attrib;
+ points %Points.datatype; #REQUIRED
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.polyline.attlist -->]]>
+
+<!-- polygon: Polygon Element .......................... -->
+
+<!ENTITY % SVG.polygon.extra.content "" >
+
+<!ENTITY % SVG.polygon.element "INCLUDE" >
+<![%SVG.polygon.element;[
+<!ENTITY % SVG.polygon.content
+ "(( %SVG.Description.class; )*, ( %SVG.Animation.class;
+ %SVG.polygon.extra.content; )*)"
+>
+<!ELEMENT %SVG.polygon.qname; %SVG.polygon.content; >
+<!-- end of SVG.polygon.element -->]]>
+
+<!ENTITY % SVG.polygon.attlist "INCLUDE" >
+<![%SVG.polygon.attlist;[
+<!ATTLIST %SVG.polygon.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.External.attrib;
+ points %Points.datatype; #REQUIRED
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.polygon.attlist -->]]>
+
+<!-- end of svg-shape.mod -->
+]]>
+
+<!-- Text Module ................................................. -->
+<!ENTITY % svg-text.module "INCLUDE" >
+<![%svg-text.module;[
+<!ENTITY % svg-text.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Text//EN"
+ "svg-text.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Text Module ................................................... -->
+<!-- file: svg-text.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg12-flat.dtd 201394 2004-11-18 01:47:06Z deweese $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Text//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-text.mod"
+
+ ....................................................................... -->
+
+<!-- Text
+
+ text, tspan, tref, textPath, altGlyph, altGlyphDef, altGlyphItem,
+ glyphRef
+
+ This module declares markup to provide support for alternate glyph.
+-->
+
+<!-- 'baseline-shift' property/attribute value (e.g., 'baseline', 'sub', etc.) -->
+<!ENTITY % BaselineShiftValue.datatype "CDATA" >
+
+<!-- 'font-family' property/attribute value (i.e., list of fonts) -->
+<!ENTITY % FontFamilyValue.datatype "CDATA" >
+
+<!-- 'font-size' property/attribute value -->
+<!ENTITY % FontSizeValue.datatype "CDATA" >
+
+<!-- 'font-size-adjust' property/attribute value -->
+<!ENTITY % FontSizeAdjustValue.datatype "CDATA" >
+
+<!-- 'glyph-orientation-horizontal' property/attribute value (e.g., <angle>) -->
+<!ENTITY % GlyphOrientationHorizontalValue.datatype "CDATA" >
+
+<!-- 'glyph-orientation-vertical' property/attribute value (e.g., 'auto', <angle>) -->
+<!ENTITY % GlyphOrientationVerticalValue.datatype "CDATA" >
+
+<!-- 'kerning' property/attribute value (e.g., 'auto', <length>) -->
+<!ENTITY % KerningValue.datatype "CDATA" >
+
+<!-- 'letter-spacing' or 'word-spacing' property/attribute value (e.g., 'normal', <length>) -->
+<!ENTITY % SpacingValue.datatype "CDATA" >
+
+<!-- 'text-decoration' property/attribute value (e.g., 'none', 'underline') -->
+<!ENTITY % TextDecorationValue.datatype "CDATA" >
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.text.qname "text" >
+<!ENTITY % SVG.tspan.qname "tspan" >
+<!ENTITY % SVG.tref.qname "tref" >
+<!ENTITY % SVG.textPath.qname "textPath" >
+<!ENTITY % SVG.altGlyph.qname "altGlyph" >
+<!ENTITY % SVG.altGlyphDef.qname "altGlyphDef" >
+<!ENTITY % SVG.altGlyphItem.qname "altGlyphItem" >
+<!ENTITY % SVG.glyphRef.qname "glyphRef" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Conditional.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Paint.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Clip.attrib "" >
+<!ENTITY % SVG.Mask.attrib "" >
+<!ENTITY % SVG.Filter.attrib "" >
+<!ENTITY % SVG.GraphicalEvents.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.XLink.attrib "" >
+<!ENTITY % SVG.XLinkRequired.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Text.class .................................... -->
+
+<!ENTITY % SVG.Text.extra.class "" >
+
+<!ENTITY % SVG.Text.class
+ "| %SVG.text.qname; | %SVG.altGlyphDef.qname; %SVG.Text.extra.class;"
+>
+
+<!-- SVG.TextContent.class ............................. -->
+
+<!ENTITY % SVG.TextContent.extra.class "" >
+
+<!ENTITY % SVG.TextContent.class
+ "| %SVG.tspan.qname; | %SVG.tref.qname; | %SVG.textPath.qname;
+ | %SVG.altGlyph.qname; %SVG.TextContent.extra.class;"
+>
+
+<!-- SVG.Text.attrib ................................... -->
+
+<!ENTITY % SVG.Text.extra.attrib "" >
+
+<!ENTITY % SVG.Text.attrib
+ "writing-mode ( lr-tb | rl-tb | tb-rl | lr | rl | tb | inherit ) #IMPLIED
+ %SVG.Text.extra.attrib;"
+>
+
+<!-- SVG.TextContent.attrib ............................ -->
+
+<!ENTITY % SVG.TextContent.extra.attrib "" >
+
+<!ENTITY % SVG.TextContent.attrib
+ "alignment-baseline ( auto | baseline | before-edge | text-before-edge |
+ middle | central | after-edge | text-after-edge |
+ ideographic | alphabetic | hanging | mathematical |
+ inherit ) #IMPLIED
+ baseline-shift %BaselineShiftValue.datatype; #IMPLIED
+ direction ( ltr | rtl | inherit ) #IMPLIED
+ dominant-baseline ( auto | use-script | no-change | reset-size |
+ ideographic | alphabetic | hanging | mathematical |
+ central | middle | text-after-edge | text-before-edge |
+ inherit ) #IMPLIED
+ glyph-orientation-horizontal %GlyphOrientationHorizontalValue.datatype;
+ #IMPLIED
+ glyph-orientation-vertical %GlyphOrientationVerticalValue.datatype;
+ #IMPLIED
+ kerning %KerningValue.datatype; #IMPLIED
+ letter-spacing %SpacingValue.datatype; #IMPLIED
+ text-anchor ( start | middle | end | inherit ) #IMPLIED
+ text-decoration %TextDecorationValue.datatype; #IMPLIED
+ unicode-bidi ( normal | embed | bidi-override | inherit ) #IMPLIED
+ word-spacing %SpacingValue.datatype; #IMPLIED
+ %SVG.TextContent.extra.attrib;"
+>
+
+<!-- SVG.Font.attrib ................................... -->
+
+<!ENTITY % SVG.Font.extra.attrib "" >
+
+<!ENTITY % SVG.Font.attrib
+ "font-family %FontFamilyValue.datatype; #IMPLIED
+ font-size %FontSizeValue.datatype; #IMPLIED
+ font-size-adjust %FontSizeAdjustValue.datatype; #IMPLIED
+ font-stretch ( normal | wider | narrower | ultra-condensed |
+ extra-condensed | condensed | semi-condensed |
+ semi-expanded | expanded | extra-expanded |
+ ultra-expanded | inherit ) #IMPLIED
+ font-style ( normal | italic | oblique | inherit ) #IMPLIED
+ font-variant ( normal | small-caps | inherit ) #IMPLIED
+ font-weight ( normal | bold | bolder | lighter | 100 | 200 | 300 | 400 |
+ 500 | 600 | 700 | 800 | 900 | inherit ) #IMPLIED
+ %SVG.Font.extra.attrib;"
+>
+
+<!-- text: Text Element ................................ -->
+
+<!ENTITY % SVG.text.extra.content "" >
+
+<!ENTITY % SVG.text.element "INCLUDE" >
+<![%SVG.text.element;[
+<!ENTITY % SVG.text.content
+ "( #PCDATA | %SVG.Description.class; | %SVG.Animation.class;
+ %SVG.TextContent.class; %SVG.Hyperlink.class;
+ %SVG.text.extra.content; )*"
+>
+<!ELEMENT %SVG.text.qname; %SVG.text.content; >
+<!-- end of SVG.text.element -->]]>
+
+<!ENTITY % SVG.text.attlist "INCLUDE" >
+<![%SVG.text.attlist;[
+<!ATTLIST %SVG.text.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Text.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.External.attrib;
+ x %Coordinates.datatype; #IMPLIED
+ y %Coordinates.datatype; #IMPLIED
+ dx %Lengths.datatype; #IMPLIED
+ dy %Lengths.datatype; #IMPLIED
+ rotate %Numbers.datatype; #IMPLIED
+ textLength %Length.datatype; #IMPLIED
+ lengthAdjust ( spacing | spacingAndGlyphs ) #IMPLIED
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.text.attlist -->]]>
+
+<!-- tspan: Text Span Element .......................... -->
+
+<!ENTITY % SVG.tspan.extra.content "" >
+
+<!ENTITY % SVG.tspan.element "INCLUDE" >
+<![%SVG.tspan.element;[
+<!ENTITY % SVG.tspan.content
+ "( #PCDATA | %SVG.tspan.qname; | %SVG.tref.qname; | %SVG.altGlyph.qname;
+ | %SVG.animate.qname; | %SVG.set.qname; | %SVG.animateColor.qname;
+ | %SVG.Description.class; %SVG.Hyperlink.class;
+ %SVG.tspan.extra.content; )*"
+>
+<!ELEMENT %SVG.tspan.qname; %SVG.tspan.content; >
+<!-- end of SVG.tspan.element -->]]>
+
+<!ENTITY % SVG.tspan.attlist "INCLUDE" >
+<![%SVG.tspan.attlist;[
+<!ATTLIST %SVG.tspan.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.External.attrib;
+ x %Coordinates.datatype; #IMPLIED
+ y %Coordinates.datatype; #IMPLIED
+ dx %Lengths.datatype; #IMPLIED
+ dy %Lengths.datatype; #IMPLIED
+ rotate %Numbers.datatype; #IMPLIED
+ textLength %Length.datatype; #IMPLIED
+ lengthAdjust ( spacing | spacingAndGlyphs ) #IMPLIED
+>
+<!-- end of SVG.tspan.attlist -->]]>
+
+<!-- tref: Text Reference Element ...................... -->
+
+<!ENTITY % SVG.tref.extra.content "" >
+
+<!ENTITY % SVG.tref.element "INCLUDE" >
+<![%SVG.tref.element;[
+<!ENTITY % SVG.tref.content
+ "( %SVG.animate.qname; | %SVG.set.qname; | %SVG.animateColor.qname;
+ | %SVG.Description.class; %SVG.tref.extra.content; )*"
+>
+<!ELEMENT %SVG.tref.qname; %SVG.tref.content; >
+<!-- end of SVG.tref.element -->]]>
+
+<!ENTITY % SVG.tref.attlist "INCLUDE" >
+<![%SVG.tref.attlist;[
+<!ATTLIST %SVG.tref.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.XLinkRequired.attrib;
+ %SVG.External.attrib;
+ x %Coordinates.datatype; #IMPLIED
+ y %Coordinates.datatype; #IMPLIED
+ dx %Lengths.datatype; #IMPLIED
+ dy %Lengths.datatype; #IMPLIED
+ rotate %Numbers.datatype; #IMPLIED
+ textLength %Length.datatype; #IMPLIED
+ lengthAdjust ( spacing | spacingAndGlyphs ) #IMPLIED
+>
+<!-- end of SVG.tref.attlist -->]]>
+
+<!-- textPath: Text Path Element ....................... -->
+
+<!ENTITY % SVG.textPath.extra.content "" >
+
+<!ENTITY % SVG.textPath.element "INCLUDE" >
+<![%SVG.textPath.element;[
+<!ENTITY % SVG.textPath.content
+ "( #PCDATA | %SVG.tspan.qname; | %SVG.tref.qname; | %SVG.altGlyph.qname;
+ | %SVG.animate.qname; | %SVG.set.qname; | %SVG.animateColor.qname;
+ | %SVG.Description.class; %SVG.Hyperlink.class;
+ %SVG.textPath.extra.content; )*"
+>
+<!ELEMENT %SVG.textPath.qname; %SVG.textPath.content; >
+<!-- end of SVG.textPath.element -->]]>
+
+<!ENTITY % SVG.textPath.attlist "INCLUDE" >
+<![%SVG.textPath.attlist;[
+<!ATTLIST %SVG.textPath.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.XLinkRequired.attrib;
+ %SVG.External.attrib;
+ startOffset %Length.datatype; #IMPLIED
+ textLength %Length.datatype; #IMPLIED
+ lengthAdjust ( spacing | spacingAndGlyphs ) #IMPLIED
+ method ( align | stretch ) #IMPLIED
+ spacing ( auto | exact ) #IMPLIED
+>
+<!-- end of SVG.textPath.attlist -->]]>
+
+<!-- altGlyph: Alternate Glyph Element ................. -->
+
+<!ENTITY % SVG.altGlyph.extra.content "" >
+
+<!ENTITY % SVG.altGlyph.element "INCLUDE" >
+<![%SVG.altGlyph.element;[
+<!ENTITY % SVG.altGlyph.content
+ "( #PCDATA %SVG.altGlyph.extra.content; )*"
+>
+<!ELEMENT %SVG.altGlyph.qname; %SVG.altGlyph.content; >
+<!-- end of SVG.altGlyph.element -->]]>
+
+<!ENTITY % SVG.altGlyph.attlist "INCLUDE" >
+<![%SVG.altGlyph.attlist;[
+<!ATTLIST %SVG.altGlyph.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.XLink.attrib;
+ %SVG.External.attrib;
+ x %Coordinates.datatype; #IMPLIED
+ y %Coordinates.datatype; #IMPLIED
+ dx %Lengths.datatype; #IMPLIED
+ dy %Lengths.datatype; #IMPLIED
+ glyphRef CDATA #IMPLIED
+ format CDATA #IMPLIED
+ rotate %Numbers.datatype; #IMPLIED
+>
+<!-- end of SVG.altGlyph.attlist -->]]>
+
+<!-- altGlyphDef: Alternate Glyph Definition Element ... -->
+
+<!ENTITY % SVG.altGlyphDef.extra.content "" >
+
+<!ENTITY % SVG.altGlyphDef.element "INCLUDE" >
+<![%SVG.altGlyphDef.element;[
+<!ENTITY % SVG.altGlyphDef.content
+ "(( %SVG.glyphRef.qname;+ | %SVG.altGlyphItem.qname;+ )
+ %SVG.altGlyphDef.extra.content; )"
+>
+<!ELEMENT %SVG.altGlyphDef.qname; %SVG.altGlyphDef.content; >
+<!-- end of SVG.altGlyphDef.element -->]]>
+
+<!ENTITY % SVG.altGlyphDef.attlist "INCLUDE" >
+<![%SVG.altGlyphDef.attlist;[
+<!ATTLIST %SVG.altGlyphDef.qname;
+ %SVG.Core.attrib;
+>
+<!-- end of SVG.altGlyphDef.attlist -->]]>
+
+<!-- altGlyphItem: Alternate Glyph Item Element ........ -->
+
+<!ENTITY % SVG.altGlyphItem.extra.content "" >
+
+<!ENTITY % SVG.altGlyphItem.element "INCLUDE" >
+<![%SVG.altGlyphItem.element;[
+<!ENTITY % SVG.altGlyphItem.content
+ "( %SVG.glyphRef.qname;+ %SVG.altGlyphItem.extra.content; )"
+>
+<!ELEMENT %SVG.altGlyphItem.qname; %SVG.altGlyphItem.content; >
+<!-- end of SVG.altGlyphItem.element -->]]>
+
+<!ENTITY % SVG.altGlyphItem.attlist "INCLUDE" >
+<![%SVG.altGlyphItem.attlist;[
+<!ATTLIST %SVG.altGlyphItem.qname;
+ %SVG.Core.attrib;
+>
+<!-- end of SVG.altGlyphItem.attlist -->]]>
+
+<!-- glyphRef: Glyph Reference Element ................. -->
+
+<!ENTITY % SVG.glyphRef.element "INCLUDE" >
+<![%SVG.glyphRef.element;[
+<!ENTITY % SVG.glyphRef.content "EMPTY" >
+<!ELEMENT %SVG.glyphRef.qname; %SVG.glyphRef.content; >
+<!-- end of SVG.glyphRef.element -->]]>
+
+<!ENTITY % SVG.glyphRef.attlist "INCLUDE" >
+<![%SVG.glyphRef.attlist;[
+<!ATTLIST %SVG.glyphRef.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Font.attrib;
+ %SVG.XLink.attrib;
+ x %Number.datatype; #IMPLIED
+ y %Number.datatype; #IMPLIED
+ dx %Number.datatype; #IMPLIED
+ dy %Number.datatype; #IMPLIED
+ glyphRef CDATA #IMPLIED
+ format CDATA #IMPLIED
+>
+<!-- end of SVG.glyphRef.attlist -->]]>
+
+<!-- end of svg-text.mod -->
+]]>
+
+<!-- Marker Module ............................................... -->
+<!ENTITY % svg-marker.module "INCLUDE" >
+<![%svg-marker.module;[
+<!ENTITY % svg-marker.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Marker//EN"
+ "svg-marker.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Marker Module ................................................. -->
+<!-- file: svg-marker.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg12-flat.dtd 201394 2004-11-18 01:47:06Z deweese $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Marker//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-marker.mod"
+
+ ....................................................................... -->
+
+<!-- Marker
+
+ marker
+
+ This module declares markup to provide support for marker.
+-->
+
+<!-- 'marker' property/attribute value (e.g., 'none', <uri>) -->
+<!ENTITY % MarkerValue.datatype "CDATA" >
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.marker.qname "marker" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Container.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Viewport.attrib "" >
+<!ENTITY % SVG.Text.attrib "" >
+<!ENTITY % SVG.TextContent.attrib "" >
+<!ENTITY % SVG.Font.attrib "" >
+<!ENTITY % SVG.Paint.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Profile.attrib "" >
+<!ENTITY % SVG.Gradient.attrib "" >
+<!ENTITY % SVG.Clip.attrib "" >
+<!ENTITY % SVG.Mask.attrib "" >
+<!ENTITY % SVG.Filter.attrib "" >
+<!ENTITY % SVG.FilterColor.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Marker.class .................................. -->
+
+<!ENTITY % SVG.Marker.extra.class "" >
+
+<!ENTITY % SVG.Marker.class
+ "| %SVG.marker.qname; %SVG.Marker.extra.class;"
+>
+
+<!-- SVG.Marker.attrib ................................. -->
+
+<!ENTITY % SVG.Marker.extra.attrib "" >
+
+<!ENTITY % SVG.Marker.attrib
+ "marker-start %MarkerValue.datatype; #IMPLIED
+ marker-mid %MarkerValue.datatype; #IMPLIED
+ marker-end %MarkerValue.datatype; #IMPLIED
+ %SVG.Marker.extra.attrib;"
+>
+
+<!-- SVG.Presentation.attrib ........................... -->
+
+<!ENTITY % SVG.Presentation.extra.attrib "" >
+
+<!ENTITY % SVG.Presentation.attrib
+ "%SVG.Container.attrib;
+ %SVG.Viewport.attrib;
+ %SVG.Text.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Profile.attrib;
+ %SVG.Gradient.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.Cursor.attrib;
+ flood-color %SVGColor.datatype; #IMPLIED
+ flood-opacity %OpacityValue.datatype; #IMPLIED
+ lighting-color %SVGColor.datatype; #IMPLIED
+ %SVG.Presentation.extra.attrib;"
+>
+
+<!-- marker: Marker Element ............................ -->
+
+<!ENTITY % SVG.marker.extra.content "" >
+
+<!ENTITY % SVG.marker.element "INCLUDE" >
+<![%SVG.marker.element;[
+<!ENTITY % SVG.marker.content
+ "( %SVG.Description.class; | %SVG.Animation.class; %SVG.Structure.class;
+ %SVG.Conditional.class; %SVG.Image.class; %SVG.Style.class;
+ %SVG.Shape.class; %SVG.Text.class; %SVG.Marker.class; %SVG.Profile.class;
+ %SVG.Gradient.class; %SVG.Pattern.class; %SVG.Clip.class;
+ %SVG.Mask.class; %SVG.Filter.class; %SVG.Cursor.class;
+ %SVG.Hyperlink.class; %SVG.View.class; %SVG.Script.class;
+ %SVG.Font.class; %SVG.marker.extra.content; )*"
+>
+<!ELEMENT %SVG.marker.qname; %SVG.marker.content; >
+<!-- end of SVG.marker.element -->]]>
+
+<!ENTITY % SVG.marker.attlist "INCLUDE" >
+<![%SVG.marker.attlist;[
+<!ATTLIST %SVG.marker.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.External.attrib;
+ refX %Coordinate.datatype; #IMPLIED
+ refY %Coordinate.datatype; #IMPLIED
+ markerUnits ( strokeWidth | userSpaceOnUse ) #IMPLIED
+ markerWidth %Length.datatype; #IMPLIED
+ markerHeight %Length.datatype; #IMPLIED
+ orient CDATA #IMPLIED
+ viewBox %ViewBoxSpec.datatype; #IMPLIED
+ preserveAspectRatio %PreserveAspectRatioSpec.datatype; 'xMidYMid meet'
+>
+<!-- end of SVG.marker.attlist -->]]>
+
+<!-- end of svg-marker.mod -->
+]]>
+
+<!-- Color Profile Module ........................................ -->
+<!ENTITY % svg-profile.module "INCLUDE" >
+<![%svg-profile.module;[
+<!ENTITY % svg-profile.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Color Profile//EN"
+ "svg-profile.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Color Profile Module .......................................... -->
+<!-- file: svg-profile.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg12-flat.dtd 201394 2004-11-18 01:47:06Z deweese $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Color Profile//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-profile.mod"
+
+ ....................................................................... -->
+
+<!-- Color Profile
+
+ color-profile
+
+ This module declares markup to provide support for color profile.
+-->
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.color-profile.qname "color-profile" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.XLink.attrib "" >
+
+<!-- SVG.Profile.class ................................. -->
+
+<!ENTITY % SVG.Profile.extra.class "" >
+
+<!ENTITY % SVG.Profile.class
+ "| %SVG.color-profile.qname; %SVG.Profile.extra.class;"
+>
+
+<!-- SVG.Profile.attrib ................................ -->
+
+<!ENTITY % SVG.Profile.extra.attrib "" >
+
+<!ENTITY % SVG.Profile.attrib
+ "color-profile CDATA #IMPLIED
+ %SVG.Profile.extra.attrib;"
+>
+
+<!-- color-profile: Color Profile Element .............. -->
+
+<!ENTITY % SVG.color-profile.extra.content "" >
+
+<!ENTITY % SVG.color-profile.element "INCLUDE" >
+<![%SVG.color-profile.element;[
+<!ENTITY % SVG.color-profile.content
+ "( %SVG.Description.class; %SVG.color-profile.extra.content; )*"
+>
+<!ELEMENT %SVG.color-profile.qname; %SVG.color-profile.content; >
+<!-- end of SVG.color-profile.element -->]]>
+
+<!ENTITY % SVG.color-profile.attlist "INCLUDE" >
+<![%SVG.color-profile.attlist;[
+<!ATTLIST %SVG.color-profile.qname;
+ %SVG.Core.attrib;
+ %SVG.XLink.attrib;
+ local CDATA #IMPLIED
+ name CDATA #REQUIRED
+ rendering-intent ( auto | perceptual | relative-colorimetric | saturation |
+ absolute-colorimetric ) 'auto'
+>
+<!-- end of SVG.color-profile.attlist -->]]>
+
+<!-- end of svg-profile.mod -->
+]]>
+
+<!-- Gradient Module ............................................. -->
+<!ENTITY % svg-gradient.module "INCLUDE" >
+<![%svg-gradient.module;[
+<!ENTITY % svg-gradient.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Gradient//EN"
+ "svg-gradient.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Gradient Module ............................................... -->
+<!-- file: svg-gradient.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg12-flat.dtd 201394 2004-11-18 01:47:06Z deweese $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Gradient//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-gradient.mod"
+
+ ....................................................................... -->
+
+<!-- Gradient
+
+ linearGradient, radialGradient, stop
+
+ This module declares markup to provide support for gradient fill.
+-->
+
+<!-- a <number> or a <percentage> -->
+<!ENTITY % NumberOrPercentage.datatype "CDATA" >
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.linearGradient.qname "linearGradient" >
+<!ENTITY % SVG.radialGradient.qname "radialGradient" >
+<!ENTITY % SVG.stop.qname "stop" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.XLink.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Gradient.class ................................ -->
+
+<!ENTITY % SVG.Gradient.extra.class "" >
+
+<!ENTITY % SVG.Gradient.class
+ "| %SVG.linearGradient.qname; | %SVG.radialGradient.qname;
+ %SVG.Gradient.extra.class;"
+>
+
+<!-- SVG.Gradient.attrib ............................... -->
+
+<!ENTITY % SVG.Gradient.extra.attrib "" >
+
+<!ENTITY % SVG.Gradient.attrib
+ "stop-color %SVGColor.datatype; #IMPLIED
+ stop-opacity %OpacityValue.datatype; #IMPLIED
+ %SVG.Gradient.extra.attrib;"
+>
+
+<!-- linearGradient: Linear Gradient Element ........... -->
+
+<!ENTITY % SVG.linearGradient.extra.content "" >
+
+<!ENTITY % SVG.linearGradient.element "INCLUDE" >
+<![%SVG.linearGradient.element;[
+<!ENTITY % SVG.linearGradient.content
+ "(( %SVG.Description.class; )*, ( %SVG.stop.qname; | %SVG.animate.qname;
+ | %SVG.set.qname; | %SVG.animateTransform.qname;
+ %SVG.linearGradient.extra.content; )*)"
+>
+<!ELEMENT %SVG.linearGradient.qname; %SVG.linearGradient.content; >
+<!-- end of SVG.linearGradient.element -->]]>
+
+<!ENTITY % SVG.linearGradient.attlist "INCLUDE" >
+<![%SVG.linearGradient.attlist;[
+<!ATTLIST %SVG.linearGradient.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Color.attrib;
+ %SVG.Gradient.attrib;
+ %SVG.XLink.attrib;
+ %SVG.External.attrib;
+ x1 %Coordinate.datatype; #IMPLIED
+ y1 %Coordinate.datatype; #IMPLIED
+ x2 %Coordinate.datatype; #IMPLIED
+ y2 %Coordinate.datatype; #IMPLIED
+ gradientUnits ( userSpaceOnUse | objectBoundingBox ) #IMPLIED
+ gradientTransform %TransformList.datatype; #IMPLIED
+ spreadMethod ( pad | reflect | repeat ) #IMPLIED
+>
+<!-- end of SVG.linearGradient.attlist -->]]>
+
+<!-- radialGradient: Radial Gradient Element ........... -->
+
+<!ENTITY % SVG.radialGradient.extra.content "" >
+
+<!ENTITY % SVG.radialGradient.element "INCLUDE" >
+<![%SVG.radialGradient.element;[
+<!ENTITY % SVG.radialGradient.content
+ "(( %SVG.Description.class; )*, ( %SVG.stop.qname; | %SVG.animate.qname;
+ | %SVG.set.qname; | %SVG.animateTransform.qname;
+ %SVG.radialGradient.extra.content; )*)"
+>
+<!ELEMENT %SVG.radialGradient.qname; %SVG.radialGradient.content; >
+<!-- end of SVG.radialGradient.element -->]]>
+
+<!ENTITY % SVG.radialGradient.attlist "INCLUDE" >
+<![%SVG.radialGradient.attlist;[
+<!ATTLIST %SVG.radialGradient.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Color.attrib;
+ %SVG.Gradient.attrib;
+ %SVG.XLink.attrib;
+ %SVG.External.attrib;
+ cx %Coordinate.datatype; #IMPLIED
+ cy %Coordinate.datatype; #IMPLIED
+ r %Length.datatype; #IMPLIED
+ fx %Coordinate.datatype; #IMPLIED
+ fy %Coordinate.datatype; #IMPLIED
+ gradientUnits ( userSpaceOnUse | objectBoundingBox ) #IMPLIED
+ gradientTransform %TransformList.datatype; #IMPLIED
+ spreadMethod ( pad | reflect | repeat ) #IMPLIED
+>
+<!-- end of SVG.radialGradient.attlist -->]]>
+
+<!-- stop: Stop Element ................................ -->
+
+<!ENTITY % SVG.stop.extra.content "" >
+
+<!ENTITY % SVG.stop.element "INCLUDE" >
+<![%SVG.stop.element;[
+<!ENTITY % SVG.stop.content
+ "( %SVG.animate.qname; | %SVG.set.qname; | %SVG.animateColor.qname;
+ %SVG.stop.extra.content; )*"
+>
+<!ELEMENT %SVG.stop.qname; %SVG.stop.content; >
+<!-- end of SVG.stop.element -->]]>
+
+<!ENTITY % SVG.stop.attlist "INCLUDE" >
+<![%SVG.stop.attlist;[
+<!ATTLIST %SVG.stop.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Color.attrib;
+ %SVG.Gradient.attrib;
+ offset %NumberOrPercentage.datatype; #REQUIRED
+>
+<!-- end of SVG.stop.attlist -->]]>
+
+<!-- end of svg-gradient.mod -->
+]]>
+
+<!-- Pattern Module .............................................. -->
+<!ENTITY % svg-pattern.module "INCLUDE" >
+<![%svg-pattern.module;[
+<!ENTITY % svg-pattern.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Pattern//EN"
+ "svg-pattern.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Pattern Module ................................................ -->
+<!-- file: svg-pattern.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg12-flat.dtd 201394 2004-11-18 01:47:06Z deweese $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Pattern//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-pattern.mod"
+
+ ....................................................................... -->
+
+<!-- Pattern
+
+ pattern
+
+ This module declares markup to provide support for pattern fill.
+-->
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.pattern.qname "pattern" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Container.attrib "" >
+<!ENTITY % SVG.Conditional.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Viewport.attrib "" >
+<!ENTITY % SVG.Text.attrib "" >
+<!ENTITY % SVG.TextContent.attrib "" >
+<!ENTITY % SVG.Font.attrib "" >
+<!ENTITY % SVG.Paint.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Marker.attrib "" >
+<!ENTITY % SVG.Profile.attrib "" >
+<!ENTITY % SVG.Gradient.attrib "" >
+<!ENTITY % SVG.Clip.attrib "" >
+<!ENTITY % SVG.Mask.attrib "" >
+<!ENTITY % SVG.Filter.attrib "" >
+<!ENTITY % SVG.FilterColor.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.XLink.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Pattern.class ................................. -->
+
+<!ENTITY % SVG.Pattern.extra.class "" >
+
+<!ENTITY % SVG.Pattern.class
+ "| %SVG.pattern.qname; %SVG.Pattern.extra.class;"
+>
+
+<!-- SVG.Presentation.attrib ........................... -->
+
+<!ENTITY % SVG.Presentation.extra.attrib "" >
+
+<!ENTITY % SVG.Presentation.attrib
+ "%SVG.Container.attrib;
+ %SVG.Viewport.attrib;
+ %SVG.Text.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Profile.attrib;
+ %SVG.Gradient.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.Cursor.attrib;
+ flood-color %SVGColor.datatype; #IMPLIED
+ flood-opacity %OpacityValue.datatype; #IMPLIED
+ lighting-color %SVGColor.datatype; #IMPLIED
+ %SVG.Presentation.extra.attrib;"
+>
+
+<!-- pattern: Pattern Element .......................... -->
+
+<!ENTITY % SVG.pattern.extra.content "" >
+
+<!ENTITY % SVG.pattern.element "INCLUDE" >
+<![%SVG.pattern.element;[
+<!ENTITY % SVG.pattern.content
+ "( %SVG.Description.class; | %SVG.Animation.class; %SVG.Structure.class;
+ %SVG.Conditional.class; %SVG.Image.class; %SVG.Style.class;
+ %SVG.Shape.class; %SVG.Text.class; %SVG.Marker.class; %SVG.Profile.class;
+ %SVG.Gradient.class; %SVG.Pattern.class; %SVG.Clip.class;
+ %SVG.Mask.class; %SVG.Filter.class; %SVG.Cursor.class;
+ %SVG.Hyperlink.class; %SVG.View.class; %SVG.Script.class;
+ %SVG.Font.class; %SVG.pattern.extra.content; )*"
+>
+<!ELEMENT %SVG.pattern.qname; %SVG.pattern.content; >
+<!-- end of SVG.pattern.element -->]]>
+
+<!ENTITY % SVG.pattern.attlist "INCLUDE" >
+<![%SVG.pattern.attlist;[
+<!ATTLIST %SVG.pattern.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.XLink.attrib;
+ %SVG.External.attrib;
+ x %Coordinate.datatype; #IMPLIED
+ y %Coordinate.datatype; #IMPLIED
+ width %Length.datatype; #IMPLIED
+ height %Length.datatype; #IMPLIED
+ patternUnits ( userSpaceOnUse | objectBoundingBox ) #IMPLIED
+ patternContentUnits ( userSpaceOnUse | objectBoundingBox ) #IMPLIED
+ patternTransform %TransformList.datatype; #IMPLIED
+ viewBox %ViewBoxSpec.datatype; #IMPLIED
+ preserveAspectRatio %PreserveAspectRatioSpec.datatype; 'xMidYMid meet'
+>
+<!-- end of SVG.pattern.attlist -->]]>
+
+<!-- end of svg-pattern.mod -->
+]]>
+
+<!-- Clip Module ................................................. -->
+<!ENTITY % svg-clip.module "INCLUDE" >
+<![%svg-clip.module;[
+<!ENTITY % svg-clip.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Clip//EN"
+ "svg-clip.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Clip Module ................................................... -->
+<!-- file: svg-clip.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg12-flat.dtd 201394 2004-11-18 01:47:06Z deweese $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Clip//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-clip.mod"
+
+ ....................................................................... -->
+
+<!-- Clip
+
+ clipPath
+
+ This module declares markup to provide support for clipping.
+-->
+
+<!-- 'clip-path' property/attribute value (e.g., 'none', <uri>) -->
+<!ENTITY % ClipPathValue.datatype "CDATA" >
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.clipPath.qname "clipPath" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Conditional.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Text.attrib "" >
+<!ENTITY % SVG.TextContent.attrib "" >
+<!ENTITY % SVG.Font.attrib "" >
+<!ENTITY % SVG.Paint.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Mask.attrib "" >
+<!ENTITY % SVG.Filter.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Clip.class .................................... -->
+
+<!ENTITY % SVG.Clip.extra.class "" >
+
+<!ENTITY % SVG.Clip.class
+ "| %SVG.clipPath.qname; %SVG.Clip.extra.class;"
+>
+
+<!-- SVG.Clip.attrib ................................... -->
+
+<!ENTITY % SVG.Clip.extra.attrib "" >
+
+<!ENTITY % SVG.Clip.attrib
+ "clip-path %ClipPathValue.datatype; #IMPLIED
+ clip-rule %ClipFillRule.datatype; #IMPLIED
+ %SVG.Clip.extra.attrib;"
+>
+
+<!-- clipPath: Clip Path Element ....................... -->
+
+<!ENTITY % SVG.clipPath.extra.content "" >
+
+<!ENTITY % SVG.clipPath.element "INCLUDE" >
+<![%SVG.clipPath.element;[
+<!ENTITY % SVG.clipPath.content
+ "(( %SVG.Description.class; )*, ( %SVG.Animation.class; %SVG.Use.class;
+ %SVG.Shape.class; %SVG.Text.class; %SVG.clipPath.extra.content; )*)"
+>
+<!ELEMENT %SVG.clipPath.qname; %SVG.clipPath.content; >
+<!-- end of SVG.clipPath.element -->]]>
+
+<!ENTITY % SVG.clipPath.attlist "INCLUDE" >
+<![%SVG.clipPath.attlist;[
+<!ATTLIST %SVG.clipPath.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Text.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.Cursor.attrib;
+ %SVG.External.attrib;
+ transform %TransformList.datatype; #IMPLIED
+ clipPathUnits ( userSpaceOnUse | objectBoundingBox ) #IMPLIED
+>
+<!-- end of SVG.clipPath.attlist -->]]>
+
+<!-- end of svg-clip.mod -->
+]]>
+
+<!-- Mask Module ................................................. -->
+<!ENTITY % svg-mask.module "INCLUDE" >
+<![%svg-mask.module;[
+<!ENTITY % svg-mask.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Mask//EN"
+ "svg-mask.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Mask Module ................................................... -->
+<!-- file: svg-mask.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg12-flat.dtd 201394 2004-11-18 01:47:06Z deweese $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Mask//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-mask.mod"
+
+ ....................................................................... -->
+
+<!-- Mask
+
+ mask
+
+ This module declares markup to provide support for masking.
+-->
+
+<!-- 'mask' property/attribute value (e.g., 'none', <uri>) -->
+<!ENTITY % MaskValue.datatype "CDATA" >
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.mask.qname "mask" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Container.attrib "" >
+<!ENTITY % SVG.Conditional.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Viewport.attrib "" >
+<!ENTITY % SVG.Text.attrib "" >
+<!ENTITY % SVG.TextContent.attrib "" >
+<!ENTITY % SVG.Font.attrib "" >
+<!ENTITY % SVG.Paint.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Marker.attrib "" >
+<!ENTITY % SVG.Profile.attrib "" >
+<!ENTITY % SVG.Gradient.attrib "" >
+<!ENTITY % SVG.Clip.attrib "" >
+<!ENTITY % SVG.Filter.attrib "" >
+<!ENTITY % SVG.FilterColor.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Mask.class .................................... -->
+
+<!ENTITY % SVG.Mask.extra.class "" >
+
+<!ENTITY % SVG.Mask.class
+ "| %SVG.mask.qname; %SVG.Mask.extra.class;"
+>
+
+<!-- SVG.Mask.attrib ................................... -->
+
+<!ENTITY % SVG.Mask.extra.attrib "" >
+
+<!ENTITY % SVG.Mask.attrib
+ "mask %MaskValue.datatype; #IMPLIED
+ %SVG.Mask.extra.attrib;"
+>
+
+<!-- SVG.Presentation.attrib ........................... -->
+
+<!ENTITY % SVG.Presentation.extra.attrib "" >
+
+<!ENTITY % SVG.Presentation.attrib
+ "%SVG.Container.attrib;
+ %SVG.Viewport.attrib;
+ %SVG.Text.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Profile.attrib;
+ %SVG.Gradient.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.Cursor.attrib;
+ flood-color %SVGColor.datatype; #IMPLIED
+ flood-opacity %OpacityValue.datatype; #IMPLIED
+ lighting-color %SVGColor.datatype; #IMPLIED
+ %SVG.Presentation.extra.attrib;"
+>
+
+<!-- mask: Mask Element ................................ -->
+
+<!ENTITY % SVG.mask.extra.content "" >
+
+<!ENTITY % SVG.mask.element "INCLUDE" >
+<![%SVG.mask.element;[
+<!ENTITY % SVG.mask.content
+ "( %SVG.Description.class; | %SVG.Animation.class; %SVG.Structure.class;
+ %SVG.Conditional.class; %SVG.Image.class; %SVG.Style.class;
+ %SVG.Shape.class; %SVG.Text.class; %SVG.Marker.class; %SVG.Profile.class;
+ %SVG.Gradient.class; %SVG.Pattern.class; %SVG.Clip.class;
+ %SVG.Mask.class; %SVG.Filter.class; %SVG.Cursor.class;
+ %SVG.Hyperlink.class; %SVG.View.class; %SVG.Script.class;
+ %SVG.Font.class; %SVG.mask.extra.content; )*"
+>
+<!ELEMENT %SVG.mask.qname; %SVG.mask.content; >
+<!-- end of SVG.mask.element -->]]>
+
+<!ENTITY % SVG.mask.attlist "INCLUDE" >
+<![%SVG.mask.attlist;[
+<!ATTLIST %SVG.mask.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.External.attrib;
+ x %Coordinate.datatype; #IMPLIED
+ y %Coordinate.datatype; #IMPLIED
+ width %Length.datatype; #IMPLIED
+ height %Length.datatype; #IMPLIED
+ maskUnits ( userSpaceOnUse | objectBoundingBox ) #IMPLIED
+ maskContentUnits ( userSpaceOnUse | objectBoundingBox ) #IMPLIED
+>
+<!-- end of SVG.mask.attlist -->]]>
+
+<!-- end of svg-mask.mod -->
+]]>
+
+<!-- Filter Module ............................................... -->
+<!ENTITY % svg-filter.module "INCLUDE" >
+<![%svg-filter.module;[
+<!ENTITY % svg-filter.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Filter//EN"
+ "svg-filter.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Filter Module ................................................. -->
+<!-- file: svg-filter.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg12-flat.dtd 201394 2004-11-18 01:47:06Z deweese $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Filter//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-filter.mod"
+
+ ....................................................................... -->
+
+<!-- Filter
+
+ filter, feBlend, feColorMatrix, feComponentTransfer, feComposite,
+ feConvolveMatrix, feDiffuseLighting, feDisplacementMap, feFlood,
+ feGaussianBlur, feImage, feMerge, feMergeNode, feMorphology, feOffset,
+ feSpecularLighting, feTile, feTurbulence, feDistantLight, fePointLight,
+ feSpotLight, feFuncR, feFuncG, feFuncB, feFuncA
+
+ This module declares markup to provide support for filter effect.
+-->
+
+<!-- 'filter' property/attribute value (e.g., 'none', <uri>) -->
+<!ENTITY % FilterValue.datatype "CDATA" >
+
+<!-- list of <number>s, but at least one and at most two -->
+<!ENTITY % NumberOptionalNumber.datatype "CDATA" >
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.filter.qname "filter" >
+<!ENTITY % SVG.feBlend.qname "feBlend" >
+<!ENTITY % SVG.feColorMatrix.qname "feColorMatrix" >
+<!ENTITY % SVG.feComponentTransfer.qname "feComponentTransfer" >
+<!ENTITY % SVG.feComposite.qname "feComposite" >
+<!ENTITY % SVG.feConvolveMatrix.qname "feConvolveMatrix" >
+<!ENTITY % SVG.feDiffuseLighting.qname "feDiffuseLighting" >
+<!ENTITY % SVG.feDisplacementMap.qname "feDisplacementMap" >
+<!ENTITY % SVG.feFlood.qname "feFlood" >
+<!ENTITY % SVG.feGaussianBlur.qname "feGaussianBlur" >
+<!ENTITY % SVG.feImage.qname "feImage" >
+<!ENTITY % SVG.feMerge.qname "feMerge" >
+<!ENTITY % SVG.feMergeNode.qname "feMergeNode" >
+<!ENTITY % SVG.feMorphology.qname "feMorphology" >
+<!ENTITY % SVG.feOffset.qname "feOffset" >
+<!ENTITY % SVG.feSpecularLighting.qname "feSpecularLighting" >
+<!ENTITY % SVG.feTile.qname "feTile" >
+<!ENTITY % SVG.feTurbulence.qname "feTurbulence" >
+<!ENTITY % SVG.feDistantLight.qname "feDistantLight" >
+<!ENTITY % SVG.fePointLight.qname "fePointLight" >
+<!ENTITY % SVG.feSpotLight.qname "feSpotLight" >
+<!ENTITY % SVG.feFuncR.qname "feFuncR" >
+<!ENTITY % SVG.feFuncG.qname "feFuncG" >
+<!ENTITY % SVG.feFuncB.qname "feFuncB" >
+<!ENTITY % SVG.feFuncA.qname "feFuncA" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Container.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Viewport.attrib "" >
+<!ENTITY % SVG.Text.attrib "" >
+<!ENTITY % SVG.TextContent.attrib "" >
+<!ENTITY % SVG.Font.attrib "" >
+<!ENTITY % SVG.Paint.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Marker.attrib "" >
+<!ENTITY % SVG.Profile.attrib "" >
+<!ENTITY % SVG.Gradient.attrib "" >
+<!ENTITY % SVG.Clip.attrib "" >
+<!ENTITY % SVG.Mask.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.XLink.attrib "" >
+<!ENTITY % SVG.XLinkEmbed.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Filter.class .................................. -->
+
+<!ENTITY % SVG.Filter.extra.class "" >
+
+<!ENTITY % SVG.Filter.class
+ "| %SVG.filter.qname; %SVG.Filter.extra.class;"
+>
+
+<!-- SVG.FilterPrimitive.class ......................... -->
+
+<!ENTITY % SVG.FilterPrimitive.extra.class "" >
+
+<!ENTITY % SVG.FilterPrimitive.class
+ "| %SVG.feBlend.qname; | %SVG.feColorMatrix.qname;
+ | %SVG.feComponentTransfer.qname; | %SVG.feComposite.qname;
+ | %SVG.feConvolveMatrix.qname; | %SVG.feDiffuseLighting.qname;
+ | %SVG.feDisplacementMap.qname; | %SVG.feFlood.qname;
+ | %SVG.feGaussianBlur.qname; | %SVG.feImage.qname; | %SVG.feMerge.qname;
+ | %SVG.feMorphology.qname; | %SVG.feOffset.qname;
+ | %SVG.feSpecularLighting.qname; | %SVG.feTile.qname;
+ | %SVG.feTurbulence.qname; %SVG.FilterPrimitive.extra.class;"
+>
+
+<!-- SVG.Filter.attrib ................................. -->
+
+<!ENTITY % SVG.Filter.extra.attrib "" >
+
+<!ENTITY % SVG.Filter.attrib
+ "filter %FilterValue.datatype; #IMPLIED
+ %SVG.Filter.extra.attrib;"
+>
+
+<!-- SVG.FilterColor.attrib ............................ -->
+
+<!ENTITY % SVG.FilterColor.extra.attrib "" >
+
+<!ENTITY % SVG.FilterColor.attrib
+ "color-interpolation-filters ( auto | sRGB | linearRGB | inherit )
+ #IMPLIED
+ %SVG.FilterColor.extra.attrib;"
+>
+
+<!-- SVG.FilterPrimitive.attrib ........................ -->
+
+<!ENTITY % SVG.FilterPrimitive.extra.attrib "" >
+
+<!ENTITY % SVG.FilterPrimitive.attrib
+ "x %Coordinate.datatype; #IMPLIED
+ y %Coordinate.datatype; #IMPLIED
+ width %Length.datatype; #IMPLIED
+ height %Length.datatype; #IMPLIED
+ result CDATA #IMPLIED
+ %SVG.FilterPrimitive.extra.attrib;"
+>
+
+<!-- SVG.FilterPrimitiveWithIn.attrib .................. -->
+
+<!ENTITY % SVG.FilterPrimitiveWithIn.extra.attrib "" >
+
+<!ENTITY % SVG.FilterPrimitiveWithIn.attrib
+ "%SVG.FilterPrimitive.attrib;
+ in CDATA #IMPLIED
+ %SVG.FilterPrimitiveWithIn.extra.attrib;"
+>
+
+<!-- SVG.Presentation.attrib ........................... -->
+
+<!ENTITY % SVG.Presentation.extra.attrib "" >
+
+<!ENTITY % SVG.Presentation.attrib
+ "%SVG.Container.attrib;
+ %SVG.Viewport.attrib;
+ %SVG.Text.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Profile.attrib;
+ %SVG.Gradient.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.Cursor.attrib;
+ flood-color %SVGColor.datatype; #IMPLIED
+ flood-opacity %OpacityValue.datatype; #IMPLIED
+ lighting-color %SVGColor.datatype; #IMPLIED
+ %SVG.Presentation.extra.attrib;"
+>
+
+<!-- filter: Filter Element ............................ -->
+
+<!ENTITY % SVG.filter.extra.content "" >
+
+<!ENTITY % SVG.filter.element "INCLUDE" >
+<![%SVG.filter.element;[
+<!ENTITY % SVG.filter.content
+ "(( %SVG.Description.class; )*, ( %SVG.animate.qname; | %SVG.set.qname;
+ %SVG.FilterPrimitive.class; %SVG.filter.extra.content; )*)"
+>
+<!ELEMENT %SVG.filter.qname; %SVG.filter.content; >
+<!-- end of SVG.filter.element -->]]>
+
+<!ENTITY % SVG.filter.attlist "INCLUDE" >
+<![%SVG.filter.attlist;[
+<!ATTLIST %SVG.filter.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.XLink.attrib;
+ %SVG.External.attrib;
+ x %Coordinate.datatype; #IMPLIED
+ y %Coordinate.datatype; #IMPLIED
+ width %Length.datatype; #IMPLIED
+ height %Length.datatype; #IMPLIED
+ filterRes %NumberOptionalNumber.datatype; #IMPLIED
+ filterUnits ( userSpaceOnUse | objectBoundingBox ) #IMPLIED
+ primitiveUnits ( userSpaceOnUse | objectBoundingBox ) #IMPLIED
+>
+<!-- end of SVG.filter.attlist -->]]>
+
+<!-- feBlend: Filter Effect Blend Element .............. -->
+
+<!ENTITY % SVG.feBlend.extra.content "" >
+
+<!ENTITY % SVG.feBlend.element "INCLUDE" >
+<![%SVG.feBlend.element;[
+<!ENTITY % SVG.feBlend.content
+ "( %SVG.animate.qname; | %SVG.set.qname; %SVG.feBlend.extra.content; )*"
+>
+<!ELEMENT %SVG.feBlend.qname; %SVG.feBlend.content; >
+<!-- end of SVG.feBlend.element -->]]>
+
+<!ENTITY % SVG.feBlend.attlist "INCLUDE" >
+<![%SVG.feBlend.attlist;[
+<!ATTLIST %SVG.feBlend.qname;
+ %SVG.Core.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitiveWithIn.attrib;
+ in2 CDATA #REQUIRED
+ mode ( normal | multiply | screen | darken | lighten ) 'normal'
+>
+<!-- end of SVG.feBlend.attlist -->]]>
+
+<!-- feColorMatrix: Filter Effect Color Matrix Element . -->
+
+<!ENTITY % SVG.feColorMatrix.extra.content "" >
+
+<!ENTITY % SVG.feColorMatrix.element "INCLUDE" >
+<![%SVG.feColorMatrix.element;[
+<!ENTITY % SVG.feColorMatrix.content
+ "( %SVG.animate.qname; | %SVG.set.qname;
+ %SVG.feColorMatrix.extra.content; )*"
+>
+<!ELEMENT %SVG.feColorMatrix.qname; %SVG.feColorMatrix.content; >
+<!-- end of SVG.feColorMatrix.element -->]]>
+
+<!ENTITY % SVG.feColorMatrix.attlist "INCLUDE" >
+<![%SVG.feColorMatrix.attlist;[
+<!ATTLIST %SVG.feColorMatrix.qname;
+ %SVG.Core.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitiveWithIn.attrib;
+ type ( matrix | saturate | hueRotate | luminanceToAlpha ) 'matrix'
+ values CDATA #IMPLIED
+>
+<!-- end of SVG.feColorMatrix.attlist -->]]>
+
+<!-- feComponentTransfer: Filter Effect Component Transfer Element -->
+
+<!ENTITY % SVG.feComponentTransfer.extra.content "" >
+
+<!ENTITY % SVG.feComponentTransfer.element "INCLUDE" >
+<![%SVG.feComponentTransfer.element;[
+<!ENTITY % SVG.feComponentTransfer.content
+ "( %SVG.feFuncR.qname;?, %SVG.feFuncG.qname;?, %SVG.feFuncB.qname;?,
+ %SVG.feFuncA.qname;? %SVG.feComponentTransfer.extra.content; )"
+>
+<!ELEMENT %SVG.feComponentTransfer.qname; %SVG.feComponentTransfer.content; >
+<!-- end of SVG.feComponentTransfer.element -->]]>
+
+<!ENTITY % SVG.feComponentTransfer.attlist "INCLUDE" >
+<![%SVG.feComponentTransfer.attlist;[
+<!ATTLIST %SVG.feComponentTransfer.qname;
+ %SVG.Core.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitiveWithIn.attrib;
+>
+<!-- end of SVG.feComponentTransfer.attlist -->]]>
+
+<!-- feComposite: Filter Effect Composite Element ...... -->
+
+<!ENTITY % SVG.feComposite.extra.content "" >
+
+<!ENTITY % SVG.feComposite.element "INCLUDE" >
+<![%SVG.feComposite.element;[
+<!ENTITY % SVG.feComposite.content
+ "( %SVG.animate.qname; | %SVG.set.qname; %SVG.feComposite.extra.content; )*"
+>
+<!ELEMENT %SVG.feComposite.qname; %SVG.feComposite.content; >
+<!-- end of SVG.feComposite.element -->]]>
+
+<!ENTITY % SVG.feComposite.attlist "INCLUDE" >
+<![%SVG.feComposite.attlist;[
+<!ATTLIST %SVG.feComposite.qname;
+ %SVG.Core.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitiveWithIn.attrib;
+ in2 CDATA #REQUIRED
+ operator ( over | in | out | atop | xor | arithmetic ) 'over'
+ k1 %Number.datatype; #IMPLIED
+ k2 %Number.datatype; #IMPLIED
+ k3 %Number.datatype; #IMPLIED
+ k4 %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.feComposite.attlist -->]]>
+
+<!-- feConvolveMatrix: Filter Effect Convolve Matrix Element -->
+
+<!ENTITY % SVG.feConvolveMatrix.extra.content "" >
+
+<!ENTITY % SVG.feConvolveMatrix.element "INCLUDE" >
+<![%SVG.feConvolveMatrix.element;[
+<!ENTITY % SVG.feConvolveMatrix.content
+ "( %SVG.animate.qname; | %SVG.set.qname;
+ %SVG.feConvolveMatrix.extra.content; )*"
+>
+<!ELEMENT %SVG.feConvolveMatrix.qname; %SVG.feConvolveMatrix.content; >
+<!-- end of SVG.feConvolveMatrix.element -->]]>
+
+<!ENTITY % SVG.feConvolveMatrix.attlist "INCLUDE" >
+<![%SVG.feConvolveMatrix.attlist;[
+<!ATTLIST %SVG.feConvolveMatrix.qname;
+ %SVG.Core.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitiveWithIn.attrib;
+ order %NumberOptionalNumber.datatype; #REQUIRED
+ kernelMatrix CDATA #REQUIRED
+ divisor %Number.datatype; #IMPLIED
+ bias %Number.datatype; #IMPLIED
+ targetX %Integer.datatype; #IMPLIED
+ targetY %Integer.datatype; #IMPLIED
+ edgeMode ( duplicate | wrap | none ) 'duplicate'
+ kernelUnitLength %NumberOptionalNumber.datatype; #IMPLIED
+ preserveAlpha %Boolean.datatype; #IMPLIED
+>
+<!-- end of SVG.feConvolveMatrix.attlist -->]]>
+
+<!-- feDiffuseLighting: Filter Effect Diffuse Lighting Element -->
+
+<!ENTITY % SVG.feDiffuseLighting.extra.content "" >
+
+<!ENTITY % SVG.feDiffuseLighting.element "INCLUDE" >
+<![%SVG.feDiffuseLighting.element;[
+<!ENTITY % SVG.feDiffuseLighting.content
+ "(( %SVG.feDistantLight.qname; | %SVG.fePointLight.qname;
+ | %SVG.feSpotLight.qname; ), ( %SVG.animate.qname; | %SVG.set.qname;
+ | %SVG.animateColor.qname; %SVG.feDiffuseLighting.extra.content; )*)"
+>
+<!ELEMENT %SVG.feDiffuseLighting.qname; %SVG.feDiffuseLighting.content; >
+<!-- end of SVG.feDiffuseLighting.element -->]]>
+
+<!ENTITY % SVG.feDiffuseLighting.attlist "INCLUDE" >
+<![%SVG.feDiffuseLighting.attlist;[
+<!ATTLIST %SVG.feDiffuseLighting.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Color.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitiveWithIn.attrib;
+ lighting-color %SVGColor.datatype; #IMPLIED
+ surfaceScale %Number.datatype; #IMPLIED
+ diffuseConstant %Number.datatype; #IMPLIED
+ kernelUnitLength %NumberOptionalNumber.datatype; #IMPLIED
+>
+<!-- end of SVG.feDiffuseLighting.attlist -->]]>
+
+<!-- feDisplacementMap: Filter Effect Displacement Map Element -->
+
+<!ENTITY % SVG.feDisplacementMap.extra.content "" >
+
+<!ENTITY % SVG.feDisplacementMap.element "INCLUDE" >
+<![%SVG.feDisplacementMap.element;[
+<!ENTITY % SVG.feDisplacementMap.content
+ "( %SVG.animate.qname; | %SVG.set.qname;
+ %SVG.feDisplacementMap.extra.content; )*"
+>
+<!ELEMENT %SVG.feDisplacementMap.qname; %SVG.feDisplacementMap.content; >
+<!-- end of SVG.feDisplacementMap.element -->]]>
+
+<!ENTITY % SVG.feDisplacementMap.attlist "INCLUDE" >
+<![%SVG.feDisplacementMap.attlist;[
+<!ATTLIST %SVG.feDisplacementMap.qname;
+ %SVG.Core.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitiveWithIn.attrib;
+ in2 CDATA #REQUIRED
+ scale %Number.datatype; #IMPLIED
+ xChannelSelector ( R | G | B | A ) 'A'
+ yChannelSelector ( R | G | B | A ) 'A'
+>
+<!-- end of SVG.feDisplacementMap.attlist -->]]>
+
+<!-- feFlood: Filter Effect Flood Element .............. -->
+
+<!ENTITY % SVG.feFlood.extra.content "" >
+
+<!ENTITY % SVG.feFlood.element "INCLUDE" >
+<![%SVG.feFlood.element;[
+<!ENTITY % SVG.feFlood.content
+ "( %SVG.animate.qname; | %SVG.set.qname; | %SVG.animateColor.qname;
+ %SVG.feFlood.extra.content; )*"
+>
+<!ELEMENT %SVG.feFlood.qname; %SVG.feFlood.content; >
+<!-- end of SVG.feFlood.element -->]]>
+
+<!ENTITY % SVG.feFlood.attlist "INCLUDE" >
+<![%SVG.feFlood.attlist;[
+<!ATTLIST %SVG.feFlood.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Color.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitiveWithIn.attrib;
+ flood-color %SVGColor.datatype; #IMPLIED
+ flood-opacity %OpacityValue.datatype; #IMPLIED
+>
+<!-- end of SVG.feFlood.attlist -->]]>
+
+<!-- feGaussianBlur: Filter Effect Gaussian Blur Element -->
+
+<!ENTITY % SVG.feGaussianBlur.extra.content "" >
+
+<!ENTITY % SVG.feGaussianBlur.element "INCLUDE" >
+<![%SVG.feGaussianBlur.element;[
+<!ENTITY % SVG.feGaussianBlur.content
+ "( %SVG.animate.qname; | %SVG.set.qname;
+ %SVG.feGaussianBlur.extra.content; )*"
+>
+<!ELEMENT %SVG.feGaussianBlur.qname; %SVG.feGaussianBlur.content; >
+<!-- end of SVG.feGaussianBlur.element -->]]>
+
+<!ENTITY % SVG.feGaussianBlur.attlist "INCLUDE" >
+<![%SVG.feGaussianBlur.attlist;[
+<!ATTLIST %SVG.feGaussianBlur.qname;
+ %SVG.Core.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitiveWithIn.attrib;
+ stdDeviation %NumberOptionalNumber.datatype; #IMPLIED
+>
+<!-- end of SVG.feGaussianBlur.attlist -->]]>
+
+<!-- feImage: Filter Effect Image Element .............. -->
+
+<!ENTITY % SVG.feImage.extra.content "" >
+
+<!ENTITY % SVG.feImage.element "INCLUDE" >
+<![%SVG.feImage.element;[
+<!ENTITY % SVG.feImage.content
+ "( %SVG.animate.qname; | %SVG.set.qname; | %SVG.animateTransform.qname;
+ %SVG.feImage.extra.content; )*"
+>
+<!ELEMENT %SVG.feImage.qname; %SVG.feImage.content; >
+<!-- end of SVG.feImage.element -->]]>
+
+<!ENTITY % SVG.feImage.attlist "INCLUDE" >
+<![%SVG.feImage.attlist;[
+<!ATTLIST %SVG.feImage.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.FilterPrimitive.attrib;
+ %SVG.XLinkEmbed.attrib;
+ %SVG.External.attrib;
+ preserveAspectRatio %PreserveAspectRatioSpec.datatype; 'xMidYMid meet'
+>
+<!-- end of SVG.feImage.attlist -->]]>
+
+<!-- feMerge: Filter Effect Merge Element .............. -->
+
+<!ENTITY % SVG.feMerge.extra.content "" >
+
+<!ENTITY % SVG.feMerge.element "INCLUDE" >
+<![%SVG.feMerge.element;[
+<!ENTITY % SVG.feMerge.content
+ "( %SVG.feMergeNode.qname; %SVG.feMerge.extra.content; )*"
+>
+<!ELEMENT %SVG.feMerge.qname; %SVG.feMerge.content; >
+<!-- end of SVG.feMerge.element -->]]>
+
+<!ENTITY % SVG.feMerge.attlist "INCLUDE" >
+<![%SVG.feMerge.attlist;[
+<!ATTLIST %SVG.feMerge.qname;
+ %SVG.Core.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitive.attrib;
+>
+<!-- end of SVG.feMerge.attlist -->]]>
+
+<!-- feMergeNode: Filter Effect Merge Node Element ..... -->
+
+<!ENTITY % SVG.feMergeNode.extra.content "" >
+
+<!ENTITY % SVG.feMergeNode.element "INCLUDE" >
+<![%SVG.feMergeNode.element;[
+<!ENTITY % SVG.feMergeNode.content
+ "( %SVG.animate.qname; | %SVG.set.qname; %SVG.feMergeNode.extra.content; )*"
+>
+<!ELEMENT %SVG.feMergeNode.qname; %SVG.feMergeNode.content; >
+<!-- end of SVG.feMergeNode.element -->]]>
+
+<!ENTITY % SVG.feMergeNode.attlist "INCLUDE" >
+<![%SVG.feMergeNode.attlist;[
+<!ATTLIST %SVG.feMergeNode.qname;
+ %SVG.Core.attrib;
+ in CDATA #IMPLIED
+>
+<!-- end of SVG.feMergeNode.attlist -->]]>
+
+<!-- feMorphology: Filter Effect Morphology Element .... -->
+
+<!ENTITY % SVG.feMorphology.extra.content "" >
+
+<!ENTITY % SVG.feMorphology.element "INCLUDE" >
+<![%SVG.feMorphology.element;[
+<!ENTITY % SVG.feMorphology.content
+ "( %SVG.animate.qname; | %SVG.set.qname;
+ %SVG.feMorphology.extra.content; )*"
+>
+<!ELEMENT %SVG.feMorphology.qname; %SVG.feMorphology.content; >
+<!-- end of SVG.feMorphology.element -->]]>
+
+<!ENTITY % SVG.feMorphology.attlist "INCLUDE" >
+<![%SVG.feMorphology.attlist;[
+<!ATTLIST %SVG.feMorphology.qname;
+ %SVG.Core.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitiveWithIn.attrib;
+ operator ( erode | dilate ) 'erode'
+ radius %NumberOptionalNumber.datatype; #IMPLIED
+>
+<!-- end of SVG.feMorphology.attlist -->]]>
+
+<!-- feOffset: Filter Effect Offset Element ............ -->
+
+<!ENTITY % SVG.feOffset.extra.content "" >
+
+<!ENTITY % SVG.feOffset.element "INCLUDE" >
+<![%SVG.feOffset.element;[
+<!ENTITY % SVG.feOffset.content
+ "( %SVG.animate.qname; | %SVG.set.qname; %SVG.feOffset.extra.content; )*"
+>
+<!ELEMENT %SVG.feOffset.qname; %SVG.feOffset.content; >
+<!-- end of SVG.feOffset.element -->]]>
+
+<!ENTITY % SVG.feOffset.attlist "INCLUDE" >
+<![%SVG.feOffset.attlist;[
+<!ATTLIST %SVG.feOffset.qname;
+ %SVG.Core.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitiveWithIn.attrib;
+ dx %Number.datatype; #IMPLIED
+ dy %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.feOffset.attlist -->]]>
+
+<!-- feSpecularLighting: Filter Effect Specular Lighting Element -->
+
+<!ENTITY % SVG.feSpecularLighting.extra.content "" >
+
+<!ENTITY % SVG.feSpecularLighting.element "INCLUDE" >
+<![%SVG.feSpecularLighting.element;[
+<!ENTITY % SVG.feSpecularLighting.content
+ "(( %SVG.feDistantLight.qname; | %SVG.fePointLight.qname;
+ | %SVG.feSpotLight.qname; ), ( %SVG.animate.qname; | %SVG.set.qname;
+ | %SVG.animateColor.qname; %SVG.feSpecularLighting.extra.content; )*)"
+>
+<!ELEMENT %SVG.feSpecularLighting.qname; %SVG.feSpecularLighting.content; >
+<!-- end of SVG.feSpecularLighting.element -->]]>
+
+<!ENTITY % SVG.feSpecularLighting.attlist "INCLUDE" >
+<![%SVG.feSpecularLighting.attlist;[
+<!ATTLIST %SVG.feSpecularLighting.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Color.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitiveWithIn.attrib;
+ lighting-color %SVGColor.datatype; #IMPLIED
+ surfaceScale %Number.datatype; #IMPLIED
+ specularConstant %Number.datatype; #IMPLIED
+ specularExponent %Number.datatype; #IMPLIED
+ kernelUnitLength %NumberOptionalNumber.datatype; #IMPLIED
+>
+<!-- end of SVG.feSpecularLighting.attlist -->]]>
+
+<!-- feTile: Filter Effect Tile Element ................ -->
+
+<!ENTITY % SVG.feTile.extra.content "" >
+
+<!ENTITY % SVG.feTile.element "INCLUDE" >
+<![%SVG.feTile.element;[
+<!ENTITY % SVG.feTile.content
+ "( %SVG.animate.qname; | %SVG.set.qname; %SVG.feTile.extra.content; )*"
+>
+<!ELEMENT %SVG.feTile.qname; %SVG.feTile.content; >
+<!-- end of SVG.feTile.element -->]]>
+
+<!ENTITY % SVG.feTile.attlist "INCLUDE" >
+<![%SVG.feTile.attlist;[
+<!ATTLIST %SVG.feTile.qname;
+ %SVG.Core.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitiveWithIn.attrib;
+>
+<!-- end of SVG.feTile.attlist -->]]>
+
+<!-- feTurbulence: Filter Effect Turbulence Element .... -->
+
+<!ENTITY % SVG.feTurbulence.extra.content "" >
+
+<!ENTITY % SVG.feTurbulence.element "INCLUDE" >
+<![%SVG.feTurbulence.element;[
+<!ENTITY % SVG.feTurbulence.content
+ "( %SVG.animate.qname; | %SVG.set.qname;
+ %SVG.feTurbulence.extra.content; )*"
+>
+<!ELEMENT %SVG.feTurbulence.qname; %SVG.feTurbulence.content; >
+<!-- end of SVG.feTurbulence.element -->]]>
+
+<!ENTITY % SVG.feTurbulence.attlist "INCLUDE" >
+<![%SVG.feTurbulence.attlist;[
+<!ATTLIST %SVG.feTurbulence.qname;
+ %SVG.Core.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.FilterPrimitive.attrib;
+ baseFrequency %NumberOptionalNumber.datatype; #IMPLIED
+ numOctaves %Integer.datatype; #IMPLIED
+ seed %Number.datatype; #IMPLIED
+ stitchTiles ( stitch | noStitch ) 'noStitch'
+ type ( fractalNoise | turbulence ) 'turbulence'
+>
+<!-- end of SVG.feTurbulence.attlist -->]]>
+
+<!-- feDistantLight: Filter Effect Distant Light Element -->
+
+<!ENTITY % SVG.feDistantLight.extra.content "" >
+
+<!ENTITY % SVG.feDistantLight.element "INCLUDE" >
+<![%SVG.feDistantLight.element;[
+<!ENTITY % SVG.feDistantLight.content
+ "( %SVG.animate.qname; | %SVG.set.qname;
+ %SVG.feDistantLight.extra.content; )*"
+>
+<!ELEMENT %SVG.feDistantLight.qname; %SVG.feDistantLight.content; >
+<!-- end of SVG.feDistantLight.element -->]]>
+
+<!ENTITY % SVG.feDistantLight.attlist "INCLUDE" >
+<![%SVG.feDistantLight.attlist;[
+<!ATTLIST %SVG.feDistantLight.qname;
+ %SVG.Core.attrib;
+ azimuth %Number.datatype; #IMPLIED
+ elevation %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.feDistantLight.attlist -->]]>
+
+<!-- fePointLight: Filter Effect Point Light Element ... -->
+
+<!ENTITY % SVG.fePointLight.extra.content "" >
+
+<!ENTITY % SVG.fePointLight.element "INCLUDE" >
+<![%SVG.fePointLight.element;[
+<!ENTITY % SVG.fePointLight.content
+ "( %SVG.animate.qname; | %SVG.set.qname;
+ %SVG.fePointLight.extra.content; )*"
+>
+<!ELEMENT %SVG.fePointLight.qname; %SVG.fePointLight.content; >
+<!-- end of SVG.fePointLight.element -->]]>
+
+<!ENTITY % SVG.fePointLight.attlist "INCLUDE" >
+<![%SVG.fePointLight.attlist;[
+<!ATTLIST %SVG.fePointLight.qname;
+ %SVG.Core.attrib;
+ x %Number.datatype; #IMPLIED
+ y %Number.datatype; #IMPLIED
+ z %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.fePointLight.attlist -->]]>
+
+<!-- feSpotLight: Filter Effect Spot Light Element ..... -->
+
+<!ENTITY % SVG.feSpotLight.extra.content "" >
+
+<!ENTITY % SVG.feSpotLight.element "INCLUDE" >
+<![%SVG.feSpotLight.element;[
+<!ENTITY % SVG.feSpotLight.content
+ "( %SVG.animate.qname; | %SVG.set.qname; %SVG.feSpotLight.extra.content; )*"
+>
+<!ELEMENT %SVG.feSpotLight.qname; %SVG.feSpotLight.content; >
+<!-- end of SVG.feSpotLight.element -->]]>
+
+<!ENTITY % SVG.feSpotLight.attlist "INCLUDE" >
+<![%SVG.feSpotLight.attlist;[
+<!ATTLIST %SVG.feSpotLight.qname;
+ %SVG.Core.attrib;
+ x %Number.datatype; #IMPLIED
+ y %Number.datatype; #IMPLIED
+ z %Number.datatype; #IMPLIED
+ pointsAtX %Number.datatype; #IMPLIED
+ pointsAtY %Number.datatype; #IMPLIED
+ pointsAtZ %Number.datatype; #IMPLIED
+ specularExponent %Number.datatype; #IMPLIED
+ limitingConeAngle %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.feSpotLight.attlist -->]]>
+
+<!-- feFuncR: Filter Effect Function Red Element ....... -->
+
+<!ENTITY % SVG.feFuncR.extra.content "" >
+
+<!ENTITY % SVG.feFuncR.element "INCLUDE" >
+<![%SVG.feFuncR.element;[
+<!ENTITY % SVG.feFuncR.content
+ "( %SVG.animate.qname; | %SVG.set.qname; %SVG.feFuncR.extra.content; )*"
+>
+<!ELEMENT %SVG.feFuncR.qname; %SVG.feFuncR.content; >
+<!-- end of SVG.feFuncR.element -->]]>
+
+<!ENTITY % SVG.feFuncR.attlist "INCLUDE" >
+<![%SVG.feFuncR.attlist;[
+<!ATTLIST %SVG.feFuncR.qname;
+ %SVG.Core.attrib;
+ type ( identity | table | discrete | linear | gamma ) #REQUIRED
+ tableValues CDATA #IMPLIED
+ slope %Number.datatype; #IMPLIED
+ intercept %Number.datatype; #IMPLIED
+ amplitude %Number.datatype; #IMPLIED
+ exponent %Number.datatype; #IMPLIED
+ offset %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.feFuncR.attlist -->]]>
+
+<!-- feFuncG: Filter Effect Function Green Element ..... -->
+
+<!ENTITY % SVG.feFuncG.extra.content "" >
+
+<!ENTITY % SVG.feFuncG.element "INCLUDE" >
+<![%SVG.feFuncG.element;[
+<!ENTITY % SVG.feFuncG.content
+ "( %SVG.animate.qname; | %SVG.set.qname; %SVG.feFuncG.extra.content; )*"
+>
+<!ELEMENT %SVG.feFuncG.qname; %SVG.feFuncG.content; >
+<!-- end of SVG.feFuncG.element -->]]>
+
+<!ENTITY % SVG.feFuncG.attlist "INCLUDE" >
+<![%SVG.feFuncG.attlist;[
+<!ATTLIST %SVG.feFuncG.qname;
+ %SVG.Core.attrib;
+ type ( identity | table | discrete | linear | gamma ) #REQUIRED
+ tableValues CDATA #IMPLIED
+ slope %Number.datatype; #IMPLIED
+ intercept %Number.datatype; #IMPLIED
+ amplitude %Number.datatype; #IMPLIED
+ exponent %Number.datatype; #IMPLIED
+ offset %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.feFuncG.attlist -->]]>
+
+<!-- feFuncB: Filter Effect Function Blue Element ...... -->
+
+<!ENTITY % SVG.feFuncB.extra.content "" >
+
+<!ENTITY % SVG.feFuncB.element "INCLUDE" >
+<![%SVG.feFuncB.element;[
+<!ENTITY % SVG.feFuncB.content
+ "( %SVG.animate.qname; | %SVG.set.qname; %SVG.feFuncB.extra.content; )*"
+>
+<!ELEMENT %SVG.feFuncB.qname; %SVG.feFuncB.content; >
+<!-- end of SVG.feFuncB.element -->]]>
+
+<!ENTITY % SVG.feFuncB.attlist "INCLUDE" >
+<![%SVG.feFuncB.attlist;[
+<!ATTLIST %SVG.feFuncB.qname;
+ %SVG.Core.attrib;
+ type ( identity | table | discrete | linear | gamma ) #REQUIRED
+ tableValues CDATA #IMPLIED
+ slope %Number.datatype; #IMPLIED
+ intercept %Number.datatype; #IMPLIED
+ amplitude %Number.datatype; #IMPLIED
+ exponent %Number.datatype; #IMPLIED
+ offset %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.feFuncB.attlist -->]]>
+
+<!-- feFuncA: Filter Effect Function Alpha Element ..... -->
+
+<!ENTITY % SVG.feFuncA.extra.content "" >
+
+<!ENTITY % SVG.feFuncA.element "INCLUDE" >
+<![%SVG.feFuncA.element;[
+<!ENTITY % SVG.feFuncA.content
+ "( %SVG.animate.qname; | %SVG.set.qname; %SVG.feFuncA.extra.content; )*"
+>
+<!ELEMENT %SVG.feFuncA.qname; %SVG.feFuncA.content; >
+<!-- end of SVG.feFuncA.element -->]]>
+
+<!ENTITY % SVG.feFuncA.attlist "INCLUDE" >
+<![%SVG.feFuncA.attlist;[
+<!ATTLIST %SVG.feFuncA.qname;
+ %SVG.Core.attrib;
+ type ( identity | table | discrete | linear | gamma ) #REQUIRED
+ tableValues CDATA #IMPLIED
+ slope %Number.datatype; #IMPLIED
+ intercept %Number.datatype; #IMPLIED
+ amplitude %Number.datatype; #IMPLIED
+ exponent %Number.datatype; #IMPLIED
+ offset %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.feFuncA.attlist -->]]>
+
+<!-- end of svg-filter.mod -->
+]]>
+
+<!-- Cursor Module ............................................... -->
+<!ENTITY % svg-cursor.module "INCLUDE" >
+<![%svg-cursor.module;[
+<!ENTITY % svg-cursor.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Cursor//EN"
+ "svg-cursor.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Cursor Module ................................................. -->
+<!-- file: svg-cursor.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg12-flat.dtd 201394 2004-11-18 01:47:06Z deweese $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Cursor//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-cursor.mod"
+
+ ....................................................................... -->
+
+<!-- Cursor
+
+ cursor
+
+ This module declares markup to provide support for cursor.
+-->
+
+<!-- 'cursor' property/attribute value (e.g., 'crosshair', <uri>) -->
+<!ENTITY % CursorValue.datatype "CDATA" >
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.cursor.qname "cursor" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Conditional.attrib "" >
+<!ENTITY % SVG.XLinkRequired.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Cursor.class .................................. -->
+
+<!ENTITY % SVG.Cursor.extra.class "" >
+
+<!ENTITY % SVG.Cursor.class
+ "| %SVG.cursor.qname; %SVG.Cursor.extra.class;"
+>
+
+<!-- SVG.Cursor.attrib ................................. -->
+
+<!ENTITY % SVG.Cursor.extra.attrib "" >
+
+<!ENTITY % SVG.Cursor.attrib
+ "cursor %CursorValue.datatype; #IMPLIED
+ %SVG.Cursor.extra.attrib;"
+>
+
+<!-- cursor: Cursor Element ............................ -->
+
+<!ENTITY % SVG.cursor.extra.content "" >
+
+<!ENTITY % SVG.cursor.element "INCLUDE" >
+<![%SVG.cursor.element;[
+<!ENTITY % SVG.cursor.content
+ "( %SVG.Description.class; %SVG.cursor.extra.content; )*"
+>
+<!ELEMENT %SVG.cursor.qname; %SVG.cursor.content; >
+<!-- end of SVG.cursor.element -->]]>
+
+<!ENTITY % SVG.cursor.attlist "INCLUDE" >
+<![%SVG.cursor.attlist;[
+<!ATTLIST %SVG.cursor.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.XLinkRequired.attrib;
+ %SVG.External.attrib;
+ x %Coordinate.datatype; #IMPLIED
+ y %Coordinate.datatype; #IMPLIED
+>
+<!-- end of SVG.cursor.attlist -->]]>
+
+<!-- end of svg-cursor.mod -->
+]]>
+
+<!-- Hyperlinking Module ......................................... -->
+<!ENTITY % svg-hyperlink.module "INCLUDE" >
+<![%svg-hyperlink.module;[
+<!ENTITY % svg-hyperlink.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Hyperlinking//EN"
+ "svg-hyperlink.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Hyperlinking Module ........................................... -->
+<!-- file: svg-hyperlink.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg12-flat.dtd 201394 2004-11-18 01:47:06Z deweese $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Hyperlinking//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-hyperlink.mod"
+
+ ....................................................................... -->
+
+<!-- Hyperlinking
+
+ a
+
+ This module declares markup to provide support for hyper linking.
+-->
+
+<!-- link to this target -->
+<!ENTITY % LinkTarget.datatype "NMTOKEN" >
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.a.qname "a" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Conditional.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Viewport.attrib "" >
+<!ENTITY % SVG.Text.attrib "" >
+<!ENTITY % SVG.TextContent.attrib "" >
+<!ENTITY % SVG.Font.attrib "" >
+<!ENTITY % SVG.Paint.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Marker.attrib "" >
+<!ENTITY % SVG.Gradient.attrib "" >
+<!ENTITY % SVG.Clip.attrib "" >
+<!ENTITY % SVG.Mask.attrib "" >
+<!ENTITY % SVG.Filter.attrib "" >
+<!ENTITY % SVG.FilterColor.attrib "" >
+<!ENTITY % SVG.GraphicalEvents.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.XLinkReplace.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Hyperlink.class ............................... -->
+
+<!ENTITY % SVG.Hyperlink.extra.class "" >
+
+<!ENTITY % SVG.Hyperlink.class
+ "| %SVG.a.qname; %SVG.Hyperlink.extra.class;"
+>
+
+<!-- SVG.Presentation.attrib ........................... -->
+
+<!ENTITY % SVG.Presentation.extra.attrib "" >
+
+<!ENTITY % SVG.Presentation.attrib
+ "%SVG.Container.attrib;
+ %SVG.Viewport.attrib;
+ %SVG.Text.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Profile.attrib;
+ %SVG.Gradient.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.Cursor.attrib;
+ flood-color %SVGColor.datatype; #IMPLIED
+ flood-opacity %OpacityValue.datatype; #IMPLIED
+ lighting-color %SVGColor.datatype; #IMPLIED
+ %SVG.Presentation.extra.attrib;"
+>
+
+<!-- a: Anchor Element ................................. -->
+
+<!ENTITY % SVG.a.extra.content "" >
+
+<!ENTITY % SVG.a.element "INCLUDE" >
+<![%SVG.a.element;[
+<!ENTITY % SVG.a.content
+ "( #PCDATA | %SVG.Description.class; | %SVG.Animation.class;
+ %SVG.Structure.class; %SVG.Conditional.class; %SVG.Image.class;
+ %SVG.Style.class; %SVG.Shape.class; %SVG.Text.class; %SVG.Marker.class;
+ %SVG.Profile.class; %SVG.Gradient.class; %SVG.Pattern.class;
+ %SVG.Clip.class; %SVG.Mask.class; %SVG.Filter.class; %SVG.Cursor.class;
+ %SVG.Hyperlink.class; %SVG.View.class; %SVG.Script.class;
+ %SVG.Font.class; %SVG.a.extra.content; )*"
+>
+<!ELEMENT %SVG.a.qname; %SVG.a.content; >
+<!-- end of SVG.a.element -->]]>
+
+<!ENTITY % SVG.a.attlist "INCLUDE" >
+<![%SVG.a.attlist;[
+<!ATTLIST %SVG.a.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.XLinkReplace.attrib;
+ %SVG.External.attrib;
+ transform %TransformList.datatype; #IMPLIED
+ target %LinkTarget.datatype; #IMPLIED
+>
+<!-- end of SVG.a.attlist -->]]>
+
+<!-- end of svg-hyperlink.mod -->
+]]>
+
+<!-- View Module ................................................. -->
+<!ENTITY % svg-view.module "INCLUDE" >
+<![%svg-view.module;[
+<!ENTITY % svg-view.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 View//EN"
+ "svg-view.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 View Module ................................................... -->
+<!-- file: svg-view.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg12-flat.dtd 201394 2004-11-18 01:47:06Z deweese $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 View//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-view.mod"
+
+ ....................................................................... -->
+
+<!-- View
+
+ view
+
+ This module declares markup to provide support for view.
+-->
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.view.qname "view" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.View.class .................................... -->
+
+<!ENTITY % SVG.View.extra.class "" >
+
+<!ENTITY % SVG.View.class
+ "| %SVG.view.qname; %SVG.View.extra.class;"
+>
+
+<!-- view: View Element ................................ -->
+
+<!ENTITY % SVG.view.extra.content "" >
+
+<!ENTITY % SVG.view.element "INCLUDE" >
+<![%SVG.view.element;[
+<!ENTITY % SVG.view.content
+ "( %SVG.Description.class; %SVG.view.extra.content; )*"
+>
+<!ELEMENT %SVG.view.qname; %SVG.view.content; >
+<!-- end of SVG.view.element -->]]>
+
+<!ENTITY % SVG.view.attlist "INCLUDE" >
+<![%SVG.view.attlist;[
+<!ATTLIST %SVG.view.qname;
+ %SVG.Core.attrib;
+ %SVG.External.attrib;
+ viewBox %ViewBoxSpec.datatype; #IMPLIED
+ preserveAspectRatio %PreserveAspectRatioSpec.datatype; 'xMidYMid meet'
+ zoomAndPan ( disable | magnify ) 'magnify'
+ viewTarget CDATA #IMPLIED
+>
+<!-- end of SVG.view.attlist -->]]>
+
+<!-- end of svg-view.mod -->
+]]>
+
+<!-- Scripting Module ............................................ -->
+<!ENTITY % svg-script.module "INCLUDE" >
+<![%svg-script.module;[
+<!ENTITY % svg-script.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Scripting//EN"
+ "svg-script.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Scripting Module .............................................. -->
+<!-- file: svg-script.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg12-flat.dtd 201394 2004-11-18 01:47:06Z deweese $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Scripting//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-script.mod"
+
+ ....................................................................... -->
+
+<!-- Scripting
+
+ script
+
+ This module declares markup to provide support for scripting.
+-->
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.script.qname "script" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.XLink.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Script.class .................................. -->
+
+<!ENTITY % SVG.Script.extra.class "" >
+
+<!ENTITY % SVG.Script.class
+ "| %SVG.script.qname; %SVG.Script.extra.class;"
+>
+
+<!-- script: Script Element ............................ -->
+
+<!ENTITY % SVG.script.extra.content "" >
+
+<!ENTITY % SVG.script.element "INCLUDE" >
+<![%SVG.script.element;[
+<!ENTITY % SVG.script.content
+ "( #PCDATA %SVG.script.extra.content; )*"
+>
+<!ELEMENT %SVG.script.qname; %SVG.script.content; >
+<!-- end of SVG.script.element -->]]>
+
+<!ENTITY % SVG.script.attlist "INCLUDE" >
+<![%SVG.script.attlist;[
+<!ATTLIST %SVG.script.qname;
+ %SVG.Core.attrib;
+ %SVG.XLink.attrib;
+ %SVG.External.attrib;
+ type %ContentType.datatype; #REQUIRED
+>
+<!-- end of SVG.script.attlist -->]]>
+
+<!-- end of svg-script.mod -->
+]]>
+
+<!-- Animation Module ............................................ -->
+<!ENTITY % svg-animation.module "INCLUDE" >
+<![%svg-animation.module;[
+<!ENTITY % svg-animation.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Animation//EN"
+ "svg-animation.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Animation Module .............................................. -->
+<!-- file: svg-animation.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg12-flat.dtd 201394 2004-11-18 01:47:06Z deweese $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Animation//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-animation.mod"
+
+ ....................................................................... -->
+
+<!-- Animation
+
+ animate, set, animateMotion, animateColor, animateTransform, mpath
+
+ This module declares markup to provide support for animation.
+-->
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.animate.qname "animate" >
+<!ENTITY % SVG.set.qname "set" >
+<!ENTITY % SVG.animateMotion.qname "animateMotion" >
+<!ENTITY % SVG.animateColor.qname "animateColor" >
+<!ENTITY % SVG.animateTransform.qname "animateTransform" >
+<!ENTITY % SVG.mpath.qname "mpath" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Conditional.attrib "" >
+<!ENTITY % SVG.AnimationEvents.attrib "" >
+<!ENTITY % SVG.XLink.attrib "" >
+<!ENTITY % SVG.XLinkRequired.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Animation.class ............................... -->
+
+<!ENTITY % SVG.Animation.extra.class "" >
+
+<!ENTITY % SVG.Animation.class
+ "%SVG.animate.qname; | %SVG.set.qname; | %SVG.animateMotion.qname; |
+ %SVG.animateColor.qname; | %SVG.animateTransform.qname;
+ %SVG.Animation.extra.class;"
+>
+
+<!-- SVG.Animation.attrib .............................. -->
+
+<!ENTITY % SVG.Animation.extra.attrib "" >
+
+<!ENTITY % SVG.Animation.attrib
+ "%SVG.XLink.attrib;
+ %SVG.Animation.extra.attrib;"
+>
+
+<!-- SVG.AnimationAttribute.attrib ..................... -->
+
+<!ENTITY % SVG.AnimationAttribute.extra.attrib "" >
+
+<!ENTITY % SVG.AnimationAttribute.attrib
+ "attributeName CDATA #REQUIRED
+ attributeType CDATA #IMPLIED
+ %SVG.AnimationAttribute.extra.attrib;"
+>
+
+<!-- SVG.AnimationTiming.attrib ........................ -->
+
+<!ENTITY % SVG.AnimationTiming.extra.attrib "" >
+
+<!ENTITY % SVG.AnimationTiming.attrib
+ "begin CDATA #IMPLIED
+ dur CDATA #IMPLIED
+ end CDATA #IMPLIED
+ min CDATA #IMPLIED
+ max CDATA #IMPLIED
+ restart ( always | never | whenNotActive ) 'always'
+ repeatCount CDATA #IMPLIED
+ repeatDur CDATA #IMPLIED
+ fill ( remove | freeze ) 'remove'
+ %SVG.AnimationTiming.extra.attrib;"
+>
+
+<!-- SVG.AnimationValue.attrib ......................... -->
+
+<!ENTITY % SVG.AnimationValue.extra.attrib "" >
+
+<!ENTITY % SVG.AnimationValue.attrib
+ "calcMode ( discrete | linear | paced | spline ) 'linear'
+ values CDATA #IMPLIED
+ keyTimes CDATA #IMPLIED
+ keySplines CDATA #IMPLIED
+ from CDATA #IMPLIED
+ to CDATA #IMPLIED
+ by CDATA #IMPLIED
+ %SVG.AnimationValue.extra.attrib;"
+>
+
+<!-- SVG.AnimationAddtion.attrib ....................... -->
+
+<!ENTITY % SVG.AnimationAddtion.extra.attrib "" >
+
+<!ENTITY % SVG.AnimationAddtion.attrib
+ "additive ( replace | sum ) 'replace'
+ accumulate ( none | sum ) 'none'
+ %SVG.AnimationAddtion.extra.attrib;"
+>
+
+<!-- animate: Animate Element .......................... -->
+
+<!ENTITY % SVG.animate.extra.content "" >
+
+<!ENTITY % SVG.animate.element "INCLUDE" >
+<![%SVG.animate.element;[
+<!ENTITY % SVG.animate.content
+ "( %SVG.Description.class; %SVG.animate.extra.content; )*"
+>
+<!ELEMENT %SVG.animate.qname; %SVG.animate.content; >
+<!-- end of SVG.animate.element -->]]>
+
+<!ENTITY % SVG.animate.attlist "INCLUDE" >
+<![%SVG.animate.attlist;[
+<!ATTLIST %SVG.animate.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.AnimationEvents.attrib;
+ %SVG.External.attrib;
+ %SVG.Animation.attrib;
+ %SVG.AnimationAttribute.attrib;
+ %SVG.AnimationTiming.attrib;
+ %SVG.AnimationValue.attrib;
+ %SVG.AnimationAddtion.attrib;
+>
+<!-- end of SVG.animate.attlist -->]]>
+
+<!-- set: Set Element .................................. -->
+
+<!ENTITY % SVG.set.extra.content "" >
+
+<!ENTITY % SVG.set.element "INCLUDE" >
+<![%SVG.set.element;[
+<!ENTITY % SVG.set.content
+ "( %SVG.Description.class; %SVG.set.extra.content; )*"
+>
+<!ELEMENT %SVG.set.qname; %SVG.set.content; >
+<!-- end of SVG.set.element -->]]>
+
+<!ENTITY % SVG.set.attlist "INCLUDE" >
+<![%SVG.set.attlist;[
+<!ATTLIST %SVG.set.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.AnimationEvents.attrib;
+ %SVG.External.attrib;
+ %SVG.Animation.attrib;
+ %SVG.AnimationAttribute.attrib;
+ %SVG.AnimationTiming.attrib;
+ to CDATA #IMPLIED
+>
+<!-- end of SVG.set.attlist -->]]>
+
+<!-- animateMotion: Animate Motion Element ............. -->
+
+<!ENTITY % SVG.animateMotion.extra.content "" >
+
+<!ENTITY % SVG.animateMotion.element "INCLUDE" >
+<![%SVG.animateMotion.element;[
+<!ENTITY % SVG.animateMotion.content
+ "(( %SVG.Description.class; )*, %SVG.mpath.qname;?
+ %SVG.animateMotion.extra.content; )"
+>
+<!ELEMENT %SVG.animateMotion.qname; %SVG.animateMotion.content; >
+<!-- end of SVG.animateMotion.element -->]]>
+
+<!ENTITY % SVG.animateMotion.attlist "INCLUDE" >
+<![%SVG.animateMotion.attlist;[
+<!ATTLIST %SVG.animateMotion.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.AnimationEvents.attrib;
+ %SVG.External.attrib;
+ %SVG.Animation.attrib;
+ %SVG.AnimationTiming.attrib;
+ %SVG.AnimationAddtion.attrib;
+ calcMode ( discrete | linear | paced | spline ) 'paced'
+ values CDATA #IMPLIED
+ keyTimes CDATA #IMPLIED
+ keySplines CDATA #IMPLIED
+ from CDATA #IMPLIED
+ to CDATA #IMPLIED
+ by CDATA #IMPLIED
+ path CDATA #IMPLIED
+ keyPoints CDATA #IMPLIED
+ rotate CDATA #IMPLIED
+ origin CDATA #IMPLIED
+>
+<!-- end of SVG.animateMotion.attlist -->]]>
+
+<!-- animateColor: Animate Color Element ............... -->
+
+<!ENTITY % SVG.animateColor.extra.content "" >
+
+<!ENTITY % SVG.animateColor.element "INCLUDE" >
+<![%SVG.animateColor.element;[
+<!ENTITY % SVG.animateColor.content
+ "( %SVG.Description.class; %SVG.animateColor.extra.content; )*"
+>
+<!ELEMENT %SVG.animateColor.qname; %SVG.animateColor.content; >
+<!-- end of SVG.animateColor.element -->]]>
+
+<!ENTITY % SVG.animateColor.attlist "INCLUDE" >
+<![%SVG.animateColor.attlist;[
+<!ATTLIST %SVG.animateColor.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.AnimationEvents.attrib;
+ %SVG.External.attrib;
+ %SVG.Animation.attrib;
+ %SVG.AnimationAttribute.attrib;
+ %SVG.AnimationTiming.attrib;
+ %SVG.AnimationValue.attrib;
+ %SVG.AnimationAddtion.attrib;
+>
+<!-- end of SVG.animateColor.attlist -->]]>
+
+<!-- animateTransform: Animate Transform Element ....... -->
+
+<!ENTITY % SVG.animateTransform.extra.content "" >
+
+<!ENTITY % SVG.animateTransform.element "INCLUDE" >
+<![%SVG.animateTransform.element;[
+<!ENTITY % SVG.animateTransform.content
+ "( %SVG.Description.class; %SVG.animateTransform.extra.content; )*"
+>
+<!ELEMENT %SVG.animateTransform.qname; %SVG.animateTransform.content; >
+<!-- end of SVG.animateTransform.element -->]]>
+
+<!ENTITY % SVG.animateTransform.attlist "INCLUDE" >
+<![%SVG.animateTransform.attlist;[
+<!ATTLIST %SVG.animateTransform.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.AnimationEvents.attrib;
+ %SVG.External.attrib;
+ %SVG.Animation.attrib;
+ %SVG.AnimationAttribute.attrib;
+ %SVG.AnimationTiming.attrib;
+ %SVG.AnimationValue.attrib;
+ %SVG.AnimationAddtion.attrib;
+ type ( translate | scale | rotate | skewX | skewY ) 'translate'
+>
+<!-- end of SVG.animateTransform.attlist -->]]>
+
+<!-- mpath: Motion Path Element ........................ -->
+
+<!ENTITY % SVG.mpath.extra.content "" >
+
+<!ENTITY % SVG.mpath.element "INCLUDE" >
+<![%SVG.mpath.element;[
+<!ENTITY % SVG.mpath.content
+ "( %SVG.Description.class; %SVG.mpath.extra.content; )*"
+>
+<!ELEMENT %SVG.mpath.qname; %SVG.mpath.content; >
+<!-- end of SVG.mpath.element -->]]>
+
+<!ENTITY % SVG.mpath.attlist "INCLUDE" >
+<![%SVG.mpath.attlist;[
+<!ATTLIST %SVG.mpath.qname;
+ %SVG.Core.attrib;
+ %SVG.XLinkRequired.attrib;
+ %SVG.External.attrib;
+>
+<!-- end of SVG.mpath.attlist -->]]>
+
+<!-- end of svg-animation.mod -->
+]]>
+
+<!-- Font Module ................................................. -->
+<!ENTITY % svg-font.module "INCLUDE" >
+<![%svg-font.module;[
+<!ENTITY % svg-font.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Font//EN"
+ "svg-font.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Font Module ................................................... -->
+<!-- file: svg-font.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg12-flat.dtd 201394 2004-11-18 01:47:06Z deweese $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Font//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-font.mod"
+
+ ....................................................................... -->
+
+<!-- Font
+
+ font, font-face, glyph, missing-glyph, hkern, vkern, font-face-src,
+ font-face-uri, font-face-format, font-face-name, definition-src
+
+ This module declares markup to provide support for template.
+-->
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.font.qname "font" >
+<!ENTITY % SVG.font-face.qname "font-face" >
+<!ENTITY % SVG.glyph.qname "glyph" >
+<!ENTITY % SVG.missing-glyph.qname "missing-glyph" >
+<!ENTITY % SVG.hkern.qname "hkern" >
+<!ENTITY % SVG.vkern.qname "vkern" >
+<!ENTITY % SVG.font-face-src.qname "font-face-src" >
+<!ENTITY % SVG.font-face-uri.qname "font-face-uri" >
+<!ENTITY % SVG.font-face-format.qname "font-face-format" >
+<!ENTITY % SVG.font-face-name.qname "font-face-name" >
+<!ENTITY % SVG.definition-src.qname "definition-src" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Container.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Viewport.attrib "" >
+<!ENTITY % SVG.Text.attrib "" >
+<!ENTITY % SVG.TextContent.attrib "" >
+<!ENTITY % SVG.Font.attrib "" >
+<!ENTITY % SVG.Paint.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Marker.attrib "" >
+<!ENTITY % SVG.Profile.attrib "" >
+<!ENTITY % SVG.Gradient.attrib "" >
+<!ENTITY % SVG.Clip.attrib "" >
+<!ENTITY % SVG.Mask.attrib "" >
+<!ENTITY % SVG.Filter.attrib "" >
+<!ENTITY % SVG.FilterColor.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.XLinkRequired.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Font.class .................................... -->
+
+<!ENTITY % SVG.Font.extra.class "" >
+
+<!ENTITY % SVG.Font.class
+ "| %SVG.font.qname; | %SVG.font-face.qname; %SVG.Font.extra.class;"
+>
+
+<!-- SVG.Presentation.attrib ........................... -->
+
+<!ENTITY % SVG.Presentation.extra.attrib "" >
+
+<!ENTITY % SVG.Presentation.attrib
+ "%SVG.Container.attrib;
+ %SVG.Viewport.attrib;
+ %SVG.Text.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Profile.attrib;
+ %SVG.Gradient.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.Cursor.attrib;
+ flood-color %SVGColor.datatype; #IMPLIED
+ flood-opacity %OpacityValue.datatype; #IMPLIED
+ lighting-color %SVGColor.datatype; #IMPLIED
+ %SVG.Presentation.extra.attrib;"
+>
+
+<!-- font: Font Element ................................ -->
+
+<!ENTITY % SVG.font.extra.content "" >
+
+<!ENTITY % SVG.font.element "INCLUDE" >
+<![%SVG.font.element;[
+<!ENTITY % SVG.font.content
+ "(( %SVG.Description.class; )*, %SVG.font-face.qname;,
+ %SVG.missing-glyph.qname;, ( %SVG.glyph.qname; | %SVG.hkern.qname;
+ | %SVG.vkern.qname; %SVG.font.extra.content; )*)"
+>
+<!ELEMENT %SVG.font.qname; %SVG.font.content; >
+<!-- end of SVG.font.element -->]]>
+
+<!ENTITY % SVG.font.attlist "INCLUDE" >
+<![%SVG.font.attlist;[
+<!ATTLIST %SVG.font.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.External.attrib;
+ horiz-origin-x %Number.datatype; #IMPLIED
+ horiz-origin-y %Number.datatype; #IMPLIED
+ horiz-adv-x %Number.datatype; #REQUIRED
+ vert-origin-x %Number.datatype; #IMPLIED
+ vert-origin-y %Number.datatype; #IMPLIED
+ vert-adv-y %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.font.attlist -->]]>
+
+<!-- font-face: Font Face Element ...................... -->
+
+<!ENTITY % SVG.font-face.extra.content "" >
+
+<!ENTITY % SVG.font-face.element "INCLUDE" >
+<![%SVG.font-face.element;[
+<!ENTITY % SVG.font-face.content
+ "(( %SVG.Description.class; )*, %SVG.font-face-src.qname;?,
+ %SVG.definition-src.qname;? %SVG.font-face.extra.content; )"
+>
+<!ELEMENT %SVG.font-face.qname; %SVG.font-face.content; >
+<!-- end of SVG.font-face.element -->]]>
+
+<!ENTITY % SVG.font-face.attlist "INCLUDE" >
+<![%SVG.font-face.attlist;[
+<!ATTLIST %SVG.font-face.qname;
+ %SVG.Core.attrib;
+ font-family CDATA #IMPLIED
+ font-style CDATA #IMPLIED
+ font-variant CDATA #IMPLIED
+ font-weight CDATA #IMPLIED
+ font-stretch CDATA #IMPLIED
+ font-size CDATA #IMPLIED
+ unicode-range CDATA #IMPLIED
+ units-per-em %Number.datatype; #IMPLIED
+ panose-1 CDATA #IMPLIED
+ stemv %Number.datatype; #IMPLIED
+ stemh %Number.datatype; #IMPLIED
+ slope %Number.datatype; #IMPLIED
+ cap-height %Number.datatype; #IMPLIED
+ x-height %Number.datatype; #IMPLIED
+ accent-height %Number.datatype; #IMPLIED
+ ascent %Number.datatype; #IMPLIED
+ descent %Number.datatype; #IMPLIED
+ widths CDATA #IMPLIED
+ bbox CDATA #IMPLIED
+ ideographic %Number.datatype; #IMPLIED
+ alphabetic %Number.datatype; #IMPLIED
+ mathematical %Number.datatype; #IMPLIED
+ hanging %Number.datatype; #IMPLIED
+ v-ideographic %Number.datatype; #IMPLIED
+ v-alphabetic %Number.datatype; #IMPLIED
+ v-mathematical %Number.datatype; #IMPLIED
+ v-hanging %Number.datatype; #IMPLIED
+ underline-position %Number.datatype; #IMPLIED
+ underline-thickness %Number.datatype; #IMPLIED
+ strikethrough-position %Number.datatype; #IMPLIED
+ strikethrough-thickness %Number.datatype; #IMPLIED
+ overline-position %Number.datatype; #IMPLIED
+ overline-thickness %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.font-face.attlist -->]]>
+
+<!-- glyph: Glyph Element .............................. -->
+
+<!ENTITY % SVG.glyph.extra.content "" >
+
+<!ENTITY % SVG.glyph.element "INCLUDE" >
+<![%SVG.glyph.element;[
+<!ENTITY % SVG.glyph.content
+ "( %SVG.Description.class; | %SVG.Animation.class; %SVG.Structure.class;
+ %SVG.Conditional.class; %SVG.Image.class; %SVG.Style.class;
+ %SVG.Shape.class; %SVG.Text.class; %SVG.Marker.class; %SVG.Profile.class;
+ %SVG.Gradient.class; %SVG.Pattern.class; %SVG.Clip.class;
+ %SVG.Mask.class; %SVG.Filter.class; %SVG.Cursor.class;
+ %SVG.Hyperlink.class; %SVG.View.class; %SVG.Script.class;
+ %SVG.Font.class; %SVG.glyph.extra.content; )*"
+>
+<!ELEMENT %SVG.glyph.qname; %SVG.glyph.content; >
+<!-- end of SVG.glyph.element -->]]>
+
+<!ENTITY % SVG.glyph.attlist "INCLUDE" >
+<![%SVG.glyph.attlist;[
+<!ATTLIST %SVG.glyph.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ unicode CDATA #IMPLIED
+ glyph-name CDATA #IMPLIED
+ d %PathData.datatype; #IMPLIED
+ orientation CDATA #IMPLIED
+ arabic-form CDATA #IMPLIED
+ lang %LanguageCodes.datatype; #IMPLIED
+ horiz-adv-x %Number.datatype; #IMPLIED
+ vert-origin-x %Number.datatype; #IMPLIED
+ vert-origin-y %Number.datatype; #IMPLIED
+ vert-adv-y %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.glyph.attlist -->]]>
+
+<!-- missing-glyph: Missing Glyph Element .............. -->
+
+<!ENTITY % SVG.missing-glyph.extra.content "" >
+
+<!ENTITY % SVG.missing-glyph.element "INCLUDE" >
+<![%SVG.missing-glyph.element;[
+<!ENTITY % SVG.missing-glyph.content
+ "( %SVG.Description.class; | %SVG.Animation.class; %SVG.Structure.class;
+ %SVG.Conditional.class; %SVG.Image.class; %SVG.Style.class;
+ %SVG.Shape.class; %SVG.Text.class; %SVG.Marker.class; %SVG.Profile.class;
+ %SVG.Gradient.class; %SVG.Pattern.class; %SVG.Clip.class;
+ %SVG.Mask.class; %SVG.Filter.class; %SVG.Cursor.class;
+ %SVG.Hyperlink.class; %SVG.View.class; %SVG.Script.class;
+ %SVG.Font.class; %SVG.missing-glyph.extra.content; )*"
+>
+<!ELEMENT %SVG.missing-glyph.qname; %SVG.missing-glyph.content; >
+<!-- end of SVG.missing-glyph.element -->]]>
+
+<!ENTITY % SVG.missing-glyph.attlist "INCLUDE" >
+<![%SVG.missing-glyph.attlist;[
+<!ATTLIST %SVG.missing-glyph.qname;
+ %SVG.Core.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ d %PathData.datatype; #IMPLIED
+ horiz-adv-x %Number.datatype; #IMPLIED
+ vert-origin-x %Number.datatype; #IMPLIED
+ vert-origin-y %Number.datatype; #IMPLIED
+ vert-adv-y %Number.datatype; #IMPLIED
+>
+<!-- end of SVG.missing-glyph.attlist -->]]>
+
+<!-- hkern: Horizontal Kerning Element ................. -->
+
+<!ENTITY % SVG.hkern.element "INCLUDE" >
+<![%SVG.hkern.element;[
+<!ENTITY % SVG.hkern.content "EMPTY" >
+<!ELEMENT %SVG.hkern.qname; %SVG.hkern.content; >
+<!-- end of SVG.hkern.element -->]]>
+
+<!ENTITY % SVG.hkern.attlist "INCLUDE" >
+<![%SVG.hkern.attlist;[
+<!ATTLIST %SVG.hkern.qname;
+ %SVG.Core.attrib;
+ u1 CDATA #IMPLIED
+ g1 CDATA #IMPLIED
+ u2 CDATA #IMPLIED
+ g2 CDATA #IMPLIED
+ k %Number.datatype; #REQUIRED
+>
+<!-- end of SVG.hkern.attlist -->]]>
+
+<!-- vkern: Vertical Kerning Element ................... -->
+
+<!ENTITY % SVG.vkern.element "INCLUDE" >
+<![%SVG.vkern.element;[
+<!ENTITY % SVG.vkern.content "EMPTY" >
+<!ELEMENT %SVG.vkern.qname; %SVG.vkern.content; >
+<!-- end of SVG.vkern.element -->]]>
+
+<!ENTITY % SVG.vkern.attlist "INCLUDE" >
+<![%SVG.vkern.attlist;[
+<!ATTLIST %SVG.vkern.qname;
+ %SVG.Core.attrib;
+ u1 CDATA #IMPLIED
+ g1 CDATA #IMPLIED
+ u2 CDATA #IMPLIED
+ g2 CDATA #IMPLIED
+ k %Number.datatype; #REQUIRED
+>
+<!-- end of SVG.vkern.attlist -->]]>
+
+<!-- font-face-src: Font Face Source Element ........... -->
+
+<!ENTITY % SVG.font-face-src.extra.content "" >
+
+<!ENTITY % SVG.font-face-src.element "INCLUDE" >
+<![%SVG.font-face-src.element;[
+<!ENTITY % SVG.font-face-src.content
+ "( %SVG.font-face-uri.qname; | %SVG.font-face-name.qname;
+ %SVG.font-face-src.extra.content; )+"
+>
+<!ELEMENT %SVG.font-face-src.qname; %SVG.font-face-src.content; >
+<!-- end of SVG.font-face-src.element -->]]>
+
+<!ENTITY % SVG.font-face-src.attlist "INCLUDE" >
+<![%SVG.font-face-src.attlist;[
+<!ATTLIST %SVG.font-face-src.qname;
+ %SVG.Core.attrib;
+>
+<!-- end of SVG.font-face-src.attlist -->]]>
+
+<!-- font-face-uri: Font Face URI Element .............. -->
+
+<!ENTITY % SVG.font-face-uri.extra.content "" >
+
+<!ENTITY % SVG.font-face-uri.element "INCLUDE" >
+<![%SVG.font-face-uri.element;[
+<!ENTITY % SVG.font-face-uri.content
+ "( %SVG.font-face-format.qname; %SVG.font-face-uri.extra.content; )*"
+>
+<!ELEMENT %SVG.font-face-uri.qname; %SVG.font-face-uri.content; >
+<!-- end of SVG.font-face-uri.element -->]]>
+
+<!ENTITY % SVG.font-face-uri.attlist "INCLUDE" >
+<![%SVG.font-face-uri.attlist;[
+<!ATTLIST %SVG.font-face-uri.qname;
+ %SVG.Core.attrib;
+ %SVG.XLinkRequired.attrib;
+>
+<!-- end of SVG.font-face-uri.attlist -->]]>
+
+<!-- font-face-format: Font Face Format Element ........ -->
+
+<!ENTITY % SVG.font-face-format.element "INCLUDE" >
+<![%SVG.font-face-format.element;[
+<!ENTITY % SVG.font-face-format.content "EMPTY" >
+<!ELEMENT %SVG.font-face-format.qname; %SVG.font-face-format.content; >
+<!-- end of SVG.font-face-format.element -->]]>
+
+<!ENTITY % SVG.font-face-format.attlist "INCLUDE" >
+<![%SVG.font-face-format.attlist;[
+<!ATTLIST %SVG.font-face-format.qname;
+ %SVG.Core.attrib;
+ string CDATA #IMPLIED
+>
+<!-- end of SVG.font-face-format.attlist -->]]>
+
+<!-- font-face-name: Font Face Name Element ............ -->
+
+<!ENTITY % SVG.font-face-name.element "INCLUDE" >
+<![%SVG.font-face-name.element;[
+<!ENTITY % SVG.font-face-name.content "EMPTY" >
+<!ELEMENT %SVG.font-face-name.qname; %SVG.font-face-name.content; >
+<!-- end of SVG.font-face-name.element -->]]>
+
+<!ENTITY % SVG.font-face-name.attlist "INCLUDE" >
+<![%SVG.font-face-name.attlist;[
+<!ATTLIST %SVG.font-face-name.qname;
+ %SVG.Core.attrib;
+ name CDATA #IMPLIED
+>
+<!-- end of SVG.font-face-name.attlist -->]]>
+
+<!-- definition-src: Definition Source Element ......... -->
+
+<!ENTITY % SVG.definition-src.element "INCLUDE" >
+<![%SVG.definition-src.element;[
+<!ENTITY % SVG.definition-src.content "EMPTY" >
+<!ELEMENT %SVG.definition-src.qname; %SVG.definition-src.content; >
+<!-- end of SVG.definition-src.element -->]]>
+
+<!ENTITY % SVG.definition-src.attlist "INCLUDE" >
+<![%SVG.definition-src.attlist;[
+<!ATTLIST %SVG.definition-src.qname;
+ %SVG.Core.attrib;
+ %SVG.XLinkRequired.attrib;
+>
+<!-- end of SVG.definition-src.attlist -->]]>
+
+<!-- end of svg-font.mod -->
+]]>
+
+<!-- Extensibility Module ........................................ -->
+<!ENTITY % svg-extensibility.module "INCLUDE" >
+<![%svg-extensibility.module;[
+<!ENTITY % svg-extensibility.mod
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Extensibility//EN"
+ "svg-extensibility.mod" >
+<!-- ....................................................................... -->
+<!-- SVG 1.1 Extensibility Module .......................................... -->
+<!-- file: svg-extensibility.mod
+
+ This is SVG, a language for describing two-dimensional graphics in XML.
+ Copyright 2001, 2002 W3C (MIT, INRIA, Keio), All Rights Reserved.
+ Revision: $Id: svg12-flat.dtd 201394 2004-11-18 01:47:06Z deweese $
+
+ This DTD module is identified by the PUBLIC and SYSTEM identifiers:
+
+ PUBLIC "-//W3C//ELEMENTS SVG 1.1 Extensibility//EN"
+ SYSTEM "http://www.w3.org/Graphics/SVG/1.1/DTD/svg-extensibility.mod"
+
+ ....................................................................... -->
+
+<!-- Extensibility
+
+ foreignObject
+
+ This module declares markup to provide support for extensibility.
+-->
+
+<!-- Qualified Names (Default) ......................... -->
+
+<!ENTITY % SVG.foreignObject.qname "foreignObject" >
+
+<!-- Attribute Collections (Default) ................... -->
+
+<!ENTITY % SVG.Core.attrib "" >
+<!ENTITY % SVG.Conditional.attrib "" >
+<!ENTITY % SVG.Style.attrib "" >
+<!ENTITY % SVG.Viewport.attrib "" >
+<!ENTITY % SVG.Text.attrib "" >
+<!ENTITY % SVG.TextContent.attrib "" >
+<!ENTITY % SVG.Font.attrib "" >
+<!ENTITY % SVG.Paint.attrib "" >
+<!ENTITY % SVG.Color.attrib "" >
+<!ENTITY % SVG.Opacity.attrib "" >
+<!ENTITY % SVG.Graphics.attrib "" >
+<!ENTITY % SVG.Marker.attrib "" >
+<!ENTITY % SVG.Gradient.attrib "" >
+<!ENTITY % SVG.Clip.attrib "" >
+<!ENTITY % SVG.Mask.attrib "" >
+<!ENTITY % SVG.Filter.attrib "" >
+<!ENTITY % SVG.FilterColor.attrib "" >
+<!ENTITY % SVG.GraphicalEvents.attrib "" >
+<!ENTITY % SVG.Cursor.attrib "" >
+<!ENTITY % SVG.External.attrib "" >
+
+<!-- SVG.Extensibility.class ........................... -->
+
+<!ENTITY % SVG.Extensibility.extra.class "" >
+
+<!ENTITY % SVG.Extensibility.class
+ "| %SVG.foreignObject.qname; %SVG.Extensibility.extra.class;"
+>
+
+<!-- SVG.Presentation.attrib ........................... -->
+
+<!ENTITY % SVG.Presentation.extra.attrib "" >
+
+<!ENTITY % SVG.Presentation.attrib
+ "%SVG.Container.attrib;
+ %SVG.Viewport.attrib;
+ %SVG.Text.attrib;
+ %SVG.TextContent.attrib;
+ %SVG.Font.attrib;
+ %SVG.Paint.attrib;
+ %SVG.Color.attrib;
+ %SVG.Opacity.attrib;
+ %SVG.Graphics.attrib;
+ %SVG.Marker.attrib;
+ %SVG.Profile.attrib;
+ %SVG.Gradient.attrib;
+ %SVG.Clip.attrib;
+ %SVG.Mask.attrib;
+ %SVG.Filter.attrib;
+ %SVG.FilterColor.attrib;
+ %SVG.Cursor.attrib;
+ flood-color %SVGColor.datatype; #IMPLIED
+ flood-opacity %OpacityValue.datatype; #IMPLIED
+ lighting-color %SVGColor.datatype; #IMPLIED
+ %SVG.Presentation.extra.attrib;"
+>
+
+<!-- foreignObject: Foreign Object Element ............. -->
+
+<!ENTITY % SVG.foreignObject.extra.content "" >
+
+<!ENTITY % SVG.foreignObject.element "INCLUDE" >
+<![%SVG.foreignObject.element;[
+<!ENTITY % SVG.foreignObject.content
+ "( #PCDATA %SVG.foreignObject.extra.content; )*"
+>
+<!ELEMENT %SVG.foreignObject.qname; %SVG.foreignObject.content; >
+<!-- end of SVG.foreignObject.element -->]]>
+
+<!ENTITY % SVG.foreignObject.attlist "INCLUDE" >
+<![%SVG.foreignObject.attlist;[
+<!ATTLIST %SVG.foreignObject.qname;
+ %SVG.Core.attrib;
+ %SVG.Conditional.attrib;
+ %SVG.Style.attrib;
+ %SVG.Presentation.attrib;
+ %SVG.GraphicalEvents.attrib;
+ %SVG.External.attrib;
+ x %Coordinate.datatype; #IMPLIED
+ y %Coordinate.datatype; #IMPLIED
+ width %Length.datatype; #REQUIRED
+ height %Length.datatype; #REQUIRED
+ transform %TransformList.datatype; #IMPLIED
+>
+<!-- end of SVG.foreignObject.attlist -->]]>
+
+<!-- end of svg-extensibility.mod -->
+]]>
+
+<!-- end of SVG 1.1 DTD .................................................... -->
+<!-- ....................................................................... -->
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diff --git a/org/apache/batik/ext/awt/image/spi/URLRegistryEntry.class b/org/apache/batik/ext/awt/image/spi/URLRegistryEntry.class
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diff --git a/org/apache/batik/ext/awt/image/spi/resources/Messages.properties b/org/apache/batik/ext/awt/image/spi/resources/Messages.properties
new file mode 100644
index 0000000..014d1f3
--- /dev/null
+++ b/org/apache/batik/ext/awt/image/spi/resources/Messages.properties
@@ -0,0 +1,34 @@
+# -----------------------------------------------------------------------------
+#
+# Licensed to the Apache Software Foundation (ASF) under one or more
+# contributor license agreements. See the NOTICE file distributed with
+# this work for additional information regarding copyright ownership.
+# The ASF licenses this file to You under the Apache License, Version 2.0
+# (the "License"); you may not use this file except in compliance with
+# the License. You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+# $Id: Messages.properties 475477 2006-11-15 22:44:28Z cam $
+# -----------------------------------------------------------------------------
+
+stream.unreadable = \
+Stream data is corrupt or unsupported format
+
+stream.format.unreadable = \
+{0} stream is corrupt or unsupported variant
+
+url.unreachable = \
+Unable to access URL
+
+url.uninterpretable = \
+URL data in unsupported format or corrupt
+
+url.format.unreadable =\
+{0} URL is corrupt or unsupported variant
diff --git a/org/apache/batik/ext/swing/AffineTransformTracker.class b/org/apache/batik/ext/swing/AffineTransformTracker.class
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diff --git a/org/apache/batik/ext/swing/Resources.class b/org/apache/batik/ext/swing/Resources.class
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diff --git a/org/apache/batik/ext/swing/resources/Messages.properties b/org/apache/batik/ext/swing/resources/Messages.properties
new file mode 100644
index 0000000..ef1c2be
--- /dev/null
+++ b/org/apache/batik/ext/swing/resources/Messages.properties
@@ -0,0 +1,64 @@
+# -----------------------------------------------------------------------------
+#
+# Licensed to the Apache Software Foundation (ASF) under one or more
+# contributor license agreements. See the NOTICE file distributed with
+# this work for additional information regarding copyright ownership.
+# The ASF licenses this file to You under the Apache License, Version 2.0
+# (the "License"); you may not use this file except in compliance with
+# the License. You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+# $Id: Messages.properties 475477 2006-11-15 22:44:28Z cam $
+# -----------------------------------------------------------------------------
+
+JAffineTransformChooser.label.angle = Angle
+
+JAffineTransformChooser.label.degree = �
+
+JAffineTransformChooser.label.percent = %
+
+JAffineTransformChooser.label.rotate = Rotate
+
+JAffineTransformChooser.label.scale = Scale
+
+JAffineTransformChooser.label.rx = rx
+
+JAffineTransformChooser.label.ry = ry
+
+JAffineTransformChooser.label.sx = sx
+
+JAffineTransformChooser.label.sy = sy
+
+JAffineTransformChooser.label.translate = Translate
+
+JAffineTransformChooser.label.tx = tx
+
+JAffineTransformChooser.label.ty = ty
+
+JAffineTransformChooser.label.ok = OK
+
+JAffineTransformChooser.label.cancel = Cancel
+
+JAffineTransformChooser.label.reset = Reset
+
+#
+# JAffineTransformChooser config
+#
+
+JAffineTransformChooser.config.text.field.width = 7
+
+JAffineTransformChooser.config.top.pad = 5
+
+JAffineTransformChooser.config.left.pad = 10
+
+JAffineTransformChooser.config.bottom.pad = 5
+
+JAffineTransformChooser.config.right.pad = 10
+
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diff --git a/org/apache/batik/parser/resources/Messages.properties b/org/apache/batik/parser/resources/Messages.properties
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index 0000000..bd95089
--- /dev/null
+++ b/org/apache/batik/parser/resources/Messages.properties
@@ -0,0 +1,37 @@
+# -----------------------------------------------------------------------------
+#
+# Licensed to the Apache Software Foundation (ASF) under one or more
+# contributor license agreements. See the NOTICE file distributed with
+# this work for additional information regarding copyright ownership.
+# The ASF licenses this file to You under the Apache License, Version 2.0
+# (the "License"); you may not use this file except in compliance with
+# the License. You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+# The messages for the micro-parsers API.
+#
+# $Id: Messages.properties 475477 2006-11-15 22:44:28Z cam $
+# -----------------------------------------------------------------------------
+
+character.expected = \
+The character ''{0}'' was expected. The current character code is: {1}.
+
+end.of.stream = \
+Unexpected end of stream.
+
+character.unexpected = \
+Unexpected character (code: {0}).
+
+float.format = \
+Wrong float: ''{0}''.
+
+end.of.stream.expected = \
+End of stream expected. Instead, a character with code {0} has been \
+encountered.
diff --git a/org/apache/batik/parser/style/resources/Messages.properties b/org/apache/batik/parser/style/resources/Messages.properties
new file mode 100644
index 0000000..4dcb546
--- /dev/null
+++ b/org/apache/batik/parser/style/resources/Messages.properties
@@ -0,0 +1,51 @@
+# -----------------------------------------------------------------------------
+#
+# Licensed to the Apache Software Foundation (ASF) under one or more
+# contributor license agreements. See the NOTICE file distributed with
+# this work for additional information regarding copyright ownership.
+# The ASF licenses this file to You under the Apache License, Version 2.0
+# (the "License"); you may not use this file except in compliance with
+# the License. You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+# The default messages for the style package, in english.
+#
+# $Id: Messages.properties 475477 2006-11-15 22:44:28Z cam $
+# -----------------------------------------------------------------------------
+
+unknown.attribute = \
+The attribute with namespace URI "{0}" and local name "{1}" do\n \
+not have an associated CSSValueFactory.
+
+parser.exception = \
+An exception occured while parsing an attribute. The original message was:\n\
+{0}.
+
+creation.exception = \
+An exception occured while creating a parser. The original message was:\n\
+{0}.
+
+readonly.value = \
+This value cannot be modified.
+
+illegal.operation = \
+The invoked method is not supported by this object.
+
+invalid.conversion = \
+Cannot convert this value to the given unit ({0}).
+
+illegal.unit.type = \
+The requested unit type ({0}) do not exist.
+
+invalid.lexical.unit = \
+The given SAC unit type ({0}) is invalid in this context.
+
+invalid.identifier = \
+The given identifier ({0}) is illegal in this context.
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--- /dev/null
+++ b/org/apache/batik/svggen/font/resources/Messages.properties
@@ -0,0 +1,42 @@
+# -----------------------------------------------------------------------------
+#
+# Licensed to the Apache Software Foundation (ASF) under one or more
+# contributor license agreements. See the NOTICE file distributed with
+# this work for additional information regarding copyright ownership.
+# The ASF licenses this file to You under the Apache License, Version 2.0
+# (the "License"); you may not use this file except in compliance with
+# the License. You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+# $Id: Messages.properties 475477 2006-11-15 22:44:28Z cam $
+# -----------------------------------------------------------------------------
+
+SVGFont.config.usage = \
+usage: java org.apache.batik.svggen.font.SVGFont <ttf-path> [-l <range-begin>] [-h <range-end>] [-autorange] [-ascii] [-id <id>] [-o <output-path>] [-testcard]
+
+SVGFont.config.svg.begin = \
+<?xml version="1.0" standalone="no"?> \
+<!DOCTYPE svg PUBLIC "{0}" \
+"{1}" > \
+<svg xmlns="http://www.w3.org/2000/svg" width="100%" height="100%">
+
+SVGFont.config.svg.test.card.start = \
+<g style="font-family:'
+
+SVGFont.config.svg.test.card.end = '; font-size:18;fill:black"> \n\
+<text x="20" y="60"> !"#$%&'()*+,-./0123456789:;<>?</text> \n\
+<text x="20" y="120">@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\\]^_</text> \n\
+<text x="20" y="180">`abcdefghijklmnopqrstuvwxyz|{}~</text> \n\
+<text x="20" y="240">€‚ƒ„…†‡ˆ‰Š‹ŒŽ‘’“”•–—˜™š›œžŸ</text> \n\
+<text x="20" y="300"> ¡¢£¤¥¦§¨©ª«¬­®¯°±²³´µ¶·¸¹º»¼½¾¿</text> \n\
+<text x="20" y="360">ÀÁÂÃÄÅÆÇÈÉÊËÌÍÎÏÐÑÒÓÔÕÖ×ØÙÚÛÜÝÞß</text> \n\
+<text x="20" y="420">àáâãäåæçèéêëìíîïðñòóôõö÷øùúûüýþÿ</text> \n\
+</g>
+
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@@ -0,0 +1,37 @@
+# -----------------------------------------------------------------------------
+#
+# Licensed to the Apache Software Foundation (ASF) under one or more
+# contributor license agreements. See the NOTICE file distributed with
+# this work for additional information regarding copyright ownership.
+# The ASF licenses this file to You under the Apache License, Version 2.0
+# (the "License"); you may not use this file except in compliance with
+# the License. You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+# The error messages for the image transcoder.
+#
+# Author: Thierry Kormann
+# $Id: Messages.properties 475477 2006-11-15 22:44:28Z cam $
+# -----------------------------------------------------------------------------
+
+notsvg = \
+The specified XML document fragment is not an SVG document
+
+jpeg.badoutput = \
+Invalid output. JPEG transcoder only supports a byte stream output
+
+jpeg.unspecifiedQuality = \
+The JPEG quality has not been specified. Use the default one: no compression
+
+png.badoutput = \
+Invalid output. PNG transcoder only supports a byte stream output
+
+tiff.badoutput = \
+Invalid output. TIFF transcoder only supports a byte stream output
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diff --git a/org/apache/batik/util/gui/resource/MenuFactory.class b/org/apache/batik/util/gui/resource/MenuFactory.class
new file mode 100644
index 0000000..c799341
Binary files /dev/null and b/org/apache/batik/util/gui/resource/MenuFactory.class differ
diff --git a/org/apache/batik/util/gui/resource/MissingListenerException.class b/org/apache/batik/util/gui/resource/MissingListenerException.class
new file mode 100644
index 0000000..206cb04
Binary files /dev/null and b/org/apache/batik/util/gui/resource/MissingListenerException.class differ
diff --git a/org/apache/batik/util/gui/resource/ToolBarFactory.class b/org/apache/batik/util/gui/resource/ToolBarFactory.class
new file mode 100644
index 0000000..2ec013e
Binary files /dev/null and b/org/apache/batik/util/gui/resource/ToolBarFactory.class differ
diff --git a/org/apache/batik/util/gui/resources/CSSMediaPanel.properties b/org/apache/batik/util/gui/resources/CSSMediaPanel.properties
new file mode 100644
index 0000000..00f767d
--- /dev/null
+++ b/org/apache/batik/util/gui/resources/CSSMediaPanel.properties
@@ -0,0 +1,49 @@
+# -----------------------------------------------------------------------------
+#
+# Licensed to the Apache Software Foundation (ASF) under one or more
+# contributor license agreements. See the NOTICE file distributed with
+# this work for additional information regarding copyright ownership.
+# The ASF licenses this file to You under the Apache License, Version 2.0
+# (the "License"); you may not use this file except in compliance with
+# the License. You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+# The resources for the location bar
+#
+# Author: tkormann at ilog.fr
+# $Id: CSSMediaPanel.properties 496986 2007-01-17 10:50:57Z cam $
+# -----------------------------------------------------------------------------
+
+OKButton.text = OK
+OKButton.mnemonic = O
+OKButton.action = OKButtonAction
+
+CancelButton.text = Cancel
+CancelButton.mnemonic = C
+CancelButton.action = CancelButtonAction
+
+AddButton.text = Add
+AddButton.mnemonic = A
+AddButton.action = AddButtonAction
+
+RemoveButton.text = Remove
+RemoveButton.mnemonic = R
+RemoveButton.action = RemoveButtonAction
+
+ClearButton.text = Clear
+ClearButton.mnemonic = l
+ClearButton.action = ClearButtonAction
+
+Panel.title = CSS Media
+
+Media.list = aural braille embossed handheld print projection screen tty tv
+AddMediumDialog.title = Add a new CSS medium
+AddMediumDialog.label = Medium Name:
+
diff --git a/org/apache/batik/util/gui/resources/JErrorPane.properties b/org/apache/batik/util/gui/resources/JErrorPane.properties
new file mode 100644
index 0000000..0677cdd
--- /dev/null
+++ b/org/apache/batik/util/gui/resources/JErrorPane.properties
@@ -0,0 +1,35 @@
+# -----------------------------------------------------------------------------
+#
+# Licensed to the Apache Software Foundation (ASF) under one or more
+# contributor license agreements. See the NOTICE file distributed with
+# this work for additional information regarding copyright ownership.
+# The ASF licenses this file to You under the Apache License, Version 2.0
+# (the "License"); you may not use this file except in compliance with
+# the License. You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+# The resources for the JErrorPane
+#
+# Author: tkormann at ilog.fr
+# $Id: JErrorPane.properties 475477 2006-11-15 22:44:28Z cam $
+# -----------------------------------------------------------------------------
+
+Heading.text = SVG Error:
+
+ShowDetailButton.text = Show Details
+ShowDetailButton.text2 = Hide Details
+ShowDetailButton.mnemonic = D
+ShowDetailButton.action = ShowDetailButtonAction
+
+OKButton.text = OK
+OKButton.mnemonic = O
+OKButton.action = OKButtonAction
+
+
diff --git a/org/apache/batik/util/gui/resources/LanguageDialogMessages.properties b/org/apache/batik/util/gui/resources/LanguageDialogMessages.properties
new file mode 100644
index 0000000..a477b25
--- /dev/null
+++ b/org/apache/batik/util/gui/resources/LanguageDialogMessages.properties
@@ -0,0 +1,476 @@
+# -----------------------------------------------------------------------------
+#
+# Licensed to the Apache Software Foundation (ASF) under one or more
+# contributor license agreements. See the NOTICE file distributed with
+# this work for additional information regarding copyright ownership.
+# The ASF licenses this file to You under the Apache License, Version 2.0
+# (the "License"); you may not use this file except in compliance with
+# the License. You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+# The resource file for the language dialog.
+#
+# stephane at hillion.org
+# $Id: LanguageDialogMessages.properties 496986 2007-01-17 10:50:57Z cam $
+# -----------------------------------------------------------------------------
+
+Dialog.title = Language Options
+Panel.title = User Languages Selection
+Languages.title = Available languages:
+User.title = User languages:
+
+InfoLabel.text = The user languages are used while processing \
+the SVG switch element.
+
+AddLanguageButton.text = >>
+AddLanguageButton.tooltip = Add the selected language to the user languages
+AddLanguageButton.action = AddLanguageButtonAction
+
+RemoveLanguageButton.text = <<
+RemoveLanguageButton.tooltip = Remove the selected language from the user \
+ languages
+RemoveLanguageButton.action = RemoveLanguageButtonAction
+
+UpLanguageButton.text = Up
+UpLanguageButton.tooltip = Move up the selected language
+UpLanguageButton.action = UpLanguageButtonAction
+
+DownLanguageButton.text = Down
+DownLanguageButton.tooltip = Move down the selected language
+DownLanguageButton.action = DownLanguageButtonAction
+
+ClearLanguageButton.text = Clear
+ClearLanguageButton.tooltip = Clear the user language list
+ClearLanguageButton.action = ClearLanguageButtonAction
+
+OKButton.text = OK
+OKButton.mnemonic = O
+OKButton.action = OKButtonAction
+
+CancelButton.text = Cancel
+CancelButton.mnemonic = C
+CancelButton.action = CancelButtonAction
+
+#
+# The countries
+#
+
+Country.list = aa ab af am ar as ay az ba be bg bh bi bn bo br ca co cs cy da de de-CH dz el en en-UK eo es et eu fa fi fj fo fr fr-CA fr-CH fy ga gd gl gn gu ha he hi hr hu hy ij ik id is it ja ji jv ka kk kl km kn ko ks ku ky la ln lo lt lv mg mi mk ml mn mo mr ms mt my na ne nl no or pa pl ps pt pt-BR qu rm rn ro ru rw sa sd sg si sk sl sm sn so sq sr ss st su sv sw ta te tg th ti tk tl tn to tr ts tt tw uk ur uz vi vo xh yo zh zu
+
+aa.text = Afar (aa)
+aa.icon = resources/flags/flag_aa.gif
+
+ab.text = Abkhazian (ab)
+ab.icon = resources/flags/flag_ab.gif
+
+af.text = Afrikaans (af)
+af.icon = resources/flags/flag_af.gif
+
+am.text = Amharic (am)
+am.icon = resources/flags/flag_aa.gif
+
+ar.text = Arabic (ar)
+ar.icon = resources/flags/flag_ar.gif
+
+as.text = Assamese (as)
+as.icon = resources/flags/flag_as.gif
+
+ay.text = Aymara (ay)
+ay.icon = resources/flags/flag_ay.gif
+
+az.text = Azerbaijani (az)
+az.icon = resources/flags/flag_az.gif
+
+ba.text = Bashkir (ba)
+ba.icon = resources/flags/flag_ru.gif
+
+be.text = Byelorussian (be)
+be.icon = resources/flags/flag_be.gif
+
+bg.text = Bulgarian (bg)
+bg.icon = resources/flags/flag_bg.gif
+
+bh.text = Bihari (bh)
+bh.icon = resources/flags/flag_ne.gif
+
+bi.text = Bislama (bi)
+bi.icon = resources/flags/flag_bi.gif
+
+bn.text = Bengali (bn)
+bn.icon = resources/flags/flag_bn.gif
+
+bo.text = Tibetan (bo)
+bo.icon = resources/flags/flag_bo.gif
+
+br.text = Breton (br)
+br.icon = resources/flags/flag_br.gif
+
+ca.text = Catalan (ca)
+ca.icon = resources/flags/flag_ca.gif
+
+co.text = Corsican (co)
+co.icon = resources/flags/flag_co.gif
+
+cs.text = Czech (cs)
+cs.icon = resources/flags/flag_cs.gif
+
+cy.text = Welsh (cy)
+cy.icon = resources/flags/flag_cy.gif
+
+da.text = Danish (da)
+da.icon = resources/flags/flag_da.gif
+
+de.text = German (de)
+de.icon = resources/flags/flag_de.gif
+
+de-CH.text = Swiss German (de-CH)
+de-CH.icon = resources/flags/flag_ch.gif
+
+dz.text = Bhutani (dz)
+dz.icon = resources/flags/flag_dz.gif
+
+el.text = Greek (el)
+el.icon = resources/flags/flag_el.gif
+
+en.text = English US (en)
+en.icon = resources/flags/flag_en.gif
+
+en-UK.text = English UK (en-UK)
+en-UK.icon = resources/flags/flag_en_UK.gif
+
+eo.text = Esperanto (eo)
+eo.icon = resources/flags/flag_eo.gif
+
+es.text = Spanish (es)
+es.icon = resources/flags/flag_es.gif
+
+et.text = Estonian (et)
+et.icon = resources/flags/flag_et.gif
+
+eu.text = Basque (eu)
+eu.icon = resources/flags/flag_eu.gif
+
+fa.text = Persian (fa)
+fa.icon = resources/flags/flag_fa.gif
+
+fi.text = Finnish (fi)
+fi.icon = resources/flags/flag_fi.gif
+
+fj.text = Fiji (fj)
+fj.icon = resources/flags/flag_fj.gif
+
+fo.text = Faeroese (fo)
+fo.icon = resources/flags/flag_fo.gif
+
+fr.text = French (fr)
+fr.icon = resources/flags/flag_fr.gif
+
+fr-CA.text = Canadian French (fr-CA)
+fr-CA.icon = resources/flags/flag_fr_CA.gif
+
+fr-CH.text = Swiss French (fr-CH)
+fr-CH.icon = resources/flags/flag_ch.gif
+
+fy.text = Frisian (fy)
+fy.icon = resources/flags/flag_de.gif
+
+ga.text = Irish (ga)
+ga.icon = resources/flags/flag_ga.gif
+
+gd.text = Scots Gaelic (gd)
+gd.icon = resources/flags/flag_gd.gif
+
+gl.text = Galician (gl)
+gl.icon = resources/flags/flag_es.gif
+
+gn.text = Guarani (gn)
+gn.icon = resources/flags/flag_gn.gif
+
+gu.text = Gujarati (gu)
+gu.icon = resources/flags/flag_as.gif
+
+ha.text = Hausa (ha)
+ha.icon = resources/flags/flag_ha.gif
+
+he.text = Hebrew (he)
+he.icon = resources/flags/flag_he.gif
+
+hi.text = Hindi (hi)
+hi.icon = resources/flags/flag_as.gif
+
+hr.text = Croatian (hr)
+hr.icon = resources/flags/flag_hr.gif
+
+hu.text = Hungarian (hu)
+hu.icon = resources/flags/flag_hu.gif
+
+hy.text = Armenian (hy)
+hy.icon = resources/flags/flag_hy.gif
+
+ij.text = Inuktitut (ij)
+ij.icon = resources/flags/flag_ij.gif
+
+ik.text = Inupiak (ik)
+ik.icon = resources/flags/flag_kl.gif
+
+id.text = Indonesian (id)
+id.icon = resources/flags/flag_in.gif
+
+is.text = Icelandic (is)
+is.icon = resources/flags/flag_is.gif
+
+it.text = Italian (it)
+it.icon = resources/flags/flag_it.gif
+
+ja.text = Japanese (ja)
+ja.icon = resources/flags/flag_ja.gif
+
+ji.text = Yiddish (ji)
+ji.icon = resources/flags/flag_he.gif
+
+jv.text = Javanese (jv)
+jv.icon = resources/flags/flag_in.gif
+
+ka.text = Georgian (ka)
+ka.icon = resources/flags/flag_ka.gif
+
+kk.text = Kazakh (kk)
+kk.icon = resources/flags/flag_kk.gif
+
+kl.text = Greenlandic (kl)
+kl.icon = resources/flags/flag_kl.gif
+
+km.text = Cambodian (km)
+km.icon = resources/flags/flag_km.gif
+
+kn.text = Kannada (kn)
+kn.icon = resources/flags/flag_as.gif
+
+ko.text = Korean (ko)
+ko.icon = resources/flags/flag_ko.gif
+
+ks.text = Kashmiri (ks)
+ks.icon = resources/flags/flag_tg.gif
+
+ku.text = Kurdish (ku)
+ku.icon = resources/flags/flag_ku.gif
+
+ky.text = Kirghiz (ky)
+ky.icon = resources/flags/flag_ky.gif
+
+la.text = Latin (la)
+la.icon = resources/flags/flag_la.gif
+
+ln.text = Lingala (ln)
+ln.icon = resources/flags/flag_ln.gif
+
+lo.text = Laothian (lo)
+lo.icon = resources/flags/flag_lo.gif
+
+lt.text = Lithuanian (lt)
+lt.icon = resources/flags/flag_lt.gif
+
+lv.text = Latvian (lv)
+lv.icon = resources/flags/flag_lv.gif
+
+mg.text = Malagasy (mg)
+mg.icon = resources/flags/flag_mg.gif
+
+mi.text = Maori (mi)
+mi.icon = resources/flags/flag_mi.gif
+
+mk.text = Macedonian (mk)
+mk.icon = resources/flags/flag_mk.gif
+
+ml.text = Malayalam (ml)
+ml.icon = resources/flags/flag_as.gif
+
+mn.text = Mongolian (mn)
+mn.icon = resources/flags/flag_mn.gif
+
+mo.text = Moldavian (mo)
+mo.icon = resources/flags/flag_mo.gif
+
+mr.text = Marathi (mr)
+mr.icon = resources/flags/flag_as.gif
+
+ms.text = Malay (ms)
+ms.icon = resources/flags/flag_ms.gif
+
+mt.text = Maltese (mt)
+mt.icon = resources/flags/flag_mt.gif
+
+my.text = Burmese (my)
+my.icon = resources/flags/flag_my.gif
+
+na.text = Nauru (na)
+na.icon = resources/flags/flag_na.gif
+
+ne.text = Nepali (ne)
+ne.icon = resources/flags/flag_ne.gif
+
+nl.text = Dutch (nl)
+nl.icon = resources/flags/flag_nl.gif
+
+no.text = Norwegian (no)
+no.icon = resources/flags/flag_no.gif
+
+or.text = Oriya (or)
+or.icon = resources/flags/flag_or.gif
+
+pa.text = Punjabi (pa)
+pa.icon = resources/flags/flag_as.gif
+
+pl.text = Polish (pl)
+pl.icon = resources/flags/flag_pl.gif
+
+ps.text = Pashto (ps)
+ps.icon = resources/flags/flag_ps.gif
+
+pt.text = Portuguese (pt)
+pt.icon = resources/flags/flag_pt.gif
+
+pt-BR.text = Brazilian Portuguese (pt-BR)
+pt-BR.icon = resources/flags/flag_pt_BR.gif
+
+qu.text = Quechua (qu)
+qu.icon = resources/flags/flag_qu.gif
+
+rm.text = Rhaeto-Romance (rm)
+rm.icon = resources/flags/flag_ch.gif
+
+rn.text = Kirundi (rn)
+rn.icon = resources/flags/flag_rn.gif
+
+ro.text = Romanian (ro)
+ro.icon = resources/flags/flag_ro.gif
+
+ru.text = Russian (ru)
+ru.icon = resources/flags/flag_ru.gif
+
+rw.text = Kinyarwanda (rw)
+rw.icon = resources/flags/flag_rw.gif
+
+sa.text = Sanskrit (sa)
+sa.icon = resources/flags/flag_as.gif
+
+sd.text = Sindhi (sd)
+sd.icon = resources/flags/flag_as.gif
+
+sg.text = Sangro (sg)
+sg.icon = resources/flags/flag_blank.gif
+
+si.text = Singhalese (si)
+si.icon = resources/flags/flag_si.gif
+
+sk.text = Slovak (sk)
+sk.icon = resources/flags/flag_sk.gif
+
+sl.text = Slovenian (sl)
+sl.icon = resources/flags/flag_sl.gif
+
+sm.text = Samoan (sm)
+sm.icon = resources/flags/flag_sm.gif
+
+sn.text = Shona (sn)
+sn.icon = resources/flags/flag_si.gif
+
+so.text = Somali (so)
+so.icon = resources/flags/flag_so.gif
+
+sq.text = Albanian (sq)
+sq.icon = resources/flags/flag_sq.gif
+
+sr.text = Serbian (sr)
+sr.icon = resources/flags/flag_sr.gif
+
+ss.text = Siswati (ss)
+ss.icon = resources/flags/flag_ss.gif
+
+st.text = Sesotho (st)
+st.icon = resources/flags/flag_st.gif
+
+su.text = Sundanese (su)
+su.icon = resources/flags/flag_in.gif
+
+sv.text = Swedish (sv)
+sv.icon = resources/flags/flag_sv.gif
+
+sw.text = Swahili (sw)
+sw.icon = resources/flags/flag_sw.gif
+
+ta.text = Tamil (ta)
+ta.icon = resources/flags/flag_as.gif
+
+te.text = Telugu (te)
+te.icon = resources/flags/flag_tw.gif
+
+tg.text = Tajik (tg)
+tg.icon = resources/flags/flag_tg.gif
+
+th.text = Thai (th)
+th.icon = resources/flags/flag_th.gif
+
+ti.text = Tigrinya (ti)
+ti.icon = resources/flags/flag_aa.gif
+
+tk.text = Turkmen (tk)
+tk.icon = resources/flags/flag_tk.gif
+
+tl.text = Tagalog (tl)
+tl.icon = resources/flags/flag_tl.gif
+
+tn.text = Setswana (tn)
+tn.icon = resources/flags/flag_tn.gif
+
+to.text = Tonga (to)
+to.icon = resources/flags/flag_to.gif
+
+tr.text = Turkish (tr)
+tr.icon = resources/flags/flag_tr.gif
+
+ts.text = Tsonga (ts)
+ts.icon = resources/flags/flag_ts.gif
+
+tt.text = Tatar (tt)
+tt.icon = resources/flags/flag_ru.gif
+
+tw.text = Twi (tw)
+tw.icon = resources/flags/flag_tw.gif
+
+uk.text = Ukrainian (uk)
+uk.icon = resources/flags/flag_uk.gif
+
+ur.text = Urdu (ur)
+ur.icon = resources/flags/flag_ps.gif
+
+uz.text = Uzbek (uz)
+uz.icon = resources/flags/flag_uz.gif
+
+vi.text = Vietnamese (vi)
+vi.icon = resources/flags/flag_vi.gif
+
+vo.text = Volapuk (vo)
+vo.icon = resources/flags/flag_vo.gif
+
+wo.text = Wolof (wo)
+wo.icon = resources/flags/flag_wo.gif
+
+xh.text = Xhosa (xh)
+xh.icon = resources/flags/flag_xh.gif
+
+yo.text = Yoruba (yo)
+yo.icon = resources/flags/flag_ha.gif
+
+zh.text = Chinese (zh)
+zh.icon = resources/flags/flag_zh.gif
+
+zu.text = Zulu (zu)
+zu.icon = resources/flags/flag_zu.gif
diff --git a/org/apache/batik/util/gui/resources/LocationBar.properties b/org/apache/batik/util/gui/resources/LocationBar.properties
new file mode 100644
index 0000000..fb1cae4
--- /dev/null
+++ b/org/apache/batik/util/gui/resources/LocationBar.properties
@@ -0,0 +1,25 @@
+# -----------------------------------------------------------------------------
+#
+# Licensed to the Apache Software Foundation (ASF) under one or more
+# contributor license agreements. See the NOTICE file distributed with
+# this work for additional information regarding copyright ownership.
+# The ASF licenses this file to You under the Apache License, Version 2.0
+# (the "License"); you may not use this file except in compliance with
+# the License. You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+# The resources for the location bar
+#
+# Author: stephane at hillion.org
+# $Id: LocationBar.properties 498555 2007-01-22 08:09:33Z cam $
+# -----------------------------------------------------------------------------
+
+Panel.label = Location:
+Panel.icon = resources/text-html.png
diff --git a/org/apache/batik/util/gui/resources/MemoryMonitorMessages.properties b/org/apache/batik/util/gui/resources/MemoryMonitorMessages.properties
new file mode 100644
index 0000000..09a51ce
--- /dev/null
+++ b/org/apache/batik/util/gui/resources/MemoryMonitorMessages.properties
@@ -0,0 +1,41 @@
+# -----------------------------------------------------------------------------
+#
+# Licensed to the Apache Software Foundation (ASF) under one or more
+# contributor license agreements. See the NOTICE file distributed with
+# this work for additional information regarding copyright ownership.
+# The ASF licenses this file to You under the Apache License, Version 2.0
+# (the "License"); you may not use this file except in compliance with
+# the License. You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+# The resources for the memory monitor components.
+#
+# stephane at hillion.org
+# $Id: MemoryMonitorMessages.properties 475477 2006-11-15 22:44:28Z cam $
+# -----------------------------------------------------------------------------
+
+Frame.title = Memory Monitor
+Frame.border_title = Memory Usage & History
+
+CollectButton.text = Collect
+CollectButton.mnemonic = l
+CollectButton.tooltip = Collect the unused memory
+CollectButton.action = CollectButtonAction
+
+CloseButton.text = Close
+CloseButton.mnemonic = C
+CloseButton.tooltip = Close the memory monitor frame
+CloseButton.action = CloseButtonAction
+
+Usage.units = K
+Usage.total = total
+Usage.used = used
+
+Usage.postfix = true
diff --git a/org/apache/batik/util/gui/resources/ScrollablePopupMenuMessages.properties b/org/apache/batik/util/gui/resources/ScrollablePopupMenuMessages.properties
new file mode 100644
index 0000000..c2f4157
--- /dev/null
+++ b/org/apache/batik/util/gui/resources/ScrollablePopupMenuMessages.properties
@@ -0,0 +1,27 @@
+# -----------------------------------------------------------------------------
+#
+# Licensed to the Apache Software Foundation (ASF) under one or more
+# contributor license agreements. See the NOTICE file distributed with
+# this work for additional information regarding copyright ownership.
+# The ASF licenses this file to You under the Apache License, Version 2.0
+# (the "License"); you may not use this file except in compliance with
+# the License. You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+# $Id$
+# -----------------------------------------------------------------------------
+
+PreferredHeight = 218
+
+ScrollPane.minWidth = 240
+ScrollPane.minHeight = 40
+ScrollPane.maxWidth = 1200
+ScrollPane.maxHeight = 400
+
diff --git a/org/apache/batik/util/gui/resources/URIChooserMessages.properties b/org/apache/batik/util/gui/resources/URIChooserMessages.properties
new file mode 100644
index 0000000..069e269
--- /dev/null
+++ b/org/apache/batik/util/gui/resources/URIChooserMessages.properties
@@ -0,0 +1,41 @@
+# -----------------------------------------------------------------------------
+#
+# Licensed to the Apache Software Foundation (ASF) under one or more
+# contributor license agreements. See the NOTICE file distributed with
+# this work for additional information regarding copyright ownership.
+# The ASF licenses this file to You under the Apache License, Version 2.0
+# (the "License"); you may not use this file except in compliance with
+# the License. You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+# URI Chooser properties file
+#
+# Author: stephane at hillion.org
+# $Id: URIChooserMessages.properties 475477 2006-11-15 22:44:28Z cam $
+# -----------------------------------------------------------------------------
+
+Dialog.title = Select a path
+Dialog.label = Choose an URI or a local file:
+
+BrowseButton.text = Browse...
+BrowseButton.mnemonic = B
+BrowseButton.action = BrowseButtonAction
+
+OKButton.text = OK
+OKButton.mnemonic = O
+OKButton.action = OKButtonAction
+
+CancelButton.text = Cancel
+CancelButton.mnemonic = C
+CancelButton.action = CancelButtonAction
+
+ClearButton.text = Clear
+ClearButton.mnemonic = r
+ClearButton.action = ClearButtonAction
diff --git a/org/apache/batik/util/gui/resources/UserStyleDialog.properties b/org/apache/batik/util/gui/resources/UserStyleDialog.properties
new file mode 100644
index 0000000..a78667b
--- /dev/null
+++ b/org/apache/batik/util/gui/resources/UserStyleDialog.properties
@@ -0,0 +1,47 @@
+# -----------------------------------------------------------------------------
+#
+# Licensed to the Apache Software Foundation (ASF) under one or more
+# contributor license agreements. See the NOTICE file distributed with
+# this work for additional information regarding copyright ownership.
+# The ASF licenses this file to You under the Apache License, Version 2.0
+# (the "License"); you may not use this file except in compliance with
+# the License. You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+# The resource file for the user style dialog.
+#
+# Author: stephane at hillion.org
+# $Id: UserStyleDialog.properties 475477 2006-11-15 22:44:28Z cam $
+# -----------------------------------------------------------------------------
+
+Dialog.title = Style Options
+
+OKButton.text = OK
+OKButton.mnemonic = O
+OKButton.action = OKButtonAction
+
+CancelButton.text = Cancel
+CancelButton.mnemonic = C
+CancelButton.action = CancelButtonAction
+
+# UserStyleSheetPanel #########################
+
+Panel.title = User Style Sheet
+
+PanelFileCheckBox.text = Enable user style sheet
+PanelFileLabel.text = Choose an URL or a local file:
+
+PanelFileBrowseButton.text = Browse...
+PanelFileBrowseButton.mnemonic = B
+
+StyleDialogError.text = A file name must be given or\n\
+the checkbox must be unselected.
+
+StyleDialogError.title = Style Options Error
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diff --git a/org/apache/batik/util/io/resources/Messages.properties b/org/apache/batik/util/io/resources/Messages.properties
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index 0000000..f0983c3
--- /dev/null
+++ b/org/apache/batik/util/io/resources/Messages.properties
@@ -0,0 +1,27 @@
+# -----------------------------------------------------------------------------
+#
+# Licensed to the Apache Software Foundation (ASF) under one or more
+# contributor license agreements. See the NOTICE file distributed with
+# this work for additional information regarding copyright ownership.
+# The ASF licenses this file to You under the Apache License, Version 2.0
+# (the "License"); you may not use this file except in compliance with
+# the License. You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+# The error messages for the IO utilities.
+#
+# $Id: Messages.properties 475477 2006-11-15 22:44:28Z cam $
+# -----------------------------------------------------------------------------
+
+invalid.char = \
+The input stream represents an invalid {0} stream.
+
+end.of.stream = \
+Unexpected end of stream while decoding a {0} stream.
diff --git a/org/apache/batik/util/resources/Messages.class b/org/apache/batik/util/resources/Messages.class
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diff --git a/org/apache/batik/util/resources/Messages.properties b/org/apache/batik/util/resources/Messages.properties
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index 0000000..91f6e3e
--- /dev/null
+++ b/org/apache/batik/util/resources/Messages.properties
@@ -0,0 +1,42 @@
+# -----------------------------------------------------------------------------
+#
+# Licensed to the Apache Software Foundation (ASF) under one or more
+# contributor license agreements. See the NOTICE file distributed with
+# this work for additional information regarding copyright ownership.
+# The ASF licenses this file to You under the Apache License, Version 2.0
+# (the "License"); you may not use this file except in compliance with
+# the License. You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+# The error messages for the utility package
+#
+# Author: Thierry Kormann
+# $Id: Messages.properties 475477 2006-11-15 22:44:28Z cam $
+# -----------------------------------------------------------------------------
+
+#
+# UnitProcessor
+#
+
+invalid.svg.unit=The given unit is invalid : {0}
+invalid.css.unit=The given CSS unit is invalid : {0}
+
+
+#
+# Security Enforcer
+#
+
+ApplicationSecurityEnforcer.message.security.exception.alien.security.manager=\
+The application cannot install or remove a security manager when there is \
+already one it place that it did not install.
+
+ApplicationSecurityEnforcer.message.null.pointer.exception.no.policy.file=\
+The application could not load the specificed security policy ({0})
+
diff --git a/org/apache/batik/util/resources/ResourceFormatException.class b/org/apache/batik/util/resources/ResourceFormatException.class
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diff --git a/org/apache/batik/util/resources/XMLResourceDescriptor.properties b/org/apache/batik/util/resources/XMLResourceDescriptor.properties
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--- /dev/null
+++ b/org/apache/batik/util/resources/XMLResourceDescriptor.properties
@@ -0,0 +1,24 @@
+# -----------------------------------------------------------------------------
+#
+# Licensed to the Apache Software Foundation (ASF) under one or more
+# contributor license agreements. See the NOTICE file distributed with
+# this work for additional information regarding copyright ownership.
+# The ASF licenses this file to You under the Apache License, Version 2.0
+# (the "License"); you may not use this file except in compliance with
+# the License. You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+# Author: Thierry Kormann
+#
+# $Id: XMLResourceDescriptor.properties 475477 2006-11-15 22:44:28Z cam $
+# -----------------------------------------------------------------------------
+
+#org.xml.sax.driver = org.apache.xerces.parsers.SAXParser
+org.w3c.css.sac.driver = org.apache.batik.css.parser.Parser
diff --git a/org/apache/batik/xml/LexicalUnits.class b/org/apache/batik/xml/LexicalUnits.class
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diff --git a/org/apache/batik/xml/scanner/resources/Messages.properties b/org/apache/batik/xml/scanner/resources/Messages.properties
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--- /dev/null
+++ b/org/apache/batik/xml/scanner/resources/Messages.properties
@@ -0,0 +1,55 @@
+# -----------------------------------------------------------------------------
+#
+# Licensed to the Apache Software Foundation (ASF) under one or more
+# contributor license agreements. See the NOTICE file distributed with
+# this work for additional information regarding copyright ownership.
+# The ASF licenses this file to You under the Apache License, Version 2.0
+# (the "License"); you may not use this file except in compliance with
+# the License. You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+# The error messages for the XML scanner.
+#
+# Author: stephane at hillion.org
+# $Id: Messages.properties 475477 2006-11-15 22:44:28Z cam $
+# -----------------------------------------------------------------------------
+
+character = \
+Invalid character.
+
+comment = \
+Malformed comment.
+
+eof = \
+Unexpected end of stream.
+
+character.reference = \
+Malformed character reference.
+
+parameter.entity = \
+Malformed parameter entity.
+
+pi.target = \
+Invalid processing instruction target.
+
+xml.reserved = \
+'x' or 'X', 'm' or 'M' and 'l' or 'L' cannot start PI targets.
+
+comment.or.doctype = \
+Comment or DOCTYPE expected.
+
+tag.end = \
+Malformed end of tag.
+
+pi.end = \
+Malformed end of processing instruction.
+
+name = \
+Malformed name.
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+++ b/org/apache/log4j/lf5/config/defaultconfig.properties
@@ -0,0 +1,31 @@
+# Licensed to the Apache Software Foundation (ASF) under one or more
+# contributor license agreements. See the NOTICE file distributed with
+# this work for additional information regarding copyright ownership.
+# The ASF licenses this file to You under the Apache License, Version 2.0
+# (the "License"); you may not use this file except in compliance with
+# the License. You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+# For the general syntax of property based configuration files see the
+# documenation of org.apache.log4j.PropertyConfigurator.
+
+# The root category uses the appender called A1. Since no priority is
+# specified, the root category assumes the default priority for root
+# which is DEBUG in log4j. The root category is the only category that
+# has a default priority. All other categories need not be assigned a
+# priority in which case they inherit their priority from the
+# hierarchy.
+
+log4j.rootCategory=, A1
+
+# A1 is set to be a LogMonitorAppender which outputs to a swing
+# logging console.
+
+log4j.appender.A1=org.apache.log4j.lf5.LF5Appender
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diff --git a/org/apache/log4j/xml/log4j.dtd b/org/apache/log4j/xml/log4j.dtd
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--- /dev/null
+++ b/org/apache/log4j/xml/log4j.dtd
@@ -0,0 +1,227 @@
+<?xml version="1.0" encoding="UTF-8" ?>
+<!--
+ Licensed to the Apache Software Foundation (ASF) under one or more
+ contributor license agreements. See the NOTICE file distributed with
+ this work for additional information regarding copyright ownership.
+ The ASF licenses this file to You under the Apache License, Version 2.0
+ (the "License"); you may not use this file except in compliance with
+ the License. You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing, software
+ distributed under the License is distributed on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ See the License for the specific language governing permissions and
+ limitations under the License.
+-->
+
+<!-- Authors: Chris Taylor, Ceki Gulcu. -->
+
+<!-- Version: 1.2 -->
+
+<!-- A configuration element consists of optional renderer
+elements,appender elements, categories and an optional root
+element. -->
+
+<!ELEMENT log4j:configuration (renderer*, appender*,plugin*, (category|logger)*,root?,
+ (categoryFactory|loggerFactory)?)>
+
+<!-- The "threshold" attribute takes a level value below which -->
+<!-- all logging statements are disabled. -->
+
+<!-- Setting the "debug" enable the printing of internal log4j logging -->
+<!-- statements. -->
+
+<!-- By default, debug attribute is "null", meaning that we not do touch -->
+<!-- internal log4j logging settings. The "null" value for the threshold -->
+<!-- attribute can be misleading. The threshold field of a repository -->
+<!-- cannot be set to null. The "null" value for the threshold attribute -->
+<!-- simply means don't touch the threshold field, the threshold field -->
+<!-- keeps its old value. -->
+
+<!ATTLIST log4j:configuration
+ xmlns:log4j CDATA #FIXED "http://jakarta.apache.org/log4j/"
+ threshold (all|trace|debug|info|warn|error|fatal|off|null) "null"
+ debug (true|false|null) "null"
+ reset (true|false) "false"
+>
+
+<!-- renderer elements allow the user to customize the conversion of -->
+<!-- message objects to String. -->
+
+<!ELEMENT renderer EMPTY>
+<!ATTLIST renderer
+ renderedClass CDATA #REQUIRED
+ renderingClass CDATA #REQUIRED
+>
+
+<!-- Appenders must have a name and a class. -->
+<!-- Appenders may contain an error handler, a layout, optional parameters -->
+<!-- and filters. They may also reference (or include) other appenders. -->
+<!ELEMENT appender (errorHandler?, param*,
+ rollingPolicy?, triggeringPolicy?, connectionSource?,
+ layout?, filter*, appender-ref*)>
+<!ATTLIST appender
+ name CDATA #REQUIRED
+ class CDATA #REQUIRED
+>
+
+<!ELEMENT layout (param*)>
+<!ATTLIST layout
+ class CDATA #REQUIRED
+>
+
+<!ELEMENT filter (param*)>
+<!ATTLIST filter
+ class CDATA #REQUIRED
+>
+
+<!-- ErrorHandlers can be of any class. They can admit any number of -->
+<!-- parameters. -->
+
+<!ELEMENT errorHandler (param*, root-ref?, logger-ref*, appender-ref?)>
+<!ATTLIST errorHandler
+ class CDATA #REQUIRED
+>
+
+<!ELEMENT root-ref EMPTY>
+
+<!ELEMENT logger-ref EMPTY>
+<!ATTLIST logger-ref
+ ref CDATA #REQUIRED
+>
+
+<!ELEMENT param EMPTY>
+<!ATTLIST param
+ name CDATA #REQUIRED
+ value CDATA #REQUIRED
+>
+
+
+<!-- The priority class is org.apache.log4j.Level by default -->
+<!ELEMENT priority (param*)>
+<!ATTLIST priority
+ class CDATA #IMPLIED
+ value CDATA #REQUIRED
+>
+
+<!-- The level class is org.apache.log4j.Level by default -->
+<!ELEMENT level (param*)>
+<!ATTLIST level
+ class CDATA #IMPLIED
+ value CDATA #REQUIRED
+>
+
+
+<!-- If no level element is specified, then the configurator MUST not -->
+<!-- touch the level of the named category. -->
+<!ELEMENT category (param*,(priority|level)?,appender-ref*)>
+<!ATTLIST category
+ class CDATA #IMPLIED
+ name CDATA #REQUIRED
+ additivity (true|false) "true"
+>
+
+<!-- If no level element is specified, then the configurator MUST not -->
+<!-- touch the level of the named logger. -->
+<!ELEMENT logger (level?,appender-ref*)>
+<!ATTLIST logger
+ name CDATA #REQUIRED
+ additivity (true|false) "true"
+>
+
+
+<!ELEMENT categoryFactory (param*)>
+<!ATTLIST categoryFactory
+ class CDATA #REQUIRED>
+
+<!ELEMENT loggerFactory (param*)>
+<!ATTLIST loggerFactory
+ class CDATA #REQUIRED>
+
+<!ELEMENT appender-ref EMPTY>
+<!ATTLIST appender-ref
+ ref CDATA #REQUIRED
+>
+
+<!-- plugins must have a name and class and can have optional parameters -->
+<!ELEMENT plugin (param*, connectionSource?)>
+<!ATTLIST plugin
+ name CDATA #REQUIRED
+ class CDATA #REQUIRED
+>
+
+<!ELEMENT connectionSource (dataSource?, param*)>
+<!ATTLIST connectionSource
+ class CDATA #REQUIRED
+>
+
+<!ELEMENT dataSource (param*)>
+<!ATTLIST dataSource
+ class CDATA #REQUIRED
+>
+
+<!ELEMENT triggeringPolicy ((param|filter)*)>
+<!ATTLIST triggeringPolicy
+ name CDATA #IMPLIED
+ class CDATA #REQUIRED
+>
+
+<!ELEMENT rollingPolicy (param*)>
+<!ATTLIST rollingPolicy
+ name CDATA #IMPLIED
+ class CDATA #REQUIRED
+>
+
+
+<!-- If no priority element is specified, then the configurator MUST not -->
+<!-- touch the priority of root. -->
+<!-- The root category always exists and cannot be subclassed. -->
+<!ELEMENT root (param*, (priority|level)?, appender-ref*)>
+
+
+<!-- ==================================================================== -->
+<!-- A logging event -->
+<!-- ==================================================================== -->
+<!ELEMENT log4j:eventSet (log4j:event*)>
+<!ATTLIST log4j:eventSet
+ xmlns:log4j CDATA #FIXED "http://jakarta.apache.org/log4j/"
+ version (1.1|1.2) "1.2"
+ includesLocationInfo (true|false) "true"
+>
+
+
+
+<!ELEMENT log4j:event (log4j:message, log4j:NDC?, log4j:throwable?,
+ log4j:locationInfo?, log4j:properties?) >
+
+<!-- The timestamp format is application dependent. -->
+<!ATTLIST log4j:event
+ logger CDATA #REQUIRED
+ level CDATA #REQUIRED
+ thread CDATA #REQUIRED
+ timestamp CDATA #REQUIRED
+ time CDATA #IMPLIED
+>
+
+<!ELEMENT log4j:message (#PCDATA)>
+<!ELEMENT log4j:NDC (#PCDATA)>
+
+<!ELEMENT log4j:throwable (#PCDATA)>
+
+<!ELEMENT log4j:locationInfo EMPTY>
+<!ATTLIST log4j:locationInfo
+ class CDATA #REQUIRED
+ method CDATA #REQUIRED
+ file CDATA #REQUIRED
+ line CDATA #REQUIRED
+>
+
+<!ELEMENT log4j:properties (log4j:data*)>
+
+<!ELEMENT log4j:data EMPTY>
+<!ATTLIST log4j:data
+ name CDATA #REQUIRED
+ value CDATA #REQUIRED
+>
diff --git a/org/apache/tomcat/util/Ascii.class b/org/apache/tomcat/util/Ascii.class
new file mode 100644
index 0000000..c286436
Binary files /dev/null and b/org/apache/tomcat/util/Ascii.class differ
diff --git a/org/apache/tomcat/util/HttpDate.class b/org/apache/tomcat/util/HttpDate.class
new file mode 100644
index 0000000..b709c93
Binary files /dev/null and b/org/apache/tomcat/util/HttpDate.class differ
diff --git a/org/apache/xmlcommons/Version.class b/org/apache/xmlcommons/Version.class
new file mode 100644
index 0000000..0e6d1a1
Binary files /dev/null and b/org/apache/xmlcommons/Version.class differ
diff --git a/org/broad/igv/DirectoryManager.class b/org/broad/igv/DirectoryManager.class
new file mode 100644
index 0000000..e2e321e
Binary files /dev/null and b/org/broad/igv/DirectoryManager.class differ
diff --git a/org/broad/igv/Globals.class b/org/broad/igv/Globals.class
new file mode 100644
index 0000000..06e4ab5
Binary files /dev/null and b/org/broad/igv/Globals.class differ
diff --git a/org/broad/igv/IGVPreferences.class b/org/broad/igv/IGVPreferences.class
new file mode 100644
index 0000000..f49619e
Binary files /dev/null and b/org/broad/igv/IGVPreferences.class differ
diff --git a/org/broad/igv/PreferenceManager$1.class b/org/broad/igv/PreferenceManager$1.class
new file mode 100644
index 0000000..b209f7f
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diff --git a/org/broad/igv/PreferenceManager.class b/org/broad/igv/PreferenceManager.class
new file mode 100644
index 0000000..5eb95ef
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diff --git a/org/broad/igv/batch/BatchRunner.class b/org/broad/igv/batch/BatchRunner.class
new file mode 100644
index 0000000..b2dfce3
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diff --git a/org/broad/igv/batch/CommandExecutor.class b/org/broad/igv/batch/CommandExecutor.class
new file mode 100644
index 0000000..fad7083
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diff --git a/org/broad/igv/batch/CommandListener.class b/org/broad/igv/batch/CommandListener.class
new file mode 100644
index 0000000..a01a25a
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diff --git a/org/broad/igv/batch/Exec.class b/org/broad/igv/batch/Exec.class
new file mode 100644
index 0000000..d9b55f8
Binary files /dev/null and b/org/broad/igv/batch/Exec.class differ
diff --git a/org/broad/igv/batch/TestClient.class b/org/broad/igv/batch/TestClient.class
new file mode 100644
index 0000000..255cb88
Binary files /dev/null and b/org/broad/igv/batch/TestClient.class differ
diff --git a/org/broad/igv/bbfile/BBFileHeader.class b/org/broad/igv/bbfile/BBFileHeader.class
new file mode 100644
index 0000000..06ab280
Binary files /dev/null and b/org/broad/igv/bbfile/BBFileHeader.class differ
diff --git a/org/broad/igv/bbfile/BBFileReader.class b/org/broad/igv/bbfile/BBFileReader.class
new file mode 100644
index 0000000..66fe91a
Binary files /dev/null and b/org/broad/igv/bbfile/BBFileReader.class differ
diff --git a/org/broad/igv/bbfile/BBTotalSummaryBlock.class b/org/broad/igv/bbfile/BBTotalSummaryBlock.class
new file mode 100644
index 0000000..76d7020
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diff --git a/org/broad/igv/bbfile/BBZoomLevelFormat.class b/org/broad/igv/bbfile/BBZoomLevelFormat.class
new file mode 100644
index 0000000..a1d715c
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diff --git a/org/broad/igv/bbfile/BBZoomLevelHeader.class b/org/broad/igv/bbfile/BBZoomLevelHeader.class
new file mode 100644
index 0000000..934d24c
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diff --git a/org/broad/igv/bbfile/BBZoomLevels.class b/org/broad/igv/bbfile/BBZoomLevels.class
new file mode 100644
index 0000000..6906620
Binary files /dev/null and b/org/broad/igv/bbfile/BBZoomLevels.class differ
diff --git a/org/broad/igv/bbfile/BPTree.class b/org/broad/igv/bbfile/BPTree.class
new file mode 100644
index 0000000..5142d24
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diff --git a/org/broad/igv/bbfile/BPTreeChildNode.class b/org/broad/igv/bbfile/BPTreeChildNode.class
new file mode 100644
index 0000000..3e19c6a
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diff --git a/org/broad/igv/bbfile/BPTreeChildNodeItem.class b/org/broad/igv/bbfile/BPTreeChildNodeItem.class
new file mode 100644
index 0000000..48a2149
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diff --git a/org/broad/igv/bbfile/BPTreeHeader.class b/org/broad/igv/bbfile/BPTreeHeader.class
new file mode 100644
index 0000000..6869140
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diff --git a/org/broad/igv/bbfile/BPTreeLeafNode.class b/org/broad/igv/bbfile/BPTreeLeafNode.class
new file mode 100644
index 0000000..35756e3
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diff --git a/org/broad/igv/bbfile/BPTreeLeafNodeItem.class b/org/broad/igv/bbfile/BPTreeLeafNodeItem.class
new file mode 100644
index 0000000..b5f1526
Binary files /dev/null and b/org/broad/igv/bbfile/BPTreeLeafNodeItem.class differ
diff --git a/org/broad/igv/bbfile/BPTreeNode.class b/org/broad/igv/bbfile/BPTreeNode.class
new file mode 100644
index 0000000..e2b0c23
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diff --git a/org/broad/igv/bbfile/BPTreeNodeItem.class b/org/broad/igv/bbfile/BPTreeNodeItem.class
new file mode 100644
index 0000000..2f83130
Binary files /dev/null and b/org/broad/igv/bbfile/BPTreeNodeItem.class differ
diff --git a/org/broad/igv/bbfile/BedFeature.class b/org/broad/igv/bbfile/BedFeature.class
new file mode 100644
index 0000000..81e069b
Binary files /dev/null and b/org/broad/igv/bbfile/BedFeature.class differ
diff --git a/org/broad/igv/bbfile/BigBedDataBlock.class b/org/broad/igv/bbfile/BigBedDataBlock.class
new file mode 100644
index 0000000..9793c29
Binary files /dev/null and b/org/broad/igv/bbfile/BigBedDataBlock.class differ
diff --git a/org/broad/igv/bbfile/BigBedIterator.class b/org/broad/igv/bbfile/BigBedIterator.class
new file mode 100644
index 0000000..4230985
Binary files /dev/null and b/org/broad/igv/bbfile/BigBedIterator.class differ
diff --git a/org/broad/igv/bbfile/BigWigDataBlock.class b/org/broad/igv/bbfile/BigWigDataBlock.class
new file mode 100644
index 0000000..2f6e3f0
Binary files /dev/null and b/org/broad/igv/bbfile/BigWigDataBlock.class differ
diff --git a/org/broad/igv/bbfile/BigWigIterator.class b/org/broad/igv/bbfile/BigWigIterator.class
new file mode 100644
index 0000000..0dc4b62
Binary files /dev/null and b/org/broad/igv/bbfile/BigWigIterator.class differ
diff --git a/org/broad/igv/bbfile/BigWigSection.class b/org/broad/igv/bbfile/BigWigSection.class
new file mode 100644
index 0000000..6f5d60c
Binary files /dev/null and b/org/broad/igv/bbfile/BigWigSection.class differ
diff --git a/org/broad/igv/bbfile/BigWigSectionHeader$WigItemType.class b/org/broad/igv/bbfile/BigWigSectionHeader$WigItemType.class
new file mode 100644
index 0000000..d32c77a
Binary files /dev/null and b/org/broad/igv/bbfile/BigWigSectionHeader$WigItemType.class differ
diff --git a/org/broad/igv/bbfile/BigWigSectionHeader.class b/org/broad/igv/bbfile/BigWigSectionHeader.class
new file mode 100644
index 0000000..4277464
Binary files /dev/null and b/org/broad/igv/bbfile/BigWigSectionHeader.class differ
diff --git a/org/broad/igv/bbfile/RPChromosomeRegion.class b/org/broad/igv/bbfile/RPChromosomeRegion.class
new file mode 100644
index 0000000..35c6672
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diff --git a/org/broad/igv/bbfile/RPTree.class b/org/broad/igv/bbfile/RPTree.class
new file mode 100644
index 0000000..45afc4a
Binary files /dev/null and b/org/broad/igv/bbfile/RPTree.class differ
diff --git a/org/broad/igv/bbfile/RPTreeChildNodeItem.class b/org/broad/igv/bbfile/RPTreeChildNodeItem.class
new file mode 100644
index 0000000..7feecd9
Binary files /dev/null and b/org/broad/igv/bbfile/RPTreeChildNodeItem.class differ
diff --git a/org/broad/igv/bbfile/RPTreeHeader.class b/org/broad/igv/bbfile/RPTreeHeader.class
new file mode 100644
index 0000000..35a31ac
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diff --git a/org/broad/igv/bbfile/RPTreeLeafNodeItem.class b/org/broad/igv/bbfile/RPTreeLeafNodeItem.class
new file mode 100644
index 0000000..bf1369d
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diff --git a/org/broad/igv/bbfile/RPTreeNode.class b/org/broad/igv/bbfile/RPTreeNode.class
new file mode 100644
index 0000000..c8bb5e7
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diff --git a/org/broad/igv/bbfile/RPTreeNodeItem.class b/org/broad/igv/bbfile/RPTreeNodeItem.class
new file mode 100644
index 0000000..6a373cb
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diff --git a/org/broad/igv/bbfile/RPTreeNodeProxy.class b/org/broad/igv/bbfile/RPTreeNodeProxy.class
new file mode 100644
index 0000000..d62d715
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diff --git a/org/broad/igv/bbfile/WigItem.class b/org/broad/igv/bbfile/WigItem.class
new file mode 100644
index 0000000..a096d11
Binary files /dev/null and b/org/broad/igv/bbfile/WigItem.class differ
diff --git a/org/broad/igv/bbfile/ZoomDataBlock.class b/org/broad/igv/bbfile/ZoomDataBlock.class
new file mode 100644
index 0000000..5a2bdeb
Binary files /dev/null and b/org/broad/igv/bbfile/ZoomDataBlock.class differ
diff --git a/org/broad/igv/bbfile/ZoomDataRecord.class b/org/broad/igv/bbfile/ZoomDataRecord.class
new file mode 100644
index 0000000..e2c9f96
Binary files /dev/null and b/org/broad/igv/bbfile/ZoomDataRecord.class differ
diff --git a/org/broad/igv/bbfile/ZoomLevelIterator$EmptyIterator.class b/org/broad/igv/bbfile/ZoomLevelIterator$EmptyIterator.class
new file mode 100644
index 0000000..1b84dc2
Binary files /dev/null and b/org/broad/igv/bbfile/ZoomLevelIterator$EmptyIterator.class differ
diff --git a/org/broad/igv/bbfile/ZoomLevelIterator.class b/org/broad/igv/bbfile/ZoomLevelIterator.class
new file mode 100644
index 0000000..5f05f10
Binary files /dev/null and b/org/broad/igv/bbfile/ZoomLevelIterator.class differ
diff --git a/org/broad/igv/bigwig/BigWigDataSource$1.class b/org/broad/igv/bigwig/BigWigDataSource$1.class
new file mode 100644
index 0000000..ac17d04
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diff --git a/org/broad/igv/bigwig/BigWigDataSource$RawDataInterval.class b/org/broad/igv/bigwig/BigWigDataSource$RawDataInterval.class
new file mode 100644
index 0000000..fd852b0
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diff --git a/org/broad/igv/bigwig/BigWigDataSource$WrappedIterator.class b/org/broad/igv/bigwig/BigWigDataSource$WrappedIterator.class
new file mode 100644
index 0000000..445f668
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diff --git a/org/broad/igv/bigwig/BigWigDataSource.class b/org/broad/igv/bigwig/BigWigDataSource.class
new file mode 100644
index 0000000..ffa3bb3
Binary files /dev/null and b/org/broad/igv/bigwig/BigWigDataSource.class differ
diff --git a/org/broad/igv/cbio/AttributeFilter.class b/org/broad/igv/cbio/AttributeFilter.class
new file mode 100644
index 0000000..d5d0575
Binary files /dev/null and b/org/broad/igv/cbio/AttributeFilter.class differ
diff --git a/org/broad/igv/cbio/AttributeFilter.jfd b/org/broad/igv/cbio/AttributeFilter.jfd
new file mode 100644
index 0000000..a985173
--- /dev/null
+++ b/org/broad/igv/cbio/AttributeFilter.jfd
@@ -0,0 +1,306 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<java version="1.6.0_31" class="java.beans.XMLDecoder">
+ <object class="com.jformdesigner.model.FormModel">
+ <void property="contentType">
+ <string>form/swing</string>
+ </void>
+ <void property="root">
+ <object class="com.jformdesigner.model.FormRoot">
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.BorderLayout</class>
+ </object>
+ <void property="name">
+ <string>panel1</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>javax.swing.BoxLayout</class>
+ <void method="setProperty">
+ <string>axis</string>
+ <int>0</int>
+ </void>
+ </object>
+ <void method="setProperty">
+ <string>maximumSize</string>
+ <object class="java.awt.Dimension">
+ <int>100000</int>
+ <int>29</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>preferredSize</string>
+ <object class="java.awt.Dimension">
+ <int>600</int>
+ <int>29</int>
+ </object>
+ </void>
+ <void property="name">
+ <string>filterRow</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JComboBox</string>
+ <void method="setProperty">
+ <string>maximumRowCount</string>
+ <int>12</int>
+ </void>
+ <void method="setProperty">
+ <string>maximumSize</string>
+ <object class="java.awt.Dimension">
+ <int>300</int>
+ <int>28</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>toolTipText</string>
+ <string>Attribute by which to filter</string>
+ </void>
+ <void method="setProperty">
+ <string>alignmentX</string>
+ <float>0.0</float>
+ </void>
+ <void property="name">
+ <string>attrName</string>
+ </void>
+ <void method="auxiliary">
+ <void method="setProperty">
+ <string>JavaCodeGenerator.variableGetter</string>
+ <boolean>true</boolean>
+ </void>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Min</string>
+ </void>
+ <void property="name">
+ <string>label1</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>0.0</string>
+ </void>
+ <void method="setProperty">
+ <string>maximumSize</string>
+ <object class="java.awt.Dimension">
+ <int>80</int>
+ <int>28</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>preferredSize</string>
+ <object class="java.awt.Dimension">
+ <int>50</int>
+ <int>28</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>minimumSize</string>
+ <object class="java.awt.Dimension">
+ <int>50</int>
+ <int>28</int>
+ </object>
+ </void>
+ <void property="name">
+ <string>minVal</string>
+ </void>
+ <void method="auxiliary">
+ <void method="setProperty">
+ <string>JavaCodeGenerator.variableModifiers</string>
+ <int>0</int>
+ </void>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Max</string>
+ </void>
+ <void property="name">
+ <string>label2</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>100.0</string>
+ </void>
+ <void method="setProperty">
+ <string>maximumSize</string>
+ <object class="java.awt.Dimension">
+ <int>80</int>
+ <int>28</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>preferredSize</string>
+ <object class="java.awt.Dimension">
+ <int>50</int>
+ <int>28</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>minimumSize</string>
+ <object class="java.awt.Dimension">
+ <int>50</int>
+ <int>28</int>
+ </object>
+ </void>
+ <void property="name">
+ <string>maxVal</string>
+ </void>
+ <void method="auxiliary">
+ <void method="setProperty">
+ <string>JavaCodeGenerator.variableModifiers</string>
+ <int>0</int>
+ </void>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>-</string>
+ </void>
+ <void method="setProperty">
+ <string>maximumSize</string>
+ <object id="Dimension0" class="java.awt.Dimension">
+ <int>20</int>
+ <int>29</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>minimumSize</string>
+ <object id="Dimension1" class="java.awt.Dimension">
+ <int>20</int>
+ <int>29</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>preferredSize</string>
+ <object id="Dimension2" class="java.awt.Dimension">
+ <int>20</int>
+ <int>29</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>toolTipText</string>
+ <string>Delete this filter</string>
+ </void>
+ <void method="setProperty">
+ <string>margin</string>
+ <object class="java.awt.Insets">
+ <int>2</int>
+ <int>2</int>
+ <int>2</int>
+ <int>2</int>
+ </object>
+ </void>
+ <void property="name">
+ <string>delRow</string>
+ </void>
+ <void method="auxiliary">
+ <void method="setProperty">
+ <string>JavaCodeGenerator.variableGetter</string>
+ <boolean>true</boolean>
+ </void>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>+</string>
+ </void>
+ <void method="setProperty">
+ <string>maximumSize</string>
+ <object idref="Dimension0"/>
+ </void>
+ <void method="setProperty">
+ <string>minimumSize</string>
+ <object idref="Dimension1"/>
+ </void>
+ <void method="setProperty">
+ <string>preferredSize</string>
+ <object idref="Dimension2"/>
+ </void>
+ <void method="setProperty">
+ <string>toolTipText</string>
+ <string>Add a new filter</string>
+ </void>
+ <void method="setProperty">
+ <string>margin</string>
+ <object class="java.awt.Insets">
+ <int>2</int>
+ <int>2</int>
+ <int>2</int>
+ <int>2</int>
+ </object>
+ </void>
+ <void property="name">
+ <string>addRow</string>
+ </void>
+ <void method="auxiliary">
+ <void method="setProperty">
+ <string>JavaCodeGenerator.variableGetter</string>
+ <boolean>true</boolean>
+ </void>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>Center</string>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <null/>
+ <void method="setProperty">
+ <string>location</string>
+ <object class="java.awt.Point">
+ <int>0</int>
+ <int>0</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>size</string>
+ <object class="java.awt.Dimension">
+ <int>500</int>
+ <int>300</int>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+</java>
diff --git a/org/broad/igv/cbio/FilterGeneNetworkUI$1.class b/org/broad/igv/cbio/FilterGeneNetworkUI$1.class
new file mode 100644
index 0000000..df861ca
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diff --git a/org/broad/igv/cbio/FilterGeneNetworkUI$10.class b/org/broad/igv/cbio/FilterGeneNetworkUI$10.class
new file mode 100644
index 0000000..59dae7c
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diff --git a/org/broad/igv/cbio/FilterGeneNetworkUI$11.class b/org/broad/igv/cbio/FilterGeneNetworkUI$11.class
new file mode 100644
index 0000000..dfb1bb6
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diff --git a/org/broad/igv/cbio/FilterGeneNetworkUI$2.class b/org/broad/igv/cbio/FilterGeneNetworkUI$2.class
new file mode 100644
index 0000000..2172124
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diff --git a/org/broad/igv/cbio/FilterGeneNetworkUI$3.class b/org/broad/igv/cbio/FilterGeneNetworkUI$3.class
new file mode 100644
index 0000000..6b9e79a
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diff --git a/org/broad/igv/cbio/FilterGeneNetworkUI$4.class b/org/broad/igv/cbio/FilterGeneNetworkUI$4.class
new file mode 100644
index 0000000..c242d12
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diff --git a/org/broad/igv/cbio/FilterGeneNetworkUI$5.class b/org/broad/igv/cbio/FilterGeneNetworkUI$5.class
new file mode 100644
index 0000000..4a4e5e5
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diff --git a/org/broad/igv/cbio/FilterGeneNetworkUI$6.class b/org/broad/igv/cbio/FilterGeneNetworkUI$6.class
new file mode 100644
index 0000000..20f7894
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diff --git a/org/broad/igv/cbio/FilterGeneNetworkUI$7.class b/org/broad/igv/cbio/FilterGeneNetworkUI$7.class
new file mode 100644
index 0000000..455f536
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diff --git a/org/broad/igv/cbio/FilterGeneNetworkUI$8.class b/org/broad/igv/cbio/FilterGeneNetworkUI$8.class
new file mode 100644
index 0000000..097ae3e
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diff --git a/org/broad/igv/cbio/FilterGeneNetworkUI$9.class b/org/broad/igv/cbio/FilterGeneNetworkUI$9.class
new file mode 100644
index 0000000..9765da1
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diff --git a/org/broad/igv/cbio/FilterGeneNetworkUI$GraphListModel.class b/org/broad/igv/cbio/FilterGeneNetworkUI$GraphListModel.class
new file mode 100644
index 0000000..cacb966
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diff --git a/org/broad/igv/cbio/FilterGeneNetworkUI$RefreshListener.class b/org/broad/igv/cbio/FilterGeneNetworkUI$RefreshListener.class
new file mode 100644
index 0000000..7141276
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diff --git a/org/broad/igv/cbio/FilterGeneNetworkUI.class b/org/broad/igv/cbio/FilterGeneNetworkUI.class
new file mode 100644
index 0000000..7a4f636
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diff --git a/org/broad/igv/cbio/FilterGeneNetworkUI.jfd b/org/broad/igv/cbio/FilterGeneNetworkUI.jfd
new file mode 100644
index 0000000..449d908
--- /dev/null
+++ b/org/broad/igv/cbio/FilterGeneNetworkUI.jfd
@@ -0,0 +1,911 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<java version="1.6.0_31" class="java.beans.XMLDecoder">
+ <object class="com.jformdesigner.model.FormModel">
+ <void property="contentType">
+ <string>form/swing</string>
+ </void>
+ <void property="root">
+ <object class="com.jformdesigner.model.FormRoot">
+ <void method="add">
+ <object class="com.jformdesigner.model.FormWindow">
+ <string>javax.swing.JDialog</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.BorderLayout</class>
+ </object>
+ <void method="setProperty">
+ <string>minimumSize</string>
+ <object class="java.awt.Dimension">
+ <int>600</int>
+ <int>22</int>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JTabbedPane</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>javax.swing.JTabbedPane</class>
+ </object>
+ <void method="setProperty">
+ <string>preferredSize</string>
+ <object class="java.awt.Dimension">
+ <int>550</int>
+ <int>346</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>minimumSize</string>
+ <object class="java.awt.Dimension">
+ <int>550</int>
+ <int>346</int>
+ </object>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>javax.swing.event.ChangeListener</string>
+ <string>stateChanged</string>
+ <string>tabbedPaneStateChanged</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ <void property="name">
+ <string>tabbedPane</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.GridBagLayout</class>
+ <void method="setProperty">
+ <string>$columnSpecs</string>
+ <string>0:1.0</string>
+ </void>
+ <void method="setProperty">
+ <string>$rowSpecs</string>
+ <string>0, 0, 0:1.0, 0</string>
+ </void>
+ <void method="setProperty">
+ <string>$alignTop</string>
+ <boolean>true</boolean>
+ </void>
+ <void method="setProperty">
+ <string>$alignLeft</string>
+ <boolean>true</boolean>
+ </void>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="javax.swing.border.EmptyBorder">
+ <int>12</int>
+ <int>12</int>
+ <int>12</int>
+ <int>12</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>minimumSize</string>
+ <object class="java.awt.Dimension">
+ <int>443</int>
+ <int>300</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>preferredSize</string>
+ <object class="java.awt.Dimension">
+ <int>443</int>
+ <int>300</int>
+ </object>
+ </void>
+ <void property="name">
+ <string>dialogPane</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.GridBagLayout</class>
+ <void method="setProperty">
+ <string>$columnSpecs</string>
+ <string>0, 0</string>
+ </void>
+ <void method="setProperty">
+ <string>$rowSpecs</string>
+ <string>0</string>
+ </void>
+ <void method="setProperty">
+ <string>$hGap</string>
+ <int>5</int>
+ </void>
+ <void method="setProperty">
+ <string>$vGap</string>
+ <int>5</int>
+ </void>
+ <void method="setProperty">
+ <string>$alignLeft</string>
+ <boolean>true</boolean>
+ </void>
+ <void method="setProperty">
+ <string>$alignTop</string>
+ <boolean>true</boolean>
+ </void>
+ </object>
+ <void property="name">
+ <string>panel1</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Add Filter</string>
+ </void>
+ <void method="setProperty">
+ <string>maximumSize</string>
+ <object class="java.awt.Dimension">
+ <int>200</int>
+ <int>28</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>minimumSize</string>
+ <object class="java.awt.Dimension">
+ <int>100</int>
+ <int>28</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>preferredSize</string>
+ <object class="java.awt.Dimension">
+ <int>150</int>
+ <int>28</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>visible</string>
+ <boolean>false</boolean>
+ </void>
+ <void property="name">
+ <string>addRow</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>addRowActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridwidth</string>
+ <int>2</int>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>javax.swing.BoxLayout</class>
+ <void method="setProperty">
+ <string>axis</string>
+ <int>1</int>
+ </void>
+ </object>
+ <void property="name">
+ <string>contentPane</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>1</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.GridBagLayout</class>
+ <void method="setProperty">
+ <string>$columnSpecs</string>
+ <string>0:1.0, 80, 80, 80</string>
+ </void>
+ <void method="setProperty">
+ <string>$rowSpecs</string>
+ <string>0, 0, 0</string>
+ </void>
+ <void method="setProperty">
+ <string>$hGap</string>
+ <int>5</int>
+ </void>
+ <void method="setProperty">
+ <string>$vGap</string>
+ <int>5</int>
+ </void>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="javax.swing.border.EmptyBorder">
+ <int>12</int>
+ <int>0</int>
+ <int>0</int>
+ <int>0</int>
+ </object>
+ </void>
+ <void property="name">
+ <string>buttonBar</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JCheckBox</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Keep Isolated Genes</string>
+ </void>
+ <void method="setProperty">
+ <string>visible</string>
+ <boolean>false</boolean>
+ </void>
+ <void property="name">
+ <string>keepIsolated</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>1</int>
+ </void>
+ <void method="setProperty">
+ <string>gridwidth</string>
+ <int>2</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>View Network</string>
+ </void>
+ <void method="setProperty">
+ <string>toolTipText</string>
+ <string>Display the network in a web browser</string>
+ </void>
+ <void property="name">
+ <string>okButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>okButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>2</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Refresh Filter</string>
+ </void>
+ <void method="setProperty">
+ <string>visible</string>
+ <boolean>false</boolean>
+ </void>
+ <void property="name">
+ <string>refFilter</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>refFilterActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>1</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Cancel</string>
+ </void>
+ <void property="name">
+ <string>cancelButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>cancelButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>2</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Help</string>
+ </void>
+ <void method="setProperty">
+ <string>visible</string>
+ <boolean>false</boolean>
+ </void>
+ <void property="name">
+ <string>helpButton</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>3</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>2</int>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>3</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JScrollPane</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>javax.swing.JScrollPane</class>
+ </object>
+ <void property="name">
+ <string>scrollPane1</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTable</string>
+ <void method="setProperty">
+ <string>autoCreateRowSorter</string>
+ <boolean>true</boolean>
+ </void>
+ <void property="name">
+ <string>geneTable</string>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>2</int>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <null/>
+ <void method="setProperty">
+ <string>title</string>
+ <string>Filter</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.BorderLayout</class>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="javax.swing.border.EmptyBorder">
+ <int>12</int>
+ <int>12</int>
+ <int>12</int>
+ <int>12</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>preferredSize</string>
+ <object class="java.awt.Dimension">
+ <int>550</int>
+ <int>196</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>minimumSize</string>
+ <object class="java.awt.Dimension">
+ <int>550</int>
+ <int>196</int>
+ </object>
+ </void>
+ <void property="name">
+ <string>thresholds</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.GridBagLayout</class>
+ <void method="setProperty">
+ <string>$columnSpecs</string>
+ <string>0:1.0, 0, 0, 0:1.0, 0:1.0</string>
+ </void>
+ <void method="setProperty">
+ <string>$rowSpecs</string>
+ <string>0:1.0, 0:1.0, 0:1.0, 0:1.0</string>
+ </void>
+ <void method="setProperty">
+ <string>$hGap</string>
+ <int>5</int>
+ </void>
+ <void method="setProperty">
+ <string>$vGap</string>
+ <int>10</int>
+ </void>
+ <void method="setProperty">
+ <string>$alignTop</string>
+ <boolean>true</boolean>
+ </void>
+ <void method="setProperty">
+ <string>$alignLeft</string>
+ <boolean>true</boolean>
+ </void>
+ </object>
+ <void property="name">
+ <string>contentPanel</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Mutation:</string>
+ </void>
+ <void method="setProperty">
+ <string>horizontalAlignment</string>
+ <int>4</int>
+ </void>
+ <void method="setProperty">
+ <string>labelFor</string>
+ <object class="com.jformdesigner.model.FormReference">
+ <string>mutInput</string>
+ </object>
+ </void>
+ <void property="name">
+ <string>label1</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>1</string>
+ </void>
+ <void method="setProperty">
+ <string>autoscrolls</string>
+ <boolean>false</boolean>
+ </void>
+ <void method="setProperty">
+ <string>minimumSize</string>
+ <object class="java.awt.Dimension">
+ <int>34</int>
+ <int>28</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>preferredSize</string>
+ <object class="java.awt.Dimension">
+ <int>45</int>
+ <int>28</int>
+ </object>
+ </void>
+ <void property="name">
+ <string>mutInput</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>1</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Amplification:</string>
+ </void>
+ <void method="setProperty">
+ <string>horizontalAlignment</string>
+ <int>4</int>
+ </void>
+ <void method="setProperty">
+ <string>labelFor</string>
+ <object class="com.jformdesigner.model.FormReference">
+ <string>ampInput</string>
+ </object>
+ </void>
+ <void property="name">
+ <string>label2</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>1</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>0.7</string>
+ </void>
+ <void method="setProperty">
+ <string>minimumSize</string>
+ <object class="java.awt.Dimension">
+ <int>34</int>
+ <int>28</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>preferredSize</string>
+ <object class="java.awt.Dimension">
+ <int>45</int>
+ <int>28</int>
+ </object>
+ </void>
+ <void property="name">
+ <string>ampInput</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>1</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>1</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Deletion:</string>
+ </void>
+ <void method="setProperty">
+ <string>horizontalAlignment</string>
+ <int>4</int>
+ </void>
+ <void method="setProperty">
+ <string>labelFor</string>
+ <object class="com.jformdesigner.model.FormReference">
+ <string>delInput</string>
+ </object>
+ </void>
+ <void property="name">
+ <string>label3</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>1</int>
+ </void>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>2</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>0.7</string>
+ </void>
+ <void method="setProperty">
+ <string>minimumSize</string>
+ <object class="java.awt.Dimension">
+ <int>34</int>
+ <int>28</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>preferredSize</string>
+ <object class="java.awt.Dimension">
+ <int>45</int>
+ <int>28</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>maximumSize</string>
+ <object class="java.awt.Dimension">
+ <int>50</int>
+ <int>2147483647</int>
+ </object>
+ </void>
+ <void property="name">
+ <string>delInput</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>3</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>1</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Expression Up:</string>
+ </void>
+ <void method="setProperty">
+ <string>horizontalAlignment</string>
+ <int>4</int>
+ </void>
+ <void method="setProperty">
+ <string>labelFor</string>
+ <object class="com.jformdesigner.model.FormReference">
+ <string>expUpInput</string>
+ </object>
+ </void>
+ <void property="name">
+ <string>label4</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>2</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>0.1</string>
+ </void>
+ <void method="setProperty">
+ <string>minimumSize</string>
+ <object class="java.awt.Dimension">
+ <int>34</int>
+ <int>28</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>preferredSize</string>
+ <object class="java.awt.Dimension">
+ <int>35</int>
+ <int>28</int>
+ </object>
+ </void>
+ <void property="name">
+ <string>expUpInput</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>1</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>2</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Expression Down:</string>
+ </void>
+ <void method="setProperty">
+ <string>horizontalAlignment</string>
+ <int>4</int>
+ </void>
+ <void method="setProperty">
+ <string>labelFor</string>
+ <object class="com.jformdesigner.model.FormReference">
+ <string>expDownInput</string>
+ </object>
+ </void>
+ <void property="name">
+ <string>label7</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>2</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>0.1</string>
+ </void>
+ <void method="setProperty">
+ <string>preferredSize</string>
+ <object class="java.awt.Dimension">
+ <int>45</int>
+ <int>28</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>minimumSize</string>
+ <object class="java.awt.Dimension">
+ <int>34</int>
+ <int>28</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>maximumSize</string>
+ <object class="java.awt.Dimension">
+ <int>50</int>
+ <int>2147483647</int>
+ </object>
+ </void>
+ <void property="name">
+ <string>expDownInput</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>3</int>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>Center</string>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <null/>
+ <void method="setProperty">
+ <string>title</string>
+ <string>Thresholds</string>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>North</string>
+ </void>
+ </object>
+ </void>
+ <void property="name">
+ <string>this</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <null/>
+ <void method="setProperty">
+ <string>location</string>
+ <object class="java.awt.Point">
+ <int>0</int>
+ <int>0</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>size</string>
+ <object class="java.awt.Dimension">
+ <int>550</int>
+ <int>370</int>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+</java>
diff --git a/org/broad/igv/cbio/GeneNetwork$1.class b/org/broad/igv/cbio/GeneNetwork$1.class
new file mode 100644
index 0000000..65a943b
Binary files /dev/null and b/org/broad/igv/cbio/GeneNetwork$1.class differ
diff --git a/org/broad/igv/cbio/GeneNetwork$2.class b/org/broad/igv/cbio/GeneNetwork$2.class
new file mode 100644
index 0000000..35de149
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diff --git a/org/broad/igv/cbio/GeneNetwork$ByteArrayOutputStreamChild.class b/org/broad/igv/cbio/GeneNetwork$ByteArrayOutputStreamChild.class
new file mode 100644
index 0000000..cb8090d
Binary files /dev/null and b/org/broad/igv/cbio/GeneNetwork$ByteArrayOutputStreamChild.class differ
diff --git a/org/broad/igv/cbio/GeneNetwork$ScoreData.class b/org/broad/igv/cbio/GeneNetwork$ScoreData.class
new file mode 100644
index 0000000..13ac330
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diff --git a/org/broad/igv/cbio/GeneNetwork.class b/org/broad/igv/cbio/GeneNetwork.class
new file mode 100644
index 0000000..46c0b47
Binary files /dev/null and b/org/broad/igv/cbio/GeneNetwork.class differ
diff --git a/org/broad/igv/cbio/resources/post_stub.html b/org/broad/igv/cbio/resources/post_stub.html
new file mode 100644
index 0000000..c7903f4
--- /dev/null
+++ b/org/broad/igv/cbio/resources/post_stub.html
@@ -0,0 +1,39 @@
+<!--
+ ~ Copyright (c) 2007-2012 The Broad Institute, Inc.
+ ~ SOFTWARE COPYRIGHT NOTICE
+ ~ This software and its documentation are the copyright of the Broad Institute, Inc. All rights are reserved.
+ ~
+ ~ This software is supplied without any warranty or guaranteed support whatsoever. The Broad Institute is not responsible for its use, misuse, or functionality.
+ ~
+ ~ This software is licensed under the terms of the GNU Lesser General Public License (LGPL),
+ ~ Version 2.1 which is available at http://www.opensource.org/licenses/lgpl-2.1.php.
+ -->
+
+<!--This document is a template. The intention is to generate GraphML, generate a new file
+based on this template with the GraphML data in the appropriate location,
+and use javascript to automatically post it to cBio. This way, IGV directs a browser to
+post a large amount of data. For testing purposes, this document should be well-formed XML-->
+<html>
+<head>
+ <script type="text/javascript">
+ function formSubmit() {
+ document.getElementById("gmlform").submit();
+ }
+ </script>
+</head>
+
+<body onload="formSubmit()">
+
+<form id="gmlform" name="input" action="http://www.cbioportal.org/public-portal/netviz.jsp"
+ enctype="multipart/form-data" method="post" display="none">
+ <textarea rows="10" cols="530" id="graphml" name="graphml">
+ allthegraphmldatagoeshere
+ </textarea>
+ <input type="hidden" name="format" value="graphml.gz.base64"></input>
+ <input type="submit" name="submit_button" value="Submit Data"></input>
+</form>
+If you are not redirected, most likely you have javascript disabled.
+The cBio viewer requires javascript.
+Click the "Submit Data" button above to submit the data manually
+</body>
+</html>
\ No newline at end of file
diff --git a/org/broad/igv/charts/Axis$Orientation.class b/org/broad/igv/charts/Axis$Orientation.class
new file mode 100644
index 0000000..26914ae
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diff --git a/org/broad/igv/charts/Axis.class b/org/broad/igv/charts/Axis.class
new file mode 100644
index 0000000..a8d1b31
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diff --git a/org/broad/igv/charts/AxisPanel.class b/org/broad/igv/charts/AxisPanel.class
new file mode 100644
index 0000000..16c0bf6
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diff --git a/org/broad/igv/charts/ChartLayout.class b/org/broad/igv/charts/ChartLayout.class
new file mode 100644
index 0000000..de1e5c4
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diff --git a/org/broad/igv/charts/ChartPanel$LegendIcon.class b/org/broad/igv/charts/ChartPanel$LegendIcon.class
new file mode 100644
index 0000000..6d4b7b7
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diff --git a/org/broad/igv/charts/ChartPanel$LegendPanel$1.class b/org/broad/igv/charts/ChartPanel$LegendPanel$1.class
new file mode 100644
index 0000000..411ef3e
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diff --git a/org/broad/igv/charts/ChartPanel$LegendPanel$2.class b/org/broad/igv/charts/ChartPanel$LegendPanel$2.class
new file mode 100644
index 0000000..43e5562
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diff --git a/org/broad/igv/charts/ChartPanel$LegendPanel.class b/org/broad/igv/charts/ChartPanel$LegendPanel.class
new file mode 100644
index 0000000..0d97cf4
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diff --git a/org/broad/igv/charts/ChartPanel$PlotPanel$1.class b/org/broad/igv/charts/ChartPanel$PlotPanel$1.class
new file mode 100644
index 0000000..92e81fd
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diff --git a/org/broad/igv/charts/ChartPanel$PlotPanel.class b/org/broad/igv/charts/ChartPanel$PlotPanel.class
new file mode 100644
index 0000000..1571622
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diff --git a/org/broad/igv/charts/ChartPanel.class b/org/broad/igv/charts/ChartPanel.class
new file mode 100644
index 0000000..905325a
Binary files /dev/null and b/org/broad/igv/charts/ChartPanel.class differ
diff --git a/org/broad/igv/charts/ScatterPlot.class b/org/broad/igv/charts/ScatterPlot.class
new file mode 100644
index 0000000..4518128
Binary files /dev/null and b/org/broad/igv/charts/ScatterPlot.class differ
diff --git a/org/broad/igv/charts/ScatterPlotData.class b/org/broad/igv/charts/ScatterPlotData.class
new file mode 100644
index 0000000..3575c87
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diff --git a/org/broad/igv/charts/ScatterPlotDemo$1.class b/org/broad/igv/charts/ScatterPlotDemo$1.class
new file mode 100644
index 0000000..68c3dbb
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diff --git a/org/broad/igv/charts/ScatterPlotDemo.class b/org/broad/igv/charts/ScatterPlotDemo.class
new file mode 100644
index 0000000..867af54
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diff --git a/org/broad/igv/charts/ScatterPlotFrame$1.class b/org/broad/igv/charts/ScatterPlotFrame$1.class
new file mode 100644
index 0000000..e47c9c4
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diff --git a/org/broad/igv/charts/ScatterPlotFrame$2.class b/org/broad/igv/charts/ScatterPlotFrame$2.class
new file mode 100644
index 0000000..8e2d23d
Binary files /dev/null and b/org/broad/igv/charts/ScatterPlotFrame$2.class differ
diff --git a/org/broad/igv/charts/ScatterPlotFrame$3.class b/org/broad/igv/charts/ScatterPlotFrame$3.class
new file mode 100644
index 0000000..d75b6f8
Binary files /dev/null and b/org/broad/igv/charts/ScatterPlotFrame$3.class differ
diff --git a/org/broad/igv/charts/ScatterPlotFrame$4.class b/org/broad/igv/charts/ScatterPlotFrame$4.class
new file mode 100644
index 0000000..3a0a772
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diff --git a/org/broad/igv/charts/ScatterPlotFrame.class b/org/broad/igv/charts/ScatterPlotFrame.class
new file mode 100644
index 0000000..8f9bc98
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diff --git a/org/broad/igv/charts/ScatterPlotFrame.jfd b/org/broad/igv/charts/ScatterPlotFrame.jfd
new file mode 100644
index 0000000..d76f3bb
--- /dev/null
+++ b/org/broad/igv/charts/ScatterPlotFrame.jfd
@@ -0,0 +1,359 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<java version="1.6.0_26" class="java.beans.XMLDecoder">
+ <object class="com.jformdesigner.model.FormModel">
+ <void property="contentType">
+ <string>form/swing</string>
+ </void>
+ <void property="root">
+ <object class="com.jformdesigner.model.FormRoot">
+ <void method="add">
+ <object class="com.jformdesigner.model.FormWindow">
+ <string>javax.swing.JFrame</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.BorderLayout</class>
+ </object>
+ <void method="setProperty">
+ <string>focusTraversalPolicyProvider</string>
+ <boolean>true</boolean>
+ </void>
+ <void method="setProperty">
+ <string>$sizePolicy</string>
+ <int>1</int>
+ </void>
+ <void method="setProperty">
+ <string>defaultCloseOperation</string>
+ <int>2</int>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>javax.swing.BoxLayout</class>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="javax.swing.border.BevelBorder">
+ <int>1</int>
+ <null/>
+ <null/>
+ <null/>
+ <null/>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>preferredSize</string>
+ <object class="java.awt.Dimension">
+ <int>420</int>
+ <int>45</int>
+ </object>
+ </void>
+ <void property="name">
+ <string>commandBar</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>com.jformdesigner.designer.wrapper.HSpacer</string>
+ <void property="name">
+ <string>hSpacer3</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>javax.swing.BoxLayout</class>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="com.jformdesigner.model.FormObject" field="NULL_VALUE"/>
+ </void>
+ <void method="setProperty">
+ <string>preferredSize</string>
+ <object class="java.awt.Dimension">
+ <int>180</int>
+ <int>41</int>
+ </object>
+ </void>
+ <void property="name">
+ <string>panel2</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>X: </string>
+ </void>
+ <void property="name">
+ <string>label1</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JComboBox</string>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="com.jformdesigner.model.FormObject" field="NULL_VALUE"/>
+ </void>
+ <void method="setProperty">
+ <string>preferredSize</string>
+ <object class="java.awt.Dimension">
+ <int>120</int>
+ <int>27</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>toolTipText</string>
+ <string>Set data type for X axis</string>
+ </void>
+ <void property="name">
+ <string>xAxisComboBox</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>axisChanged</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>com.jformdesigner.designer.wrapper.HSpacer</string>
+ <void property="name">
+ <string>hSpacer1</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>javax.swing.BoxLayout</class>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="com.jformdesigner.model.FormObject" field="NULL_VALUE"/>
+ </void>
+ <void method="setProperty">
+ <string>preferredSize</string>
+ <object class="java.awt.Dimension">
+ <int>180</int>
+ <int>41</int>
+ </object>
+ </void>
+ <void property="name">
+ <string>panel3</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Y:</string>
+ </void>
+ <void property="name">
+ <string>label2</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JComboBox</string>
+ <void method="setProperty">
+ <string>preferredSize</string>
+ <object class="java.awt.Dimension">
+ <int>120</int>
+ <int>27</int>
+ </object>
+ </void>
+ <void property="name">
+ <string>yAxisComboBox</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>axisChanged</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>com.jformdesigner.designer.wrapper.HSpacer</string>
+ <void property="name">
+ <string>hSpacer2</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>javax.swing.BoxLayout</class>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="com.jformdesigner.model.FormObject" field="NULL_VALUE"/>
+ </void>
+ <void method="setProperty">
+ <string>preferredSize</string>
+ <object class="java.awt.Dimension">
+ <int>250</int>
+ <int>27</int>
+ </object>
+ </void>
+ <void property="name">
+ <string>panel4</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Classify By:</string>
+ </void>
+ <void property="name">
+ <string>label3</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JComboBox</string>
+ <void method="setProperty">
+ <string>preferredSize</string>
+ <object class="java.awt.Dimension">
+ <int>150</int>
+ <int>27</int>
+ </object>
+ </void>
+ <void property="name">
+ <string>classifyComboBox</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>attributeChanged</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>com.jformdesigner.designer.wrapper.HSpacer</string>
+ <void property="name">
+ <string>hSpacer4</string>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>North</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>org.broad.igv.charts.ChartPanel</string>
+ <void property="name">
+ <string>chartPanel</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>Center</string>
+ </void>
+ </object>
+ </void>
+ <void property="menuBar">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JMenuBar</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>javax.swing.JMenuBar</class>
+ </object>
+ <void property="name">
+ <string>menuBar</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JMenu</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>javax.swing.JMenu</class>
+ </object>
+ <void method="setProperty">
+ <string>text</string>
+ <string>File</string>
+ </void>
+ <void property="name">
+ <string>fileMenu</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JMenuItem</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Close</string>
+ </void>
+ <void property="name">
+ <string>closeMenuItem</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>closeMenuItemActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+ </void>
+ <void property="name">
+ <string>this</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <null/>
+ <void method="setProperty">
+ <string>location</string>
+ <object class="java.awt.Point">
+ <int>0</int>
+ <int>0</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>size</string>
+ <object class="java.awt.Dimension">
+ <int>815</int>
+ <int>660</int>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+</java>
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+This package, and sub-pacakges, contain development code for special projects.
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Binary files /dev/null and b/org/broad/igv/feature/genome/FastaIndex.class differ
diff --git a/org/broad/igv/feature/genome/FastaIndexedSequence.class b/org/broad/igv/feature/genome/FastaIndexedSequence.class
new file mode 100644
index 0000000..9c538ac
Binary files /dev/null and b/org/broad/igv/feature/genome/FastaIndexedSequence.class differ
diff --git a/org/broad/igv/feature/genome/FastaSequence.class b/org/broad/igv/feature/genome/FastaSequence.class
new file mode 100644
index 0000000..9d910ed
Binary files /dev/null and b/org/broad/igv/feature/genome/FastaSequence.class differ
diff --git a/org/broad/igv/feature/genome/FastaUtils.class b/org/broad/igv/feature/genome/FastaUtils.class
new file mode 100644
index 0000000..02005a7
Binary files /dev/null and b/org/broad/igv/feature/genome/FastaUtils.class differ
diff --git a/org/broad/igv/feature/genome/Genome.class b/org/broad/igv/feature/genome/Genome.class
new file mode 100644
index 0000000..01125f4
Binary files /dev/null and b/org/broad/igv/feature/genome/Genome.class differ
diff --git a/org/broad/igv/feature/genome/GenomeBuilderDialog$1.class b/org/broad/igv/feature/genome/GenomeBuilderDialog$1.class
new file mode 100644
index 0000000..0dc440a
Binary files /dev/null and b/org/broad/igv/feature/genome/GenomeBuilderDialog$1.class differ
diff --git a/org/broad/igv/feature/genome/GenomeBuilderDialog$2.class b/org/broad/igv/feature/genome/GenomeBuilderDialog$2.class
new file mode 100644
index 0000000..208c268
Binary files /dev/null and b/org/broad/igv/feature/genome/GenomeBuilderDialog$2.class differ
diff --git a/org/broad/igv/feature/genome/GenomeBuilderDialog.class b/org/broad/igv/feature/genome/GenomeBuilderDialog.class
new file mode 100644
index 0000000..518549b
Binary files /dev/null and b/org/broad/igv/feature/genome/GenomeBuilderDialog.class differ
diff --git a/org/broad/igv/feature/genome/GenomeBuilderDialog.jfd b/org/broad/igv/feature/genome/GenomeBuilderDialog.jfd
new file mode 100644
index 0000000..88f08b9
--- /dev/null
+++ b/org/broad/igv/feature/genome/GenomeBuilderDialog.jfd
@@ -0,0 +1,209 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<java version="1.6.0_31" class="java.beans.XMLDecoder">
+ <object class="com.jformdesigner.model.FormModel">
+ <void property="contentType">
+ <string>form/swing</string>
+ </void>
+ <void property="root">
+ <object class="com.jformdesigner.model.FormRoot">
+ <void method="add">
+ <object class="com.jformdesigner.model.FormWindow">
+ <string>javax.swing.JDialog</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.BorderLayout</class>
+ </object>
+ <void method="setProperty">
+ <string>$sizePolicy</string>
+ <int>1</int>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.BorderLayout</class>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="javax.swing.border.EmptyBorder">
+ <int>12</int>
+ <int>12</int>
+ <int>12</int>
+ <int>12</int>
+ </object>
+ </void>
+ <void property="name">
+ <string>dialogPane</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.BorderLayout</class>
+ </object>
+ <void property="name">
+ <string>contentPanel</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>org.broad.igv.feature.genome.GenomeBuilderPane</string>
+ <void property="name">
+ <string>panel1</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>Center</string>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>Center</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.GridBagLayout</class>
+ <void method="setProperty">
+ <string>$columnSpecs</string>
+ <string>0:1.0, 80, 80</string>
+ </void>
+ <void method="setProperty">
+ <string>$rowSpecs</string>
+ <string>0</string>
+ </void>
+ <void method="setProperty">
+ <string>$hGap</string>
+ <int>5</int>
+ </void>
+ <void method="setProperty">
+ <string>$vGap</string>
+ <int>5</int>
+ </void>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="javax.swing.border.EmptyBorder">
+ <int>12</int>
+ <int>0</int>
+ <int>0</int>
+ <int>0</int>
+ </object>
+ </void>
+ <void property="name">
+ <string>buttonBar</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>OK</string>
+ </void>
+ <void property="name">
+ <string>okButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>okButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>1</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>0</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Cancel</string>
+ </void>
+ <void property="name">
+ <string>cancelButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>cancelButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>0</int>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>South</string>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>Center</string>
+ </void>
+ </object>
+ </void>
+ <void property="name">
+ <string>this</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <null/>
+ <void method="setProperty">
+ <string>location</string>
+ <object class="java.awt.Point">
+ <int>0</int>
+ <int>0</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>size</string>
+ <object class="java.awt.Dimension">
+ <int>870</int>
+ <int>430</int>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+</java>
diff --git a/org/broad/igv/feature/genome/GenomeBuilderPane$1.class b/org/broad/igv/feature/genome/GenomeBuilderPane$1.class
new file mode 100644
index 0000000..4b51036
Binary files /dev/null and b/org/broad/igv/feature/genome/GenomeBuilderPane$1.class differ
diff --git a/org/broad/igv/feature/genome/GenomeBuilderPane$2.class b/org/broad/igv/feature/genome/GenomeBuilderPane$2.class
new file mode 100644
index 0000000..9a49f25
Binary files /dev/null and b/org/broad/igv/feature/genome/GenomeBuilderPane$2.class differ
diff --git a/org/broad/igv/feature/genome/GenomeBuilderPane$3.class b/org/broad/igv/feature/genome/GenomeBuilderPane$3.class
new file mode 100644
index 0000000..636e932
Binary files /dev/null and b/org/broad/igv/feature/genome/GenomeBuilderPane$3.class differ
diff --git a/org/broad/igv/feature/genome/GenomeBuilderPane$4.class b/org/broad/igv/feature/genome/GenomeBuilderPane$4.class
new file mode 100644
index 0000000..bea18d0
Binary files /dev/null and b/org/broad/igv/feature/genome/GenomeBuilderPane$4.class differ
diff --git a/org/broad/igv/feature/genome/GenomeBuilderPane.class b/org/broad/igv/feature/genome/GenomeBuilderPane.class
new file mode 100644
index 0000000..8f334bd
Binary files /dev/null and b/org/broad/igv/feature/genome/GenomeBuilderPane.class differ
diff --git a/org/broad/igv/feature/genome/GenomeBuilderPane.jfd b/org/broad/igv/feature/genome/GenomeBuilderPane.jfd
new file mode 100644
index 0000000..e04b48d
--- /dev/null
+++ b/org/broad/igv/feature/genome/GenomeBuilderPane.jfd
@@ -0,0 +1,800 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<java version="1.6.0_31" class="java.beans.XMLDecoder">
+ <object class="com.jformdesigner.model.FormModel">
+ <void property="contentType">
+ <string>form/swing</string>
+ </void>
+ <void property="root">
+ <object class="com.jformdesigner.model.FormRoot">
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.BorderLayout</class>
+ </object>
+ <void method="setProperty">
+ <string>font</string>
+ <object class="java.awt.Font">
+ <string>Tahoma</string>
+ <int>2</int>
+ <int>12</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>maximumSize</string>
+ <object class="java.awt.Dimension">
+ <int>900</int>
+ <int>500</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>minimumSize</string>
+ <object class="java.awt.Dimension">
+ <int>400</int>
+ <int>200</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>preferredSize</string>
+ <object class="java.awt.Dimension">
+ <int>700</int>
+ <int>200</int>
+ </object>
+ </void>
+ <void property="name">
+ <string>this</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>javax.swing.BoxLayout</class>
+ <void method="setProperty">
+ <string>axis</string>
+ <int>1</int>
+ </void>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="javax.swing.border.EmptyBorder">
+ <int>20</int>
+ <int>20</int>
+ <int>20</int>
+ <int>20</int>
+ </object>
+ </void>
+ <void property="name">
+ <string>panel3</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>com.jformdesigner.runtime.NullLayout</class>
+ <void method="setProperty">
+ <string>autoSize</string>
+ <boolean>false</boolean>
+ </void>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="javax.swing.border.EmptyBorder">
+ <int>0</int>
+ <int>0</int>
+ <int>30</int>
+ <int>0</int>
+ </object>
+ </void>
+ <void property="name">
+ <string>panel2</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Unique identifier</string>
+ </void>
+ <void method="setProperty">
+ <string>toolTipText</string>
+ <string>Unique identifier (e.g. hg18)</string>
+ </void>
+ <void method="setProperty">
+ <string>maximumSize</string>
+ <object class="java.awt.Dimension">
+ <int>84</int>
+ <int>16</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>minimumSize</string>
+ <object class="java.awt.Dimension">
+ <int>84</int>
+ <int>16</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>preferredSize</string>
+ <object class="java.awt.Dimension">
+ <int>14</int>
+ <int>16</int>
+ </object>
+ </void>
+ <void property="name">
+ <string>genomeDisplayNameLabel2</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>15</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>22</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>125</int>
+ </void>
+ <void method="setProperty">
+ <string>height</string>
+ <int>28</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void method="setProperty">
+ <string>toolTipText</string>
+ <string>A uniqe identifier for the genome</string>
+ </void>
+ <void property="name">
+ <string>idField</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>145</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>22</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>548</int>
+ </void>
+ <void method="setProperty">
+ <string>height</string>
+ <int>29</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Descriptive name</string>
+ </void>
+ <void property="name">
+ <string>genomeDisplayNameLabel</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>15</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>56</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>175</int>
+ </void>
+ <void method="setProperty">
+ <string>height</string>
+ <int>28</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void method="setProperty">
+ <string>toolTipText</string>
+ <string>The user-readable name of the genome</string>
+ </void>
+ <void method="setProperty">
+ <string>preferredSize</string>
+ <object class="java.awt.Dimension">
+ <int>400</int>
+ <int>28</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>minimumSize</string>
+ <object class="java.awt.Dimension">
+ <int>25</int>
+ <int>28</int>
+ </object>
+ </void>
+ <void property="name">
+ <string>genomeDisplayNameTextField</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>145</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>56</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>548</int>
+ </void>
+ <void method="setProperty">
+ <string>height</string>
+ <int>29</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>FASTA file</string>
+ </void>
+ <void property="name">
+ <string>fastaFileLabel</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>15</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>88</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>175</int>
+ </void>
+ <void method="setProperty">
+ <string>height</string>
+ <int>29</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void method="setProperty">
+ <string>toolTipText</string>
+ <string>A FASTA data file</string>
+ </void>
+ <void method="setProperty">
+ <string>preferredSize</string>
+ <object class="java.awt.Dimension">
+ <int>400</int>
+ <int>28</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>minimumSize</string>
+ <object class="java.awt.Dimension">
+ <int>25</int>
+ <int>28</int>
+ </object>
+ </void>
+ <void property="name">
+ <string>fastaFileTextField</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>145</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>88</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>548</int>
+ </void>
+ <void method="setProperty">
+ <string>height</string>
+ <int>29</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>label</string>
+ <string>...</string>
+ </void>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Browse</string>
+ </void>
+ <void property="name">
+ <string>fastaFileButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>fastaFileButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>698</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>88</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>83</int>
+ </void>
+ </object>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>com.jformdesigner.runtime.NullLayout</class>
+ <void method="setProperty">
+ <string>autoSize</string>
+ <boolean>false</boolean>
+ </void>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="javax.swing.border.TitledBorder">
+ <null/>
+ <string>Optional</string>
+ <int>4</int>
+ <int>0</int>
+ <object class="java.awt.Font">
+ <string>Lucida Grande</string>
+ <int>1</int>
+ <int>13</int>
+ </object>
+ <null/>
+ </object>
+ </void>
+ <void property="name">
+ <string>panel1</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Cytoband file</string>
+ </void>
+ <void property="name">
+ <string>cytobandFileLabel</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>15</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>25</int>
+ </void>
+ <void method="setProperty">
+ <string>height</string>
+ <int>29</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>105</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void method="setProperty">
+ <string>toolTipText</string>
+ <string>A cytoband data file</string>
+ </void>
+ <void method="setProperty">
+ <string>preferredSize</string>
+ <object class="java.awt.Dimension">
+ <int>400</int>
+ <int>28</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>minimumSize</string>
+ <object class="java.awt.Dimension">
+ <int>25</int>
+ <int>28</int>
+ </object>
+ </void>
+ <void property="name">
+ <string>cytobandFileTextField</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>145</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>22</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>548</int>
+ </void>
+ <void method="setProperty">
+ <string>height</string>
+ <int>29</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>label</string>
+ <string>...</string>
+ </void>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Browse</string>
+ </void>
+ <void property="name">
+ <string>cytobandFileButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>cytobandFileButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>698</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>22</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>83</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Gene file</string>
+ </void>
+ <void property="name">
+ <string>refFlatFileLabel</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>15</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>56</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>84</int>
+ </void>
+ <void method="setProperty">
+ <string>height</string>
+ <int>29</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void method="setProperty">
+ <string>toolTipText</string>
+ <string>An annotation file</string>
+ </void>
+ <void method="setProperty">
+ <string>preferredSize</string>
+ <object class="java.awt.Dimension">
+ <int>400</int>
+ <int>28</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>minimumSize</string>
+ <object class="java.awt.Dimension">
+ <int>25</int>
+ <int>28</int>
+ </object>
+ </void>
+ <void property="name">
+ <string>refFlatFileTextField</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>145</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>56</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>548</int>
+ </void>
+ <void method="setProperty">
+ <string>height</string>
+ <int>29</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>label</string>
+ <string>...</string>
+ </void>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Browse</string>
+ </void>
+ <void property="name">
+ <string>refFlatFileButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>refFlatFileButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>698</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>56</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>83</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Alias file</string>
+ </void>
+ <void property="name">
+ <string>refFlatFileLabel2</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>15</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>90</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>84</int>
+ </void>
+ <void method="setProperty">
+ <string>height</string>
+ <int>29</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void method="setProperty">
+ <string>preferredSize</string>
+ <object class="java.awt.Dimension">
+ <int>400</int>
+ <int>28</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>minimumSize</string>
+ <object class="java.awt.Dimension">
+ <int>25</int>
+ <int>28</int>
+ </object>
+ </void>
+ <void property="name">
+ <string>chrAliasField</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>145</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>90</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>548</int>
+ </void>
+ <void method="setProperty">
+ <string>height</string>
+ <int>29</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>label</string>
+ <string>...</string>
+ </void>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Browse</string>
+ </void>
+ <void property="name">
+ <string>chrAliasButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>chrAliasButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>698</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>90</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>83</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>com.jformdesigner.designer.wrapper.VSpacer</string>
+ <void property="name">
+ <string>vSpacer2</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>6</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>124</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>84</int>
+ </void>
+ <void method="setProperty">
+ <string>height</string>
+ <int>20</int>
+ </void>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>Center</string>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <null/>
+ <void method="setProperty">
+ <string>size</string>
+ <object class="java.awt.Dimension">
+ <int>845</int>
+ <int>425</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>location</string>
+ <object class="java.awt.Point">
+ <int>25</int>
+ <int>5</int>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+</java>
diff --git a/org/broad/igv/feature/genome/GenomeDescriptor.class b/org/broad/igv/feature/genome/GenomeDescriptor.class
new file mode 100644
index 0000000..40a86cd
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diff --git a/org/broad/igv/feature/genome/GenomeException.class b/org/broad/igv/feature/genome/GenomeException.class
new file mode 100644
index 0000000..7bc252d
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diff --git a/org/broad/igv/feature/genome/GenomeImpl$ChromosomeComparator.class b/org/broad/igv/feature/genome/GenomeImpl$ChromosomeComparator.class
new file mode 100644
index 0000000..7fd605d
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diff --git a/org/broad/igv/feature/genome/GenomeImpl.class b/org/broad/igv/feature/genome/GenomeImpl.class
new file mode 100644
index 0000000..c92c713
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diff --git a/org/broad/igv/feature/genome/GenomeImporter.class b/org/broad/igv/feature/genome/GenomeImporter.class
new file mode 100644
index 0000000..2021dd5
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diff --git a/org/broad/igv/feature/genome/GenomeListItem.class b/org/broad/igv/feature/genome/GenomeListItem.class
new file mode 100644
index 0000000..ec7c7fd
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diff --git a/org/broad/igv/feature/genome/GenomeManager.class b/org/broad/igv/feature/genome/GenomeManager.class
new file mode 100644
index 0000000..ba33edd
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diff --git a/org/broad/igv/feature/genome/GenomeServerException.class b/org/broad/igv/feature/genome/GenomeServerException.class
new file mode 100644
index 0000000..6b01ce2
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diff --git a/org/broad/igv/feature/genome/GenomeZipDescriptor.class b/org/broad/igv/feature/genome/GenomeZipDescriptor.class
new file mode 100644
index 0000000..bc28532
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diff --git a/org/broad/igv/feature/genome/IGVSequence.class b/org/broad/igv/feature/genome/IGVSequence.class
new file mode 100644
index 0000000..4e65229
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diff --git a/org/broad/igv/feature/genome/Sequence.class b/org/broad/igv/feature/genome/Sequence.class
new file mode 100644
index 0000000..6d49aee
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diff --git a/org/broad/igv/feature/genome/SequenceHelper$SequenceTile.class b/org/broad/igv/feature/genome/SequenceHelper$SequenceTile.class
new file mode 100644
index 0000000..b47bca7
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diff --git a/org/broad/igv/feature/genome/SequenceHelper.class b/org/broad/igv/feature/genome/SequenceHelper.class
new file mode 100644
index 0000000..fb61c0b
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diff --git a/org/broad/igv/feature/genome/SequenceServletWrapper.class b/org/broad/igv/feature/genome/SequenceServletWrapper.class
new file mode 100644
index 0000000..9dcc40a
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diff --git a/org/broad/igv/feature/genome/ServletSequence.class b/org/broad/igv/feature/genome/ServletSequence.class
new file mode 100644
index 0000000..e057c32
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diff --git a/org/broad/igv/feature/tribble/CachingFeatureReader$Bin.class b/org/broad/igv/feature/tribble/CachingFeatureReader$Bin.class
new file mode 100644
index 0000000..0b1bc10
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diff --git a/org/broad/igv/feature/tribble/CachingFeatureReader$BinIterator.class b/org/broad/igv/feature/tribble/CachingFeatureReader$BinIterator.class
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index 0000000..cb6f959
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diff --git a/org/broad/igv/feature/tribble/CachingFeatureReader.class b/org/broad/igv/feature/tribble/CachingFeatureReader.class
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index 0000000..76b2510
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diff --git a/org/broad/igv/feature/tribble/CodecFactory.class b/org/broad/igv/feature/tribble/CodecFactory.class
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diff --git a/org/broad/igv/feature/tribble/FeatureFileHeader.class b/org/broad/igv/feature/tribble/FeatureFileHeader.class
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diff --git a/org/broad/igv/feature/tribble/GFFCodec$GFF2Helper.class b/org/broad/igv/feature/tribble/GFFCodec$GFF2Helper.class
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index 0000000..47be23d
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diff --git a/org/broad/igv/feature/tribble/GFFCodec$GFF3Helper.class b/org/broad/igv/feature/tribble/GFFCodec$GFF3Helper.class
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index 0000000..98f375d
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diff --git a/org/broad/igv/feature/tribble/GFFCodec$Helper.class b/org/broad/igv/feature/tribble/GFFCodec$Helper.class
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diff --git a/org/broad/igv/feature/tribble/GFFCodec$Version.class b/org/broad/igv/feature/tribble/GFFCodec$Version.class
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diff --git a/org/broad/igv/feature/tribble/IGVBEDCodec.class b/org/broad/igv/feature/tribble/IGVBEDCodec.class
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diff --git a/org/broad/igv/feature/tribble/Locus.class b/org/broad/igv/feature/tribble/Locus.class
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index 0000000..20f6d83
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diff --git a/org/broad/igv/feature/tribble/PSLCodec.class b/org/broad/igv/feature/tribble/PSLCodec.class
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index 0000000..eb66bda
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diff --git a/org/broad/igv/feature/tribble/REPMaskCodec.class b/org/broad/igv/feature/tribble/REPMaskCodec.class
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index 0000000..00206eb
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diff --git a/org/broad/igv/feature/tribble/SAMCodec.class b/org/broad/igv/feature/tribble/SAMCodec.class
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index 0000000..7cf6865
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diff --git a/org/broad/igv/feature/tribble/UCSCCodec.class b/org/broad/igv/feature/tribble/UCSCCodec.class
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index 0000000..b4fc689
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diff --git a/org/broad/igv/feature/tribble/UCSCGeneTableCodec$1.class b/org/broad/igv/feature/tribble/UCSCGeneTableCodec$1.class
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diff --git a/org/broad/igv/feature/tribble/UCSCGeneTableCodec$Type.class b/org/broad/igv/feature/tribble/UCSCGeneTableCodec$Type.class
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diff --git a/org/broad/igv/feature/tribble/VCFFeature.class b/org/broad/igv/feature/tribble/VCFFeature.class
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diff --git a/org/broad/igv/goby/GobyAlignment$1.class b/org/broad/igv/goby/GobyAlignment$1.class
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diff --git a/org/broad/igv/goby/GobyAlignmentIterator.class b/org/broad/igv/goby/GobyAlignmentIterator.class
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diff --git a/org/broad/igv/goby/GobyAlignmentQueryReader.class b/org/broad/igv/goby/GobyAlignmentQueryReader.class
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diff --git a/org/broad/igv/goby/GobyCountArchiveDataSource.class b/org/broad/igv/goby/GobyCountArchiveDataSource.class
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diff --git a/org/broad/igv/goby/GobyCountArchiveDataSourceTest.class b/org/broad/igv/goby/GobyCountArchiveDataSourceTest.class
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diff --git a/org/broad/igv/goby/package.html b/org/broad/igv/goby/package.html
new file mode 100644
index 0000000..618adb1
--- /dev/null
+++ b/org/broad/igv/goby/package.html
@@ -0,0 +1,4 @@
+
+<body>
+This package provides <a href="http://goby.campagnelab.org/">Goby</a> support for IGV.
+</body>
diff --git a/org/broad/igv/graph/Edge.class b/org/broad/igv/graph/Edge.class
new file mode 100644
index 0000000..9e54353
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diff --git a/org/broad/igv/graph/GeneUtils$1.class b/org/broad/igv/graph/GeneUtils$1.class
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diff --git a/org/broad/igv/graph/GeneUtils.class b/org/broad/igv/graph/GeneUtils.class
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diff --git a/org/broad/igv/graph/Graph$1.class b/org/broad/igv/graph/Graph$1.class
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diff --git a/org/broad/igv/graph/Graph$NodeGrid.class b/org/broad/igv/graph/Graph$NodeGrid.class
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diff --git a/org/broad/igv/graph/GraphPanel2.class b/org/broad/igv/graph/GraphPanel2.class
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index 0000000..214987e
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diff --git a/org/broad/igv/graph/MainWindow.class b/org/broad/igv/graph/MainWindow.class
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index 0000000..3188291
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diff --git a/org/broad/igv/graph/Node.class b/org/broad/igv/graph/Node.class
new file mode 100644
index 0000000..865ea5c
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diff --git a/org/broad/igv/graph/SubGraph.class b/org/broad/igv/graph/SubGraph.class
new file mode 100644
index 0000000..1c01420
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diff --git a/org/broad/igv/gs/GSFileBrowser$1.class b/org/broad/igv/gs/GSFileBrowser$1.class
new file mode 100644
index 0000000..3162b2e
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diff --git a/org/broad/igv/gs/GSFileBrowser$2.class b/org/broad/igv/gs/GSFileBrowser$2.class
new file mode 100644
index 0000000..46c13f8
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diff --git a/org/broad/igv/gs/GSFileBrowser$3.class b/org/broad/igv/gs/GSFileBrowser$3.class
new file mode 100644
index 0000000..ecb0964
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diff --git a/org/broad/igv/gs/GSFileBrowser$4.class b/org/broad/igv/gs/GSFileBrowser$4.class
new file mode 100644
index 0000000..8f046f2
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diff --git a/org/broad/igv/gs/GSFileBrowser$CellRenderer.class b/org/broad/igv/gs/GSFileBrowser$CellRenderer.class
new file mode 100644
index 0000000..061c804
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diff --git a/org/broad/igv/gs/GSFileBrowser$ListModel.class b/org/broad/igv/gs/GSFileBrowser$ListModel.class
new file mode 100644
index 0000000..de9a4ce
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diff --git a/org/broad/igv/gs/GSFileBrowser$Mode.class b/org/broad/igv/gs/GSFileBrowser$Mode.class
new file mode 100644
index 0000000..173b797
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diff --git a/org/broad/igv/gs/GSFileBrowser.class b/org/broad/igv/gs/GSFileBrowser.class
new file mode 100644
index 0000000..f2a111d
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diff --git a/org/broad/igv/gs/GSFileBrowser.jfd b/org/broad/igv/gs/GSFileBrowser.jfd
new file mode 100644
index 0000000..90fbe52
--- /dev/null
+++ b/org/broad/igv/gs/GSFileBrowser.jfd
@@ -0,0 +1,280 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<java version="1.6.0_26" class="java.beans.XMLDecoder">
+ <object class="com.jformdesigner.model.FormModel">
+ <void property="contentType">
+ <string>form/swing</string>
+ </void>
+ <void property="root">
+ <object class="com.jformdesigner.model.FormRoot">
+ <void method="add">
+ <object class="com.jformdesigner.model.FormWindow">
+ <string>javax.swing.JDialog</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.BorderLayout</class>
+ </object>
+ <void method="setProperty">
+ <string>$sizePolicy</string>
+ <int>1</int>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.BorderLayout</class>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="javax.swing.border.EmptyBorder">
+ <object class="java.awt.Insets">
+ <int>12</int>
+ <int>12</int>
+ <int>12</int>
+ <int>12</int>
+ </object>
+ </object>
+ </void>
+ <void property="name">
+ <string>dialogPane</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>javax.swing.BoxLayout</class>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="javax.swing.border.EmptyBorder">
+ <object class="java.awt.Insets">
+ <int>12</int>
+ <int>0</int>
+ <int>0</int>
+ <int>0</int>
+ </object>
+ </object>
+ </void>
+ <void property="name">
+ <string>buttonBar</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>com.jformdesigner.designer.wrapper.HSpacer</string>
+ <void property="name">
+ <string>hSpacer2</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>New Folder</string>
+ </void>
+ <void property="name">
+ <string>newFolderButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>newFolderButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>com.jformdesigner.designer.wrapper.HSpacer</string>
+ <void property="name">
+ <string>hSpacer1</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Cancel</string>
+ </void>
+ <void property="name">
+ <string>cancelButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>cancelButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Open</string>
+ </void>
+ <void property="name">
+ <string>openButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>loadButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>South</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>javax.swing.BoxLayout</class>
+ </object>
+ <void method="setProperty">
+ <string>visible</string>
+ <boolean>false</boolean>
+ </void>
+ <void property="name">
+ <string>savePanel</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Save As: </string>
+ </void>
+ <void property="name">
+ <string>label2</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void property="name">
+ <string>selectedFileTextField</string>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>North</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>javax.swing.BoxLayout</class>
+ <void method="setProperty">
+ <string>axis</string>
+ <int>1</int>
+ </void>
+ </object>
+ <void property="name">
+ <string>splitPane1</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JScrollPane</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>javax.swing.JScrollPane</class>
+ </object>
+ <void property="name">
+ <string>scrollPane1</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JList</string>
+ <void property="name">
+ <string>fileList</string>
+ </void>
+ </object>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>horizontalAlignment</string>
+ <int>0</int>
+ </void>
+ <void method="setProperty">
+ <string>icon</string>
+ <object class="com.jformdesigner.model.SwingIcon">
+ <int>0</int>
+ <string>/images/genomespacelogo.png</string>
+ </object>
+ </void>
+ <void property="name">
+ <string>label1</string>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>Center</string>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>Center</string>
+ </void>
+ </object>
+ </void>
+ <void property="name">
+ <string>this</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <null/>
+ <void method="setProperty">
+ <string>location</string>
+ <object class="java.awt.Point">
+ <int>0</int>
+ <int>0</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>size</string>
+ <object class="java.awt.Dimension">
+ <int>490</int>
+ <int>530</int>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+</java>
diff --git a/org/broad/igv/gs/GSOpenSessionMenuAction$1.class b/org/broad/igv/gs/GSOpenSessionMenuAction$1.class
new file mode 100644
index 0000000..0159162
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diff --git a/org/broad/igv/gs/GSOpenSessionMenuAction.class b/org/broad/igv/gs/GSOpenSessionMenuAction.class
new file mode 100644
index 0000000..420ae9d
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diff --git a/org/broad/igv/gs/GSSaveSessionMenuAction.class b/org/broad/igv/gs/GSSaveSessionMenuAction.class
new file mode 100644
index 0000000..fe54c6b
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diff --git a/org/broad/igv/gs/GSUtils.class b/org/broad/igv/gs/GSUtils.class
new file mode 100644
index 0000000..f75c83b
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diff --git a/org/broad/igv/gs/atm/ATMUtils.class b/org/broad/igv/gs/atm/ATMUtils.class
new file mode 100644
index 0000000..9006643
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diff --git a/org/broad/igv/gs/atm/FileParameter.class b/org/broad/igv/gs/atm/FileParameter.class
new file mode 100644
index 0000000..6a5984d
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diff --git a/org/broad/igv/gs/atm/GSDataFormat.class b/org/broad/igv/gs/atm/GSDataFormat.class
new file mode 100644
index 0000000..67fe9b0
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diff --git a/org/broad/igv/gs/atm/SubToolDescriptor.class b/org/broad/igv/gs/atm/SubToolDescriptor.class
new file mode 100644
index 0000000..07ea8e5
Binary files /dev/null and b/org/broad/igv/gs/atm/SubToolDescriptor.class differ
diff --git a/org/broad/igv/gs/atm/WebToolDescriptor.class b/org/broad/igv/gs/atm/WebToolDescriptor.class
new file mode 100644
index 0000000..63b2be8
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diff --git a/org/broad/igv/gs/dm/DMUtils.class b/org/broad/igv/gs/dm/DMUtils.class
new file mode 100644
index 0000000..275e300
Binary files /dev/null and b/org/broad/igv/gs/dm/DMUtils.class differ
diff --git a/org/broad/igv/gs/dm/GSDataFormat.class b/org/broad/igv/gs/dm/GSDataFormat.class
new file mode 100644
index 0000000..7e276b7
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diff --git a/org/broad/igv/gs/dm/GSDirectoryListing.class b/org/broad/igv/gs/dm/GSDirectoryListing.class
new file mode 100644
index 0000000..6e09028
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diff --git a/org/broad/igv/gs/dm/GSFileMetadata.class b/org/broad/igv/gs/dm/GSFileMetadata.class
new file mode 100644
index 0000000..090b81c
Binary files /dev/null and b/org/broad/igv/gs/dm/GSFileMetadata.class differ
diff --git a/org/broad/igv/gwas/DescriptionCache.class b/org/broad/igv/gwas/DescriptionCache.class
new file mode 100644
index 0000000..e5ed283
Binary files /dev/null and b/org/broad/igv/gwas/DescriptionCache.class differ
diff --git a/org/broad/igv/gwas/GWASData.class b/org/broad/igv/gwas/GWASData.class
new file mode 100644
index 0000000..ed179ae
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diff --git a/org/broad/igv/gwas/GWASParser.class b/org/broad/igv/gwas/GWASParser.class
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index 0000000..a55621f
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diff --git a/org/broad/igv/gwas/GWASTrack$1.class b/org/broad/igv/gwas/GWASTrack$1.class
new file mode 100644
index 0000000..3b02402
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diff --git a/org/broad/igv/gwas/GWASTrack$2.class b/org/broad/igv/gwas/GWASTrack$2.class
new file mode 100644
index 0000000..2a08f6c
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diff --git a/org/broad/igv/gwas/GWASTrack$3.class b/org/broad/igv/gwas/GWASTrack$3.class
new file mode 100644
index 0000000..d4c4d64
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diff --git a/org/broad/igv/gwas/GWASTrack$4.class b/org/broad/igv/gwas/GWASTrack$4.class
new file mode 100644
index 0000000..2ecf6fd
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diff --git a/org/broad/igv/gwas/GWASTrack$5.class b/org/broad/igv/gwas/GWASTrack$5.class
new file mode 100644
index 0000000..c96155e
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diff --git a/org/broad/igv/gwas/GWASTrack$6.class b/org/broad/igv/gwas/GWASTrack$6.class
new file mode 100644
index 0000000..fe27a95
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diff --git a/org/broad/igv/gwas/GWASTrack$7.class b/org/broad/igv/gwas/GWASTrack$7.class
new file mode 100644
index 0000000..1383b18
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diff --git a/org/broad/igv/gwas/GWASTrack$8.class b/org/broad/igv/gwas/GWASTrack$8.class
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index 0000000..b4ee1c4
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diff --git a/org/broad/igv/gwas/GWASTrack.class b/org/broad/igv/gwas/GWASTrack.class
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index 0000000..6e5b4dd
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diff --git a/org/broad/igv/hic/ColorRangeDialog$1.class b/org/broad/igv/hic/ColorRangeDialog$1.class
new file mode 100644
index 0000000..956d616
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diff --git a/org/broad/igv/hic/ColorRangeDialog$2.class b/org/broad/igv/hic/ColorRangeDialog$2.class
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index 0000000..2993e13
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diff --git a/org/broad/igv/hic/ColorRangeDialog.class b/org/broad/igv/hic/ColorRangeDialog.class
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index 0000000..d376859
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diff --git a/org/broad/igv/hic/ColorRangeDialog.jfd b/org/broad/igv/hic/ColorRangeDialog.jfd
new file mode 100644
index 0000000..fd905cf
--- /dev/null
+++ b/org/broad/igv/hic/ColorRangeDialog.jfd
@@ -0,0 +1,403 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<java version="1.6.0_26" class="java.beans.XMLDecoder">
+ <object class="com.jformdesigner.model.FormModel">
+ <void property="contentType">
+ <string>form/swing</string>
+ </void>
+ <void property="root">
+ <object class="com.jformdesigner.model.FormRoot">
+ <void method="add">
+ <object class="com.jformdesigner.model.FormWindow">
+ <string>javax.swing.JDialog</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.BorderLayout</class>
+ </object>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.BorderLayout</class>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="javax.swing.border.EmptyBorder">
+ <int>12</int>
+ <int>12</int>
+ <int>12</int>
+ <int>12</int>
+ </object>
+ </void>
+ <void property="name">
+ <string>dialogPane</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.FlowLayout</class>
+ <void method="setProperty">
+ <string>alignment</string>
+ <int>0</int>
+ </void>
+ <void method="setProperty">
+ <string>vgap</string>
+ <int>25</int>
+ </void>
+ </object>
+ <void property="name">
+ <string>panel3</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Set color scale range in counts / mb^2</string>
+ </void>
+ <void property="name">
+ <string>label1</string>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>North</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>javax.swing.BoxLayout</class>
+ <void method="setProperty">
+ <string>axis</string>
+ <int>1</int>
+ </void>
+ </object>
+ <void property="name">
+ <string>contentPanel</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.FlowLayout</class>
+ <void method="setProperty">
+ <string>alignment</string>
+ <int>0</int>
+ </void>
+ </object>
+ <void property="name">
+ <string>panel2</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Minimum:</string>
+ </void>
+ <void property="name">
+ <string>label4</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>text</string>
+ </void>
+ <void method="setProperty">
+ <string>maximumSize</string>
+ <object class="java.awt.Dimension">
+ <int>100</int>
+ <int>16</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>minimumSize</string>
+ <object class="java.awt.Dimension">
+ <int>100</int>
+ <int>16</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>preferredSize</string>
+ <object class="java.awt.Dimension">
+ <int>100</int>
+ <int>16</int>
+ </object>
+ </void>
+ <void property="name">
+ <string>minimumField</string>
+ </void>
+ </object>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.FlowLayout</class>
+ <void method="setProperty">
+ <string>alignment</string>
+ <int>3</int>
+ </void>
+ </object>
+ <void property="name">
+ <string>panel1</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Maximum</string>
+ </void>
+ <void property="name">
+ <string>label2</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>text</string>
+ </void>
+ <void method="setProperty">
+ <string>maximumSize</string>
+ <object id="Dimension0" class="java.awt.Dimension">
+ <int>100</int>
+ <int>16</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>minimumSize</string>
+ <object id="Dimension1" class="java.awt.Dimension">
+ <int>100</int>
+ <int>16</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>preferredSize</string>
+ <object id="Dimension2" class="java.awt.Dimension">
+ <int>100</int>
+ <int>16</int>
+ </object>
+ </void>
+ <void property="name">
+ <string>maximumField</string>
+ </void>
+ </object>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.FlowLayout</class>
+ <void method="setProperty">
+ <string>alignment</string>
+ <int>3</int>
+ </void>
+ </object>
+ <void property="name">
+ <string>panel4</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Tick spacing:</string>
+ </void>
+ <void property="name">
+ <string>label3</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>text</string>
+ </void>
+ <void method="setProperty">
+ <string>maximumSize</string>
+ <object idref="Dimension0"/>
+ </void>
+ <void method="setProperty">
+ <string>minimumSize</string>
+ <object idref="Dimension1"/>
+ </void>
+ <void method="setProperty">
+ <string>preferredSize</string>
+ <object idref="Dimension2"/>
+ </void>
+ <void property="name">
+ <string>tickSpacingField</string>
+ </void>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>Center</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.GridBagLayout</class>
+ <void method="setProperty">
+ <string>$columnSpecs</string>
+ <string>0:1.0, 80, 80</string>
+ </void>
+ <void method="setProperty">
+ <string>$rowSpecs</string>
+ <string>0</string>
+ </void>
+ <void method="setProperty">
+ <string>$hGap</string>
+ <int>5</int>
+ </void>
+ <void method="setProperty">
+ <string>$vGap</string>
+ <int>5</int>
+ </void>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="javax.swing.border.EmptyBorder">
+ <int>12</int>
+ <int>0</int>
+ <int>0</int>
+ <int>0</int>
+ </object>
+ </void>
+ <void property="name">
+ <string>buttonBar</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>OK</string>
+ </void>
+ <void property="name">
+ <string>okButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>okButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>1</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>0</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Cancel</string>
+ </void>
+ <void property="name">
+ <string>cancelButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>cancelButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>0</int>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>South</string>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>Center</string>
+ </void>
+ </object>
+ </void>
+ <void property="name">
+ <string>this</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <null/>
+ <void method="setProperty">
+ <string>location</string>
+ <object class="java.awt.Point">
+ <int>0</int>
+ <int>0</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>size</string>
+ <object class="java.awt.Dimension">
+ <int>475</int>
+ <int>300</int>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+</java>
diff --git a/org/broad/igv/hic/ColorScalePanel.class b/org/broad/igv/hic/ColorScalePanel.class
new file mode 100644
index 0000000..73bcbe7
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diff --git a/org/broad/igv/hic/Context.class b/org/broad/igv/hic/Context.class
new file mode 100644
index 0000000..e101757
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diff --git a/org/broad/igv/hic/EigenvectorTrack.class b/org/broad/igv/hic/EigenvectorTrack.class
new file mode 100644
index 0000000..0f9c1c6
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diff --git a/org/broad/igv/hic/HeatmapPanel$1.class b/org/broad/igv/hic/HeatmapPanel$1.class
new file mode 100644
index 0000000..c517ae1
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diff --git a/org/broad/igv/hic/HeatmapPanel$DragMode.class b/org/broad/igv/hic/HeatmapPanel$DragMode.class
new file mode 100644
index 0000000..bca855a
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diff --git a/org/broad/igv/hic/HeatmapPanel$HeatmapMouseHandler.class b/org/broad/igv/hic/HeatmapPanel$HeatmapMouseHandler.class
new file mode 100644
index 0000000..a8ac8cb
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diff --git a/org/broad/igv/hic/HeatmapPanel$ImageTile.class b/org/broad/igv/hic/HeatmapPanel$ImageTile.class
new file mode 100644
index 0000000..9c7fe20
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diff --git a/org/broad/igv/hic/HeatmapPanel.class b/org/broad/igv/hic/HeatmapPanel.class
new file mode 100644
index 0000000..a9cdba3
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diff --git a/org/broad/igv/hic/HeatmapRenderer$1.class b/org/broad/igv/hic/HeatmapRenderer$1.class
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index 0000000..bf86788
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diff --git a/org/broad/igv/hic/HeatmapRenderer.class b/org/broad/igv/hic/HeatmapRenderer.class
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index 0000000..b871cff
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diff --git a/org/broad/igv/hic/HiC$1.class b/org/broad/igv/hic/HiC$1.class
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index 0000000..d3deb4c
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diff --git a/org/broad/igv/hic/HiC$2.class b/org/broad/igv/hic/HiC$2.class
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index 0000000..88ec984
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index 0000000..1abab0f
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index 0000000..b8542ea
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diff --git a/org/broad/igv/hic/HiC.class b/org/broad/igv/hic/HiC.class
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index 0000000..a255d48
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diff --git a/org/broad/igv/hic/HiCColorScale.class b/org/broad/igv/hic/HiCColorScale.class
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index 0000000..bce690a
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diff --git a/org/broad/igv/hic/HiCGlobals.class b/org/broad/igv/hic/HiCGlobals.class
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index 0000000..5c47894
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diff --git a/org/broad/igv/hic/HiCLayout.class b/org/broad/igv/hic/HiCLayout.class
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index 0000000..e177f8e
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diff --git a/org/broad/igv/hic/HiCReferenceFrame.class b/org/broad/igv/hic/HiCReferenceFrame.class
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index 0000000..b71b45b
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diff --git a/org/broad/igv/hic/HiCRenderContext.class b/org/broad/igv/hic/HiCRenderContext.class
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index 0000000..4603965
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diff --git a/org/broad/igv/hic/HiCRulerPanel$ClickLink.class b/org/broad/igv/hic/HiCRulerPanel$ClickLink.class
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index 0000000..2468037
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diff --git a/org/broad/igv/hic/HiCRulerPanel$Orientation.class b/org/broad/igv/hic/HiCRulerPanel$Orientation.class
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index 0000000..a5ade56
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diff --git a/org/broad/igv/hic/HiCRulerPanel$TickSpacing.class b/org/broad/igv/hic/HiCRulerPanel$TickSpacing.class
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diff --git a/org/broad/igv/hic/ThumbnailPanel$SquareDonut.class b/org/broad/igv/hic/ThumbnailPanel$SquareDonut.class
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diff --git a/org/broad/igv/hic/TrackPanel.class b/org/broad/igv/hic/TrackPanel.class
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diff --git a/org/broad/igv/hic/data.uml b/org/broad/igv/hic/data.uml
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index 0000000..ea8b994
--- /dev/null
+++ b/org/broad/igv/hic/data.uml
@@ -0,0 +1,85 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<Diagram>
+ <ID>JAVA</ID>
+ <OriginalElement>org.broad.igv.hic.data</OriginalElement>
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diff --git a/org/broad/igv/hic/data/HumanAugust.densities.txt b/org/broad/igv/hic/data/HumanAugust.densities.txt
new file mode 100644
index 0000000..3024a86
--- /dev/null
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diff --git a/org/broad/igv/hic/data/Matrix.class b/org/broad/igv/hic/data/Matrix.class
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index 0000000..046c051
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new file mode 100644
index 0000000..197d45f
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diff --git a/org/broad/igv/hic/data/MatrixZoomData$PearsonsMinMax.class b/org/broad/igv/hic/data/MatrixZoomData$PearsonsMinMax.class
new file mode 100644
index 0000000..7e37cdc
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index 0000000..5e45071
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diff --git a/org/broad/igv/hic/data/binary_file_layout.txt b/org/broad/igv/hic/data/binary_file_layout.txt
new file mode 100644
index 0000000..af9c82d
--- /dev/null
+++ b/org/broad/igv/hic/data/binary_file_layout.txt
@@ -0,0 +1,80 @@
+------
+Header
+------
+
+ masterIndexPointer
+
+
+ --------
+ Chr dictionary
+ --------
+ numberOfChromosomes
+
+ ------------
+ Chromosome // repeat for each chromosome
+ ------------
+ name
+ size
+
+ ---------
+ Attribute dictionary
+ ---------
+ attributeCount
+ attKey
+ attValue
+ attKey
+ attValue
+ ....
+
+ --------
+ Matrix
+ --------
+ chr1 // lowest index chromosome
+ chr2 // highest index chromosome
+ numberOfZooms
+
+ --------------
+ MatrixZoomData //repeat for each zoom
+ --------------
+
+ zoom
+ sum // Sum of counts over all records
+ binSize // in bp
+ blockBinCount // in # bin columns
+ columnCount
+ numberOfBlocks
+
+ -----------
+ Block Index // repeat for each block
+ -----------
+ blockNumber
+ filePosition
+ sizeInbytes
+
+
+
+ ----------
+ Block // repeat for each block
+ ----------
+ numberOfRecords
+
+ -----------
+ ContactRecord // repeat for each contact record
+ -----------
+ bin1
+ bin2
+ counts // int
+
+
+------------
+Master Index
+------------
+numberOfEntries
+
+ -----
+ Entry // repeat for each entry
+ -----
+ matrixKey // chr1_chr2
+ filePosition
+ sizeInBytes
+
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diff --git a/org/broad/igv/hic/tools/Preprocessor$MatrixZoomDataPP.class b/org/broad/igv/hic/tools/Preprocessor$MatrixZoomDataPP.class
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index 0000000..77e545f
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diff --git a/org/broad/igv/hic/tools/Preprocessor.class b/org/broad/igv/hic/tools/Preprocessor.class
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diff --git a/org/broad/igv/hic/tools/b37.chrom.sizes b/org/broad/igv/hic/tools/b37.chrom.sizes
new file mode 100644
index 0000000..6a627d1
--- /dev/null
+++ b/org/broad/igv/hic/tools/b37.chrom.sizes
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diff --git a/org/broad/igv/hic/tools/dMel.chrom.sizes b/org/broad/igv/hic/tools/dMel.chrom.sizes
new file mode 100644
index 0000000..0c14773
--- /dev/null
+++ b/org/broad/igv/hic/tools/dMel.chrom.sizes
@@ -0,0 +1,7 @@
+2L 22407834
+2R 20766785
+3L 23771897
+3R 27905053
+4 1281640
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diff --git a/org/broad/igv/hic/tools/hg18.chrom.sizes b/org/broad/igv/hic/tools/hg18.chrom.sizes
new file mode 100644
index 0000000..0e88729
--- /dev/null
+++ b/org/broad/igv/hic/tools/hg18.chrom.sizes
@@ -0,0 +1,25 @@
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diff --git a/org/broad/igv/hic/tools/mm9.chrom.sizes b/org/broad/igv/hic/tools/mm9.chrom.sizes
new file mode 100644
index 0000000..29f8f8c
--- /dev/null
+++ b/org/broad/igv/hic/tools/mm9.chrom.sizes
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+chr14 125194864
+chr15 103494974
+chr16 98319150
+chr17 95272651
+chr18 90772031
+chr19 61342430
+chrX 166650296
+chrY 15902555
+chrM 16300
diff --git a/org/broad/igv/lists/GeneList$1.class b/org/broad/igv/lists/GeneList$1.class
new file mode 100644
index 0000000..818f436
Binary files /dev/null and b/org/broad/igv/lists/GeneList$1.class differ
diff --git a/org/broad/igv/lists/GeneList.class b/org/broad/igv/lists/GeneList.class
new file mode 100644
index 0000000..2aa1598
Binary files /dev/null and b/org/broad/igv/lists/GeneList.class differ
diff --git a/org/broad/igv/lists/GeneListEditDialog$1.class b/org/broad/igv/lists/GeneListEditDialog$1.class
new file mode 100644
index 0000000..ffe2fd4
Binary files /dev/null and b/org/broad/igv/lists/GeneListEditDialog$1.class differ
diff --git a/org/broad/igv/lists/GeneListEditDialog$2.class b/org/broad/igv/lists/GeneListEditDialog$2.class
new file mode 100644
index 0000000..8a454aa
Binary files /dev/null and b/org/broad/igv/lists/GeneListEditDialog$2.class differ
diff --git a/org/broad/igv/lists/GeneListEditDialog.class b/org/broad/igv/lists/GeneListEditDialog.class
new file mode 100644
index 0000000..c2912c2
Binary files /dev/null and b/org/broad/igv/lists/GeneListEditDialog.class differ
diff --git a/org/broad/igv/lists/GeneListEditDialog.jfd b/org/broad/igv/lists/GeneListEditDialog.jfd
new file mode 100644
index 0000000..d328ae5
--- /dev/null
+++ b/org/broad/igv/lists/GeneListEditDialog.jfd
@@ -0,0 +1,374 @@
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+ <void property="name">
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+ <object class="com.jformdesigner.model.FormContainer">
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+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
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+ <void method="setProperty">
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+ <string><html>Enter or paste genes or loci below <i>(e.g EGFR or chr1:1000-2000)</string>
+ </void>
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diff --git a/org/broad/igv/lists/GeneListGroup.class b/org/broad/igv/lists/GeneListGroup.class
new file mode 100644
index 0000000..e344085
Binary files /dev/null and b/org/broad/igv/lists/GeneListGroup.class differ
diff --git a/org/broad/igv/lists/GeneListManager.class b/org/broad/igv/lists/GeneListManager.class
new file mode 100644
index 0000000..c800c3b
Binary files /dev/null and b/org/broad/igv/lists/GeneListManager.class differ
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new file mode 100644
index 0000000..7f8b782
Binary files /dev/null and b/org/broad/igv/lists/GeneListManagerUI$1.class differ
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new file mode 100644
index 0000000..dc415f5
Binary files /dev/null and b/org/broad/igv/lists/GeneListManagerUI$10.class differ
diff --git a/org/broad/igv/lists/GeneListManagerUI$11.class b/org/broad/igv/lists/GeneListManagerUI$11.class
new file mode 100644
index 0000000..71f587c
Binary files /dev/null and b/org/broad/igv/lists/GeneListManagerUI$11.class differ
diff --git a/org/broad/igv/lists/GeneListManagerUI$12.class b/org/broad/igv/lists/GeneListManagerUI$12.class
new file mode 100644
index 0000000..709be53
Binary files /dev/null and b/org/broad/igv/lists/GeneListManagerUI$12.class differ
diff --git a/org/broad/igv/lists/GeneListManagerUI$13.class b/org/broad/igv/lists/GeneListManagerUI$13.class
new file mode 100644
index 0000000..bec86a6
Binary files /dev/null and b/org/broad/igv/lists/GeneListManagerUI$13.class differ
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new file mode 100644
index 0000000..7cce8c8
Binary files /dev/null and b/org/broad/igv/lists/GeneListManagerUI$14.class differ
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new file mode 100644
index 0000000..67230d6
Binary files /dev/null and b/org/broad/igv/lists/GeneListManagerUI$15.class differ
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new file mode 100644
index 0000000..e9747ae
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new file mode 100644
index 0000000..875119b
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new file mode 100644
index 0000000..ed6aed0
Binary files /dev/null and b/org/broad/igv/lists/GeneListManagerUI$18.class differ
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new file mode 100644
index 0000000..ee9f0c0
Binary files /dev/null and b/org/broad/igv/lists/GeneListManagerUI$2.class differ
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new file mode 100644
index 0000000..1bc06cf
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new file mode 100644
index 0000000..9ab39f0
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new file mode 100644
index 0000000..6737eea
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new file mode 100644
index 0000000..9c47838
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new file mode 100644
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new file mode 100644
index 0000000..c6391e1
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new file mode 100644
index 0000000..a5da574
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index 0000000..a41abab
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diff --git a/org/broad/igv/lists/GeneListManagerUI$ListListModel.class b/org/broad/igv/lists/GeneListManagerUI$ListListModel.class
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diff --git a/org/broad/igv/lists/GeneListManagerUI.class b/org/broad/igv/lists/GeneListManagerUI.class
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index 0000000..d505ac6
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diff --git a/org/broad/igv/lists/GeneListManagerUI.jfd b/org/broad/igv/lists/GeneListManagerUI.jfd
new file mode 100644
index 0000000..dec032e
--- /dev/null
+++ b/org/broad/igv/lists/GeneListManagerUI.jfd
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+ </void>
+ <void method="setProperty">
+ <string>opaque</string>
+ <boolean>false</boolean>
+ </void>
+ <void property="name">
+ <string>panel6</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Search</string>
+ </void>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="javax.swing.border.EmptyBorder">
+ <int>0</int>
+ <int>0</int>
+ <int>0</int>
+ <int>10</int>
+ </object>
+ </void>
+ <void property="name">
+ <string>label1</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="javax.swing.border.BevelBorder">
+ <int>1</int>
+ <null/>
+ <null/>
+ <null/>
+ <null/>
+ </object>
+ </void>
+ <void property="name">
+ <string>searchBox</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.KeyListener</string>
+ <string>keyReleased</string>
+ <string>searchBoxKeyReleased</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>com.jformdesigner.runtime.NullLayout</class>
+ <void method="setProperty">
+ <string>autoSize</string>
+ <boolean>false</boolean>
+ </void>
+ </object>
+ <void method="setProperty">
+ <string>preferredSize</string>
+ <object class="java.awt.Dimension">
+ <int>5</int>
+ <int>0</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>minimumSize</string>
+ <object class="java.awt.Dimension">
+ <int>5</int>
+ <int>0</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>opaque</string>
+ <boolean>false</boolean>
+ </void>
+ <void property="name">
+ <string>panel10</string>
+ </void>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>North</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JSplitPane</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>javax.swing.JSplitPane</class>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="com.jformdesigner.model.FormObject" field="NULL_VALUE"/>
+ </void>
+ <void method="setProperty">
+ <string>dividerLocation</string>
+ <int>600</int>
+ </void>
+ <void property="name">
+ <string>splitPane2</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JSplitPane</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>javax.swing.JSplitPane</class>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="com.jformdesigner.model.FormObject" field="NULL_VALUE"/>
+ </void>
+ <void method="setProperty">
+ <string>dividerLocation</string>
+ <int>270</int>
+ </void>
+ <void property="name">
+ <string>splitPane1</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.BorderLayout</class>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object id="LineBorder0" class="javax.swing.border.LineBorder">
+ <object class="java.awt.Color" field="black"/>
+ <int>1</int>
+ <boolean>false</boolean>
+ </object>
+ </void>
+ <void property="name">
+ <string>panel3</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Group</string>
+ </void>
+ <void property="name">
+ <string>label3</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>North</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JScrollPane</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>javax.swing.JScrollPane</class>
+ </object>
+ <void method="setProperty">
+ <string>preferredSize</string>
+ <object class="java.awt.Dimension">
+ <int>80</int>
+ <int>140</int>
+ </object>
+ </void>
+ <void property="name">
+ <string>scrollPane1</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JList</string>
+ <void method="setProperty">
+ <string>model</string>
+ <object class="javax.swing.DefaultListModel">
+ <void method="addElement">
+ <string>All</string>
+ </void>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>selectionMode</string>
+ <int>0</int>
+ </void>
+ <void property="name">
+ <string>groupJList</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>javax.swing.event.ListSelectionListener</string>
+ <string>valueChanged</string>
+ <string>groupsValueChanged</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>Center</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>javax.swing.BoxLayout</class>
+ <void method="setProperty">
+ <string>axis</string>
+ <int>0</int>
+ </void>
+ </object>
+ <void property="name">
+ <string>panel7</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>icon</string>
+ <object class="com.jformdesigner.model.FormObject" field="NULL_VALUE"/>
+ </void>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Import</string>
+ </void>
+ <void method="setProperty">
+ <string>toolTipText</string>
+ <string>Import a .gmt file</string>
+ </void>
+ <void property="name">
+ <string>importButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>importButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Export</string>
+ </void>
+ <void property="name">
+ <string>exportButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>exportButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Delete</string>
+ </void>
+ <void method="setProperty">
+ <string>enabled</string>
+ <boolean>false</boolean>
+ </void>
+ <void property="name">
+ <string>deleteGroupButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>deleteGroupButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>South</string>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>left</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.BorderLayout</class>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object idref="LineBorder0"/>
+ </void>
+ <void property="name">
+ <string>panel4</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>List</string>
+ </void>
+ <void property="name">
+ <string>listLabel</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.MouseListener</string>
+ <string>mouseClicked</string>
+ <string>listLabelMouseClicked</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>First</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JScrollPane</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>javax.swing.JScrollPane</class>
+ </object>
+ <void property="name">
+ <string>scrollPane2</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JList</string>
+ <void method="setProperty">
+ <string>selectionMode</string>
+ <int>0</int>
+ </void>
+ <void property="name">
+ <string>glJList</string>
+ </void>
+ <void method="auxiliary">
+ <void method="setProperty">
+ <string>JavaCodeGenerator.customCreate</string>
+ <boolean>true</boolean>
+ </void>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>javax.swing.event.ListSelectionListener</string>
+ <string>valueChanged</string>
+ <string>listsValueChanged</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.MouseListener</string>
+ <string>mouseClicked</string>
+ <string>glJListMouseClicked</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>Center</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>javax.swing.BoxLayout</class>
+ </object>
+ <void property="name">
+ <string>panel8</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>icon</string>
+ <object class="com.jformdesigner.model.FormObject" field="NULL_VALUE"/>
+ </void>
+ <void method="setProperty">
+ <string>text</string>
+ <string>New</string>
+ </void>
+ <void property="name">
+ <string>newList</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>newListActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Copy</string>
+ </void>
+ <void property="name">
+ <string>copyListButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>copyListButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Edit</string>
+ </void>
+ <void method="setProperty">
+ <string>enabled</string>
+ <boolean>false</boolean>
+ </void>
+ <void property="name">
+ <string>editButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>editButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>icon</string>
+ <object class="com.jformdesigner.model.FormObject" field="NULL_VALUE"/>
+ </void>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Delete</string>
+ </void>
+ <void method="setProperty">
+ <string>enabled</string>
+ <boolean>false</boolean>
+ </void>
+ <void property="name">
+ <string>deleteButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>deleteButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>Last</string>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>right</string>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>left</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.BorderLayout</class>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object idref="LineBorder0"/>
+ </void>
+ <void property="name">
+ <string>panel5</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Loci</string>
+ </void>
+ <void property="name">
+ <string>label4</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>North</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JScrollPane</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>javax.swing.JScrollPane</class>
+ </object>
+ <void property="name">
+ <string>scrollPane3</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JList</string>
+ <void property="name">
+ <string>lociJList</string>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>Center</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>javax.swing.BoxLayout</class>
+ <void method="setProperty">
+ <string>axis</string>
+ <int>0</int>
+ </void>
+ </object>
+ <void property="name">
+ <string>panel9</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>South</string>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>right</string>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>Center</string>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>Center</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.FlowLayout</class>
+ <void method="setProperty">
+ <string>alignment</string>
+ <int>2</int>
+ </void>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="com.jformdesigner.model.FormObject" field="NULL_VALUE"/>
+ </void>
+ <void property="name">
+ <string>buttonBar</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>cBio Network</string>
+ </void>
+ <void method="setProperty">
+ <string>visible</string>
+ <boolean>false</boolean>
+ </void>
+ <void property="name">
+ <string>viewNetworkButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>viewNetworkButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Load</string>
+ </void>
+ <void method="setProperty">
+ <string>enabled</string>
+ <boolean>false</boolean>
+ </void>
+ <void property="name">
+ <string>loadButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>loadButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Close</string>
+ </void>
+ <void property="name">
+ <string>closeButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>closeButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>South</string>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>Center</string>
+ </void>
+ </object>
+ </void>
+ <void property="name">
+ <string>this</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <null/>
+ <void method="setProperty">
+ <string>location</string>
+ <object class="java.awt.Point">
+ <int>0</int>
+ <int>0</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>size</string>
+ <object class="java.awt.Dimension">
+ <int>845</int>
+ <int>580</int>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+</java>
diff --git a/org/broad/igv/lists/Preloader.class b/org/broad/igv/lists/Preloader.class
new file mode 100644
index 0000000..ae8274e
Binary files /dev/null and b/org/broad/igv/lists/Preloader.class differ
diff --git a/org/broad/igv/lists/VariantListEntry.class b/org/broad/igv/lists/VariantListEntry.class
new file mode 100644
index 0000000..222467e
Binary files /dev/null and b/org/broad/igv/lists/VariantListEntry.class differ
diff --git a/org/broad/igv/lists/VariantListManager.class b/org/broad/igv/lists/VariantListManager.class
new file mode 100644
index 0000000..c59adfa
Binary files /dev/null and b/org/broad/igv/lists/VariantListManager.class differ
diff --git a/org/broad/igv/lists/VariantListNavigator$1.class b/org/broad/igv/lists/VariantListNavigator$1.class
new file mode 100644
index 0000000..a3d182f
Binary files /dev/null and b/org/broad/igv/lists/VariantListNavigator$1.class differ
diff --git a/org/broad/igv/lists/VariantListNavigator$2.class b/org/broad/igv/lists/VariantListNavigator$2.class
new file mode 100644
index 0000000..ff1a965
Binary files /dev/null and b/org/broad/igv/lists/VariantListNavigator$2.class differ
diff --git a/org/broad/igv/lists/VariantListNavigator$3$1.class b/org/broad/igv/lists/VariantListNavigator$3$1.class
new file mode 100644
index 0000000..67b838a
Binary files /dev/null and b/org/broad/igv/lists/VariantListNavigator$3$1.class differ
diff --git a/org/broad/igv/lists/VariantListNavigator$3.class b/org/broad/igv/lists/VariantListNavigator$3.class
new file mode 100644
index 0000000..7af65a3
Binary files /dev/null and b/org/broad/igv/lists/VariantListNavigator$3.class differ
diff --git a/org/broad/igv/lists/VariantListNavigator.class b/org/broad/igv/lists/VariantListNavigator.class
new file mode 100644
index 0000000..c75394f
Binary files /dev/null and b/org/broad/igv/lists/VariantListNavigator.class differ
diff --git a/org/broad/igv/lists/VariantListNavigator.jfd b/org/broad/igv/lists/VariantListNavigator.jfd
new file mode 100644
index 0000000..411e675
--- /dev/null
+++ b/org/broad/igv/lists/VariantListNavigator.jfd
@@ -0,0 +1,123 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<java version="1.6.0_22" class="java.beans.XMLDecoder">
+ <object class="com.jformdesigner.model.FormModel">
+ <void property="contentType">
+ <string>form/swing</string>
+ </void>
+ <void property="root">
+ <object class="com.jformdesigner.model.FormRoot">
+ <void method="add">
+ <object class="com.jformdesigner.model.FormWindow">
+ <string>javax.swing.JDialog</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.BorderLayout</class>
+ </object>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JScrollPane</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>javax.swing.JScrollPane</class>
+ </object>
+ <void property="name">
+ <string>scrollPane1</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JList</string>
+ <void property="name">
+ <string>variantList</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>javax.swing.event.ListSelectionListener</string>
+ <string>valueChanged</string>
+ <string>variantListValueChanged</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>Center</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>com.jformdesigner.runtime.NullLayout</class>
+ </object>
+ <void property="name">
+ <string>panel1</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Load variants...</string>
+ </void>
+ <void property="name">
+ <string>loadVariantsButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>loadVariantsButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>0</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>0</int>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>North</string>
+ </void>
+ </object>
+ </void>
+ <void property="name">
+ <string>this</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <null/>
+ <void method="setProperty">
+ <string>location</string>
+ <object class="java.awt.Point">
+ <int>0</int>
+ <int>0</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>size</string>
+ <object class="java.awt.Dimension">
+ <int>295</int>
+ <int>325</int>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+</java>
diff --git a/org/broad/igv/lists/biocarta_cancer_cp.gmt b/org/broad/igv/lists/biocarta_cancer_cp.gmt
new file mode 100644
index 0000000..adba7fb
--- /dev/null
+++ b/org/broad/igv/lists/biocarta_cancer_cp.gmt
@@ -0,0 +1,21 @@
+#name=Biocarta canonical cancer pathways
+BIOCARTA_41BB_PATHWAY > The 4-1BB-dependent immune response ATF2 CHUK IFNG IKBKB IL2 IL4 JUN MAP3K1 MAP3K5 MAP4K5 MAPK14 MAPK8 NFKB1 NFKBIA RELA TNFRSF9 TRAF2
+BIOCARTA_ATRBRCA_PATHWAY > Role of BRCA1, BRCA2 and ATR in Cancer Susceptibility ATM ATR BRCA1 BRCA2 CHEK1 CHEK2 FANCC FANCD2 FANCE FANCF FANCG HUS1 MRE11A NBN RAD1 RAD17 RAD50 RAD51 RAD9A TP53 TREX1
+BIOCARTA_CD40_PATHWAY > CD40L Signaling Pathway CD40 CD40LG CHUK DUSP1 IKBKAP IKBKB IKBKG MAP3K1 MAP3K14 NFKB1 NFKBIA RELA TNFAIP3 TRAF3 TRAF6
+BIOCARTA_CDC42RAC_PATHWAY > Role of PI3K subunit p85 in regulation of Actin Organization and Cell Migration ACTR2 ACTR3 ARPC1A ARPC1B ARPC2 ARPC3 ARPC4 ARPC5 CDC42 PAK1 PDGFRA PIK3CA PIK3R1 RAC1 RHOA WASL
+BIOCARTA_CDMAC_PATHWAY > Cadmium induces DNA synthesis and proliferation in macrophages CUZD1 FOS HRAS JUN MAP2K1 MAPK1 MAPK3 MYC NFKB1 NFKBIA PLCB1 PRKCA PRKCB RAF1 RELA TNF
+BIOCARTA_CELL2CELL_PATHWAY > Cell to Cell Adhesion Signaling ACTN1 ACTN2 ACTN3 BCAR1 CSK CTNNA1 CTNNA2 CTNNA3 CTNNB1 PECAM1 PTK2 PXN SRC VCL
+BIOCARTA_CTL_PATHWAY > CTL mediated immune response against target cells B2M CD247 CD3D CD3E CD3G FAS FASLG GZMB HLA-A ICAM1 ITGAL ITGB2 PRF1 TRA@ TRB@
+BIOCARTA_EGF_PATHWAY > EGF Signaling Pathway CSNK2A1 EGF EGFR ELK1 FOS GRB2 HRAS JAK1 JUN MAP2K1 MAP2K4 MAP3K1 MAPK3 MAPK8 PIK3CA PIK3R1 PLCG1 PRKCA PRKCB RAF1 RASA1 SHC1 SOS1 SRF STAT1 STAT2 STAT3 STAT4 STAT5A STAT5B STAT6
+BIOCARTA_GLEEVEC_PATHWAY > Inhibition of Cellular Proliferation by Gleevec AKT1 BAD BCR CRKL FOS GRB2 HRAS JAK2 JUN MAP2K1 MAP2K4 MAP3K1 MAPK3 MAPK8 MYC PIK3CA PIK3CG PIK3R1 RAF1 SOS1 STAT1 STAT5A STAT5B
+BIOCARTA_GLYCOLYSIS_PATHWAY > Glycolysis Pathway ALDOB ENO1 GAPDH GPI HK1 PFKL PGAM1 PGK1 PKLR TPI1
+BIOCARTA_HER2_PATHWAY > Role of ERBB2 in Signal Transduction and Oncology CARM1 EGFR EP300 ERBB3 ERBB4 ESR1 GRB2 GRIP1 HRAS IL6 IL6R IL6ST MAP2K1 MAPK1 MAPK3 PIK3CA PIK3CG PIK3R1 RAF1 SHC1 SOS1 STAT3
+BIOCARTA_IGF1R_PATHWAY > Multiple antiapoptotic pathways from IGF-1R signaling lead to BAD phosphorylation ADCY1 AKT1 BAD GRB2 HRAS IGF1R IRS1 MAP2K1 MAPK1 MAPK3 PIK3CA PIK3R1 PRKACB PRKACG PRKAR1A PRKAR1B PRKAR2A PRKAR2B RAF1 RPS6KA1 SHC1 SOS1 YWHAH
+BIOCARTA_LONGEVITY_PATHWAY > The IGF-1 Receptor and Longevity AKT1 CAT FOXO3 GH1 GHR HRAS IGF1 IGF1R PIK3CA PIK3CG PIK3R1 SHC1 SOD1 SOD2 SOD3
+BIOCARTA_MET_PATHWAY > Signaling of Hepatocyte Growth Factor Receptor ACTA1 CRK CRKL DOCK1 ELK1 FOS GAB1 GRB2 HGF HRAS ITGA1 ITGB1 JUN MAP2K1 MAP2K2 MAP4K1 MAPK1 MAPK3 MAPK8 MET PAK1 PIK3CA PIK3CG PIK3R1 PTEN PTK2 PTK2B PTPN11 PXN RAF1 RAP1A RAP1B RAPGEF1 RASA1 SOS1 SRC STAT3
+BIOCARTA_P27_PATHWAY > Regulation of p27 Phosphorylation during Cell Cycle Progression CCNE1 CDK2 CDKN1B CKS1B CUL1 E2F1 NEDD8 RB1 RBX1 SKP1 SKP2 TFDP1 UBE2M
+BIOCARTA_SET_PATHWAY > Granzyme A mediated Apoptosis Pathway ANP32A APEX1 CREBBP DFFA DFFB GZMA GZMB HMGB2 NME1 PRF1 SET
+BIOCARTA_SHH_PATHWAY > Sonic Hedgehog (Shh) Pathway DYRK1A DYRK1B GLI1 GLI2 GLI3 GSK3B PRKACB PRKACG PRKAR1A PRKAR1B PRKAR2A PRKAR2B PTCH1 SHH SMO SUFU
+BIOCARTA_STATHMIN_PATHWAY > Stathmin and breast cancer resistance to antimicrotubule agents CAMK2A CAMK2B CAMK2D CAMK2G CAMK4 CCNB1 CD2 CD247 CD3D CD3E CD3G CDK1 MAPK13 PRKACB PRKACG PRKAR1A PRKAR1B PRKAR2A PRKAR2B
+BIOCARTA_TGFB_PATHWAY > TGF beta signaling pathway APC CDH1 CREBBP EP300 MAP2K1 MAP3K7 MAPK3 SKIL SMAD2 SMAD3 SMAD4 SMAD7 TAB1 TGFB1 TGFB2 TGFB3 TGFBR1 TGFBR2 ZFYVE9
+BIOCARTA_VDR_PATHWAY > Control of Gene Expression by Vitamin D Receptor CARM1 CREBBP EP300 HDAC1 KAT2B MED1 NCOA1 NCOA2 NCOA3 NCOR1 RXRA TSC2
\ No newline at end of file
diff --git a/org/broad/igv/lists/examples.gmt b/org/broad/igv/lists/examples.gmt
new file mode 100644
index 0000000..fd8d88c
--- /dev/null
+++ b/org/broad/igv/lists/examples.gmt
@@ -0,0 +1,10 @@
+#name=Example gene lists
+Proneural dev genes Proneural dev genes SOX1 SOX2 SOX3 SOX21 DCX DLL3 ASCL1 TCF4
+Microglia markers Microglia markers CD68 PTPRC TNF
+MMR genes MMR genes MGMT MLH1 MSH2 MSH6 PMS2
+PI(3)K complex PI(3)K complex PIK3CA PIK3R1
+Oligodendrocytic dev genes Oligodendrocytic dev genes PDGFRA NKX2-2 NG2 OLIG2 CDKN1A
+P53 signaling P53 signaling CDKN2A TP53 MDM2 MDM4
+RB signaling RB signaling CDKN2A CDKN2B CDKN2C CDK4 CDK6 CCND1 CCND2 RB1
+AKT signaling AKT signaling PIK3CA PTEN PIP3 AKT1 AKT2 AKT3
+RTK/RAS signaling RTK/RAS signaling PDGFRA PDGFRB ERBB3 EGFR ERBB2 FGFR1 FGFR2 MET GRB2 NF1 NRAS KRAS HRAS ARAF BRAF RAF1 SPRY2
diff --git a/org/broad/igv/lists/kegg_cancer_cp.gmt b/org/broad/igv/lists/kegg_cancer_cp.gmt
new file mode 100644
index 0000000..65177b9
--- /dev/null
+++ b/org/broad/igv/lists/kegg_cancer_cp.gmt
@@ -0,0 +1,12 @@
+#name=KEGG canonical cancer pathways
+KEGG_BLADDER_CANCER > Bladder cancer ARAF BRAF CCND1 CDH1 CDK4 CDKN1A CDKN2A DAPK1 DAPK2 DAPK3 E2F1 E2F2 E2F3 EGF EGFR ERBB2 FGFR3 FIGF HRAS IL8 KRAS MAP2K1 MAP2K2 MAPK1 MAPK3 MDM2 MMP1 MMP2 MMP9 MYC NRAS PGF RAF1 RASSF1 RB1 RPS6KA5 THBS1 TP53 TYMP VEGFA VEGFB VEGFC
+KEGG_THYROID_CANCER > Thyroid cancer BRAF CCDC6 CCND1 CDH1 CTNNB1 HRAS KRAS LEF1 MAP2K1 MAP2K2 MAPK1 MAPK3 MYC NCOA4 NRAS NTRK1 PAX8 PPARG RET RXRA RXRB RXRG TCF7 TCF7L1 TCF7L2 TFG TP53 TPM3 TPR
+KEGG_COLORECTAL_CANCER > Colorectal cancer AKT1 AKT2 AKT3 APC APC2 APPL1 ARAF AXIN1 AXIN2 BAD BAX BCL2 BIRC5 BRAF CASP3 CASP9 CCND1 CTNNB1 CYCS DCC FOS GSK3B JUN KRAS LEF1 MAP2K1 MAPK1 MAPK10 MAPK3 MAPK8 MAPK9 MLH1 MSH2 MSH3 MSH6 MYC PIK3CA PIK3CB PIK3CD PIK3CG PIK3R1 PIK3R2 PIK3R3 PIK3R5 RAC1 RAC2 RAC3 RAF1 RALGDS RHOA SMAD2 SMAD3 SMAD4 TCF7 TCF7L1 TCF7L2 TGFB1 TGFB2 TGFB3 TGFBR1 TGFBR2 TP53
+KEGG_ENDOMETRIAL_CANCER > Endometrial cancer AKT1 AKT2 AKT3 APC APC2 ARAF AXIN1 AXIN2 BAD BRAF CASP9 CCND1 CDH1 CTNNA1 CTNNA2 CTNNA3 CTNNB1 EGF EGFR ELK1 ERBB2 FOXO3 GRB2 GSK3B HRAS ILK KRAS LEF1 MAP2K1 MAP2K2 MAPK1 MAPK3 MLH1 MYC NRAS PDPK1 PIK3CA PIK3CB PIK3CD PIK3CG PIK3R1 PIK3R2 PIK3R3 PIK3R5 PTEN RAF1 SOS1 SOS2 TCF7 TCF7L1 TCF7L2 TP53
+KEGG_HOMOLOGOUS_RECOMBINATION > Homologous recombination BLM BRCA2 EME1 MRE11A MUS81 NBN POLD1 POLD2 POLD3 POLD4 RAD50 RAD51 RAD51C RAD51L1 RAD51L3 RAD52 RAD54B RAD54L RPA1 RPA2 RPA3 RPA4 SHFM1 SSBP1 TOP3A TOP3B XRCC2 XRCC3
+KEGG_MISMATCH_REPAIR > Mismatch repair EXO1 LIG1 MLH1 MLH3 MSH2 MSH3 MSH6 PCNA PMS2 POLD1 POLD2 POLD3 POLD4 RFC1 RFC2 RFC3 RFC4 RFC5 RPA1 RPA2 RPA3 RPA4 SSBP1
+KEGG_NON_SMALL_CELL_LUNG_CANCER > Non-small cell lung cancer AKT1 AKT2 AKT3 ARAF BAD BRAF CASP9 CCND1 CDK4 CDK6 CDKN2A E2F1 E2F2 E2F3 EGF EGFR ERBB2 FHIT FOXO3 GRB2 HRAS KRAS MAP2K1 MAP2K2 MAPK1 MAPK3 NRAS PDPK1 PIK3CA PIK3CB PIK3CD PIK3CG PIK3R1 PIK3R2 PIK3R3 PIK3R5 PLCG1 PLCG2 PRKCA PRKCB PRKCG RAF1 RARB RASSF1 RASSF5 RB1 RXRA RXRB RXRG SOS1 SOS2 STK4 TGFA TP53
+KEGG_PANCREATIC_CANCER > Pancreatic cancer AKT1 AKT2 AKT3 ARAF ARHGEF6 BAD BCL2L1 BRAF BRCA2 CASP9 CCND1 CDC42 CDK4 CDK6 CDKN2A CHUK E2F1 E2F2 E2F3 EGF EGFR ERBB2 FIGF IKBKB IKBKG JAK1 KRAS MAP2K1 MAPK1 MAPK10 MAPK3 MAPK8 MAPK9 NFKB1 PGF PIK3CA PIK3CB PIK3CD PIK3CG PIK3R1 PIK3R2 PIK3R3 PIK3R5 PLD1 RAC1 RAC2 RAC3 RAD51 RAF1 RALA RALB RALBP1 RALGDS RB1 RELA SMAD2 SMAD3 SMAD4 STAT1 STAT3 TGFA TGFB1 TGFB2 TGFB3 TGFBR1 TGFBR2 TP53 VEGFA VEGFB VEGFC
+KEGG_PROSTATE_CANCER > Prostate cancer AKT1 AKT2 AKT3 AR ARAF ATF4 BAD BCL2 BRAF CASP9 CCND1 CCNE1 CCNE2 CDK2 CDKN1A CDKN1B CHUK CREB1 CREB3 CREB3L1 CREB3L2 CREB3L3 CREB3L4 CREB5 CREBBP CTNNB1 E2F1 E2F2 E2F3 EGF EGFR EP300 ERBB2 FGFR1 FGFR2 FOXO1 GRB2 GSK3B GSTP1 HRAS HSP90AA1 HSP90AB1 HSP90B1 IGF1 IGF1R IKBKB IKBKG INS INSRR KLK3 KRAS LEF1 MAP2K1 MAP2K2 MAPK1 MAPK3 MDM2 MTOR NFKB1 NFKBIA NKX3-1 NRAS PDGFA PDGFB PDGFC PDGFD PDGFRA PDGFRB PDPK1 PIK3CA PIK3CB PIK3CD PIK3CG PIK3R1 PIK3R2 PI [...]
+KEGG_RENAL_CELL_CARCINOMA > Renal cell carcinoma AKT1 AKT2 AKT3 ARAF ARNT ARNT2 BRAF CDC42 CREBBP CRK CRKL CUL2 EGLN1 EGLN2 EGLN3 EP300 EPAS1 ETS1 FH FIGF FLCN GAB1 GRB2 HGF HIF1A HRAS JUN KRAS MAP2K1 MAP2K2 MAPK1 MAPK3 MET NRAS PAK1 PAK2 PAK3 PAK4 PAK6 PAK7 PDGFB PGF PIK3CA PIK3CB PIK3CD PIK3CG PIK3R1 PIK3R2 PIK3R3 PIK3R5 PTPN11 RAC1 RAF1 RAP1A RAP1B RAPGEF1 RBX1 SLC2A1 SOS1 SOS2 TCEB1 TCEB2 TGFA TGFB1 TGFB2 TGFB3 VEGFA VEGFB VEGFC VHL
+KEGG_SMALL_CELL_LUNG_CANCER > Small cell lung cancer AKT1 AKT2 AKT3 APAF1 BCL2 BCL2L1 BIRC2 BIRC3 CASP9 CCND1 CCNE1 CCNE2 CDK2 CDK4 CDK6 CDKN1B CDKN2B CHUK CKS1B COL4A1 COL4A2 COL4A4 COL4A6 CYCS E2F1 E2F2 E2F3 FHIT FN1 IKBKB IKBKG ITGA2 ITGA2B ITGA3 ITGA6 ITGAV ITGB1 LAMA1 LAMA2 LAMA3 LAMA4 LAMA5 LAMB1 LAMB2 LAMB3 LAMB4 LAMC1 LAMC2 LAMC3 MAX MYC NFKB1 NFKBIA NOS2 PIAS1 PIAS2 PIAS3 PIAS4 PIK3CA PIK3CB PIK3CD PIK3CG PIK3R1 PIK3R2 PIK3R3 PIK3R5 PTEN PTGS2 PTK2 RARB RB1 RELA RXRA RXRB RXRG S [...]
\ No newline at end of file
diff --git a/org/broad/igv/lists/mckd1.gmt b/org/broad/igv/lists/mckd1.gmt
new file mode 100644
index 0000000..963a3e5
--- /dev/null
+++ b/org/broad/igv/lists/mckd1.gmt
@@ -0,0 +1,9 @@
+#name=MKCD1
+MCKD1_1 > . IL6R SHE TDRD10 UBE2Q1 CHRNB2 ADAR KCNN3 PMVK PBXIP1 PYGO2
+MCKD1_2 > . ADAR KCNN3 PMVK PBXIP1 PYGO2 SHC1 CKS1B FLAD1 LENEP ZBTB7B
+MCKD1_3 > . DCST2 DCST1 ADAM15 EFNA4 RAG1AP1 DPM3 KRTCAP2 TRIM46 MUC1 MIR92B
+MCKD1_4 > . THBS3 MTX1 GBAP1 GBA FAM189B SCAMP3 CLK2 HCN3 PKLR FDPS
+MCKD1_5 > . FDPS C1orf104 RUSC1 ASH1L MIR555 LOC645676 MSTO1 YY1AP1 DAP3 MSTO2P
+MCKD1_6 > . GON4L SYT11 RIT1 KIAA0907 SNORA42 SCARNA4 RXFP4 ARHGEF2 SSR2 UBQLN4
+MCKD1_7 > . ROBLD3 RAB25 MEX3A LMNA SEMA4A SLC25A44 PMF1 BGLAP PAQR6 SMG5
+MCKD1_8 > . TMEM79 TMEM79 C1orf85 VHLL CCT3 C1orf182 RHBG C1orf61 MIR9-1 MEF2D
diff --git a/org/broad/igv/lists/reactome_cp.gmt b/org/broad/igv/lists/reactome_cp.gmt
new file mode 100644
index 0000000..ac1723d
--- /dev/null
+++ b/org/broad/igv/lists/reactome_cp.gmt
@@ -0,0 +1,431 @@
+#name=Reactome canonical pathways
+REACTOME_A_THIRD_PROTEOLYTIC_CLEAVAGE_RELEASES_NICD > Genes involved in A third proteolytic cleavage releases NICD APH1A APH1B NCSTN NOTCH1 NOTCH2 NOTCH3 NOTCH4 PSEN1 PSEN2 PSENEN
+REACTOME_ABORTIVE_ELONGATION_OF_HIV1_TRANSCRIPT_IN_THE_ABSENCE_OF_TAT > Genes involved in Abortive elongation of HIV-1 transcript in the absence of Tat COBRA1 CTDP1 GTF2F1 GTF2F2 NCBP1 NCBP2 POLR2A POLR2B POLR2C POLR2D POLR2E POLR2F POLR2G POLR2H POLR2I POLR2J POLR2K POLR2L RDBP SUPT4H1 SUPT5H TH1L WHSC2
+REACTOME_ACETYLCHOLINE_NEUROTRANSMITTER_RELEASE_CYCLE > Genes involved in Acetylcholine Neurotransmitter Release Cycle CHAT CPLX1 RAB3A RIMS1 SLC18A3 SLC5A7 SNAP25 STX1A STXBP1 SYT1 VAMP2
+REACTOME_ACTIVATED_AMPK_STIMULATES_FATTY_ACID_OXIDATION_IN_MUSCLE > Genes involved in Activated AMPK stimulates fatty-acid oxidation in muscle ACACB ACSL1 CAB39 CAB39L CPT1B CPT2 PRKAA1 PRKAA2 PRKAB1 PRKAB2 PRKAG1 PRKAG2 PRKAG3 SLC25A20 STK11 STRADA STRADB
+REACTOME_ACTIVATED_TAK1_MEDIATES_P38_MAPK_ACTIVATION > Genes involved in activated TAK1 mediates p38 MAPK activation MAP2K3 MAP2K6 MAP3K7 MAPK11 MAPK14 MAPKAPK2 MAPKAPK3 TAB1 TAB2 TAB3 TICAM1 TLR3 TRAF6
+REACTOME_ACTIVATED_TLR4_SIGNALLING > Genes involved in Activated TLR4 signalling ECSIT IRAK1 IRAK3 IRAK4 IRF3 LY96 MAP3K1 MYD88 RIPK1 SIGIRR TBK1 TICAM1 TICAM2 TIRAP TLR1 TLR10 TLR2 TLR4 TLR5 TLR6 TLR7 TLR8 TLR9 TRAF6
+REACTOME_ACTIVATION_OF_ATR_IN_RESPONSE_TO_REPLICATION_STRESS > Genes involved in Activation of ATR in response to replication stress ATR ATRIP CDC25A CDC25C CDC45 CDC6 CDC7 CDK2 CHEK1 CLSPN DBF4 HUS1 MCM10 MCM2 MCM3 MCM4 MCM5 MCM6 MCM7 MCM8 ORC1L ORC2L ORC3L ORC4L ORC5L ORC6L RAD1 RAD17 RAD9A RAD9B RFC2 RFC3 RFC4 RFC5 RPA1 RPA2 RPA3
+REACTOME_ACTIVATION_OF_BH3_ONLY_PROTEINS > Genes involved in Activation of BH3-only proteins AKT1 BAD BBC3 BCL2 BCL2L11 BID BMF DYNLL1 DYNLL2 E2F1 MAPK8 PMAIP1 PPP3CC PPP3R1 TFDP1 YWHAB
+REACTOME_ACTIVATION_OF_CHAPERONES_BY_IRE1_ALPHA > Genes involved in Activation of Chaperones by IRE1alpha DNAJB11 DNAJB9 DNAJC3 EDEM1 ERN1 HSPA5 NFYA PDIA6 SERP1 XBP1
+REACTOME_ACTIVATION_OF_KAINATE_RECEPTORS_UPON_GLUTAMATE_BINDING > Genes involved in Activation of Kainate Receptors upon glutamate binding CALM1 CALM2 CALM3 DLG1 DLG3 DLG4 GNB1 GNB2 GNB3 GNB4 GNB5 GNG10 GNG11 GNG12 GNG13 GNG2 GNG3 GNG4 GNG5 GNG7 GNG8 GNGT1 GNGT2 GRIK1 GRIK2 GRIK3 GRIK4 GRIK5 NCALD PLCB1 PLCB2 PLCB3
+REACTOME_ACTIVATION_OF_NMDA_RECEPTOR_UPON_GLUTAMATE_BINDING_AND_POSTSYNAPTIC_EVENTS > Genes involved in Activation of NMDA receptor upon glutamate binding and postsynaptic events ACTN2 ADCY1 ADCY3 ADCY8 CALM1 CALM2 CALM3 CAMK2A CAMK2B CAMK2D CAMK2G CAMK4 CAMKK1 CREB1 DLG4 GRIA1 GRIA2 GRIA3 GRIA4 GRIN1 GRIN2A GRIN2B GRIN2C GRIN2D HRAS MAPK1 NEFL PDPK1 PRKACB RAF1 RASGRF1 RASGRF2 RPS6KA1 RPS6KA2 RPS6KA3 RPS6KA6
+REACTOME_ACTIVATION_OF_RAC > Genes involved in Activation of Rac GPC1 NCK1 NCK2 PAK1 PAK2 PAK3 PAK4 PAK6 PAK7 RAC1 ROBO1 SLIT2 SOS1 SOS2
+REACTOME_ACTIVATION_OF_THE_AP1_FAMILY_OF_TRANSCRIPTION_FACTORS > Genes involved in Activation of the AP-1 family of transcription factors ATF2 FOS JUN MAPK1 MAPK10 MAPK11 MAPK14 MAPK3 MAPK8 MAPK9
+REACTOME_ACTIVATION_OF_THE_PRE_REPLICATIVE_COMPLEX > Genes involved in Activation of the pre-replicative complex CDC45 CDC6 CDC7 CDK2 CDT1 DBF4 MCM10 MCM2 MCM3 MCM4 MCM5 MCM6 MCM7 MCM8 ORC1L ORC2L ORC3L ORC4L ORC5L ORC6L POLA1 POLA2 POLE POLE2 PRIM1 PRIM2 RPA1 RPA2 RPA3 RPA4
+REACTOME_ADENYLATE_CYCLASE_ACTIVATING_PATHWAY > Genes involved in Adenylate cyclase activating pathway ADCY1 ADCY10 ADCY2 ADCY3 ADCY4 ADCY5 ADCY6 ADCY7 ADCY8 ADCY9 GNAL
+REACTOME_ADHERENS_JUNCTIONS_INTERACTIONS > Genes involved in Adherens junctions interactions CADM1 CADM2 CADM3 CDH1 CDH10 CDH11 CDH12 CDH13 CDH15 CDH18 CDH2 CDH24 CDH3 CDH4 CDH5 CDH6 CDH7 CDH8 CDH9 CTNNA1 CTNNB1 CTNND1 JUP MLLT4 PVR PVRL1 PVRL2 PVRL3 PVRL4
+REACTOME_ADP_SIGNALLING_THROUGH_P2Y_PURINOCEPTOR_1 > Genes involved in ADP signalling through P2Y purinoceptor 1 GNA11 GNA14 GNA15 GNAQ GNB1 GNB2 GNB3 GNB4 GNB5 GNG10 GNG11 GNG12 GNG13 GNG2 GNG3 GNG4 GNG5 GNG7 GNG8 GNGT1 GNGT2 MAPK14 P2RY1 PLA2G4A SRC
+REACTOME_ADP_SIGNALLING_THROUGH_P2Y_PURINOCEPTOR_12 > Genes involved in ADP signalling through P2Y purinoceptor 12 GNAI1 GNAI2 GNAI3 GNB1 GNB2 GNB3 GNB4 GNB5 GNG10 GNG11 GNG12 GNG13 GNG2 GNG3 GNG4 GNG5 GNG7 GNG8 GNGT1 GNGT2 P2RY12
+REACTOME_AKT_PHOSPHORYLATES_TARGETS_IN_THE_CYTOSOL > Genes involved in AKT phosphorylates targets in the cytosol AKT1 AKT1S1 AKT2 AKT3 BAD CASP9 CDKN1A CDKN1B CHUK GSK3A GSK3B MDM2 PDPK1 TSC2
+REACTOME_AMINE_COMPOUND_SLC_TRANSPORTERS > Genes involved in Amine compound SLC transporters RHAG RHBG RHCG SLC14A1 SLC14A2 SLC18A1 SLC18A2 SLC22A2 SLC44A1 SLC44A2 SLC44A3 SLC44A4 SLC44A5 SLC5A7 SLC6A1 SLC6A11 SLC6A12 SLC6A13 SLC6A14 SLC6A15 SLC6A18 SLC6A19 SLC6A2 SLC6A20 SLC6A3 SLC6A5 SLC6A6 SLC6A7 SLC6A9
+REACTOME_AMINE_DERIVED_HORMONES > Genes involved in Amine-derived hormones AANAT ASMT DBH DDC DIO1 DIO2 DIO3 IYD PNMT SLC5A5 TH TPH1 TPO
+REACTOME_AMINE_LIGAND_BINDING_RECEPTORS > Genes involved in Amine ligand-binding receptors ADRA1A ADRA1B ADRA1D ADRA2A ADRA2B ADRA2C ADRB1 ADRB2 ADRB3 CHRM1 CHRM2 CHRM3 CHRM4 CHRM5 DRD1 DRD2 DRD3 DRD4 DRD5 HRH1 HRH2 HRH3 HRH4 HTR1A HTR1B HTR1D HTR1E HTR1F HTR2A HTR2B HTR2C HTR4 HTR5A HTR6 HTR7 TAAR1 TAAR2 TAAR3 TAAR5 TAAR6 TAAR8 TAAR9
+REACTOME_AMINO_ACID_AND_OLIGOPEPTIDE_SLC_TRANSPORTERS > Genes involved in Amino acid and oligopeptide SLC transporters SLC15A1 SLC15A2 SLC15A3 SLC15A4 SLC16A10 SLC17A1 SLC17A5 SLC17A6 SLC17A7 SLC17A8 SLC1A1 SLC1A2 SLC1A3 SLC1A4 SLC1A5 SLC1A6 SLC1A7 SLC32A1 SLC36A1 SLC36A2 SLC38A1 SLC38A2 SLC38A3 SLC38A4 SLC38A5 SLC3A1 SLC3A2 SLC43A1 SLC43A2 SLC5A5 SLC5A8 SLC6A12 SLC6A14 SLC6A15 SLC6A18 SLC6A19 SLC6A20 SLC6A6 SLC7A1 SLC7A10 SLC7A11 SLC7A2 SLC7A3 SLC7A5 SLC7A6 SLC7A7 SLC7A8 SLC7A9
+REACTOME_AMINO_ACID_SYNTHESIS_AND_INTERCONVERSION > Genes involved in Amino acid synthesis and interconversion (transamination) ALDH18A1 ASNS GLS GLS2 GLUD1 GLUL GOT1 GOT2 GPT GPT2 OAT PYCR1
+REACTOME_AMINO_ACID_TRANSPORT_ACROSS_THE_PLASMA_MEMBRANE > Genes involved in Amino acid transport across the plasma membrane SLC16A10 SLC1A4 SLC1A5 SLC36A1 SLC36A2 SLC38A1 SLC38A2 SLC38A3 SLC38A4 SLC38A5 SLC3A1 SLC3A2 SLC43A1 SLC43A2 SLC6A12 SLC6A14 SLC6A15 SLC6A18 SLC6A19 SLC6A20 SLC6A6 SLC7A1 SLC7A10 SLC7A11 SLC7A2 SLC7A3 SLC7A5 SLC7A6 SLC7A7 SLC7A8 SLC7A9
+REACTOME_APCDC20_MEDIATED_DEGRADATION_OF_CYCLIN_B > Genes involved in APC/C:Cdc20 mediated degradation of Cyclin B ANAPC1 ANAPC10 ANAPC11 ANAPC2 ANAPC4 ANAPC5 ANAPC7 CCNB1 CDC16 CDC20 CDC23 CDC26 CDC27 CDK1 UBB UBE2C UBE2D1 UBE2E1
+REACTOME_APOPTOSIS > Genes involved in Apoptosis ACIN1 ADD1 AKT1 APAF1 APC ARHGAP10 BAD BAK1 BAX BBC3 BCAP31 BCL2 BCL2L1 BCL2L11 BID BIRC2 BMF BMX CASP10 CASP3 CASP6 CASP7 CASP8 CASP9 CDH1 CFLAR CLSPN CTNNB1 CYCS DBNL DFFA DFFB DIABLO DSG1 DSG2 DSG3 DSP DYNLL1 DYNLL2 E2F1 FADD FAS FASLG FNTA GAS2 GSN GZMB H1F0 HIST1H1A HIST1H1B HIST1H1C HIST1H1D HIST1H1E KPNA1 KPNB1 LMNA LMNB1 MAPK8 MAPT MST4 NMT1 OCLN PAK2 PKP1 PLEC PMAIP1 PPP3CC PPP3R1 PRKCD PRKCQ PSMA1 PSMA2 PSMA3 PSMA4 PSMA5 PSMA6 PS [...]
+REACTOME_APOPTOSIS_INDUCED_DNA_FRAGMENTATION > Genes involved in Apoptosis induced DNA fragmentation CASP3 DFFA DFFB H1F0 HIST1H1A HIST1H1B HIST1H1C HIST1H1D HIST1H1E KPNA1 KPNB1
+REACTOME_APOPTOTIC_CLEAVAGE_OF_CELL_ADHESION_PROTEINS > Genes involved in Apoptotic cleavage of cell adhesion proteins CASP3 CDH1 CTNNB1 DSG1 DSG2 DSG3 DSP OCLN PKP1 TJP1 TJP2
+REACTOME_APOPTOTIC_EXECUTION_PHASE > Genes involved in Apoptotic execution phase ACIN1 ADD1 APC BCAP31 BIRC2 BMX CASP3 CASP6 CASP7 CASP8 CDH1 CLSPN CTNNB1 DBNL DFFA DFFB DSG1 DSG2 DSG3 DSP FNTA GAS2 GSN H1F0 HIST1H1A HIST1H1B HIST1H1C HIST1H1D HIST1H1E KPNA1 KPNB1 LMNA LMNB1 MAPT MST4 OCLN PAK2 PKP1 PLEC PRKCD PRKCQ PTK2 ROCK1 SPTAN1 STK24 TJP1 TJP2 VIM
+REACTOME_ASSOCIATION_OF_LICENSING_FACTORS_WITH_THE_PREREPLICATIVE_COMPLEX > Genes involved in Association of licensing factors with the pre-replicative complex CDC6 CDT1 E2F1 E2F2 E2F3 GMNN ORC1L ORC2L ORC3L ORC4L ORC5L UBB
+REACTOME_ASSOCIATION_OF_TRIC_CCT_WITH_TARGET_PROTEINS_DURING_BIOSYNTHESIS > Genes involved in Association of TriC/CCT with target proteins during biosynthesis AP3M1 ARFGEF2 CCT2 CCT3 CCT4 CCT5 CCT6A CCT7 CCT8 FBXL3 FBXL5 FBXO4 FBXO6 FBXW10 FBXW2 FBXW4 FBXW5 FBXW7 FBXW9 FKBP9 KIF13A KIFC3 LONP2 NOP56 SKIV2L SPHK1 TCP1 USP11 XRN2
+REACTOME_AUTODEGRADATION_OF_CDH1_BY_CDH1_APC > Genes involved in Autodegradation of Cdh1 by Cdh1:APC/C ANAPC1 ANAPC10 ANAPC11 ANAPC2 ANAPC4 ANAPC5 ANAPC7 CDC16 CDC23 CDC26 CDC27 FZR1 PSMA1 PSMA2 PSMA3 PSMA4 PSMA5 PSMA6 PSMA7 PSMB1 PSMB10 PSMB2 PSMB3 PSMB4 PSMB5 PSMB6 PSMB7 PSMB8 PSMB9 PSMC1 PSMC2 PSMC3 PSMC4 PSMC5 PSMC6 PSMD1 PSMD10 PSMD11 PSMD12 PSMD13 PSMD14 PSMD2 PSMD3 PSMD4 PSMD5 PSMD6 PSMD7 PSMD8 PSMD9 PSME1 PSME2 PSME3 PSMF1 UBB UBE2C UBE2D1 UBE2E1
+REACTOME_AXON_GUIDANCE > Genes involved in Axon guidance ABL1 ABL2 AGRN ARHGAP39 ARHGEF11 ARHGEF12 ARTN CACNA1C CACNA1D CACNA1F CACNA1G CACNA1H CACNA1I CACNA1S CACNB1 CACNB2 CACNB3 CACNB4 CAP1 CAP2 CD72 CDC42 CDK5 CDK5R1 CFL1 CLASP1 CLASP2 CNTN2 COL1A1 COL1A2 COL29A1 COL2A1 COL3A1 COL4A1 COL4A2 COL4A3 COL4A4 COL4A5 COL5A1 COL5A2 COL6A1 COL6A2 COL6A3 COL6A6 COL9A1 COL9A2 COL9A3 CREB1 CRMP1 DPYSL2 DPYSL3 DPYSL4 DPYSL5 ENAH ERBB2 EVL FARP2 FES FGFR1 FYN GDNF GFRA1 GFRA2 GFRA4 GPC1 GRB2 GRLF [...]
+REACTOME_BASE_EXCISION_REPAIR > Genes involved in Base Excision Repair APEX1 CCNO FEN1 LIG1 LIG3 MBD4 MPG MUTYH NTHL1 OGG1 POLB POLD1 POLD2 POLD3 POLD4 SMUG1 TDG XRCC1
+REACTOME_BASE_FREE_SUGAR_PHOSPHATE_REMOVAL_VIA_THE_SINGLE_NUCLEOTIDE_REPLACEMENT_PATHWAY > Genes involved in Base-free sugar-phosphate removal via the single-nucleotide replacement pathway APEX1 CCNO MBD4 MPG MUTYH NTHL1 OGG1 POLB SMUG1 TDG
+REACTOME_BASIGIN_INTERACTIONS > Genes involved in Basigin interactions ATP1B1 ATP1B2 ATP1B3 BSG CAV1 ITGA3 ITGA6 ITGB1 L1CAM MAG MMP1 PPIA PPIL2 SLC16A1 SLC16A3 SLC16A8 SLC3A2 SLC7A10 SLC7A11 SLC7A5 SLC7A6 SLC7A7 SLC7A8 SLC7A9 SPN
+REACTOME_BETACATENIN_PHOSPHORYLATION_CASCADE > Genes involved in Beta-catenin phosphorylation cascade APC AXIN1 CSNK1A1 CTNNB1 GSK3B PPP2CA PPP2CB PPP2R1A PPP2R1B PPP2R5A PPP2R5B PPP2R5C PPP2R5D
+REACTOME_BILE_SALT_AND_ORGANIC_ANION_SLC_TRANSPORTERS > Genes involved in Bile salt and organic anion SLC transporters SLC10A6 SLC13A1 SLC13A2 SLC13A3 SLC13A4 SLC13A5 SLC16A1 SLC16A3 SLC16A7 SLC16A8 SLC47A1 SLC47A2
+REACTOME_BIOLOGICAL_OXIDATIONS > Genes involved in Biological oxidations ACSM1 ACSM2B ACSS1 ACSS2 ADH1A ADH1B ADH1C ADH4 ADH6 ADH7 AHCY ALDH1A1 ALDH2 COMT CYP11A1 CYP11B1 CYP11B2 CYP17A1 CYP19A1 CYP1A1 CYP1A2 CYP1B1 CYP21A2 CYP24A1 CYP26A1 CYP26B1 CYP26C1 CYP27A1 CYP27B1 CYP2A13 CYP2A6 CYP2B6 CYP2C18 CYP2C19 CYP2C8 CYP2C9 CYP2D6 CYP2E1 CYP2F1 CYP2J2 CYP2R1 CYP2S1 CYP2U1 CYP2W1 CYP39A1 CYP3A4 CYP3A43 CYP3A5 CYP3A7 CYP46A1 CYP4A11 CYP4B1 CYP4F11 CYP4F12 CYP4F2 CYP4F3 CYP4F8 CYP51A1 CYP7A1 [...]
+REACTOME_BOTULINUM_NEUROTOXICITY > Genes involved in Botulinum neurotoxicity SNAP25 STX10 STX11 STX12 STX16 STX1A STX1B STX2 STX3 STX4 STX5 STX6 STX7 STX8 SYT1 SYT2 VAMP1 VAMP2
+REACTOME_BRANCHED_CHAIN_AMINO_ACID_CATABOLISM > Genes involved in Branched-chain amino acid catabolism ACAD8 ACADSB ACAT1 ALDH6A1 AUH BCAT1 BCAT2 BCKDHA BCKDHB DBT DLD HIBADH HIBCH HSD17B10 IVD MCCC1 MCCC2
+REACTOME_CALCITONIN_LIKE_LIGAND_RECEPTORS > Genes involved in Calcitonin-like ligand receptors ADM ADM2 CALCA CALCB CALCR CALCRL IAPP RAMP1 RAMP2 RAMP3
+REACTOME_CAM_PATHWAY > Genes involved in CaM pathway ADCY1 ADCY10 ADCY2 ADCY3 ADCY4 ADCY5 ADCY6 ADCY7 ADCY8 ADCY9 ADRBK1 CALM1 CALM2 CALM3 CAMK4 CREB1 PDE1A PDE1B PDE1C PRKACA PRKACB PRKACG PRKAR1A PRKAR1B PRKAR2A PRKAR2B
+REACTOME_CASPASE_MEDIATED_CLEAVAGE_OF_CYTOSKELETAL_PROTEINS > Genes involved in Caspase-mediated cleavage of cytoskeletal proteins ADD1 CASP3 CASP6 CASP7 CASP8 DBNL GAS2 GSN MAPT PLEC SPTAN1 VIM
+REACTOME_CD28_CO_STIMULATION > Genes involved in CD28 co-stimulation AKT1 AKT2 AKT3 CD28 CD80 CD86 CDC42 FYN GRAP2 GRB2 LCK LYN MAP3K14 MAP3K8 MAPKAP1 MLST8 MTOR PAK1 PAK2 PDPK1 PIK3CA PIK3R1 RAC1 RICTOR SRC THEM4 TRIB3 VAV1 YES1
+REACTOME_CD28_DEPENDENT_PI3K_AKT_SIGNALING > Genes involved in CD28 dependent PI3K/Akt signaling AKT1 AKT2 AKT3 CD28 CD80 CD86 FYN LCK MAP3K14 MAP3K8 MAPKAP1 MLST8 MTOR PDPK1 PIK3CA PIK3R1 RICTOR THEM4 TRIB3
+REACTOME_CD28_DEPENDENT_VAV1_PATHWAY > Genes involved in CD28 dependent Vav1 pathway CD28 CD80 CD86 CDC42 FYN GRB2 LCK PAK1 PAK2 RAC1 VAV1
+REACTOME_CDC20_PHOSPHO_APC_MEDIATED_DEGRADATION_OF_CYCLIN_A > Genes involved in Cdc20:Phospho-APC/C mediated degradation of Cyclin A ANAPC1 ANAPC10 ANAPC11 ANAPC2 ANAPC4 ANAPC5 ANAPC7 BUB1B BUB3 CCNA1 CCNA2 CDC16 CDC20 CDC23 CDC26 CDC27 CDK1 MAD2L1 PSMA1 PSMA2 PSMA3 PSMA4 PSMA5 PSMA6 PSMA7 PSMB1 PSMB10 PSMB2 PSMB3 PSMB4 PSMB5 PSMB6 PSMB7 PSMB8 PSMB9 PSMC1 PSMC2 PSMC3 PSMC4 PSMC5 PSMC6 PSMD1 PSMD10 PSMD11 PSMD12 PSMD13 PSMD14 PSMD2 PSMD3 PSMD4 PSMD5 PSMD6 PSMD7 PSMD8 PSMD9 PSME1 PSME2 PSM [...]
+REACTOME_CDC6_ASSOCIATION_WITH_THE_ORC:ORIGIN_COMPLEX > Genes involved in CDC6 association with the ORC:origin complex CDC6 E2F1 E2F2 E2F3 MCM8 ORC1L ORC2L ORC3L ORC4L ORC5L ORC6L
+REACTOME_CDT1_ASSOCIATION_WITH_THE_CDC6_ORC_ORIGIN_COMPLEX > Genes involved in CDT1 association with the CDC6:ORC:origin complex CDC6 CDT1 GMNN MCM8 ORC1L ORC2L ORC3L ORC4L ORC5L ORC6L PSMA1 PSMA2 PSMA3 PSMA4 PSMA5 PSMA6 PSMA7 PSMB1 PSMB10 PSMB2 PSMB3 PSMB4 PSMB5 PSMB6 PSMB7 PSMB8 PSMB9 PSMC1 PSMC2 PSMC3 PSMC4 PSMC5 PSMC6 PSMD1 PSMD10 PSMD11 PSMD12 PSMD13 PSMD14 PSMD2 PSMD3 PSMD4 PSMD5 PSMD6 PSMD7 PSMD8 PSMD9 PSME1 PSME2 PSME3 PSMF1 UBB
+REACTOME_CELL_CELL_ADHESION_SYSTEMS > Genes involved in Cell-cell adhesion systems CADM1 CADM2 CADM3 CDH1 CDH10 CDH11 CDH12 CDH13 CDH15 CDH18 CDH2 CDH24 CDH3 CDH4 CDH5 CDH6 CDH7 CDH8 CDH9 CLDN1 CLDN10 CLDN11 CLDN12 CLDN14 CLDN15 CLDN16 CLDN17 CLDN18 CLDN19 CLDN2 CLDN20 CLDN22 CLDN23 CLDN3 CLDN4 CLDN5 CLDN6 CLDN7 CLDN8 CLDN9 CRB3 CTNNA1 CTNNB1 CTNND1 F11R INADL JUP MLLT4 MPP5 PARD3 PARD6A PARD6B PARD6G PRKCI PVR PVRL1 PVRL2 PVRL3 PVRL4
+REACTOME_CELL_CYCLE_CHECKPOINTS > Genes involved in Cell Cycle Checkpoints ANAPC1 ANAPC10 ANAPC11 ANAPC2 ANAPC4 ANAPC5 ANAPC7 ATM ATR ATRIP BUB1B BUB3 CCNB1 CCNB2 CCNE1 CCNE2 CDC16 CDC20 CDC23 CDC25A CDC25C CDC26 CDC27 CDC45 CDC6 CDC7 CDK1 CDK2 CDKN1A CHEK1 CHEK2 CLSPN DBF4 HUS1 MAD1L1 MAD2L1 MCM10 MCM2 MCM3 MCM4 MCM5 MCM6 MCM7 MCM8 MDM2 ORC1L ORC2L ORC3L ORC4L ORC5L ORC6L PSMA1 PSMA2 PSMA3 PSMA4 PSMA5 PSMA6 PSMA7 PSMB1 PSMB10 PSMB2 PSMB3 PSMB4 PSMB5 PSMB6 PSMB7 PSMB8 PSMB9 PSMC1 PSMC2 P [...]
+REACTOME_CELL_CYCLE_MITOTIC > Genes involved in Cell Cycle, Mitotic ACTR1A AHCTF1 AKAP9 ALMS1 ANAPC1 ANAPC10 ANAPC11 ANAPC2 ANAPC4 ANAPC5 ANAPC7 APITD1 AURKA AURKB AZI1 B9D2 BIRC5 BTRC BUB1 BUB1B BUB3 CASC5 CCDC99 CCNA1 CCNA2 CCNB1 CCNB2 CCND1 CCND2 CCND3 CCNE1 CCNE2 CCNH CDC14A CDC16 CDC20 CDC23 CDC25A CDC25B CDC25C CDC26 CDC27 CDC45 CDC6 CDC7 CDCA8 CDK1 CDK11A CDK11B CDK2 CDK4 CDK5RAP2 CDK6 CDK7 CDKN1A CDT1 CENPA CENPC1 CENPE CENPF CENPH CENPI CENPJ CENPK CENPL CENPM CENPN CENPO CENPP [...]
+REACTOME_CELL_DEATH_SIGNALLING_VIA_NRAGE_NRIF_AND_NADE > Genes involved in Cell death signalling via NRAGE, NRIF and NADE AATF ABR AKAP13 APH1A APH1B ARHGAP4 ARHGEF11 ARHGEF12 ARHGEF16 ARHGEF17 ARHGEF18 ARHGEF2 ARHGEF3 ARHGEF4 ARHGEF6 ARHGEF7 ARHGEF9 BAD BCL2L11 CASP2 CASP3 ECT2 FGD1 FGD2 FGD3 FGD4 ITGB3BP ITSN1 KALRN MAGED1 MAPK8 MCF2 MCF2L NCSTN NET1 NGEF NGF NGFR NGFRAP1 OBSCN PLEKHG2 PLEKHG5 PREX1 PSEN1 PSEN2 PSENEN RAC1 RASGRF1 RASGRF2 SOS1 SOS2 SQSTM1 TIAM1 TIAM2 TRAF6 TRIO UBB VAV [...]
+REACTOME_CELL_JUNCTION_ORGANIZATION > Genes involved in Cell junction organization ACTN1 ARHGEF6 CADM1 CADM2 CADM3 CD151 CDH1 CDH10 CDH11 CDH12 CDH13 CDH15 CDH18 CDH2 CDH24 CDH3 CDH4 CDH5 CDH6 CDH7 CDH8 CDH9 CLDN1 CLDN10 CLDN11 CLDN12 CLDN14 CLDN15 CLDN16 CLDN17 CLDN18 CLDN19 CLDN2 CLDN20 CLDN22 CLDN23 CLDN3 CLDN4 CLDN5 CLDN6 CLDN7 CLDN8 CLDN9 COL17A1 CRB3 CTNNA1 CTNNB1 CTNND1 DST F11R FBLIM1 FERMT2 FLNA FLNC ILK INADL ITGA6 ITGB1 ITGB4 JUP LAMA3 LAMB3 LAMC2 LIMS1 LIMS2 MLLT4 MPP5 PARD3 [...]
+REACTOME_CELL_SURFACE_INTERACTIONS_AT_THE_VASCULAR_WALL > Genes involved in Cell surface interactions at the vascular wall AMICA1 ANGPT1 ANGPT2 ANGPT4 APOB ATP1B1 ATP1B2 ATP1B3 BSG CAV1 CD177 CD2 CD244 CD47 CD48 CD58 CD84 COL1A1 COL1A2 CXADR DOK2 ESAM F11R F2 FCER1G FN1 FYN GAS6 GP6 GRB14 GRB2 GRB7 HRAS INPP5D ITGA3 ITGA4 ITGA5 ITGA6 ITGAL ITGAM ITGAV ITGAX ITGB1 ITGB2 ITGB3 JAM2 JAM3 KRAS L1CAM LCK LYN MAG MERTK MMP1 NRAS OLR1 PECAM1 PF4 PF4V1 PIK3CA PIK3CB PIK3R1 PIK3R2 PLCG1 PPIA PPIL [...]
+REACTOME_CELLEXTRACELLULAR_MATRIX_INTERACTIONS > Genes involved in Cell-extracellular matrix interactions ACTN1 ARHGEF6 FBLIM1 FERMT2 FLNA FLNC ILK ITGB1 LIMS1 LIMS2 PARVA PARVB PXN RSU1 TESK1 VASP
+REACTOME_CENTROSOME_MATURATION > Genes involved in Centrosome maturation ACTR1A AKAP9 ALMS1 AZI1 CCNB1 CDK1 CDK11A CDK11B CDK5RAP2 CENPJ CEP110 CEP135 CEP152 CEP164 CEP192 CEP250 CEP290 CEP57 CEP63 CEP70 CEP72 CEP76 CEP78 CETN2 CKAP5 CLASP1 CP110 CSNK1D CSNK1E DCTN1 DCTN2 DCTN3 DYNC1H1 DYNC1I2 DYNLL1 FGFR1OP HAUS2 HSP90AA1 MAPRE1 NDE1 NEDD1 NEK2 NINL NUMA1 ODF2 OFD1 PAFAH1B1 PCM1 PCNT PLK1 PLK4 PPP2R1A PRKACA PRKAR2B SDCCAG8 SFI1 SSNA1 TSGA14 TUBA1A TUBA4A TUBB TUBB2C TUBB4 TUBG1 TUBG2 T [...]
+REACTOME_CHAPERONIN_MEDIATED_PROTEIN_FOLDING > Genes involved in Chaperonin-mediated protein folding ACTB AP3M1 ARFGEF2 CCT2 CCT3 CCT4 CCT5 CCT6A CCT7 CCT8 FBXL3 FBXL5 FBXO4 FBXO6 FBXW10 FBXW2 FBXW4 FBXW5 FBXW7 FBXW9 FKBP9 KIF13A KIFC3 LONP2 NOP56 PFDN1 PFDN2 PFDN4 PFDN5 PFDN6 SKIV2L SPHK1 TCP1 TUBA1A TUBA1B TUBA1C TUBA3C TUBA3D TUBA4A TUBB1 TUBB2A TUBB2B TUBB2C TUBB3 TUBB4 TUBB4Q TUBB6 USP11 VBP1 XRN2
+REACTOME_CHEMOKINE_RECEPTORS_BIND_CHEMOKINES > Genes involved in Chemokine receptors bind chemokines CCBP2 CCL11 CCL16 CCL17 CCL19 CCL2 CCL20 CCL21 CCL22 CCL25 CCL27 CCL28 CCL3 CCL3L1 CCL3L3 CCL4 CCL5 CCL7 CCR1 CCR10 CCR2 CCR3 CCR4 CCR5 CCR6 CCR7 CCR8 CCR9 CCRL1 CX3CL1 CX3CR1 CXCL1 CXCL10 CXCL11 CXCL12 CXCL13 CXCL16 CXCL2 CXCL3 CXCL5 CXCL6 CXCL9 CXCR1 CXCR2 CXCR3 CXCR4 CXCR5 CXCR6 CXCR7 IL8 PF4 PPBP XCL1 XCL2 XCR1
+REACTOME_CHOLESTEROL_BIOSYNTHESIS > Genes involved in Cholesterol biosynthesis CYP51A1 DHCR24 DHCR7 EBP FDFT1 GGPS1 HMGCR HMGCS1 HSD17B7 IDI1 IDI2 LBR LSS MVD MVK NSDHL PMVK SC4MOL SC5DL SQLE TM7SF2
+REACTOME_CHYLOMICRON_MEDIATED_LIPID_TRANSPORT > Genes involved in Chylomicron-mediated lipid transport APOA1 APOA2 APOA4 APOA5 APOB APOC2 APOC3 APOE HSPG2 LDLR LDLRAP1 LIPC LPL MTTP P4HB SAR1B SDC1
+REACTOME_CITRIC_ACID_CYCLE > Genes involved in Citric acid cycle (TCA cycle) ACO2 CS DLD DLST FH IDH2 IDH3A IDH3B IDH3G MDH2 NNT OGDH SDHA SDHB SDHC SDHD SUCLA2 SUCLG1 SUCLG2
+REACTOME_CLASS_A1_RHODOPSIN_LIKE_RECEPTORS > Genes involved in Class A/1 (Rhodopsin-like receptors) ADORA1 ADORA2A ADORA2B ADORA3 ADRA1A ADRA1B ADRA1D ADRA2A ADRA2B ADRA2C ADRB1 ADRB2 ADRB3 AGT AGTR1 AGTR2 ANXA1 APLN APLNR AVP AVPR1A AVPR1B AVPR2 BDKRB1 BDKRB2 C3 C3AR1 C5 C5AR1 CCBP2 CCK CCKAR CCKBR CCL11 CCL16 CCL17 CCL19 CCL2 CCL20 CCL21 CCL22 CCL23 CCL25 CCL27 CCL28 CCL3 CCL3L1 CCL3L3 CCL4 CCL5 CCL7 CCR1 CCR10 CCR2 CCR3 CCR4 CCR5 CCR6 CCR7 CCR8 CCR9 CCRL1 CGA CGB CHRM1 CHRM2 CHRM3 CHR [...]
+REACTOME_CLASS_B2_SECRETIN_FAMILY_RECEPTORS > Genes involved in Class B/2 (Secretin family receptors) ADCYAP1 ADCYAP1R1 ADM ADM2 CALCA CALCB CALCR CALCRL CRH CRHR1 CRHR2 DHH FZD1 FZD10 FZD2 FZD3 FZD4 FZD5 FZD6 FZD7 FZD8 FZD9 GCG GCGR GHRH GHRHR GIP GIPR GLP1R GLP2R GNAS GNB1 GNB2 GNB3 GNB4 GNB5 GNG10 GNG11 GNG12 GNG13 GNG2 GNG3 GNG4 GNG5 GNG7 GNG8 GNGT1 GNGT2 IAPP IHH PTCH1 PTCH2 PTH PTH1R PTH2 PTH2R PTHLH RAMP1 RAMP2 RAMP3 SCT SCTR SHH SMO VIP VIPR1 VIPR2 WNT1 WNT10A WNT10B WNT11 WNT16 [...]
+REACTOME_CLASS_C3_METABOTROPIC_GLUTAMATE_PHEROMONE_RECEPTORS > Genes involved in Class C/3 (Metabotropic glutamateheromone receptors) CASR GABBR1 GABBR2 GPRC6A GRM1 GRM2 GRM3 GRM4 GRM5 GRM6 GRM7 GRM8 TAS1R1 TAS1R2 TAS1R3
+REACTOME_CLASSICAL_ANTIBODY_MEDIATED_COMPLEMENT_ACTIVATION > Genes involved in Classical antibody-mediated complement activation C1QA C1QB C1QC C1R C1S IGHV3-23 IGHV7-81 IGKC IGKV1-5 IGKV4-1 IGLC1 IGLC2 IGLC3 IGLV1-36 IGLV1-40 IGLV1-44 IGLV10-54 IGLV11-55 IGLV2-11 IGLV2-18 IGLV2-23 IGLV2-33 IGLV3-12 IGLV3-16 IGLV3-22 IGLV3-25 IGLV3-27 IGLV4-3 IGLV4-60 IGLV4-69 IGLV5-37 IGLV5-45 IGLV7-43 IGLV7-46 IGLV8-61
+REACTOME_CLATHRIN_DERIVED_VESICLE_BUDDING > Genes involved in Clathrin derived vesicle budding AP1B1 AP1G1 AP1M1 AP1M2 AP1S1 AP1S2 AP1S3 AP3B1 AP3S1 AP4B1 AP4E1 ARF1 ARRB1 BLOC1S1 BLOC1S3 CLINT1 CLTA CLTC CNO CPD CTSZ DNAJC6 DNASE2 DNM2 DTNBP1 FTH1 FTL GAK GBF1 GNS HIP1R HSPA8 IGF2R M6PR NAPA NECAP1 OCRL PICALM PIK3C2A PLDN PUM1 RAB5C SH3D19 SH3GL2 SNAP23 SNAPIN SNX2 SNX5 SNX9 SORT1 STX4 TBC1D8B TFRC TGOLN2 TPD52 TPD52L1 TXNDC5 VAMP2 VAMP7 VAMP8 YIPF6
+REACTOME_COLLAGEN_MEDIATED_ACTIVATION_CASCADE > Genes involved in Collagen-mediated activation cascade AKT1 AKT2 AKT3 COL1A1 COL1A2 FCER1G FYN GP6 LCP2 LYN PDPK1 PIK3CA PIK3CB PIK3CG PIK3R1 PIK3R5 PIK3R6 PLCG2 PRKCZ SYK VAV1 VAV2 VAV3
+REACTOME_COMMON_PATHWAY > Genes involved in Common Pathway F10 F13A1 F13B F2 F5 FGA FGB FGG PF4 PF4V1 PROC PROS1 SERPINC1 THBD
+REACTOME_COMPLEMENT_CASCADE > Genes involved in Complement cascade C1QA C1QB C1QC C1R C1S C2 C3 C4A C5 C6 C7 C8A C8B C8G C9 CFB CFD IGHV3-23 IGHV7-81 IGKC IGKV1-5 IGKV4-1 IGLC1 IGLC2 IGLC3 IGLV1-36 IGLV1-40 IGLV1-44 IGLV10-54 IGLV11-55 IGLV2-11 IGLV2-18 IGLV2-23 IGLV2-33 IGLV3-12 IGLV3-16 IGLV3-22 IGLV3-25 IGLV3-27 IGLV4-3 IGLV4-60 IGLV4-69 IGLV5-37 IGLV5-45 IGLV7-43 IGLV7-46 IGLV8-61 MASP1 MASP2 MBL2
+REACTOME_CONVERSION_FROM_APC_CDC20_TO_APC_CDH1_IN_LATE_ANAPHASE > Genes involved in Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase ANAPC1 ANAPC10 ANAPC11 ANAPC2 ANAPC4 ANAPC5 ANAPC7 CDC14A CDC16 CDC20 CDC23 CDC26 CDC27 FZR1 UBE2C UBE2D1 UBE2E1
+REACTOME_COPI_MEDIATED_TRANSPORT > Genes involved in COPI Mediated Transport ARCN1 ARF1 ARFGAP1 COPA COPB1 COPB2 COPE COPG COPZ1 GBF1
+REACTOME_COSTIMULATION_BY_THE_CD28_FAMILY > Genes involved in Costimulation by the CD28 family AKT1 AKT2 AKT3 BTLA CD247 CD274 CD28 CD3D CD3E CD3G CD4 CD80 CD86 CDC42 CSK CTLA4 FYN GRAP2 GRB2 HLA-DMA HLA-DMB HLA-DOA HLA-DOB HLA-DPA1 HLA-DPB1 HLA-DQA1 HLA-DQA2 HLA-DQB1 HLA-DRA HLA-DRB1 HLA-DRB3 HLA-DRB5 ICOS ICOSLG LCK LYN MAP3K14 MAP3K8 MAPKAP1 MLST8 MTOR PAK1 PAK2 PDCD1 PDCD1LG2 PDPK1 PIK3CA PIK3R1 PPP2CA PPP2CB PPP2R1A PPP2R1B PPP2R5A PPP2R5B PPP2R5C PPP2R5D PTPN11 PTPN6 RAC1 RICTOR SR [...]
+REACTOME_CREB_PHOPHORYLATION_THROUGH_THE_ACTIVATION_OF_RAS > Genes involved in CREB phophorylation through the activation of Ras ACTN2 CALM1 CALM2 CALM3 CAMK2A CAMK2B CAMK2D CAMK2G CREB1 DLG4 GRIN1 GRIN2A GRIN2B GRIN2C GRIN2D HRAS MAPK1 NEFL PDPK1 RAF1 RASGRF1 RASGRF2 RPS6KA1 RPS6KA2 RPS6KA3 RPS6KA6
+REACTOME_CREB_PHOSPHORYLATION_THROUGH_THE_ACTIVATION_OF_CAMKII > Genes involved in CREB phosphorylation through the activation of CaMKII ACTN2 CALM1 CALM2 CALM3 CAMK2A CAMK2B CAMK2D CAMK2G CREB1 DLG4 GRIN1 GRIN2A GRIN2B GRIN2C GRIN2D NEFL
+REACTOME_CRMPS_IN_SEMA3A_SIGNALING > Genes involved in CRMPs in Sema3A signaling CDK5 CDK5R1 CRMP1 DPYSL2 DPYSL3 DPYSL4 DPYSL5 FES FYN GSK3B NRP1 PLXNA1 PLXNA2 PLXNA3 PLXNA4 SEMA3A
+REACTOME_CTLA4_INHIBITORY_SIGNALING > Genes involved in CTLA4 inhibitory signaling AKT1 AKT2 AKT3 CD80 CD86 CTLA4 FYN LCK LYN PDPK1 PPP2CA PPP2CB PPP2R1A PPP2R1B PPP2R5A PPP2R5B PPP2R5C PPP2R5D PTPN11 SRC YES1
+REACTOME_CYCLIN_A1_ASSOCIATED_EVENTS_DURING_G2_M_TRANSITION > Genes involved in Cyclin A1 associated events during G2/M transition CCNA1 CCNA2 CCNB1 CCNB2 CCNH CDC25A CDC25B CDC25C CDK1 CDK7 MNAT1 PKMYT1 PLK1 WEE1 XPO1
+REACTOME_CYCLIN_E_ASSOCIATED_EVENTS_DURING_G1_S_TRANSITION_ > Genes involved in Cyclin E associated events during G1/S transition CCNA1 CCNA2 CCNE1 CCNE2 CCNH CDC25A CDK2 CDK7 CDKN1A CKS1B CUL1 MNAT1 PSMA1 PSMA2 PSMA3 PSMA4 PSMA5 PSMA6 PSMA7 PSMB1 PSMB10 PSMB2 PSMB3 PSMB4 PSMB5 PSMB6 PSMB7 PSMB8 PSMB9 PSMC1 PSMC2 PSMC3 PSMC4 PSMC5 PSMC6 PSMD1 PSMD10 PSMD11 PSMD12 PSMD13 PSMD14 PSMD2 PSMD3 PSMD4 PSMD5 PSMD6 PSMD7 PSMD8 PSMD9 PSME1 PSME2 PSME3 PSMF1 RB1 SKP1 SKP2 UBB WEE1
+REACTOME_CYTOCHROME_P450_ARRANGED_BY_SUBSTRATE_TYPE > Genes involved in Cytochrome P450 - arranged by substrate type CYP11A1 CYP11B1 CYP11B2 CYP17A1 CYP19A1 CYP1A1 CYP1A2 CYP1B1 CYP21A2 CYP24A1 CYP26A1 CYP26B1 CYP26C1 CYP27A1 CYP27B1 CYP2A13 CYP2A6 CYP2B6 CYP2C18 CYP2C19 CYP2C8 CYP2C9 CYP2D6 CYP2E1 CYP2F1 CYP2J2 CYP2R1 CYP2S1 CYP2U1 CYP2W1 CYP39A1 CYP3A4 CYP3A43 CYP3A5 CYP3A7 CYP46A1 CYP4A11 CYP4B1 CYP4F11 CYP4F12 CYP4F2 CYP4F3 CYP4F8 CYP51A1 CYP7A1 CYP7B1 CYP8B1 PTGIS TBXAS1
+REACTOME_CYTOSOLIC_SULFONATION_OF_SMALL_MOLECULES > Genes involved in Cytosolic sulfonation of small molecules SULT1A1 SULT1A2 SULT1A3 SULT1A4 SULT1B1 SULT1C2 SULT1C4 SULT1E1 SULT2A1 SULT2B1 SULT4A1
+REACTOME_CYTOSOLIC_TRNA_AMINOACYLATION > Genes involved in Cytosolic tRNA aminoacylation AARS AIMP1 AIMP2 CARS DARS EEF1E1 EPRS FARSA FARSB GARS HARS IARS KARS LARS MARS NARS QARS RARS SARS TARS VARS WARS YARS
+REACTOME_DARPP32_EVENTS > Genes involved in DARPP-32 events CALM1 CALM2 CALM3 CDK5 PDE4A PDE4B PDE4C PDE4D PPP1CA PPP1R1B PPP2CA PPP2CB PPP2R1A PPP2R1B PPP2R5D PPP3CA PPP3CB PPP3CC PPP3R1 PRKACA PRKACB PRKACG PRKAR1A PRKAR1B PRKAR2A PRKAR2B
+REACTOME_DEADENYLATION_OF_MRNA > Genes involved in Deadenylation of mRNA C2ORF29 CNOT1 CNOT10 CNOT2 CNOT3 CNOT4 CNOT6 CNOT6L CNOT7 CNOT8 EIF4A1 EIF4A2 EIF4B EIF4E EIF4G1 PABPC1 PAIP1 PAN2 PAN3 PARN RQCD1 TNKS1BP1
+REACTOME_DEATH_RECEPTOR_SIGNALLING > Genes involved in Death Receptor Signalling CASP10 CASP8 CFLAR FADD FAS FASLG RIPK1 TNF TNFRSF10B TNFRSF1A TNFSF10 TRADD TRAF2
+REACTOME_DEPOLARIZATION_OF_THE_PRESYNAPTIC_TERMINAL_TRIGGERS_THE_OPENING_OF_CALCIUM_CHANNELS > Genes involved in Depolarization of the Presynaptic Terminal Triggers the Opening of Calcium Channels CACNA1A CACNA1B CACNA1E CACNA2D1 CACNA2D2 CACNA2D3 CACNB1 CACNB2 CACNB3 CACNB4 CACNG2 CACNG4
+REACTOME_DIABETES_PATHWAYS > Genes involved in Diabetes pathways ABCC8 ACO2 ADCY5 ADCY6 ADCY8 ADRA2A ADRA2C AKAP5 ALDOA ALDOB ALDOC ATF3 ATF4 ATF6 ATP5A1 ATP5B ATP5C1 ATP5D ATP5E ATP5F1 ATP5G1 ATP5H ATP5I ATP5J ATP5J2 ATP5L ATP5O ATP6 ATP8 BCHE CACNA1A CACNA1C CACNA1D CACNA1E CACNA2D2 CACNB2 CACNB3 CHRM3 COX1 COX2 COX3 COX4I1 COX5A COX5B COX6A1 COX6B1 COX6C COX7A2L COX7B COX7C COX8A CPE CS CTSL1 CYC1 CYCS DDIT3 DDOST DLAT DLD DLST DNAJB11 DNAJB9 DNAJC3 EDEM1 EIF2AK3 EIF2S1 ENO1 ENO2 ENO3 [...]
+REACTOME_DNA_REPAIR > Genes involved in DNA Repair ALKBH2 ALKBH3 APEX1 ATM ATR BRCA1 BRCA2 C17ORF70 C19ORF40 CCNH CCNO CDK7 DDB1 DDB2 ERCC1 ERCC2 ERCC3 ERCC4 ERCC5 ERCC6 ERCC8 FANCA FANCB FANCC FANCD2 FANCE FANCF FANCG FANCI FANCL FANCM FEN1 GTF2H1 GTF2H2 GTF2H3 GTF2H4 H2AFX LIG1 LIG3 LIG4 MAD2L2 MBD4 MDC1 MGMT MNAT1 MPG MRE11A MUTYH NBN NTHL1 OGG1 PALB2 PCNA POLB POLD1 POLD2 POLD3 POLD4 POLE POLE2 POLH POLR2A POLR2B POLR2C POLR2D POLR2E POLR2F POLR2G POLR2H POLR2I POLR2J POLR2K POLR2L P [...]
+REACTOME_DNA_REPLICATION_PRE_INITIATION > Genes involved in DNA Replication Pre-Initiation CDC45 CDC6 CDC7 CDK2 CDT1 DBF4 E2F1 E2F2 E2F3 GMNN MCM10 MCM2 MCM3 MCM4 MCM5 MCM6 MCM7 MCM8 ORC1L ORC2L ORC3L ORC4L ORC5L ORC6L POLA1 POLA2 POLE POLE2 PRIM1 PRIM2 PSMA1 PSMA2 PSMA3 PSMA4 PSMA5 PSMA6 PSMA7 PSMB1 PSMB10 PSMB2 PSMB3 PSMB4 PSMB5 PSMB6 PSMB7 PSMB8 PSMB9 PSMC1 PSMC2 PSMC3 PSMC4 PSMC5 PSMC6 PSMD1 PSMD10 PSMD11 PSMD12 PSMD13 PSMD14 PSMD2 PSMD3 PSMD4 PSMD5 PSMD6 PSMD7 PSMD8 PSMD9 PSME1 PSME [...]
+REACTOME_DNA_STRAND_ELONGATION > Genes involved in DNA strand elongation CDC45 DNA2 FEN1 GINS1 GINS2 GINS4 LIG1 MCM2 MCM3 MCM4 MCM5 MCM6 MCM7 MCM8 PCNA POLA1 POLA2 POLD1 POLD2 POLD3 POLD4 PRIM1 PRIM2 RFC1 RFC2 RFC3 RFC4 RFC5 RPA1 RPA2 RPA3
+REACTOME_DOPAMINE_NEUROTRANSMITTER_RELEASE_CYCLE > Genes involved in Dopamine Neurotransmitter Release Cycle CPLX1 DDC RAB3A RIMS1 SLC18A2 SNAP25 STX1A STXBP1 SYN1 SYN2 SYN3 SYT1 TH VAMP2
+REACTOME_DOUBLE_STRAND_BREAK_REPAIR > Genes involved in Double-Strand Break Repair ATM BRCA1 BRCA2 H2AFX LIG1 LIG4 MDC1 MRE11A NBN PRKDC RAD50 RAD51 RAD52 RPA1 RPA2 RPA3 TDP1 TP53BP1 XRCC4 XRCC5 XRCC6
+REACTOME_DOWN_STREAM_SIGNAL_TRANSDUCTION > Genes involved in Down-stream signal transduction BCAR1 CRK CRKL GRB2 GRB7 HRAS KRAS MAP2K1 MAP2K2 MAPK1 MAPK3 NCK1 NCK2 NRAS PDGFA PDGFB PDGFRA PDGFRB PIK3CA PIK3CB PIK3R1 PIK3R2 PLCG1 PTPN11 RAF1 RAPGEF1 RASA1 SOS1 SRC STAT1 STAT3 STAT5A STAT5B STAT6 YWHAB
+REACTOME_DOWNSTREAM_EVENTS_IN_GPCR_SIGNALING > Genes involved in Downstream events in GPCR signaling ABR ADCY1 ADCY10 ADCY2 ADCY3 ADCY4 ADCY5 ADCY6 ADCY7 ADCY8 ADCY9 ADCYAP1 ADCYAP1R1 ADM ADM2 ADORA1 ADORA2A ADORA2B ADORA3 ADRA1A ADRA1B ADRA1D ADRA2A ADRA2B ADRA2C ADRB1 ADRB2 ADRB3 ADRBK1 AGT AGTR1 AGTR2 AKAP13 AKT1 AKT2 AKT3 ANXA1 APLN APLNR ARHGAP4 ARHGEF1 ARHGEF11 ARHGEF12 ARHGEF16 ARHGEF17 ARHGEF18 ARHGEF2 ARHGEF3 ARHGEF4 ARHGEF6 ARHGEF7 ARHGEF9 AVP AVPR1A AVPR1B AVPR2 BDKRB1 BDKRB2 [...]
+REACTOME_DOWNSTREAM_SIGNALING_OF_ACTIVATED_FGFR > Genes involved in Downstream signaling of activated FGFR DOK1 FGF1 FGF10 FGF16 FGF17 FGF18 FGF19 FGF2 FGF20 FGF22 FGF23 FGF3 FGF4 FGF5 FGF6 FGF7 FGF8 FGF9 FGFR1 FGFR2 FGFR3 FGFR4 FRS2 FRS3 GAB1 GRB2 INS INSR IRS1 IRS2 KL PIK3C3 PIK3CA PIK3CB PIK3R1 PIK3R2 PIK3R4 PLCG1 PTPN11 SHC1 SOS1 SRC TLR9
+REACTOME_DOWNSTREAM_TCR_SIGNALING > Genes involved in Downstream TCR signaling BCL10 CARD11 CD247 CD3D CD3E CD3G CD4 CHUK HLA-DMA HLA-DMB HLA-DOA HLA-DOB HLA-DPA1 HLA-DPB1 HLA-DQA1 HLA-DQA2 HLA-DQB1 HLA-DRA HLA-DRB1 HLA-DRB3 HLA-DRB5 IKBKB IKBKG INPP5D LCK MALT1 MAP3K7 NFKB1 NFKBIA PDPK1 PIK3CA PIK3CB PIK3R1 PIK3R2 PRKCQ PTEN RELA RIPK2 TAB2 TRA@ TRAF6 TRAT1 TRB@ TRBC1 TRBV12-3 UBE2N UBE2V1
+REACTOME_DUAL_INCISION_REACTION_IN_GG_NER > Genes involved in Dual incision reaction in GG-NER CCNH CDK7 DDB1 DDB2 ERCC1 ERCC2 ERCC3 ERCC4 ERCC5 GTF2H1 GTF2H2 GTF2H3 GTF2H4 MNAT1 RAD23B RPA1 RPA2 RPA3 XPA XPC
+REACTOME_DUAL_INCISION_REACTION_IN_TC_NER > Genes involved in Dual incision reaction in TC-NER CCNH CDK7 ERCC1 ERCC2 ERCC3 ERCC4 ERCC5 ERCC6 ERCC8 GTF2H1 GTF2H2 GTF2H3 GTF2H4 MNAT1 POLR2A POLR2B POLR2C POLR2D POLR2E POLR2F POLR2G POLR2H POLR2I POLR2J POLR2K POLR2L TCEA1 XAB2
+REACTOME_E2F_ENABLED_INHIBITION_OF_PRE_REPLICATION_COMPLEX_FORMATION > Genes involved in E2F-enabled inhibition of pre-replication complex formation CCNB1 CDC25A CDK1 MCM8 ORC1L ORC2L ORC3L ORC4L ORC5L ORC6L
+REACTOME_E2F_MEDIATED_REGULATION_OF_DNA_REPLICATION > Genes involved in E2F mediated regulation of DNA replication CCNA1 CCNB1 CCNE1 CDC25A CDC45 CDC6 CDK1 CDT1 DHFR E2F1 E2F2 E2F3 FBXO5 MCM8 NANOG ORC1L ORC2L ORC3L ORC4L ORC5L ORC6L PCNA POLA1 POLA2 POU5F1 PRIM1 PRIM2 RB1 RRM2 SOX2 TFDP1 TK2 TYMS
+REACTOME_E2F_TRANSCRIPTIONAL_TARGETS_AT_G1_S > Genes involved in E2F transcriptional targets at G1/S CCNA1 CCNE1 CDC25A CDC45 CDC6 CDK1 CDT1 DHFR E2F1 E2F2 E2F3 FBXO5 NANOG ORC1L PCNA POLA1 POU5F1 RRM2 SOX2 TFDP1 TK2 TYMS
+REACTOME_EARLY_PHASE_OF_HIV_LIFE_CYCLE > Genes involved in Early Phase of HIV Life Cycle BANF1 CCR5 CD4 CXCR4 FEN1 HMGA1 LIG1 LIG4 PPIA PSIP1 XRCC4 XRCC5 XRCC6
+REACTOME_EFFECTS_OF_PIP2_HYDROLYSIS > Genes involved in Effects of PIP2 hydrolysis DAGLA DAGLB DGKA DGKB DGKD DGKE DGKG DGKH DGKI DGKK DGKQ DGKZ ITPR1 ITPR2 ITPR3 MGLL
+REACTOME_EGFR_DOWNREGULATION > Genes involved in EGFR downregulation AP2A1 AP2A2 AP2B1 AP2M1 AP2S1 ARHGEF7 CBL CDC42 CLTA CLTC EGF EGFR EPN1 EPS15 EPS15L1 GRB2 HGS SH3GL2 SH3KBP1 SPRY1 SPRY2 STAM STAM2 UBB
+REACTOME_EICOSANOID_LIGAND_BINDING_RECEPTORS > Genes involved in Eicosanoid ligand-binding receptors CYSLTR1 CYSLTR2 GPR17 GPR44 LTB4R LTB4R2 OXER1 PTGDR PTGER1 PTGER2 PTGER3 PTGER4 PTGFR PTGIR TBXA2R
+REACTOME_ELECTRON_TRANSPORT_CHAIN > Genes involved in Electron Transport Chain COX1 COX2 COX3 COX4I1 COX5A COX5B COX6A1 COX6B1 COX6C COX7A2L COX7B COX7C COX8A CYC1 CYCS ETFA ETFB ETFDH ND1 ND2 ND3 ND4 ND4L ND5 ND6 NDUFA1 NDUFA10 NDUFA11 NDUFA12 NDUFA13 NDUFA2 NDUFA3 NDUFA4 NDUFA5 NDUFA6 NDUFA7 NDUFA8 NDUFA9 NDUFAB1 NDUFB1 NDUFB10 NDUFB11 NDUFB2 NDUFB3 NDUFB4 NDUFB5 NDUFB6 NDUFB7 NDUFB8 NDUFB9 NDUFC1 NDUFC2 NDUFS1 NDUFS2 NDUFS3 NDUFS4 NDUFS5 NDUFS6 NDUFS7 NDUFS8 NDUFV1 NDUFV2 NDUFV3 SDHA [...]
+REACTOME_ELONGATION_AND_PROCESSING_OF_CAPPED_TRANSCRIPTS > Genes involved in Elongation and Processing of Capped Transcripts CCAR1 CCNH CCNT1 CCNT2 CD2BP2 CDC40 CDK7 CDK9 CLP1 COBRA1 CPSF1 CPSF2 CPSF3 CPSF7 CSTF1 CSTF2 CSTF3 CTDP1 DDX23 DHX38 DHX9 DNAJC8 EFTUD2 ELL ERCC2 ERCC3 FUS GTF2F1 GTF2F2 GTF2H1 GTF2H2 GTF2H3 GTF2H4 HNRNPA0 HNRNPA1 HNRNPA2B1 HNRNPA3 HNRNPC HNRNPD HNRNPF HNRNPH1 HNRNPH2 HNRNPK HNRNPL HNRNPM HNRNPR HNRNPU HNRNPUL1 LSM2 MAGOH METTL3 MNAT1 NCBP1 NCBP2 NFX1 NHP2L1 NUDT2 [...]
+REACTOME_ENDOGENOUS_STEROLS > Genes involved in Endogenous sterols CYP11A1 CYP11B1 CYP11B2 CYP17A1 CYP19A1 CYP1B1 CYP21A2 CYP27A1 CYP39A1 CYP46A1 CYP51A1 CYP7A1 CYP7B1 CYP8B1
+REACTOME_ENERGY_DEPENDENT_REGULATION_OF_MTOR_BY_LKB1_AMPK > Genes involved in Energy dependent regulation of mTOR by LKB1-AMPK CAB39 CAB39L PPM1A PRKAA1 PRKAA2 PRKAB1 PRKAB2 PRKAG1 PRKAG2 PRKAG3 RHEB RPTOR STK11 STRADA STRADB TSC1 TSC2
+REACTOME_ERK_MAPK_TARGETS > Genes involved in ERK/MAPK targets DUSP3 DUSP4 DUSP6 DUSP7 ELK1 MAPK1 MAPK11 MAPK14 MAPK3 MAPK7 MEF2A MEF2C PPP2CA PPP2CB PPP2R1A PPP2R1B PPP2R5D RPS6KA1 RPS6KA2 RPS6KA3 RPS6KA5
+REACTOME_ERKS_ARE_INACTIVATED > Genes involved in ERKs are inactivated DUSP3 DUSP4 DUSP6 DUSP7 MAPK1 MAPK3 MAPK7 PPP2CA PPP2CB PPP2R1A PPP2R1B PPP2R5D
+REACTOME_ETHANOL_OXIDATION > Genes involved in Ethanol oxidation ACSS1 ACSS2 ADH1A ADH1B ADH1C ADH4 ADH6 ADH7 ALDH1A1 ALDH2
+REACTOME_EXTENSION_OF_TELOMERES > Genes involved in Extension of Telomeres DKC1 DNA2 FEN1 LIG1 NHP2 PCNA POLA1 POLA2 POLD1 POLD2 POLD3 POLD4 POLE POLE2 PRIM1 PRIM2 RFC1 RFC2 RFC3 RFC4 RFC5 RPA1 RPA2 RPA3 RUVBL1 RUVBL2 TERT WRAP53
+REACTOME_FACILITATIVE_NA_INDEPENDENT_GLUCOSE_TRANSPORTERS > Genes involved in Facilitative Na+-independent glucose transporters SLC2A1 SLC2A10 SLC2A11 SLC2A12 SLC2A2 SLC2A3 SLC2A4 SLC2A5 SLC2A6 SLC2A7 SLC2A8 SLC2A9
+REACTOME_FANCONI_ANEMIA_PATHWAY > Genes involved in Fanconi Anemia pathway BRCA1 BRCA2 C17ORF70 C19ORF40 FANCA FANCB FANCC FANCD2 FANCE FANCF FANCG FANCI FANCL FANCM PALB2 UBB UBE2T
+REACTOME_FGFR_LIGAND_BINDING_AND_ACTIVATION > Genes involved in FGFR ligand binding and activation CBL FGF1 FGF10 FGF16 FGF17 FGF18 FGF19 FGF2 FGF20 FGF22 FGF23 FGF3 FGF4 FGF5 FGF6 FGF7 FGF8 FGF9 FGFR1 FGFR2 FGFR3 FGFR4 FRS2 FRS3 GRB2 KL SDC2
+REACTOME_FORMATION_AND_MATURATION_OF_MRNA_TRANSCRIPT > Genes involved in Formation and Maturation of mRNA Transcript CCAR1 CCNH CCNT1 CCNT2 CD2BP2 CDC40 CDK7 CDK9 CLP1 COBRA1 CPSF1 CPSF2 CPSF3 CPSF7 CSTF1 CSTF2 CSTF3 CTDP1 DDX23 DHX38 DHX9 DNAJC8 EFTUD2 ELL ERCC2 ERCC3 FUS GTF2A1 GTF2A2 GTF2B GTF2E1 GTF2E2 GTF2F1 GTF2F2 GTF2H1 GTF2H2 GTF2H3 GTF2H4 HNRNPA0 HNRNPA1 HNRNPA2B1 HNRNPA3 HNRNPC HNRNPD HNRNPF HNRNPH1 HNRNPH2 HNRNPK HNRNPL HNRNPM HNRNPR HNRNPU HNRNPUL1 LSM2 MAGOH METTL3 MNAT1 NCB [...]
+REACTOME_FORMATION_OF_A_POOL_OF_FREE_40S_SUBUNITS > Genes involved in Formation of a pool of free 40S subunits EIF1AX EIF3A EIF3B EIF3C EIF3CL EIF3D EIF3E EIF3F EIF3G EIF3H EIF3I EIF3J EIF3K FAU RPL10 RPL10A RPL11 RPL12 RPL13 RPL13A RPL14 RPL15 RPL17 RPL18 RPL18A RPL19 RPL21 RPL22 RPL23 RPL23A RPL24 RPL26 RPL26L1 RPL27 RPL27A RPL28 RPL29 RPL3 RPL30 RPL31 RPL32 RPL34 RPL35 RPL35A RPL36 RPL36A RPL37 RPL37A RPL38 RPL39 RPL3L RPL4 RPL41 RPL5 RPL6 RPL7 RPL7A RPL8 RPL9 RPLP0 RPLP1 RPLP2 RPS10 [...]
+REACTOME_FORMATION_OF_ATP_BY_CHEMIOSMOTIC_COUPLING > Genes involved in Formation of ATP by chemiosmotic coupling ATP5A1 ATP5B ATP5C1 ATP5D ATP5E ATP5F1 ATP5G1 ATP5H ATP5I ATP5J ATP5J2 ATP5L ATP5O ATP6 ATP8
+REACTOME_FORMATION_OF_FIBRIN_CLOT_CLOTTING_CASCADE > Genes involved in Formation of Fibrin Clot (Clotting Cascade) A2M C1QBP F10 F11 F12 F13A1 F13B F2 F3 F5 F7 F8 F9 FGA FGB FGG GP1BA GP1BB GP5 GP9 KLKB1 KNG1 PF4 PF4V1 PRCP PROC PROS1 SERPINC1 SERPING1 TFPI THBD VWF
+REACTOME_FORMATION_OF_PLATELET_PLUG > Genes involved in Formation of Platelet plug A2M ACTN1 ACTN2 ACTN4 ADRA2A ADRA2B ADRA2C AKT1 AKT2 AKT3 ALB ALDOA APBB1IP APOA1 APP BCAR1 BRPF3 CALM1 CALM2 CALM3 CALU CAP1 CD36 CD63 CD9 CFD CFL1 CLU COL1A1 COL1A2 CRK CSK DAGLA DAGLB DGKA DGKB DGKD DGKE DGKG DGKH DGKI DGKK DGKQ DGKZ EGF F13A1 F2 F2R F2RL2 F2RL3 F5 F8 FCER1G FGA FGB FGG FIGF FLNA FN1 FYN GAS6 GNA11 GNA12 GNA13 GNA14 GNA15 GNAI1 GNAI2 GNAI3 GNAQ GNB1 GNB2 GNB3 GNB4 GNB5 GNG10 GNG11 GNG12 [...]
+REACTOME_FORMATION_OF_THE_EARLY_ELONGATION_COMPLEX > Genes involved in Formation of the Early Elongation Complex CCNH CDK7 COBRA1 CTDP1 ERCC2 ERCC3 GTF2F1 GTF2F2 GTF2H1 GTF2H2 GTF2H3 GTF2H4 MNAT1 NCBP1 NCBP2 POLR2A POLR2B POLR2C POLR2D POLR2E POLR2F POLR2G POLR2H POLR2I POLR2J POLR2K POLR2L RDBP SUPT4H1 SUPT5H TH1L WHSC2
+REACTOME_FORMATION_OF_THE_TERNARY_COMPLEX_AND_SUBSEQUENTLY_THE_43S_COMPLEX > Genes involved in Formation of the ternary complex, and subsequently, the 43S complex EIF1AX EIF2S1 EIF2S2 EIF2S3 EIF3A EIF3B EIF3C EIF3CL EIF3D EIF3E EIF3F EIF3G EIF3H EIF3I EIF3J EIF3K FAU RPS10 RPS11 RPS12 RPS13 RPS14 RPS15 RPS15A RPS16 RPS17 RPS18 RPS19 RPS2 RPS20 RPS21 RPS23 RPS24 RPS25 RPS26 RPS27 RPS27A RPS28 RPS29 RPS3 RPS3A RPS4X RPS4Y1 RPS5 RPS6 RPS7 RPS8 RPS9 RPSA
+REACTOME_FORMATION_OF_TUBULIN_FOLDING_INTERMEDIATES_BY_CCT_TRIC > Genes involved in Formation of tubulin folding intermediates by CCT/TriC CCT2 CCT3 CCT4 CCT5 CCT6A CCT7 CCT8 TCP1 TUBA1A TUBA1B TUBA1C TUBA3C TUBA3D TUBA4A TUBB1 TUBB2A TUBB2B TUBB2C TUBB3 TUBB4 TUBB4Q TUBB6
+REACTOME_FRS2_MEDIATED_ACTIVATION > Genes involved in Frs2-mediated activation BRAF CRK FRS2 HRAS KRAS MAP2K1 MAP2K2 MAPK1 MAPK3 NGF NRAS NTRK1 RAF1 RAP1A RAPGEF1 YWHAB
+REACTOME_FRS2MEDIATED_CASCADE > Genes involved in FRS2-mediated cascade FGF1 FGF10 FGF16 FGF17 FGF18 FGF19 FGF2 FGF20 FGF22 FGF23 FGF3 FGF4 FGF5 FGF6 FGF7 FGF8 FGF9 FGFR1 FGFR2 FGFR3 FGFR4 FRS2 FRS3 GAB1 GRB2 KL PTPN11
+REACTOME_FURTHER_PLATELET_RELEASATE > Genes involved in Further platelet releasate APOA1 BRPF3 CALM1 CALM2 CALM3 CALU CAP1 CFL1 FLNA HABP4 HSPA5 PFN1 PLEK POTEKP PPIA PSAP SCG3 SOD1 TF TLN1 TTN TUBA4A VCL WDR1
+REACTOME_G1_PHASE > Genes involved in G1 Phase CCND1 CCND2 CCND3 CCNH CDK4 CDK6 CDK7 CDKN1A E2F1 E2F2 E2F3 E2F4 E2F5 MNAT1 RB1 TFDP1
+REACTOME_G1_S_TRANSITION > Genes involved in G1/S Transition CCNA1 CCNA2 CCNB1 CCNE1 CCNE2 CCNH CDC25A CDC45 CDC6 CDC7 CDK1 CDK2 CDK7 CDKN1A CDT1 CKS1B CUL1 DBF4 DHFR E2F1 E2F2 E2F3 FBXO5 MCM10 MCM2 MCM3 MCM4 MCM5 MCM6 MCM7 MCM8 MNAT1 NANOG ORC1L ORC2L ORC3L ORC4L ORC5L ORC6L PCNA POLA1 POLA2 POLE POLE2 POU5F1 PRIM1 PRIM2 PSMA1 PSMA2 PSMA3 PSMA4 PSMA5 PSMA6 PSMA7 PSMB1 PSMB10 PSMB2 PSMB3 PSMB4 PSMB5 PSMB6 PSMB7 PSMB8 PSMB9 PSMC1 PSMC2 PSMC3 PSMC4 PSMC5 PSMC6 PSMD1 PSMD10 PSMD11 PSMD12 PS [...]
+REACTOME_G2_M_CHECKPOINTS > Genes involved in G2/M Checkpoints ATM ATR ATRIP CCNB1 CCNB2 CDC25A CDC25C CDC45 CDC6 CDC7 CDK1 CDK2 CHEK1 CHEK2 CLSPN DBF4 HUS1 MCM10 MCM2 MCM3 MCM4 MCM5 MCM6 MCM7 MCM8 ORC1L ORC2L ORC3L ORC4L ORC5L ORC6L RAD1 RAD17 RAD9A RAD9B RFC2 RFC3 RFC4 RFC5 RPA1 RPA2 RPA3 WEE1
+REACTOME_G2_M_TRANSITION > Genes involved in G2/M Transition ACTR1A AKAP9 ALMS1 AZI1 CCNA1 CCNA2 CCNB1 CCNB2 CCNH CDC25A CDC25B CDC25C CDK1 CDK11A CDK11B CDK5RAP2 CDK7 CENPJ CEP110 CEP135 CEP152 CEP164 CEP192 CEP250 CEP290 CEP57 CEP63 CEP70 CEP72 CEP76 CEP78 CETN2 CKAP5 CLASP1 CP110 CSNK1D CSNK1E DCTN1 DCTN2 DCTN3 DYNC1H1 DYNC1I2 DYNLL1 FGFR1OP HAUS2 HSP90AA1 MAPRE1 MNAT1 NDE1 NEDD1 NEK2 NINL NUMA1 ODF2 OFD1 PAFAH1B1 PCM1 PCNT PKMYT1 PLK1 PLK4 PPP2R1A PRKACA PRKAR2B SDCCAG8 SFI1 SSNA1 TS [...]
+REACTOME_G_ALPHA_12_13_SIGNALLING_EVENTS > Genes involved in G alpha (12/13) signalling events ABR AKAP13 ARHGAP4 ARHGEF1 ARHGEF11 ARHGEF12 ARHGEF16 ARHGEF17 ARHGEF18 ARHGEF2 ARHGEF3 ARHGEF4 ARHGEF6 ARHGEF7 ARHGEF9 CDC42 ECT2 FGD1 FGD2 FGD3 FGD4 GNA12 GNA13 ITSN1 KALRN MCF2 MCF2L NET1 NGEF OBSCN PIK3CA PIK3R1 PLEKHG2 PLEKHG5 PLXNB1 PREX1 RAC1 RAC2 RASGRF1 RASGRF2 RHOA RHOB RHOC RHOG ROCK1 ROCK2 SOS1 SOS2 TIAM1 TIAM2 TRIO VAV1 VAV2 VAV3
+REACTOME_G_ALPHA_I_SIGNALLING_EVENTS > Genes involved in G alpha (i) signalling events ADCY1 ADCY10 ADCY2 ADCY3 ADCY4 ADCY5 ADCY6 ADCY7 ADCY8 ADCY9 ADORA1 ADORA3 ADRA2A ADRA2B ADRA2C AGT AGTR2 ANXA1 APLN APLNR BDKRB1 BDKRB2 C3 C3AR1 C5 C5AR1 CASR CCL16 CCL19 CCL20 CCL21 CCL23 CCL25 CCL27 CCL28 CCL5 CCR1 CCR10 CCR2 CCR3 CCR4 CCR5 CCR6 CCR7 CCR8 CCR9 CHRM2 CHRM4 CNR1 CNR2 CXCL1 CXCL10 CXCL11 CXCL12 CXCL13 CXCL16 CXCL2 CXCL3 CXCL5 CXCL6 CXCL9 CXCR1 CXCR2 CXCR3 CXCR4 CXCR5 CXCR6 CXCR7 DRD2 D [...]
+REACTOME_G_ALPHA_Q_SIGNALLING_EVENTS > Genes involved in G alpha (q) signalling events ADRA1A ADRA1B ADRA1D ADRBK1 AGT AGTR1 ANXA1 AVP AVPR1A AVPR1B BDKRB1 BDKRB2 CASR CCK CCKAR CCKBR CCL23 CGA CGB CHRM1 CHRM3 CHRM5 CYSLTR1 CYSLTR2 DAGLA DAGLB DGKA DGKB DGKD DGKE DGKG DGKH DGKI DGKK DGKQ DGKZ EDN1 EDN2 EDN3 EDNRA EDNRB F2 F2R F2RL1 F2RL2 F2RL3 FFAR1 FFAR2 FFAR3 FPR2 GCG GCGR GEFT GNA11 GNA14 GNA15 GNAQ GNB1 GNB2 GNB3 GNB4 GNB5 GNG10 GNG11 GNG12 GNG13 GNG2 GNG3 GNG4 GNG5 GNG7 GNG8 GNGT1 G [...]
+REACTOME_G_ALPHA_S_SIGNALLING_EVENTS > Genes involved in G alpha (s) signalling events ADCY1 ADCY10 ADCY2 ADCY3 ADCY4 ADCY5 ADCY6 ADCY7 ADCY8 ADCY9 ADCYAP1 ADCYAP1R1 ADM ADM2 ADORA2A ADORA2B ADRB1 ADRB2 ADRB3 AVP AVPR2 CALCA CALCB CALCR CALCRL CGA CRH CRHR1 CRHR2 DRD1 DRD5 FSHB FSHR GCG GCGR GHRH GHRHR GIP GIPR GLP1R GLP2R GNAI1 GNAI2 GNAI3 GNAS GNAZ GNB1 GNB2 GNB3 GNB4 GNB5 GNG10 GNG11 GNG12 GNG13 GNG2 GNG3 GNG4 GNG5 GNG7 GNG8 GNGT1 GNGT2 GPBAR1 HRH2 HTR4 HTR6 HTR7 IAPP INSL3 LHB LHCGR [...]
+REACTOME_G_ALPHA_Z_SIGNALLING_EVENTS > Genes involved in G alpha (z) signalling events ADCY1 ADCY10 ADCY2 ADCY3 ADCY4 ADCY5 ADCY6 ADCY7 ADCY8 ADCY9 GNAI1 GNAI2 GNAI3 GNAZ
+REACTOME_G_BETA_GAMMA_SIGNALLING_THROUGH_PI3KGAMMA > Genes involved in G beta:gamma signalling through PI3Kgamma AKT1 AKT2 AKT3 GNB1 GNB2 GNB3 GNB4 GNB5 GNG10 GNG11 GNG12 GNG13 GNG2 GNG3 GNG4 GNG5 GNG7 GNG8 GNGT1 GNGT2 PDPK1 PIK3CG PIK3R5 PIK3R6 RHOA
+REACTOME_G_BETA_GAMMA_SIGNALLING_THROUGH_PLC_BETA > Genes involved in G beta:gamma signalling through PLC beta GNB1 GNB2 GNB3 GNB4 GNB5 GNG10 GNG11 GNG12 GNG13 GNG2 GNG3 GNG4 GNG5 GNG7 GNG8 GNGT1 GNGT2 PLCB1 PLCB2 PLCB3
+REACTOME_G_PROTEIN_ACTIVATION > Genes involved in G-protein activation GNAI1 GNAI2 GNAI3 GNAO1 GNAT1 GNAT2 GNAT3 GNAZ GNB1 GNB2 GNB3 GNB4 GNB5 GNG10 GNG11 GNG12 GNG13 GNG2 GNG3 GNG4 GNG5 GNG7 GNG8 GNGT1 GNGT2 OPRM1 PDYN POMC
+REACTOME_G_PROTEIN_BETA_GAMMA_SIGNALLING > Genes involved in G-protein beta:gamma signalling AKT1 AKT2 AKT3 GNB1 GNB2 GNB3 GNB4 GNB5 GNG10 GNG11 GNG12 GNG13 GNG2 GNG3 GNG4 GNG5 GNG7 GNG8 GNGT1 GNGT2 PDPK1 PIK3CG PIK3R5 PIK3R6 PLCB1 PLCB2 PLCB3 RHOA
+REACTOME_GAB1_SIGNALOSOME > Genes involved in Gab1 signalosome CSK EGF EGFR GAB1 GRB2 PAG1 PIK3CA PIK3R1 PTPN11 PXN SRC
+REACTOME_GAMMA_CARBOXYLATION_TRANSPORT_AND_AMINO_TERMINAL_CLEAVAGE_OF_PROTEINS > Genes involved in Gamma-carboxylation, transport, and amino-terminal cleavage of proteins F10 F2 F7 F9 FURIN GAS6 GGCX PROC PROS1 PROZ
+REACTOME_GAP_JUNCTION_ASSEMBLY > Genes involved in Gap junction assembly GJA1 GJA10 GJA3 GJA4 GJA5 GJA8 GJA9 GJB1 GJB2 GJB3 GJB4 GJB5 GJB6 GJB7 GJC1 GJC2 GJD2 GJD3 GJD4
+REACTOME_GAP_JUNCTION_DEGRADATION > Genes involved in Gap junction degradation AP2M1 CLTA CLTB CLTC CLTCL1 DAB2 DNM1 DNM2 GJA1 MYO6
+REACTOME_GAP_JUNCTION_TRAFFICKING > Genes involved in Gap junction trafficking AP2M1 CLTA CLTB CLTC CLTCL1 DAB2 DNM1 DNM2 GJA1 GJA10 GJA3 GJA4 GJA5 GJA8 GJA9 GJB1 GJB2 GJB3 GJB4 GJB5 GJB6 GJB7 GJC1 GJC2 GJD2 GJD3 GJD4 MYO6
+REACTOME_GENE_EXPRESSION > Genes involved in Gene Expression AAAS AARS AARS2 AIMP1 AIMP2 AR CARS CARS2 CCAR1 CCNC CCNH CCNT1 CCNT2 CD2BP2 CDC40 CDK7 CDK8 CDK9 CLP1 COBRA1 CPSF1 CPSF2 CPSF3 CPSF7 CREBBP CSTF1 CSTF2 CSTF3 CTDP1 DARS DARS2 DDX23 DHX38 DHX9 DNAJC8 EARS2 EEF1A1 EEF1B2 EEF1D EEF1E1 EEF1G EEF2 EFTUD2 EIF1AX EIF2B1 EIF2B2 EIF2B3 EIF2B4 EIF2B5 EIF2S1 EIF2S2 EIF2S3 EIF3A EIF3B EIF3C EIF3CL EIF3D EIF3E EIF3F EIF3G EIF3H EIF3I EIF3J EIF3K EIF4A1 EIF4A2 EIF4B EIF4E EIF4EBP1 EIF4G1 EI [...]
+REACTOME_GENERATION_OF_SECOND_MESSENGER_MOLECULES > Genes involved in Generation of second messenger molecules CD247 CD3D CD3E CD3G CD4 ENAH EVL FYB GRAP2 HLA-DMA HLA-DMB HLA-DOA HLA-DOB HLA-DPA1 HLA-DPB1 HLA-DQA1 HLA-DQA2 HLA-DQB1 HLA-DRA HLA-DRB1 HLA-DRB3 HLA-DRB5 ITK LAT LCK LCP2 NCK1 PAK1 PAK2 PLCG1 TRA@ TRB@ TRBC1 TRBV12-3 VASP WAS ZAP70
+REACTOME_GENERIC_TRANSCRIPTION_PATHWAY > Genes involved in Generic Transcription Pathway CCNC CDK8 CREBBP KAT2A KAT2B MAML1 MAML2 MAML3 MAMLD1 MED1 MED10 MED12 MED13 MED14 MED15 MED16 MED17 MED20 MED23 MED24 MED25 MED26 MED27 MED30 MED31 MED4 MED6 MED7 MED8 NOTCH1 NOTCH2 NOTCH3 NOTCH4 RBPJ SNW1
+REACTOME_GENES_INVOLVED_IN_APOPTOTIC_CLEAVAGE_OF_CELLULAR_PROTEINS > Genes involved in Apoptotic cleavage of cellular proteins ACIN1 ADD1 APC BCAP31 BIRC2 BMX CASP3 CASP6 CASP7 CASP8 CDH1 CLSPN CTNNB1 DBNL DSG1 DSG2 DSG3 DSP FNTA GAS2 GSN LMNA LMNB1 MAPT MST4 OCLN PKP1 PLEC PRKCD PRKCQ PTK2 ROCK1 SPTAN1 STK24 TJP1 TJP2 VIM
+REACTOME_GLOBAL_GENOMIC_NER > Genes involved in Global Genomic NER (GG-NER) CCNH CDK7 DDB1 DDB2 ERCC1 ERCC2 ERCC3 ERCC4 ERCC5 GTF2H1 GTF2H2 GTF2H3 GTF2H4 LIG1 MNAT1 PCNA POLD1 POLD2 POLD3 POLD4 POLE POLE2 RAD23B RFC1 RFC2 RFC3 RFC4 RFC5 RPA1 RPA2 RPA3 XPA XPC
+REACTOME_GLUCAGON_SIGNALING_IN_METABOLIC_REGULATION > Genes involved in Glucagon signaling in metabolic regulation ADCY1 ADCY10 ADCY2 ADCY3 ADCY4 ADCY5 ADCY6 ADCY7 ADCY8 ADCY9 GCG GCGR GNAS GNB1 GNB2 GNB3 GNB4 GNG10 GNG11 GNG12 GNG13 GNG2 GNG3 GNG4 GNG5 GNG7 GNG8 PRKACA PRKACB PRKACG PRKAR1A PRKAR1B PRKAR2A PRKAR2B
+REACTOME_GLUCAGON_TYPE_LIGAND_RECEPTORS > Genes involved in Glucagon-type ligand receptors ADCYAP1 ADCYAP1R1 GCG GCGR GHRH GHRHR GIP GIPR GLP1R GLP2R GNAS GNB1 GNB2 GNB3 GNB4 GNB5 GNG10 GNG11 GNG12 GNG13 GNG2 GNG3 GNG4 GNG5 GNG7 GNG8 GNGT1 GNGT2 SCT SCTR VIP VIPR1 VIPR2
+REACTOME_GLUCONEOGENESIS > Genes involved in Gluconeogenesis ALDOA ALDOB ALDOC ENO1 ENO2 ENO3 FBP1 FBP2 GAPDH GAPDHS GOT1 GOT2 GPI MDH1 MDH2 PC PCK1 PCK2 PFKFB1 PFKFB2 PFKFB3 PFKFB4 PGAM1 PGAM2 PGK1 SLC25A1 SLC25A10 SLC25A11 SLC25A12 SLC25A13 TPI1
+REACTOME_GLUCOSE_AND_OTHER_SUGAR_SLC_TRANSPORTERS > Genes involved in Glucose and other sugar SLC transporters RHAG RHBG RHCG SLC10A6 SLC11A1 SLC11A2 SLC13A1 SLC13A2 SLC13A3 SLC13A4 SLC13A5 SLC14A1 SLC14A2 SLC16A1 SLC16A3 SLC16A7 SLC16A8 SLC18A1 SLC18A2 SLC22A2 SLC2A1 SLC2A10 SLC2A11 SLC2A12 SLC2A13 SLC2A2 SLC2A3 SLC2A4 SLC2A5 SLC2A6 SLC2A7 SLC2A8 SLC2A9 SLC30A1 SLC30A2 SLC30A3 SLC30A5 SLC30A6 SLC30A7 SLC30A8 SLC31A1 SLC39A1 SLC39A10 SLC39A14 SLC39A2 SLC39A3 SLC39A4 SLC39A5 SLC39A6 SLC39 [...]
+REACTOME_GLUCOSE_METABOLISM > Genes involved in Glucose metabolism AGL ALDOA ALDOB ALDOC CALM1 CALM2 CALM3 ENO1 ENO2 ENO3 FBP1 FBP2 GAPDH GAPDHS GBE1 GOT1 GOT2 GPI GYG1 GYG2 GYS1 GYS2 MDH1 MDH2 PC PCK1 PCK2 PFKFB1 PFKFB2 PFKFB3 PFKFB4 PFKL PFKM PFKP PGAM1 PGAM2 PGK1 PGM1 PGM2 PHKA1 PHKA2 PHKB PHKG1 PHKG2 PKLR PKM2 PYGB PYGL PYGM SLC25A1 SLC25A10 SLC25A11 SLC25A12 SLC25A13 TPI1 UGP2
+REACTOME_GLUCOSE_REGULATION_OF_INSULIN_SECRETION > Genes involved in Glucose Regulation of Insulin Secretion ABCC8 ACO2 ALDOA ALDOB ALDOC ATP5A1 ATP5B ATP5C1 ATP5D ATP5E ATP5F1 ATP5G1 ATP5H ATP5I ATP5J ATP5J2 ATP5L ATP5O ATP6 ATP8 CACNA1A CACNA1C CACNA1D CACNA1E CACNA2D2 CACNB2 CACNB3 COX1 COX2 COX3 COX4I1 COX5A COX5B COX6A1 COX6B1 COX6C COX7A2L COX7B COX7C COX8A CS CYC1 CYCS DLAT DLD DLST ENO1 ENO2 ENO3 ETFA ETFB ETFDH FH GAPDH GAPDHS GCK GNAI1 GNAI2 GNAO1 GPI IDH2 IDH3A IDH3B IDH3G INS [...]
+REACTOME_GLUCOSE_TRANSPORT > Genes involved in Glucose transport AAAS G6PC GCK GCKR HK1 HK2 HK3 NUP107 NUP133 NUP153 NUP155 NUP160 NUP188 NUP205 NUP210 NUP214 NUP35 NUP37 NUP43 NUP50 NUP54 NUP62 NUP85 NUP88 NUP93 NUP98 NUPL1 NUPL2 POM121 RAE1 RANBP2 SEH1L SLC2A1 SLC2A2 SLC2A3 SLC2A4 SLC37A4 TPR
+REACTOME_GLUCURONIDATION > Genes involved in Glucuronidation SLC35D1 UGDH UGP2 UGT1A1 UGT1A3 UGT1A4 UGT1A5 UGT1A6 UGT1A7 UGT1A8 UGT1A9 UGT2A1 UGT2B10 UGT2B11 UGT2B15 UGT2B17 UGT2B28 UGT2B4 UGT2B7
+REACTOME_GLUTAMATE_NEUROTRANSMITTER_RELEASE_CYCLE > Genes involved in Glutamate Neurotransmitter Release Cycle CPLX1 FNBP1L GLS RAB3A RIMS1 SLC17A7 SLC1A1 SLC1A6 SLC1A7 SNAP25 STX1A STXBP1 SYT1 UNC13B VAMP2
+REACTOME_GLUTATHIONE_CONJUGATION > Genes involved in Glutathione conjugation GCLC GCLM GSS GSTA1 GSTA2 GSTA3 GSTA4 GSTA5 GSTM1 GSTM4 GSTM5 GSTO1 GSTO2 GSTP1 MGST1 MGST2 MGST3
+REACTOME_GLYCOGEN_BREAKDOWN_GLYCOGENOLYSIS > Genes involved in Glycogen breakdown (glycogenolysis) AGL CALM1 CALM2 CALM3 GYG1 GYG2 PGM1 PGM2 PHKA1 PHKA2 PHKB PHKG1 PHKG2 PYGB PYGL PYGM
+REACTOME_GLYCOLYSIS > Genes involved in Glycolysis ALDOA ALDOB ALDOC ENO1 ENO2 ENO3 GAPDH GAPDHS GPI PFKFB1 PFKFB2 PFKFB3 PFKFB4 PFKL PFKM PFKP PGAM1 PGAM2 PGK1 PKLR PKM2 TPI1
+REACTOME_GOLGI_ASSOCIATED_VESICLE_BIOGENESIS > Genes involved in Golgi Associated Vesicle Biogenesis AP1B1 AP1G1 AP1M1 AP1M2 AP1S1 AP1S2 AP1S3 AP3B1 AP3S1 AP4B1 AP4E1 ARF1 ARRB1 BLOC1S1 BLOC1S3 CLINT1 CLTA CLTC CNO CPD DNAJC6 DNM2 DTNBP1 FTH1 FTL GAK HIP1R HSPA8 IGF2R NAPA NECAP1 OCRL PICALM PIK3C2A PLDN PUM1 RAB5C SH3D19 SH3GL2 SNAPIN SNX2 SNX5 SNX9 SORT1 TBC1D8B TFRC TGOLN2 TPD52 TPD52L1 TXNDC5 VAMP2 VAMP7 VAMP8 YIPF6
+REACTOME_GPCR_LIGAND_BINDING > Genes involved in GPCR ligand binding ADCYAP1 ADCYAP1R1 ADM ADM2 ADORA1 ADORA2A ADORA2B ADORA3 ADRA1A ADRA1B ADRA1D ADRA2A ADRA2B ADRA2C ADRB1 ADRB2 ADRB3 AGT AGTR1 AGTR2 ANXA1 APLN APLNR AVP AVPR1A AVPR1B AVPR2 BDKRB1 BDKRB2 C3 C3AR1 C5 C5AR1 CALCA CALCB CALCR CALCRL CASR CCBP2 CCK CCKAR CCKBR CCL11 CCL16 CCL17 CCL19 CCL2 CCL20 CCL21 CCL22 CCL23 CCL25 CCL27 CCL28 CCL3 CCL3L1 CCL3L3 CCL4 CCL5 CCL7 CCR1 CCR10 CCR2 CCR3 CCR4 CCR5 CCR6 CCR7 CCR8 CCR9 CCRL1 CGA [...]
+REACTOME_GRB2_EVENTS_IN_EGFR_SIGNALING > Genes involved in Grb2 events in EGFR signaling EGF EGFR GRB2 HRAS KRAS MAP2K1 MAP2K2 MAPK1 MAPK3 NRAS RAF1 SOS1 YWHAB
+REACTOME_GRB2_SOS_PROVIDES_LINKAGE_TO_MAPK_SIGNALING_FOR_INTERGRINS_ > Genes involved in Grb2:SOS provides linkage to MAPK signaling for Intergrins APBB1IP FGA FGB FGG FN1 GRB2 ITGA2B ITGB3 PTK2 RAP1A RAP1B SOS1 SRC TLN1 VWF
+REACTOME_GS_ALPHA_MEDIATED_EVENTS_IN_GLUCAGON_SIGNALLING > Genes involved in G(s)-alpha mediated events in glucagon signalling ADCY1 ADCY10 ADCY2 ADCY3 ADCY4 ADCY5 ADCY6 ADCY7 ADCY8 ADCY9 GCG GCGR GNAS GNB1 GNB2 GNB3 GNB4 GNG10 GNG11 GNG12 GNG13 GNG2 GNG3 GNG4 GNG5 GNG7 GNG8
+REACTOME_GTP_HYDROLYSIS_AND_JOINING_OF_THE_60S_RIBOSOMAL_SUBUNIT > Genes involved in GTP hydrolysis and joining of the 60S ribosomal subunit EIF1AX EIF2S1 EIF2S2 EIF2S3 EIF3A EIF3B EIF3C EIF3CL EIF3D EIF3E EIF3F EIF3G EIF3H EIF3I EIF3J EIF3K EIF4A1 EIF4A2 EIF4B EIF4E EIF4G1 EIF4H EIF5 EIF5B FAU RPL10 RPL10A RPL11 RPL12 RPL13 RPL13A RPL14 RPL15 RPL17 RPL18 RPL18A RPL19 RPL21 RPL22 RPL23 RPL23A RPL24 RPL26 RPL26L1 RPL27 RPL27A RPL28 RPL29 RPL3 RPL30 RPL31 RPL32 RPL34 RPL35 RPL35A RPL36 RPL [...]
+REACTOME_HDL_MEDIATED_LIPID_TRANSPORT > Genes involved in HDL-mediated lipid transport A2M ABCA1 ABCG1 ALB AMN APOA1 BMP1 CETP CUBN LCAT SCARB1
+REACTOME_HEMOSTASIS > Genes involved in Hemostasis A2M ACTN1 ACTN2 ACTN4 ADRA2A ADRA2B ADRA2C AKT1 AKT2 AKT3 ALB ALDOA AMICA1 ANGPT1 ANGPT2 ANGPT4 APBB1IP APOA1 APOB APP ATP1B1 ATP1B2 ATP1B3 BCAR1 BRPF3 BSG C1QBP CALM1 CALM2 CALM3 CALU CAP1 CAV1 CD177 CD2 CD244 CD36 CD47 CD48 CD58 CD63 CD84 CD9 CFD CFL1 CLU COL1A1 COL1A2 CRK CSK CXADR DAGLA DAGLB DGKA DGKB DGKD DGKE DGKG DGKH DGKI DGKK DGKQ DGKZ DOK2 EGF ESAM F10 F11 F11R F12 F13A1 F13B F2 F2R F2RL2 F2RL3 F3 F5 F7 F8 F9 FCER1G FGA FGB FG [...]
+REACTOME_HIV1_TRANSCRIPTION_ELONGATION > Genes involved in HIV-1 Transcription Elongation CCNH CCNT1 CDK7 CDK9 COBRA1 CTDP1 ELL ERCC2 ERCC3 GTF2F1 GTF2F2 GTF2H1 GTF2H2 GTF2H3 GTF2H4 MNAT1 NCBP1 NCBP2 POLR2A POLR2B POLR2C POLR2D POLR2E POLR2F POLR2G POLR2H POLR2I POLR2J POLR2K POLR2L RDBP SSRP1 SUPT16H SUPT4H1 SUPT5H TCEA1 TCEB1 TCEB2 TCEB3 TH1L WHSC2
+REACTOME_HIV1_TRANSCRIPTION_INITIATION > Genes involved in HIV-1 Transcription Initiation CCNH CDK7 ERCC2 ERCC3 GTF2A1 GTF2A2 GTF2B GTF2E1 GTF2E2 GTF2F1 GTF2F2 GTF2H1 GTF2H2 GTF2H3 GTF2H4 MNAT1 POLR2A POLR2B POLR2C POLR2D POLR2E POLR2F POLR2G POLR2H POLR2I POLR2J POLR2K POLR2L TAF1 TAF10 TAF11 TAF12 TAF13 TAF4 TAF4B TAF5 TAF6 TAF9 TBP
+REACTOME_HIV_INFECTION > Genes involved in HIV Infection AAAS AP1B1 AP1G1 AP1M1 AP1M2 AP1S1 AP1S2 AP1S3 AP2A1 AP2A2 AP2B1 AP2M1 AP2S1 APOBEC3G ARF1 ATP6V1H B2M BANF1 BTRC CCNH CCNT1 CCR5 CD247 CD28 CD4 CD8B CDK7 CDK9 COBRA1 CTDP1 CUL5 CXCR4 DOCK2 ELL ELMO1 ERCC2 ERCC3 FEN1 FYN GTF2A1 GTF2A2 GTF2B GTF2E1 GTF2E2 GTF2F1 GTF2F2 GTF2H1 GTF2H2 GTF2H3 GTF2H4 HCK HLA-A HMGA1 KPNA1 KPNB1 LCK LIG1 LIG4 MNAT1 NCBP1 NCBP2 NPM1 NUP107 NUP133 NUP153 NUP155 NUP160 NUP188 NUP205 NUP210 NUP214 NUP35 NUP3 [...]
+REACTOME_HIV_LIFE_CYCLE > Genes involved in HIV Life Cycle AAAS BANF1 CCNH CCNT1 CCR5 CD4 CDK7 CDK9 COBRA1 CTDP1 CXCR4 ELL ERCC2 ERCC3 FEN1 GTF2A1 GTF2A2 GTF2B GTF2E1 GTF2E2 GTF2F1 GTF2F2 GTF2H1 GTF2H2 GTF2H3 GTF2H4 HMGA1 LIG1 LIG4 MNAT1 NCBP1 NCBP2 NUP107 NUP133 NUP153 NUP155 NUP160 NUP188 NUP205 NUP210 NUP214 NUP35 NUP37 NUP43 NUP50 NUP54 NUP62 NUP85 NUP88 NUP93 NUP98 NUPL1 NUPL2 POLR2A POLR2B POLR2C POLR2D POLR2E POLR2F POLR2G POLR2H POLR2I POLR2J POLR2K POLR2L POM121 PPIA PSIP1 RAE1 [...]
+REACTOME_HOMOLOGOUS_RECOMBINATION_REPAIR > Genes involved in Homologous Recombination Repair ATM BRCA1 BRCA2 H2AFX LIG1 MDC1 MRE11A NBN RAD50 RAD51 RAD52 RPA1 RPA2 RPA3 TP53BP1
+REACTOME_HORMONE_BIOSYNTHESIS > Genes involved in Hormone biosynthesis AANAT ABCC1 ALOX5 ASMT CGA CGB CUBN CYP11A1 CYP11B1 CYP11B2 CYP17A1 CYP19A1 CYP21A2 CYP24A1 CYP27B1 CYP2R1 DBH DDC DIO1 DIO2 DIO3 DPEP2 FSHB GC GGT5 HSD11B1 HSD17B3 HSD3B1 HSD3B2 IYD LGMN LHB LRP2 LTA4H LTC4S PCSK1 PNMT POMC PTGES3 PTGIS PTGS1 PTGS2 SLC5A5 STAR STARD4 STARD5 STARD6 TBXAS1 TH TPH1 TPO TSHB
+REACTOME_HORMONE_LIGAND_BINDING_RECEPTORS > Genes involved in Hormone ligand-binding receptors CGA CGB FSHB FSHR GNRHR GNRHR2 LHB LHCGR TSHB TSHR
+REACTOME_HORMONE_SENSITIVE_LIPASE_HSL_MEDIATED_TRIACYLGLYCEROL_HYDROLYSIS > Genes involved in Hormone-sensitive lipase (HSL)-mediated triacylglycerol hydrolysis ABHD5 CAV1 FABP4 LIPE MGLL PLIN1 PPP1CA PPP1CB PPP1CC PRKACA PRKACB PRKACG
+REACTOME_HOST_INTERACTIONS_OF_HIV_FACTORS > Genes involved in Host Interactions of HIV factors AAAS AP1B1 AP1G1 AP1M1 AP1M2 AP1S1 AP1S2 AP1S3 AP2A1 AP2A2 AP2B1 AP2M1 AP2S1 APOBEC3G ARF1 ATP6V1H B2M BANF1 BTRC CCNT1 CD247 CD28 CD4 CD8B CDK9 CUL5 DOCK2 ELMO1 FYN HCK HLA-A HMGA1 KPNA1 KPNB1 LCK NPM1 NUP107 NUP133 NUP153 NUP155 NUP160 NUP188 NUP205 NUP210 NUP214 NUP35 NUP37 NUP43 NUP50 NUP54 NUP62 NUP85 NUP88 NUP93 NUP98 NUPL1 NUPL2 PACS1 PAK2 POM121 PPIA PSIP1 PSMA1 PSMA2 PSMA3 PSMA4 PSMA5 [...]
+REACTOME_HUMAN_TAK1_ACTIVATES_NFKB_BY_PHOSPHORYLATION_AND_ACTIVATION_OF_IKKS_COMPLEX > Genes involved in human TAK1 activates NFkB by phosphorylation and activation of IKKs complex CHUK IKBKB IKBKG MAP3K7 NFKB1 NFKB2 NFKBIA NFKBIB RELA TAB1 TAB2 TAB3 TICAM1 TLR3 TRAF6
+REACTOME_IMMUNOREGULATORY_INTERACTIONS_BETWEEN_A_LYMPHOID_AND_A_NON_LYMPHOID_CELL > Genes involved in Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell AMICA1 B2M C3 CD160 CD19 CD200 CD200R1 CD226 CD247 CD34 CD3D CD3E CD3G CD40 CD40LG CD81 CD8A CD8B CD96 CDH1 CRTAM CXADR FCGR2B FCGR3A GLYCAM1 HCST HLA-A HLA-B HLA-C HLA-E HLA-F HLA-G ICAM1 ICAM2 ICAM3 ICAM4 IFITM1 IGHV3-23 IGHV7-81 IGKC IGKV1-5 IGKV4-1 IGLC1 IGLC2 IGLC3 IGLV1-36 IGLV1-40 IGLV1-44 IGLV10-54 IGLV11-55 [...]
+REACTOME_INACTIVATION_OF_APC_VIA_DIRECT_INHIBITION_OF_THE_APCOMPLEX > Genes involved in Inactivation of APC/C via direct inhibition of the APC/C complex ANAPC1 ANAPC10 ANAPC11 ANAPC2 ANAPC4 ANAPC5 ANAPC7 BUB1B BUB3 CDC16 CDC20 CDC23 CDC26 CDC27 MAD2L1 UBE2C UBE2D1 UBE2E1
+REACTOME_INFLUENZA_LIFE_CYCLE > Genes involved in Influenza Life Cycle AAAS CALR CANX CLTA CLTC DNAJC3 FAU GRSF1 GTF2F1 GTF2F2 HSP90AA1 HSPA1A HSPA1B IPO5 KPNA1 KPNB1 NUP107 NUP133 NUP153 NUP155 NUP160 NUP188 NUP205 NUP210 NUP214 NUP35 NUP37 NUP43 NUP50 NUP54 NUP62 NUP85 NUP88 NUP93 NUP98 NUPL1 NUPL2 POLR2A POLR2B POLR2C POLR2D POLR2E POLR2F POLR2G POLR2H POLR2I POLR2J POLR2K POLR2L POM121 RAE1 RAN RANBP2 RPL10 RPL10A RPL11 RPL12 RPL13 RPL13A RPL14 RPL15 RPL17 RPL18 RPL18A RPL19 RPL21 RP [...]
+REACTOME_INFLUENZA_VIRAL_RNA_TRANSCRIPTION_AND_REPLICATION > Genes involved in Influenza Viral RNA Transcription and Replication DNAJC3 FAU GRSF1 GTF2F1 GTF2F2 HSP90AA1 IPO5 POLR2A POLR2B POLR2C POLR2D POLR2E POLR2F POLR2G POLR2H POLR2I POLR2J POLR2K POLR2L RPL10 RPL10A RPL11 RPL12 RPL13 RPL13A RPL14 RPL15 RPL17 RPL18 RPL18A RPL19 RPL21 RPL22 RPL23 RPL23A RPL24 RPL26 RPL26L1 RPL27 RPL27A RPL28 RPL29 RPL3 RPL30 RPL31 RPL32 RPL34 RPL35 RPL35A RPL36 RPL36A RPL37 RPL37A RPL38 RPL39 RPL3L RPL [...]
+REACTOME_INHIBITION_OF_INSULIN_SECRETION_BY_ADRENALINE_NORADRENALINE > Genes involved in Inhibition of Insulin Secretion by Adrenaline/Noradrenaline ADCY5 ADCY6 ADRA2A ADRA2C CACNA1C CACNA1D CACNA2D2 CACNB2 CACNB3 GNAI1 GNAI2 GNAO1 GNB1 GNB2 GNB3 GNB4 GNB5 GNG10 GNG11 GNG12 GNG13 GNG2 GNG3 GNG4 GNG5 GNG7 GNG8 GNGT1 GNGT2 INS
+REACTOME_INITIAL_TRIGGERING_OF_COMPLEMENT > Genes involved in Initial triggering of complement C1QA C1QB C1QC C1R C1S C2 C3 C4A CFB CFD IGHV3-23 IGHV7-81 IGKC IGKV1-5 IGKV4-1 IGLC1 IGLC2 IGLC3 IGLV1-36 IGLV1-40 IGLV1-44 IGLV10-54 IGLV11-55 IGLV2-11 IGLV2-18 IGLV2-23 IGLV2-33 IGLV3-12 IGLV3-16 IGLV3-22 IGLV3-25 IGLV3-27 IGLV4-3 IGLV4-60 IGLV4-69 IGLV5-37 IGLV5-45 IGLV7-43 IGLV7-46 IGLV8-61 MASP1 MASP2 MBL2
+REACTOME_INNATE_IMMUNITY_SIGNALING > Genes involved in Innate Immunity Signaling ATF1 ATF2 C1QA C1QB C1QC C1R C1S C2 C3 C4A C5 C6 C7 C8A C8B C8G C9 CD14 CD180 CFB CFD CHUK CREB1 DUSP3 DUSP4 DUSP6 DUSP7 ECSIT EEA1 ELK1 FOS IGHV3-23 IGHV7-81 IGKC IGKV1-5 IGKV4-1 IGLC1 IGLC2 IGLC3 IGLV1-36 IGLV1-40 IGLV1-44 IGLV10-54 IGLV11-55 IGLV2-11 IGLV2-18 IGLV2-23 IGLV2-33 IGLV3-12 IGLV3-16 IGLV3-22 IGLV3-25 IGLV3-27 IGLV4-3 IGLV4-60 IGLV4-69 IGLV5-37 IGLV5-45 IGLV7-43 IGLV7-46 IGLV8-61 IKBKB IKBKE IK [...]
+REACTOME_INORGANIC_CATION_ANION_SLC_TRANSPORTERS > Genes involved in Inorganic cation/anion SLC transporters SLC12A1 SLC12A2 SLC12A3 SLC12A4 SLC12A5 SLC12A6 SLC12A7 SLC15A1 SLC15A2 SLC15A3 SLC15A4 SLC16A10 SLC17A1 SLC17A5 SLC17A6 SLC17A7 SLC17A8 SLC1A1 SLC1A2 SLC1A3 SLC1A4 SLC1A5 SLC1A6 SLC1A7 SLC20A1 SLC20A2 SLC24A1 SLC24A2 SLC24A3 SLC24A4 SLC24A5 SLC24A6 SLC26A1 SLC26A2 SLC26A3 SLC26A4 SLC26A6 SLC26A7 SLC26A9 SLC32A1 SLC34A1 SLC34A2 SLC34A3 SLC36A1 SLC36A2 SLC38A1 SLC38A2 SLC38A3 SLC38 [...]
+REACTOME_INSULIN_SYNTHESIS_AND_SECRETION > Genes involved in Insulin Synthesis and Secretion CPE DDOST ERO1L FAU GNAI1 GNAI2 GNAO1 INS KIF5B MAFA MYO5A NKX2-2 PAX6 PCSK1 PCSK2 PDX1 RAB27A RPL10 RPL10A RPL11 RPL12 RPL13 RPL13A RPL14 RPL15 RPL17 RPL18 RPL18A RPL19 RPL21 RPL22 RPL23 RPL23A RPL24 RPL26 RPL26L1 RPL27 RPL27A RPL28 RPL29 RPL3 RPL30 RPL31 RPL32 RPL34 RPL35 RPL35A RPL36 RPL36A RPL37 RPL37A RPL38 RPL39 RPL3L RPL4 RPL41 RPL5 RPL6 RPL7 RPL7A RPL8 RPL9 RPLP0 RPLP1 RPLP2 RPN1 RPN2 RPS [...]
+REACTOME_INTEGRATION_OF_ENERGY_METABOLISM > Genes involved in Integration of energy metabolism ABCC8 ACACA ACACB ACLY ACO2 ACSL1 ADCY1 ADCY10 ADCY2 ADCY3 ADCY4 ADCY5 ADCY6 ADCY7 ADCY8 ADCY9 AGPAT1 ALDOA ALDOB ALDOC ATP5A1 ATP5B ATP5C1 ATP5D ATP5E ATP5F1 ATP5G1 ATP5H ATP5I ATP5J ATP5J2 ATP5L ATP5O ATP6 ATP8 CAB39 CAB39L CACNA1A CACNA1C CACNA1D CACNA1E CACNA2D2 CACNB2 CACNB3 COX1 COX2 COX3 COX4I1 COX5A COX5B COX6A1 COX6B1 COX6C COX7A2L COX7B COX7C COX8A CPT1B CPT2 CS CYC1 CYCS DLAT DLD DLS [...]
+REACTOME_INTEGRIN_ALPHAIIBBETA3_SIGNALING > Genes involved in Integrin alphaIIbbeta3 signaling APBB1IP BCAR1 CRK CSK FGA FGB FGG FN1 GRB2 ITGA2B ITGB3 PTK2 PTPN1 RAP1A RAP1B RAPGEF3 RAPGEF4 RASGRP2 RASGRP3 SOS1 SRC TLN1 VWF
+REACTOME_INTEGRIN_CELL_SURFACE_INTERACTIONS > Genes involved in Integrin cell surface interactions AMICA1 APBB1IP BCAR1 BSG CDH1 COL1A1 COL1A2 COL2A1 COL4A1 COL4A2 COL4A3 COL4A4 COL4A5 CRK CSK F11R FBN1 FGA FGB FGG FN1 GRB2 IBSP ICAM1 ICAM2 ICAM3 ICAM4 ITGA1 ITGA10 ITGA11 ITGA2 ITGA2B ITGA3 ITGA4 ITGA5 ITGA6 ITGA7 ITGA8 ITGA9 ITGAD ITGAE ITGAL ITGAM ITGAV ITGAX ITGB1 ITGB2 ITGB3 ITGB4 ITGB5 ITGB6 ITGB7 ITGB8 JAM2 JAM3 LAMA1 LAMA2 LAMA5 LAMB1 LAMB2 LAMC1 LAMC3 MADCAM1 PECAM1 PTK2 PTPN1 RA [...]
+REACTOME_INTRINSIC_PATHWAY > Genes involved in Intrinsic Pathway A2M C1QBP F10 F11 F12 F2 F8 F9 GP1BA GP1BB GP5 GP9 KLKB1 KNG1 PRCP SERPING1 VWF
+REACTOME_INTRINSIC_PATHWAY_FOR_APOPTOSIS > Genes involved in Intrinsic Pathway for Apoptosis AKT1 APAF1 BAD BAK1 BAX BBC3 BCL2 BCL2L1 BCL2L11 BID BMF CASP3 CASP7 CASP8 CASP9 CYCS DIABLO DYNLL1 DYNLL2 E2F1 GZMB MAPK8 NMT1 PMAIP1 PPP3CC PPP3R1 TFDP1 XIAP YWHAB
+REACTOME_IONOTROPIC_ACTIVITY_OF_KAINATE_RECEPTORS > Genes involved in Ionotropic activity of Kainate Receptors CALM1 CALM2 CALM3 DLG1 DLG3 DLG4 GRIK1 GRIK2 GRIK3 GRIK4 GRIK5 NCALD
+REACTOME_IRS_RELATED_EVENTS > Genes involved in IRS-related events AKT2 CAB39 CAB39L DOK1 EEF2K EIF4B EIF4E EIF4EBP1 EIF4G1 FGF1 FGF10 FGF16 FGF17 FGF18 FGF19 FGF2 FGF20 FGF22 FGF23 FGF3 FGF4 FGF5 FGF6 FGF7 FGF8 FGF9 FGFR1 FGFR2 FGFR3 FGFR4 FRS2 GAB1 GRB2 HRAS INS INSR IRS1 IRS2 KL KRAS MAP2K1 MAP2K2 MAPK1 MAPK3 MLST8 MTOR NRAS PDE3B PDPK1 PIK3C3 PIK3CA PIK3CB PIK3R1 PIK3R2 PIK3R4 PPM1A PRKAA1 PRKAA2 PRKAB1 PRKAB2 PRKAG1 PRKAG2 PRKAG3 PTPN11 RAF1 RHEB RPS6 RPS6KB1 RPTOR SOS1 STK11 STRADA [...]
+REACTOME_JNK_PHOSPHORYLATION_AND_ACTIVATION_MEDIATED_BY_ACTIVATED_HUMAN_TAK1 > Genes involved in JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 MAP2K4 MAP2K7 MAP3K7 MAPK10 MAPK8 MAPK9 TAB1 TAB2 TAB3 TICAM1 TLR3 TRAF6
+REACTOME_LAGGING_STRAND_SYNTHESIS > Genes involved in Lagging Strand Synthesis DNA2 FEN1 LIG1 PCNA POLA1 POLA2 POLD1 POLD2 POLD3 POLD4 PRIM1 PRIM2 RFC1 RFC2 RFC3 RFC4 RFC5 RPA1 RPA2 RPA3
+REACTOME_LATE_PHASE_OF_HIV_LIFE_CYCLE > Genes involved in Late Phase of HIV Life Cycle AAAS CCNH CCNT1 CDK7 CDK9 COBRA1 CTDP1 ELL ERCC2 ERCC3 GTF2A1 GTF2A2 GTF2B GTF2E1 GTF2E2 GTF2F1 GTF2F2 GTF2H1 GTF2H2 GTF2H3 GTF2H4 MNAT1 NCBP1 NCBP2 NUP107 NUP133 NUP153 NUP155 NUP160 NUP188 NUP205 NUP210 NUP214 NUP35 NUP37 NUP43 NUP50 NUP54 NUP62 NUP85 NUP88 NUP93 NUP98 NUPL1 NUPL2 POLR2A POLR2B POLR2C POLR2D POLR2E POLR2F POLR2G POLR2H POLR2I POLR2J POLR2K POLR2L POM121 RAE1 RAN RANBP1 RANBP2 RANGAP1 [...]
+REACTOME_LIPOPROTEIN_METABOLISM > Genes involved in Lipoprotein metabolism A2M ABCA1 ABCG1 ALB AMN APOA1 APOA2 APOA4 APOA5 APOB APOC2 APOC3 APOE BMP1 CETP CUBN HSPG2 LCAT LDLR LDLRAP1 LIPC LPL MTTP P4HB SAR1B SCARB1 SDC1
+REACTOME_LOSS_OF_NLP_FROM_MITOTIC_CENTROSOMES > Genes involved in Loss of Nlp from mitotic centrosomes ACTR1A AKAP9 ALMS1 AZI1 CDK1 CDK5RAP2 CENPJ CEP110 CEP135 CEP152 CEP164 CEP192 CEP250 CEP290 CEP57 CEP63 CEP70 CEP72 CEP76 CEP78 CETN2 CKAP5 CLASP1 CP110 CSNK1D CSNK1E DCTN1 DCTN2 DCTN3 DYNC1H1 DYNC1I2 DYNLL1 FGFR1OP HAUS2 HSP90AA1 MAPRE1 NDE1 NEDD1 NEK2 NINL ODF2 OFD1 PAFAH1B1 PCM1 PCNT PLK1 PLK4 PPP2R1A PRKACA PRKAR2B SDCCAG8 SFI1 SSNA1 TSGA14 TUBA1A TUBA4A TUBB TUBB2C TUBB4 TUBG1 YWH [...]
+REACTOME_LYSOSOME_VESICLE_BIOGENESIS > Genes involved in Lysosome Vesicle Biogenesis AP1B1 AP1G1 AP1M1 AP1M2 AP1S1 AP1S2 AP1S3 ARF1 ARRB1 BLOC1S1 CLTA CLTC CTSZ DNAJC6 DNASE2 DNM2 GNS HSPA8 M6PR SH3GL2 TXNDC5 VAMP2 VAMP7 VAMP8
+REACTOME_M_G1_TRANSITION > Genes involved in M/G1 Transition CDC6 CDT1 E2F1 E2F2 E2F3 GMNN MCM2 MCM3 MCM4 MCM5 MCM6 MCM7 MCM8 ORC1L ORC2L ORC3L ORC4L ORC5L ORC6L PSMA1 PSMA2 PSMA3 PSMA4 PSMA5 PSMA6 PSMA7 PSMB1 PSMB10 PSMB2 PSMB3 PSMB4 PSMB5 PSMB6 PSMB7 PSMB8 PSMB9 PSMC1 PSMC2 PSMC3 PSMC4 PSMC5 PSMC6 PSMD1 PSMD10 PSMD11 PSMD12 PSMD13 PSMD14 PSMD2 PSMD3 PSMD4 PSMD5 PSMD6 PSMD7 PSMD8 PSMD9 PSME1 PSME2 PSME3 PSMF1 UBB
+REACTOME_MAP_KINASES_ACTIVATION_IN_TLR_CASCADE > Genes involved in MAP kinases activation in TLR cascade ATF1 ATF2 CREB1 DUSP3 DUSP4 DUSP6 DUSP7 ELK1 FOS JUN MAP2K1 MAP2K2 MAP2K3 MAP2K4 MAP2K6 MAP2K7 MAP3K7 MAPK1 MAPK10 MAPK11 MAPK14 MAPK3 MAPK7 MAPK8 MAPK9 MAPKAPK2 MAPKAPK3 MEF2A MEF2C PPP2CA PPP2CB PPP2R1A PPP2R1B PPP2R5D RPS6KA1 RPS6KA2 RPS6KA3 RPS6KA5 TAB1 TAB2 TAB3 TICAM1 TLR3 TRAF6
+REACTOME_MAPK_TARGETS_NUCLEAR_EVENTS_MEDIATED_BY_MAP_KINASES > Genes involved in MAPK targets/Nuclear events mediated by MAP kinases ATF1 ATF2 CREB1 DUSP3 DUSP4 DUSP6 DUSP7 ELK1 FOS JUN MAPK1 MAPK10 MAPK11 MAPK14 MAPK3 MAPK7 MAPK8 MAPK9 MAPKAPK2 MEF2A MEF2C PPP2CA PPP2CB PPP2R1A PPP2R1B PPP2R5D RPS6KA1 RPS6KA2 RPS6KA3 RPS6KA5
+REACTOME_MEMBRANE_TRAFFICKING > Genes involved in Membrane Trafficking AP1B1 AP1G1 AP1M1 AP1M2 AP1S1 AP1S2 AP1S3 AP3B1 AP3S1 AP4B1 AP4E1 ARCN1 ARF1 ARFGAP1 ARRB1 BLOC1S1 BLOC1S3 CLINT1 CLTA CLTC CNO COPA COPB1 COPB2 COPE COPG COPZ1 CPD CTSZ DNAJC6 DNASE2 DNM2 DTNBP1 FTH1 FTL GAK GBF1 GNS HIP1R HSPA8 IGF2R M6PR NAPA NECAP1 OCRL PICALM PIK3C2A PLDN PREB PUM1 RAB5C SAR1B SEC13 SEC23A SEC24A SEC24B SEC24C SEC24D SEC31A SH3D19 SH3GL2 SNAP23 SNAPIN SNX2 SNX5 SNX9 SORT1 STX4 TBC1D8B TFRC TGOLN2 [...]
+REACTOME_METABLISM_OF_NUCLEOTIDES > Genes involved in Metablism of nucleotides ADA ADK ADSL ADSS ADSSL1 AK1 AK2 AK5 AMPD1 AMPD2 AMPD3 APRT ATIC CAD CDA CMPK1 CTPS CTPS2 DCK DCTD DGUOK DHODH DPYD DPYS DTYMK DUT GART GDA GLRX GMPR GMPR2 GMPS GSR GUK1 HPRT1 IMPDH1 IMPDH2 NME1 NME2 NME4 NT5C NT5C1A NT5C1B NT5C2 NT5C3 NT5E NT5M PAICS PFAS PNP PPAT RRM1 RRM2 RRM2B SLC28A1 SLC28A2 SLC28A3 SLC29A1 SLC29A2 TK1 TK2 TXN TXNRD1 TYMP TYMS UCK1 UCK2 UMPS UPB1 UPP1 XDH
+REACTOME_METABOLISM_OF_AMINO_ACIDS > Genes involved in Metabolism of amino acids AADAT AASS ACAD8 ACADSB ACAT1 ACMSD ADC AFMID AGMAT ALDH18A1 ALDH4A1 ALDH6A1 ALDH7A1 ALDH9A1 AMD1 AMDHD1 ARG1 ARG2 ASL ASNS ASS1 AUH AZIN1 BBOX1 BCAT1 BCAT2 BCKDHA BCKDHB CKB CKM CKMT1A CKMT1B CKMT2 CPS1 DBT DLD DLST FAH FTCD GAMT GATM GCDH GLS GLS2 GLUD1 GLUL GOT1 GOT2 GPT GPT2 GSTZ1 HAAO HAL HGD HIBADH HIBCH HPD HSD17B10 IDO1 IVD KMO KYNU MCCC1 MCCC2 NAGS NQO1 OAT OAZ1 OAZ2 OAZ3 ODC1 OGDH OTC PAH PCBD1 PRO [...]
+REACTOME_METABOLISM_OF_BILE_ACIDS_AND_BILE_SALTS > Genes involved in Metabolism of bile acids and bile salts ABCB11 ABCC3 ACOT8 ACOX2 AKR1C4 AKR1D1 ALB AMACR BAAT CH25H CYP27A1 CYP39A1 CYP46A1 CYP7A1 CYP7B1 CYP8B1 FABP6 HSD17B4 HSD3B7 SCP2 SLC10A1 SLC10A2 SLC27A2 SLC27A5 SLCO1A2 SLCO1B1 SLCO1B3
+REACTOME_METABOLISM_OF_CARBOHYDRATES > Genes involved in Metabolism of carbohydrates AAAS AGL ALDOA ALDOB ALDOC AMY1A AMY1B AMY1C AMY2A AMY2B CALM1 CALM2 CALM3 ENO1 ENO2 ENO3 FBP1 FBP2 G6PC G6PD GALE GALK1 GALT GAPDH GAPDHS GBE1 GCK GCKR GOT1 GOT2 GPI GYG1 GYG2 GYS1 GYS2 HK1 HK2 HK3 KHK LCT MDH1 MDH2 MGAM NUP107 NUP133 NUP153 NUP155 NUP160 NUP188 NUP205 NUP210 NUP214 NUP35 NUP37 NUP43 NUP50 NUP54 NUP62 NUP85 NUP88 NUP93 NUP98 NUPL1 NUPL2 PC PCK1 PCK2 PFKFB1 PFKFB2 PFKFB3 PFKFB4 PFKL PFKM [...]
+REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS > Genes involved in Metabolism of lipids and lipoproteins A2M ABCA1 ABCB11 ABCB4 ABCC3 ABCD1 ABCG1 ABCG5 ABCG8 ABHD5 ACAA1 ACACA ACACB ACADL ACADM ACADS ACADVL ACAT1 ACER1 ACER2 ACER3 ACOT8 ACOX1 ACOX2 ACOX3 ACSL1 AGPAT1 AGPAT2 AGPAT3 AGPAT4 AGPAT5 AGPS AGT AKR1C4 AKR1D1 ALB AMACR AMN ANGPTL4 APOA1 APOA2 APOA4 APOA5 APOB APOC2 APOC3 APOE BAAT BDH1 BMP1 CARM1 CAV1 CD36 CEL CETP CH25H CHD9 CLPS COL4A3BP CPT1A CPT1B CPT2 CRAT CREBBP CROT CSNK1G [...]
+REACTOME_METABOLISM_OF_MRNA > Genes involved in Metabolism of mRNA C2ORF29 CNOT1 CNOT10 CNOT2 CNOT3 CNOT4 CNOT6 CNOT6L CNOT7 CNOT8 DCP1A DCP1B DCP2 DCPS DDX6 DIS3 EDC3 EDC4 EIF4A1 EIF4A2 EIF4B EIF4E EIF4G1 EXOSC1 EXOSC2 EXOSC3 EXOSC4 EXOSC5 EXOSC6 EXOSC7 EXOSC8 EXOSC9 LSM1 LSM2 LSM3 LSM4 LSM5 LSM6 PABPC1 PAIP1 PAN2 PAN3 PARN RQCD1 TNKS1BP1 XRN1
+REACTOME_METABOLISM_OF_NITRIC_OXIDE > Genes involved in Metabolism of nitric oxide AKT1 CALM1 CALM2 CALM3 CAV1 DNM2 HSP90AA1 LYPLA1 NOS3 NOSIP NOSTRIN WASL ZDHHC21
+REACTOME_METABOLISM_OF_PROTEINS > Genes involved in Metabolism of proteins ACTB AP3M1 ARFGEF2 CCT2 CCT3 CCT4 CCT5 CCT6A CCT7 CCT8 DHPS DOHH DPM1 DPM2 DPM3 EEF1A1 EEF1B2 EEF1D EEF1G EEF2 EIF1AX EIF2B1 EIF2B2 EIF2B3 EIF2B4 EIF2B5 EIF2S1 EIF2S2 EIF2S3 EIF3A EIF3B EIF3C EIF3CL EIF3D EIF3E EIF3F EIF3G EIF3H EIF3I EIF3J EIF3K EIF4A1 EIF4A2 EIF4B EIF4E EIF4EBP1 EIF4G1 EIF4H EIF5 EIF5A EIF5A2 EIF5B ETF1 F10 F2 F7 F9 FAU FBXL3 FBXL5 FBXO4 FBXO6 FBXW10 FBXW2 FBXW4 FBXW5 FBXW7 FBXW9 FKBP9 FURIN GAS [...]
+REACTOME_METABOLISM_OF_RNA > Genes involved in Metabolism of RNA AAAS C2ORF29 CLNS1A CNOT1 CNOT10 CNOT2 CNOT3 CNOT4 CNOT6 CNOT6L CNOT7 CNOT8 DCP1A DCP1B DCP2 DCPS DDX20 DDX6 DIS3 EDC3 EDC4 EIF4A1 EIF4A2 EIF4B EIF4E EIF4G1 EXOSC1 EXOSC2 EXOSC3 EXOSC4 EXOSC5 EXOSC6 EXOSC7 EXOSC8 EXOSC9 GEMIN4 GEMIN5 GEMIN6 GEMIN7 LSM1 LSM2 LSM3 LSM4 LSM5 LSM6 NCBP1 NCBP2 NUP107 NUP133 NUP153 NUP155 NUP160 NUP188 NUP205 NUP210 NUP214 NUP35 NUP37 NUP43 NUP50 NUP54 NUP62 NUP85 NUP88 NUP93 NUP98 NUPL1 NUPL2 PA [...]
+REACTOME_METABOLISM_OF_VITAMINS_AND_COFACTORS > Genes involved in Metabolism of vitamins and cofactors AASDHPPT ACP5 COASY CYB5A CYB5R3 DHFR ENPP1 FASN FLAD1 FPGS GSTO1 GSTO2 MTHFD1 MTHFR NADK NADSYN1 NAMPT NAPRT1 NMNAT1 NMNAT2 NMNAT3 PANK1 PANK2 PANK3 PANK4 PPCDC PPCS QPRT RFK SHMT1 SLC19A1 SLC19A2 SLC19A3 SLC23A1 SLC23A2 SLC25A16 SLC25A32 SLC2A1 SLC2A3 SLC46A1 SLC5A6 TPK1
+REACTOME_METAL_ION_SLC_TRANSPORTERS > Genes involved in Metal ion SLC transporters SLC11A1 SLC11A2 SLC30A1 SLC30A2 SLC30A3 SLC30A5 SLC30A6 SLC30A7 SLC30A8 SLC31A1 SLC39A1 SLC39A10 SLC39A14 SLC39A2 SLC39A3 SLC39A4 SLC39A5 SLC39A6 SLC39A7 SLC39A8 SLC40A1 SLC41A1 SLC41A2
+REACTOME_MICRORNA_BIOGENESIS > Genes involved in MicroRNA biogenesis DGCR8 DICER1 POLR2A POLR2B POLR2C POLR2D POLR2E POLR2F POLR2G POLR2H POLR2I POLR2J POLR2K POLR2L RAN RNASEN TARBP2 XPO5
+REACTOME_MITOCHONDRIAL_FATTY_ACID_BETA_OXIDATION > Genes involved in Mitochondrial Fatty Acid Beta-Oxidation ACADL ACADM ACADS ACADVL DCI DECR1 ECHS1 HADH HADHA HADHB
+REACTOME_MITOCHONDRIAL_TRNA_AMINOACYLATION > Genes involved in Mitochondrial tRNA aminoacylation AARS2 CARS2 DARS2 EARS2 FARS2 GARS HARS2 IARS2 KARS LARS2 MARS2 NARS2 PARS2 QARS RARS2 SARS2 TARS2 VARS2 WARS2 YARS2
+REACTOME_MITOTIC_M_M_G1_PHASES > Genes involved in Mitotic M-M/G1 phases AHCTF1 APITD1 AURKB B9D2 BIRC5 BUB1 BUB1B BUB3 CASC5 CCDC99 CDC20 CDC6 CDCA8 CDT1 CENPA CENPC1 CENPE CENPF CENPH CENPI CENPK CENPL CENPM CENPN CENPO CENPP CENPQ CENPT CKAP5 CLASP1 CLASP2 CLIP1 DSN1 E2F1 E2F2 E2F3 ERCC6L FBXO5 GMNN GORASP1 INCENP ITGB3BP KIF18A KIF20A KIF23 KIF2A KIF2B KIF2C KNTC1 MAD1L1 MAD2L1 MAPRE1 MCM2 MCM3 MCM4 MCM5 MCM6 MCM7 MCM8 MIS12 MLF1IP NDC80 NDE1 NDEL1 NSL1 NUDC NUF2 NUP107 NUP133 NUP160 [...]
+REACTOME_MITOTIC_PROMETAPHASE > Genes involved in Mitotic Prometaphase AHCTF1 APITD1 AURKB B9D2 BIRC5 BUB1 BUB1B BUB3 CASC5 CCDC99 CDC20 CDCA8 CENPA CENPC1 CENPE CENPF CENPH CENPI CENPK CENPL CENPM CENPN CENPO CENPP CENPQ CENPT CKAP5 CLASP1 CLASP2 CLIP1 DSN1 ERCC6L INCENP ITGB3BP KIF18A KIF2A KIF2B KIF2C KNTC1 MAD1L1 MAD2L1 MAPRE1 MIS12 MLF1IP NDC80 NDE1 NDEL1 NSL1 NUDC NUF2 NUP107 NUP133 NUP160 NUP37 NUP43 NUP85 NUP98 PAFAH1B1 PLK1 PMF1 PPP1CC PPP2CA PPP2CB PPP2R1A PPP2R1B PPP2R5A PPP2R [...]
+REACTOME_MRNA_3_END_PROCESSING > Genes involved in mRNA 3-end processing CDC40 CLP1 CPSF1 CPSF2 CPSF3 CPSF7 CSTF1 CSTF2 CSTF3 DHX38 MAGOH NCBP1 NCBP2 NFX1 NUDT21 PABPN1 PAPOLA PCF11 RBM8A RNPS1 SFRS1 SFRS11 SFRS2 SFRS3 SFRS4 SFRS5 SFRS6 SFRS7 SFRS9 SRRM1 THOC4 U2AF1 U2AF2 UPF3B
+REACTOME_MRNA_DECAY_BY_3_TO_5_EXORIBONUCLEASE > Genes involved in mRNA Decay by 3' to 5' Exoribonuclease DCPS DIS3 EXOSC1 EXOSC2 EXOSC3 EXOSC4 EXOSC5 EXOSC6 EXOSC7 EXOSC8 EXOSC9
+REACTOME_MRNA_DECAY_BY_5_TO_3_EXORIBONUCLEASE > Genes involved in mRNA Decay by 5' to 3' Exoribonuclease DCP1A DCP1B DCP2 DDX6 EDC3 EDC4 LSM1 LSM2 LSM3 LSM4 LSM5 LSM6 XRN1
+REACTOME_MRNA_PROCESSING > Genes involved in mRNA Processing A1CF ADAR ADARB1 APOBEC1 CCNH CDK7 ERCC2 ERCC3 GTF2F1 GTF2F2 GTF2H1 GTF2H2 GTF2H3 GTF2H4 MNAT1 NCBP1 NCBP2 POLR2A POLR2B POLR2C POLR2D POLR2E POLR2F POLR2G POLR2H POLR2I POLR2J POLR2K POLR2L RNGTT RNMT SUPT5H
+REACTOME_MRNA_SPLICING > Genes involved in mRNA Splicing CCAR1 CD2BP2 CDC40 CLP1 CPSF1 CPSF2 CPSF3 CPSF7 CSTF1 CSTF2 CSTF3 DDX23 DHX38 DHX9 DNAJC8 EFTUD2 FUS GTF2F1 GTF2F2 HNRNPA0 HNRNPA1 HNRNPA2B1 HNRNPA3 HNRNPC HNRNPD HNRNPF HNRNPH1 HNRNPH2 HNRNPK HNRNPL HNRNPM HNRNPR HNRNPU HNRNPUL1 LSM2 MAGOH NCBP1 NCBP2 NFX1 NHP2L1 NUDT21 PABPN1 PAPOLA PCBP1 PCBP2 PCF11 PHF5A POLR2A POLR2B POLR2C POLR2D POLR2E POLR2F POLR2G POLR2H POLR2I POLR2J POLR2K POLR2L PRPF4 PRPF6 PRPF8 PTBP1 RBM5 RBM8A RBMX R [...]
+REACTOME_MRNA_SPLICING_MINOR_PATHWAY > Genes involved in mRNA Splicing - Minor Pathway DDX23 EFTUD2 GTF2F1 GTF2F2 LSM2 NCBP1 NCBP2 NHP2L1 POLR2A POLR2B POLR2C POLR2D POLR2E POLR2F POLR2G POLR2H POLR2I POLR2J POLR2K POLR2L PRPF6 PRPF8 SF3B1 SF3B14 SF3B2 SF3B3 SF3B4 SF3B5 SFRS1 SFRS2 SFRS6 SFRS7 SNRNP200 SNRNP40 SNRPB SNRPD1 SNRPD2 SNRPD3 SNRPE SNRPF SNRPG TXNL4A
+REACTOME_MTOR_SIGNALLING > Genes involved in mTOR signalling AKT2 CAB39 CAB39L EEF2K EIF4B EIF4E EIF4EBP1 EIF4G1 MLST8 MTOR PPM1A PRKAA1 PRKAA2 PRKAB1 PRKAB2 PRKAG1 PRKAG2 PRKAG3 RHEB RPS6 RPS6KB1 RPTOR STK11 STRADA STRADB TSC1 TSC2
+REACTOME_MTORC1_MEDIATED_SIGNALLING > Genes involved in mTORC1-mediated signalling EEF2K EIF4B EIF4E EIF4EBP1 EIF4G1 MLST8 MTOR RHEB RPS6 RPS6KB1 RPTOR
+REACTOME_MUSCLE_CONTRACTION > Genes involved in Muscle contraction ACTA2 ACTG2 ACTN2 ACTN3 CALD1 CALM1 CALM2 CALM3 DES DMD ITGA1 ITGB5 LMOD1 MYBPC1 MYBPC2 MYBPC3 MYH11 MYH3 MYH6 MYH8 MYL1 MYL12B MYL2 MYL3 MYL4 MYL6 MYL6B MYL9 MYLK NEB PXN SORBS1 SORBS3 TCAP TLN1 TMOD1 TNNC1 TNNC2 TNNI1 TNNI2 TNNI3 TNNT1 TNNT2 TNNT3 TPM1 TPM2 TPM3 TPM4 TTN VCL VIM
+REACTOME_MYD88_CASCADE > Genes involved in MyD88 cascade ECSIT IRAK1 IRAK3 IRAK4 LY96 MAP3K1 MYD88 SIGIRR TIRAP TLR1 TLR10 TLR2 TLR4 TLR5 TLR6 TLR7 TLR8 TLR9 TRAF6
+REACTOME_MYOGENESSIS > Genes involved in MyoGenessis ABL1 BNIP2 BOC CDC42 CDH15 CDH2 CDH4 CDON CTNNA1 CTNNA2 CTNNB1 MAP2K6 MAPK11 MAPK12 MAPK14 MEF2A MEF2B MEF2C MEF2D MYF5 MYF6 MYOD1 MYOG NEO1 NTN3 SPAG9 TCF12 TCF3 TCF4
+REACTOME_NA_CL_DEPENDENT_NEUROTRANSMITTER_TRANSPORTERS > Genes involved in Na+/Cl- dependent neurotransmitter transporters SLC18A1 SLC18A2 SLC22A2 SLC6A1 SLC6A11 SLC6A12 SLC6A13 SLC6A14 SLC6A15 SLC6A18 SLC6A19 SLC6A2 SLC6A20 SLC6A3 SLC6A5 SLC6A6 SLC6A7 SLC6A9
+REACTOME_NCAM1_INTERACTIONS > Genes involved in NCAM1 interactions AGRN ARTN CACNA1C CACNA1D CACNA1F CACNA1G CACNA1H CACNA1I CACNA1S CACNB1 CACNB2 CACNB3 CACNB4 CNTN2 COL1A1 COL1A2 COL29A1 COL2A1 COL3A1 COL4A1 COL4A2 COL4A3 COL4A4 COL4A5 COL5A1 COL5A2 COL6A1 COL6A2 COL6A3 COL6A6 COL9A1 COL9A2 COL9A3 GDNF GFRA1 GFRA2 GFRA4 NCAM1 NCAN NRTN PRNP PSPN ST8SIA2 ST8SIA4
+REACTOME_NCAM_SIGNALING_FOR_NEURITE_OUT_GROWTH > Genes involved in NCAM signaling for neurite out-growth AGRN ARTN CACNA1C CACNA1D CACNA1F CACNA1G CACNA1H CACNA1I CACNA1S CACNB1 CACNB2 CACNB3 CACNB4 CNTN2 COL1A1 COL1A2 COL29A1 COL2A1 COL3A1 COL4A1 COL4A2 COL4A3 COL4A4 COL4A5 COL5A1 COL5A2 COL6A1 COL6A2 COL6A3 COL6A6 COL9A1 COL9A2 COL9A3 CREB1 FGFR1 FYN GDNF GFRA1 GFRA2 GFRA4 GRB2 HRAS KRAS MAP2K1 MAP2K2 MAPK1 MAPK3 NCAM1 NCAN NRAS NRTN PRNP PSPN PTK2 PTPRA RAF1 RPS6KA5 SOS1 SPTA1 SPTAN1 [...]
+REACTOME_NEF_MEDIATED_DOWNREGULATION_OF_MHC_CLASS_I_COMPLEX_CELL_SURFACE_EXPRESSION > Genes involved in Nef mediated downregulation of MHC classcomplex cell surface expression AP1B1 AP1G1 AP1M1 AP1M2 AP1S1 AP1S2 AP1S3 B2M HLA-A PACS1
+REACTOME_NEF_MEDIATES_DOWN_MODULATION_OF_CELL_SURFACE_RECEPTORS_BY_RECRUITING_THEM_TO_CLATHRIN_ADAPTERS > Genes involved in Nef-mediates down modulation of cell surface receptors by recruiting them to clathrin adapters AP1B1 AP1G1 AP1M1 AP1M2 AP1S1 AP1S2 AP1S3 AP2A1 AP2A2 AP2B1 AP2M1 AP2S1 ARF1 ATP6V1H B2M CD28 CD4 CD8B HLA-A LCK PACS1
+REACTOME_NEP_NS2_INTERACTS_WITH_THE_CELLULAR_EXPORT_MACHINERY > Genes involved in NEP/NS2 Interacts with the Cellular Export Machinery AAAS NUP107 NUP133 NUP153 NUP155 NUP160 NUP188 NUP205 NUP210 NUP214 NUP35 NUP37 NUP43 NUP50 NUP54 NUP62 NUP85 NUP88 NUP93 NUP98 NUPL1 NUPL2 POM121 RAE1 RAN RANBP2 SEH1L TPR XPO1
+REACTOME_NEURORANSMITTER_RECEPTOR_BINDING_AND_DOWNSTREAM_TRANSMISSION_IN_THE_POSTSYNAPTIC_CELL > Genes involved in Neuroransmitter Receptor Binding And Downstream Transmission In The Postsynaptic Cell ACTN2 ADCY1 ADCY3 ADCY8 AKAP5 AP2A1 AP2A2 AP2B1 AP2M1 AP2S1 CACNG2 CACNG3 CACNG4 CACNG8 CALM1 CALM2 CALM3 CAMK2A CAMK2B CAMK2D CAMK2G CAMK4 CAMKK1 CREB1 DLG1 DLG3 DLG4 EPB41L1 GNB1 GNB2 GNB3 GNB4 GNB5 GNG10 GNG11 GNG12 GNG13 GNG2 GNG3 GNG4 GNG5 GNG7 GNG8 GNGT1 GNGT2 GRIA1 GRIA2 GRIA3 GRIA4 [...]
+REACTOME_NEUROTRANSMITTER_RELEASE_CYCLE > Genes involved in Neurotransmitter Release Cycle CHAT CPLX1 DBH DDC FNBP1L GLS MAOA RAB3A RIMS1 SLC17A7 SLC18A2 SLC18A3 SLC1A1 SLC1A6 SLC1A7 SLC22A2 SLC5A7 SNAP25 STX1A STXBP1 SYN1 SYN2 SYN3 SYT1 TH TPH1 UNC13B VAMP2
+REACTOME_NF_KB_IS_ACTIVATED_AND_SIGNALS_SURVIVAL > Genes involved in NF-kB is activated and signals survival IKBKB IRAK1 NFKB1 NFKBIA NGF NGFR RELA SQSTM1 TRAF6 UBB
+REACTOME_NOREPINEPHRINE_NEUROTRANSMITTER_RELEASE_CYCLE > Genes involved in Norepinephrine Neurotransmitter Release Cycle CPLX1 DBH MAOA RAB3A RIMS1 SLC18A2 SLC22A2 SNAP25 STX1A STXBP1 SYT1 VAMP2
+REACTOME_NOTCH_HLH_TRANSCRIPTION_PATHWAY > Genes involved in Notch-HLH transcription pathway CREBBP KAT2A KAT2B MAML1 MAML2 MAML3 MAMLD1 NOTCH1 NOTCH2 NOTCH3 NOTCH4 RBPJ SNW1
+REACTOME_NRAGE_SIGNALS_DEATH_THROUGH_JNK > Genes involved in NRAGE signals death through JNK AATF ABR AKAP13 ARHGAP4 ARHGEF11 ARHGEF12 ARHGEF16 ARHGEF17 ARHGEF18 ARHGEF2 ARHGEF3 ARHGEF4 ARHGEF6 ARHGEF7 ARHGEF9 BAD BCL2L11 ECT2 FGD1 FGD2 FGD3 FGD4 ITSN1 KALRN MAGED1 MAPK8 MCF2 MCF2L NET1 NGEF NGF NGFR OBSCN PLEKHG2 PLEKHG5 PREX1 RAC1 RASGRF1 RASGRF2 SOS1 SOS2 TIAM1 TIAM2 TRIO VAV1 VAV2 VAV3
+REACTOME_NRIF_SIGNALS_CELL_DEATH_FROM_THE_NUCLEUS > Genes involved in NRIF signals cell death from the nucleus APH1A APH1B ITGB3BP MAPK8 NCSTN NGF NGFR PSEN1 PSEN2 PSENEN SQSTM1 TRAF6 UBB
+REACTOME_NUCLEAR_EVENTS_KINASE_AND_TRANSCRIPTION_FACTOR_ACTIVATION > Genes involved in Nuclear Events (kinase and transcription factor activation) ATF1 CREB1 DUSP3 DUSP4 DUSP6 DUSP7 ELK1 MAPK1 MAPK11 MAPK14 MAPK3 MAPK7 MAPKAPK2 MEF2A MEF2C PPP2CA PPP2CB PPP2R1A PPP2R1B PPP2R5D RPS6KA1 RPS6KA2 RPS6KA3 RPS6KA5
+REACTOME_NUCLEAR_IMPORT_OF_REV_PROTEIN > Genes involved in Nuclear import of Rev protein AAAS KPNB1 NPM1 NUP107 NUP133 NUP153 NUP155 NUP160 NUP188 NUP205 NUP210 NUP214 NUP35 NUP37 NUP43 NUP50 NUP54 NUP62 NUP85 NUP88 NUP93 NUP98 NUPL1 NUPL2 POM121 RAE1 RAN RANBP2 SEH1L TPR
+REACTOME_NUCLEAR_RECEPTOR_TRANSCRIPTION_PATHWAY > Genes involved in Nuclear Receptor transcription pathway AR ESR1 ESR2 ESRRA ESRRB ESRRG HNF4A HNF4G MED1 NR0B1 NR0B2 NR1D1 NR1D2 NR1H2 NR1H3 NR1H4 NR1I2 NR1I3 NR2C1 NR2C2 NR2C2AP NR2E1 NR2E3 NR2F1 NR2F6 NR3C1 NR3C2 NR4A1 NR4A2 NR4A3 NR5A2 NR6A1 NRBF2 NRBP1 PGR PPARA PPARD PPARG RARA RARB RARG RORA RORB RORC RXRA RXRB RXRG THRA THRB VDR
+REACTOME_NUCLEOTIDE_EXCISION_REPAIR > Genes involved in Nucleotide Excision Repair CCNH CDK7 DDB1 DDB2 ERCC1 ERCC2 ERCC3 ERCC4 ERCC5 ERCC6 ERCC8 GTF2H1 GTF2H2 GTF2H3 GTF2H4 LIG1 MNAT1 PCNA POLD1 POLD2 POLD3 POLD4 POLE POLE2 POLR2A POLR2B POLR2C POLR2D POLR2E POLR2F POLR2G POLR2H POLR2I POLR2J POLR2K POLR2L RAD23B RFC1 RFC2 RFC3 RFC4 RFC5 RPA1 RPA2 RPA3 TCEA1 XAB2 XPA XPC
+REACTOME_NUCLEOTIDE_LIKE_PURINERGIC_RECEPTORS > Genes involved in Nucleotide-like (purinergic) receptors ADORA1 ADORA2A ADORA2B ADORA3 GPR17 LPAR4 LPAR6 P2RY1 P2RY10 P2RY11 P2RY12 P2RY13 P2RY14 P2RY2 P2RY4 P2RY6 P2RY8
+REACTOME_OLFACTORY_SIGNALING_PATHWAY > Genes involved in Olfactory Signaling Pathway GNAL GNB1 GNGT1 OR10A2 OR10A3 OR10A4 OR10A5 OR10A6 OR10A7 OR10AD1 OR10AG1 OR10C1 OR10D4P OR10G2 OR10G3 OR10G4 OR10G6 OR10G7 OR10G8 OR10G9 OR10H1 OR10H2 OR10H3 OR10H4 OR10H5 OR10J1 OR10J3 OR10J4 OR10J5 OR10J6P OR10K1 OR10K2 OR10P1 OR10Q1 OR10R2 OR10S1 OR10T2 OR10V1 OR10W1 OR10X1 OR10Z1 OR14A2 OR14C36 OR14I1 OR14J1 OR1A1 OR1A2 OR1B1 OR1C1 OR1D2 OR1D4 OR1D5 OR1E1 OR1E2 OR1F1 OR1F12 OR1F2P OR1G1 OR1I1 OR1J1 [...]
+REACTOME_OPIOID_SIGNALLING > Genes involved in Opioid Signalling ADCY1 ADCY10 ADCY2 ADCY3 ADCY4 ADCY5 ADCY6 ADCY7 ADCY8 ADCY9 ADRBK1 CALM1 CALM2 CALM3 CAMK4 CDK5 CREB1 GNA11 GNA14 GNA15 GNAI1 GNAI2 GNAI3 GNAL GNAO1 GNAQ GNAT1 GNAT2 GNAT3 GNAZ GNB1 GNB2 GNB3 GNB4 GNB5 GNG10 GNG11 GNG12 GNG13 GNG2 GNG3 GNG4 GNG5 GNG7 GNG8 GNGT1 GNGT2 ITPR1 ITPR2 ITPR3 OPRM1 PDE1A PDE1B PDE1C PDE4A PDE4B PDE4C PDE4D PDYN PLA2G4A PLCB1 PLCB2 PLCB3 PLCB4 POMC PPP1CA PPP1R1B PPP2CA PPP2CB PPP2R1A PPP2R1B PPP2R [...]
+REACTOME_OPSINS > Genes involved in Opsins OPN1LW OPN1MW OPN1MW2 OPN1SW OPN3 OPN4 OPN5 RGR RHO RRH
+REACTOME_ORC1_REMOVAL_FROM_CHROMATIN > Genes involved in Orc1 removal from chromatin CCNA1 CCNA2 CDC6 CDK2 CDKN1A CDT1 FZR1 MCM2 MCM3 MCM4 MCM5 MCM6 MCM7 MCM8 ORC1L ORC2L ORC3L ORC4L ORC5L ORC6L PSMA1 PSMA2 PSMA3 PSMA4 PSMA5 PSMA6 PSMA7 PSMB1 PSMB10 PSMB2 PSMB3 PSMB4 PSMB5 PSMB6 PSMB7 PSMB8 PSMB9 PSMC1 PSMC2 PSMC3 PSMC4 PSMC5 PSMC6 PSMD1 PSMD10 PSMD11 PSMD12 PSMD13 PSMD14 PSMD2 PSMD3 PSMD4 PSMD5 PSMD6 PSMD7 PSMD8 PSMD9 PSME1 PSME2 PSME3 PSMF1 RB1 UBB
+REACTOME_OTHER_SEMAPHORIN_INTERACTIONS > Genes involved in Other semaphorin interactions ITGA1 ITGB1 PLXNA1 PLXNA2 PLXNA4 PLXNB3 PLXNC1 PLXND1 SEMA3E SEMA4A SEMA5A SEMA6A SEMA6D SEMA7A TREM2 TYROBP
+REACTOME_P130CAS_LINKAGE_TO_MAPK_SIGNALING_FOR_INTEGRINS > Genes involved in p130Cas linkage to MAPK signaling for integrins APBB1IP BCAR1 CRK FGA FGB FGG FN1 ITGA2B ITGB3 PTK2 RAP1A RAP1B SRC TLN1 VWF
+REACTOME_P2Y_RECEPTORS > Genes involved in P2Y receptors GPR17 LPAR4 LPAR6 P2RY1 P2RY10 P2RY11 P2RY12 P2RY13 P2RY14 P2RY2 P2RY4 P2RY6 P2RY8
+REACTOME_P38MAPK_EVENTS > Genes involved in p38MAPK events HRAS KRAS MAPK11 MAPK12 MAPK13 MAPK14 MAPKAPK2 MAPKAPK3 NRAS RALA RALB RALGDS SRC
+REACTOME_P53_INDEPENDENT_DNA_DAMAGE_RESPONSE > Genes involved in p53-Independent DNA Damage Response CDC25A PSMA1 PSMA2 PSMA3 PSMA4 PSMA5 PSMA6 PSMA7 PSMB1 PSMB10 PSMB2 PSMB3 PSMB4 PSMB5 PSMB6 PSMB7 PSMB8 PSMB9 PSMC1 PSMC2 PSMC3 PSMC4 PSMC5 PSMC6 PSMD1 PSMD10 PSMD11 PSMD12 PSMD13 PSMD14 PSMD2 PSMD3 PSMD4 PSMD5 PSMD6 PSMD7 PSMD8 PSMD9 PSME1 PSME2 PSME3 PSMF1 UBB
+REACTOME_P75_NTR_RECEPTOR_MEDIATED_SIGNALLING > Genes involved in p75 NTR receptor-mediated signalling AATF ABR ADAM17 AKAP13 APH1A APH1B ARHGAP4 ARHGDIA ARHGEF1 ARHGEF11 ARHGEF12 ARHGEF16 ARHGEF17 ARHGEF18 ARHGEF2 ARHGEF3 ARHGEF4 ARHGEF6 ARHGEF7 ARHGEF9 BAD BCL2L11 CASP2 CASP3 ECT2 FGD1 FGD2 FGD3 FGD4 HDAC1 HDAC2 HDAC3 IKBKB IRAK1 ITGB3BP ITSN1 KALRN MAG MAGED1 MAPK8 MCF2 MCF2L MYD88 NCSTN NET1 NFKB1 NFKBIA NGEF NGF NGFR NGFRAP1 OBSCN OMG PLEKHG2 PLEKHG5 PRDM4 PREX1 PRKCI PSEN1 PSEN2 PS [...]
+REACTOME_P75NTR_RECRUITS_SIGNALLING_COMPLEXES > Genes involved in p75NTR recruits signalling complexes IKBKB IRAK1 MYD88 NGF NGFR PRKCI RIPK2 SQSTM1 TRAF6 UBB
+REACTOME_P75NTR_SIGNALS_VIA_NFKB > Genes involved in p75NTR signals via NF-kB IKBKB IRAK1 MYD88 NFKB1 NFKBIA NGF NGFR PRKCI RELA RIPK2 SQSTM1 TRAF6 UBB
+REACTOME_PACKAGING_OF_TELOMERE_ENDS > Genes involved in Packaging Of Telomere Ends ACD H2AFB1 H2AFX H2AFZ H2BFS HIST1H2AB HIST1H2AC HIST1H2AD HIST1H2AE HIST1H2AK HIST1H2BA HIST1H2BB HIST1H2BC HIST1H2BD HIST1H2BE HIST1H2BF HIST1H2BG HIST1H2BH HIST1H2BI HIST1H2BJ HIST1H2BK HIST1H2BL HIST1H2BM HIST1H2BN HIST1H2BO HIST1H4A HIST1H4B HIST1H4C HIST1H4D HIST1H4E HIST1H4F HIST1H4H HIST1H4I HIST1H4J HIST1H4K HIST1H4L HIST2H2AA3 HIST2H2AC HIST2H2BE HIST2H4A HIST2H4B HIST3H2BB HIST3H3 HIST4H4 POT1 T [...]
+REACTOME_PD1_SIGNALING > Genes involved in PD-1 signaling CD247 CD274 CD3D CD3E CD3G CD4 CSK HLA-DMA HLA-DMB HLA-DOA HLA-DOB HLA-DPA1 HLA-DPB1 HLA-DQA1 HLA-DQA2 HLA-DQB1 HLA-DRA HLA-DRB1 HLA-DRB3 HLA-DRB5 LCK PDCD1 PDCD1LG2 PTPN11 PTPN6 TRA@ TRB@ TRBC1 TRBV12-3
+REACTOME_PECAM1_INTERACTIONS > Genes involved in PECAM1 interactions FYN INPP5D ITGAV ITGB3 LCK LYN PECAM1 PLCG1 PTPN11 PTPN6 SRC YES1
+REACTOME_PEPTIDE_CHAIN_ELONGATION > Genes involved in Peptide chain elongation EEF1A1 EEF2 FAU RPL10 RPL10A RPL11 RPL12 RPL13 RPL13A RPL14 RPL15 RPL17 RPL18 RPL18A RPL19 RPL21 RPL22 RPL23 RPL23A RPL24 RPL26 RPL26L1 RPL27 RPL27A RPL28 RPL29 RPL3 RPL30 RPL31 RPL32 RPL34 RPL35 RPL35A RPL36 RPL36A RPL37 RPL37A RPL38 RPL39 RPL3L RPL4 RPL41 RPL5 RPL6 RPL7 RPL7A RPL8 RPL9 RPLP0 RPLP1 RPLP2 RPS10 RPS11 RPS12 RPS13 RPS14 RPS15 RPS15A RPS16 RPS17 RPS18 RPS19 RPS2 RPS20 RPS21 RPS23 RPS24 RPS25 RPS2 [...]
+REACTOME_PEPTIDE_LIGAND_BINDING_RECEPTORS > Genes involved in Peptide ligand-binding receptors AGT AGTR1 AGTR2 ANXA1 APLN APLNR AVP AVPR1A AVPR1B AVPR2 BDKRB1 BDKRB2 C3 C3AR1 C5 C5AR1 CCBP2 CCK CCKAR CCKBR CCL11 CCL16 CCL17 CCL19 CCL2 CCL20 CCL21 CCL22 CCL23 CCL25 CCL27 CCL28 CCL3 CCL3L1 CCL3L3 CCL4 CCL5 CCL7 CCR1 CCR10 CCR2 CCR3 CCR4 CCR5 CCR6 CCR7 CCR8 CCR9 CCRL1 CX3CL1 CX3CR1 CXCL1 CXCL10 CXCL11 CXCL12 CXCL13 CXCL16 CXCL2 CXCL3 CXCL5 CXCL6 CXCL9 CXCR1 CXCR2 CXCR3 CXCR4 CXCR5 CXCR6 CXC [...]
+REACTOME_PEROXISOMAL_LIPID_METABOLISM > Genes involved in Peroxisomal lipid metabolism ABCD1 ACAA1 ACOT8 ACOX1 ACOX2 ACOX3 AGPS AMACR CRAT CROT FAR1 FAR2 GNPAT HACL1 HSD17B4 IDH1 PHYH SCP2 SLC25A17 SLC27A2
+REACTOME_PHASE_1_FUNCTIONALIZATION > Genes involved in Phase 1 functionalization CYP1A1 CYP1A2 CYP2A6 CYP2D6 CYP2E1 CYP3A4 CYP4A11 FMO3 MAOA MAOB PTGIS PTGS1 PTGS2 SMOX TBXAS1
+REACTOME_PHASE_1_FUNCTIONALIZATION_OF_COMPOUNDS > Genes involved in Phase 1 - Functionalization of compounds ACSS1 ACSS2 ADH1A ADH1B ADH1C ADH4 ADH6 ADH7 ALDH1A1 ALDH2 CYP11A1 CYP11B1 CYP11B2 CYP17A1 CYP19A1 CYP1A1 CYP1A2 CYP1B1 CYP21A2 CYP24A1 CYP26A1 CYP26B1 CYP26C1 CYP27A1 CYP27B1 CYP2A13 CYP2A6 CYP2B6 CYP2C18 CYP2C19 CYP2C8 CYP2C9 CYP2D6 CYP2E1 CYP2F1 CYP2J2 CYP2R1 CYP2S1 CYP2U1 CYP2W1 CYP39A1 CYP3A4 CYP3A43 CYP3A5 CYP3A7 CYP46A1 CYP4A11 CYP4B1 CYP4F11 CYP4F12 CYP4F2 CYP4F3 CYP4F8 CY [...]
+REACTOME_PHASE_II_CONJUGATION > Genes involved in Phase II conjugation ACSM1 ACSM2B AHCY COMT GCLC GCLM GLYAT GSS GSTA1 GSTA2 GSTA3 GSTA4 GSTA5 GSTM1 GSTM4 GSTM5 GSTO1 GSTO2 GSTP1 MAT1A MAT2A MAT2B MGST1 MGST2 MGST3 MTR NAT1 NAT2 NNMT SLC35D1 SULT1A1 SULT1A2 SULT1A3 SULT1A4 SULT1B1 SULT1C2 SULT1C4 SULT1E1 SULT2A1 SULT2B1 SULT4A1 TPMT UGDH UGP2 UGT1A1 UGT1A3 UGT1A4 UGT1A5 UGT1A6 UGT1A7 UGT1A8 UGT1A9 UGT2A1 UGT2B10 UGT2B11 UGT2B15 UGT2B17 UGT2B28 UGT2B4 UGT2B7
+REACTOME_PHOSPHOLIPASE_CMEDIATED_CASCADE > Genes involved in Phospholipase C-mediated cascade FGF1 FGF10 FGF16 FGF17 FGF18 FGF19 FGF2 FGF20 FGF22 FGF23 FGF3 FGF4 FGF5 FGF6 FGF7 FGF8 FGF9 FGFR1 FGFR2 FGFR3 FGFR4 KL PLCG1
+REACTOME_PHOSPHORYLATION_OF_CD3_AND_TCR_ZETA_CHAINS > Genes involved in Phosphorylation of CD3 and TCR zeta chains CD247 CD3D CD3E CD3G CD4 CSK HLA-DMA HLA-DMB HLA-DOA HLA-DOB HLA-DPA1 HLA-DPB1 HLA-DQA1 HLA-DQA2 HLA-DQB1 HLA-DRA HLA-DRB1 HLA-DRB3 HLA-DRB5 LCK PAG1 PTPRC TRA@ TRB@ TRBC1 TRBV12-3
+REACTOME_PHOSPHORYLATION_OF_THE_APC > Genes involved in Phosphorylation of the APC/C ANAPC1 ANAPC10 ANAPC11 ANAPC2 ANAPC4 ANAPC5 ANAPC7 CCNB1 CDC16 CDC23 CDC26 CDC27 CDK1 PLK1 UBE2C UBE2D1 UBE2E1
+REACTOME_PI3K_AKT_SIGNALLING > Genes involved in PI3K/AKT signalling AKT1 AKT1S1 AKT2 AKT3 BAD CASP9 CDKN1A CDKN1B CHUK CREB1 FOXO1 FOXO3 FOXO4 GSK3A GSK3B IRS1 IRS2 MAPKAP1 MDM2 MLST8 MTOR NGF NR4A1 NTRK1 PDPK1 PHLPP1 PIK3CA PIK3CB PIK3R1 PIK3R2 PTEN RHOA RICTOR RPS6KB2 THEM4 TRIB3 TSC2
+REACTOME_PI3K_CASCADE > Genes involved in PI-3K cascade DOK1 FGF1 FGF10 FGF16 FGF17 FGF18 FGF19 FGF2 FGF20 FGF22 FGF23 FGF3 FGF4 FGF5 FGF6 FGF7 FGF8 FGF9 FGFR1 FGFR2 FGFR3 FGFR4 FRS2 GAB1 GRB2 INS INSR IRS1 IRS2 KL PIK3C3 PIK3CA PIK3CB PIK3R1 PIK3R2 PIK3R4 PTPN11 TLR9
+REACTOME_PKA_ACTIVATION > Genes involved in PKA activation ADCY1 ADCY10 ADCY2 ADCY3 ADCY4 ADCY5 ADCY6 ADCY7 ADCY8 ADCY9 PRKACA PRKACB PRKACG PRKAR1A PRKAR1B PRKAR2A PRKAR2B
+REACTOME_PLATELET_ACTIVATION > Genes involved in Platelet Activation A2M ACTN1 ACTN2 ACTN4 AKT1 AKT2 AKT3 ALB ALDOA APOA1 APP BRPF3 CALM1 CALM2 CALM3 CALU CAP1 CD36 CD63 CD9 CFD CFL1 CLU COL1A1 COL1A2 DAGLA DAGLB DGKA DGKB DGKD DGKE DGKG DGKH DGKI DGKK DGKQ DGKZ EGF F13A1 F2 F2R F2RL2 F2RL3 F5 F8 FCER1G FGA FGB FGG FIGF FLNA FN1 FYN GAS6 GNA11 GNA12 GNA13 GNA14 GNA15 GNAI1 GNAI2 GNAI3 GNAQ GNB1 GNB2 GNB3 GNB4 GNB5 GNG10 GNG11 GNG12 GNG13 GNG2 GNG3 GNG4 GNG5 GNG7 GNG8 GNGT1 GNGT2 GP1BA GP [...]
+REACTOME_PLATELET_ACTIVATION_TRIGGERS > Genes involved in Platelet activation triggers AKT1 AKT2 AKT3 COL1A1 COL1A2 F2 F2R F2RL2 F2RL3 FCER1G FYN GNA11 GNA12 GNA13 GNA14 GNA15 GNAI1 GNAI2 GNAI3 GNAQ GNB1 GNB2 GNB3 GNB4 GNB5 GNG10 GNG11 GNG12 GNG13 GNG2 GNG3 GNG4 GNG5 GNG7 GNG8 GNGT1 GNGT2 GP6 LCP2 LYN MAPK14 P2RY1 P2RY12 PDPK1 PIK3CA PIK3CB PIK3CG PIK3R1 PIK3R5 PIK3R6 PLA2G4A PLCG2 PRKCZ SRC SYK TBXA2R VAV1 VAV2 VAV3
+REACTOME_PLATELET_ADHESION_TO_EXPOSED_COLLAGEN > Genes involved in Platelet Adhesion to exposed collagen CD36 COL1A1 COL1A2 FCER1G FYN GP1BA GP1BB GP5 GP6 GP9 ITGA2 ITGB1 LYN VWF
+REACTOME_PLATELET_AGGREGATION_PLUG_FORMATION > Genes involved in Platelet Aggregation (Plug Formation) ADRA2A ADRA2B ADRA2C APBB1IP BCAR1 CRK CSK FGA FGB FGG FN1 GRB2 ITGA2B ITGB3 PTK2 PTPN1 RAP1A RAP1B RAPGEF3 RAPGEF4 RASGRP2 RASGRP3 SOS1 SRC TLN1 VWF
+REACTOME_PLATELET_DEGRANULATION > Genes involved in Platelet degranulation A2M ACTN1 ACTN2 ACTN4 ALB ALDOA APOA1 APP BRPF3 CALM1 CALM2 CALM3 CALU CAP1 CD36 CD63 CD9 CFD CFL1 CLU EGF F13A1 F5 F8 FGA FGB FGG FIGF FLNA FN1 GAS6 GP1BA GP1BB GP5 GP9 HABP4 HGF HRG HSPA5 IGF1 ITGA2B ITGB3 KNG1 LAMP2 LEFTY2 MMRN1 PDGFA PDGFB PECAM1 PF4 PFN1 PLEK PLG POTEKP PPBP PPIA PROS1 PSAP SCG3 SELP SERPINA1 SERPINE1 SERPINF2 SERPING1 SOD1 SPARC SRGN TF TGFB1 TGFB2 TGFB3 THBS1 THBS2 THBS3 THBS4 TIMP1 TLN1 TM [...]
+REACTOME_PLC_BETA_MEDIATED_EVENTS > Genes involved in PLC beta mediated events ADCY1 ADCY10 ADCY2 ADCY3 ADCY4 ADCY5 ADCY6 ADCY7 ADCY8 ADCY9 ADRBK1 CALM1 CALM2 CALM3 CAMK4 CREB1 GNA11 GNA14 GNA15 GNAQ ITPR1 ITPR2 ITPR3 PDE1A PDE1B PDE1C PLA2G4A PLCB1 PLCB2 PLCB3 PLCB4 PRKACA PRKACB PRKACG PRKAR1A PRKAR1B PRKAR2A PRKAR2B
+REACTOME_PLC_GAMMA1_SIGNALLING > Genes involved in PLC-gamma1 signalling ADCY1 ADCY10 ADCY2 ADCY3 ADCY4 ADCY5 ADCY6 ADCY7 ADCY8 ADCY9 ADRBK1 CALM1 CALM2 CALM3 CAMK4 CREB1 FRS2 ITPR1 ITPR2 ITPR3 NGF NTRK1 PDE1A PDE1B PDE1C PLCG1 PRKACA PRKACB PRKACG PRKAR1A PRKAR1B PRKAR2A PRKAR2B PRKCD PRKCE
+REACTOME_POLYMERASE_SWITCHING > Genes involved in Polymerase switching PCNA POLA1 POLA2 POLD1 POLD2 POLD3 POLD4 PRIM1 PRIM2 RFC1 RFC2 RFC3 RFC4 RFC5
+REACTOME_POST_CHAPERONIN_TUBULIN_FOLDING_PATHWAY > Genes involved in Post-chaperonin tubulin folding pathway TBCA TBCB TBCC TBCD TBCE TUBA1A TUBA1B TUBA1C TUBA3C TUBA3D TUBA4A TUBB1 TUBB2A TUBB2B TUBB2C TUBB3 TUBB4 TUBB4Q TUBB6
+REACTOME_POST_NMDA_RECEPTOR_ACTIVATION_EVENTS > Genes involved in Post NMDA receptor activation events ACTN2 ADCY1 ADCY3 ADCY8 CALM1 CALM2 CALM3 CAMK2A CAMK2B CAMK2D CAMK2G CAMK4 CAMKK1 CREB1 DLG4 GRIN1 GRIN2A GRIN2B GRIN2C GRIN2D HRAS MAPK1 NEFL PDPK1 PRKACB RAF1 RASGRF1 RASGRF2 RPS6KA1 RPS6KA2 RPS6KA3 RPS6KA6
+REACTOME_POST_TRANSLATIONAL_PROTEIN_MODIFICATION > Genes involved in Post-translational protein modification DHPS DOHH DPM1 DPM2 DPM3 EIF5A EIF5A2 F10 F2 F7 F9 FURIN GAS6 GGCX GPAA1 PGAP1 PIGA PIGB PIGC PIGF PIGG PIGH PIGK PIGL PIGM PIGN PIGO PIGP PIGQ PIGS PIGT PIGU PIGV PIGW PIGX PLAUR PROC PROS1 PROZ SEMA6D
+REACTOME_PP2A_MEDIATED_DEPHOSPHORYLATION_OF_KEY_METABOLIC_FACTORS > Genes involved in PP2A-mediated dephosphorylation of key metabolic factors MLXIPL PFKFB1 PFKFB2 PFKFB3 PFKFB4 PPP2CA PPP2CB PPP2R1A PPP2R1B PPP2R5D
+REACTOME_PREFOLDIN_MEDIATED_TRANSFER_OF_SUBSTRATE_TO_CCT_TRIC > Genes involved in Prefoldin mediated transfer of substrate to CCT/TriC ACTB CCT2 CCT3 CCT4 CCT5 CCT6A CCT7 CCT8 PFDN1 PFDN2 PFDN4 PFDN5 PFDN6 TCP1 TUBA1A TUBA1C TUBA3C TUBA3D TUBA4A TUBB1 TUBB2A TUBB2B TUBB2C TUBB3 TUBB4 TUBB4Q TUBB6 VBP1
+REACTOME_PROCESSING_OF_CAPPED_INTRON_CONTAINING_PRE_MRNA > Genes involved in Processing of Capped Intron-Containing Pre-mRNA AAAS CCAR1 CD2BP2 CDC40 CLP1 CPSF1 CPSF2 CPSF3 CPSF7 CSTF1 CSTF2 CSTF3 DDX23 DHX38 DHX9 DNAJC8 EFTUD2 EIF4E FUS GTF2F1 GTF2F2 HNRNPA0 HNRNPA1 HNRNPA2B1 HNRNPA3 HNRNPC HNRNPD HNRNPF HNRNPH1 HNRNPH2 HNRNPK HNRNPL HNRNPM HNRNPR HNRNPU HNRNPUL1 LSM2 MAGOH METTL3 NCBP1 NCBP2 NFX1 NHP2L1 NUDT21 NUP107 NUP133 NUP153 NUP155 NUP160 NUP188 NUP205 NUP210 NUP214 NUP35 NUP37 NU [...]
+REACTOME_PROSTANOID_HORMONES > Genes involved in Prostanoid hormones ABCC1 ALOX5 DPEP2 GGT5 LTA4H LTC4S PTGES3 PTGIS PTGS1 PTGS2 TBXAS1
+REACTOME_PROTEOLYTIC_CLEAVAGE_OF_SNARE_COMPLEX_PROTEINS > Genes involved in Proteolytic cleavage of SNARE complex proteins SNAP25 STX10 STX11 STX12 STX16 STX1A STX1B STX2 STX3 STX4 STX5 STX6 STX7 STX8 VAMP1 VAMP2
+REACTOME_PURINE_METABOLISM > Genes involved in Purine metabolism ADA ADK ADSL ADSS ADSSL1 AMPD1 AMPD2 AMPD3 APRT ATIC DCK DGUOK GART GDA GMPR GMPR2 GMPS HPRT1 IMPDH1 IMPDH2 NT5C NT5C1A NT5C1B NT5C2 NT5E PAICS PFAS PNP PPAT XDH
+REACTOME_PURINE_RIBONUCLEOSIDE_MONOPHOSPHATE_BIOSYNTHESIS > Genes involved in Purine ribonucleoside monophosphate biosynthesis ADSL ADSS ADSSL1 ATIC GART GMPS IMPDH1 IMPDH2 PAICS PFAS PPAT
+REACTOME_PURINE_SALVAGE_REACTIONS > Genes involved in Purine salvage reactions ADA ADK AMPD1 AMPD2 AMPD3 APRT DCK DGUOK GMPR GMPR2 HPRT1 PNP
+REACTOME_PYRIMIDINE_CATABOLISM > Genes involved in Pyrimidine catabolism DPYD DPYS NT5C NT5C1A NT5C3 NT5E NT5M TYMP UPB1 UPP1
+REACTOME_PYRIMIDINE_METABOLISM > Genes involved in Pyrimidine metabolism CAD CDA DCK DCTD DHODH DPYD DPYS DUT NT5C NT5C1A NT5C3 NT5E NT5M TK1 TK2 TYMP TYMS UCK1 UCK2 UMPS UPB1 UPP1
+REACTOME_PYRUVATE_METABOLISM > Genes involved in Pyruvate metabolism BSG DLAT DLD LDHA LDHB PDHA1 PDHB PDHX PDK1 PDK2 PDK3 PDK4 PDP1 PDP2 PDPR SLC16A1 SLC16A3 SLC16A8
+REACTOME_PYRUVATE_METABOLISM_AND_TCA_CYCLE > Genes involved in Pyruvate metabolism and TCA cycle ACO2 BSG CS DLAT DLD DLST FH IDH2 IDH3A IDH3B IDH3G LDHA LDHB MDH2 NNT OGDH PDHA1 PDHB PDHX PDK1 PDK2 PDK3 PDK4 PDP1 PDP2 PDPR SDHA SDHB SDHC SDHD SLC16A1 SLC16A3 SLC16A8 SUCLA2 SUCLG1 SUCLG2
+REACTOME_RAS_ACTIVATION_UOPN_CA2_INFUX_THROUGH_NMDA_RECEPTOR > Genes involved in Ras activation uopn Ca2+ infux through NMDA receptor ACTN2 CALM1 CALM2 CALM3 CAMK2A CAMK2B CAMK2D CAMK2G DLG4 GRIN1 GRIN2A GRIN2B GRIN2C GRIN2D HRAS NEFL RASGRF1 RASGRF2
+REACTOME_RECRUITMENT_OF_NUMA_TO_MITOTIC_CENTROSOMES > Genes involved in Recruitment of NuMA to mitotic centrosomes CCNB1 CDK1 NEDD1 NUMA1 TUBG1 TUBG2 TUBGCP2 TUBGCP3 TUBGCP4 TUBGCP5 TUBGCP6
+REACTOME_RECYCLING_OF_BILE_ACIDS_AND_SALTS > Genes involved in Recycling of bile acids and salts ABCB11 ABCC3 ALB BAAT FABP6 SLC10A1 SLC10A2 SLC27A5 SLCO1A2 SLCO1B1 SLCO1B3
+REACTOME_REGULATED_PROTEOLYSIS_OF_P75NTR > Genes involved in Regulated proteolysis of p75NTR ADAM17 APH1A APH1B NCSTN NFKB1 NGFR PSEN1 PSEN2 PSENEN RELA TRAF6
+REACTOME_REGULATION_OF_AMPK_ACTIVITY_VIA_LKB1 > Genes involved in Regulation of AMPK activity via LKB1 CAB39 CAB39L PPM1A PRKAA1 PRKAA2 PRKAB1 PRKAB2 PRKAG1 PRKAG2 PRKAG3 RPTOR STK11 STRADA STRADB
+REACTOME_REGULATION_OF_APC_ACTIVATORS_BETWEEN_G1_S_AND_EARLY_ANAPHASE > Genes involved in Regulation of APC/C activators between G1/S and early anaphase ANAPC1 ANAPC10 ANAPC11 ANAPC2 ANAPC4 ANAPC5 ANAPC7 BTRC BUB1B BUB3 CCNA1 CCNA2 CCNB1 CDC16 CDC20 CDC23 CDC26 CDC27 CDK1 CDK2 CUL1 FBXO5 FZR1 MAD2L1 PLK1 PSMA1 PSMA2 PSMA3 PSMA4 PSMA5 PSMA6 PSMA7 PSMB1 PSMB10 PSMB2 PSMB3 PSMB4 PSMB5 PSMB6 PSMB7 PSMB8 PSMB9 PSMC1 PSMC2 PSMC3 PSMC4 PSMC5 PSMC6 PSMD1 PSMD10 PSMD11 PSMD12 PSMD13 PSMD14 PSMD2 [...]
+REACTOME_REGULATION_OF_BETA_CELL_DEVELOPMENT > Genes involved in Regulation of beta-cell development AKT1 AKT2 AKT3 FAU FGF10 FOXA2 FOXA3 FOXO1 GCK HES1 HNF1A HNF1B HNF4A HNF4G IAPP INS INSM1 MAFA NEUROD1 NEUROG3 NKX2-2 NKX6-1 NOTCH1 NR5A2 ONECUT1 ONECUT3 PAX4 PAX6 PDX1 PKLR PTF1A RBPJ RPL10 RPL10A RPL11 RPL12 RPL13 RPL13A RPL14 RPL15 RPL17 RPL18 RPL18A RPL19 RPL21 RPL22 RPL23 RPL23A RPL24 RPL26 RPL26L1 RPL27 RPL27A RPL28 RPL29 RPL3 RPL30 RPL31 RPL32 RPL34 RPL35 RPL35A RPL36 RPL36A RPL37 [...]
+REACTOME_REGULATION_OF_GENE_EXPRESSION_IN_BETA_CELLS > Genes involved in Regulation of gene expression in beta cells AKT1 AKT2 AKT3 FAU FOXA2 FOXA3 FOXO1 GCK HNF1A HNF4A HNF4G IAPP INS MAFA NKX2-2 NKX6-1 PAX6 PDX1 PKLR RPL10 RPL10A RPL11 RPL12 RPL13 RPL13A RPL14 RPL15 RPL17 RPL18 RPL18A RPL19 RPL21 RPL22 RPL23 RPL23A RPL24 RPL26 RPL26L1 RPL27 RPL27A RPL28 RPL29 RPL3 RPL30 RPL31 RPL32 RPL34 RPL35 RPL35A RPL36 RPL36A RPL37 RPL37A RPL38 RPL39 RPL3L RPL4 RPL41 RPL5 RPL6 RPL7 RPL7A RPL8 RPL9 [...]
+REACTOME_REGULATION_OF_GLUCOKINASE_BY_GLUCOKINASE_REGULATORY_PROTEIN > Genes involved in Regulation of Glucokinase by Glucokinase Regulatory Protein AAAS GCK GCKR NUP107 NUP133 NUP153 NUP155 NUP160 NUP188 NUP205 NUP210 NUP214 NUP35 NUP37 NUP43 NUP50 NUP54 NUP62 NUP85 NUP88 NUP93 NUP98 NUPL1 NUPL2 POM121 RAE1 RANBP2 SEH1L TPR
+REACTOME_REGULATION_OF_INSULIN_LIKE_GROWTH_FACTOR_ACTIVITY_BY_INSULIN_LIKE_GROWTH_FACTOR_BINDING_PROTEINS > Genes involved in Regulation of Insulin-like Growth Factor (IGF) Activity by Insulin-like Growth Factor Binding Proteins CTSL1 F2 IGF1 IGF2 IGFALS IGFBP1 IGFBP2 IGFBP3 IGFBP4 IGFBP5 IGFBP6 KLK3 MMP1 MMP2 PAPPA PAPPA2 PLG
+REACTOME_REGULATION_OF_INSULIN_SECRETION > Genes involved in Regulation of Insulin Secretion ABCC8 ACO2 ADCY5 ADCY6 ADCY8 ADRA2A ADRA2C AKAP5 ALDOA ALDOB ALDOC ATP5A1 ATP5B ATP5C1 ATP5D ATP5E ATP5F1 ATP5G1 ATP5H ATP5I ATP5J ATP5J2 ATP5L ATP5O ATP6 ATP8 CACNA1A CACNA1C CACNA1D CACNA1E CACNA2D2 CACNB2 CACNB3 CHRM3 COX1 COX2 COX3 COX4I1 COX5A COX5B COX6A1 COX6B1 COX6C COX7A2L COX7B COX7C COX8A CS CYC1 CYCS DLAT DLD DLST ENO1 ENO2 ENO3 ETFA ETFB ETFDH FFAR1 FH GAPDH GAPDHS GCG GCK GLP1R GNA1 [...]
+REACTOME_REGULATION_OF_INSULIN_SECRETION_BY_ACETYLCHOLINE > Genes involved in Regulation of Insulin Secretion by Acetylcholine CHRM3 GNA11 GNA14 GNA15 GNAI1 GNAI2 GNAO1 GNAQ INS ITPR1 ITPR2 ITPR3 MARCKS PLCB1 PLCB2 PLCB3 PRKCA SNAP25 STX1A STXBP1 SYT5 VAMP2
+REACTOME_REGULATION_OF_INSULIN_SECRETION_BY_FREE_FATTY_ACIDS > Genes involved in Regulation of Insulin Secretion by Free Fatty Acids FFAR1 GNA11 GNA14 GNA15 GNAI1 GNAI2 GNAO1 GNAQ INS ITPR1 ITPR2 ITPR3 PLCB1 PLCB2 PLCB3 SNAP25 STX1A STXBP1 SYT5 VAMP2
+REACTOME_REGULATION_OF_INSULIN_SECRETION_BY_GLUCAGON_LIKE_PEPTIDE_1 > Genes involved in Regulation of Insulin Secretion by Glucagon-like Peptide-1 ABCC8 ADCY5 ADCY6 ADCY8 AKAP5 CACNA1A CACNA1C CACNA1D CACNA1E CACNA2D2 CACNB2 CACNB3 GCG GLP1R GNAI1 GNAI2 GNAO1 GNAS GNB1 GNB2 GNB3 GNB4 GNB5 GNG10 GNG11 GNG12 GNG13 GNG2 GNG3 GNG4 GNG5 GNG7 GNG8 GNGT1 GNGT2 INS IQGAP1 ITPR1 ITPR2 ITPR3 KCNB1 KCNC2 KCNG2 KCNJ11 KCNS3 PRKACA PRKACB PRKACG PRKAR1A PRKAR1B PRKAR2A PRKAR2B RAP1A RAP1B RAPGEF3 RAP [...]
+REACTOME_REGULATION_OF_LIPID_METABOLISM_BY_PEROXISOME_PROLIFERATOR_ACTIVATED_RECEPTOR_ALPHA > Genes involved in Regulation of Lipid Metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha) ABCA1 ABCB4 ACACA ACADM ACOX1 ACSL1 AGT ANGPTL4 APOA1 APOA2 APOA5 CARM1 CD36 CHD9 CPT1A CPT2 CREBBP CYP4A11 CYP4A22 CYP7A1 DGAT1 EHHADH FABP4 FADS1 FADS2 FASN HDAC3 LPL ME1 MED1 MTTP NCOA1 NCOA2 NCOA3 NCOA6 NCOR1 NCOR2 NR1H3 PEX11A PLIN1 PLIN2 PLTP PPARA PRIC285 RXRA SCD SCP2 SIN3A SI [...]
+REACTOME_REGULATION_OF_ORNITHINE_DECARBOXYLASE > Genes involved in Regulation of ornithine decarboxylase (ODC) AZIN1 NQO1 OAZ1 OAZ2 OAZ3 ODC1 PSMA1 PSMA2 PSMA3 PSMA4 PSMA5 PSMA6 PSMA7 PSMB1 PSMB10 PSMB2 PSMB3 PSMB4 PSMB5 PSMB6 PSMB7 PSMB8 PSMB9 PSMC1 PSMC2 PSMC3 PSMC4 PSMC5 PSMC6 PSMD1 PSMD10 PSMD11 PSMD12 PSMD13 PSMD14 PSMD2 PSMD3 PSMD4 PSMD5 PSMD6 PSMD7 PSMD8 PSMD9 PSME1 PSME2 PSME3 PSMF1
+REACTOME_REGULATION_OF_PYRUVATE_DEHYDROGENASE_COMPLEX > Genes involved in Regulation of pyruvate dehydrogenase (PDH) complex DLAT DLD PDHA1 PDHB PDHX PDK1 PDK2 PDK3 PDK4 PDP1 PDP2 PDPR
+REACTOME_REGULATION_OF_RHEB_GTPASE_ACTIVITY_BY_AMPK > Genes involved in Regulation of Rheb GTPase activity by AMPK PRKAA1 PRKAA2 PRKAB1 PRKAB2 PRKAG1 PRKAG2 PRKAG3 RHEB TSC1 TSC2
+REACTOME_REMOVAL_OF_DNA_PATCH_CONTAINING_ABASIC_RESIDUE > Genes involved in Removal of DNA patch containing abasic residue APEX1 CCNO FEN1 MBD4 MPG MUTYH NTHL1 OGG1 POLB POLD1 POLD2 POLD3 POLD4 SMUG1 TDG
+REACTOME_REMOVAL_OF_THE_FLAP_INTERMEDIATE > Genes involved in Removal of the Flap Intermediate DNA2 FEN1 PCNA POLA1 POLA2 POLD1 POLD2 POLD3 POLD4 PRIM1 PRIM2 RPA1 RPA2 RPA3
+REACTOME_REMOVAL_OF_THE_FLAP_INTERMEDIATE_FROM_THE_C_STRAND > Genes involved in Removal of the Flap Intermediate from the C-strand DNA2 FEN1 PCNA POLD1 POLD2 POLD3 POLD4 RPA1 RPA2 RPA3
+REACTOME_REPAIR_SYNTHESIS_OF_PATCH_27_30_BASES_LONG_BY_DNA_POLYMERASE > Genes involved in Repair synthesis of patch ~27-30 bases long by DNA polymerase PCNA POLD1 POLD2 POLD3 POLD4 POLE POLE2 RFC1 RFC2 RFC3 RFC4 RFC5 RPA1 RPA2 RPA3
+REACTOME_RESOLUTION_OF_AP_SITES_VIA_THE_SINGLE_NUCLEOTIDE_REPLACEMENT_PATHWAY > Genes involved in Resolution of AP sites via the single-nucleotide replacement pathway APEX1 CCNO LIG3 MBD4 MPG MUTYH NTHL1 OGG1 POLB SMUG1 TDG XRCC1
+REACTOME_RETROGRADE_NEUROTROPHIN_SIGNALLING > Genes involved in Retrograde neurotrophin signalling AP2A1 AP2A2 AP2B1 AP2M1 AP2S1 CLTA CLTC DNAL4 DNM1 NGF NTRK1 SH3GL2
+REACTOME_REV_MEDIATED_NUCLEAR_EXPORT_OF_HIV1_RNA > Genes involved in Rev-mediated nuclear export of HIV-1 RNA AAAS NUP107 NUP133 NUP153 NUP155 NUP160 NUP188 NUP205 NUP210 NUP214 NUP35 NUP37 NUP43 NUP50 NUP54 NUP62 NUP85 NUP88 NUP93 NUP98 NUPL1 NUPL2 POM121 RAE1 RAN RANBP1 RANBP2 RANGAP1 SEH1L TPR XPO1
+REACTOME_RHO_GTPASE_CYCLE > Genes involved in Rho GTPase cycle A2M ABR AKAP13 ARAP1 ARAP2 ARAP3 ARHGAP1 ARHGAP10 ARHGAP11A ARHGAP11B ARHGAP12 ARHGAP15 ARHGAP17 ARHGAP18 ARHGAP19 ARHGAP20 ARHGAP22 ARHGAP24 ARHGAP25 ARHGAP26 ARHGAP28 ARHGAP29 ARHGAP30 ARHGAP31 ARHGAP32 ARHGAP36 ARHGAP39 ARHGAP4 ARHGAP40 ARHGAP5 ARHGAP6 ARHGAP8 ARHGAP9 ARHGDIA ARHGDIB ARHGDIG ARHGEF11 ARHGEF12 ARHGEF16 ARHGEF17 ARHGEF18 ARHGEF2 ARHGEF3 ARHGEF4 ARHGEF6 ARHGEF7 ARHGEF9 BCR CDC42 CHN1 CHN2 DEPDC1 DEPDC1B DEPDC [...]
+REACTOME_RNA_POL_II_CTD_PHOSPHORYLATION_AND_INTERACTION_WITH_CE > Genes involved in RNA Pol II CTD phosphorylation and interaction with CE CCNH CDK7 ERCC2 ERCC3 GTF2F1 GTF2F2 GTF2H1 GTF2H2 GTF2H3 GTF2H4 MNAT1 POLR2A POLR2B POLR2C POLR2D POLR2E POLR2F POLR2G POLR2H POLR2I POLR2J POLR2K POLR2L RNGTT RNMT SUPT5H
+REACTOME_RNA_POLYMERASE_I_CHAIN_ELONGATION > Genes involved in RNA PolymeraseChain Elongation CBX3 CCNH CDK7 ERCC2 ERCC3 GTF2H1 GTF2H2 GTF2H3 GTF2H4 H3F3A H3F3B HIST1H3A HIST1H3B HIST1H3C HIST1H3E HIST1H3F HIST1H3G HIST1H3H HIST1H3I HIST1H3J HIST2H3A HIST2H3C HIST2H3D MNAT1 POLR1A POLR1B POLR1C POLR1D POLR2H POLR2K TAF1A TAF1B TAF1C UBTF
+REACTOME_RNA_POLYMERASE_I_III_AND_MITOCHONDRIAL_TRANSCRIPTION > Genes involved in RNA Polymerase I, RNA Polymerase III, and Mitochondrial Transcription BDP1 BRF1 BRF2 CBX3 CCNH CDK7 EHMT2 ERCC2 ERCC3 ERCC6 GTF2H1 GTF2H2 GTF2H3 GTF2H4 GTF3A GTF3C1 GTF3C2 GTF3C3 GTF3C4 GTF3C5 H2AFB1 H2AFX H2AFZ H2BFS H3F3A H3F3B HIST1H2AB HIST1H2AC HIST1H2AD HIST1H2AE HIST1H2AK HIST1H2BA HIST1H2BB HIST1H2BC HIST1H2BD HIST1H2BE HIST1H2BF HIST1H2BG HIST1H2BH HIST1H2BI HIST1H2BJ HIST1H2BK HIST1H2BL HIST1H2BM [...]
+REACTOME_RNA_POLYMERASE_I_PROMOTER_CLEARANCE > Genes involved in RNA PolymerasePromoter Clearance CCNH CDK7 EHMT2 ERCC2 ERCC3 ERCC6 GTF2H1 GTF2H2 GTF2H3 GTF2H4 H2AFB1 H2AFX H2AFZ H2BFS H3F3A H3F3B HIST1H2AB HIST1H2AC HIST1H2AD HIST1H2AE HIST1H2AK HIST1H2BA HIST1H2BB HIST1H2BC HIST1H2BD HIST1H2BE HIST1H2BF HIST1H2BG HIST1H2BH HIST1H2BI HIST1H2BJ HIST1H2BK HIST1H2BL HIST1H2BM HIST1H2BN HIST1H2BO HIST1H3A HIST1H3B HIST1H3C HIST1H3E HIST1H3F HIST1H3G HIST1H3H HIST1H3I HIST1H3J HIST1H4A HIST1 [...]
+REACTOME_RNA_POLYMERASE_I_PROMOTER_ESCAPE > Genes involved in RNA Polymerase I Promoter Escape CCNH CDK7 ERCC2 ERCC3 GTF2H1 GTF2H2 GTF2H3 GTF2H4 MNAT1 POLR1A POLR1B POLR1C POLR1D POLR2H POLR2K RRN3 TAF1A TAF1B TAF1C UBTF
+REACTOME_RNA_POLYMERASE_I_PROMOTER_OPENING > Genes involved in RNA Polymerase I Promoter Opening H2AFB1 H2AFX H2AFZ H2BFS H3F3A H3F3B HIST1H2AB HIST1H2AC HIST1H2AD HIST1H2AE HIST1H2AK HIST1H2BA HIST1H2BB HIST1H2BC HIST1H2BD HIST1H2BE HIST1H2BF HIST1H2BG HIST1H2BH HIST1H2BI HIST1H2BJ HIST1H2BK HIST1H2BL HIST1H2BM HIST1H2BN HIST1H2BO HIST1H3A HIST1H3B HIST1H3C HIST1H3E HIST1H3F HIST1H3G HIST1H3H HIST1H3I HIST1H3J HIST1H4A HIST1H4B HIST1H4C HIST1H4D HIST1H4E HIST1H4F HIST1H4H HIST1H4I HIST1 [...]
+REACTOME_RNA_POLYMERASE_I_TRANSCRIPTION_INITIATION > Genes involved in RNA PolymeraseTranscription Initiation CCNH CDK7 EHMT2 ERCC2 ERCC3 ERCC6 GTF2H1 GTF2H2 GTF2H3 GTF2H4 KAT2B MNAT1 POLR1A POLR1B POLR1C POLR1D POLR2H POLR2K RRN3 TAF1A TAF1B TAF1C TTF1 UBTF
+REACTOME_RNA_POLYMERASE_I_TRANSCRIPTION_TERMINATION > Genes involved in RNA PolymeraseTranscription Termination CCNH CDK7 ERCC2 ERCC3 GTF2H1 GTF2H2 GTF2H3 GTF2H4 MNAT1 POLR1A POLR1B POLR1C POLR1D POLR2H POLR2K PTRF TAF1A TAF1B TAF1C TTF1 UBTF
+REACTOME_RNA_POLYMERASE_II_TRANSCRIPTION > Genes involved in RNA Polymerase II Transcription CCNH CCNT1 CCNT2 CDC40 CDK7 CDK9 CLP1 COBRA1 CPSF1 CPSF2 CPSF3 CPSF7 CSTF1 CSTF2 CSTF3 CTDP1 DHX38 ELL ERCC2 ERCC3 GTF2A1 GTF2A2 GTF2B GTF2E1 GTF2E2 GTF2F1 GTF2F2 GTF2H1 GTF2H2 GTF2H3 GTF2H4 MAGOH MNAT1 NCBP1 NCBP2 NFX1 NUDT21 PABPN1 PAPOLA PCF11 POLR2A POLR2B POLR2C POLR2D POLR2E POLR2F POLR2G POLR2H POLR2I POLR2J POLR2K POLR2L RBM8A RDBP RNGTT RNMT RNPS1 SFRS1 SFRS11 SFRS2 SFRS3 SFRS4 SFRS5 SFR [...]
+REACTOME_RNA_POLYMERASE_III_CHAIN_ELONGATION > Genes involved in RNA Polymerase III Chain Elongation LZTS1 POLR2E POLR2F POLR2H POLR2K POLR2L POLR3A POLR3B POLR3D POLR3E POLR3F POLR3H
+REACTOME_RNA_POLYMERASE_III_TRANSCRIPTION > Genes involved in RNA Polymerase III Transcription BDP1 BRF1 BRF2 GTF3A GTF3C1 GTF3C2 GTF3C3 GTF3C4 GTF3C5 LZTS1 NFIA NFIB NFIC NFIX POLR2E POLR2F POLR2H POLR2K POLR2L POLR3A POLR3B POLR3D POLR3E POLR3F POLR3H POU2F1 SNAPC1 SNAPC2 SNAPC3 SNAPC4 SNAPC5 SSB TBP ZNF143
+REACTOME_RNA_POLYMERASE_III_TRANSCRIPTION_INITIATION > Genes involved in RNA Polymerase III Transcription Initiation BDP1 BRF1 BRF2 GTF3A GTF3C1 GTF3C2 GTF3C3 GTF3C4 GTF3C5 LZTS1 POLR2E POLR2F POLR2H POLR2K POLR2L POLR3A POLR3B POLR3D POLR3E POLR3F POLR3H POU2F1 SNAPC1 SNAPC2 SNAPC3 SNAPC4 SNAPC5 TBP ZNF143
+REACTOME_RNA_POLYMERASE_III_TRANSCRIPTION_INITIATION_FROM_TYPE_2_PROMOTER > Genes involved in RNA Polymerase III Transcription Initiation From Type 2 Promoter BDP1 BRF1 GTF3C1 GTF3C2 GTF3C3 GTF3C4 GTF3C5 LZTS1 POLR2E POLR2F POLR2H POLR2K POLR2L POLR3A POLR3B POLR3D POLR3E POLR3F POLR3H TBP
+REACTOME_RNA_POLYMERASE_III_TRANSCRIPTION_INITIATION_FROM_TYPE_3_PROMOTER > Genes involved in RNA Polymerase III Transcription Initiation From Type 3 Promoter BDP1 BRF2 LZTS1 POLR2E POLR2F POLR2H POLR2K POLR2L POLR3A POLR3B POLR3D POLR3E POLR3F POLR3H POU2F1 SNAPC1 SNAPC2 SNAPC3 SNAPC4 SNAPC5 TBP ZNF143
+REACTOME_RNA_POLYMERASE_III_TRANSCRIPTION_TERMINATION > Genes involved in RNA Polymerase III Transcription Termination LZTS1 NFIA NFIB NFIC NFIX POLR2E POLR2F POLR2H POLR2K POLR2L POLR3A POLR3B POLR3D POLR3E POLR3F POLR3H SSB
+REACTOME_S_PHASE > Genes involved in S Phase CCNA1 CCNA2 CCND1 CCNE1 CCNE2 CCNH CDC25A CDC25B CDC45 CDC6 CDK2 CDK4 CDK7 CDKN1A CDT1 CKS1B CUL1 DNA2 FEN1 FZR1 GINS1 GINS2 GINS4 LIG1 MCM2 MCM3 MCM4 MCM5 MCM6 MCM7 MCM8 MNAT1 ORC1L ORC2L ORC3L ORC4L ORC5L ORC6L PCNA POLA1 POLA2 POLD1 POLD2 POLD3 POLD4 POLE POLE2 PRIM1 PRIM2 PSMA1 PSMA2 PSMA3 PSMA4 PSMA5 PSMA6 PSMA7 PSMB1 PSMB10 PSMB2 PSMB3 PSMB4 PSMB5 PSMB6 PSMB7 PSMB8 PSMB9 PSMC1 PSMC2 PSMC3 PSMC4 PSMC5 PSMC6 PSMD1 PSMD10 PSMD11 PSMD12 PSMD [...]
+REACTOME_SCF_BETA_TRCP_MEDIATED_DEGRADATION_OF_EMI1 > Genes involved in SCF-beta-TrCP mediated degradation of Emi1 BTRC CDC20 CUL1 FBXO5 FZR1 PSMA1 PSMA2 PSMA3 PSMA4 PSMA5 PSMA6 PSMA7 PSMB1 PSMB10 PSMB2 PSMB3 PSMB4 PSMB5 PSMB6 PSMB7 PSMB8 PSMB9 PSMC1 PSMC2 PSMC3 PSMC4 PSMC5 PSMC6 PSMD1 PSMD10 PSMD11 PSMD12 PSMD13 PSMD14 PSMD2 PSMD3 PSMD4 PSMD5 PSMD6 PSMD7 PSMD8 PSMD9 PSME1 PSME2 PSME3 PSMF1 SKP1 UBB
+REACTOME_SCF_SKP2_MEDIATED_DEGRADATION_OF_P27_P21 > Genes involved in SCF(Skp2)-mediated degradation of p2721 CCNA1 CCNA2 CCNE1 CCNE2 CDK2 CDKN1A CKS1B CUL1 PSMA1 PSMA2 PSMA3 PSMA4 PSMA5 PSMA6 PSMA7 PSMB1 PSMB10 PSMB2 PSMB3 PSMB4 PSMB5 PSMB6 PSMB7 PSMB8 PSMB9 PSMC1 PSMC2 PSMC3 PSMC4 PSMC5 PSMC6 PSMD1 PSMD10 PSMD11 PSMD12 PSMD13 PSMD14 PSMD2 PSMD3 PSMD4 PSMD5 PSMD6 PSMD7 PSMD8 PSMD9 PSME1 PSME2 PSME3 PSMF1 SKP1 SKP2 UBB
+REACTOME_SEMA3A_PAK_DEPENDENT_AXON_REPULSION > Genes involved in Sema3A PAK dependent Axon repulsion CFL1 FES FYN HSP90AA1 HSP90AB1 LIMK1 NRP1 PAK1 PAK2 PLXNA1 PLXNA2 PLXNA3 PLXNA4 RAC1 SEMA3A
+REACTOME_SEMA3A_PLEXIN_REPULSION_SIGNALING_BY_INHIBITING_INTEGRIN_ADHESION > Genes involved in SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion FARP2 FES FYN NRP1 PIP5K1C PLXNA1 PLXNA2 PLXNA3 PLXNA4 RAC1 RND1 RRAS SEMA3A TLN1
+REACTOME_SEMA4D_IN_SEMAPHORIN_SIGNALING > Genes involved in Sema4D in semaphorin signaling ARHGEF11 ARHGEF12 CD72 CDC42 ERBB2 GRLF1 LIMK1 LIMK2 MET MYH10 MYH11 MYH14 MYH9 MYL12B MYL6 MYL9 PLXNB1 PTPRC RAC1 RAC2 RHOA RHOB RHOC RHOG RND1 ROCK1 ROCK2 RRAS SEMA4D
+REACTOME_SEMA4D_INDUCED_CELL_MIGRATION_AND_GROWTH_CONE_COLLAPSE > Genes involved in Sema4D induced cell migration and growth-cone collapse ARHGEF11 ARHGEF12 CDC42 ERBB2 LIMK1 LIMK2 MYH10 MYH11 MYH14 MYH9 MYL12B MYL6 MYL9 PLXNB1 RAC1 RAC2 RHOA RHOB RHOC RHOG RND1 ROCK1 ROCK2 SEMA4D
+REACTOME_SEMAPHORIN_INTERACTIONS > Genes involved in Semaphorin interactions ARHGEF11 ARHGEF12 CD72 CDC42 CDK5 CDK5R1 CFL1 CRMP1 DPYSL2 DPYSL3 DPYSL4 DPYSL5 ERBB2 FARP2 FES FYN GRLF1 GSK3B HSP90AA1 HSP90AB1 ITGA1 ITGB1 LIMK1 LIMK2 MET MYH10 MYH11 MYH14 MYH9 MYL12B MYL6 MYL9 NRP1 PAK1 PAK2 PIP5K1C PLXNA1 PLXNA2 PLXNA3 PLXNA4 PLXNB1 PLXNB3 PLXNC1 PLXND1 PTPRC RAC1 RAC2 RHOA RHOB RHOC RHOG RND1 ROCK1 ROCK2 RRAS SEMA3A SEMA3E SEMA4A SEMA4D SEMA5A SEMA6A SEMA6D SEMA7A TLN1 TREM2 TYROBP
+REACTOME_SEROTONIN_NEUROTRANSMITTER_RELEASE_CYCLE > Genes involved in Serotonin Neurotransmitter Release Cycle CPLX1 DDC RAB3A RIMS1 SLC18A2 SNAP25 STX1A STXBP1 SYN1 SYN2 SYN3 SYT1 TPH1 VAMP2
+REACTOME_SEROTONIN_RECEPTORS > Genes involved in Serotonin receptors HTR1A HTR1B HTR1D HTR1E HTR1F HTR2A HTR2B HTR2C HTR4 HTR5A HTR6 HTR7
+REACTOME_SHC_MEDIATED_SIGNALLING > Genes involved in SHC-mediated signalling GRB2 HRAS KRAS MAP2K1 MAP2K2 MAPK1 MAPK3 NRAS RAF1 SHC1 SOS1 YWHAB
+REACTOME_SHC_RELATED_EVENTS > Genes involved in SHC-related events GRB2 HRAS INS INSR KRAS MAP2K1 MAP2K2 MAPK1 MAPK3 NRAS RAF1 SHC1 SOS1 YWHAB
+REACTOME_SHCMEDIATED_CASCADE > Genes involved in SHC-mediated cascade FGF1 FGF10 FGF16 FGF17 FGF18 FGF2 FGF20 FGF22 FGF23 FGF3 FGF4 FGF5 FGF6 FGF8 FGF9 FGFR1 FGFR3 GRB2 SHC1 SOS1 SRC
+REACTOME_SIGNAL_AMPLIFICATION > Genes involved in Signal amplification GNA11 GNA13 GNA14 GNA15 GNAI1 GNAI2 GNAI3 GNAQ GNB1 GNB2 GNB3 GNB4 GNB5 GNG10 GNG11 GNG12 GNG13 GNG2 GNG3 GNG4 GNG5 GNG7 GNG8 GNGT1 GNGT2 MAPK14 P2RY1 P2RY12 PLA2G4A SRC TBXA2R
+REACTOME_SIGNAL_ATTENUATION > Genes involved in Signal attenuation CRK DOK1 GRB10 GRB2 INS INSR IRS1 IRS2 MAPK3 SHC1 SOS1
+REACTOME_SIGNALING_BY_BMP > Genes involved in Signaling by BMP ACVR2A ACVR2B BMP2 BMPR1A BMPR1B BMPR2 CER1 CHRDL1 FSTL1 GREM2 NOG SKI SMAD1 SMAD4 SMAD5 SMAD6 SMAD7 SMAD9 SMURF1 SMURF2 UBE2D1 UBE2D3 ZFYVE16
+REACTOME_SIGNALING_BY_EGFR > Genes involved in Signaling by EGFR ADAM10 ADAM12 ADAM17 AP2A1 AP2A2 AP2B1 AP2M1 AP2S1 ARHGEF7 CBL CDC42 CLTA CLTC CSK EGF EGFR EPN1 EPS15 EPS15L1 GAB1 GRB2 HGS HRAS KRAS LRIG1 MAP2K1 MAP2K2 MAPK1 MAPK3 NRAS PAG1 PIK3CA PIK3R1 PLCG1 PTPN11 PXN RAF1 SH3GL2 SH3KBP1 SHC1 SOS1 SPRY1 SPRY2 SRC STAM STAM2 UBB YWHAB
+REACTOME_SIGNALING_BY_NOTCH > Genes involved in Signaling by Notch ADAM10 APH1A APH1B DLL1 DLL4 FURIN JAG1 JAG2 NCSTN NOTCH1 NOTCH2 NOTCH3 NOTCH4 PSEN1 PSEN2 PSENEN
+REACTOME_SIGNALING_BY_PDGF > Genes involved in Signaling by PDGF BCAR1 COL1A1 COL1A2 COL29A1 COL2A1 COL3A1 COL4A1 COL4A2 COL4A3 COL4A4 COL4A5 COL5A1 COL5A2 COL6A1 COL6A2 COL6A3 COL6A6 COL9A1 COL9A2 COL9A3 CRK CRKL FURIN GRB2 GRB7 HRAS KRAS MAP2K1 MAP2K2 MAPK1 MAPK3 NCK1 NCK2 NRAS PDGFA PDGFB PDGFC PDGFD PDGFRA PDGFRB PIK3CA PIK3CB PIK3R1 PIK3R2 PLAT PLCG1 PLG PTPN11 RAF1 RAPGEF1 RASA1 SOS1 SPP1 SRC STAT1 STAT3 STAT5A STAT5B STAT6 THBS1 THBS2 THBS3 THBS4 YWHAB
+REACTOME_SIGNALING_BY_ROBO_RECEPTOR > Genes involved in Signaling by Robo receptor ABL1 ABL2 ARHGAP39 CAP1 CAP2 CDC42 CLASP1 CLASP2 ENAH EVL GPC1 NCK1 NCK2 PAK1 PAK2 PAK3 PAK4 PAK6 PAK7 PFN1 PFN2 RAC1 ROBO1 ROBO2 ROBO3 SLIT2 SOS1 SOS2 SRGAP1 SRGAP2 SRGAP3 VASP
+REACTOME_SIGNALING_BY_TGF_BETA > Genes involved in Signaling by TGF beta FURIN SKI SMAD2 SMAD3 SMAD4 SMAD6 SMAD7 SMURF1 SMURF2 TGFB1 TGFBR1 TGFBR2 UBE2D1 UBE2D3 ZFYVE9
+REACTOME_SIGNALING_BY_VEGF > Genes involved in Signaling by VEGF FIGF FLT1 FLT4 KDR NRP1 NRP2 PDGFC PGF VEGFA VEGFB VEGFC
+REACTOME_SIGNALING_BY_WNT > Genes involved in Signaling by Wnt APC AXIN1 BTRC CSNK1A1 CTNNB1 CUL1 GSK3B PPP2CA PPP2CB PPP2R1A PPP2R1B PPP2R5A PPP2R5B PPP2R5C PPP2R5D PSMA1 PSMA2 PSMA3 PSMA4 PSMA5 PSMA6 PSMA7 PSMB1 PSMB10 PSMB2 PSMB3 PSMB4 PSMB5 PSMB6 PSMB7 PSMB8 PSMB9 PSMC1 PSMC2 PSMC3 PSMC4 PSMC5 PSMC6 PSMD1 PSMD10 PSMD11 PSMD12 PSMD13 PSMD14 PSMD2 PSMD3 PSMD4 PSMD5 PSMD6 PSMD7 PSMD8 PSMD9 PSME1 PSME2 PSME3 PSMF1 SKP1 UBB
+REACTOME_SIGNALING_IN_IMMUNE_SYSTEM > Genes involved in Signaling in Immune system AKT1 AKT2 AKT3 AMICA1 ANGPT1 ANGPT2 ANGPT4 APOB ATF1 ATF2 ATP1B1 ATP1B2 ATP1B3 B2M BCL10 BSG BTLA C1QA C1QB C1QC C1R C1S C2 C3 C4A C5 C6 C7 C8A C8B C8G C9 CARD11 CAV1 CD14 CD160 CD177 CD180 CD19 CD2 CD200 CD200R1 CD226 CD244 CD247 CD274 CD28 CD34 CD3D CD3E CD3G CD4 CD40 CD40LG CD47 CD48 CD58 CD80 CD81 CD84 CD86 CD8A CD8B CD96 CDC42 CDH1 CFB CFD CHUK COL1A1 COL1A2 CREB1 CRTAM CSK CTLA4 CXADR DOK2 DUSP3 DUSP [...]
+REACTOME_SIGNALLING_BY_NGF > Genes involved in Signalling by NGF AATF ABR ADAM17 ADCY1 ADCY10 ADCY2 ADCY3 ADCY4 ADCY5 ADCY6 ADCY7 ADCY8 ADCY9 ADCYAP1 ADCYAP1R1 ADORA2A ADRBK1 AKAP13 AKT1 AKT1S1 AKT2 AKT3 AP2A1 AP2A2 AP2B1 AP2M1 AP2S1 APH1A APH1B ARHGAP4 ARHGDIA ARHGEF1 ARHGEF11 ARHGEF12 ARHGEF16 ARHGEF17 ARHGEF18 ARHGEF2 ARHGEF3 ARHGEF4 ARHGEF6 ARHGEF7 ARHGEF9 ATF1 BAD BCL2L11 BRAF CALM1 CALM2 CALM3 CAMK4 CASP2 CASP3 CASP9 CDKN1A CDKN1B CHUK CLTA CLTC CREB1 CRK DNAL4 DNM1 DUSP3 DUSP4 DUS [...]
+REACTOME_SIGNALLING_TO_ERKS > Genes involved in Signalling to ERKs BRAF CRK FRS2 GRB2 HRAS KIDINS220 KRAS MAP2K1 MAP2K2 MAPK1 MAPK11 MAPK12 MAPK13 MAPK14 MAPK3 MAPKAPK2 MAPKAPK3 NGF NRAS NTRK1 RAF1 RALA RALB RALGDS RAP1A RAPGEF1 RIT1 RIT2 SHC1 SHC2 SHC3 SOS1 SRC YWHAB
+REACTOME_SIGNALLING_TO_P38_VIA_RIT_AND_RIN > Genes involved in Signalling to p38 via RIT and RIN BRAF HRAS KRAS MAP2K1 MAP2K2 MAPK1 MAPK3 NGF NRAS NTRK1 RAF1 RIT1 RIT2 YWHAB
+REACTOME_SIGNALLING_TO_RAS > Genes involved in Signalling to RAS GRB2 HRAS KRAS MAP2K1 MAP2K2 MAPK1 MAPK11 MAPK12 MAPK13 MAPK14 MAPK3 MAPKAPK2 MAPKAPK3 NGF NRAS NTRK1 RAF1 RALA RALB RALGDS SHC1 SHC2 SHC3 SOS1 SRC YWHAB
+REACTOME_SLC_MEDIATED_TRANSMEMBRANE_TRANSPORT > Genes involved in SLC-mediated transmembrane transport RHAG RHBG RHCG SLC10A6 SLC11A1 SLC11A2 SLC12A1 SLC12A2 SLC12A3 SLC12A4 SLC12A5 SLC12A6 SLC12A7 SLC13A1 SLC13A2 SLC13A3 SLC13A4 SLC13A5 SLC14A1 SLC14A2 SLC15A1 SLC15A2 SLC15A3 SLC15A4 SLC16A1 SLC16A10 SLC16A3 SLC16A7 SLC16A8 SLC17A1 SLC17A5 SLC17A6 SLC17A7 SLC17A8 SLC18A1 SLC18A2 SLC1A1 SLC1A2 SLC1A3 SLC1A4 SLC1A5 SLC1A6 SLC1A7 SLC20A1 SLC20A2 SLC22A2 SLC24A1 SLC24A2 SLC24A3 SLC24A4 SLC2 [...]
+REACTOME_SMOOTH_MUSCLE_CONTRACTION > Genes involved in Smooth Muscle Contraction ACTA2 ACTG2 CALD1 CALM1 CALM2 CALM3 ITGA1 ITGB5 LMOD1 MYH11 MYL12B MYL6 MYL6B MYL9 MYLK PXN SORBS1 SORBS3 TLN1 TPM1 TPM2 TPM3 TPM4 VCL
+REACTOME_SNRNP_ASSEMBLY > Genes involved in snRNP Assembly AAAS CLNS1A DDX20 GEMIN4 GEMIN5 GEMIN6 GEMIN7 NCBP1 NCBP2 NUP107 NUP133 NUP153 NUP155 NUP160 NUP188 NUP205 NUP210 NUP214 NUP35 NUP37 NUP43 NUP50 NUP54 NUP62 NUP85 NUP88 NUP93 NUP98 NUPL1 NUPL2 PHAX POM121 PRMT5 RAE1 RANBP2 SEH1L SIP1 SMN1 SMN2 SNRPB SNRPD1 SNRPD2 SNRPD3 SNRPE SNRPF SNRPG SNUPN TGS1 TPR WDR77
+REACTOME_SOS_MEDIATED_SIGNALLING > Genes involved in SOS-mediated signalling GRB2 HRAS IRS1 IRS2 KRAS MAP2K1 MAP2K2 MAPK1 MAPK3 NRAS RAF1 SOS1 YWHAB
+REACTOME_SPHINGOLIPID_METABOLISM > Genes involved in Sphingolipid metabolism ACER1 ACER2 ACER3 COL4A3BP CSNK1G2 DEGS1 DEGS2 KDSR LASS1 LASS2 LASS3 LASS4 LASS5 LASS6 OSBP PPAP2A PPAP2B PPAP2C PPM1L PRKD1 SGMS1 SGMS2 SGPL1 SGPP1 SGPP2 SPHK1 SPHK2 SPTLC1 SPTLC2 SPTLC3 VAPA VAPB
+REACTOME_STABILIZATION_OF_P53 > Genes involved in Stabilization of p53 ATM MDM2 PSMA1 PSMA2 PSMA3 PSMA4 PSMA5 PSMA6 PSMA7 PSMB1 PSMB10 PSMB2 PSMB3 PSMB4 PSMB5 PSMB6 PSMB7 PSMB8 PSMB9 PSMC1 PSMC2 PSMC3 PSMC4 PSMC5 PSMC6 PSMD1 PSMD10 PSMD11 PSMD12 PSMD13 PSMD14 PSMD2 PSMD3 PSMD4 PSMD5 PSMD6 PSMD7 PSMD8 PSMD9 PSME1 PSME2 PSME3 PSMF1 RFWD2 TP53 UBB
+REACTOME_STEROID_HORMONE_BIOSYNTHESIS > Genes involved in Steroid hormone biosynthesis CYP11A1 CYP11B1 CYP11B2 CYP17A1 CYP19A1 CYP21A2 HSD11B1 HSD17B3 HSD3B1 HSD3B2 STAR STARD4 STARD5 STARD6
+REACTOME_STEROID_HORMONES > Genes involved in Steroid hormones CUBN CYP11A1 CYP11B1 CYP11B2 CYP17A1 CYP19A1 CYP21A2 CYP24A1 CYP27B1 CYP2R1 GC HSD11B1 HSD17B3 HSD3B1 HSD3B2 LGMN LRP2 STAR STARD4 STARD5 STARD6
+REACTOME_STEROID_METABOLISM > Genes involved in Steroid metabolism ABCB11 ABCC3 ACOT8 ACOX2 AKR1C4 AKR1D1 ALB AMACR BAAT CH25H CYP11A1 CYP11B1 CYP11B2 CYP17A1 CYP19A1 CYP21A2 CYP27A1 CYP39A1 CYP46A1 CYP51A1 CYP7A1 CYP7B1 CYP8B1 DHCR24 DHCR7 EBP FABP6 FDFT1 GGPS1 HMGCR HMGCS1 HSD11B1 HSD17B3 HSD17B4 HSD17B7 HSD3B1 HSD3B2 HSD3B7 IDI1 IDI2 LBR LSS MVD MVK NSDHL PMVK SC4MOL SC5DL SCP2 SLC10A1 SLC10A2 SLC27A2 SLC27A5 SLCO1A2 SLCO1B1 SLCO1B3 SQLE STAR STARD4 STARD5 STARD6 TM7SF2
+REACTOME_STRIATED_MUSCLE_CONTRACTION > Genes involved in Striated Muscle Contraction ACTN2 ACTN3 DES DMD MYBPC1 MYBPC2 MYBPC3 MYH3 MYH6 MYH8 MYL1 MYL2 MYL3 MYL4 NEB TCAP TMOD1 TNNC1 TNNC2 TNNI1 TNNI2 TNNI3 TNNT1 TNNT2 TNNT3 TPM1 TPM2 TPM3 TPM4 TTN VIM
+REACTOME_SYNTHESIS_AND_INTERCONVERSION_OF_NUCLEOTIDE_DI_AND_TRIPHOSPHATES > Genes involved in Synthesis and interconversion of nucleotide di- and triphosphates AK1 AK2 AK5 CMPK1 CTPS CTPS2 DTYMK GLRX GSR GUK1 NME1 NME2 NME4 RRM1 RRM2 RRM2B TXN TXNRD1
+REACTOME_SYNTHESIS_OF_BILE_ACIDS_AND_BILE_SALTS > Genes involved in Synthesis of bile acids and bile salts ABCB11 ACOT8 ACOX2 AKR1C4 AKR1D1 AMACR BAAT CH25H CYP27A1 CYP39A1 CYP46A1 CYP7A1 CYP7B1 CYP8B1 HSD17B4 HSD3B7 SCP2 SLC27A2 SLC27A5
+REACTOME_SYNTHESIS_OF_BILE_ACIDS_AND_BILE_SALTS_VIA_24_HYDROXYCHOLESTEROL > Genes involved in Synthesis of bile acids and bile salts via 24-hydroxycholesterol AKR1C4 AKR1D1 AMACR CYP27A1 CYP39A1 CYP46A1 CYP8B1 HSD3B7 SLC27A2 SLC27A5
+REACTOME_SYNTHESIS_OF_BILE_ACIDS_AND_BILE_SALTS_VIA_7ALPHA_HYDROXYCHOLESTEROL > Genes involved in Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol ABCB11 ACOT8 ACOX2 AKR1C4 AKR1D1 AMACR BAAT CYP27A1 CYP7A1 CYP8B1 HSD17B4 HSD3B7 SCP2 SLC27A2 SLC27A5
+REACTOME_SYNTHESIS_OF_DNA > Genes involved in Synthesis of DNA CCNA1 CCNA2 CDC45 CDC6 CDK2 CDKN1A CDT1 DNA2 FEN1 FZR1 GINS1 GINS2 GINS4 LIG1 MCM2 MCM3 MCM4 MCM5 MCM6 MCM7 MCM8 ORC1L ORC2L ORC3L ORC4L ORC5L ORC6L PCNA POLA1 POLA2 POLD1 POLD2 POLD3 POLD4 POLE POLE2 PRIM1 PRIM2 PSMA1 PSMA2 PSMA3 PSMA4 PSMA5 PSMA6 PSMA7 PSMB1 PSMB10 PSMB2 PSMB3 PSMB4 PSMB5 PSMB6 PSMB7 PSMB8 PSMB9 PSMC1 PSMC2 PSMC3 PSMC4 PSMC5 PSMC6 PSMD1 PSMD10 PSMD11 PSMD12 PSMD13 PSMD14 PSMD2 PSMD3 PSMD4 PSMD5 PSMD6 PSMD7 [...]
+REACTOME_SYNTHESIS_OF_GLYCOSYLPHOSPHATIDYLINOSITOL > Genes involved in Synthesis of glycosylphosphatidylinositol (GPI) DPM2 PIGA PIGB PIGC PIGF PIGG PIGH PIGL PIGM PIGN PIGO PIGP PIGQ PIGV PIGW PIGX SEMA6D
+REACTOME_SYNTHESIS_OF_GPI_ANCHORED_PROTEINS > Genes involved in Synthesis of GPI-anchored proteins DPM1 DPM2 DPM3 GPAA1 PGAP1 PIGA PIGB PIGC PIGF PIGG PIGH PIGK PIGL PIGM PIGN PIGO PIGP PIGQ PIGS PIGT PIGU PIGV PIGW PIGX PLAUR SEMA6D
+REACTOME_TAT_MEDIATED_HIV1_ELONGATION_ARREST_AND_RECOVERY > Genes involved in Tat-mediated HIV-1 elongation arrest and recovery CCNT1 CDK9 COBRA1 CTDP1 ELL GTF2F1 GTF2F2 POLR2A POLR2B POLR2C POLR2D POLR2E POLR2F POLR2G POLR2H POLR2I POLR2J POLR2K POLR2L RDBP SSRP1 SUPT16H SUPT4H1 SUPT5H TCEA1 TCEB1 TCEB2 TCEB3 TH1L WHSC2
+REACTOME_TCR_SIGNALING > Genes involved in TCR signaling BCL10 CARD11 CD247 CD3D CD3E CD3G CD4 CHUK CSK ENAH EVL FYB GRAP2 HLA-DMA HLA-DMB HLA-DOA HLA-DOB HLA-DPA1 HLA-DPB1 HLA-DQA1 HLA-DQA2 HLA-DQB1 HLA-DRA HLA-DRB1 HLA-DRB3 HLA-DRB5 IKBKB IKBKG INPP5D ITK LAT LCK LCP2 MALT1 MAP3K7 NCK1 NFKB1 NFKBIA PAG1 PAK1 PAK2 PDPK1 PIK3CA PIK3CB PIK3R1 PIK3R2 PLCG1 PRKCQ PTEN PTPRC RELA RIPK2 TAB2 TRA@ TRAF6 TRAT1 TRB@ TRBC1 TRBV12-3 UBE2N UBE2V1 VASP WAS ZAP70
+REACTOME_TELOMERE_MAINTENANCE > Genes involved in Telomere Maintenance ACD DKC1 DNA2 FEN1 H2AFB1 H2AFX H2AFZ H2BFS HIST1H2AB HIST1H2AC HIST1H2AD HIST1H2AE HIST1H2AK HIST1H2BA HIST1H2BB HIST1H2BC HIST1H2BD HIST1H2BE HIST1H2BF HIST1H2BG HIST1H2BH HIST1H2BI HIST1H2BJ HIST1H2BK HIST1H2BL HIST1H2BM HIST1H2BN HIST1H2BO HIST1H4A HIST1H4B HIST1H4C HIST1H4D HIST1H4E HIST1H4F HIST1H4H HIST1H4I HIST1H4J HIST1H4K HIST1H4L HIST2H2AA3 HIST2H2AC HIST2H2BE HIST2H4A HIST2H4B HIST3H2BB HIST3H3 HIST4H4 LIG [...]
+REACTOME_THE_ROLE_OF_NEF_IN_HIV1_REPLICATION_AND_DISEASE_PATHOGENESIS > Genes involved in The role of Nef in HIV-1 replication and disease pathogenesis AP1B1 AP1G1 AP1M1 AP1M2 AP1S1 AP1S2 AP1S3 AP2A1 AP2A2 AP2B1 AP2M1 AP2S1 ARF1 ATP6V1H B2M CD247 CD28 CD4 CD8B DOCK2 ELMO1 FYN HCK HLA-A LCK PACS1 PAK2 RAC1
+REACTOME_THROMBIN_SIGNALLING_THROUGH_PROTEINASE_ACTIVATED_RECEPTORS > Genes involved in Thrombin signalling through proteinase activated receptors (PARs) F2 F2R F2RL2 F2RL3 GNA11 GNA12 GNA13 GNA14 GNA15 GNAQ GNB1 GNB2 GNB3 GNB4 GNB5 GNG10 GNG11 GNG12 GNG13 GNG2 GNG3 GNG4 GNG5 GNG7 GNG8 GNGT1 GNGT2
+REACTOME_THROMBOXANE_SIGNALLING_THROUGH_TP_RECEPTOR > Genes involved in Thromboxane signalling through TP receptor GNA11 GNA13 GNA14 GNA15 GNAQ GNB1 GNB2 GNB3 GNB4 GNB5 GNG10 GNG11 GNG12 GNG13 GNG2 GNG3 GNG4 GNG5 GNG7 GNG8 GNGT1 GNGT2 TBXA2R
+REACTOME_TIE2_SIGNALING > Genes involved in Tie2 Signaling ANGPT1 ANGPT2 ANGPT4 DOK2 GRB14 GRB2 GRB7 HRAS KRAS NRAS PIK3CA PIK3CB PIK3R1 PIK3R2 PTPN11 SHC1 SOS1 TEK
+REACTOME_TIGHT_JUNCTION_INTERACTIONS > Genes involved in Tight junction interactions CLDN1 CLDN10 CLDN11 CLDN12 CLDN14 CLDN15 CLDN16 CLDN17 CLDN18 CLDN19 CLDN2 CLDN20 CLDN22 CLDN23 CLDN3 CLDN4 CLDN5 CLDN6 CLDN7 CLDN8 CLDN9 CRB3 F11R INADL MPP5 PARD3 PARD6A PARD6B PARD6G PRKCI
+REACTOME_TOLL_LIKE_RECEPTOR_3_CASCADE > Genes involved in Toll Like Receptor 3 (TLR3) Cascade ATF1 ATF2 CHUK CREB1 DUSP3 DUSP4 DUSP6 DUSP7 ELK1 FOS IKBKB IKBKE IKBKG IRF3 IRF7 JUN MAP2K1 MAP2K2 MAP2K3 MAP2K4 MAP2K6 MAP2K7 MAP3K7 MAPK1 MAPK10 MAPK11 MAPK14 MAPK3 MAPK7 MAPK8 MAPK9 MAPKAPK2 MAPKAPK3 MEF2A MEF2C NFKB1 NFKB2 NFKBIA NFKBIB PPP2CA PPP2CB PPP2R1A PPP2R1B PPP2R5D RELA RIPK1 RIPK3 RPS6KA1 RPS6KA2 RPS6KA3 RPS6KA5 TAB1 TAB2 TAB3 TBK1 TICAM1 TLR3 TRAF6 UBB
+REACTOME_TOLL_LIKE_RECEPTOR_4_CASCADE > Genes involved in Toll Like Receptor 4 (TLR4) Cascade CD14 CD180 ECSIT IRAK1 IRAK3 IRAK4 IRF3 LBP LY86 LY96 MAP3K1 MYD88 RIPK1 SIGIRR TBK1 TICAM1 TICAM2 TIRAP TLR1 TLR10 TLR2 TLR4 TLR5 TLR6 TLR7 TLR8 TLR9 TRAF6
+REACTOME_TOLL_LIKE_RECEPTOR_9_CASCADE > Genes involved in Toll Like Receptor 9 (TLR9) Cascade ECSIT EEA1 IRAK1 IRAK3 IRAK4 LY96 MAP3K1 MYD88 PIK3C3 PIK3R4 SIGIRR TIRAP TLR1 TLR10 TLR2 TLR4 TLR5 TLR6 TLR7 TLR8 TLR9 TRAF6 ZFYVE20
+REACTOME_TOLL_RECEPTOR_CASCADES > Genes involved in Toll Receptor Cascades ATF1 ATF2 CD14 CD180 CHUK CREB1 DUSP3 DUSP4 DUSP6 DUSP7 ECSIT EEA1 ELK1 FOS IKBKB IKBKE IKBKG IRAK1 IRAK3 IRAK4 IRF3 IRF7 JUN LBP LY86 LY96 MAP2K1 MAP2K2 MAP2K3 MAP2K4 MAP2K6 MAP2K7 MAP3K1 MAP3K7 MAPK1 MAPK10 MAPK11 MAPK14 MAPK3 MAPK7 MAPK8 MAPK9 MAPKAPK2 MAPKAPK3 MEF2A MEF2C MYD88 NFKB1 NFKB2 NFKBIA NFKBIB PIK3C3 PIK3R4 PPP2CA PPP2CB PPP2R1A PPP2R1B PPP2R5D RELA RIPK1 RIPK3 RPS6KA1 RPS6KA2 RPS6KA3 RPS6KA5 SIGIRR [...]
+REACTOME_TRAF6_MEDIATED_INDUCTION_OF_THE_ANTIVIRAL_CYTOKINE_IFN_ALPHA_BETA_CASCADE > Genes involved in TRAF6 Mediated Induction of the antiviral cytokine IFN-alphaeta cascade ATF1 ATF2 CHUK CREB1 DUSP3 DUSP4 DUSP6 DUSP7 ELK1 FOS IKBKB IKBKG JUN MAP2K1 MAP2K2 MAP2K3 MAP2K4 MAP2K6 MAP2K7 MAP3K7 MAPK1 MAPK10 MAPK11 MAPK14 MAPK3 MAPK7 MAPK8 MAPK9 MAPKAPK2 MAPKAPK3 MEF2A MEF2C NFKB1 NFKB2 NFKBIA NFKBIB PPP2CA PPP2CB PPP2R1A PPP2R1B PPP2R5D RELA RPS6KA1 RPS6KA2 RPS6KA3 RPS6KA5 TAB1 TAB2 TAB3 T [...]
+REACTOME_TRAFFICKING_OF_AMPA_RECEPTORS > Genes involved in Trafficking of AMPA receptors AKAP5 AP2A1 AP2A2 AP2B1 AP2M1 AP2S1 CACNG2 CACNG3 CACNG4 CACNG8 CAMK2A CAMK2B CAMK2D CAMK2G DLG1 DLG4 EPB41L1 GRIA1 GRIA2 GRIA3 GRIA4 GRIP1 GRIP2 MDM2 MYO6 NSF PICK1 PRKCA PRKCB PRKCG
+REACTOME_TRAFFICKING_OF_GLUR2_CONTAINING_AMPA_RECEPTORS > Genes involved in Trafficking of GluR2-containing AMPA receptors AP2A1 AP2A2 AP2B1 AP2M1 AP2S1 GRIA1 GRIA2 GRIA3 GRIA4 GRIP1 GRIP2 NSF PICK1 PRKCA PRKCB PRKCG
+REACTOME_TRANSCRIPTION > Genes involved in Transcription BDP1 BRF1 BRF2 CBX3 CCNH CCNT1 CCNT2 CDC40 CDK7 CDK9 CLP1 COBRA1 CPSF1 CPSF2 CPSF3 CPSF7 CSTF1 CSTF2 CSTF3 CTDP1 DHX38 EHMT2 ELL ERCC2 ERCC3 ERCC6 GTF2A1 GTF2A2 GTF2B GTF2E1 GTF2E2 GTF2F1 GTF2F2 GTF2H1 GTF2H2 GTF2H3 GTF2H4 GTF3A GTF3C1 GTF3C2 GTF3C3 GTF3C4 GTF3C5 H2AFB1 H2AFX H2AFZ H2BFS H3F3A H3F3B HIST1H2AB HIST1H2AC HIST1H2AD HIST1H2AE HIST1H2AK HIST1H2BA HIST1H2BB HIST1H2BC HIST1H2BD HIST1H2BE HIST1H2BF HIST1H2BG HIST1H2BH HIST [...]
+REACTOME_TRANSCRIPTION_COUPLED_NER > Genes involved in Transcription-coupled NER (TC-NER) CCNH CDK7 ERCC1 ERCC2 ERCC3 ERCC4 ERCC5 ERCC6 ERCC8 GTF2H1 GTF2H2 GTF2H3 GTF2H4 LIG1 MNAT1 PCNA POLD1 POLD2 POLD3 POLD4 POLE POLE2 POLR2A POLR2B POLR2C POLR2D POLR2E POLR2F POLR2G POLR2H POLR2I POLR2J POLR2K POLR2L RFC1 RFC2 RFC3 RFC4 RFC5 RPA1 RPA2 RPA3 TCEA1 XAB2
+REACTOME_TRANSCRIPTION_OF_THE_HIV_GENOME > Genes involved in Transcription of the HIV genome CCNH CCNT1 CDK7 CDK9 COBRA1 CTDP1 ELL ERCC2 ERCC3 GTF2A1 GTF2A2 GTF2B GTF2E1 GTF2E2 GTF2F1 GTF2F2 GTF2H1 GTF2H2 GTF2H3 GTF2H4 MNAT1 NCBP1 NCBP2 POLR2A POLR2B POLR2C POLR2D POLR2E POLR2F POLR2G POLR2H POLR2I POLR2J POLR2K POLR2L RDBP RNGTT RNMT SSRP1 SUPT16H SUPT4H1 SUPT5H TAF1 TAF10 TAF11 TAF12 TAF13 TAF4 TAF4B TAF5 TAF6 TAF9 TBP TCEA1 TCEB1 TCEB2 TCEB3 TH1L WHSC2
+REACTOME_TRANSFORMATION_OF_LANOSTEROL_TO_CHOLESTEROL > Genes involved in Transformation of lanosterol to cholesterol CYP51A1 DHCR24 DHCR7 EBP HSD17B7 LBR NSDHL SC4MOL SC5DL TM7SF2
+REACTOME_TRANSLATION > Genes involved in Translation EEF1A1 EEF1B2 EEF1D EEF1G EEF2 EIF1AX EIF2B1 EIF2B2 EIF2B3 EIF2B4 EIF2B5 EIF2S1 EIF2S2 EIF2S3 EIF3A EIF3B EIF3C EIF3CL EIF3D EIF3E EIF3F EIF3G EIF3H EIF3I EIF3J EIF3K EIF4A1 EIF4A2 EIF4B EIF4E EIF4EBP1 EIF4G1 EIF4H EIF5 EIF5B ETF1 FAU GSPT2 PABPC1 RPL10 RPL10A RPL11 RPL12 RPL13 RPL13A RPL14 RPL15 RPL17 RPL18 RPL18A RPL19 RPL21 RPL22 RPL23 RPL23A RPL24 RPL26 RPL26L1 RPL27 RPL27A RPL28 RPL29 RPL3 RPL30 RPL31 RPL32 RPL34 RPL35 RPL35A RPL3 [...]
+REACTOME_TRANSLATION_INITIATION_COMPLEX_FORMATION > Genes involved in Translation initiation complex formation EIF1AX EIF2S1 EIF2S2 EIF2S3 EIF3A EIF3B EIF3C EIF3CL EIF3D EIF3E EIF3F EIF3G EIF3H EIF3I EIF3J EIF3K EIF4A1 EIF4A2 EIF4B EIF4E EIF4G1 EIF4H FAU PABPC1 RPS10 RPS11 RPS12 RPS13 RPS14 RPS15 RPS15A RPS16 RPS17 RPS18 RPS19 RPS2 RPS20 RPS21 RPS23 RPS24 RPS25 RPS26 RPS27 RPS27A RPS28 RPS29 RPS3 RPS3A RPS4X RPS4Y1 RPS5 RPS6 RPS7 RPS8 RPS9 RPSA
+REACTOME_TRANSLOCATION_OF_ZAP70_TO_IMMUNOLOGICAL_SYNAPSE > Genes involved in Translocation of ZAP-70 to Immunological synapse CD247 CD3D CD3E CD3G CD4 HLA-DMA HLA-DMB HLA-DOA HLA-DOB HLA-DPA1 HLA-DPB1 HLA-DQA1 HLA-DQA2 HLA-DQB1 HLA-DRA HLA-DRB1 HLA-DRB3 HLA-DRB5 LCK TRA@ TRB@ TRBC1 TRBV12-3 ZAP70
+REACTOME_TRANSMEMBRANE_TRANSPORT_OF_SMALL_MOLECULES > Genes involved in Transmembrane transport of small molecules AAAS ABCA10 ABCA12 ABCA6 ABCA7 ABCD1 ABCD3 APOA1 CFTR G6PC GCK GCKR HK1 HK2 HK3 NUP107 NUP133 NUP153 NUP155 NUP160 NUP188 NUP205 NUP210 NUP214 NUP35 NUP37 NUP43 NUP50 NUP54 NUP62 NUP85 NUP88 NUP93 NUP98 NUPL1 NUPL2 PEX19 PEX3 POM121 RAE1 RANBP2 RHAG RHBG RHCG SEH1L SLC10A6 SLC11A1 SLC11A2 SLC12A1 SLC12A2 SLC12A3 SLC12A4 SLC12A5 SLC12A6 SLC12A7 SLC13A1 SLC13A2 SLC13A3 SLC13A4 [...]
+REACTOME_TRANSMISSION_ACROSS_CHEMICAL_SYNAPSES > Genes involved in Transmission across Chemical Synapses ACHE ACTN2 ADCY1 ADCY3 ADCY8 AKAP5 ALDH2 AP2A1 AP2A2 AP2B1 AP2M1 AP2S1 CACNA1A CACNA1B CACNA1E CACNA2D1 CACNA2D2 CACNA2D3 CACNB1 CACNB2 CACNB3 CACNB4 CACNG2 CACNG3 CACNG4 CACNG8 CALM1 CALM2 CALM3 CAMK2A CAMK2B CAMK2D CAMK2G CAMK4 CAMKK1 CHAT COMT CPLX1 CREB1 DBH DDC DLG1 DLG3 DLG4 EPB41L1 FNBP1L GLS GLUL GNB1 GNB2 GNB3 GNB4 GNB5 GNG10 GNG11 GNG12 GNG13 GNG2 GNG3 GNG4 GNG5 GNG7 GNG8 GN [...]
+REACTOME_TRANSPORT_OF_MATURE_MRNA_DERIVED_FROM_AN_INTRON_CONTAINING_TRANSCRIPT > Genes involved in Transport of Mature mRNA derived from an Intron-Containing Transcript AAAS CDC40 DHX38 EIF4E MAGOH NCBP1 NCBP2 NFX1 NUP107 NUP133 NUP153 NUP155 NUP160 NUP188 NUP205 NUP210 NUP214 NUP35 NUP37 NUP43 NUP50 NUP54 NUP62 NUP85 NUP88 NUP93 NUP98 NUPL1 NUPL2 NXF1 POM121 RAE1 RANBP2 RBM8A RNPS1 SEH1L SFRS1 SFRS11 SFRS2 SFRS3 SFRS4 SFRS5 SFRS6 SFRS7 SFRS9 SRRM1 THOC4 TPR U2AF1 U2AF2 UPF3B
+REACTOME_TRANSPORT_OF_RIBONUCLEOPROTEINS_INTO_THE_HOST_NUCLEUS > Genes involved in Transport of Ribonucleoproteins into the Host Nucleus AAAS KPNA1 KPNB1 NUP107 NUP133 NUP153 NUP155 NUP160 NUP188 NUP205 NUP210 NUP214 NUP35 NUP37 NUP43 NUP50 NUP54 NUP62 NUP85 NUP88 NUP93 NUP98 NUPL1 NUPL2 POM121 RAE1 RANBP2 SEH1L TPR
+REACTOME_TRANSPORT_OF_THE_SLBP_INDEPENDENT_MATURE_MRNA > Genes involved in Transport of the SLBP independent Mature mRNA AAAS EIF4E NCBP1 NCBP2 NUP107 NUP133 NUP153 NUP155 NUP160 NUP188 NUP205 NUP210 NUP214 NUP35 NUP37 NUP43 NUP50 NUP54 NUP62 NUP85 NUP88 NUP93 NUP98 NUPL1 NUPL2 NXF1 POM121 RAE1 RANBP2 SEH1L THOC4 TPR
+REACTOME_TRIACYLGLYCERIDE_BIOSYNTHESIS > Genes involved in Triacylglyceride Biosynthesis ACACB AGPAT1 AGPAT2 AGPAT3 AGPAT4 AGPAT5 DGAT1 FASN GK GPAM GPD1 PPAP2A PPAP2B PPAP2C
+REACTOME_TRKA_SIGNALLING_FROM_THE_PLASMA_MEMBRANE > Genes involved in TRKA signalling from the plasma membrane ADCY1 ADCY10 ADCY2 ADCY3 ADCY4 ADCY5 ADCY6 ADCY7 ADCY8 ADCY9 ADRBK1 AKT1 AKT1S1 AKT2 AKT3 BAD BRAF CALM1 CALM2 CALM3 CAMK4 CASP9 CDKN1A CDKN1B CHUK CREB1 CRK FOXO1 FOXO3 FOXO4 FRS2 GRB2 GSK3A GSK3B HRAS IRS1 IRS2 ITPR1 ITPR2 ITPR3 KIDINS220 KRAS MAP2K1 MAP2K2 MAP2K5 MAPK1 MAPK11 MAPK12 MAPK13 MAPK14 MAPK3 MAPK7 MAPKAP1 MAPKAPK2 MAPKAPK3 MDM2 MLST8 MTOR NGF NR4A1 NRAS NTRK1 PDE1A [...]
+REACTOME_TRNA_AMINOACYLATION > Genes involved in tRNA Aminoacylation AARS AARS2 AIMP1 AIMP2 CARS CARS2 DARS DARS2 EARS2 EEF1E1 EPRS FARS2 FARSA FARSB GARS HARS HARS2 IARS IARS2 KARS LARS LARS2 MARS MARS2 NARS NARS2 PARS2 QARS RARS RARS2 SARS SARS2 TARS TARS2 VARS VARS2 WARS WARS2 YARS YARS2
+REACTOME_UNFOLDED_PROTEIN_RESPONSE > Genes involved in Unfolded Protein Response ATF3 ATF4 ATF6 DDIT3 DNAJB11 DNAJB9 DNAJC3 EDEM1 EIF2AK3 EIF2S1 ERN1 HERPUD1 HSPA5 MBTPS1 MBTPS2 NFYA PDIA6 SERP1 XBP1
+REACTOME_UNWINDING_OF_DNA > Genes involved in Unwinding of DNA CDC45 GINS1 GINS2 GINS4 MCM2 MCM3 MCM4 MCM5 MCM6 MCM7 MCM8
+REACTOME_VIF_MEDIATED_DEGRADATION_OF_APOBEC3G > Genes involved in Vif-mediated degradation of APOBEC3G APOBEC3G CUL5 PSMA1 PSMA2 PSMA3 PSMA4 PSMA5 PSMA6 PSMA7 PSMB1 PSMB10 PSMB2 PSMB3 PSMB4 PSMB5 PSMB6 PSMB7 PSMB8 PSMB9 PSMC1 PSMC2 PSMC3 PSMC4 PSMC5 PSMC6 PSMD1 PSMD10 PSMD11 PSMD12 PSMD13 PSMD14 PSMD2 PSMD3 PSMD4 PSMD5 PSMD6 PSMD7 PSMD8 PSMD9 PSME1 PSME2 PSME3 PSMF1 RBX1 TCEB1 TCEB2 UBB
+REACTOME_VIRAL_DSRNA_TLR3_TRIF_COMPLEX_ACTIVATES_RIP1 > Genes involved in Viral dsRNA:TLR3:TRIF Complex Activates RIP1 CHUK IKBKB IKBKG NFKB1 NFKB2 NFKBIA NFKBIB RELA RIPK1 RIPK3 TICAM1 TLR3
+REACTOME_VIRAL_MESSENGER_RNA_SYNTHESIS > Genes involved in Viral Messenger RNA Synthesis GTF2F1 GTF2F2 POLR2A POLR2B POLR2C POLR2D POLR2E POLR2F POLR2G POLR2H POLR2I POLR2J POLR2K POLR2L
+REACTOME_VIRAL_MRNA_TRANSLATION > Genes involved in Viral mRNA Translation DNAJC3 FAU GRSF1 RPL10 RPL10A RPL11 RPL12 RPL13 RPL13A RPL14 RPL15 RPL17 RPL18 RPL18A RPL19 RPL21 RPL22 RPL23 RPL23A RPL24 RPL26 RPL26L1 RPL27 RPL27A RPL28 RPL29 RPL3 RPL30 RPL31 RPL32 RPL34 RPL35 RPL35A RPL36 RPL36A RPL37 RPL37A RPL38 RPL39 RPL3L RPL4 RPL41 RPL5 RPL6 RPL7 RPL7A RPL8 RPL9 RPLP0 RPLP1 RPLP2 RPS10 RPS11 RPS12 RPS13 RPS14 RPS15 RPS15A RPS16 RPS17 RPS18 RPS19 RPS2 RPS20 RPS21 RPS23 RPS24 RPS25 RPS26 R [...]
+REACTOME_VITAMIN_B5_(PANTOTHENATE)_METABOLISM > Genes involved in Vitamin B5 (pantothenate) metabolism AASDHPPT COASY FASN PANK1 PANK2 PANK3 PANK4 PPCDC PPCS SLC25A16 SLC5A6
+REACTOME_VPR_MEDIATED_NUCLEAR_IMPORT_OF_PICS > Genes involved in Vpr-mediated nuclear import of PICs AAAS BANF1 HMGA1 KPNA1 NUP107 NUP133 NUP153 NUP155 NUP160 NUP188 NUP205 NUP210 NUP214 NUP35 NUP37 NUP43 NUP50 NUP54 NUP62 NUP85 NUP88 NUP93 NUP98 NUPL1 NUPL2 POM121 PSIP1 RAE1 RANBP2 SEH1L TPR
+REACTOME_XENOBIOTICS > Genes involved in Xenobiotics CYP1A1 CYP1A2 CYP2A13 CYP2A6 CYP2B6 CYP2C18 CYP2C19 CYP2C8 CYP2C9 CYP2D6 CYP2E1 CYP2F1 CYP3A4 CYP3A5 CYP3A7
+REACTOME_ZINC_INFLUX_INTO_CELLS_BY_THE_SLC39_GENES_FAMILY > Genes involved in Zinc influx into cells by the SLC39 Genes family SLC39A1 SLC39A10 SLC39A14 SLC39A2 SLC39A3 SLC39A4 SLC39A5 SLC39A6 SLC39A7 SLC39A8
+REACTOME_ZINC_TRANSPORTATION > Genes involved in Zinc transportation SLC30A1 SLC30A2 SLC30A3 SLC30A5 SLC30A6 SLC30A7 SLC30A8 SLC39A1 SLC39A10 SLC39A14 SLC39A2 SLC39A3 SLC39A4 SLC39A5 SLC39A6 SLC39A7 SLC39A8
\ No newline at end of file
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diff --git a/org/broad/igv/maf/MAFConfigurationDialog$3.class b/org/broad/igv/maf/MAFConfigurationDialog$3.class
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index 0000000..2446d28
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diff --git a/org/broad/igv/maf/MAFConfigurationDialog$4.class b/org/broad/igv/maf/MAFConfigurationDialog$4.class
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index 0000000..2f70b54
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diff --git a/org/broad/igv/maf/MAFConfigurationDialog$5.class b/org/broad/igv/maf/MAFConfigurationDialog$5.class
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index 0000000..a093c9b
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diff --git a/org/broad/igv/maf/MAFConfigurationDialog$6.class b/org/broad/igv/maf/MAFConfigurationDialog$6.class
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index 0000000..cb924ef
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diff --git a/org/broad/igv/maf/MAFConfigurationDialog$Category.class b/org/broad/igv/maf/MAFConfigurationDialog$Category.class
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index 0000000..71de4af
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diff --git a/org/broad/igv/maf/MAFConfigurationDialog$SpeciesSelectionPanel$1.class b/org/broad/igv/maf/MAFConfigurationDialog$SpeciesSelectionPanel$1.class
new file mode 100644
index 0000000..7dd3a66
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diff --git a/org/broad/igv/maf/MAFConfigurationDialog$SpeciesSelectionPanel.class b/org/broad/igv/maf/MAFConfigurationDialog$SpeciesSelectionPanel.class
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index 0000000..4836b03
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diff --git a/org/broad/igv/maf/MAFConfigurationDialog.class b/org/broad/igv/maf/MAFConfigurationDialog.class
new file mode 100644
index 0000000..8f06f12
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diff --git a/org/broad/igv/maf/MAFListReader$1.class b/org/broad/igv/maf/MAFListReader$1.class
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index 0000000..7a6831a
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diff --git a/org/broad/igv/maf/MAFListReader.class b/org/broad/igv/maf/MAFListReader.class
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index 0000000..ead1d77
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diff --git a/org/broad/igv/maf/MAFLocalReader.class b/org/broad/igv/maf/MAFLocalReader.class
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index 0000000..44c30b1
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diff --git a/org/broad/igv/maf/MAFManager$1.class b/org/broad/igv/maf/MAFManager$1.class
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index 0000000..c45f4ce
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diff --git a/org/broad/igv/maf/MAFManager.class b/org/broad/igv/maf/MAFManager.class
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index 0000000..cc185c2
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diff --git a/org/broad/igv/maf/MAFReader.class b/org/broad/igv/maf/MAFReader.class
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index 0000000..e27806c
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diff --git a/org/broad/igv/maf/MAFRemoteReader.class b/org/broad/igv/maf/MAFRemoteReader.class
new file mode 100644
index 0000000..a4ba647
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diff --git a/org/broad/igv/maf/MAFRenderer.class b/org/broad/igv/maf/MAFRenderer.class
new file mode 100644
index 0000000..a8af717
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diff --git a/org/broad/igv/maf/MAFTile$Gap.class b/org/broad/igv/maf/MAFTile$Gap.class
new file mode 100644
index 0000000..6fa8dc3
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diff --git a/org/broad/igv/maf/MAFTile$MASequence.class b/org/broad/igv/maf/MAFTile$MASequence.class
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index 0000000..0f37042
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diff --git a/org/broad/igv/maf/MAFTile.class b/org/broad/igv/maf/MAFTile.class
new file mode 100644
index 0000000..3ab871d
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diff --git a/org/broad/igv/maf/MAFTileCodec.class b/org/broad/igv/maf/MAFTileCodec.class
new file mode 100644
index 0000000..6c7d33e
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diff --git a/org/broad/igv/maf/MAFTrack$1.class b/org/broad/igv/maf/MAFTrack$1.class
new file mode 100644
index 0000000..6fe5f4f
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diff --git a/org/broad/igv/maf/MAFTrack$2.class b/org/broad/igv/maf/MAFTrack$2.class
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index 0000000..051b353
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diff --git a/org/broad/igv/maf/MAFTrack.class b/org/broad/igv/maf/MAFTrack.class
new file mode 100644
index 0000000..5ceb891
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diff --git a/org/broad/igv/maf/MAFUtils.class b/org/broad/igv/maf/MAFUtils.class
new file mode 100644
index 0000000..b9b8c36
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diff --git a/org/broad/igv/maf/species.properties b/org/broad/igv/maf/species.properties
new file mode 100644
index 0000000..c7f5972
--- /dev/null
+++ b/org/broad/igv/maf/species.properties
@@ -0,0 +1,62 @@
+#
+# Copyright (c) 2007-2011 by The Broad Institute of MIT and Harvard. All Rights Reserved.
+#
+# This software is licensed under the terms of the GNU Lesser General Public License (LGPL),
+# Version 2.1 which is available at http://www.opensource.org/licenses/lgpl-2.1.php.
+#
+# THE SOFTWARE IS PROVIDED "AS IS." THE BROAD AND MIT MAKE NO REPRESENTATIONS OR
+# WARRANTES OF ANY KIND CONCERNING THE SOFTWARE, EXPRESS OR IMPLIED, INCLUDING,
+# WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR
+# PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER
+# OR NOT DISCOVERABLE. IN NO EVENT SHALL THE BROAD OR MIT, OR THEIR RESPECTIVE
+# TRUSTEES, DIRECTORS, OFFICERS, EMPLOYEES, AND AFFILIATES BE LIABLE FOR ANY DAMAGES
+# OF ANY KIND, INCLUDING, WITHOUT LIMITATION, INCIDENTAL OR CONSEQUENTIAL DAMAGES,
+# ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER
+# THE BROAD OR MIT SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT
+# SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
+#
+
+hg18=Human
+panTro2=Chimp
+gorGor1=Gorilla
+ponAbe2=Orangutan
+rheMac2=Rhesus
+calJac1=Marmoset
+tarSyr1=Tarsier
+micMur1=Mouse Lemur
+otoGar1=Bushbaby
+tupBel1=TreeShrew
+mm9=Mouse
+rn4=Rat
+dipOrd1=Kangaroo Rat
+cavPor3=Guinea Pig
+speTri1=Squirrel
+oryCun1=Rabbit
+ochPri2=Pika
+vicPac1=Alpaca
+turTru1=Dolphin
+bosTau4=Cow
+equCab2=Horse
+felCat3=Cat
+canFam2=Dog
+myoLuc1=Microbat
+pteVam1=Megabat
+eriEur1=Hedgehog
+sorAra1=Shrew
+loxAfr2=Elephant
+proCap1=Rock Hyrax
+echTel1=Tenrec
+dasNov2=Armadillo
+choHof1=Sloth
+monDom4=Opossum
+ornAna1=Platypus
+galGal3=Chicken
+taeGut1=Zebra Finch
+anoCar1=Lizard
+xenTro2=X. tropicalis
+tetNig1=Tetraodon
+fr2=Fugu
+gasAcu1=Stickleback
+oryLat28=Medaka
+danRer5=Zebrafish
+petMar1=Lamprey
diff --git a/org/broad/igv/methyl/BBMethylDataSource$Type.class b/org/broad/igv/methyl/BBMethylDataSource$Type.class
new file mode 100644
index 0000000..7bb9f0b
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diff --git a/org/broad/igv/methyl/BBMethylDataSource$WrappedIterator.class b/org/broad/igv/methyl/BBMethylDataSource$WrappedIterator.class
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index 0000000..c15972b
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diff --git a/org/broad/igv/methyl/BBMethylDataSource.class b/org/broad/igv/methyl/BBMethylDataSource.class
new file mode 100644
index 0000000..69c0a0d
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diff --git a/org/broad/igv/methyl/CachingMethylSource$Bin.class b/org/broad/igv/methyl/CachingMethylSource$Bin.class
new file mode 100644
index 0000000..2b563ae
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diff --git a/org/broad/igv/methyl/CachingMethylSource$BinIterator.class b/org/broad/igv/methyl/CachingMethylSource$BinIterator.class
new file mode 100644
index 0000000..b350bf6
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diff --git a/org/broad/igv/methyl/CachingMethylSource.class b/org/broad/igv/methyl/CachingMethylSource.class
new file mode 100644
index 0000000..9cbc05b
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diff --git a/org/broad/igv/methyl/MethylDataSource.class b/org/broad/igv/methyl/MethylDataSource.class
new file mode 100644
index 0000000..b2826c8
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diff --git a/org/broad/igv/methyl/MethylScore.class b/org/broad/igv/methyl/MethylScore.class
new file mode 100644
index 0000000..f4b47b0
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diff --git a/org/broad/igv/methyl/MethylTrack$1.class b/org/broad/igv/methyl/MethylTrack$1.class
new file mode 100644
index 0000000..e400741
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diff --git a/org/broad/igv/methyl/MethylTrack$Interval.class b/org/broad/igv/methyl/MethylTrack$Interval.class
new file mode 100644
index 0000000..42c0d7c
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diff --git a/org/broad/igv/methyl/MethylTrack.class b/org/broad/igv/methyl/MethylTrack.class
new file mode 100644
index 0000000..4546617
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diff --git a/org/broad/igv/methyl/ZillerDataSource2$RawDataInterval.class b/org/broad/igv/methyl/ZillerDataSource2$RawDataInterval.class
new file mode 100644
index 0000000..565e436
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diff --git a/org/broad/igv/methyl/ZillerDataSource2.class b/org/broad/igv/methyl/ZillerDataSource2.class
new file mode 100644
index 0000000..492a03c
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diff --git a/org/broad/igv/methyl/readme b/org/broad/igv/methyl/readme
new file mode 100644
index 0000000..8f883ec
--- /dev/null
+++ b/org/broad/igv/methyl/readme
@@ -0,0 +1 @@
+Package contains classes, many experimental, for dna methylation displays.
\ No newline at end of file
diff --git a/org/broad/igv/peaks/BedToPeaks$PeakRecord.class b/org/broad/igv/peaks/BedToPeaks$PeakRecord.class
new file mode 100644
index 0000000..bf77422
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diff --git a/org/broad/igv/peaks/BedToPeaks.class b/org/broad/igv/peaks/BedToPeaks.class
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index 0000000..0be51c5
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diff --git a/org/broad/igv/peaks/Peak.class b/org/broad/igv/peaks/Peak.class
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index 0000000..a491b65
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diff --git a/org/broad/igv/peaks/PeakCodec.class b/org/broad/igv/peaks/PeakCodec.class
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index 0000000..a6b1415
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diff --git a/org/broad/igv/peaks/PeakCommandBar$1.class b/org/broad/igv/peaks/PeakCommandBar$1.class
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index 0000000..f847aef
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index 0000000..f106e37
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index 0000000..0b3dfd2
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index 0000000..d56341a
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diff --git a/org/broad/igv/peaks/PeakCommandBar$5.class b/org/broad/igv/peaks/PeakCommandBar$5.class
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index 0000000..5f348b3
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diff --git a/org/broad/igv/peaks/PeakCommandBar$6.class b/org/broad/igv/peaks/PeakCommandBar$6.class
new file mode 100644
index 0000000..9dfab95
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diff --git a/org/broad/igv/peaks/PeakCommandBar$7.class b/org/broad/igv/peaks/PeakCommandBar$7.class
new file mode 100644
index 0000000..c0d79e9
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diff --git a/org/broad/igv/peaks/PeakCommandBar$8.class b/org/broad/igv/peaks/PeakCommandBar$8.class
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index 0000000..0e21229
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diff --git a/org/broad/igv/peaks/PeakCommandBar.class b/org/broad/igv/peaks/PeakCommandBar.class
new file mode 100644
index 0000000..4a458bd
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diff --git a/org/broad/igv/peaks/PeakCommandBar.jfd b/org/broad/igv/peaks/PeakCommandBar.jfd
new file mode 100644
index 0000000..a1ce555
--- /dev/null
+++ b/org/broad/igv/peaks/PeakCommandBar.jfd
@@ -0,0 +1,479 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<java version="1.6.0_26" class="java.beans.XMLDecoder">
+ <object class="com.jformdesigner.model.FormModel">
+ <void property="contentType">
+ <string>form/swing</string>
+ </void>
+ <void property="root">
+ <object class="com.jformdesigner.model.FormRoot">
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.FlowLayout</class>
+ <void method="setProperty">
+ <string>alignment</string>
+ <int>0</int>
+ </void>
+ <void method="setProperty">
+ <string>vgap</string>
+ <int>0</int>
+ </void>
+ </object>
+ <void property="name">
+ <string>this</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.FlowLayout</class>
+ </object>
+ <void property="name">
+ <string>panel3</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string><html>Fold change<br>threshold</string>
+ </void>
+ <void property="name">
+ <string>label1</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JSlider</string>
+ <void method="setProperty">
+ <string>paintTicks</string>
+ <boolean>true</boolean>
+ </void>
+ <void method="setProperty">
+ <string>toolTipText</string>
+ <string>Adjust score threshold</string>
+ </void>
+ <void method="setProperty">
+ <string>majorTickSpacing</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>minorTickSpacing</string>
+ <int>1</int>
+ </void>
+ <void method="setProperty">
+ <string>maximum</string>
+ <int>10</int>
+ </void>
+ <void method="setProperty">
+ <string>value</string>
+ <int>0</int>
+ </void>
+ <void method="setProperty">
+ <string>paintLabels</string>
+ <boolean>true</boolean>
+ </void>
+ <void method="setProperty">
+ <string>preferredSize</string>
+ <object class="java.awt.Dimension">
+ <int>150</int>
+ <int>52</int>
+ </object>
+ </void>
+ <void property="name">
+ <string>foldChangeSlider</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>javax.swing.event.ChangeListener</string>
+ <string>stateChanged</string>
+ <string>foldChangeSliderStateChanged</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.FlowLayout</class>
+ </object>
+ <void property="name">
+ <string>panel2</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string><html>Score<br>threshold</string>
+ </void>
+ <void property="name">
+ <string>label2</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JSlider</string>
+ <void method="setProperty">
+ <string>paintTicks</string>
+ <boolean>true</boolean>
+ </void>
+ <void method="setProperty">
+ <string>toolTipText</string>
+ <string>Adjust score threshold</string>
+ </void>
+ <void method="setProperty">
+ <string>majorTickSpacing</string>
+ <int>20</int>
+ </void>
+ <void method="setProperty">
+ <string>paintLabels</string>
+ <boolean>true</boolean>
+ </void>
+ <void method="setProperty">
+ <string>preferredSize</string>
+ <object class="java.awt.Dimension">
+ <int>150</int>
+ <int>52</int>
+ </object>
+ </void>
+ <void property="name">
+ <string>scoreSlider</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>javax.swing.event.ChangeListener</string>
+ <string>stateChanged</string>
+ <string>scoreSliderStateChanged</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>com.jformdesigner.designer.wrapper.HSpacer</string>
+ <void property="name">
+ <string>hSpacer1</string>
+ </void>
+ </object>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.FlowLayout</class>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object id="EtchedBorder0" class="javax.swing.border.EtchedBorder">
+ <int>0</int>
+ <null/>
+ <null/>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>minimumSize</string>
+ <object class="java.awt.Dimension">
+ <int>250</int>
+ <int>37</int>
+ </object>
+ </void>
+ <void property="name">
+ <string>panel1</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Show:</string>
+ </void>
+ <void property="name">
+ <string>label3</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JRadioButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Peaks</string>
+ </void>
+ <void method="setProperty">
+ <string>$buttonGroup</string>
+ <object class="com.jformdesigner.model.FormReference">
+ <string>buttonGroup1</string>
+ </object>
+ </void>
+ <void property="name">
+ <string>peaksButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>radioButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>peaksButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JRadioButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Signals</string>
+ </void>
+ <void method="setProperty">
+ <string>$buttonGroup</string>
+ <object class="com.jformdesigner.model.FormReference">
+ <string>buttonGroup1</string>
+ </object>
+ </void>
+ <void property="name">
+ <string>signalsButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>radioButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>signalsButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JRadioButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Both</string>
+ </void>
+ <void method="setProperty">
+ <string>$buttonGroup</string>
+ <object class="com.jformdesigner.model.FormReference">
+ <string>buttonGroup1</string>
+ </object>
+ </void>
+ <void property="name">
+ <string>bothButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>radioButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>bothButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>com.jformdesigner.designer.wrapper.HSpacer</string>
+ <void property="name">
+ <string>hSpacer2</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.FlowLayout</class>
+ <void method="setProperty">
+ <string>alignment</string>
+ <int>0</int>
+ </void>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object idref="EtchedBorder0"/>
+ </void>
+ <void property="name">
+ <string>colorByPanel</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Color peaks by:</string>
+ </void>
+ <void property="name">
+ <string>label4</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JRadioButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Factor</string>
+ </void>
+ <void method="setProperty">
+ <string>$buttonGroup</string>
+ <object class="com.jformdesigner.model.FormReference">
+ <string>buttonGroup2</string>
+ </object>
+ </void>
+ <void property="name">
+ <string>colorByScoresButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>colorByActionPeformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JRadioButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Change</string>
+ </void>
+ <void method="setProperty">
+ <string>$buttonGroup</string>
+ <object class="com.jformdesigner.model.FormReference">
+ <string>buttonGroup2</string>
+ </object>
+ </void>
+ <void property="name">
+ <string>colorByChangeButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>colorByActionPeformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Sort</string>
+ </void>
+ <void property="name">
+ <string>sortButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>sortButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <null/>
+ <void method="setProperty">
+ <string>location</string>
+ <object class="java.awt.Point">
+ <int>0</int>
+ <int>0</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>size</string>
+ <object class="java.awt.Dimension">
+ <int>1325</int>
+ <int>55</int>
+ </object>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormNonVisual">
+ <string>javax.swing.ButtonGroup</string>
+ <void property="name">
+ <string>buttonGroup1</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <null/>
+ <void method="setProperty">
+ <string>location</string>
+ <object class="java.awt.Point">
+ <int>0</int>
+ <int>65</int>
+ </object>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormNonVisual">
+ <string>javax.swing.ButtonGroup</string>
+ <void property="name">
+ <string>buttonGroup2</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <null/>
+ <void method="setProperty">
+ <string>location</string>
+ <object class="java.awt.Point">
+ <int>0</int>
+ <int>119</int>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+</java>
diff --git a/org/broad/igv/peaks/PeakControlDialog$1.class b/org/broad/igv/peaks/PeakControlDialog$1.class
new file mode 100644
index 0000000..614e741
Binary files /dev/null and b/org/broad/igv/peaks/PeakControlDialog$1.class differ
diff --git a/org/broad/igv/peaks/PeakControlDialog$2.class b/org/broad/igv/peaks/PeakControlDialog$2.class
new file mode 100644
index 0000000..d4a9606
Binary files /dev/null and b/org/broad/igv/peaks/PeakControlDialog$2.class differ
diff --git a/org/broad/igv/peaks/PeakControlDialog.class b/org/broad/igv/peaks/PeakControlDialog.class
new file mode 100644
index 0000000..c835c10
Binary files /dev/null and b/org/broad/igv/peaks/PeakControlDialog.class differ
diff --git a/org/broad/igv/peaks/PeakControlDialog.jfd b/org/broad/igv/peaks/PeakControlDialog.jfd
new file mode 100644
index 0000000..02d0f28
--- /dev/null
+++ b/org/broad/igv/peaks/PeakControlDialog.jfd
@@ -0,0 +1,243 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<java version="1.6.0_22" class="java.beans.XMLDecoder">
+ <object class="com.jformdesigner.model.FormModel">
+ <void property="contentType">
+ <string>form/swing</string>
+ </void>
+ <void property="root">
+ <object class="com.jformdesigner.model.FormRoot">
+ <void method="add">
+ <object class="com.jformdesigner.model.FormWindow">
+ <string>javax.swing.JDialog</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.BorderLayout</class>
+ </object>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.BorderLayout</class>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="javax.swing.border.EmptyBorder">
+ <object class="java.awt.Insets">
+ <int>12</int>
+ <int>12</int>
+ <int>12</int>
+ <int>12</int>
+ </object>
+ </object>
+ </void>
+ <void property="name">
+ <string>dialogPane</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>com.jformdesigner.runtime.NullLayout</class>
+ </object>
+ <void property="name">
+ <string>contentPanel</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JSlider</string>
+ <void method="setProperty">
+ <string>paintTicks</string>
+ <boolean>true</boolean>
+ </void>
+ <void method="setProperty">
+ <string>paintLabels</string>
+ <boolean>true</boolean>
+ </void>
+ <void method="setProperty">
+ <string>toolTipText</string>
+ <string>Adjust score threshold</string>
+ </void>
+ <void method="setProperty">
+ <string>majorTickSpacing</string>
+ <int>20</int>
+ </void>
+ <void property="name">
+ <string>scoreSlider</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>javax.swing.event.ChangeListener</string>
+ <string>stateChanged</string>
+ <string>scoreSliderStateChanged</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>5</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>15</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>215</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Score threshold:</string>
+ </void>
+ <void property="name">
+ <string>label1</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>5</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>0</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Fold change threshold:</string>
+ </void>
+ <void property="name">
+ <string>label2</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>5</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>85</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JSlider</string>
+ <void method="setProperty">
+ <string>paintTicks</string>
+ <boolean>true</boolean>
+ </void>
+ <void method="setProperty">
+ <string>paintLabels</string>
+ <boolean>true</boolean>
+ </void>
+ <void method="setProperty">
+ <string>toolTipText</string>
+ <string>Adjust score threshold</string>
+ </void>
+ <void method="setProperty">
+ <string>majorTickSpacing</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>minorTickSpacing</string>
+ <int>1</int>
+ </void>
+ <void method="setProperty">
+ <string>maximum</string>
+ <int>10</int>
+ </void>
+ <void method="setProperty">
+ <string>value</string>
+ <int>0</int>
+ </void>
+ <void property="name">
+ <string>foldChangeSlider</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>javax.swing.event.ChangeListener</string>
+ <string>stateChanged</string>
+ <string>foldChangeSliderStateChanged</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>width</string>
+ <int>215</int>
+ </void>
+ <void method="setProperty">
+ <string>height</string>
+ <int>52</int>
+ </void>
+ <void method="setProperty">
+ <string>x</string>
+ <int>5</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>100</int>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>Center</string>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>Center</string>
+ </void>
+ </object>
+ </void>
+ <void property="name">
+ <string>this</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <null/>
+ <void method="setProperty">
+ <string>location</string>
+ <object class="java.awt.Point">
+ <int>0</int>
+ <int>0</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>size</string>
+ <object class="java.awt.Dimension">
+ <int>250</int>
+ <int>205</int>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+</java>
diff --git a/org/broad/igv/peaks/PeakParser.class b/org/broad/igv/peaks/PeakParser.class
new file mode 100644
index 0000000..e0976b3
Binary files /dev/null and b/org/broad/igv/peaks/PeakParser.class differ
diff --git a/org/broad/igv/peaks/PeakRenderer.class b/org/broad/igv/peaks/PeakRenderer.class
new file mode 100644
index 0000000..125d495
Binary files /dev/null and b/org/broad/igv/peaks/PeakRenderer.class differ
diff --git a/org/broad/igv/peaks/PeakTimePlotFrame.class b/org/broad/igv/peaks/PeakTimePlotFrame.class
new file mode 100644
index 0000000..825ae3e
Binary files /dev/null and b/org/broad/igv/peaks/PeakTimePlotFrame.class differ
diff --git a/org/broad/igv/peaks/PeakTimePlotFrame.jfd b/org/broad/igv/peaks/PeakTimePlotFrame.jfd
new file mode 100644
index 0000000..169ce2a
--- /dev/null
+++ b/org/broad/igv/peaks/PeakTimePlotFrame.jfd
@@ -0,0 +1,136 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<java version="1.6.0_22" class="java.beans.XMLDecoder">
+ <object class="com.jformdesigner.model.FormModel">
+ <void property="contentType">
+ <string>form/swing</string>
+ </void>
+ <void property="root">
+ <object class="com.jformdesigner.model.FormRoot">
+ <void method="add">
+ <object class="com.jformdesigner.model.FormWindow">
+ <string>javax.swing.JFrame</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.BorderLayout</class>
+ </object>
+ <void method="setProperty">
+ <string>$sizePolicy</string>
+ <int>1</int>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.BorderLayout</class>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="javax.swing.border.EmptyBorder">
+ <object class="java.awt.Insets">
+ <int>12</int>
+ <int>12</int>
+ <int>12</int>
+ <int>12</int>
+ </object>
+ </object>
+ </void>
+ <void property="name">
+ <string>dialogPane</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.BorderLayout</class>
+ </object>
+ <void property="name">
+ <string>contentPanel</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>Center</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.GridBagLayout</class>
+ <void method="setProperty">
+ <string>$columnSpecs</string>
+ <string>0:1.0, 80</string>
+ </void>
+ <void method="setProperty">
+ <string>$rowSpecs</string>
+ <string>0</string>
+ </void>
+ <void method="setProperty">
+ <string>$hGap</string>
+ <int>5</int>
+ </void>
+ <void method="setProperty">
+ <string>$vGap</string>
+ <int>5</int>
+ </void>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="javax.swing.border.EmptyBorder">
+ <object class="java.awt.Insets">
+ <int>12</int>
+ <int>0</int>
+ <int>0</int>
+ <int>0</int>
+ </object>
+ </object>
+ </void>
+ <void property="name">
+ <string>buttonBar</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>South</string>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>Center</string>
+ </void>
+ </object>
+ </void>
+ <void property="name">
+ <string>this</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <null/>
+ <void method="setProperty">
+ <string>location</string>
+ <object class="java.awt.Point">
+ <int>0</int>
+ <int>0</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>size</string>
+ <object class="java.awt.Dimension">
+ <int>495</int>
+ <int>370</int>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+</java>
diff --git a/org/broad/igv/peaks/PeakToolTip.class b/org/broad/igv/peaks/PeakToolTip.class
new file mode 100644
index 0000000..1403e67
Binary files /dev/null and b/org/broad/igv/peaks/PeakToolTip.class differ
diff --git a/org/broad/igv/peaks/PeakTrack$1.class b/org/broad/igv/peaks/PeakTrack$1.class
new file mode 100644
index 0000000..869c2d1
Binary files /dev/null and b/org/broad/igv/peaks/PeakTrack$1.class differ
diff --git a/org/broad/igv/peaks/PeakTrack$ColorOption.class b/org/broad/igv/peaks/PeakTrack$ColorOption.class
new file mode 100644
index 0000000..3d80dff
Binary files /dev/null and b/org/broad/igv/peaks/PeakTrack$ColorOption.class differ
diff --git a/org/broad/igv/peaks/PeakTrack$InViewInterval.class b/org/broad/igv/peaks/PeakTrack$InViewInterval.class
new file mode 100644
index 0000000..2b060bb
Binary files /dev/null and b/org/broad/igv/peaks/PeakTrack$InViewInterval.class differ
diff --git a/org/broad/igv/peaks/PeakTrack$WrappedDataSource.class b/org/broad/igv/peaks/PeakTrack$WrappedDataSource.class
new file mode 100644
index 0000000..4df6359
Binary files /dev/null and b/org/broad/igv/peaks/PeakTrack$WrappedDataSource.class differ
diff --git a/org/broad/igv/peaks/PeakTrack.class b/org/broad/igv/peaks/PeakTrack.class
new file mode 100644
index 0000000..de96406
Binary files /dev/null and b/org/broad/igv/peaks/PeakTrack.class differ
diff --git a/org/broad/igv/peaks/PeakTrackMenu$1.class b/org/broad/igv/peaks/PeakTrackMenu$1.class
new file mode 100644
index 0000000..f292050
Binary files /dev/null and b/org/broad/igv/peaks/PeakTrackMenu$1.class differ
diff --git a/org/broad/igv/peaks/PeakTrackMenu$2.class b/org/broad/igv/peaks/PeakTrackMenu$2.class
new file mode 100644
index 0000000..9796c16
Binary files /dev/null and b/org/broad/igv/peaks/PeakTrackMenu$2.class differ
diff --git a/org/broad/igv/peaks/PeakTrackMenu$3.class b/org/broad/igv/peaks/PeakTrackMenu$3.class
new file mode 100644
index 0000000..568d57d
Binary files /dev/null and b/org/broad/igv/peaks/PeakTrackMenu$3.class differ
diff --git a/org/broad/igv/peaks/PeakTrackMenu$4.class b/org/broad/igv/peaks/PeakTrackMenu$4.class
new file mode 100644
index 0000000..f7a3148
Binary files /dev/null and b/org/broad/igv/peaks/PeakTrackMenu$4.class differ
diff --git a/org/broad/igv/peaks/PeakTrackMenu$5.class b/org/broad/igv/peaks/PeakTrackMenu$5.class
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index 0000000..7bc304e
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--- /dev/null
+++ b/org/broad/igv/peaks/descriptor.txt
@@ -0,0 +1,4 @@
+timePoints=0,30,60,120
+peaks -- igv (or tdf) file, compressed + time signals
+compressedSignals -- tdf file
+timeSignals -- 4 tdf files
\ No newline at end of file
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--- /dev/null
+++ b/org/broad/igv/sam/notes.txt
@@ -0,0 +1,41 @@
+
+Goal: Do interval queries on BAM files remotely by http.
+
+ reader = new SAMFileReader(url);
+
+ header = reader.getFileHeader()
+
+ reader.query(sequence, start, end, contained)
+
+
+
+Approach: Use byte range request for queries.
+
+ RandomAccessStream
+ / \
+ / \
+ RandomAccessHTTPStream RandomAccessFileStream
+
+
+* readHeader() -- just read from URL connection stream
+
+* query -- replace RandomAccessFile in BlockCompressedInputStream with wrapper class
+
+ uses of RandomAccessFile:
+
+ - close();
+
+ - seek(compressedOffset);
+
+ - read(buffer, offset + bytesRead, length - bytesRead);
+
+ - length()
+ only used to test for EOF
+ mFile.length() == mFile.getFilePointer();
+
+* index ???
+
+ Current implementation uses a MappedByteBuffer & file nio. Its not obvious
+ how to map this to url streams. Would it work to just copy the index file
+ to the client machine, then use the current code on the copied tmp file?
+ Other ideas?
\ No newline at end of file
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+
+ General layout
+ [Header]
+ [Tiles]
+ [Datasets]
+ [Groups]
+ [Master Index]
+
+ Header
+ ------
+ magic number (32 bit int)
+ version (32 bit int
+ index position (64 bit long)
+ index size (bytes) (32 bit int)
+ header size (bytes) (32 bit int -- # of bytes for rest of header).
+ # of window functions
+ [window functions]
+ track type (string)
+ track line (string)
+ # of tracks
+ [track names]
+
+ FixedTile
+ ---------
+ Type
+ # Positions
+ Start location
+ Span
+ Data
+
+ Features
+ ---------
+ magic number (32 bit int) <= 'F','E', 'A', 'T'
+ format (string) <= bed, gff, other
+ [chr (string)
+ start (int)
+ rest of record (string)]
+
+ FeatureIndex
+ ------------
+
+
+ Dataset
+ -------
+ # attributes
+ [attribute key (string)
+ attribute value (string]
+ data type
+ tile width
+ # tiles
+ [tile position
+ tile size (bytes)] <= THIS IS NOT NECCESSARY
+
+ Group
+ ------
+ # attributes
+ [attribute key (string)
+ attribute value (string]
+
+ Master Index
+ -----------
+ feature index position (long) (-1 if no features)
+ # datasets
+ [dataset name (string)
+ position (long)
+ size in bytes (int)] <= THIS IS NOT NECCESSARY
+ # groups
+ [group name
+ position (long)
+ size in bytes (int)] <= THIS IS NOT NECCESSARY
+
+
+
+
+seek(long position)
+read(buffer, offset, length)
+length() <== Only used for testing end of file
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diff --git a/org/broad/igv/tools/IgvToolsGui.jfd b/org/broad/igv/tools/IgvToolsGui.jfd
new file mode 100644
index 0000000..d9e2aaa
--- /dev/null
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+<?xml version="1.0" encoding="UTF-8"?>
+<java version="1.6.0_20" class="java.beans.XMLDecoder">
+ <object class="com.jformdesigner.model.FormModel">
+ <void property="contentType">
+ <string>form/swing</string>
+ </void>
+ <void property="root">
+ <object class="com.jformdesigner.model.FormRoot">
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.GridBagLayout</class>
+ <void method="setProperty">
+ <string>$columnSpecs</string>
+ <string>0, 0</string>
+ </void>
+ <void method="setProperty">
+ <string>$rowSpecs</string>
+ <string>0, 0, 0, 0, 0, 0, 0, 0</string>
+ </void>
+ <void method="setProperty">
+ <string>$vGap</string>
+ <int>10</int>
+ </void>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="javax.swing.border.TitledBorder">
+ <object class="javax.swing.border.EtchedBorder">
+ <int>1</int>
+ <null/>
+ <null/>
+ </object>
+ <string></string>
+ <int>4</int>
+ <int>0</int>
+ <null/>
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+ <void property="name">
+ <string>mainPanel</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.GridBagLayout</class>
+ <void method="setProperty">
+ <string>$columnSpecs</string>
+ <string>0, 0, 0, 0</string>
+ </void>
+ <void method="setProperty">
+ <string>$rowSpecs</string>
+ <string>0, 0, 0, 0, 0</string>
+ </void>
+ </object>
+ <void property="name">
+ <string>requiredPanel</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JComboBox</string>
+ <void property="name">
+ <string>toolCombo</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>toolComboActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>1</int>
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+ <void method="setProperty">
+ <string>vAlign</string>
+ <int>0</int>
+ </void>
+ <void method="setProperty">
+ <string>weightx</string>
+ <double>1.0</double>
+ </void>
+ <void method="setProperty">
+ <string>weighty</string>
+ <double>1.0</double>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Command</string>
+ </void>
+ <void property="name">
+ <string>label1</string>
+ </void>
+ <void method="auxiliary">
+ <void method="setProperty">
+ <string>JavaCodeGenerator.variableLocal</string>
+ <boolean>true</boolean>
+ </void>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>1</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>1</int>
+ </void>
+ <void method="setProperty">
+ <string>hAlign</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>vAlign</string>
+ <int>0</int>
+ </void>
+ <void method="setProperty">
+ <string>weighty</string>
+ <double>1.0</double>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Input File</string>
+ </void>
+ <void property="name">
+ <string>label2</string>
+ </void>
+ <void method="auxiliary">
+ <void method="setProperty">
+ <string>JavaCodeGenerator.variableLocal</string>
+ <boolean>true</boolean>
+ </void>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>1</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>hAlign</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>vAlign</string>
+ <int>0</int>
+ </void>
+ <void method="setProperty">
+ <string>weighty</string>
+ <double>1.0</double>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Output File</string>
+ </void>
+ <void property="name">
+ <string>outputLabel</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>1</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>3</int>
+ </void>
+ <void method="setProperty">
+ <string>hAlign</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>vAlign</string>
+ <int>0</int>
+ </void>
+ <void method="setProperty">
+ <string>weighty</string>
+ <double>1.0</double>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Browse</string>
+ </void>
+ <void property="name">
+ <string>outputButton</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>3</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>3</int>
+ </void>
+ <void method="setProperty">
+ <string>vAlign</string>
+ <int>0</int>
+ </void>
+ <void method="setProperty">
+ <string>weighty</string>
+ <double>1.0</double>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void property="name">
+ <string>inputField</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.FocusListener</string>
+ <string>focusLost</string>
+ <string>inputFieldFocusLost</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>inputFieldActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>2</int>
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+ <void method="setProperty">
+ <string>vAlign</string>
+ <int>0</int>
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+ <void method="setProperty">
+ <string>weightx</string>
+ <double>1.0</double>
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+ <void method="setProperty">
+ <string>weighty</string>
+ <double>1.0</double>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Browse</string>
+ </void>
+ <void property="name">
+ <string>inputButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>inputButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>3</int>
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+ <void method="setProperty">
+ <string>gridy</string>
+ <int>2</int>
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+ <void method="setProperty">
+ <string>vAlign</string>
+ <int>0</int>
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+ <void method="setProperty">
+ <string>weighty</string>
+ <double>1.0</double>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void property="name">
+ <string>outputField</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>3</int>
+ </void>
+ <void method="setProperty">
+ <string>vAlign</string>
+ <int>0</int>
+ </void>
+ <void method="setProperty">
+ <string>weightx</string>
+ <double>1.0</double>
+ </void>
+ <void method="setProperty">
+ <string>weighty</string>
+ <double>1.0</double>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>toolTipText</string>
+ <string>Either a genome ID (e.g. hg18) or the full path to a .genome file.</string>
+ </void>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Genome</string>
+ </void>
+ <void property="name">
+ <string>genomeLabel</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>1</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>4</int>
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+ <void method="setProperty">
+ <string>hAlign</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>vAlign</string>
+ <int>0</int>
+ </void>
+ <void method="setProperty">
+ <string>weighty</string>
+ <double>1.0</double>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void property="name">
+ <string>genomeField</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>4</int>
+ </void>
+ <void method="setProperty">
+ <string>vAlign</string>
+ <int>0</int>
+ </void>
+ <void method="setProperty">
+ <string>weightx</string>
+ <double>1.0</double>
+ </void>
+ <void method="setProperty">
+ <string>weighty</string>
+ <double>1.0</double>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Browse</string>
+ </void>
+ <void property="name">
+ <string>genomeButton</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>3</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>4</int>
+ </void>
+ <void method="setProperty">
+ <string>vAlign</string>
+ <int>0</int>
+ </void>
+ <void method="setProperty">
+ <string>weighty</string>
+ <double>1.0</double>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>1</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>1</int>
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+ <void method="setProperty">
+ <string>weightx</string>
+ <double>1.0</double>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.GridBagLayout</class>
+ <void method="setProperty">
+ <string>$columnSpecs</string>
+ <string>0, 0, 0, 0</string>
+ </void>
+ <void method="setProperty">
+ <string>$rowSpecs</string>
+ <string>0, 0, 0, 0, 0</string>
+ </void>
+ </object>
+ <void method="setProperty">
+ <string>enabled</string>
+ <boolean>true</boolean>
+ </void>
+ <void method="setProperty">
+ <string>font</string>
+ <object class="com.jformdesigner.model.SwingDerivedFont">
+ <null/>
+ <int>65538</int>
+ <int>10</int>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="javax.swing.border.TitledBorder">
+ <null/>
+ <string>Tile and Count Options</string>
+ <int>4</int>
+ <int>2</int>
+ <null/>
+ <null/>
+ </object>
+ </void>
+ <void property="name">
+ <string>tilePanel</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>toolTipText</string>
+ <string><html>Specifies the maximum zoom level to precompute. The default value is 7.<br>To reduce file size at the expense of Iperformance this value can be reduced.</string>
+ </void>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Zoom Levels</string>
+ </void>
+ <void property="name">
+ <string>zoomLabel</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>1</int>
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+ <void method="setProperty">
+ <string>gridy</string>
+ <int>1</int>
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+ <void method="setProperty">
+ <string>hAlign</string>
+ <int>2</int>
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+ <void method="setProperty">
+ <string>vAlign</string>
+ <int>0</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>toolTipText</string>
+ <string>Window functions to use for summarizing data. </string>
+ </void>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Window Functions</string>
+ </void>
+ <void property="name">
+ <string>windowFunctionLabel</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>1</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>2</int>
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+ <void method="setProperty">
+ <string>hAlign</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>vAlign</string>
+ <int>1</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.GridLayout</class>
+ <void method="setProperty">
+ <string>rows</string>
+ <int>2</int>
+ </void>
+ </object>
+ <void property="name">
+ <string>windowFunctionPanel</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JCheckBox</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Min</string>
+ </void>
+ <void property="name">
+ <string>minCheckBox</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JCheckBox</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Max</string>
+ </void>
+ <void property="name">
+ <string>maxCheckBox</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JCheckBox</string>
+ <void method="setProperty">
+ <string>selected</string>
+ <boolean>true</boolean>
+ </void>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Mean</string>
+ </void>
+ <void property="name">
+ <string>meanCheckBox</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JCheckBox</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Median</string>
+ </void>
+ <void property="name">
+ <string>medianCheckBox</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JCheckBox</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>2%</string>
+ </void>
+ <void property="name">
+ <string>a2CheckBox</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JCheckBox</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>10%</string>
+ </void>
+ <void property="name">
+ <string>a10CheckBox</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JCheckBox</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>90%</string>
+ </void>
+ <void property="name">
+ <string>a90CheckBox</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JCheckBox</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>98%</string>
+ </void>
+ <void property="name">
+ <string>a98CheckBox</string>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>weightx</string>
+ <double>1.0</double>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>font</string>
+ <object class="com.jformdesigner.model.SwingDerivedFont">
+ <null/>
+ <int>0</int>
+ <int>0</int>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>toolTipText</string>
+ <string><html>Specifies a "bed" file to be used to map probe identifiers to locations. This option is useful <br>when preprocessing gct files. The bed file should contain 4 columns: chr start end name
+<br>where name is the probe name in the gct file.</string>
+ </void>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Probe to Loci Mapping</string>
+ </void>
+ <void property="name">
+ <string>probeLabel</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>1</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>3</int>
+ </void>
+ <void method="setProperty">
+ <string>hAlign</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>vAlign</string>
+ <int>0</int>
+ </void>
+ <void method="setProperty">
+ <string>weighty</string>
+ <double>1.0</double>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void property="name">
+ <string>probeField</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>3</int>
+ </void>
+ <void method="setProperty">
+ <string>vAlign</string>
+ <int>0</int>
+ </void>
+ <void method="setProperty">
+ <string>weightx</string>
+ <double>1.0</double>
+ </void>
+ <void method="setProperty">
+ <string>weighty</string>
+ <double>1.0</double>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Browse</string>
+ </void>
+ <void property="name">
+ <string>probeButton</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>3</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>3</int>
+ </void>
+ <void method="setProperty">
+ <string>vAlign</string>
+ <int>0</int>
+ </void>
+ <void method="setProperty">
+ <string>weighty</string>
+ <double>1.0</double>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JComboBox</string>
+ <void method="setProperty">
+ <string>editable</string>
+ <boolean>false</boolean>
+ </void>
+ <void method="setProperty">
+ <string>model</string>
+ <object class="javax.swing.DefaultComboBoxModel"/>
+ </void>
+ <void property="name">
+ <string>zoomCombo</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>1</int>
+ </void>
+ <void method="setProperty">
+ <string>hAlign</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>vAlign</string>
+ <int>0</int>
+ </void>
+ <void method="setProperty">
+ <string>weightx</string>
+ <double>1.0</double>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>toolTipText</string>
+ <string>The window size over which coverage computed when using the count command. Defaults to 25 bp.</string>
+ </void>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Window Size</string>
+ </void>
+ <void property="name">
+ <string>windowSizeLabel</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>1</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>4</int>
+ </void>
+ <void method="setProperty">
+ <string>hAlign</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>vAlign</string>
+ <int>0</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void property="name">
+ <string>windowSizeField</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>4</int>
+ </void>
+ <void method="setProperty">
+ <string>vAlign</string>
+ <int>0</int>
+ </void>
+ <void method="setProperty">
+ <string>weightx</string>
+ <double>1.0</double>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>1</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>weightx</string>
+ <double>1.0</double>
+ </void>
+ <void method="setProperty">
+ <string>weighty</string>
+ <double>1.0</double>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.GridBagLayout</class>
+ <void method="setProperty">
+ <string>$columnSpecs</string>
+ <string>0, 0, 0, 0, 0</string>
+ </void>
+ <void method="setProperty">
+ <string>$rowSpecs</string>
+ <string>0, 0, 0</string>
+ </void>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="javax.swing.border.TitledBorder">
+ <null/>
+ <string>Sort Options</string>
+ <int>4</int>
+ <int>2</int>
+ <null/>
+ <null/>
+ </object>
+ </void>
+ <void property="name">
+ <string>sortPanel</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>toolTipText</string>
+ <string><html>Specify a temporary working directory. For large input files this directory will be used to <br>store intermediate results of the sort. The default is the users temp directory.</string>
+ </void>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Temp Directory</string>
+ </void>
+ <void property="name">
+ <string>tmpDirectoryLabel</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>1</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>1</int>
+ </void>
+ <void method="setProperty">
+ <string>hAlign</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>vAlign</string>
+ <int>0</int>
+ </void>
+ <void method="setProperty">
+ <string>weighty</string>
+ <double>1.0</double>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>toolTipText</string>
+ <string><html>The maximum number of records to keep in memory during the sort. The default value is <br>500000. Increase this number if you receive "too many open files" errors. Decrease it if you <br>experience "out of memory" errors.</string>
+ </void>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Max Records</string>
+ </void>
+ <void property="name">
+ <string>maxRecordsLabel</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>1</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>hAlign</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>vAlign</string>
+ <int>0</int>
+ </void>
+ <void method="setProperty">
+ <string>weighty</string>
+ <double>1.0</double>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Browse</string>
+ </void>
+ <void property="name">
+ <string>tempButton</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>4</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>1</int>
+ </void>
+ <void method="setProperty">
+ <string>vAlign</string>
+ <int>0</int>
+ </void>
+ <void method="setProperty">
+ <string>weighty</string>
+ <double>1.0</double>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void property="name">
+ <string>tmpDirectoryField</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>3</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>1</int>
+ </void>
+ <void method="setProperty">
+ <string>vAlign</string>
+ <int>0</int>
+ </void>
+ <void method="setProperty">
+ <string>weightx</string>
+ <double>1.0</double>
+ </void>
+ <void method="setProperty">
+ <string>weighty</string>
+ <double>1.0</double>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void property="name">
+ <string>maxRecordsField</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>3</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>vAlign</string>
+ <int>0</int>
+ </void>
+ <void method="setProperty">
+ <string>weightx</string>
+ <double>1.0</double>
+ </void>
+ <void method="setProperty">
+ <string>weighty</string>
+ <double>1.0</double>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>1</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>3</int>
+ </void>
+ <void method="setProperty">
+ <string>weightx</string>
+ <double>1.0</double>
+ </void>
+ <void method="setProperty">
+ <string>weighty</string>
+ <double>1.0</double>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.GridBagLayout</class>
+ <void method="setProperty">
+ <string>$columnSpecs</string>
+ <string>0, 0, 0</string>
+ </void>
+ <void method="setProperty">
+ <string>$rowSpecs</string>
+ <string>0</string>
+ </void>
+ </object>
+ <void property="name">
+ <string>buttonPanel</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Run</string>
+ </void>
+ <void property="name">
+ <string>runButton</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>vAlign</string>
+ <int>0</int>
+ </void>
+ <void method="setProperty">
+ <string>weighty</string>
+ <double>1.0</double>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Close</string>
+ </void>
+ <void property="name">
+ <string>closeButton</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>1</int>
+ </void>
+ <void method="setProperty">
+ <string>vAlign</string>
+ <int>0</int>
+ </void>
+ <void method="setProperty">
+ <string>weighty</string>
+ <double>1.0</double>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>1</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>4</int>
+ </void>
+ <void method="setProperty">
+ <string>weightx</string>
+ <double>1.0</double>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>com.jformdesigner.runtime.NullLayout</class>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="javax.swing.border.TitledBorder">
+ <object class="javax.swing.border.EmptyBorder">
+ <object class="java.awt.Insets">
+ <int>0</int>
+ <int>0</int>
+ <int>0</int>
+ <int>0</int>
+ </object>
+ </object>
+ <string>Messages</string>
+ <int>4</int>
+ <int>2</int>
+ <null/>
+ <null/>
+ </object>
+ </void>
+ <void property="name">
+ <string>OutputPanel</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JScrollPane</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>javax.swing.JScrollPane</class>
+ </object>
+ <void property="name">
+ <string>outputScroll</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextArea</string>
+ <void method="setProperty">
+ <string>editable</string>
+ <boolean>false</boolean>
+ </void>
+ <void method="setProperty">
+ <string>text</string>
+ <string></string>
+ </void>
+ <void method="setProperty">
+ <string>rows</string>
+ <int>10</int>
+ </void>
+ <void property="name">
+ <string>outputText</string>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>4</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>20</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>881</int>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>1</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>6</int>
+ </void>
+ <void method="setProperty">
+ <string>weightx</string>
+ <double>1.0</double>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JSeparator</string>
+ <void property="name">
+ <string>separator1</string>
+ </void>
+ <void method="auxiliary">
+ <void method="setProperty">
+ <string>JavaCodeGenerator.variableLocal</string>
+ <boolean>true</boolean>
+ </void>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>1</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>5</int>
+ </void>
+ <void method="setProperty">
+ <string>weightx</string>
+ <double>1.0</double>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JProgressBar</string>
+ <void property="name">
+ <string>progressBar</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>1</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>7</int>
+ </void>
+ <void method="setProperty">
+ <string>vAlign</string>
+ <int>0</int>
+ </void>
+ <void method="setProperty">
+ <string>weightx</string>
+ <double>1.0</double>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <null/>
+ <void method="setProperty">
+ <string>location</string>
+ <object class="java.awt.Point">
+ <int>0</int>
+ <int>0</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>size</string>
+ <object class="java.awt.Dimension">
+ <int>921</int>
+ <int>1347</int>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+</java>
diff --git a/org/broad/igv/tools/ListAccumulator$1.class b/org/broad/igv/tools/ListAccumulator$1.class
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diff --git a/org/broad/igv/tools/ui/CoverageGui.jfd b/org/broad/igv/tools/ui/CoverageGui.jfd
new file mode 100644
index 0000000..7dbbed1
--- /dev/null
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+<?xml version="1.0" encoding="UTF-8"?>
+<java version="1.6.0_20" class="java.beans.XMLDecoder">
+ <object class="com.jformdesigner.model.FormModel">
+ <void property="contentType">
+ <string>form/swing</string>
+ </void>
+ <void property="root">
+ <object class="com.jformdesigner.model.FormRoot">
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.GridBagLayout</class>
+ <void method="setProperty">
+ <string>$columnSpecs</string>
+ <string>0, 0</string>
+ </void>
+ <void method="setProperty">
+ <string>$rowSpecs</string>
+ <string>0, 0, 0, 0, 0, 0, 0, 0</string>
+ </void>
+ <void method="setProperty">
+ <string>$vGap</string>
+ <int>10</int>
+ </void>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="javax.swing.border.TitledBorder">
+ <object class="javax.swing.border.EtchedBorder">
+ <int>1</int>
+ <null/>
+ <null/>
+ </object>
+ <string></string>
+ <int>4</int>
+ <int>0</int>
+ <null/>
+ <null/>
+ </object>
+ </void>
+ <void property="name">
+ <string>mainPanel</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Compute coverage for an alignment or feature file.</string>
+ </void>
+ <void method="setProperty">
+ <string>font</string>
+ <object class="java.awt.Font">
+ <string>Lucida Grande</string>
+ <int>1</int>
+ <int>14</int>
+ </object>
+ </void>
+ <void property="name">
+ <string>label1</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>1</int>
+ </void>
+ <void method="setProperty">
+ <string>hAlign</string>
+ <int>0</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.GridBagLayout</class>
+ <void method="setProperty">
+ <string>$columnSpecs</string>
+ <string>0, 0, 0, 0</string>
+ </void>
+ <void method="setProperty">
+ <string>$rowSpecs</string>
+ <string>0, 0, 0, 0, 0</string>
+ </void>
+ </object>
+ <void property="name">
+ <string>requiredPanel</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Input File</string>
+ </void>
+ <void property="name">
+ <string>label2</string>
+ </void>
+ <void method="auxiliary">
+ <void method="setProperty">
+ <string>JavaCodeGenerator.variableLocal</string>
+ <boolean>true</boolean>
+ </void>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>1</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>hAlign</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>vAlign</string>
+ <int>0</int>
+ </void>
+ <void method="setProperty">
+ <string>weighty</string>
+ <double>1.0</double>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Output File</string>
+ </void>
+ <void property="name">
+ <string>outputLabel</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>1</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>3</int>
+ </void>
+ <void method="setProperty">
+ <string>hAlign</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>vAlign</string>
+ <int>0</int>
+ </void>
+ <void method="setProperty">
+ <string>weighty</string>
+ <double>1.0</double>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Browse</string>
+ </void>
+ <void property="name">
+ <string>outputButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>outputButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>3</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>3</int>
+ </void>
+ <void method="setProperty">
+ <string>vAlign</string>
+ <int>0</int>
+ </void>
+ <void method="setProperty">
+ <string>weighty</string>
+ <double>1.0</double>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void property="name">
+ <string>inputField</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.FocusListener</string>
+ <string>focusLost</string>
+ <string>inputFieldFocusLost</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>inputFieldActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>vAlign</string>
+ <int>0</int>
+ </void>
+ <void method="setProperty">
+ <string>weightx</string>
+ <double>1.0</double>
+ </void>
+ <void method="setProperty">
+ <string>weighty</string>
+ <double>1.0</double>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Browse</string>
+ </void>
+ <void property="name">
+ <string>inputButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>inputButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>inputButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>3</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>vAlign</string>
+ <int>0</int>
+ </void>
+ <void method="setProperty">
+ <string>weighty</string>
+ <double>1.0</double>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void property="name">
+ <string>outputField</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>3</int>
+ </void>
+ <void method="setProperty">
+ <string>vAlign</string>
+ <int>0</int>
+ </void>
+ <void method="setProperty">
+ <string>weightx</string>
+ <double>1.0</double>
+ </void>
+ <void method="setProperty">
+ <string>weighty</string>
+ <double>1.0</double>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>toolTipText</string>
+ <string>Either a genome ID (e.g. hg18) or the full path to a .genome file.</string>
+ </void>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Genome</string>
+ </void>
+ <void property="name">
+ <string>genomeLabel</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>1</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>4</int>
+ </void>
+ <void method="setProperty">
+ <string>hAlign</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>vAlign</string>
+ <int>0</int>
+ </void>
+ <void method="setProperty">
+ <string>weighty</string>
+ <double>1.0</double>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void property="name">
+ <string>genomeField</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>4</int>
+ </void>
+ <void method="setProperty">
+ <string>vAlign</string>
+ <int>0</int>
+ </void>
+ <void method="setProperty">
+ <string>weightx</string>
+ <double>1.0</double>
+ </void>
+ <void method="setProperty">
+ <string>weighty</string>
+ <double>1.0</double>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>1</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>1</int>
+ </void>
+ <void method="setProperty">
+ <string>weightx</string>
+ <double>1.0</double>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.GridBagLayout</class>
+ <void method="setProperty">
+ <string>$columnSpecs</string>
+ <string>0, 0, 0, 0</string>
+ </void>
+ <void method="setProperty">
+ <string>$rowSpecs</string>
+ <string>0, 0, 0, 0, 0, 0</string>
+ </void>
+ </object>
+ <void method="setProperty">
+ <string>enabled</string>
+ <boolean>true</boolean>
+ </void>
+ <void method="setProperty">
+ <string>font</string>
+ <object class="com.jformdesigner.model.SwingDerivedFont">
+ <null/>
+ <int>65538</int>
+ <int>10</int>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="javax.swing.border.TitledBorder">
+ <null/>
+ <string>Advanced Options</string>
+ <int>4</int>
+ <int>2</int>
+ <null/>
+ <null/>
+ </object>
+ </void>
+ <void property="name">
+ <string>tilePanel</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>toolTipText</string>
+ <string><html>Specifies the maximum zoom level to precompute. The default value is 7.<br>To reduce file size at the expense of Iperformance this value can be reduced.</string>
+ </void>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Zoom Levels</string>
+ </void>
+ <void property="name">
+ <string>zoomLabel</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>1</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>1</int>
+ </void>
+ <void method="setProperty">
+ <string>hAlign</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>vAlign</string>
+ <int>0</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>toolTipText</string>
+ <string>Window functions to use for summarizing data. </string>
+ </void>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Window Functions</string>
+ </void>
+ <void property="name">
+ <string>windowFunctionLabel</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>1</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>hAlign</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>vAlign</string>
+ <int>1</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.GridLayout</class>
+ <void method="setProperty">
+ <string>rows</string>
+ <int>2</int>
+ </void>
+ </object>
+ <void property="name">
+ <string>windowFunctionPanel</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JCheckBox</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Min</string>
+ </void>
+ <void property="name">
+ <string>minCheckBox</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JCheckBox</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Max</string>
+ </void>
+ <void property="name">
+ <string>maxCheckBox</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JCheckBox</string>
+ <void method="setProperty">
+ <string>selected</string>
+ <boolean>true</boolean>
+ </void>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Mean</string>
+ </void>
+ <void property="name">
+ <string>meanCheckBox</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JCheckBox</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Median</string>
+ </void>
+ <void property="name">
+ <string>medianCheckBox</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JCheckBox</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>2%</string>
+ </void>
+ <void property="name">
+ <string>a2CheckBox</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JCheckBox</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>10%</string>
+ </void>
+ <void property="name">
+ <string>a10CheckBox</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JCheckBox</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>90%</string>
+ </void>
+ <void property="name">
+ <string>a90CheckBox</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JCheckBox</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>98%</string>
+ </void>
+ <void property="name">
+ <string>a98CheckBox</string>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>weightx</string>
+ <double>1.0</double>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JComboBox</string>
+ <void method="setProperty">
+ <string>editable</string>
+ <boolean>false</boolean>
+ </void>
+ <void method="setProperty">
+ <string>model</string>
+ <object class="javax.swing.DefaultComboBoxModel"/>
+ </void>
+ <void property="name">
+ <string>zoomCombo</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>1</int>
+ </void>
+ <void method="setProperty">
+ <string>hAlign</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>vAlign</string>
+ <int>0</int>
+ </void>
+ <void method="setProperty">
+ <string>weightx</string>
+ <double>1.0</double>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>toolTipText</string>
+ <string>The window size over which coverage computed when using the count command. Defaults to 25 bp.</string>
+ </void>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Window Size</string>
+ </void>
+ <void property="name">
+ <string>windowSizeLabel</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>1</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>4</int>
+ </void>
+ <void method="setProperty">
+ <string>hAlign</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>vAlign</string>
+ <int>0</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void property="name">
+ <string>windowSizeField</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>4</int>
+ </void>
+ <void method="setProperty">
+ <string>vAlign</string>
+ <int>0</int>
+ </void>
+ <void method="setProperty">
+ <string>weightx</string>
+ <double>1.0</double>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>font</string>
+ <object class="com.jformdesigner.model.SwingDerivedFont">
+ <null/>
+ <int>0</int>
+ <int>0</int>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>toolTipText</string>
+ <string><html>Specifies a "bed" file to be used to map probe identifiers to locations. This option is useful <br>when preprocessing gct files. The bed file should contain 4 columns: chr start end name
+<br>where name is the probe name in the gct file.</string>
+ </void>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Probe to Loci Mapping</string>
+ </void>
+ <void property="name">
+ <string>probeLabel</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>5</int>
+ </void>
+ <void method="setProperty">
+ <string>hAlign</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>vAlign</string>
+ <int>0</int>
+ </void>
+ <void method="setProperty">
+ <string>weighty</string>
+ <double>1.0</double>
+ </void>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>1</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void property="name">
+ <string>probeField</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>5</int>
+ </void>
+ <void method="setProperty">
+ <string>vAlign</string>
+ <int>0</int>
+ </void>
+ <void method="setProperty">
+ <string>weightx</string>
+ <double>1.0</double>
+ </void>
+ <void method="setProperty">
+ <string>weighty</string>
+ <double>1.0</double>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Browse</string>
+ </void>
+ <void property="name">
+ <string>probeButton</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>3</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>5</int>
+ </void>
+ <void method="setProperty">
+ <string>vAlign</string>
+ <int>0</int>
+ </void>
+ <void method="setProperty">
+ <string>weighty</string>
+ <double>1.0</double>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>1</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>weightx</string>
+ <double>1.0</double>
+ </void>
+ <void method="setProperty">
+ <string>weighty</string>
+ <double>1.0</double>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.GridBagLayout</class>
+ <void method="setProperty">
+ <string>$columnSpecs</string>
+ <string>0, 0, 0</string>
+ </void>
+ <void method="setProperty">
+ <string>$rowSpecs</string>
+ <string>0</string>
+ </void>
+ </object>
+ <void property="name">
+ <string>buttonPanel</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Run</string>
+ </void>
+ <void property="name">
+ <string>runButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>runButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>vAlign</string>
+ <int>0</int>
+ </void>
+ <void method="setProperty">
+ <string>weighty</string>
+ <double>1.0</double>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Close</string>
+ </void>
+ <void property="name">
+ <string>closeButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>closeButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>1</int>
+ </void>
+ <void method="setProperty">
+ <string>vAlign</string>
+ <int>0</int>
+ </void>
+ <void method="setProperty">
+ <string>weighty</string>
+ <double>1.0</double>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>1</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>4</int>
+ </void>
+ <void method="setProperty">
+ <string>weightx</string>
+ <double>1.0</double>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>com.jformdesigner.runtime.NullLayout</class>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="javax.swing.border.TitledBorder">
+ <object class="javax.swing.border.EmptyBorder">
+ <object class="java.awt.Insets">
+ <int>0</int>
+ <int>0</int>
+ <int>0</int>
+ <int>0</int>
+ </object>
+ </object>
+ <string>Messages</string>
+ <int>4</int>
+ <int>2</int>
+ <null/>
+ <null/>
+ </object>
+ </void>
+ <void property="name">
+ <string>OutputPanel</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JScrollPane</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>javax.swing.JScrollPane</class>
+ </object>
+ <void property="name">
+ <string>outputScroll</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextArea</string>
+ <void method="setProperty">
+ <string>editable</string>
+ <boolean>false</boolean>
+ </void>
+ <void method="setProperty">
+ <string>text</string>
+ <string></string>
+ </void>
+ <void method="setProperty">
+ <string>rows</string>
+ <int>10</int>
+ </void>
+ <void property="name">
+ <string>outputText</string>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>4</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>20</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>881</int>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>1</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>6</int>
+ </void>
+ <void method="setProperty">
+ <string>weightx</string>
+ <double>1.0</double>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JSeparator</string>
+ <void property="name">
+ <string>separator1</string>
+ </void>
+ <void method="auxiliary">
+ <void method="setProperty">
+ <string>JavaCodeGenerator.variableLocal</string>
+ <boolean>true</boolean>
+ </void>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>1</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>5</int>
+ </void>
+ <void method="setProperty">
+ <string>weightx</string>
+ <double>1.0</double>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JProgressBar</string>
+ <void property="name">
+ <string>progressBar</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>1</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>7</int>
+ </void>
+ <void method="setProperty">
+ <string>vAlign</string>
+ <int>0</int>
+ </void>
+ <void method="setProperty">
+ <string>weightx</string>
+ <double>1.0</double>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <null/>
+ <void method="setProperty">
+ <string>location</string>
+ <object class="java.awt.Point">
+ <int>0</int>
+ <int>0</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>size</string>
+ <object class="java.awt.Dimension">
+ <int>921</int>
+ <int>1347</int>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+</java>
diff --git a/org/broad/igv/tools/ui/IndexGui$1.class b/org/broad/igv/tools/ui/IndexGui$1.class
new file mode 100644
index 0000000..1ddc4b7
Binary files /dev/null and b/org/broad/igv/tools/ui/IndexGui$1.class differ
diff --git a/org/broad/igv/tools/ui/IndexGui$2.class b/org/broad/igv/tools/ui/IndexGui$2.class
new file mode 100644
index 0000000..bfa5ea6
Binary files /dev/null and b/org/broad/igv/tools/ui/IndexGui$2.class differ
diff --git a/org/broad/igv/tools/ui/IndexGui$3.class b/org/broad/igv/tools/ui/IndexGui$3.class
new file mode 100644
index 0000000..2572547
Binary files /dev/null and b/org/broad/igv/tools/ui/IndexGui$3.class differ
diff --git a/org/broad/igv/tools/ui/IndexGui$4.class b/org/broad/igv/tools/ui/IndexGui$4.class
new file mode 100644
index 0000000..6ce1f24
Binary files /dev/null and b/org/broad/igv/tools/ui/IndexGui$4.class differ
diff --git a/org/broad/igv/tools/ui/IndexGui.class b/org/broad/igv/tools/ui/IndexGui.class
new file mode 100644
index 0000000..b586c2a
Binary files /dev/null and b/org/broad/igv/tools/ui/IndexGui.class differ
diff --git a/org/broad/igv/tools/ui/IndexGui.jfd b/org/broad/igv/tools/ui/IndexGui.jfd
new file mode 100644
index 0000000..4b5caa8
--- /dev/null
+++ b/org/broad/igv/tools/ui/IndexGui.jfd
@@ -0,0 +1,590 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<java version="1.6.0_20" class="java.beans.XMLDecoder">
+ <object class="com.jformdesigner.model.FormModel">
+ <void property="contentType">
+ <string>form/swing</string>
+ </void>
+ <void property="root">
+ <object class="com.jformdesigner.model.FormRoot">
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.GridBagLayout</class>
+ <void method="setProperty">
+ <string>$columnSpecs</string>
+ <string>0, 0</string>
+ </void>
+ <void method="setProperty">
+ <string>$rowSpecs</string>
+ <string>0, 0, 0, 0, 0, 0, 0, 0</string>
+ </void>
+ <void method="setProperty">
+ <string>$vGap</string>
+ <int>10</int>
+ </void>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="javax.swing.border.TitledBorder">
+ <object class="javax.swing.border.EtchedBorder">
+ <int>1</int>
+ <null/>
+ <null/>
+ </object>
+ <string></string>
+ <int>4</int>
+ <int>0</int>
+ <null/>
+ <null/>
+ </object>
+ </void>
+ <void property="name">
+ <string>mainPanel</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.GridBagLayout</class>
+ <void method="setProperty">
+ <string>$columnSpecs</string>
+ <string>0, 0, 0, 0</string>
+ </void>
+ <void method="setProperty">
+ <string>$rowSpecs</string>
+ <string>0, 0, 0, 0, 0</string>
+ </void>
+ </object>
+ <void property="name">
+ <string>requiredPanel</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Input File</string>
+ </void>
+ <void property="name">
+ <string>label2</string>
+ </void>
+ <void method="auxiliary">
+ <void method="setProperty">
+ <string>JavaCodeGenerator.variableLocal</string>
+ <boolean>true</boolean>
+ </void>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>1</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>hAlign</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>vAlign</string>
+ <int>0</int>
+ </void>
+ <void method="setProperty">
+ <string>weighty</string>
+ <double>1.0</double>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Output File</string>
+ </void>
+ <void property="name">
+ <string>outputLabel</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>1</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>3</int>
+ </void>
+ <void method="setProperty">
+ <string>hAlign</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>vAlign</string>
+ <int>0</int>
+ </void>
+ <void method="setProperty">
+ <string>weighty</string>
+ <double>1.0</double>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Browse</string>
+ </void>
+ <void property="name">
+ <string>outputButton</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>3</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>3</int>
+ </void>
+ <void method="setProperty">
+ <string>vAlign</string>
+ <int>0</int>
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+ <void method="setProperty">
+ <string>weighty</string>
+ <double>1.0</double>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void property="name">
+ <string>inputField</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.FocusListener</string>
+ <string>focusLost</string>
+ <string>inputFieldFocusLost</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>inputFieldActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>vAlign</string>
+ <int>0</int>
+ </void>
+ <void method="setProperty">
+ <string>weightx</string>
+ <double>1.0</double>
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+ <void method="setProperty">
+ <string>weighty</string>
+ <double>1.0</double>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Browse</string>
+ </void>
+ <void property="name">
+ <string>inputButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>inputButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>3</int>
+ </void>
+ <void method="setProperty">
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+ <void method="setProperty">
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+ <void method="setProperty">
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+ <double>1.0</double>
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+ </void>
+ <void method="add">
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+ <string>javax.swing.JTextField</string>
+ <void property="name">
+ <string>outputField</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
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+ </void>
+ <void method="setProperty">
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+ <void method="setProperty">
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+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Browse</string>
+ </void>
+ <void property="name">
+ <string>genomeButton</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
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+ </void>
+ <void method="setProperty">
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+ <double>1.0</double>
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+ <object class="com.jformdesigner.model.FormLayoutConstraints">
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+ <void method="setProperty">
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+ </void>
+ <void method="setProperty">
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+ <void method="setProperty">
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+ <double>1.0</double>
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+ </object>
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+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.GridBagLayout</class>
+ <void method="setProperty">
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+ </void>
+ <void method="setProperty">
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+ </object>
+ <void property="name">
+ <string>buttonPanel</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Run</string>
+ </void>
+ <void property="name">
+ <string>runButton</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
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+ <double>1.0</double>
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+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Close</string>
+ </void>
+ <void property="name">
+ <string>closeButton</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
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+ </void>
+ <void method="setProperty">
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+ <void method="setProperty">
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+ <double>1.0</double>
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+ <object class="com.jformdesigner.model.FormLayoutConstraints">
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+ <void method="setProperty">
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+ <void method="setProperty">
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+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
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+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>com.jformdesigner.runtime.NullLayout</class>
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+ <void method="setProperty">
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+ <object class="javax.swing.border.TitledBorder">
+ <object class="javax.swing.border.EmptyBorder">
+ <object class="java.awt.Insets">
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+ <void property="name">
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+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JScrollPane</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>javax.swing.JScrollPane</class>
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+ <void property="name">
+ <string>outputScroll</string>
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+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextArea</string>
+ <void method="setProperty">
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+ <void method="setProperty">
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+ <string></string>
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+ <void property="name">
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+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
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+ <void method="setProperty">
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+ <void method="setProperty">
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+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
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+ <void method="setProperty">
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+ <void method="setProperty">
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+ <double>1.0</double>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JSeparator</string>
+ <void property="name">
+ <string>separator1</string>
+ </void>
+ <void method="auxiliary">
+ <void method="setProperty">
+ <string>JavaCodeGenerator.variableLocal</string>
+ <boolean>true</boolean>
+ </void>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
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+ <void method="setProperty">
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+ <double>1.0</double>
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+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JProgressBar</string>
+ <void property="name">
+ <string>progressBar</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>1</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>7</int>
+ </void>
+ <void method="setProperty">
+ <string>vAlign</string>
+ <int>0</int>
+ </void>
+ <void method="setProperty">
+ <string>weightx</string>
+ <double>1.0</double>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <null/>
+ <void method="setProperty">
+ <string>location</string>
+ <object class="java.awt.Point">
+ <int>0</int>
+ <int>0</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>size</string>
+ <object class="java.awt.Dimension">
+ <int>921</int>
+ <int>1347</int>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+</java>
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index 0000000..8bf30a0
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new file mode 100644
index 0000000..554a15b
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diff --git a/org/broad/igv/ui/InsertSizeSettingsDialog$10.class b/org/broad/igv/ui/InsertSizeSettingsDialog$10.class
new file mode 100644
index 0000000..7c5f784
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diff --git a/org/broad/igv/ui/InsertSizeSettingsDialog$11.class b/org/broad/igv/ui/InsertSizeSettingsDialog$11.class
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index 0000000..99ddd15
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diff --git a/org/broad/igv/ui/InsertSizeSettingsDialog$2.class b/org/broad/igv/ui/InsertSizeSettingsDialog$2.class
new file mode 100644
index 0000000..bb19d76
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diff --git a/org/broad/igv/ui/InsertSizeSettingsDialog$3.class b/org/broad/igv/ui/InsertSizeSettingsDialog$3.class
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diff --git a/org/broad/igv/ui/InsertSizeSettingsDialog$4.class b/org/broad/igv/ui/InsertSizeSettingsDialog$4.class
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diff --git a/org/broad/igv/ui/InsertSizeSettingsDialog$5.class b/org/broad/igv/ui/InsertSizeSettingsDialog$5.class
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diff --git a/org/broad/igv/ui/InsertSizeSettingsDialog$6.class b/org/broad/igv/ui/InsertSizeSettingsDialog$6.class
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diff --git a/org/broad/igv/ui/InsertSizeSettingsDialog$8.class b/org/broad/igv/ui/InsertSizeSettingsDialog$8.class
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diff --git a/org/broad/igv/ui/InsertSizeSettingsDialog$9.class b/org/broad/igv/ui/InsertSizeSettingsDialog$9.class
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diff --git a/org/broad/igv/ui/InsertSizeSettingsDialog.class b/org/broad/igv/ui/InsertSizeSettingsDialog.class
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diff --git a/org/broad/igv/ui/InsertSizeSettingsDialog.jfd b/org/broad/igv/ui/InsertSizeSettingsDialog.jfd
new file mode 100644
index 0000000..0bcaa82
--- /dev/null
+++ b/org/broad/igv/ui/InsertSizeSettingsDialog.jfd
@@ -0,0 +1,620 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<java version="1.6.0_22" class="java.beans.XMLDecoder">
+ <object class="com.jformdesigner.model.FormModel">
+ <void property="contentType">
+ <string>form/swing</string>
+ </void>
+ <void property="root">
+ <object class="com.jformdesigner.model.FormRoot">
+ <void method="add">
+ <object class="com.jformdesigner.model.FormWindow">
+ <string>javax.swing.JDialog</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.BorderLayout</class>
+ </object>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.BorderLayout</class>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="javax.swing.border.EmptyBorder">
+ <object class="java.awt.Insets">
+ <int>12</int>
+ <int>12</int>
+ <int>12</int>
+ <int>12</int>
+ </object>
+ </object>
+ </void>
+ <void property="name">
+ <string>dialogPane</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>com.jformdesigner.runtime.NullLayout</class>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="com.jformdesigner.model.FormObject" field="NULL_VALUE"/>
+ </void>
+ <void property="name">
+ <string>contentPanel</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string><html>These settings control color-coding of paired reads based on the inferred insert size.</string>
+ </void>
+ <void property="name">
+ <string>label1</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>20</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>15</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>405</int>
+ </void>
+ <void method="setProperty">
+ <string>height</string>
+ <int>60</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>com.jformdesigner.runtime.NullLayout</class>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="javax.swing.border.TitledBorder">
+ <null/>
+ <string>Dynamic options</string>
+ <int>4</int>
+ <int>0</int>
+ <null/>
+ <null/>
+ </object>
+ </void>
+ <void property="name">
+ <string>panel1</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JCheckBox</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Compute thresholds</string>
+ </void>
+ <void property="name">
+ <string>computeIsizeCB</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>computeIsizeCBActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>10</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>25</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Minimum percentile:</string>
+ </void>
+ <void property="name">
+ <string>label4</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>y</string>
+ <int>70</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>175</int>
+ </void>
+ <void method="setProperty">
+ <string>x</string>
+ <int>10</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Maximum percentile:</string>
+ </void>
+ <void property="name">
+ <string>label5</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>width</string>
+ <int>175</int>
+ </void>
+ <void method="setProperty">
+ <string>height</string>
+ <int>16</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>100</int>
+ </void>
+ <void method="setProperty">
+ <string>x</string>
+ <int>10</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void method="setProperty">
+ <string>enabled</string>
+ <boolean>false</boolean>
+ </void>
+ <void property="name">
+ <string>minPercentileField</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>minPercentileFieldActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.FocusListener</string>
+ <string>focusLost</string>
+ <string>minPercentileFieldFocusLost</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>220</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>64</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>135</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void method="setProperty">
+ <string>enabled</string>
+ <boolean>false</boolean>
+ </void>
+ <void property="name">
+ <string>maxPercentileField</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>maxPercentileFieldActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.FocusListener</string>
+ <string>focusLost</string>
+ <string>maxPercentileFieldFocusLost</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>maxPercentileFieldActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>maxPercentileFieldActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>width</string>
+ <int>135</int>
+ </void>
+ <void method="setProperty">
+ <string>height</string>
+ <int>28</int>
+ </void>
+ <void method="setProperty">
+ <string>x</string>
+ <int>220</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>94</int>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>25</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>210</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>430</int>
+ </void>
+ <void method="setProperty">
+ <string>height</string>
+ <int>160</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>com.jformdesigner.runtime.NullLayout</class>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="javax.swing.border.TitledBorder">
+ <null/>
+ <string>Defaults</string>
+ <int>4</int>
+ <int>0</int>
+ <null/>
+ <null/>
+ </object>
+ </void>
+ <void property="name">
+ <string>panel2</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Default minimum threshold: </string>
+ </void>
+ <void property="name">
+ <string>label2</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>width</string>
+ <int>205</int>
+ </void>
+ <void method="setProperty">
+ <string>x</string>
+ <int>10</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>30</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Default maximum threshold: </string>
+ </void>
+ <void property="name">
+ <string>label3</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>width</string>
+ <int>185</int>
+ </void>
+ <void method="setProperty">
+ <string>height</string>
+ <int>16</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>60</int>
+ </void>
+ <void method="setProperty">
+ <string>x</string>
+ <int>10</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void property="name">
+ <string>minThresholdField</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>minThresholdFieldActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.FocusListener</string>
+ <string>focusLost</string>
+ <string>minThresholdFieldFocusLost</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>215</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>24</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>145</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void property="name">
+ <string>maxThresholdField</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>maxThresholdFieldActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.FocusListener</string>
+ <string>focusLost</string>
+ <string>maxThresholdFieldFocusLost</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>width</string>
+ <int>145</int>
+ </void>
+ <void method="setProperty">
+ <string>height</string>
+ <int>28</int>
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+ <void method="setProperty">
+ <string>x</string>
+ <int>215</int>
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+ <void method="setProperty">
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+ <int>54</int>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>25</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>85</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>430</int>
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+ <void method="setProperty">
+ <string>height</string>
+ <int>110</int>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>Center</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.FlowLayout</class>
+ <void method="setProperty">
+ <string>alignment</string>
+ <int>2</int>
+ </void>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="javax.swing.border.EmptyBorder">
+ <object class="java.awt.Insets">
+ <int>12</int>
+ <int>0</int>
+ <int>0</int>
+ <int>0</int>
+ </object>
+ </object>
+ </void>
+ <void property="name">
+ <string>buttonBar</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Cancel</string>
+ </void>
+ <void property="name">
+ <string>cancelButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>cancelButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>cancelButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>OK</string>
+ </void>
+ <void property="name">
+ <string>okButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>okButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>South</string>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>Center</string>
+ </void>
+ </object>
+ </void>
+ <void property="name">
+ <string>this</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <null/>
+ <void method="setProperty">
+ <string>location</string>
+ <object class="java.awt.Point">
+ <int>0</int>
+ <int>0</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>size</string>
+ <object class="java.awt.Dimension">
+ <int>505</int>
+ <int>495</int>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+</java>
diff --git a/org/broad/igv/ui/Main$1.class b/org/broad/igv/ui/Main$1.class
new file mode 100644
index 0000000..895c86d
Binary files /dev/null and b/org/broad/igv/ui/Main$1.class differ
diff --git a/org/broad/igv/ui/Main$2.class b/org/broad/igv/ui/Main$2.class
new file mode 100644
index 0000000..0468b62
Binary files /dev/null and b/org/broad/igv/ui/Main$2.class differ
diff --git a/org/broad/igv/ui/Main$IGVArgs.class b/org/broad/igv/ui/Main$IGVArgs.class
new file mode 100644
index 0000000..a6168de
Binary files /dev/null and b/org/broad/igv/ui/Main$IGVArgs.class differ
diff --git a/org/broad/igv/ui/Main.class b/org/broad/igv/ui/Main.class
new file mode 100644
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+ <object class="com.jformdesigner.model.FormContainer">
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+ <object class="javax.swing.border.BevelBorder">
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+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>font</string>
+ <object class="java.awt.Font">
+ <string>Lucida Grande</string>
+ <int>2</int>
+ <int>12</int>
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+ <void method="setProperty">
+ <string>text</string>
+ <string><html>Distinguish regions with zero values from regions with no data on plots <br>(e.g. bar charts). Regions with no data are indicated with a gray background.</string>
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+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JCheckBox</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Distinguish missing data</string>
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+ <string>showMissingDataCB</string>
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+ <string>Show attribute panel</string>
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+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JCheckBox</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Zoom to features</string>
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+ <void property="name">
+ <string>searchZoomCB</string>
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+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>searchZoomCBActionPerformed</string>
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+ <int>12</int>
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+ <void method="setProperty">
+ <string>text</string>
+ <string><html>This option controls the behavior of feature searchs. If true, the zoom level is changed as required to size the view to the feature size. If false the zoom level is unchanged.</string>
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+ <string><html><i>Added before and after feature locus when zooming to a feature. Also used when defining panel extents in gene/loci list views.</string>
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+ <void method="setProperty">
+ <string>x</string>
+ <int>10</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>165</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Background color click to change): </string>
+ </void>
+ <void property="name">
+ <string>label7</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>15</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>480</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>235</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>com.jformdesigner.runtime.NullLayout</class>
+ <void method="setProperty">
+ <string>autoSize</string>
+ <boolean>false</boolean>
+ </void>
+ </object>
+ <void method="setProperty">
+ <string>preferredSize</string>
+ <object class="java.awt.Dimension">
+ <int>20</int>
+ <int>20</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="javax.swing.border.BevelBorder">
+ <int>0</int>
+ <null/>
+ <null/>
+ <null/>
+ <null/>
+ </object>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.MouseListener</string>
+ <string>mouseClicked</string>
+ <string>backgroundColorPanelMouseClicked</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ <void property="name">
+ <string>backgroundColorPanel</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>255</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>474</int>
+ </void>
+ <void method="setProperty">
+ <string>height</string>
+ <int>29</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>30</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Reset to default</string>
+ </void>
+ <void property="name">
+ <string>resetBackgroundButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>resetBackgroundButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>315</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>474</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>150</int>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>Center</string>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <null/>
+ <void method="setProperty">
+ <string>title</string>
+ <string>General</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>com.jformdesigner.runtime.NullLayout</class>
+ </object>
+ <void property="name">
+ <string>tracksPanel</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>com.jformdesigner.runtime.NullLayout</class>
+ </object>
+ <void property="name">
+ <string>jPanel6</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Default Track Height, Charts (Pixels)</string>
+ </void>
+ <void property="name">
+ <string>jLabel5</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>10</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>12</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>40</string>
+ </void>
+ <void property="name">
+ <string>defaultChartTrackHeightField</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>defaultChartTrackHeightFieldActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.FocusListener</string>
+ <string>focusLost</string>
+ <string>defaultChartTrackHeightFieldFocusLost</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>271</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>6</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>57</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Track Name Attribute</string>
+ </void>
+ <void property="name">
+ <string>trackNameAttributeLabel</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>10</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>120</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void property="name">
+ <string>trackNameAttributeField</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>trackNameAttributeFieldActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.FocusListener</string>
+ <string>focusLost</string>
+ <string>trackNameAttributeFieldFocusLost</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>150</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>115</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>216</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>font</string>
+ <object class="java.awt.Font">
+ <string>Lucida Grande</string>
+ <int>2</int>
+ <int>12</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>text</string>
+ <string><html>Name of an attribute to be used to label tracks. If provided tracks will be labeled with the corresponding attribute values from the sample information file</string>
+ </void>
+ <void method="setProperty">
+ <string>verticalAlignment</string>
+ <int>1</int>
+ </void>
+ <void property="name">
+ <string>missingDataExplanation2</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>40</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>170</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>578</int>
+ </void>
+ <void method="setProperty">
+ <string>height</string>
+ <int>54</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Default Track Height, Other (Pixels)</string>
+ </void>
+ <void property="name">
+ <string>jLabel8</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>10</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>45</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>15</string>
+ </void>
+ <void property="name">
+ <string>defaultTrackHeightField</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>defaultTrackHeightFieldActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.FocusListener</string>
+ <string>focusLost</string>
+ <string>defaultTrackHeightFieldFocusLost</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>271</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>39</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>57</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>font</string>
+ <object class="java.awt.Font">
+ <string>Lucida Grande</string>
+ <int>2</int>
+ <int>12</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>text</string>
+ <string><html>Default height of chart tracks (barcharts, scatterplots, etc)</string>
+ </void>
+ <void property="name">
+ <string>missingDataExplanation4</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>350</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>5</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>354</int>
+ </void>
+ <void method="setProperty">
+ <string>height</string>
+ <int>25</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>font</string>
+ <object class="java.awt.Font">
+ <string>Lucida Grande</string>
+ <int>2</int>
+ <int>12</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>text</string>
+ <string><html>Default height of all other tracks</string>
+ </void>
+ <void property="name">
+ <string>missingDataExplanation5</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>350</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>41</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>1141</int>
+ </void>
+ <void method="setProperty">
+ <string>height</string>
+ <int>25</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>font</string>
+ <object class="java.awt.Font">
+ <string>Lucida Grande</string>
+ <int>2</int>
+ <int>12</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>text</string>
+ <string><html><i> If selected feature tracks are expanded by default.</string>
+ </void>
+ <void property="name">
+ <string>missingDataExplanation3</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>876</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>318</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JCheckBox</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Expand Feature Tracks</string>
+ </void>
+ <void property="name">
+ <string>expandCB</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>expandCBActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>6</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>272</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JCheckBox</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Normalize Coverage Data</string>
+ </void>
+ <void property="name">
+ <string>normalizeCoverageCB</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>normalizeCoverageCBActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.FocusListener</string>
+ <string>focusLost</string>
+ <string>normalizeCoverageCBFocusLost</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>6</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>372</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>font</string>
+ <object class="java.awt.Font">
+ <string>Lucida Grande</string>
+ <int>2</int>
+ <int>12</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>text</string>
+ <string><html><i> Applies to coverage tracks computed with igvtools (.tdf files). If selected coverage values are scaled by (1,000,000 / totalCount), where totalCount is the total number of features or alignments.</string>
+ </void>
+ <void method="setProperty">
+ <string>verticalAlignment</string>
+ <int>1</int>
+ </void>
+ <void property="name">
+ <string>missingDataExplanation8</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>50</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>413</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>608</int>
+ </void>
+ <void method="setProperty">
+ <string>height</string>
+ <int>52</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JCheckBox</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Show Expand Icon</string>
+ </void>
+ <void method="setProperty">
+ <string>toolTipText</string>
+ <string>If checked displays an expand/collapse icon on feature tracks.</string>
+ </void>
+ <void property="name">
+ <string>expandIconCB</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>expandIconCBActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>6</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>318</int>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>40</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>20</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>725</int>
+ </void>
+ <void method="setProperty">
+ <string>height</string>
+ <int>480</int>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <null/>
+ <void method="setProperty">
+ <string>title</string>
+ <string>Tracks</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>com.jformdesigner.runtime.NullLayout</class>
+ </object>
+ <void property="name">
+ <string>overlaysPanel</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>com.jformdesigner.runtime.NullLayout</class>
+ </object>
+ <void property="name">
+ <string>jPanel5</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Linking attribute column:</string>
+ </void>
+ <void property="name">
+ <string>jLabel3</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>65</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>86</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>LINKING_ID</string>
+ </void>
+ <void property="name">
+ <string>overlayAttributeTextField</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>overlayAttributeTextFieldActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.FocusListener</string>
+ <string>focusLost</string>
+ <string>overlayAttributeTextFieldFocusLost</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>240</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>80</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>228</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JCheckBox</string>
+ <void method="setProperty">
+ <string>selected</string>
+ <boolean>true</boolean>
+ </void>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Overlay mutation tracks</string>
+ </void>
+ <void method="setProperty">
+ <string>actionCommand</string>
+ <string>overlayTracksCB</string>
+ </void>
+ <void property="name">
+ <string>overlayTrackCB</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>overlayTrackCBActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>6</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>51</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>font</string>
+ <object class="java.awt.Font">
+ <string>Lucida Grande</string>
+ <int>2</int>
+ <int>12</int>
+ </object>
+ </void>
+ <void property="name">
+ <string>jLabel2</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>6</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>6</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>font</string>
+ <object class="java.awt.Font">
+ <string>Lucida Grande</string>
+ <int>2</int>
+ <int>12</int>
+ </object>
+ </void>
+ <void property="name">
+ <string>jLabel4</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>6</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>12</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JCheckBox</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Color code mutations</string>
+ </void>
+ <void property="name">
+ <string>colorCodeMutationsCB</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>colorMutationsCBActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>0</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>295</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Choose colors</string>
+ </void>
+ <void method="setProperty">
+ <string>font</string>
+ <object class="com.jformdesigner.model.SwingFont">
+ <string>Button.font</string>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>verticalTextPosition</string>
+ <int>3</int>
+ </void>
+ <void property="name">
+ <string>chooseMutationColorsButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>chooseMutationColorsButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>185</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>292</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string><html><i>Name of a sample attribute column to link mutation and data tracks</string>
+ </void>
+ <void method="setProperty">
+ <string>verticalAlignment</string>
+ <int>1</int>
+ </void>
+ <void property="name">
+ <string>label11</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>110</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>115</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>360</int>
+ </void>
+ <void method="setProperty">
+ <string>height</string>
+ <int>50</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JCheckBox</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Show orphaned mutation tracks</string>
+ </void>
+ <void property="name">
+ <string>showOrphanedMutationsCB</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>showOrphanedMutationsCBActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>70</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>180</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string><html><i>Select to show mutation tracks with no corresponding data track.</string>
+ </void>
+ <void method="setProperty">
+ <string>verticalAlignment</string>
+ <int>1</int>
+ </void>
+ <void property="name">
+ <string>label12</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>110</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>210</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>360</int>
+ </void>
+ <void method="setProperty">
+ <string>height</string>
+ <int>55</int>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>28</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>55</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>673</int>
+ </void>
+ <void method="setProperty">
+ <string>height</string>
+ <int>394</int>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <null/>
+ <void method="setProperty">
+ <string>title</string>
+ <string>Mutations</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>com.jformdesigner.runtime.NullLayout</class>
+ </object>
+ <void property="name">
+ <string>chartPanel</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>com.jformdesigner.runtime.NullLayout</class>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="javax.swing.border.LineBorder">
+ <object class="java.awt.Color" field="black"/>
+ <int>1</int>
+ <boolean>false</boolean>
+ </object>
+ </void>
+ <void property="name">
+ <string>jPanel4</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JCheckBox</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Draw Top Border</string>
+ </void>
+ <void property="name">
+ <string>topBorderCB</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>topBorderCBActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>30</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>36</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>font</string>
+ <object class="com.jformdesigner.model.SwingDerivedFont">
+ <null/>
+ <int>0</int>
+ <int>0</int>
+ <boolean>false</boolean>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>text</string>
+ <string><html><b>Default settings for barcharts and scatterplots:</string>
+ </void>
+ <void property="name">
+ <string>label1</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>10</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>10</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>380</int>
+ </void>
+ <void method="setProperty">
+ <string>height</string>
+ <int>25</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JCheckBox</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Draw Track Label</string>
+ </void>
+ <void property="name">
+ <string>chartDrawTrackNameCB</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>chartDrawTrackNameCBActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>30</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>126</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JCheckBox</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Draw Bottom Border</string>
+ </void>
+ <void property="name">
+ <string>bottomBorderCB</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>bottomBorderCBActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>30</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>66</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string><html><i>Dynamically rescale to the range of the data in view.</string>
+ </void>
+ <void property="name">
+ <string>jLabel7</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>220</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>170</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>371</int>
+ </void>
+ <void method="setProperty">
+ <string>height</string>
+ <int>50</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JCheckBox</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Color Borders</string>
+ </void>
+ <void property="name">
+ <string>colorBordersCB</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>colorBordersCBActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>30</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>96</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JCheckBox</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Label Y Axis</string>
+ </void>
+ <void property="name">
+ <string>labelYAxisCB</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>labelYAxisCBActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>30</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>156</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JCheckBox</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Continuous Autoscale</string>
+ </void>
+ <void property="name">
+ <string>autoscaleCB</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>autoscaleCBActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>30</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>186</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string><html><i>Draw a label centered over the track. </string>
+ </void>
+ <void property="name">
+ <string>jLabel9</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>220</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>159</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>355</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JCheckBox</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Show Data Range</string>
+ </void>
+ <void property="name">
+ <string>showDatarangeCB</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>showDatarangeCBActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.FocusListener</string>
+ <string>focusLost</string>
+ <string>showDatarangeCBFocusLost</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>30</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>216</int>
+ </void>
+ <void method="setProperty">
+ <string>height</string>
+ <int>26</int>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>20</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>20</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>650</int>
+ </void>
+ <void method="setProperty">
+ <string>height</string>
+ <int>290</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>com.jformdesigner.runtime.NullLayout</class>
+ <void method="setProperty">
+ <string>autoSize</string>
+ <boolean>false</boolean>
+ </void>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="javax.swing.border.LineBorder">
+ <object class="java.awt.Color" field="black"/>
+ <int>1</int>
+ <boolean>false</boolean>
+ </object>
+ </void>
+ <void property="name">
+ <string>panel1</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string><html><b>Default settings for heatmaps:</string>
+ </void>
+ <void property="name">
+ <string>label13</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>width</string>
+ <int>250</int>
+ </void>
+ <void method="setProperty">
+ <string>height</string>
+ <int>30</int>
+ </void>
+ <void method="setProperty">
+ <string>x</string>
+ <int>10</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>5</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JCheckBox</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Show all features</string>
+ </void>
+ <void property="name">
+ <string>showAllHeatmapFeauresCB</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>showAllHeatmapFeauresCBActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>20</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>45</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string><html><i>Paint all features/segments with a minimum width of 1 pixel. If not checked features/segments with screen widths less than 1 pixel are not drawn.</string>
+ </void>
+ <void property="name">
+ <string>label14</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>200</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>35</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>425</int>
+ </void>
+ <void method="setProperty">
+ <string>height</string>
+ <int>60</int>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>20</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>340</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>650</int>
+ </void>
+ <void method="setProperty">
+ <string>height</string>
+ <int>135</int>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <null/>
+ <void method="setProperty">
+ <string>title</string>
+ <string>Charts</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>com.jformdesigner.runtime.NullLayout</class>
+ </object>
+ <void property="name">
+ <string>alignmentPanel</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>com.jformdesigner.runtime.NullLayout</class>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="javax.swing.border.TitledBorder">
+ <string></string>
+ </object>
+ </void>
+ <void property="name">
+ <string>jPanel11</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Visibility range threshold (kb):</string>
+ </void>
+ <void property="name">
+ <string>jLabel11</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>10</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>12</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>jTextField1</string>
+ </void>
+ <void property="name">
+ <string>samMaxWindowSizeField</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>samMaxWindowSizeFieldActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.FocusListener</string>
+ <string>focusLost</string>
+ <string>samMaxWindowSizeFieldFocusLost</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>220</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>6</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string><html><i>Nominal window size at which alignments become visible</string>
+ </void>
+ <void property="name">
+ <string>jLabel12</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>320</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>12</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string><html><i>Nominal window size at which alignments become visible</string>
+ </void>
+ <void property="name">
+ <string>jLabel14</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>width</string>
+ <int>363</int>
+ </void>
+ <void method="setProperty">
+ <string>height</string>
+ <int>16</int>
+ </void>
+ <void method="setProperty">
+ <string>x</string>
+ <int>0</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>108</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string><html><i>Nominal window size at which alignments become visible</string>
+ </void>
+ <void property="name">
+ <string>jLabel16</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>width</string>
+ <int>363</int>
+ </void>
+ <void method="setProperty">
+ <string>height</string>
+ <int>16</int>
+ </void>
+ <void method="setProperty">
+ <string>x</string>
+ <int>0</int>
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+ <void method="setProperty">
+ <string>y</string>
+ <int>129</int>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>10</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>5</int>
+ </void>
+ <void method="setProperty">
+ <string>height</string>
+ <int>45</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>755</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>com.jformdesigner.runtime.NullLayout</class>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="javax.swing.border.TitledBorder">
+ <string>Downsampling</string>
+ </object>
+ </void>
+ <void property="name">
+ <string>panel4</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JCheckBox</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Downsample reads</string>
+ </void>
+ <void property="name">
+ <string>downsampleReadsCB</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>downsampleReadsCBActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>5</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>25</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Max read count:</string>
+ </void>
+ <void property="name">
+ <string>label23</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>195</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>28</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void property="name">
+ <string>samDownsampleCountField</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>samDownsampleCountFieldActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.FocusListener</string>
+ <string>focusLost</string>
+ <string>samDownsampleCountFieldFocusLost</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>300</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>22</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>80</int>
+ </void>
+ <void method="setProperty">
+ <string>height</string>
+ <int>28</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>per window size (bases):</string>
+ </void>
+ <void property="name">
+ <string>jLabel13</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>420</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>28</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>jTextField1</string>
+ </void>
+ <void property="name">
+ <string>samSamplingWindowField</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>samSamplingWindowFieldActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.FocusListener</string>
+ <string>focusLost</string>
+ <string>samSamplingWindowFieldFocusLost</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>580</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>22</int>
+ </void>
+ <void method="setProperty">
+ <string>height</string>
+ <int>28</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>80</int>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>10</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>62</int>
+ </void>
+ <void method="setProperty">
+ <string>height</string>
+ <int>60</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>755</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>com.jformdesigner.runtime.NullLayout</class>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="javax.swing.border.TitledBorder">
+ <string>Filter and shading options</string>
+ </object>
+ </void>
+ <void property="name">
+ <string>jPanel12</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>0</string>
+ </void>
+ <void property="name">
+ <string>snpThresholdField</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>snpThresholdFieldActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.FocusListener</string>
+ <string>focusLost</string>
+ <string>snpThresholdFieldFocusLost</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>240</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>20</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>80</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Coverage allele-freq threshold</string>
+ </void>
+ <void property="name">
+ <string>jLabel26</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>32</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>25</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>200</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>0</string>
+ </void>
+ <void property="name">
+ <string>samMinBaseQualityField</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>samMinBaseQualityFieldActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.FocusListener</string>
+ <string>focusLost</string>
+ <string>samMinBaseQualityFieldFocusLost</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>605</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>140</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>50</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JCheckBox</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Shade mismatched bases by quality. </string>
+ </void>
+ <void property="name">
+ <string>samShadeMismatchedBaseCB</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>samShadeMismatchedBaseCBActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>340</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>142</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>264</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>0</string>
+ </void>
+ <void property="name">
+ <string>samMaxBaseQualityField</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>samMaxBaseQualityFieldActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.FocusListener</string>
+ <string>focusLost</string>
+ <string>samMaxBaseQualityFieldFocusLost</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>675</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>140</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>50</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JCheckBox</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Show coverage track</string>
+ </void>
+ <void property="name">
+ <string>showCovTrackCB</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>showCovTrackCBActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>340</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>49</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>270</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JCheckBox</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Filter duplicate reads</string>
+ </void>
+ <void property="name">
+ <string>samFilterDuplicatesCB</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>samShowDuplicatesCBActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>5</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>49</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>290</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JCheckBox</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Filter alignments by read group</string>
+ </void>
+ <void property="name">
+ <string>filterCB</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>filterCBActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>5</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>173</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>244</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>URL or path to filter file</string>
+ </void>
+ <void method="setProperty">
+ <string>enabled</string>
+ <boolean>false</boolean>
+ </void>
+ <void property="name">
+ <string>filterURL</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>filterURLActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.FocusListener</string>
+ <string>focusLost</string>
+ <string>filterURLFocusLost</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>265</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>173</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>440</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JCheckBox</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Flag unmapped pairs</string>
+ </void>
+ <void property="name">
+ <string>samFlagUnmappedPairCB</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>samFlagUnmappedPairCBActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>5</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>111</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>310</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JCheckBox</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Filter vendor failed reads</string>
+ </void>
+ <void property="name">
+ <string>filterFailedReadsCB</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>filterVendorFailedReadsCBActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>5</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>80</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>to</string>
+ </void>
+ <void property="name">
+ <string>label2</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>660</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>145</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JCheckBox</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Show soft-clipped bases</string>
+ </void>
+ <void property="name">
+ <string>showSoftClippedCB</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>showSoftClippedCBActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>340</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>80</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JCheckBox</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Show center line</string>
+ </void>
+ <void property="name">
+ <string>showCenterLineCB</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>showCenterLineCBActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>5</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>142</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>199</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JCheckBox</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Flag zero-quality alignments</string>
+ </void>
+ <void property="name">
+ <string>zeroQualityAlignmentCB</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>zeroQualityAlignmentCBActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>340</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>111</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Mapping quality threshold:</string>
+ </void>
+ <void property="name">
+ <string>jLabel15</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>367</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>25</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>0</string>
+ </void>
+ <void property="name">
+ <string>mappingQualityThresholdField</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>mappingQualityThresholdFieldActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.FocusListener</string>
+ <string>focusLost</string>
+ <string>mappingQualityThresholdFieldFocusLost</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>550</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>20</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>80</int>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>10</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>134</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>755</int>
+ </void>
+ <void method="setProperty">
+ <string>height</string>
+ <int>215</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>com.jformdesigner.runtime.NullLayout</class>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="javax.swing.border.TitledBorder">
+ <string>Insert Size Options</string>
+ </object>
+ </void>
+ <void property="name">
+ <string>panel2</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JCheckBox</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Compute</string>
+ </void>
+ <void property="name">
+ <string>isizeComputeCB</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>isizeComputeCBActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>isizeComputeCBActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>isizeComputeCBActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>360</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>76</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Maximum (bp):</string>
+ </void>
+ <void property="name">
+ <string>jLabel17</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>100</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>110</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>110</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>0</string>
+ </void>
+ <void property="name">
+ <string>insertSizeMinThresholdField</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>insertSizeThresholdFieldActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.FocusListener</string>
+ <string>focusLost</string>
+ <string>insertSizeThresholdFieldFocusLost</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>insertSizeMinThresholdFieldActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.FocusListener</string>
+ <string>focusLost</string>
+ <string>insertSizeMinThresholdFieldFocusLost</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>insertSizeMinThresholdFieldActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>insertSizeMinThresholdFieldActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>width</string>
+ <int>80</int>
+ </void>
+ <void method="setProperty">
+ <string>height</string>
+ <int>28</int>
+ </void>
+ <void method="setProperty">
+ <string>x</string>
+ <int>220</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>75</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Minimum (bp):</string>
+ </void>
+ <void property="name">
+ <string>jLabel20</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>width</string>
+ <int>110</int>
+ </void>
+ <void method="setProperty">
+ <string>height</string>
+ <int>16</int>
+ </void>
+ <void method="setProperty">
+ <string>x</string>
+ <int>100</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>80</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>0</string>
+ </void>
+ <void property="name">
+ <string>insertSizeThresholdField</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>insertSizeThresholdFieldActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.FocusListener</string>
+ <string>focusLost</string>
+ <string>insertSizeThresholdFieldFocusLost</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>insertSizeThresholdFieldActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>220</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>105</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>80</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Minimum (percentile):</string>
+ </void>
+ <void property="name">
+ <string>jLabel30</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>width</string>
+ <int>155</int>
+ </void>
+ <void method="setProperty">
+ <string>height</string>
+ <int>16</int>
+ </void>
+ <void method="setProperty">
+ <string>x</string>
+ <int>460</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>80</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Maximum (percentile):</string>
+ </void>
+ <void property="name">
+ <string>jLabel18</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>width</string>
+ <int>155</int>
+ </void>
+ <void method="setProperty">
+ <string>height</string>
+ <int>16</int>
+ </void>
+ <void method="setProperty">
+ <string>x</string>
+ <int>460</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>110</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>0</string>
+ </void>
+ <void property="name">
+ <string>insertSizeMinPercentileField</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>insertSizeThresholdFieldActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.FocusListener</string>
+ <string>focusLost</string>
+ <string>insertSizeThresholdFieldFocusLost</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>insertSizeMinThresholdFieldActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.FocusListener</string>
+ <string>focusLost</string>
+ <string>insertSizeMinThresholdFieldFocusLost</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>insertSizeMinThresholdFieldActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>insertSizeMinThresholdFieldActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>insertSizeMinPercentileFieldActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.FocusListener</string>
+ <string>focusLost</string>
+ <string>insertSizeMinPercentileFieldFocusLost</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>width</string>
+ <int>80</int>
+ </void>
+ <void method="setProperty">
+ <string>height</string>
+ <int>28</int>
+ </void>
+ <void method="setProperty">
+ <string>x</string>
+ <int>625</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>75</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>0</string>
+ </void>
+ <void property="name">
+ <string>insertSizeMaxPercentileField</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>insertSizeThresholdFieldActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.FocusListener</string>
+ <string>focusLost</string>
+ <string>insertSizeThresholdFieldFocusLost</string>
+ <boolean>true</boolean>
+ </object>
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+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
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+ <string>actionPerformed</string>
+ <string>insertSizeMaxPercentileFieldActionPerformed</string>
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+ <void method="addEvent">
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+ <string>java.awt.event.FocusListener</string>
+ <string>focusLost</string>
+ <string>insertSizeMaxPercentileFieldFocusLost</string>
+ <boolean>true</boolean>
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+ <int>80</int>
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+ <int>105</int>
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+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string><html><i>These options control the color coding of paired alignments by inferred insert size. Base pair values set default values. If "compute" is selected values are computed from the actual size distribution of each library.</string>
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+ <void property="name">
+ <string>label8</string>
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+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>5</int>
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+ <void method="setProperty">
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+ <int>735</int>
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+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Defaults </string>
+ </void>
+ <void property="name">
+ <string>label9</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
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+ <int>15</int>
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+ <object class="com.jformdesigner.model.FormLayoutConstraints">
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+ <void method="setProperty">
+ <string>x</string>
+ <int>10</int>
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+ <void method="setProperty">
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+ <int>442</int>
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+ <void method="setProperty">
+ <string>width</string>
+ <int>755</int>
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+ <void method="setProperty">
+ <string>height</string>
+ <int>145</int>
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+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>com.jformdesigner.runtime.NullLayout</class>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="javax.swing.border.TitledBorder">
+ <string>Splice Junction Track Options</string>
+ </object>
+ </void>
+ <void property="name">
+ <string>panel3</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JCheckBox</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Show junction track</string>
+ </void>
+ <void property="name">
+ <string>showJunctionTrackCB</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>showJunctionTrackCBActionPerformed</string>
+ <boolean>true</boolean>
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+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>5</int>
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+ <void method="setProperty">
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+ <int>25</int>
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+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void property="name">
+ <string>junctionFlankingTextField</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>junctionFlankingTextFieldActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.FocusListener</string>
+ <string>focusLost</string>
+ <string>junctionFlankingTextFieldFocusLost</string>
+ <boolean>true</boolean>
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+ <object class="com.jformdesigner.model.FormLayoutConstraints">
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+ <void method="setProperty">
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+ <int>25</int>
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+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Min flanking width:</string>
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+ <void property="name">
+ <string>label15</string>
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+ <object class="com.jformdesigner.model.FormLayoutConstraints">
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+ <void method="setProperty">
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+ <int>125</int>
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+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Min junction coverage:</string>
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+ <void property="name">
+ <string>label16</string>
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+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>460</int>
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+ <int>30</int>
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+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void property="name">
+ <string>junctionCoverageTextField</string>
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+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>junctionCoverageTextFieldActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
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+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.FocusListener</string>
+ <string>focusLost</string>
+ <string>junctionCoverageTextFieldFocusLost</string>
+ <boolean>true</boolean>
+ </object>
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+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
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+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
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+ <int>69</int>
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+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <null/>
+ <void method="setProperty">
+ <string>title</string>
+ <string>Alignments</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>com.jformdesigner.runtime.NullLayout</class>
+ </object>
+ <void property="name">
+ <string>expressionPane</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>com.jformdesigner.runtime.NullLayout</class>
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+ <void property="name">
+ <string>jPanel8</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JRadioButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Map probes to genes</string>
+ </void>
+ <void method="setProperty">
+ <string>$buttonGroup</string>
+ <object class="com.jformdesigner.model.FormReference">
+ <string>buttonGroup1</string>
+ </object>
+ </void>
+ <void property="name">
+ <string>expMapToGeneCB</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>expMapToGeneCBActionPerformed</string>
+ <boolean>true</boolean>
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+ <object class="com.jformdesigner.model.FormLayoutConstraints">
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+ <void method="setProperty">
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+ <void method="setProperty">
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+ <int>129</int>
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+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Expression probe mapping options: </string>
+ </void>
+ <void property="name">
+ <string>jLabel24</string>
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+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>20</int>
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+ <void method="setProperty">
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+ <int>20</int>
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+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JRadioButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string><html>Map probes to target loci</string>
+ </void>
+ <void method="setProperty">
+ <string>$buttonGroup</string>
+ <object class="com.jformdesigner.model.FormReference">
+ <string>buttonGroup1</string>
+ </object>
+ </void>
+ <void property="name">
+ <string>expMapToLociCB</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>expMapToLociCBActionPerformed</string>
+ <boolean>true</boolean>
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+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
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+ <void method="setProperty">
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+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string><html><i>Note: Changes will not affect currently loaded datasets.</string>
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+ <void property="name">
+ <string>jLabel21</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
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+ <void method="setProperty">
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+ <int>44</int>
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+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void property="name">
+ <string>probeMappingFileTextField</string>
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+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.FocusListener</string>
+ <string>focusLost</string>
+ <string>probeMappingFileTextFieldFocusLost</string>
+ <boolean>true</boolean>
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+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>probeMappingFileTextFieldActionPerformed</string>
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+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string><html><i>File path or URL to BED file containing genomic locations of probes.</string>
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+ <void property="name">
+ <string>label22</string>
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+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
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+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Browse</string>
+ </void>
+ <void property="name">
+ <string>probeMappingBrowseButton</string>
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+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>probeMappingBrowseButtonActionPerformed</string>
+ <boolean>true</boolean>
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+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
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+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JCheckBox</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Use probe mapping file</string>
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+ <void property="name">
+ <string>useProbeMappingCB</string>
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+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>useProbeMappingCBActionPerformed</string>
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+ <object class="com.jformdesigner.model.FormLayoutConstraints">
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+ <void method="setProperty">
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+ <void method="setProperty">
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+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <null/>
+ <void method="setProperty">
+ <string>title</string>
+ <string>Probes</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>javax.swing.BoxLayout</class>
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+ <void property="name">
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+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>com.jformdesigner.runtime.NullLayout</class>
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+ <void property="name">
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+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>com.jformdesigner.runtime.NullLayout</class>
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+ <void property="name">
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+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>jTextField1</string>
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+ <void method="setProperty">
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+ <boolean>false</boolean>
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+ <void property="name">
+ <string>proxyUsernameField</string>
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+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>proxyUsernameFieldActionPerformed</string>
+ <boolean>true</boolean>
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+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.FocusListener</string>
+ <string>focusLost</string>
+ <string>proxyUsernameFieldFocusLost</string>
+ <boolean>true</boolean>
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+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
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+ <int>127</int>
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+ <void method="setProperty">
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+ <void method="setProperty">
+ <string>width</string>
+ <int>261</int>
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+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Username</string>
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+ <void property="name">
+ <string>jLabel28</string>
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+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
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+ <int>28</int>
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+ <void method="setProperty">
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+ <int>51</int>
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+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JCheckBox</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Authentication required</string>
+ </void>
+ <void property="name">
+ <string>authenticateProxyCB</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>authenticateProxyCBActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
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+ <string>javax.swing.JTextField</string>
+ <void method="setProperty">
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+ <void method="setProperty">
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+ <void property="name">
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+ <string><html>Note: do not use these settings unless you receive error or warning messages about server connections. On most systems the correct settings will be automatically copied from your web browser.</string>
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+ <void method="setProperty">
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+ <string>Clear All</string>
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+ <void property="name">
+ <string>clearProxySettingsButton</string>
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+ <void method="addEvent">
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+ <string>java.awt.event.ActionListener</string>
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+ <string>clearProxySettingsButtonActionPerformed</string>
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+ <string>genomeUpdateCB</string>
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+ <void method="addEvent">
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+ <string>java.awt.event.ActionListener</string>
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+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Data Registry URL</string>
+ </void>
+ <void property="name">
+ <string>jLabel6</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>70</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>170</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void method="setProperty">
+ <string>enabled</string>
+ <boolean>false</boolean>
+ </void>
+ <void property="name">
+ <string>dataServerURLTextField</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>dataServerURLTextFieldActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.FocusListener</string>
+ <string>focusLost</string>
+ <string>dataServerURLTextFieldFocusLost</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>225</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>165</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>494</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Genome Server URL</string>
+ </void>
+ <void property="name">
+ <string>jLabel1</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>70</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>135</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>jTextField1</string>
+ </void>
+ <void method="setProperty">
+ <string>enabled</string>
+ <boolean>false</boolean>
+ </void>
+ <void property="name">
+ <string>genomeServerURLTextField</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>genomeServerURLTextFieldActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.FocusListener</string>
+ <string>focusLost</string>
+ <string>genomeServerURLTextFieldFocusLost</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>225</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>130</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>494</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JCheckBox</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Edit server properties</string>
+ </void>
+ <void property="name">
+ <string>editServerPropertiesCB</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>editServerPropertiesCBActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>35</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>95</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Reset to Defaults</string>
+ </void>
+ <void property="name">
+ <string>jButton1</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>jButton1ActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>225</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>95</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Move...</string>
+ </void>
+ <void property="name">
+ <string>igvDirectoryButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>igvDirectoryButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>610</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>343</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>100</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="javax.swing.border.BevelBorder">
+ <int>1</int>
+ <null/>
+ <null/>
+ <null/>
+ <null/>
+ </object>
+ </void>
+ <void property="name">
+ <string>igvDirectoryField</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>55</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>345</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>550</int>
+ </void>
+ <void method="setProperty">
+ <string>height</string>
+ <int>25</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>IGV Directory: </string>
+ </void>
+ <void property="name">
+ <string>label21</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>45</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>310</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>105</int>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <null/>
+ <void method="setProperty">
+ <string>title</string>
+ <string>Advanced</string>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>Center</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>com.jidesoft.dialog.ButtonPanel</string>
+ <null/>
+ <void property="name">
+ <string>okCancelButtonPanel</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>OK</string>
+ </void>
+ <void property="name">
+ <string>okButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>okButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Cancel</string>
+ </void>
+ <void property="name">
+ <string>cancelButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>cancelButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>South</string>
+ </void>
+ </object>
+ </void>
+ <void property="name">
+ <string>this</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <null/>
+ <void method="setProperty">
+ <string>size</string>
+ <object class="java.awt.Dimension">
+ <int>805</int>
+ <int>695</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>location</string>
+ <object class="java.awt.Point">
+ <int>0</int>
+ <int>15</int>
+ </object>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormNonVisual">
+ <string>javax.swing.ButtonGroup</string>
+ <void property="name">
+ <string>buttonGroup1</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <null/>
+ <void method="setProperty">
+ <string>location</string>
+ <object class="java.awt.Point">
+ <int>0</int>
+ <int>615</int>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+</java>
diff --git a/org/broad/igv/ui/ReadmeParser.class b/org/broad/igv/ui/ReadmeParser.class
new file mode 100644
index 0000000..4d4d619
Binary files /dev/null and b/org/broad/igv/ui/ReadmeParser.class differ
diff --git a/org/broad/igv/ui/ResourceFileBuilder.class b/org/broad/igv/ui/ResourceFileBuilder.class
new file mode 100644
index 0000000..b9fe9aa
Binary files /dev/null and b/org/broad/igv/ui/ResourceFileBuilder.class differ
diff --git a/org/broad/igv/ui/ResourceFileBuilderDialog.class b/org/broad/igv/ui/ResourceFileBuilderDialog.class
new file mode 100644
index 0000000..ef6d9cf
Binary files /dev/null and b/org/broad/igv/ui/ResourceFileBuilderDialog.class differ
diff --git a/org/broad/igv/ui/ResourceTree$1.class b/org/broad/igv/ui/ResourceTree$1.class
new file mode 100644
index 0000000..7240f60
Binary files /dev/null and b/org/broad/igv/ui/ResourceTree$1.class differ
diff --git a/org/broad/igv/ui/ResourceTree$CancelableOptionPane.class b/org/broad/igv/ui/ResourceTree$CancelableOptionPane.class
new file mode 100644
index 0000000..63997ef
Binary files /dev/null and b/org/broad/igv/ui/ResourceTree$CancelableOptionPane.class differ
diff --git a/org/broad/igv/ui/ResourceTree$CheckableResource.class b/org/broad/igv/ui/ResourceTree$CheckableResource.class
new file mode 100644
index 0000000..c0cd662
Binary files /dev/null and b/org/broad/igv/ui/ResourceTree$CheckableResource.class differ
diff --git a/org/broad/igv/ui/ResourceTree$DataResource.class b/org/broad/igv/ui/ResourceTree$DataResource.class
new file mode 100644
index 0000000..112a341
Binary files /dev/null and b/org/broad/igv/ui/ResourceTree$DataResource.class differ
diff --git a/org/broad/igv/ui/ResourceTree$NodeRenderer.class b/org/broad/igv/ui/ResourceTree$NodeRenderer.class
new file mode 100644
index 0000000..6cc360b
Binary files /dev/null and b/org/broad/igv/ui/ResourceTree$NodeRenderer.class differ
diff --git a/org/broad/igv/ui/ResourceTree$ResourceEditor$1.class b/org/broad/igv/ui/ResourceTree$ResourceEditor$1.class
new file mode 100644
index 0000000..ad6132c
Binary files /dev/null and b/org/broad/igv/ui/ResourceTree$ResourceEditor$1.class differ
diff --git a/org/broad/igv/ui/ResourceTree$ResourceEditor.class b/org/broad/igv/ui/ResourceTree$ResourceEditor.class
new file mode 100644
index 0000000..47ee0c0
Binary files /dev/null and b/org/broad/igv/ui/ResourceTree$ResourceEditor.class differ
diff --git a/org/broad/igv/ui/ResourceTree$SelectableResource.class b/org/broad/igv/ui/ResourceTree$SelectableResource.class
new file mode 100644
index 0000000..6836f11
Binary files /dev/null and b/org/broad/igv/ui/ResourceTree$SelectableResource.class differ
diff --git a/org/broad/igv/ui/ResourceTree$TreeExpansionFlag.class b/org/broad/igv/ui/ResourceTree$TreeExpansionFlag.class
new file mode 100644
index 0000000..ac92376
Binary files /dev/null and b/org/broad/igv/ui/ResourceTree$TreeExpansionFlag.class differ
diff --git a/org/broad/igv/ui/ResourceTree.class b/org/broad/igv/ui/ResourceTree.class
new file mode 100644
index 0000000..de80d79
Binary files /dev/null and b/org/broad/igv/ui/ResourceTree.class differ
diff --git a/org/broad/igv/ui/ShutdownThread.class b/org/broad/igv/ui/ShutdownThread.class
new file mode 100644
index 0000000..279bde2
Binary files /dev/null and b/org/broad/igv/ui/ShutdownThread.class differ
diff --git a/org/broad/igv/ui/SimpleFormDialog.jfd b/org/broad/igv/ui/SimpleFormDialog.jfd
new file mode 100644
index 0000000..81ac40f
--- /dev/null
+++ b/org/broad/igv/ui/SimpleFormDialog.jfd
@@ -0,0 +1,244 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<java version="1.6.0_26" class="java.beans.XMLDecoder">
+ <object class="com.jformdesigner.model.FormModel">
+ <void property="contentType">
+ <string>form/swing</string>
+ </void>
+ <void property="root">
+ <object class="com.jformdesigner.model.FormRoot">
+ <void method="add">
+ <object class="com.jformdesigner.model.FormWindow">
+ <string>javax.swing.JDialog</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.BorderLayout</class>
+ </object>
+ <void method="setProperty">
+ <string>$sizePolicy</string>
+ <int>2</int>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.BorderLayout</class>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="javax.swing.border.EmptyBorder">
+ <int>12</int>
+ <int>12</int>
+ <int>12</int>
+ <int>12</int>
+ </object>
+ </void>
+ <void property="name">
+ <string>dialogPane</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>com.jformdesigner.runtime.NullLayout</class>
+ </object>
+ <void property="name">
+ <string>contentPanel</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>Center</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.GridBagLayout</class>
+ <void method="setProperty">
+ <string>$columnSpecs</string>
+ <string>0:1.0, 80, 80</string>
+ </void>
+ <void method="setProperty">
+ <string>$rowSpecs</string>
+ <string>0</string>
+ </void>
+ <void method="setProperty">
+ <string>$hGap</string>
+ <int>5</int>
+ </void>
+ <void method="setProperty">
+ <string>$vGap</string>
+ <int>5</int>
+ </void>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="javax.swing.border.EmptyBorder">
+ <int>12</int>
+ <int>0</int>
+ <int>0</int>
+ <int>0</int>
+ </object>
+ </void>
+ <void property="name">
+ <string>buttonBar</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>OK</string>
+ </void>
+ <void property="name">
+ <string>okButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>okButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>1</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>0</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Cancel</string>
+ </void>
+ <void property="name">
+ <string>cancelButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>cancelButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>0</int>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>South</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.BorderLayout</class>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="javax.swing.border.EmptyBorder">
+ <int>5</int>
+ <int>0</int>
+ <int>15</int>
+ <int>5</int>
+ </object>
+ </void>
+ <void property="name">
+ <string>panel1</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>font</string>
+ <object class="java.awt.Font">
+ <string>Lucida Grande</string>
+ <int>1</int>
+ <int>13</int>
+ </object>
+ </void>
+ <void property="name">
+ <string>promptLabel</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>Center</string>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>North</string>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>Center</string>
+ </void>
+ </object>
+ </void>
+ <void property="name">
+ <string>this</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <null/>
+ <void method="setProperty">
+ <string>location</string>
+ <object class="java.awt.Point">
+ <int>0</int>
+ <int>0</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>size</string>
+ <object class="java.awt.Dimension">
+ <int>400</int>
+ <int>300</int>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+</java>
diff --git a/org/broad/igv/ui/StatusWindow.class b/org/broad/igv/ui/StatusWindow.class
new file mode 100644
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diff --git a/org/broad/igv/ui/StatusWindow.jfd b/org/broad/igv/ui/StatusWindow.jfd
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--- /dev/null
+++ b/org/broad/igv/ui/StatusWindow.jfd
@@ -0,0 +1,70 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<java version="1.6.0_26" class="java.beans.XMLDecoder">
+ <object class="com.jformdesigner.model.FormModel">
+ <void property="contentType">
+ <string>form/swing</string>
+ </void>
+ <void property="root">
+ <object class="com.jformdesigner.model.FormRoot">
+ <void method="add">
+ <object class="com.jformdesigner.model.FormWindow">
+ <string>javax.swing.JFrame</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.BorderLayout</class>
+ </object>
+ <void method="setProperty">
+ <string>$sizePolicy</string>
+ <int>1</int>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JScrollPane</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>javax.swing.JScrollPane</class>
+ </object>
+ <void property="name">
+ <string>scrollPane1</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JEditorPane</string>
+ <void property="name">
+ <string>editorPane1</string>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>Center</string>
+ </void>
+ </object>
+ </void>
+ <void property="name">
+ <string>this</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <null/>
+ <void method="setProperty">
+ <string>location</string>
+ <object class="java.awt.Point">
+ <int>0</int>
+ <int>0</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>size</string>
+ <object class="java.awt.Dimension">
+ <int>405</int>
+ <int>355</int>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+</java>
diff --git a/org/broad/igv/ui/TestLauncher$1.class b/org/broad/igv/ui/TestLauncher$1.class
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diff --git a/org/broad/igv/ui/TooltipTextFrame$1.class b/org/broad/igv/ui/TooltipTextFrame$1.class
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index 0000000..307a3db
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diff --git a/org/broad/igv/ui/TrackConfigurationDialog$1.class b/org/broad/igv/ui/TrackConfigurationDialog$1.class
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diff --git a/org/broad/igv/ui/TrackFilter.class b/org/broad/igv/ui/TrackFilter.class
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index 0000000..3df1574
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diff --git a/org/broad/igv/ui/TrackFilterComponent.class b/org/broad/igv/ui/TrackFilterComponent.class
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diff --git a/org/broad/igv/ui/TrackFilterElement.class b/org/broad/igv/ui/TrackFilterElement.class
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diff --git a/org/broad/igv/ui/TrackFilterPane.class b/org/broad/igv/ui/TrackFilterPane.class
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diff --git a/org/broad/igv/ui/UIConstants.class b/org/broad/igv/ui/UIConstants.class
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diff --git a/org/broad/igv/ui/UserDefinedGenomeCheckList.class b/org/broad/igv/ui/UserDefinedGenomeCheckList.class
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diff --git a/org/broad/igv/ui/UserPasswordPane.class b/org/broad/igv/ui/UserPasswordPane.class
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+<?xml version="1.0" encoding="UTF-8"?>
+<java version="1.6.0_26" class="java.beans.XMLDecoder">
+ <object class="com.jformdesigner.model.FormModel">
+ <void property="contentType">
+ <string>form/swing</string>
+ </void>
+ <void property="root">
+ <object class="com.jformdesigner.model.FormRoot">
+ <void method="add">
+ <object class="com.jformdesigner.model.FormWindow">
+ <string>javax.swing.JFrame</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.BorderLayout</class>
+ </object>
+ <void method="setProperty">
+ <string>$sizePolicy</string>
+ <int>1</int>
+ </void>
+ <void method="setProperty">
+ <string>defaultCloseOperation</string>
+ <int>3</int>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>org.broad.igv.ui.color.ColorPanel</string>
+ <void property="name">
+ <string>colorPanel</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>Center</string>
+ </void>
+ </object>
+ </void>
+ <void property="menuBar">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JMenuBar</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>javax.swing.JMenuBar</class>
+ </object>
+ <void property="name">
+ <string>menuBar1</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JMenu</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>javax.swing.JMenu</class>
+ </object>
+ <void method="setProperty">
+ <string>text</string>
+ <string>File</string>
+ </void>
+ <void property="name">
+ <string>menu1</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JMenuItem</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Save...</string>
+ </void>
+ <void property="name">
+ <string>saveItem</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>saveItemActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>com.jformdesigner.designer.wrapper.HSpacer</string>
+ <void property="name">
+ <string>hSpacer1</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JCheckBox</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>De-saturate</string>
+ </void>
+ <void property="name">
+ <string>desaturateCheckbox</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>showGrayScaleActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+ </void>
+ <void property="name">
+ <string>this</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <null/>
+ <void method="setProperty">
+ <string>location</string>
+ <object class="java.awt.Point">
+ <int>0</int>
+ <int>0</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>size</string>
+ <object class="java.awt.Dimension">
+ <int>890</int>
+ <int>570</int>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+</java>
diff --git a/org/broad/igv/ui/color/resources/colorPalettes.txt b/org/broad/igv/ui/color/resources/colorPalettes.txt
new file mode 100644
index 0000000..7e5ef6f
--- /dev/null
+++ b/org/broad/igv/ui/color/resources/colorPalettes.txt
@@ -0,0 +1,20 @@
+#Set 1
+228, 26, 28; 55, 126, 184; 77, 175, 74; 166, 86, 40; 152, 78, 163; 255, 127, 0; 247, 129, 191; 153, 153, 153; 255, 255, 51;
+#Dark 2
+27, 158, 119; 217, 95, 2; 117, 112, 179; 231, 41, 138; 102, 166, 30; 230, 171, 2; 166, 118, 29; 102, 102, 102;
+#Set 2
+102, 194, 165; 252, 141, 98; 141, 160, 203; 231, 138, 195; 166, 216, 84; 255, 217, 47; 229, 196, 148; 179, 179, 179;
+#Set 3
+141, 211, 199; 255, 255, 179; 190, 186, 218; 251, 128, 114; 128, 177, 211; 253, 180, 98; 179, 222, 105; 252, 205, 229; 217, 217, 217; 188, 128, 189; 204, 235, 197; 255, 237, 111;
+#Pastel 1
+251, 180, 174; 179, 205, 227; 204, 235, 197; 222, 203, 228; 254, 217, 166; 255, 255, 204; 229, 216, 189; 253, 218, 236;
+#Pastel 2
+173, 226, 207; 253, 205, 172; 203, 213, 232; 244, 202, 228; 230, 245, 201; 255, 242, 174; 243, 225, 206;
+#Accent
+127, 201, 127; 190, 174, 212; 253, 192, 134; 255, 255, 153; 56, 108, 176; 240, 2, 127; 191, 91, 23;
+
+
+
+
+
+
diff --git a/org/broad/igv/ui/dnd/AbstractGhostDropManager.class b/org/broad/igv/ui/dnd/AbstractGhostDropManager.class
new file mode 100644
index 0000000..24c44be
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diff --git a/org/broad/igv/ui/dnd/GhostDropAdapter.class b/org/broad/igv/ui/dnd/GhostDropAdapter.class
new file mode 100644
index 0000000..a7c60b6
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diff --git a/org/broad/igv/ui/dnd/GhostDropEvent.class b/org/broad/igv/ui/dnd/GhostDropEvent.class
new file mode 100644
index 0000000..bb44542
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diff --git a/org/broad/igv/ui/dnd/GhostDropListener.class b/org/broad/igv/ui/dnd/GhostDropListener.class
new file mode 100644
index 0000000..114ad2d
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diff --git a/org/broad/igv/ui/dnd/GhostGlassPane.class b/org/broad/igv/ui/dnd/GhostGlassPane.class
new file mode 100644
index 0000000..41a5757
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diff --git a/org/broad/igv/ui/event/AlignmentTrackEvent$Type.class b/org/broad/igv/ui/event/AlignmentTrackEvent$Type.class
new file mode 100644
index 0000000..a86eef7
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diff --git a/org/broad/igv/ui/event/AlignmentTrackEvent.class b/org/broad/igv/ui/event/AlignmentTrackEvent.class
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index 0000000..2ad1e8f
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diff --git a/org/broad/igv/ui/event/AlignmentTrackEventListener.class b/org/broad/igv/ui/event/AlignmentTrackEventListener.class
new file mode 100644
index 0000000..218a710
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diff --git a/org/broad/igv/ui/event/GlobalKeyDispatcher$1.class b/org/broad/igv/ui/event/GlobalKeyDispatcher$1.class
new file mode 100644
index 0000000..2b1cbac
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diff --git a/org/broad/igv/ui/event/GlobalKeyDispatcher$10.class b/org/broad/igv/ui/event/GlobalKeyDispatcher$10.class
new file mode 100644
index 0000000..3fca173
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diff --git a/org/broad/igv/ui/event/GlobalKeyDispatcher$11.class b/org/broad/igv/ui/event/GlobalKeyDispatcher$11.class
new file mode 100644
index 0000000..4ffaba9
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diff --git a/org/broad/igv/ui/event/GlobalKeyDispatcher$2.class b/org/broad/igv/ui/event/GlobalKeyDispatcher$2.class
new file mode 100644
index 0000000..1e27d77
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diff --git a/org/broad/igv/ui/event/GlobalKeyDispatcher$3.class b/org/broad/igv/ui/event/GlobalKeyDispatcher$3.class
new file mode 100644
index 0000000..8be93f7
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diff --git a/org/broad/igv/ui/event/GlobalKeyDispatcher$4.class b/org/broad/igv/ui/event/GlobalKeyDispatcher$4.class
new file mode 100644
index 0000000..8e7b4bb
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diff --git a/org/broad/igv/ui/event/GlobalKeyDispatcher$5.class b/org/broad/igv/ui/event/GlobalKeyDispatcher$5.class
new file mode 100644
index 0000000..6c524bb
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diff --git a/org/broad/igv/ui/event/GlobalKeyDispatcher$6.class b/org/broad/igv/ui/event/GlobalKeyDispatcher$6.class
new file mode 100644
index 0000000..0dbb599
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diff --git a/org/broad/igv/ui/event/GlobalKeyDispatcher$7.class b/org/broad/igv/ui/event/GlobalKeyDispatcher$7.class
new file mode 100644
index 0000000..8fff905
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diff --git a/org/broad/igv/ui/event/GlobalKeyDispatcher$8.class b/org/broad/igv/ui/event/GlobalKeyDispatcher$8.class
new file mode 100644
index 0000000..d119479
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diff --git a/org/broad/igv/ui/event/GlobalKeyDispatcher$9.class b/org/broad/igv/ui/event/GlobalKeyDispatcher$9.class
new file mode 100644
index 0000000..27ad068
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diff --git a/org/broad/igv/ui/event/GlobalKeyDispatcher.class b/org/broad/igv/ui/event/GlobalKeyDispatcher.class
new file mode 100644
index 0000000..c83417f
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diff --git a/org/broad/igv/ui/event/TrackGroupEvent.class b/org/broad/igv/ui/event/TrackGroupEvent.class
new file mode 100644
index 0000000..b952289
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diff --git a/org/broad/igv/ui/event/TrackGroupEventListener.class b/org/broad/igv/ui/event/TrackGroupEventListener.class
new file mode 100644
index 0000000..9bf7d18
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diff --git a/org/broad/igv/ui/filefilters/AlignmentFileFilter.class b/org/broad/igv/ui/filefilters/AlignmentFileFilter.class
new file mode 100644
index 0000000..1a542ab
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diff --git a/org/broad/igv/ui/filefilters/CoverageFileFilter.class b/org/broad/igv/ui/filefilters/CoverageFileFilter.class
new file mode 100644
index 0000000..74b944a
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diff --git a/org/broad/igv/ui/legend/ChromosomeColorLegend.class b/org/broad/igv/ui/legend/ChromosomeColorLegend.class
new file mode 100644
index 0000000..fddcc91
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diff --git a/org/broad/igv/ui/legend/ColorMapEditor$1.class b/org/broad/igv/ui/legend/ColorMapEditor$1.class
new file mode 100644
index 0000000..b92377b
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diff --git a/org/broad/igv/ui/legend/ColorMapEditor$2.class b/org/broad/igv/ui/legend/ColorMapEditor$2.class
new file mode 100644
index 0000000..54507a4
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diff --git a/org/broad/igv/ui/legend/ColorMapEditor$3.class b/org/broad/igv/ui/legend/ColorMapEditor$3.class
new file mode 100644
index 0000000..f8804d6
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diff --git a/org/broad/igv/ui/legend/ColorMapEditor.class b/org/broad/igv/ui/legend/ColorMapEditor.class
new file mode 100644
index 0000000..1620006
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diff --git a/org/broad/igv/ui/legend/HeatmapLegendEditor$1.class b/org/broad/igv/ui/legend/HeatmapLegendEditor$1.class
new file mode 100644
index 0000000..a3171f2
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diff --git a/org/broad/igv/ui/legend/HeatmapLegendEditor$2.class b/org/broad/igv/ui/legend/HeatmapLegendEditor$2.class
new file mode 100644
index 0000000..903ffe0
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diff --git a/org/broad/igv/ui/legend/HeatmapLegendEditor$3.class b/org/broad/igv/ui/legend/HeatmapLegendEditor$3.class
new file mode 100644
index 0000000..c23fede
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diff --git a/org/broad/igv/ui/legend/HeatmapLegendEditor$4.class b/org/broad/igv/ui/legend/HeatmapLegendEditor$4.class
new file mode 100644
index 0000000..bf7e9ec
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diff --git a/org/broad/igv/ui/legend/HeatmapLegendEditor.class b/org/broad/igv/ui/legend/HeatmapLegendEditor.class
new file mode 100644
index 0000000..8ae0890
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diff --git a/org/broad/igv/ui/legend/HeatmapLegendEditor.jfd b/org/broad/igv/ui/legend/HeatmapLegendEditor.jfd
new file mode 100644
index 0000000..fc7f27e
--- /dev/null
+++ b/org/broad/igv/ui/legend/HeatmapLegendEditor.jfd
@@ -0,0 +1,367 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<java version="1.6.0_22" class="java.beans.XMLDecoder">
+ <object class="com.jformdesigner.model.FormModel">
+ <void property="contentType">
+ <string>form/swing</string>
+ </void>
+ <void property="root">
+ <object class="com.jformdesigner.model.FormRoot">
+ <void method="add">
+ <object class="com.jformdesigner.model.FormWindow">
+ <string>javax.swing.JDialog</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>org.jdesktop.layout.GroupLayout</class>
+ <void method="setProperty">
+ <string>$horizontalGroup</string>
+ <string>par l {seq {space :p:35:p, par l:::p {comp doubleGradientCheckbox::l:p:175:p, comp jPanel1::l:p:184:p:1, comp negRangePanel::l:::x:1, comp posRangePanel::t:::x:1}, space ::101:x}, seq t {space ::124:x, comp okButton:::p::p, space :::p, comp cancelButton:::p::p, space :p:132:p}}</string>
+ </void>
+ <void method="setProperty">
+ <string>$verticalGroup</string>
+ <string>par l {seq l {space :p:52:p, comp doubleGradientCheckbox:::p::p, space s:::p, comp jPanel1:::p::p, space :::p, comp negRangePanel:::p:30:p, space u:::p, comp posRangePanel:::p:30:p, space s:::p, par b {comp okButton::b:p::p, comp cancelButton::b:p::p}, space :p:34:p}}</string>
+ </void>
+ </object>
+ <void method="setProperty">
+ <string>defaultCloseOperation</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>resizable</string>
+ <boolean>false</boolean>
+ </void>
+ <void method="setProperty">
+ <string>$sizePolicy</string>
+ <int>1</int>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>org.jdesktop.layout.GroupLayout</class>
+ <void method="setProperty">
+ <string>$horizontalGroup</string>
+ <string>par l {seq {par l {seq l {comp jLabel3:::p::p, space :::x, comp maxColor:4::p:50:p}, seq l {comp minColorLabel:::p::p, space ::9:x, comp minColor:4::p:75:p}, seq t {comp midColorLabel:::p::p, space ::12:x, comp midColor:4::p:50:p}}, space :p::p}}</string>
+ </void>
+ <void method="setProperty">
+ <string>$verticalGroup</string>
+ <string>par l {seq {par l {seq {comp minColorLabel:3::p::p, space u:::p, comp midColorLabel:2::p::p}, seq l {comp minColor:3::p:25:p, space :p:14:p, comp midColor:2::p:25:p}}, space :p:12:p, par l {seq t {comp jLabel3:1::p::p, space :p:20:p}, seq l {comp maxColor:1::p:25:p, space :::p}}}}</string>
+ </void>
+ </object>
+ <void property="name">
+ <string>jPanel1</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Midpoint Color</string>
+ </void>
+ <void property="name">
+ <string>midColorLabel</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Maximum Color</string>
+ </void>
+ <void property="name">
+ <string>jLabel3</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Minimum Color</string>
+ </void>
+ <void property="name">
+ <string>minColorLabel</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>com.jidesoft.combobox.ColorComboBox</string>
+ <void method="setProperty">
+ <string>colorValueVisible</string>
+ <boolean>false</boolean>
+ </void>
+ <void property="name">
+ <string>minColor</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>com.jidesoft.combobox.ColorComboBox</string>
+ <void method="setProperty">
+ <string>colorValueVisible</string>
+ <boolean>false</boolean>
+ </void>
+ <void property="name">
+ <string>midColor</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>com.jidesoft.combobox.ColorComboBox</string>
+ <void method="setProperty">
+ <string>colorValueVisible</string>
+ <boolean>false</boolean>
+ </void>
+ <void property="name">
+ <string>maxColor</string>
+ </void>
+ </object>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>OK</string>
+ </void>
+ <void property="name">
+ <string>okButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>okButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Cancel</string>
+ </void>
+ <void property="name">
+ <string>cancelButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>cancelButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>org.jdesktop.layout.GroupLayout</class>
+ <void method="setProperty">
+ <string>$horizontalGroup</string>
+ <string>par l {seq l {comp negRangeLabel:::p:115:p, space :::p, comp negRangeStart:::p:59:p, space u:::p, comp negRangeToLabel:::p:30:p:1, space :::p, comp negRangeEnd:::p:59:p:1}}</string>
+ </void>
+ <void method="setProperty">
+ <string>$verticalGroup</string>
+ <string>par l {seq {par l {comp negRangeLabel:::p:22:p, par b:l {comp negRangeStart::b:p::p, comp negRangeToLabel::b:p:22:p, comp negRangeEnd::b:p::p}}, space :::x}}</string>
+ </void>
+ </object>
+ <void property="name">
+ <string>negRangePanel</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Negative Range: </string>
+ </void>
+ <void property="name">
+ <string>negRangeLabel</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>-0.1</string>
+ </void>
+ <void property="name">
+ <string>negRangeStart</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>To:</string>
+ </void>
+ <void property="name">
+ <string>negRangeToLabel</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>-1.5</string>
+ </void>
+ <void property="name">
+ <string>negRangeEnd</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>negRangeEndActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JCheckBox</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Use Double Gradient</string>
+ </void>
+ <void property="name">
+ <string>doubleGradientCheckbox</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>doubleGradientCheckboxActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>org.jdesktop.layout.GroupLayout</class>
+ <void method="setProperty">
+ <string>$horizontalGroup</string>
+ <string>par l {seq l {comp posRangeLabel:::p:115:p, space :::p, comp posRangeStart:::p:59:p, space u:::p, comp posRangeToLabel:::p:30:p:1, space :::p, comp posRangeEnd:::p:59:p:1}}</string>
+ </void>
+ <void method="setProperty">
+ <string>$verticalGroup</string>
+ <string>par l {seq l {par l {comp posRangeLabel::l:p:22:p, par b:l {comp posRangeStart::b:p::p, comp posRangeToLabel::b:p:22:p, comp posRangeEnd::b:p::p}}, space :::x}}</string>
+ </void>
+ </object>
+ <void property="name">
+ <string>posRangePanel</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Positive Range: </string>
+ </void>
+ <void property="name">
+ <string>posRangeLabel</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>-0.1</string>
+ </void>
+ <void property="name">
+ <string>posRangeStart</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>To:</string>
+ </void>
+ <void property="name">
+ <string>posRangeToLabel</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>-1.5</string>
+ </void>
+ <void method="setProperty">
+ <string>maximumSize</string>
+ <object class="java.awt.Dimension">
+ <int>36</int>
+ <int>22</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>minimumSize</string>
+ <object class="java.awt.Dimension">
+ <int>36</int>
+ <int>22</int>
+ </object>
+ </void>
+ <void property="name">
+ <string>posRangeEnd</string>
+ </void>
+ </object>
+ </void>
+ </object>
+ </void>
+ <void property="name">
+ <string>this</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <null/>
+ <void method="setProperty">
+ <string>size</string>
+ <object class="java.awt.Dimension">
+ <int>425</int>
+ <int>405</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>location</string>
+ <object class="java.awt.Point">
+ <int>0</int>
+ <int>0</int>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+</java>
diff --git a/org/broad/igv/ui/legend/HeatmapLegendPanel$1$1.class b/org/broad/igv/ui/legend/HeatmapLegendPanel$1$1.class
new file mode 100644
index 0000000..66d3c0f
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diff --git a/org/broad/igv/ui/legend/HeatmapLegendPanel$1.class b/org/broad/igv/ui/legend/HeatmapLegendPanel$1.class
new file mode 100644
index 0000000..408fc7a
Binary files /dev/null and b/org/broad/igv/ui/legend/HeatmapLegendPanel$1.class differ
diff --git a/org/broad/igv/ui/legend/HeatmapLegendPanel$Orientation.class b/org/broad/igv/ui/legend/HeatmapLegendPanel$Orientation.class
new file mode 100644
index 0000000..1631a2e
Binary files /dev/null and b/org/broad/igv/ui/legend/HeatmapLegendPanel$Orientation.class differ
diff --git a/org/broad/igv/ui/legend/HeatmapLegendPanel.class b/org/broad/igv/ui/legend/HeatmapLegendPanel.class
new file mode 100644
index 0000000..7c8b9b2
Binary files /dev/null and b/org/broad/igv/ui/legend/HeatmapLegendPanel.class differ
diff --git a/org/broad/igv/ui/legend/LegendDialog$1.class b/org/broad/igv/ui/legend/LegendDialog$1.class
new file mode 100644
index 0000000..b513d85
Binary files /dev/null and b/org/broad/igv/ui/legend/LegendDialog$1.class differ
diff --git a/org/broad/igv/ui/legend/LegendDialog$2.class b/org/broad/igv/ui/legend/LegendDialog$2.class
new file mode 100644
index 0000000..7d0dd39
Binary files /dev/null and b/org/broad/igv/ui/legend/LegendDialog$2.class differ
diff --git a/org/broad/igv/ui/legend/LegendDialog$3.class b/org/broad/igv/ui/legend/LegendDialog$3.class
new file mode 100644
index 0000000..eade234
Binary files /dev/null and b/org/broad/igv/ui/legend/LegendDialog$3.class differ
diff --git a/org/broad/igv/ui/legend/LegendDialog$4.class b/org/broad/igv/ui/legend/LegendDialog$4.class
new file mode 100644
index 0000000..a771147
Binary files /dev/null and b/org/broad/igv/ui/legend/LegendDialog$4.class differ
diff --git a/org/broad/igv/ui/legend/LegendDialog$5.class b/org/broad/igv/ui/legend/LegendDialog$5.class
new file mode 100644
index 0000000..1bd65ef
Binary files /dev/null and b/org/broad/igv/ui/legend/LegendDialog$5.class differ
diff --git a/org/broad/igv/ui/legend/LegendDialog$6.class b/org/broad/igv/ui/legend/LegendDialog$6.class
new file mode 100644
index 0000000..e857060
Binary files /dev/null and b/org/broad/igv/ui/legend/LegendDialog$6.class differ
diff --git a/org/broad/igv/ui/legend/LegendDialog$7.class b/org/broad/igv/ui/legend/LegendDialog$7.class
new file mode 100644
index 0000000..7af1100
Binary files /dev/null and b/org/broad/igv/ui/legend/LegendDialog$7.class differ
diff --git a/org/broad/igv/ui/legend/LegendDialog$8.class b/org/broad/igv/ui/legend/LegendDialog$8.class
new file mode 100644
index 0000000..1cc416e
Binary files /dev/null and b/org/broad/igv/ui/legend/LegendDialog$8.class differ
diff --git a/org/broad/igv/ui/legend/LegendDialog$9$1.class b/org/broad/igv/ui/legend/LegendDialog$9$1.class
new file mode 100644
index 0000000..312157e
Binary files /dev/null and b/org/broad/igv/ui/legend/LegendDialog$9$1.class differ
diff --git a/org/broad/igv/ui/legend/LegendDialog$9.class b/org/broad/igv/ui/legend/LegendDialog$9.class
new file mode 100644
index 0000000..7137590
Binary files /dev/null and b/org/broad/igv/ui/legend/LegendDialog$9.class differ
diff --git a/org/broad/igv/ui/legend/LegendDialog.class b/org/broad/igv/ui/legend/LegendDialog.class
new file mode 100644
index 0000000..02fb2fc
Binary files /dev/null and b/org/broad/igv/ui/legend/LegendDialog.class differ
diff --git a/org/broad/igv/ui/legend/LegendDialog.jfd b/org/broad/igv/ui/legend/LegendDialog.jfd
new file mode 100644
index 0000000..4874aeb
--- /dev/null
+++ b/org/broad/igv/ui/legend/LegendDialog.jfd
@@ -0,0 +1,821 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<java version="1.6.0_26" class="java.beans.XMLDecoder">
+ <object class="com.jformdesigner.model.FormModel">
+ <void property="contentType">
+ <string>form/swing</string>
+ </void>
+ <void property="root">
+ <object class="com.jformdesigner.model.FormRoot">
+ <void method="add">
+ <object class="com.jformdesigner.model.FormWindow">
+ <string>javax.swing.JDialog</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>com.jformdesigner.runtime.NullLayout</class>
+ </object>
+ <void method="setProperty">
+ <string>defaultCloseOperation</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>$sizePolicy</string>
+ <int>1</int>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>font</string>
+ <object class="java.awt.Font">
+ <string>Lucida Sans</string>
+ <int>1</int>
+ <int>18</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Legends</string>
+ </void>
+ <void property="name">
+ <string>jLabel1</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>325</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>0</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>com.jformdesigner.runtime.NullLayout</class>
+ </object>
+ <void property="name">
+ <string>panel1</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Copy Number</string>
+ </void>
+ <void property="name">
+ <string>cnLabel</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
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+ <void method="setProperty">
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+ <int>7</int>
+ </void>
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+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>org.jdesktop.layout.GroupLayout</class>
+ <void method="setProperty">
+ <string>$horizontalGroup</string>
+ <string>par l {space :0:483:x}</string>
+ </void>
+ <void method="setProperty">
+ <string>$verticalGroup</string>
+ <string>par l {space :0:60:x}</string>
+ </void>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="com.jformdesigner.model.FormObject" field="NULL_VALUE"/>
+ </void>
+ <void method="auxiliary">
+ <void method="setProperty">
+ <string>JavaCodeGenerator.customCreateCode</string>
+ <string>new org.broad.igv.ui.legend.HeatmapLegendPanel(TrackType.COPY_NUMBER);</string>
+ </void>
+ </void>
+ <void property="name">
+ <string>copyNoCanvas</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
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+ <void method="add">
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+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Expression</string>
+ </void>
+ <void property="name">
+ <string>legendLabel1</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
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+ <void method="setProperty">
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+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>org.jdesktop.layout.GroupLayout</class>
+ <void method="setProperty">
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+ <void method="setProperty">
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+ <string>par l {space :0:60:x}</string>
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+ <void method="setProperty">
+ <string>minimumSize</string>
+ <object class="java.awt.Dimension">
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+ <int>100</int>
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+ </void>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="com.jformdesigner.model.FormObject" field="NULL_VALUE"/>
+ </void>
+ <void method="auxiliary">
+ <void method="setProperty">
+ <string>JavaCodeGenerator.customCreateCode</string>
+ <string>new HeatmapLegendPanel(TrackType.DNA_METHYLATION);</string>
+ </void>
+ </void>
+ <void property="name">
+ <string>methylationCanvas</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
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+ <void method="add">
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+ <class>org.jdesktop.layout.GroupLayout</class>
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+ </void>
+ <void method="setProperty">
+ <string>$verticalGroup</string>
+ <string>par l {space :0:60:x}</string>
+ </void>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="com.jformdesigner.model.FormObject" field="NULL_VALUE"/>
+ </void>
+ <void method="auxiliary">
+ <void method="setProperty">
+ <string>JavaCodeGenerator.customCreateCode</string>
+ <string>new LohLegendPanel();</string>
+ </void>
+ </void>
+ <void property="name">
+ <string>lohCanvas</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
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+ <void method="setProperty">
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+ <int>485</int>
+ </void>
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+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>LOH</string>
+ </void>
+ <void property="name">
+ <string>legendLabel2</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
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+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Methylation</string>
+ </void>
+ <void property="name">
+ <string>jLabel2</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
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+ <void method="setProperty">
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+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>org.jdesktop.layout.GroupLayout</class>
+ <void method="setProperty">
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+ <void method="setProperty">
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+ <string>par l {space :0:60:x}</string>
+ </void>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="com.jformdesigner.model.FormObject" field="NULL_VALUE"/>
+ </void>
+ <void method="auxiliary">
+ <void method="setProperty">
+ <string>JavaCodeGenerator.customCreateCode</string>
+ <string>new HeatmapLegendPanel(TrackType.GENE_EXPRESSION);</string>
+ </void>
+ </void>
+ <void property="name">
+ <string>expressionCanvas</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
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+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>org.jdesktop.layout.GroupLayout</class>
+ <void method="setProperty">
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+ <void method="setProperty">
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+ <string>par l {space :0:62:x}</string>
+ </void>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="com.jformdesigner.model.FormObject" field="NULL_VALUE"/>
+ </void>
+ <void method="auxiliary">
+ <void method="setProperty">
+ <string>JavaCodeGenerator.customCreateCode</string>
+ <string>new MutationLegendPanel();</string>
+ </void>
+ </void>
+ <void property="name">
+ <string>mutationCanvas</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
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+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Mutation</string>
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+ <void property="name">
+ <string>legendLabel3</string>
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+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
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+ <object class="com.jformdesigner.model.FormComponent">
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+ <void method="setProperty">
+ <string>text</string>
+ <string>RNAi</string>
+ </void>
+ <void property="name">
+ <string>legendLabel4</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
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+ <void method="setProperty">
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+ <object class="com.jformdesigner.model.FormLayoutManager">
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+ <void method="setProperty">
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+ <string>par l {space :0:60:x}</string>
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+ <void method="setProperty">
+ <string>border</string>
+ <object class="com.jformdesigner.model.FormObject" field="NULL_VALUE"/>
+ </void>
+ <void method="auxiliary">
+ <void method="setProperty">
+ <string>JavaCodeGenerator.customCreateCode</string>
+ <string>new HeatmapLegendPanel(TrackType.RNAI);</string>
+ </void>
+ </void>
+ <void property="name">
+ <string>rnaiPanel</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>y</string>
+ <int>167</int>
+ </void>
+ <void method="setProperty">
+ <string>height</string>
+ <int>62</int>
+ </void>
+ <void method="setProperty">
+ <string>x</string>
+ <int>110</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>485</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Edit</string>
+ </void>
+ <void property="name">
+ <string>copyNumberButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>copyNumberButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>620</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>7</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Edit</string>
+ </void>
+ <void property="name">
+ <string>expressionButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>expressionButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>620</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>87</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Edit</string>
+ </void>
+ <void property="name">
+ <string>rnaiButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>rnaiButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>620</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>167</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Edit</string>
+ </void>
+ <void property="name">
+ <string>methylationButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>methylationButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>620</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>247</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Edit</string>
+ </void>
+ <void property="name">
+ <string>lohButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>lohButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>620</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>327</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Edit</string>
+ </void>
+ <void property="name">
+ <string>mutationButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>mutationButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>620</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>424</int>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>10</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>30</int>
+ </void>
+ <void method="setProperty">
+ <string>height</string>
+ <int>495</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>720</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Reset to default</string>
+ </void>
+ <void property="name">
+ <string>resetToDefault</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>resetToDefaultActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>475</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>575</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>OK</string>
+ </void>
+ <void property="name">
+ <string>okButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>okButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>635</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>575</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string><html>* click any item to bring up its editor</string>
+ </void>
+ <void property="name">
+ <string>jLabel3</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>width</string>
+ <int>396</int>
+ </void>
+ <void method="setProperty">
+ <string>x</string>
+ <int>15</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>550</int>
+ </void>
+ </object>
+ </void>
+ <void property="name">
+ <string>this</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <null/>
+ <void method="setProperty">
+ <string>size</string>
+ <object class="java.awt.Dimension">
+ <int>755</int>
+ <int>665</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>location</string>
+ <object class="java.awt.Point">
+ <int>0</int>
+ <int>0</int>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+</java>
diff --git a/org/broad/igv/ui/legend/LegendPanel$1.class b/org/broad/igv/ui/legend/LegendPanel$1.class
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index 0000000..1fbf935
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index 0000000..eae0fd2
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index 0000000..c0c20f7
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diff --git a/org/broad/igv/ui/legend/LohLegendPanel.class b/org/broad/igv/ui/legend/LohLegendPanel.class
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index 0000000..ad5746f
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index 0000000..8a174d9
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diff --git a/org/broad/igv/ui/panel/AttributeHeaderPanel$1.class b/org/broad/igv/ui/panel/AttributeHeaderPanel$1.class
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index 0000000..71cdbb5
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diff --git a/org/broad/igv/ui/panel/AttributePanel$AttributePanelMouseAdapter.class b/org/broad/igv/ui/panel/AttributePanel$AttributePanelMouseAdapter.class
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diff --git a/org/broad/igv/ui/panel/ClickTaskScheduler.class b/org/broad/igv/ui/panel/ClickTaskScheduler.class
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index 0000000..1d1e86d
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diff --git a/org/broad/igv/ui/panel/CytobandPanel$1.class b/org/broad/igv/ui/panel/CytobandPanel$1.class
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index 0000000..6e7aebc
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diff --git a/org/broad/igv/ui/panel/DataPanel$1.class b/org/broad/igv/ui/panel/DataPanel$1.class
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diff --git a/org/broad/igv/ui/panel/DataPanel$PopupTextUpdater.class b/org/broad/igv/ui/panel/DataPanel$PopupTextUpdater.class
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diff --git a/org/broad/igv/ui/panel/DataPanelContainer$1.class b/org/broad/igv/ui/panel/DataPanelContainer$1.class
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diff --git a/org/broad/igv/ui/panel/DataPanelContainer$FileDropTargetListener.class b/org/broad/igv/ui/panel/DataPanelContainer$FileDropTargetListener.class
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diff --git a/org/broad/igv/ui/panel/DataPanelPainter.class b/org/broad/igv/ui/panel/DataPanelPainter.class
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diff --git a/org/broad/igv/ui/panel/DragAndDropTransferHandler.class b/org/broad/igv/ui/panel/DragAndDropTransferHandler.class
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diff --git a/org/broad/igv/ui/panel/DragEvent.class b/org/broad/igv/ui/panel/DragEvent.class
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diff --git a/org/broad/igv/ui/panel/HeaderPanel$1.class b/org/broad/igv/ui/panel/HeaderPanel$1.class
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diff --git a/org/broad/igv/ui/panel/MouseableRegion$TrackCltn.class b/org/broad/igv/ui/panel/MouseableRegion$TrackCltn.class
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diff --git a/org/broad/igv/ui/panel/ReferenceFrame$Range.class b/org/broad/igv/ui/panel/ReferenceFrame$Range.class
new file mode 100644
index 0000000..ad48070
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diff --git a/org/broad/igv/ui/panel/ReferenceFrame.class b/org/broad/igv/ui/panel/ReferenceFrame.class
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index 0000000..bad5f46
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diff --git a/org/broad/igv/ui/panel/RegionMenu$1.class b/org/broad/igv/ui/panel/RegionMenu$1.class
new file mode 100644
index 0000000..14ea600
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diff --git a/org/broad/igv/ui/panel/RegionMenu$2.class b/org/broad/igv/ui/panel/RegionMenu$2.class
new file mode 100644
index 0000000..f69aaae
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diff --git a/org/broad/igv/ui/panel/RegionMenu$3.class b/org/broad/igv/ui/panel/RegionMenu$3.class
new file mode 100644
index 0000000..fecc982
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diff --git a/org/broad/igv/ui/panel/RegionMenu$4.class b/org/broad/igv/ui/panel/RegionMenu$4.class
new file mode 100644
index 0000000..5f58358
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diff --git a/org/broad/igv/ui/panel/RegionMenu$5.class b/org/broad/igv/ui/panel/RegionMenu$5.class
new file mode 100644
index 0000000..0a421dc
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diff --git a/org/broad/igv/ui/panel/RegionMenu$6.class b/org/broad/igv/ui/panel/RegionMenu$6.class
new file mode 100644
index 0000000..42d3b74
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diff --git a/org/broad/igv/ui/panel/RegionMenu$7.class b/org/broad/igv/ui/panel/RegionMenu$7.class
new file mode 100644
index 0000000..0be6752
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diff --git a/org/broad/igv/ui/panel/RegionMenu.class b/org/broad/igv/ui/panel/RegionMenu.class
new file mode 100644
index 0000000..5f16b1e
Binary files /dev/null and b/org/broad/igv/ui/panel/RegionMenu.class differ
diff --git a/org/broad/igv/ui/panel/RegionNavigatorDialog$1.class b/org/broad/igv/ui/panel/RegionNavigatorDialog$1.class
new file mode 100644
index 0000000..74e5604
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diff --git a/org/broad/igv/ui/panel/RegionNavigatorDialog$2.class b/org/broad/igv/ui/panel/RegionNavigatorDialog$2.class
new file mode 100644
index 0000000..9b9c5fc
Binary files /dev/null and b/org/broad/igv/ui/panel/RegionNavigatorDialog$2.class differ
diff --git a/org/broad/igv/ui/panel/RegionNavigatorDialog$3.class b/org/broad/igv/ui/panel/RegionNavigatorDialog$3.class
new file mode 100644
index 0000000..fac8323
Binary files /dev/null and b/org/broad/igv/ui/panel/RegionNavigatorDialog$3.class differ
diff --git a/org/broad/igv/ui/panel/RegionNavigatorDialog$AddRegionAction.class b/org/broad/igv/ui/panel/RegionNavigatorDialog$AddRegionAction.class
new file mode 100644
index 0000000..468a021
Binary files /dev/null and b/org/broad/igv/ui/panel/RegionNavigatorDialog$AddRegionAction.class differ
diff --git a/org/broad/igv/ui/panel/RegionNavigatorDialog$CancelAction.class b/org/broad/igv/ui/panel/RegionNavigatorDialog$CancelAction.class
new file mode 100644
index 0000000..d121200
Binary files /dev/null and b/org/broad/igv/ui/panel/RegionNavigatorDialog$CancelAction.class differ
diff --git a/org/broad/igv/ui/panel/RegionNavigatorDialog$RegionRowFilter.class b/org/broad/igv/ui/panel/RegionNavigatorDialog$RegionRowFilter.class
new file mode 100644
index 0000000..624bead
Binary files /dev/null and b/org/broad/igv/ui/panel/RegionNavigatorDialog$RegionRowFilter.class differ
diff --git a/org/broad/igv/ui/panel/RegionNavigatorDialog$RegionTableModelListener.class b/org/broad/igv/ui/panel/RegionNavigatorDialog$RegionTableModelListener.class
new file mode 100644
index 0000000..9be121e
Binary files /dev/null and b/org/broad/igv/ui/panel/RegionNavigatorDialog$RegionTableModelListener.class differ
diff --git a/org/broad/igv/ui/panel/RegionNavigatorDialog$RegionTablePopupHandler$1.class b/org/broad/igv/ui/panel/RegionNavigatorDialog$RegionTablePopupHandler$1.class
new file mode 100644
index 0000000..cffcd1d
Binary files /dev/null and b/org/broad/igv/ui/panel/RegionNavigatorDialog$RegionTablePopupHandler$1.class differ
diff --git a/org/broad/igv/ui/panel/RegionNavigatorDialog$RegionTablePopupHandler$2.class b/org/broad/igv/ui/panel/RegionNavigatorDialog$RegionTablePopupHandler$2.class
new file mode 100644
index 0000000..3819209
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diff --git a/org/broad/igv/ui/panel/RegionNavigatorDialog$RegionTablePopupHandler.class b/org/broad/igv/ui/panel/RegionNavigatorDialog$RegionTablePopupHandler.class
new file mode 100644
index 0000000..141d2b5
Binary files /dev/null and b/org/broad/igv/ui/panel/RegionNavigatorDialog$RegionTablePopupHandler.class differ
diff --git a/org/broad/igv/ui/panel/RegionNavigatorDialog$RegionTableSelectionListener.class b/org/broad/igv/ui/panel/RegionNavigatorDialog$RegionTableSelectionListener.class
new file mode 100644
index 0000000..57550b5
Binary files /dev/null and b/org/broad/igv/ui/panel/RegionNavigatorDialog$RegionTableSelectionListener.class differ
diff --git a/org/broad/igv/ui/panel/RegionNavigatorDialog$RemoveSelectedRegionsAction.class b/org/broad/igv/ui/panel/RegionNavigatorDialog$RemoveSelectedRegionsAction.class
new file mode 100644
index 0000000..3d5473e
Binary files /dev/null and b/org/broad/igv/ui/panel/RegionNavigatorDialog$RemoveSelectedRegionsAction.class differ
diff --git a/org/broad/igv/ui/panel/RegionNavigatorDialog$SearchFieldDocumentListener.class b/org/broad/igv/ui/panel/RegionNavigatorDialog$SearchFieldDocumentListener.class
new file mode 100644
index 0000000..e0e1869
Binary files /dev/null and b/org/broad/igv/ui/panel/RegionNavigatorDialog$SearchFieldDocumentListener.class differ
diff --git a/org/broad/igv/ui/panel/RegionNavigatorDialog$ShowAllChromosomesCheckboxAction.class b/org/broad/igv/ui/panel/RegionNavigatorDialog$ShowAllChromosomesCheckboxAction.class
new file mode 100644
index 0000000..4aa04e7
Binary files /dev/null and b/org/broad/igv/ui/panel/RegionNavigatorDialog$ShowAllChromosomesCheckboxAction.class differ
diff --git a/org/broad/igv/ui/panel/RegionNavigatorDialog$ViewSelectedAction.class b/org/broad/igv/ui/panel/RegionNavigatorDialog$ViewSelectedAction.class
new file mode 100644
index 0000000..28e611c
Binary files /dev/null and b/org/broad/igv/ui/panel/RegionNavigatorDialog$ViewSelectedAction.class differ
diff --git a/org/broad/igv/ui/panel/RegionNavigatorDialog.class b/org/broad/igv/ui/panel/RegionNavigatorDialog.class
new file mode 100644
index 0000000..e7493b4
Binary files /dev/null and b/org/broad/igv/ui/panel/RegionNavigatorDialog.class differ
diff --git a/org/broad/igv/ui/panel/RegionNavigatorDialog.jfd b/org/broad/igv/ui/panel/RegionNavigatorDialog.jfd
new file mode 100644
index 0000000..8e35d6c
--- /dev/null
+++ b/org/broad/igv/ui/panel/RegionNavigatorDialog.jfd
@@ -0,0 +1,632 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<java version="1.6.0_31" class="java.beans.XMLDecoder">
+ <object class="com.jformdesigner.model.FormModel">
+ <void property="contentType">
+ <string>form/swing</string>
+ </void>
+ <void property="root">
+ <object class="com.jformdesigner.model.FormRoot">
+ <void method="add">
+ <object class="com.jformdesigner.model.FormWindow">
+ <string>javax.swing.JDialog</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.BorderLayout</class>
+ </object>
+ <void method="setProperty">
+ <string>title</string>
+ <string>Regions of Interest</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.WindowListener</string>
+ <string>windowActivated</string>
+ <string>thisWindowActivated</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.BorderLayout</class>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="com.jformdesigner.model.FormObject" field="NULL_VALUE"/>
+ </void>
+ <void property="name">
+ <string>dialogPane</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.BorderLayout</class>
+ </object>
+ <void property="name">
+ <string>contentPanel</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.FlowLayout</class>
+ <void method="setProperty">
+ <string>alignment</string>
+ <int>0</int>
+ </void>
+ </object>
+ <void method="setProperty">
+ <string>componentOrientation</string>
+ <object class="java.awt.ComponentOrientation" field="LEFT_TO_RIGHT"/>
+ </void>
+ <void method="setProperty">
+ <string>border</string>
+ <object id="LineBorder0" class="javax.swing.border.LineBorder">
+ <object class="java.awt.Color" field="black"/>
+ <int>1</int>
+ <boolean>false</boolean>
+ </object>
+ </void>
+ <void property="name">
+ <string>panel3</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JCheckBox</string>
+ <void method="setProperty">
+ <string>action</string>
+ <object class="com.jformdesigner.model.FormReference">
+ <string>showAllChromosomesCheckboxAction</string>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>toolTipText</string>
+ <string>View regions from all chromosomes (otherwise, current chromosome only)</string>
+ </void>
+ <void method="setProperty">
+ <string>selected</string>
+ <boolean>true</boolean>
+ </void>
+ <void property="name">
+ <string>checkBoxShowAllChrs</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>action</string>
+ <object class="com.jformdesigner.model.FormReference">
+ <string>addAction</string>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Add</string>
+ </void>
+ <void method="setProperty">
+ <string>actionCommand</string>
+ <string>Add</string>
+ </void>
+ <void property="name">
+ <string>addButton</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>action</string>
+ <object class="com.jformdesigner.model.FormReference">
+ <string>actionRemoveRegions</string>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Remove</string>
+ </void>
+ <void property="name">
+ <string>removeButton</string>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>North</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JScrollPane</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>javax.swing.JScrollPane</class>
+ </object>
+ <void property="name">
+ <string>scrollPane1</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTable</string>
+ <void method="setProperty">
+ <string>model</string>
+ <object class="com.jformdesigner.model.SwingTableModel">
+ <object class="java.util.Vector">
+ <void method="add">
+ <object class="java.util.Vector">
+ <void method="add">
+ <null/>
+ </void>
+ <void method="add">
+ <null/>
+ </void>
+ <void method="add">
+ <null/>
+ </void>
+ <void method="add">
+ <null/>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="java.util.Vector">
+ <void method="add">
+ <string>Chr</string>
+ </void>
+ <void method="add">
+ <string>Start</string>
+ </void>
+ <void method="add">
+ <string>End</string>
+ </void>
+ <void method="add">
+ <string>Description</string>
+ </void>
+ </object>
+ <object class="java.util.Vector">
+ <void method="add">
+ <class>java.lang.String</class>
+ </void>
+ <void method="add">
+ <class>java.lang.Integer</class>
+ </void>
+ <void method="add">
+ <class>java.lang.Integer</class>
+ </void>
+ <void method="add">
+ <null/>
+ </void>
+ </object>
+ <object class="java.util.Vector">
+ <void method="add">
+ <boolean>false</boolean>
+ </void>
+ <void method="add">
+ <null/>
+ </void>
+ <void method="add">
+ <null/>
+ </void>
+ <void method="add">
+ <null/>
+ </void>
+ </object>
+ <object class="java.util.Vector">
+ <void method="add">
+ <object class="com.jformdesigner.model.SwingTableColumn">
+ <null/>
+ <int>50</int>
+ <int>0</int>
+ <int>0</int>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.SwingTableColumn">
+ <null/>
+ <int>100</int>
+ <int>0</int>
+ <int>0</int>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.SwingTableColumn">
+ <null/>
+ <int>100</int>
+ <int>0</int>
+ <int>0</int>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.SwingTableColumn">
+ <null/>
+ <int>200</int>
+ <int>0</int>
+ <int>0</int>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>autoCreateRowSorter</string>
+ <boolean>true</boolean>
+ </void>
+ <void property="name">
+ <string>regionTable</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.MouseListener</string>
+ <string>mouseClicked</string>
+ <string>regionTableMouseClicked</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>Center</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>javax.swing.BoxLayout</class>
+ <void method="setProperty">
+ <string>axis</string>
+ <int>1</int>
+ </void>
+ </object>
+ <void property="name">
+ <string>panel1</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.FlowLayout</class>
+ <void method="setProperty">
+ <string>alignment</string>
+ <int>0</int>
+ </void>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object idref="LineBorder0"/>
+ </void>
+ <void property="name">
+ <string>panel2</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>View</string>
+ </void>
+ <void method="setProperty">
+ <string>action</string>
+ <object class="com.jformdesigner.model.FormReference">
+ <string>viewAction</string>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>actionCommand</string>
+ <string>View</string>
+ </void>
+ <void property="name">
+ <string>viewButton</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JCheckBox</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Zoom to Region</string>
+ </void>
+ <void method="setProperty">
+ <string>toolTipText</string>
+ <string>When navigating to a region, change zoom level?</string>
+ </void>
+ <void method="setProperty">
+ <string>selected</string>
+ <boolean>true</boolean>
+ </void>
+ <void property="name">
+ <string>checkBoxZoomWhenNav</string>
+ </void>
+ </object>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.FlowLayout</class>
+ <void method="setProperty">
+ <string>alignment</string>
+ <int>0</int>
+ </void>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object idref="LineBorder0"/>
+ </void>
+ <void property="name">
+ <string>panel4</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Search</string>
+ </void>
+ <void property="name">
+ <string>label1</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void method="setProperty">
+ <string>toolTipText</string>
+ <string>Search for regions containing the specified description text.</string>
+ </void>
+ <void method="setProperty">
+ <string>preferredSize</string>
+ <object class="java.awt.Dimension">
+ <int>200</int>
+ <int>28</int>
+ </object>
+ </void>
+ <void property="name">
+ <string>textFieldSearch</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>action</string>
+ <object class="com.jformdesigner.model.FormReference">
+ <string>cancelAction</string>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Clear Search</string>
+ </void>
+ <void property="name">
+ <string>clearSearchButton</string>
+ </void>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>South</string>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>Center</string>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>Center</string>
+ </void>
+ </object>
+ </void>
+ <void property="name">
+ <string>this</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <null/>
+ <void method="setProperty">
+ <string>location</string>
+ <object class="java.awt.Point">
+ <int>0</int>
+ <int>0</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>size</string>
+ <object class="java.awt.Dimension">
+ <int>480</int>
+ <int>295</int>
+ </object>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormNonVisual">
+ <string>javax.swing.AbstractAction</string>
+ <void method="setProperty">
+ <string>$action.Name</string>
+ <string>Cancel</string>
+ </void>
+ <void method="setProperty">
+ <string>$action.ShortDescription</string>
+ <string>Clear search box</string>
+ </void>
+ <void method="auxiliary">
+ <void method="setProperty">
+ <string>JavaCodeGenerator.className</string>
+ <string>CancelAction</string>
+ </void>
+ </void>
+ <void property="name">
+ <string>cancelAction</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <null/>
+ <void method="setProperty">
+ <string>location</string>
+ <object class="java.awt.Point">
+ <int>0</int>
+ <int>305</int>
+ </object>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormNonVisual">
+ <string>javax.swing.AbstractAction</string>
+ <void method="setProperty">
+ <string>$action.Name</string>
+ <string>Add</string>
+ </void>
+ <void method="setProperty">
+ <string>$action.ShortDescription</string>
+ <string>Add a new region</string>
+ </void>
+ <void method="auxiliary">
+ <void method="setProperty">
+ <string>JavaCodeGenerator.className</string>
+ <string>AddRegionAction</string>
+ </void>
+ </void>
+ <void property="name">
+ <string>addAction</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <null/>
+ <void method="setProperty">
+ <string>location</string>
+ <object class="java.awt.Point">
+ <int>0</int>
+ <int>359</int>
+ </object>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormNonVisual">
+ <string>javax.swing.AbstractAction</string>
+ <void method="setProperty">
+ <string>$action.Name</string>
+ <string>Remove</string>
+ </void>
+ <void method="setProperty">
+ <string>$action.ShortDescription</string>
+ <string>Remove all selected regions</string>
+ </void>
+ <void method="auxiliary">
+ <void method="setProperty">
+ <string>JavaCodeGenerator.className</string>
+ <string>RemoveSelectedRegionsAction</string>
+ </void>
+ </void>
+ <void property="name">
+ <string>actionRemoveRegions</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <null/>
+ <void method="setProperty">
+ <string>location</string>
+ <object class="java.awt.Point">
+ <int>0</int>
+ <int>413</int>
+ </object>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormNonVisual">
+ <string>javax.swing.AbstractAction</string>
+ <void method="setProperty">
+ <string>$action.Name</string>
+ <string>Show All Chrs</string>
+ </void>
+ <void method="auxiliary">
+ <void method="setProperty">
+ <string>JavaCodeGenerator.className</string>
+ <string>ShowAllChromosomesCheckboxAction</string>
+ </void>
+ </void>
+ <void property="name">
+ <string>showAllChromosomesCheckboxAction</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <null/>
+ <void method="setProperty">
+ <string>location</string>
+ <object class="java.awt.Point">
+ <int>0</int>
+ <int>467</int>
+ </object>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormNonVisual">
+ <string>javax.swing.AbstractAction</string>
+ <void method="setProperty">
+ <string>$action.Name</string>
+ <string>View</string>
+ </void>
+ <void method="auxiliary">
+ <void method="setProperty">
+ <string>JavaCodeGenerator.className</string>
+ <string>ViewSelectedAction</string>
+ </void>
+ </void>
+ <void property="name">
+ <string>viewAction</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <null/>
+ <void method="setProperty">
+ <string>location</string>
+ <object class="java.awt.Point">
+ <int>10</int>
+ <int>540</int>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+</java>
diff --git a/org/broad/igv/ui/panel/RegionOfInterestPanel$1.class b/org/broad/igv/ui/panel/RegionOfInterestPanel$1.class
new file mode 100644
index 0000000..98ef762
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diff --git a/org/broad/igv/ui/panel/RegionOfInterestPanel$2.class b/org/broad/igv/ui/panel/RegionOfInterestPanel$2.class
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index 0000000..6a1f28c
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diff --git a/org/broad/igv/ui/panel/RegionOfInterestPanel$3$1.class b/org/broad/igv/ui/panel/RegionOfInterestPanel$3$1.class
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index 0000000..bbea822
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index 0000000..1e96d47
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diff --git a/org/broad/igv/ui/panel/RegionOfInterestPanel$4.class b/org/broad/igv/ui/panel/RegionOfInterestPanel$4.class
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index 0000000..dee90e7
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diff --git a/org/broad/igv/ui/panel/RegionOfInterestPanel$ROIMouseAdapater.class b/org/broad/igv/ui/panel/RegionOfInterestPanel$ROIMouseAdapater.class
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index 0000000..e1c2f73
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diff --git a/org/broad/igv/ui/panel/RegionOfInterestPanel.class b/org/broad/igv/ui/panel/RegionOfInterestPanel.class
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index 0000000..f877d5e
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diff --git a/org/broad/igv/ui/panel/RegionOfInterestTool.class b/org/broad/igv/ui/panel/RegionOfInterestTool.class
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index 0000000..ae5ee06
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diff --git a/org/broad/igv/ui/panel/ReorderPanelsDialog$1.class b/org/broad/igv/ui/panel/ReorderPanelsDialog$1.class
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index 0000000..9b85502
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diff --git a/org/broad/igv/ui/panel/ReorderPanelsDialog$2.class b/org/broad/igv/ui/panel/ReorderPanelsDialog$2.class
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index 0000000..7b1aa95
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diff --git a/org/broad/igv/ui/panel/ReorderPanelsDialog$Wrapper.class b/org/broad/igv/ui/panel/ReorderPanelsDialog$Wrapper.class
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diff --git a/org/broad/igv/ui/panel/ReorderPanelsDialog.jfd b/org/broad/igv/ui/panel/ReorderPanelsDialog.jfd
new file mode 100644
index 0000000..4b4ed92
--- /dev/null
+++ b/org/broad/igv/ui/panel/ReorderPanelsDialog.jfd
@@ -0,0 +1,247 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<java version="1.6.0_22" class="java.beans.XMLDecoder">
+ <object class="com.jformdesigner.model.FormModel">
+ <void property="contentType">
+ <string>form/swing</string>
+ </void>
+ <void property="root">
+ <object class="com.jformdesigner.model.FormRoot">
+ <void method="add">
+ <object class="com.jformdesigner.model.FormWindow">
+ <string>javax.swing.JDialog</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.BorderLayout</class>
+ </object>
+ <void method="setProperty">
+ <string>title</string>
+ <string>Reorder Panels</string>
+ </void>
+ <void method="setProperty">
+ <string>defaultCloseOperation</string>
+ <int>2</int>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.BorderLayout</class>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="javax.swing.border.EmptyBorder">
+ <object class="java.awt.Insets">
+ <int>12</int>
+ <int>12</int>
+ <int>12</int>
+ <int>12</int>
+ </object>
+ </object>
+ </void>
+ <void property="name">
+ <string>dialogPane</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.BorderLayout</class>
+ </object>
+ <void property="name">
+ <string>contentPanel</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JScrollPane</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>javax.swing.JScrollPane</class>
+ </object>
+ <void property="name">
+ <string>scrollPane1</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>org.broad.igv.ui.util.ReorderableJList</string>
+ <void property="name">
+ <string>list</string>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>Center</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>To reorder panels drag and drop entries in the list below.</string>
+ </void>
+ <void property="name">
+ <string>label1</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>North</string>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>Center</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.GridBagLayout</class>
+ <void method="setProperty">
+ <string>$columnSpecs</string>
+ <string>0:1.0, 80, 80</string>
+ </void>
+ <void method="setProperty">
+ <string>$rowSpecs</string>
+ <string>0</string>
+ </void>
+ <void method="setProperty">
+ <string>$hGap</string>
+ <int>5</int>
+ </void>
+ <void method="setProperty">
+ <string>$vGap</string>
+ <int>5</int>
+ </void>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="javax.swing.border.EmptyBorder">
+ <object class="java.awt.Insets">
+ <int>12</int>
+ <int>0</int>
+ <int>0</int>
+ <int>0</int>
+ </object>
+ </object>
+ </void>
+ <void property="name">
+ <string>buttonBar</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>OK</string>
+ </void>
+ <void property="name">
+ <string>okButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>okButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>1</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>0</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Cancel</string>
+ </void>
+ <void property="name">
+ <string>cancelButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>cancelButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>0</int>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>South</string>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>Center</string>
+ </void>
+ </object>
+ </void>
+ <void property="name">
+ <string>this</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <null/>
+ <void method="setProperty">
+ <string>location</string>
+ <object class="java.awt.Point">
+ <int>0</int>
+ <int>0</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>size</string>
+ <object class="java.awt.Dimension">
+ <int>660</int>
+ <int>470</int>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+</java>
diff --git a/org/broad/igv/ui/panel/RulerPanel$1$1.class b/org/broad/igv/ui/panel/RulerPanel$1$1.class
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diff --git a/org/broad/igv/ui/panel/RulerPanel$ClickLink.class b/org/broad/igv/ui/panel/RulerPanel$ClickLink.class
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diff --git a/org/broad/igv/ui/panel/TrackPanelComponent$1.class b/org/broad/igv/ui/panel/TrackPanelComponent$1.class
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diff --git a/org/broad/igv/ui/panel/TrackPanelScrollPane$1.class b/org/broad/igv/ui/panel/TrackPanelScrollPane$1.class
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diff --git a/org/broad/igv/ui/panel/ZoomSliderPanel$1$1.class b/org/broad/igv/ui/panel/ZoomSliderPanel$1$1.class
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diff --git a/org/broad/igv/ui/panel/flowlayout.txt b/org/broad/igv/ui/panel/flowlayout.txt
new file mode 100644
index 0000000..8f4bed1
--- /dev/null
+++ b/org/broad/igv/ui/panel/flowlayout.txt
@@ -0,0 +1,577 @@
+
+KickJava Java API By Example, From Geeks To Geeks.
+Java > Open Source Codes > java > awt > FlowLayout
+
+
+
+1 /*
+2 * @(#)FlowLayout.java 1.52 03/12/19
+3 *
+4 * Copyright 2004 Sun Microsystems, Inc. All rights reserved.
+5 * SUN PROPRIETARY/CONFIDENTIAL. Use is subject to license terms.
+6 */
+7 package java.awt;
+8
+9 import java.io.ObjectInputStream JavaDoc;
+10 import java.io.IOException JavaDoc;
+11
+12 /**
+13 * A flow layout arranges components in a directional flow, much
+14 * like lines of text in a paragraph. The flow direction is
+15 * determined by the container's <code>componentOrientation</code>
+16 * property and may be one of two values:
+17 * <ul>
+18 * <li><code>ComponentOrientation.LEFT_TO_RIGHT</code>
+19 * <li><code>ComponentOrientation.RIGHT_TO_LEFT</code>
+20 * </ul>
+21 * Flow layouts are typically used
+22 * to arrange buttons in a panel. It arranges buttons
+23 * horizontally until no more buttons fit on the same line.
+24 * The line alignment is determined by the <code>align</code>
+25 * property. The possible values are:
+26 * <ul>
+27 * <li>{@link #LEFT LEFT}
+28 * <li>{@link #RIGHT RIGHT}
+29 * <li>{@link #CENTER CENTER}
+30 * <li>{@link #LEADING LEADING}
+31 * <li>{@link #TRAILING TRAILING}
+32 * </ul>
+33 * <p>
+34 * For example, the following picture shows an applet using the flow
+35 * layout manager (its default layout manager) to position three buttons:
+36 * <p>
+37 * <img SRC="doc-files/FlowLayout-1.gif"
+38 * ALT="Graphic of Layout for Three Buttons"
+39 * ALIGN=center HSPACE=10 VSPACE=7>
+40 * <p>
+41 * Here is the code for this applet:
+42 * <p>
+43 * <hr><blockquote><pre>
+44 * import java.awt.*;
+45 * import java.applet.Applet;
+46 *
+47 * public class myButtons extends Applet {
+48 * Button button1, button2, button3;
+49 * public void init() {
+50 * button1 = new Button("Ok");
+51 * button2 = new Button("Open");
+52 * button3 = new Button("Close");
+53 * add(button1);
+54 * add(button2);
+55 * add(button3);
+56 * }
+57 * }
+58 * </pre></blockquote><hr>
+59 * <p>
+60 * A flow layout lets each component assume its natural (preferred) size.
+61 *
+62 * @version 1.52, 12/19/03
+63 * @author Arthur van Hoff
+64 * @author Sami Shaio
+65 * @since JDK1.0
+66 * @see ComponentOrientation
+67 */
+68 public class FlowLayout implements LayoutManager JavaDoc, java.io.Serializable JavaDoc {
+69
+70 /**
+71 * This value indicates that each row of components
+72 * should be left-justified.
+73 */
+74 public static final int LEFT = 0;
+75
+76 /**
+77 * This value indicates that each row of components
+78 * should be centered.
+79 */
+80 public static final int CENTER = 1;
+81
+82 /**
+83 * This value indicates that each row of components
+84 * should be right-justified.
+85 */
+86 public static final int RIGHT = 2;
+87
+88 /**
+89 * This value indicates that each row of components
+90 * should be justified to the leading edge of the container's
+91 * orientation, for example, to the left in left-to-right orientations.
+92 *
+93 * @see java.awt.Component#getComponentOrientation
+94 * @see java.awt.ComponentOrientation
+95 * @since 1.2
+96 * Package-private pending API change approval
+97 */
+98 public static final int LEADING = 3;
+99
+100 /**
+101 * This value indicates that each row of components
+102 * should be justified to the trailing edge of the container's
+103 * orientation, for example, to the right in left-to-right orientations.
+104 *
+105 * @see java.awt.Component#getComponentOrientation
+106 * @see java.awt.ComponentOrientation
+107 * @since 1.2
+108 * Package-private pending API change approval
+109 */
+110 public static final int TRAILING = 4;
+111
+112 /**
+113 * <code>align</code> is the property that determines
+114 * how each row distributes empty space.
+115 * It can be one of the following values:
+116 * <ul>
+117 * <code>LEFT</code>
+118 * <code>RIGHT</code>
+119 * <code>CENTER</code>
+120 * <code>LEADING</code>
+121 * <code>TRAILING</code>
+122 * </ul>
+123 *
+124 * @serial
+125 * @see #getAlignment
+126 * @see #setAlignment
+127 */
+128 int align; // This is for 1.1 serialization compatibility
+129
+130 /**
+131 * <code>newAlign</code> is the property that determines
+132 * how each row distributes empty space for the Java 2 platform,
+133 * v1.2 and greater.
+134 * It can be one of the following three values:
+135 * <ul>
+136 * <code>LEFT</code>
+137 * <code>RIGHT</code>
+138 * <code>CENTER</code>
+139 * <code>LEADING</code>
+140 * <code>TRAILING</code>
+141 * </ul>
+142 *
+143 * @serial
+144 * @since 1.2
+145 * @see #getAlignment
+146 * @see #setAlignment
+147 */
+148 int newAlign; // This is the one we actually use
+149
+150 /**
+151 * The flow layout manager allows a seperation of
+152 * components with gaps. The horizontal gap will
+153 * specify the space between components and between
+154 * the components and the borders of the
+155 * <code>Container</code>.
+156 *
+157 * @serial
+158 * @see #getHgap()
+159 * @see #setHgap(int)
+160 */
+161 int hgap;
+162
+163 /**
+164 * The flow layout manager allows a seperation of
+165 * components with gaps. The vertical gap will
+166 * specify the space between rows and between the
+167 * the rows and the borders of the <code>Container</code>.
+168 *
+169 * @serial
+170 * @see #getHgap()
+171 * @see #setHgap(int)
+172 */
+173 int vgap;
+174
+175 /*
+176 * JDK 1.1 serialVersionUID
+177 */
+178 private static final long serialVersionUID = -7262534875583282631L;
+179
+180 /**
+181 * Constructs a new <code>FlowLayout</code> with a centered alignment and a
+182 * default 5-unit horizontal and vertical gap.
+183 */
+184 public FlowLayout() {
+185 this(CENTER, 5, 5);
+186 }
+187
+188 /**
+189 * Constructs a new <code>FlowLayout</code> with the specified
+190 * alignment and a default 5-unit horizontal and vertical gap.
+191 * The value of the alignment argument must be one of
+192 * <code>FlowLayout.LEFT</code>, <code>FlowLayout.RIGHT</code>,
+193 * <code>FlowLayout.CENTER</code>, <code>FlowLayout.LEADING</code>,
+194 * or <code>FlowLayout.TRAILING</code>.
+195 * @param align the alignment value
+196 */
+197 public FlowLayout(int align) {
+198 this(align, 5, 5);
+199 }
+200
+201 /**
+202 * Creates a new flow layout manager with the indicated alignment
+203 * and the indicated horizontal and vertical gaps.
+204 * <p>
+205 * The value of the alignment argument must be one of
+206 * <code>FlowLayout.LEFT</code>, <code>FlowLayout.RIGHT</code>,
+207 * <code>FlowLayout.CENTER</code>, <code>FlowLayout.LEADING</code>,
+208 * or <code>FlowLayout.TRAILING</code>.
+209 * @param align the alignment value
+210 * @param hgap the horizontal gap between components
+211 * and between the components and the
+212 * borders of the <code>Container</code>
+213 * @param vgap the vertical gap between components
+214 * and between the components and the
+215 * borders of the <code>Container</code>
+216 */
+217 public FlowLayout(int align, int hgap, int vgap) {
+218 this.hgap = hgap;
+219 this.vgap = vgap;
+220 setAlignment(align);
+221 }
+222
+223 /**
+224 * Gets the alignment for this layout.
+225 * Possible values are <code>FlowLayout.LEFT</code>,
+226 * <code>FlowLayout.RIGHT</code>, <code>FlowLayout.CENTER</code>,
+227 * <code>FlowLayout.LEADING</code>,
+228 * or <code>FlowLayout.TRAILING</code>.
+229 * @return the alignment value for this layout
+230 * @see java.awt.FlowLayout#setAlignment
+231 * @since JDK1.1
+232 */
+233 public int getAlignment() {
+234 return newAlign;
+235 }
+236
+237 /**
+238 * Sets the alignment for this layout.
+239 * Possible values are
+240 * <ul>
+241 * <li><code>FlowLayout.LEFT</code>
+242 * <li><code>FlowLayout.RIGHT</code>
+243 * <li><code>FlowLayout.CENTER</code>
+244 * <li><code>FlowLayout.LEADING</code>
+245 * <li><code>FlowLayout.TRAILING</code>
+246 * </ul>
+247 * @param align one of the alignment values shown above
+248 * @see #getAlignment()
+249 * @since JDK1.1
+250 */
+251 public void setAlignment(int align) {
+252 this.newAlign = align;
+253
+254 // this.align is used only for serialization compatibility,
+255 // so set it to a value compatible with the 1.1 version
+256 // of the class
+257
+258 switch (align) {
+259 case LEADING:
+260 this.align = LEFT;
+261 break;
+262 case TRAILING:
+263 this.align = RIGHT;
+264 break;
+265 default:
+266 this.align = align;
+267 break;
+268 }
+269 }
+270
+271 /**
+272 * Gets the horizontal gap between components
+273 * and between the components and the borders
+274 * of the <code>Container</code>
+275 *
+276 * @return the horizontal gap between components
+277 * and between the components and the borders
+278 * of the <code>Container</code>
+279 * @see java.awt.FlowLayout#setHgap
+280 * @since JDK1.1
+281 */
+282 public int getHgap() {
+283 return hgap;
+284 }
+285
+286 /**
+287 * Sets the horizontal gap between components and
+288 * between the components and the borders of the
+289 * <code>Container</code>.
+290 *
+291 * @param hgap the horizontal gap between components
+292 * and between the components and the borders
+293 * of the <code>Container</code>
+294 * @see java.awt.FlowLayout#getHgap
+295 * @since JDK1.1
+296 */
+297 public void setHgap(int hgap) {
+298 this.hgap = hgap;
+299 }
+300
+301 /**
+302 * Gets the vertical gap between components and
+303 * between the components and the borders of the
+304 * <code>Container</code>.
+305 *
+306 * @return the vertical gap between components
+307 * and between the components and the borders
+308 * of the <code>Container</code>
+309 * @see java.awt.FlowLayout#setVgap
+310 * @since JDK1.1
+311 */
+312 public int getVgap() {
+313 return vgap;
+314 }
+315
+316 /**
+317 * Sets the vertical gap between components and between
+318 * the components and the borders of the <code>Container</code>.
+319 *
+320 * @param vgap the vertical gap between components
+321 * and between the components and the borders
+322 * of the <code>Container</code>
+323 * @see java.awt.FlowLayout#getVgap
+324 * @since JDK1.1
+325 */
+326 public void setVgap(int vgap) {
+327 this.vgap = vgap;
+328 }
+329
+330 /**
+331 * Adds the specified component to the layout.
+332 * Not used by this class.
+333 * @param name the name of the component
+334 * @param comp the component to be added
+335 */
+336 public void addLayoutComponent(String JavaDoc name, Component JavaDoc comp) {
+337 }
+338
+339 /**
+340 * Removes the specified component from the layout.
+341 * Not used by this class.
+342 * @param comp the component to remove
+343 * @see java.awt.Container#removeAll
+344 */
+345 public void removeLayoutComponent(Component JavaDoc comp) {
+346 }
+347
+348 /**
+349 * Returns the preferred dimensions for this layout given the
+350 * <i>visible</i> components in the specified target container.
+351 *
+352 * @param target the container that needs to be laid out
+353 * @return the preferred dimensions to lay out the
+354 * subcomponents of the specified container
+355 * @see Container
+356 * @see #minimumLayoutSize
+357 * @see java.awt.Container#getPreferredSize
+358 */
+359 public Dimension JavaDoc preferredLayoutSize(Container JavaDoc target) {
+360 synchronized (target.getTreeLock()) {
+361 Dimension JavaDoc dim = new Dimension JavaDoc(0, 0);
+362 int nmembers = target.getComponentCount();
+363 boolean firstVisibleComponent = true;
+364
+365 for (int i = 0 ; i < nmembers ; i++) {
+366 Component JavaDoc m = target.getComponent(i);
+367 if (m.visible) {
+368 Dimension JavaDoc d = m.getPreferredSize();
+369 dim.height = Math.max(dim.height, d.height);
+370 if (firstVisibleComponent) {
+371 firstVisibleComponent = false;
+372 } else {
+373 dim.width += hgap;
+374 }
+375 dim.width += d.width;
+376 }
+377 }
+378 Insets JavaDoc insets = target.getInsets();
+379 dim.width += insets.left + insets.right + hgap*2;
+380 dim.height += insets.top + insets.bottom + vgap*2;
+381 return dim;
+382 }
+383 }
+384
+385 /**
+386 * Returns the minimum dimensions needed to layout the <i>visible</i>
+387 * components contained in the specified target container.
+388 * @param target the container that needs to be laid out
+389 * @return the minimum dimensions to lay out the
+390 * subcomponents of the specified container
+391 * @see #preferredLayoutSize
+392 * @see java.awt.Container
+393 * @see java.awt.Container#doLayout
+394 */
+395 public Dimension JavaDoc minimumLayoutSize(Container JavaDoc target) {
+396 synchronized (target.getTreeLock()) {
+397 Dimension JavaDoc dim = new Dimension JavaDoc(0, 0);
+398 int nmembers = target.getComponentCount();
+399
+400 for (int i = 0 ; i < nmembers ; i++) {
+401 Component JavaDoc m = target.getComponent(i);
+402 if (m.visible) {
+403 Dimension JavaDoc d = m.getMinimumSize();
+404 dim.height = Math.max(dim.height, d.height);
+405 if (i > 0) {
+406 dim.width += hgap;
+407 }
+408 dim.width += d.width;
+409 }
+410 }
+411 Insets JavaDoc insets = target.getInsets();
+412 dim.width += insets.left + insets.right + hgap*2;
+413 dim.height += insets.top + insets.bottom + vgap*2;
+414 return dim;
+415 }
+416 }
+417
+418 /**
+419 * Centers the elements in the specified row, if there is any slack.
+420 * @param target the component which needs to be moved
+421 * @param x the x coordinate
+422 * @param y the y coordinate
+423 * @param width the width dimensions
+424 * @param height the height dimensions
+425 * @param rowStart the beginning of the row
+426 * @param rowEnd the the ending of the row
+427 */
+428 private void moveComponents(Container JavaDoc target, int x, int y, int width, int height,
+429 int rowStart, int rowEnd, boolean ltr) {
+430 synchronized (target.getTreeLock()) {
+431 switch (newAlign) {
+432 case LEFT:
+433 x += ltr ? 0 : width;
+434 break;
+435 case CENTER:
+436 x += width / 2;
+437 break;
+438 case RIGHT:
+439 x += ltr ? width : 0;
+440 break;
+441 case LEADING:
+442 break;
+443 case TRAILING:
+444 x += width;
+445 break;
+446 }
+447 for (int i = rowStart ; i < rowEnd ; i++) {
+448 Component JavaDoc m = target.getComponent(i);
+449 if (m.visible) {
+450 if (ltr) {
+451 m.setLocation(x, y + (height - m.height) / 2);
+452 } else {
+453 m.setLocation(target.width - x - m.width, y + (height - m.height) / 2);
+454 }
+455 x += m.width + hgap;
+456 }
+457 }
+458 }
+459 }
+460
+461 /**
+462 * Lays out the container. This method lets each
+463 * <i>visible</i> component take
+464 * its preferred size by reshaping the components in the
+465 * target container in order to satisfy the alignment of
+466 * this <code>FlowLayout</code> object.
+467 *
+468 * @param target the specified component being laid out
+469 * @see Container
+470 * @see java.awt.Container#doLayout
+471 */
+472 public void layoutContainer(Container JavaDoc target) {
+473 synchronized (target.getTreeLock()) {
+474 Insets JavaDoc insets = target.getInsets();
+475 int maxwidth = target.width - (insets.left + insets.right + hgap*2);
+476 int nmembers = target.getComponentCount();
+477 int x = 0, y = insets.top + vgap;
+478 int rowh = 0, start = 0;
+479
+480 boolean ltr = target.getComponentOrientation().isLeftToRight();
+481
+482 for (int i = 0 ; i < nmembers ; i++) {
+483 Component JavaDoc m = target.getComponent(i);
+484 if (m.visible) {
+485 Dimension JavaDoc d = m.getPreferredSize();
+486 m.setSize(d.width, d.height);
+487
+488 if ((x == 0) || ((x + d.width) <= maxwidth)) {
+489 if (x > 0) {
+490 x += hgap;
+491 }
+492 x += d.width;
+493 rowh = Math.max(rowh, d.height);
+494 } else {
+495 moveComponents(target, insets.left + hgap, y, maxwidth - x, rowh, start, i, ltr);
+496 x = d.width;
+497 y += vgap + rowh;
+498 rowh = d.height;
+499 start = i;
+500 }
+501 }
+502 }
+503 moveComponents(target, insets.left + hgap, y, maxwidth - x, rowh, start, nmembers, ltr);
+504 }
+505 }
+506
+507 //
+508 // the internal serial version which says which version was written
+509 // - 0 (default) for versions before the Java 2 platform, v1.2
+510 // - 1 for version >= Java 2 platform v1.2, which includes "newAlign" field
+511 //
+512 private static final int currentSerialVersion = 1;
+513 /**
+514 * This represent the <code>currentSerialVersion</code>
+515 * which is bein used. It will be one of two values :
+516 * <code>0</code> versions before Java 2 platform v1.2..
+517 * <code>1</code> versions after Java 2 platform v1.2..
+518 *
+519 * @serial
+520 * @since 1.2
+521 */
+522 private int serialVersionOnStream = currentSerialVersion;
+523
+524 /**
+525 * Reads this object out of a serialization stream, handling
+526 * objects written by older versions of the class that didn't contain all
+527 * of the fields we use now..
+528 */
+529 private void readObject(ObjectInputStream JavaDoc stream)
+530 throws IOException JavaDoc, ClassNotFoundException JavaDoc
+531 {
+532 stream.defaultReadObject();
+533
+534 if (serialVersionOnStream < 1) {
+535 // "newAlign" field wasn't present, so use the old "align" field.
+536 setAlignment(this.align);
+537 }
+538 serialVersionOnStream = currentSerialVersion;
+539 }
+540
+541 /**
+542 * Returns a string representation of this <code>FlowLayout</code>
+543 * object and its values.
+544 * @return a string representation of this layout
+545 */
+546 public String JavaDoc toString() {
+547 String JavaDoc str = "";
+548 switch (align) {
+549 case LEFT: str = ",align=left"; break;
+550 case CENTER: str = ",align=center"; break;
+551 case RIGHT: str = ",align=right"; break;
+552 case LEADING: str = ",align=leading"; break;
+553 case TRAILING: str = ",align=trailing"; break;
+554 }
+555 return getClass().getName() + "[hgap=" + hgap + ",vgap=" + vgap + str + "]";
+556 }
+557
+558
+559 }
+560
+
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+Java API By Example, From Geeks To Geeks. | Our Blog | Conditions of Use | About Us_ | � 2002-2006, KickJava.com.
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+
+Read more: http://kickjava.com/src/java/awt/FlowLayout.java.htm#ixzz0z2BcRQVy
\ No newline at end of file
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+++ b/org/broad/igv/ui/util/CheckListDialog.jfd
@@ -0,0 +1,267 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<java version="1.6.0_17" class="java.beans.XMLDecoder">
+ <object class="com.jformdesigner.model.FormModel">
+ <void property="contentType">
+ <string>form/swing</string>
+ </void>
+ <void property="root">
+ <object class="com.jformdesigner.model.FormRoot">
+ <void method="add">
+ <object class="com.jformdesigner.model.FormWindow">
+ <string>javax.swing.JDialog</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>com.jformdesigner.runtime.NullLayout</class>
+ </object>
+ <void method="setProperty">
+ <string>$sizePolicy</string>
+ <int>1</int>
+ </void>
+ <void method="setProperty">
+ <string>resizable</string>
+ <boolean>false</boolean>
+ </void>
+ <void method="setProperty">
+ <string>defaultCloseOperation</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>modal</string>
+ <boolean>true</boolean>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.BorderLayout</class>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="javax.swing.border.EmptyBorder">
+ <object class="java.awt.Insets">
+ <int>12</int>
+ <int>12</int>
+ <int>12</int>
+ <int>12</int>
+ </object>
+ </object>
+ </void>
+ <void property="name">
+ <string>dialogPane</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.BorderLayout</class>
+ </object>
+ <void property="name">
+ <string>contentPanel</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JScrollPane</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>javax.swing.JScrollPane</class>
+ </object>
+ <void property="name">
+ <string>scrollPane1</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>javax.swing.BoxLayout</class>
+ <void method="setProperty">
+ <string>axis</string>
+ <int>1</int>
+ </void>
+ </object>
+ <void property="name">
+ <string>checkboxPane</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JCheckBox</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>All</string>
+ </void>
+ <void property="name">
+ <string>allCB</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>allCBActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>Center</string>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>Center</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.GridBagLayout</class>
+ <void method="setProperty">
+ <string>$columnSpecs</string>
+ <string>0:1.0, 80, 80</string>
+ </void>
+ <void method="setProperty">
+ <string>$rowSpecs</string>
+ <string>0</string>
+ </void>
+ <void method="setProperty">
+ <string>$hGap</string>
+ <int>5</int>
+ </void>
+ <void method="setProperty">
+ <string>$vGap</string>
+ <int>5</int>
+ </void>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="javax.swing.border.EmptyBorder">
+ <object class="java.awt.Insets">
+ <int>12</int>
+ <int>0</int>
+ <int>0</int>
+ <int>0</int>
+ </object>
+ </object>
+ </void>
+ <void property="name">
+ <string>buttonBar</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>OK</string>
+ </void>
+ <void property="name">
+ <string>okButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>okButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>1</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>0</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Cancel</string>
+ </void>
+ <void property="name">
+ <string>cancelButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>cancelButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>0</int>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>South</string>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>width</string>
+ <int>468</int>
+ </void>
+ <void method="setProperty">
+ <string>height</string>
+ <int>551</int>
+ </void>
+ </object>
+ </void>
+ <void property="name">
+ <string>this</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <null/>
+ <void method="setProperty">
+ <string>location</string>
+ <object class="java.awt.Point">
+ <int>0</int>
+ <int>0</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>size</string>
+ <object class="java.awt.Dimension">
+ <int>470</int>
+ <int>575</int>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+</java>
diff --git a/org/broad/igv/ui/util/ConfirmDialog$1.class b/org/broad/igv/ui/util/ConfirmDialog$1.class
new file mode 100644
index 0000000..3e71fbb
Binary files /dev/null and b/org/broad/igv/ui/util/ConfirmDialog$1.class differ
diff --git a/org/broad/igv/ui/util/ConfirmDialog$2.class b/org/broad/igv/ui/util/ConfirmDialog$2.class
new file mode 100644
index 0000000..cb55e12
Binary files /dev/null and b/org/broad/igv/ui/util/ConfirmDialog$2.class differ
diff --git a/org/broad/igv/ui/util/ConfirmDialog.class b/org/broad/igv/ui/util/ConfirmDialog.class
new file mode 100644
index 0000000..79f06ee
Binary files /dev/null and b/org/broad/igv/ui/util/ConfirmDialog.class differ
diff --git a/org/broad/igv/ui/util/ConfirmDialog.jfd b/org/broad/igv/ui/util/ConfirmDialog.jfd
new file mode 100644
index 0000000..000f8aa
--- /dev/null
+++ b/org/broad/igv/ui/util/ConfirmDialog.jfd
@@ -0,0 +1,248 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<java version="1.6.0_17" class="java.beans.XMLDecoder">
+ <object class="com.jformdesigner.model.FormModel">
+ <void property="contentType">
+ <string>form/swing</string>
+ </void>
+ <void property="root">
+ <object class="com.jformdesigner.model.FormRoot">
+ <void method="add">
+ <object class="com.jformdesigner.model.FormWindow">
+ <string>javax.swing.JDialog</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.BorderLayout</class>
+ </object>
+ <void method="setProperty">
+ <string>defaultCloseOperation</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>$sizePolicy</string>
+ <int>1</int>
+ </void>
+ <void method="setProperty">
+ <string>resizable</string>
+ <boolean>false</boolean>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.BorderLayout</class>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="javax.swing.border.EmptyBorder">
+ <object class="java.awt.Insets">
+ <int>12</int>
+ <int>12</int>
+ <int>12</int>
+ <int>12</int>
+ </object>
+ </object>
+ </void>
+ <void property="name">
+ <string>dialogPane</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>com.jformdesigner.runtime.NullLayout</class>
+ </object>
+ <void property="name">
+ <string>contentPanel</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>text</string>
+ </void>
+ <void property="name">
+ <string>label</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>10</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>0</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>565</int>
+ </void>
+ <void method="setProperty">
+ <string>height</string>
+ <int>195</int>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>Center</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.GridBagLayout</class>
+ <void method="setProperty">
+ <string>$columnSpecs</string>
+ <string>0:1.0, 0, 80</string>
+ </void>
+ <void method="setProperty">
+ <string>$rowSpecs</string>
+ <string>0, 0</string>
+ </void>
+ <void method="setProperty">
+ <string>$hGap</string>
+ <int>5</int>
+ </void>
+ <void method="setProperty">
+ <string>$vGap</string>
+ <int>5</int>
+ </void>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="javax.swing.border.EmptyBorder">
+ <object class="java.awt.Insets">
+ <int>12</int>
+ <int>0</int>
+ <int>0</int>
+ <int>0</int>
+ </object>
+ </object>
+ </void>
+ <void property="name">
+ <string>buttonBar</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JCheckBox</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Do not show this message again.</string>
+ </void>
+ <void property="name">
+ <string>doNotShowCheckbox</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Cancel</string>
+ </void>
+ <void property="name">
+ <string>cancelButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>cancelButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>1</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>OK</string>
+ </void>
+ <void property="name">
+ <string>okButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>okButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>0</int>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>South</string>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>Center</string>
+ </void>
+ </object>
+ </void>
+ <void property="name">
+ <string>this</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <null/>
+ <void method="setProperty">
+ <string>location</string>
+ <object class="java.awt.Point">
+ <int>0</int>
+ <int>0</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>size</string>
+ <object class="java.awt.Dimension">
+ <int>600</int>
+ <int>300</int>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+</java>
diff --git a/org/broad/igv/ui/util/DataPanelTool.class b/org/broad/igv/ui/util/DataPanelTool.class
new file mode 100644
index 0000000..eb5986d
Binary files /dev/null and b/org/broad/igv/ui/util/DataPanelTool.class differ
diff --git a/org/broad/igv/ui/util/FileChooser.class b/org/broad/igv/ui/util/FileChooser.class
new file mode 100644
index 0000000..ecbd4fa
Binary files /dev/null and b/org/broad/igv/ui/util/FileChooser.class differ
diff --git a/org/broad/igv/ui/util/FileChooserDialog$1.class b/org/broad/igv/ui/util/FileChooserDialog$1.class
new file mode 100644
index 0000000..e9f68e6
Binary files /dev/null and b/org/broad/igv/ui/util/FileChooserDialog$1.class differ
diff --git a/org/broad/igv/ui/util/FileChooserDialog$2.class b/org/broad/igv/ui/util/FileChooserDialog$2.class
new file mode 100644
index 0000000..79bce3b
Binary files /dev/null and b/org/broad/igv/ui/util/FileChooserDialog$2.class differ
diff --git a/org/broad/igv/ui/util/FileChooserDialog$3.class b/org/broad/igv/ui/util/FileChooserDialog$3.class
new file mode 100644
index 0000000..334efe1
Binary files /dev/null and b/org/broad/igv/ui/util/FileChooserDialog$3.class differ
diff --git a/org/broad/igv/ui/util/FileChooserDialog$4.class b/org/broad/igv/ui/util/FileChooserDialog$4.class
new file mode 100644
index 0000000..0741899
Binary files /dev/null and b/org/broad/igv/ui/util/FileChooserDialog$4.class differ
diff --git a/org/broad/igv/ui/util/FileChooserDialog.class b/org/broad/igv/ui/util/FileChooserDialog.class
new file mode 100644
index 0000000..d8c1612
Binary files /dev/null and b/org/broad/igv/ui/util/FileChooserDialog.class differ
diff --git a/org/broad/igv/ui/util/FileDialogUtils$1.class b/org/broad/igv/ui/util/FileDialogUtils$1.class
new file mode 100644
index 0000000..18e6ae5
Binary files /dev/null and b/org/broad/igv/ui/util/FileDialogUtils$1.class differ
diff --git a/org/broad/igv/ui/util/FileDialogUtils.class b/org/broad/igv/ui/util/FileDialogUtils.class
new file mode 100644
index 0000000..6fadc32
Binary files /dev/null and b/org/broad/igv/ui/util/FileDialogUtils.class differ
diff --git a/org/broad/igv/ui/util/FilterComponent$1.class b/org/broad/igv/ui/util/FilterComponent$1.class
new file mode 100644
index 0000000..de65536
Binary files /dev/null and b/org/broad/igv/ui/util/FilterComponent$1.class differ
diff --git a/org/broad/igv/ui/util/FilterComponent$2.class b/org/broad/igv/ui/util/FilterComponent$2.class
new file mode 100644
index 0000000..a8c6689
Binary files /dev/null and b/org/broad/igv/ui/util/FilterComponent$2.class differ
diff --git a/org/broad/igv/ui/util/FilterComponent$3.class b/org/broad/igv/ui/util/FilterComponent$3.class
new file mode 100644
index 0000000..4dad841
Binary files /dev/null and b/org/broad/igv/ui/util/FilterComponent$3.class differ
diff --git a/org/broad/igv/ui/util/FilterComponent$4.class b/org/broad/igv/ui/util/FilterComponent$4.class
new file mode 100644
index 0000000..d77ae85
Binary files /dev/null and b/org/broad/igv/ui/util/FilterComponent$4.class differ
diff --git a/org/broad/igv/ui/util/FilterComponent$5.class b/org/broad/igv/ui/util/FilterComponent$5.class
new file mode 100644
index 0000000..2011126
Binary files /dev/null and b/org/broad/igv/ui/util/FilterComponent$5.class differ
diff --git a/org/broad/igv/ui/util/FilterComponent$6.class b/org/broad/igv/ui/util/FilterComponent$6.class
new file mode 100644
index 0000000..f91e3a8
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diff --git a/org/broad/igv/ui/util/FilterComponent.class b/org/broad/igv/ui/util/FilterComponent.class
new file mode 100644
index 0000000..0e88788
Binary files /dev/null and b/org/broad/igv/ui/util/FilterComponent.class differ
diff --git a/org/broad/igv/ui/util/FilterPane.class b/org/broad/igv/ui/util/FilterPane.class
new file mode 100644
index 0000000..2ecdeb8
Binary files /dev/null and b/org/broad/igv/ui/util/FilterPane.class differ
diff --git a/org/broad/igv/ui/util/FontChooser$1.class b/org/broad/igv/ui/util/FontChooser$1.class
new file mode 100644
index 0000000..beb75cf
Binary files /dev/null and b/org/broad/igv/ui/util/FontChooser$1.class differ
diff --git a/org/broad/igv/ui/util/FontChooser$2.class b/org/broad/igv/ui/util/FontChooser$2.class
new file mode 100644
index 0000000..221e756
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diff --git a/org/broad/igv/ui/util/FontChooser$3.class b/org/broad/igv/ui/util/FontChooser$3.class
new file mode 100644
index 0000000..3030929
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diff --git a/org/broad/igv/ui/util/FontChooser$4.class b/org/broad/igv/ui/util/FontChooser$4.class
new file mode 100644
index 0000000..4df61e8
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diff --git a/org/broad/igv/ui/util/FontChooser$5.class b/org/broad/igv/ui/util/FontChooser$5.class
new file mode 100644
index 0000000..8e3ead0
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diff --git a/org/broad/igv/ui/util/FontChooser$6.class b/org/broad/igv/ui/util/FontChooser$6.class
new file mode 100644
index 0000000..a1586f4
Binary files /dev/null and b/org/broad/igv/ui/util/FontChooser$6.class differ
diff --git a/org/broad/igv/ui/util/FontChooser.class b/org/broad/igv/ui/util/FontChooser.class
new file mode 100644
index 0000000..f8b774f
Binary files /dev/null and b/org/broad/igv/ui/util/FontChooser.class differ
diff --git a/org/broad/igv/ui/util/FontChooser.jfd b/org/broad/igv/ui/util/FontChooser.jfd
new file mode 100644
index 0000000..834ad4d
--- /dev/null
+++ b/org/broad/igv/ui/util/FontChooser.jfd
@@ -0,0 +1,357 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<java version="1.6.0_22" class="java.beans.XMLDecoder">
+ <object class="com.jformdesigner.model.FormModel">
+ <void property="contentType">
+ <string>form/swing</string>
+ </void>
+ <void property="root">
+ <object class="com.jformdesigner.model.FormRoot">
+ <void method="add">
+ <object class="com.jformdesigner.model.FormWindow">
+ <string>javax.swing.JDialog</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.BorderLayout</class>
+ </object>
+ <void method="setProperty">
+ <string>$sizePolicy</string>
+ <int>1</int>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.BorderLayout</class>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="javax.swing.border.EmptyBorder">
+ <object class="java.awt.Insets">
+ <int>12</int>
+ <int>12</int>
+ <int>12</int>
+ <int>12</int>
+ </object>
+ </object>
+ </void>
+ <void property="name">
+ <string>dialogPane</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>org.jdesktop.layout.GroupLayout</class>
+ <void method="setProperty">
+ <string>$horizontalGroup</string>
+ <string>par l {seq l {space :::p, comp scrollPane1:::p:274:p, space :p:22:p, par t {seq {par l {seq l {comp label1:::p:52:p, space :::p, comp sizeComboBox:::p::p}, comp boldCB:::p::p, comp italicCB:::p::p}, space :p:66:p}, seq t {comp exampleLabel:::p:198:p, space :::p}}}}</string>
+ </void>
+ <void method="setProperty">
+ <string>$verticalGroup</string>
+ <string>par l {seq l {space :::p, par l {comp scrollPane1::l::264:x, seq l {par b {comp label1::b:p:22:p, comp sizeComboBox::b:p::p}, space :::p, comp boldCB:::p::p, space :p:5:p, comp italicCB:::p::p, space ::57:x, comp exampleLabel:::p:123:p}}, space :::p}}</string>
+ </void>
+ </object>
+ <void property="name">
+ <string>contentPanel</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JComboBox</string>
+ <void method="setProperty">
+ <string>model</string>
+ <object class="javax.swing.DefaultComboBoxModel">
+ <void property="selectedItem">
+ <string>6</string>
+ </void>
+ <void method="addElement">
+ <string>6</string>
+ </void>
+ <void method="addElement">
+ <string>8</string>
+ </void>
+ <void method="addElement">
+ <string>9</string>
+ </void>
+ <void method="addElement">
+ <string>10</string>
+ </void>
+ <void method="addElement">
+ <string>11</string>
+ </void>
+ <void method="addElement">
+ <string>12</string>
+ </void>
+ <void method="addElement">
+ <string>14</string>
+ </void>
+ <void method="addElement">
+ <string>16</string>
+ </void>
+ <void method="addElement">
+ <string>20</string>
+ </void>
+ <void method="addElement">
+ <string>24</string>
+ </void>
+ </object>
+ </void>
+ <void property="name">
+ <string>sizeComboBox</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>sizeComboBoxActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Size</string>
+ </void>
+ <void method="setProperty">
+ <string>labelFor</string>
+ <object class="com.jformdesigner.model.FormReference">
+ <string>sizeComboBox</string>
+ </object>
+ </void>
+ <void property="name">
+ <string>label1</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JCheckBox</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string><html><b>Bold</string>
+ </void>
+ <void property="name">
+ <string>boldCB</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>boldCBActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JCheckBox</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string><html><i>Italic</string>
+ </void>
+ <void property="name">
+ <string>italicCB</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>italicCBActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextPane</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Lorem ipsum dolor sit amet, consectetur adipiscing elit.</string>
+ </void>
+ <void property="name">
+ <string>exampleLabel</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JScrollPane</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>javax.swing.JScrollPane</class>
+ </object>
+ <void property="name">
+ <string>scrollPane1</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JList</string>
+ <void property="name">
+ <string>fontList</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>javax.swing.event.ListSelectionListener</string>
+ <string>valueChanged</string>
+ <string>fontListValueChanged</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>Center</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.GridBagLayout</class>
+ <void method="setProperty">
+ <string>$columnSpecs</string>
+ <string>0:1.0, 80, 80</string>
+ </void>
+ <void method="setProperty">
+ <string>$rowSpecs</string>
+ <string>0</string>
+ </void>
+ <void method="setProperty">
+ <string>$hGap</string>
+ <int>5</int>
+ </void>
+ <void method="setProperty">
+ <string>$vGap</string>
+ <int>5</int>
+ </void>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="javax.swing.border.EmptyBorder">
+ <object class="java.awt.Insets">
+ <int>12</int>
+ <int>0</int>
+ <int>0</int>
+ <int>0</int>
+ </object>
+ </object>
+ </void>
+ <void property="name">
+ <string>buttonBar</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>OK</string>
+ </void>
+ <void property="name">
+ <string>okButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>okButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>1</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>0</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Cancel</string>
+ </void>
+ <void property="name">
+ <string>cancelButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>cancelButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>0</int>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>South</string>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>Center</string>
+ </void>
+ </object>
+ </void>
+ <void property="name">
+ <string>this</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <null/>
+ <void method="setProperty">
+ <string>location</string>
+ <object class="java.awt.Point">
+ <int>0</int>
+ <int>0</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>size</string>
+ <object class="java.awt.Dimension">
+ <int>530</int>
+ <int>365</int>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+</java>
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diff --git a/org/broad/igv/util/LoginDialog.jfd b/org/broad/igv/util/LoginDialog.jfd
new file mode 100644
index 0000000..68f0d65
--- /dev/null
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@@ -0,0 +1,390 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<java version="1.6.0_26" class="java.beans.XMLDecoder">
+ <object class="com.jformdesigner.model.FormModel">
+ <void property="contentType">
+ <string>form/swing</string>
+ </void>
+ <void property="root">
+ <object class="com.jformdesigner.model.FormRoot">
+ <void method="add">
+ <object class="com.jformdesigner.model.FormWindow">
+ <string>javax.swing.JDialog</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.BorderLayout</class>
+ </object>
+ <void method="setProperty">
+ <string>modalityType</string>
+ <object class="java.lang.Enum" method="valueOf">
+ <class>java.awt.Dialog$ModalityType</class>
+ <string>APPLICATION_MODAL</string>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.BorderLayout</class>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="javax.swing.border.EmptyBorder">
+ <object class="java.awt.Insets">
+ <int>12</int>
+ <int>12</int>
+ <int>12</int>
+ <int>12</int>
+ </object>
+ </object>
+ </void>
+ <void property="name">
+ <string>dialogPane</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>com.jformdesigner.runtime.NullLayout</class>
+ </object>
+ <void property="name">
+ <string>contentPanel</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>icon</string>
+ <object class="com.jformdesigner.model.SwingIcon">
+ <int>0</int>
+ <string>/images/genomespacelogo.png</string>
+ </object>
+ </void>
+ <void property="name">
+ <string>iconLabel</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>20</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>160</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>320</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Enter username and password to access this resource</string>
+ </void>
+ <void method="setProperty">
+ <string>font</string>
+ <object class="java.awt.Font">
+ <string>Arial</string>
+ <int>0</int>
+ <int>14</int>
+ </object>
+ </void>
+ <void property="name">
+ <string>promptLabel</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>5</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>0</int>
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+ <int>395</int>
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+ <string>height</string>
+ <int>65</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JPasswordField</string>
+ <void property="name">
+ <string>passwordField</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>width</string>
+ <int>220</int>
+ </void>
+ <void method="setProperty">
+ <string>height</string>
+ <int>32</int>
+ </void>
+ <void method="setProperty">
+ <string>x</string>
+ <int>125</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>115</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Password:</string>
+ </void>
+ <void method="setProperty">
+ <string>font</string>
+ <object id="Font0" class="java.awt.Font">
+ <string>Arial</string>
+ <int>0</int>
+ <int>14</int>
+ </object>
+ </void>
+ <void property="name">
+ <string>label2</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>25</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>123</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void property="name">
+ <string>usernameField</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>125</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>220</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>70</int>
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+ <void method="setProperty">
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+ <int>32</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Username:</string>
+ </void>
+ <void method="setProperty">
+ <string>font</string>
+ <object idref="Font0"/>
+ </void>
+ <void property="name">
+ <string>label1</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>width</string>
+ <int>90</int>
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+ <void method="setProperty">
+ <string>height</string>
+ <int>28</int>
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+ <int>25</int>
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+ <int>72</int>
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+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>Center</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.GridBagLayout</class>
+ <void method="setProperty">
+ <string>$columnSpecs</string>
+ <string>0:1.0, 80, 80</string>
+ </void>
+ <void method="setProperty">
+ <string>$rowSpecs</string>
+ <string>0</string>
+ </void>
+ <void method="setProperty">
+ <string>$hGap</string>
+ <int>5</int>
+ </void>
+ <void method="setProperty">
+ <string>$vGap</string>
+ <int>5</int>
+ </void>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="javax.swing.border.EmptyBorder">
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+ <int>12</int>
+ <int>0</int>
+ <int>0</int>
+ <int>0</int>
+ </object>
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+ </void>
+ <void property="name">
+ <string>buttonBar</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>OK</string>
+ </void>
+ <void property="name">
+ <string>okButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>okButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>1</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>0</int>
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+ </object>
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+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Cancel</string>
+ </void>
+ <void property="name">
+ <string>cancelButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>cancelButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>0</int>
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+ </object>
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+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>South</string>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>Center</string>
+ </void>
+ </object>
+ </void>
+ <void property="name">
+ <string>this</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <null/>
+ <void method="setProperty">
+ <string>location</string>
+ <object class="java.awt.Point">
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+ </object>
+ </void>
+ <void method="setProperty">
+ <string>size</string>
+ <object class="java.awt.Dimension">
+ <int>430</int>
+ <int>350</int>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+</java>
diff --git a/org/broad/igv/util/LongRunningTask.class b/org/broad/igv/util/LongRunningTask.class
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diff --git a/org/broad/igv/util/UnzipGenomes.class b/org/broad/igv/util/UnzipGenomes.class
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diff --git a/org/broad/igv/util/UserPasswordDialog$1.class b/org/broad/igv/util/UserPasswordDialog$1.class
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diff --git a/org/broad/igv/util/UserPasswordDialog$2.class b/org/broad/igv/util/UserPasswordDialog$2.class
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diff --git a/org/broad/igv/util/UserPasswordDialog.class b/org/broad/igv/util/UserPasswordDialog.class
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diff --git a/org/broad/igv/util/UserPasswordDialog.jfd b/org/broad/igv/util/UserPasswordDialog.jfd
new file mode 100644
index 0000000..c53dc0e
--- /dev/null
+++ b/org/broad/igv/util/UserPasswordDialog.jfd
@@ -0,0 +1,378 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<java version="1.6.0_17" class="java.beans.XMLDecoder">
+ <object class="com.jformdesigner.model.FormModel">
+ <void property="contentType">
+ <string>form/swing</string>
+ </void>
+ <void property="root">
+ <object class="com.jformdesigner.model.FormRoot">
+ <void method="add">
+ <object class="com.jformdesigner.model.FormWindow">
+ <string>javax.swing.JDialog</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.BorderLayout</class>
+ </object>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.BorderLayout</class>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="javax.swing.border.EmptyBorder">
+ <object class="java.awt.Insets">
+ <int>12</int>
+ <int>12</int>
+ <int>12</int>
+ <int>12</int>
+ </object>
+ </object>
+ </void>
+ <void property="name">
+ <string>dialogPane</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.GridBagLayout</class>
+ <void method="setProperty">
+ <string>$columnSpecs</string>
+ <string>0:1.0, 80, 80</string>
+ </void>
+ <void method="setProperty">
+ <string>$rowSpecs</string>
+ <string>0</string>
+ </void>
+ <void method="setProperty">
+ <string>$hGap</string>
+ <int>5</int>
+ </void>
+ <void method="setProperty">
+ <string>$vGap</string>
+ <int>5</int>
+ </void>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="javax.swing.border.EmptyBorder">
+ <object class="java.awt.Insets">
+ <int>12</int>
+ <int>0</int>
+ <int>0</int>
+ <int>0</int>
+ </object>
+ </object>
+ </void>
+ <void property="name">
+ <string>buttonBar</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>OK</string>
+ </void>
+ <void property="name">
+ <string>okButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>okButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>1</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>0</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JButton</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Cancel</string>
+ </void>
+ <void property="name">
+ <string>cancelButton</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>cancelButtonActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+ <void method="setProperty">
+ <string>gridx</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>gridy</string>
+ <int>0</int>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>South</string>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>com.jformdesigner.runtime.NullLayout</class>
+ </object>
+ <void property="name">
+ <string>contentPanel2</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Enter user name and password for:</string>
+ </void>
+ <void property="name">
+ <string>label1</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>15</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>10</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>ftp://ftp........................................</string>
+ </void>
+ <void property="name">
+ <string>hostLabel</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>30</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>35</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>User name:</string>
+ </void>
+ <void property="name">
+ <string>label3</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>30</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>125</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Password</string>
+ </void>
+ <void property="name">
+ <string>label4</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>30</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>160</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JTextField</string>
+ <void property="name">
+ <string>userField</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>125</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>120</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>305</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JPasswordField</string>
+ <void property="name">
+ <string>passwordField</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>width</string>
+ <int>305</int>
+ </void>
+ <void method="setProperty">
+ <string>x</string>
+ <int>125</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>155</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>com.jformdesigner.runtime.NullLayout</class>
+ </object>
+ <void property="name">
+ <string>panel1</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>125</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>130</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string><html>If this is a public server try "anonymous" for user name and your<br>
+email address for password.</string>
+ </void>
+ <void property="name">
+ <string>label2</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
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+ <void method="setProperty">
+ <string>y</string>
+ <int>65</int>
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+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>North</string>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>Center</string>
+ </void>
+ </object>
+ </void>
+ <void property="name">
+ <string>this</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <null/>
+ <void method="setProperty">
+ <string>location</string>
+ <object class="java.awt.Point">
+ <int>5</int>
+ <int>20</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>size</string>
+ <object class="java.awt.Dimension">
+ <int>535</int>
+ <int>300</int>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+</java>
diff --git a/org/broad/igv/util/UserPasswordInputImpl.class b/org/broad/igv/util/UserPasswordInputImpl.class
new file mode 100644
index 0000000..c770c2b
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diff --git a/org/broad/igv/util/Utilities$1.class b/org/broad/igv/util/Utilities$1.class
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index 0000000..47d5ace
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diff --git a/org/broad/igv/util/ZipArchiveWrapper$ZipIterator.class b/org/broad/igv/util/ZipArchiveWrapper$ZipIterator.class
new file mode 100644
index 0000000..88f21d9
Binary files /dev/null and b/org/broad/igv/util/ZipArchiveWrapper$ZipIterator.class differ
diff --git a/org/broad/igv/util/ZipArchiveWrapper.class b/org/broad/igv/util/ZipArchiveWrapper.class
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index 0000000..78d991c
Binary files /dev/null and b/org/broad/igv/util/ZipArchiveWrapper.class differ
diff --git a/org/broad/igv/util/collections/DoubleArrayList.class b/org/broad/igv/util/collections/DoubleArrayList.class
new file mode 100644
index 0000000..6a2b07d
Binary files /dev/null and b/org/broad/igv/util/collections/DoubleArrayList.class differ
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index 0000000..e97cd71
Binary files /dev/null and b/org/broad/igv/util/collections/FloatArrayList.class differ
diff --git a/org/broad/igv/util/collections/IntArrayList.class b/org/broad/igv/util/collections/IntArrayList.class
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index 0000000..fd6c663
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diff --git a/org/broad/igv/util/collections/StringArrayList.class b/org/broad/igv/util/collections/StringArrayList.class
new file mode 100644
index 0000000..5a3003f
Binary files /dev/null and b/org/broad/igv/util/collections/StringArrayList.class differ
diff --git a/org/broad/igv/util/converters/DensitiesToBedGraph.class b/org/broad/igv/util/converters/DensitiesToBedGraph.class
new file mode 100644
index 0000000..0d630a7
Binary files /dev/null and b/org/broad/igv/util/converters/DensitiesToBedGraph.class differ
diff --git a/org/broad/igv/util/converters/TarjeiToBedgraph.class b/org/broad/igv/util/converters/TarjeiToBedgraph.class
new file mode 100644
index 0000000..4f34b57
Binary files /dev/null and b/org/broad/igv/util/converters/TarjeiToBedgraph.class differ
diff --git a/org/broad/igv/util/index/Interval.class b/org/broad/igv/util/index/Interval.class
new file mode 100644
index 0000000..61d9578
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diff --git a/org/broad/igv/util/index/IntervalTree$Node.class b/org/broad/igv/util/index/IntervalTree$Node.class
new file mode 100644
index 0000000..6a1acb8
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diff --git a/org/broad/igv/util/index/IntervalTree.class b/org/broad/igv/util/index/IntervalTree.class
new file mode 100644
index 0000000..a97020e
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diff --git a/org/broad/igv/util/stats/Distribution.class b/org/broad/igv/util/stats/Distribution.class
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index 0000000..7948020
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diff --git a/org/broad/igv/util/stats/KMPlotFrame$1.class b/org/broad/igv/util/stats/KMPlotFrame$1.class
new file mode 100644
index 0000000..fd620a2
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diff --git a/org/broad/igv/util/stats/KMPlotFrame$2.class b/org/broad/igv/util/stats/KMPlotFrame$2.class
new file mode 100644
index 0000000..427ad43
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diff --git a/org/broad/igv/util/stats/KMPlotFrame$3.class b/org/broad/igv/util/stats/KMPlotFrame$3.class
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index 0000000..af0bc46
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diff --git a/org/broad/igv/util/stats/KMPlotFrame$DataPoint.class b/org/broad/igv/util/stats/KMPlotFrame$DataPoint.class
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diff --git a/org/broad/igv/util/stats/KMPlotFrame.class b/org/broad/igv/util/stats/KMPlotFrame.class
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index 0000000..3b7dbaa
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diff --git a/org/broad/igv/util/stats/KMPlotFrame.jfd b/org/broad/igv/util/stats/KMPlotFrame.jfd
new file mode 100644
index 0000000..1bd775d
--- /dev/null
+++ b/org/broad/igv/util/stats/KMPlotFrame.jfd
@@ -0,0 +1,330 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<java version="1.6.0_26" class="java.beans.XMLDecoder">
+ <object class="com.jformdesigner.model.FormModel">
+ <void property="contentType">
+ <string>form/swing</string>
+ </void>
+ <void property="root">
+ <object class="com.jformdesigner.model.FormRoot">
+ <void method="add">
+ <object class="com.jformdesigner.model.FormWindow">
+ <string>javax.swing.JFrame</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.BorderLayout</class>
+ </object>
+ <void method="setProperty">
+ <string>$sizePolicy</string>
+ <int>1</int>
+ </void>
+ <void method="setProperty">
+ <string>defaultCloseOperation</string>
+ <int>2</int>
+ </void>
+ <void method="setProperty">
+ <string>title</string>
+ <string>Kaplan-Meier Plot</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.BorderLayout</class>
+ </object>
+ <void method="setProperty">
+ <string>border</string>
+ <object class="javax.swing.border.EmptyBorder">
+ <int>12</int>
+ <int>12</int>
+ <int>12</int>
+ <int>12</int>
+ </object>
+ </void>
+ <void property="name">
+ <string>dialogPane</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>java.awt.BorderLayout</class>
+ </object>
+ <void property="name">
+ <string>contentPanel</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>javax.swing.BoxLayout</class>
+ <void method="setProperty">
+ <string>axis</string>
+ <int>1</int>
+ </void>
+ </object>
+ <void method="setProperty">
+ <string>alignmentX</string>
+ <float>0.0</float>
+ </void>
+ <void property="name">
+ <string>panel1</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>com.jformdesigner.runtime.NullLayout</class>
+ </object>
+ <void method="setProperty">
+ <string>alignmentX</string>
+ <float>1.0</float>
+ </void>
+ <void property="name">
+ <string>panel2</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Survival column</string>
+ </void>
+ <void property="name">
+ <string>label2</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>5</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>10</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JComboBox</string>
+ <void property="name">
+ <string>survivalColumnControl</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>survivalColumnControlActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>120</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>5</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>235</int>
+ </void>
+ </object>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>com.jformdesigner.runtime.NullLayout</class>
+ </object>
+ <void method="setProperty">
+ <string>alignmentX</string>
+ <float>1.0</float>
+ </void>
+ <void property="name">
+ <string>panel3</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Censure column</string>
+ </void>
+ <void property="name">
+ <string>label3</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>5</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>10</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JComboBox</string>
+ <void property="name">
+ <string>censurColumnControl</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>survivalColumnControlActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>120</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>5</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>235</int>
+ </void>
+ </object>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormContainer">
+ <string>javax.swing.JPanel</string>
+ <object class="com.jformdesigner.model.FormLayoutManager">
+ <class>com.jformdesigner.runtime.NullLayout</class>
+ </object>
+ <void method="setProperty">
+ <string>alignmentX</string>
+ <float>1.0</float>
+ </void>
+ <void property="name">
+ <string>panel4</string>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JLabel</string>
+ <void method="setProperty">
+ <string>text</string>
+ <string>Group by</string>
+ </void>
+ <void property="name">
+ <string>label4</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>5</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>10</int>
+ </void>
+ </object>
+ </void>
+ <void method="add">
+ <object class="com.jformdesigner.model.FormComponent">
+ <string>javax.swing.JComboBox</string>
+ <void property="name">
+ <string>groupByControl</string>
+ </void>
+ <void method="addEvent">
+ <object class="com.jformdesigner.model.FormEvent">
+ <string>java.awt.event.ActionListener</string>
+ <string>actionPerformed</string>
+ <string>survivalColumnControlActionPerformed</string>
+ <boolean>true</boolean>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>com.jformdesigner.runtime.NullConstraints</class>
+ <void method="setProperty">
+ <string>x</string>
+ <int>120</int>
+ </void>
+ <void method="setProperty">
+ <string>y</string>
+ <int>5</int>
+ </void>
+ <void method="setProperty">
+ <string>width</string>
+ <int>235</int>
+ </void>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>North</string>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>Center</string>
+ </void>
+ </object>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <class>java.lang.String</class>
+ <void method="setProperty">
+ <string>value</string>
+ <string>Center</string>
+ </void>
+ </object>
+ </void>
+ <void property="name">
+ <string>this</string>
+ </void>
+ </object>
+ <object class="com.jformdesigner.model.FormLayoutConstraints">
+ <null/>
+ <void method="setProperty">
+ <string>location</string>
+ <object class="java.awt.Point">
+ <int>0</int>
+ <int>0</int>
+ </object>
+ </void>
+ <void method="setProperty">
+ <string>size</string>
+ <object class="java.awt.Dimension">
+ <int>565</int>
+ <int>510</int>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+ </void>
+ </object>
+</java>
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diff --git a/org/hamcrest/core/package.html b/org/hamcrest/core/package.html
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--- /dev/null
+++ b/org/hamcrest/core/package.html
@@ -0,0 +1,7 @@
+<html>
+<head>
+</head>
+<body>
+ <p>Fundamental matchers of objects and values, and composite matchers.</p>
+</body>
+</html>
diff --git a/org/hamcrest/internal/ArrayIterator.class b/org/hamcrest/internal/ArrayIterator.class
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+++ b/org/hamcrest/package.html
@@ -0,0 +1,9 @@
+<html>
+<head>
+</head>
+<body>
+ <p>The stable API defining Matcher and its associated interfaces and classes.
+ Hamcrest sub-projects define their convenience classes in the org.hamcrest package.
+ </p>
+</body>
+</html>
diff --git a/org/jdesktop/layout/AquaBaseline.class b/org/jdesktop/layout/AquaBaseline.class
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diff --git a/org/jfree/base/jcommon.properties b/org/jfree/base/jcommon.properties
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+++ b/org/jfree/base/jcommon.properties
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+#
+# The minimum loglevel that is logged
+org.jfree.base.LogLevel=Debug
+
+#
+# Where to log. Give a classname of a valid LogTarget implementation.
+# If the name is invalid, no logging is done.
+org.jfree.base.LogTarget=*none*
+
+#
+# Do not initialize the logging.
+org.jfree.base.LogAutoInit=false
+
+#
+# Should the debugging system be disabled by default. This option will suppress all
+# output, no single line of debug information will be printed. If you want to remove
+# System.out-debugging on the server side, try to switch to a Log4J-LogTarget instead.
+org.jfree.base.NoDefaultDebug=false
+
+#
+# Which ClassLoader to use for loading external resources and classes.
+# One of "ThreadContext" or "CallerContext".
+org.jfree.ClassLoader=ThreadContext
+
+#
+# Applies a workaround to fix a JDK bug. When the value is set to auto,
+# This is enabled if the JDK is not version 1.4 or higher.
+org.jfree.text.UseDrawRotatedStringWorkaround=auto
+
+#
+# Applies a workaround to fix a JDK bug. When the value is set to auto,
+# This is disabled if the JDK is not version 1.4 or higher.
+org.jfree.text.UseFontMetricsGetStringBounds=auto
+
+
+#
+# Known extra modules. Do not edit and do not delete the following lines.
+#
+# That module loading mechanism is not really extensible. A better
+# implementation might solve that at a later time.
+org.jfree.jcommon.modules.logger.Log4J.Module=org.jfree.logger.java14.Java14LogModule
+org.jfree.jcommon.modules.logger.Java14Logging.Module=org.jfree.logger.log4j.Log4JLogModule
+org.jfree.jcommon.modules.logger.JakartaLogging.Module=org.jfree.logger.jcl.JakartaLogModule
diff --git a/org/jfree/base/log/DefaultLog.class b/org/jfree/base/log/DefaultLog.class
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diff --git a/org/jfree/base/log/PadMessage.class b/org/jfree/base/log/PadMessage.class
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diff --git a/org/jfree/base/log/module.properties b/org/jfree/base/log/module.properties
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--- /dev/null
+++ b/org/jfree/base/log/module.properties
@@ -0,0 +1,14 @@
+#
+# Support for logging.
+#
+
+module-info:
+ name: base-logging-module
+ producer: The JFreeChart project - www.jfree.org/jcommon
+ description: Initialializer to configure the log system and to provide
+ a facility for logging to the System.out stream.
+ version.major: 1
+ version.minor: 0
+ version.patchlevel: 0
+ subsystem: logging
+
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diff --git a/org/jfree/chart/LocalizationBundle.properties b/org/jfree/chart/LocalizationBundle.properties
new file mode 100644
index 0000000..f111895
--- /dev/null
+++ b/org/jfree/chart/LocalizationBundle.properties
@@ -0,0 +1,19 @@
+# org.jfree.chart.ChartPanel ResourceBundle properties file
+#
+# Changes (from 31-Aug-2003)
+# --------------------------
+# 31-Aug-2003 : Initial version (AL);
+#
+
+Auto_Range=Auto Range
+All_Axes=Both Axes
+Chart_Properties=Chart Properties
+Copy=Copy
+Domain_Axis=Domain Axis
+PNG_Image_Files=PNG Image Files
+Print...=Print...
+Properties...=Properties...
+Save_as...=Save as...
+Range_Axis=Range Axis
+Zoom_In=Zoom In
+Zoom_Out=Zoom Out
diff --git a/org/jfree/chart/LocalizationBundle_de.properties b/org/jfree/chart/LocalizationBundle_de.properties
new file mode 100644
index 0000000..22efc3a
--- /dev/null
+++ b/org/jfree/chart/LocalizationBundle_de.properties
@@ -0,0 +1,20 @@
+# org.jfree.chart.ChartPanel ResourceBundle properties file - german version
+#
+# Changes (from 31-Aug-2003)
+# --------------------------
+# 31-Aug-2003 : Initial version (AL);
+# 15-Mar-2004 : Revised version (Christian W. Zuckschwerdt);
+#
+
+Auto_Range=Autojustage
+All_Axes=Beide Achsen
+Chart_Properties=Diagramm-Eigenschaften
+Copy=Kopieren
+Domain_Axis=Horizontale Achse
+PNG_Image_Files=PNG Datei (Portable Network Graphics) (*.png)
+Print...=Drucken...
+Properties...=Eigenschaften...
+Save_as...=Speichern unter...
+Range_Axis=Vertikale Achse
+Zoom_In=Hineinzoomen
+Zoom_Out=Herauszoomen
diff --git a/org/jfree/chart/LocalizationBundle_es.properties b/org/jfree/chart/LocalizationBundle_es.properties
new file mode 100644
index 0000000..0a9b7d4
--- /dev/null
+++ b/org/jfree/chart/LocalizationBundle_es.properties
@@ -0,0 +1,19 @@
+# org.jfree.chart.ChartPanel ResourceBundle properties file - spanish version
+#
+# Changes (from 16-Dec-2003)
+# --------------------------
+# 16-Dec-2003 : Initial Version: Complejo Hospitalario Universitario Juan Canalejo
+#
+
+Auto_Range=Escala autom\u00E1tica
+All_Axes=Todos los ejes
+Chart_Properties=Propiedades del gr\u00E1fico
+Copy=Copiar
+Domain_Axis=Eje horizontal
+PNG_Image_Files=Formato PNG (Portable Network Graphics) (*.png)
+Print...=Imprimir...
+Properties...=Propiedades...
+Save_as...=Grabar como...
+Range_Axis=Eje vertical
+Zoom_In=Acercar
+Zoom_Out=Alejar
diff --git a/org/jfree/chart/LocalizationBundle_fr.properties b/org/jfree/chart/LocalizationBundle_fr.properties
new file mode 100644
index 0000000..b817d9b
--- /dev/null
+++ b/org/jfree/chart/LocalizationBundle_fr.properties
@@ -0,0 +1,19 @@
+# org.jfree.chart.ChartPanel ResourceBundle properties file - french version
+#
+# Changes (from 31-Aug-2003)
+# --------------------------
+# 31-Aug-2003 : Initial version (AL);
+#
+
+Auto_Range=Echelle automatique
+All_Axes=Les deux axes
+Chart_Properties=Propri\u00E9t\u00E9s du graphique
+Copy=Copier
+Domain_Axis=Axe horizontal
+PNG_Image_Files=Format PNG (Portable Network Graphics) (*.png)
+Print...=Imprimer...
+Properties...=Propri\u00E9t\u00E9s...
+Save_as...=Enregistrer sous...
+Range_Axis=Axe vertical
+Zoom_In=Zoom avant
+Zoom_Out=Zoom arri\u00E8re
diff --git a/org/jfree/chart/LocalizationBundle_it.properties b/org/jfree/chart/LocalizationBundle_it.properties
new file mode 100644
index 0000000..0e9257c
--- /dev/null
+++ b/org/jfree/chart/LocalizationBundle_it.properties
@@ -0,0 +1,13 @@
+# org.jfree.chart.ChartPanel ResourceBundle properties file - italian version
+Auto_Range=Dimensiona Automaticamente
+All_Axes=Entrambi gli Assi
+Chart_Properties=Propriet\u00E0 del Grafico
+Copy=Copia
+Domain_Axis=Asse Orizzontale
+PNG_Image_Files=Immagine PNG
+Print...=Stampa...
+Properties...=Propriet\u00E0...
+Save_as...=Salva Come...
+Range_Axis=Asse Verticale
+Zoom_In=Ingrandisci
+Zoom_Out=Rimpicciolisci
diff --git a/org/jfree/chart/LocalizationBundle_nl.properties b/org/jfree/chart/LocalizationBundle_nl.properties
new file mode 100644
index 0000000..e1b221f
--- /dev/null
+++ b/org/jfree/chart/LocalizationBundle_nl.properties
@@ -0,0 +1,20 @@
+# org.jfree.chart.ChartPanel ResourceBundle properties file
+#
+# Changes (from 31-Aug-2003)
+# --------------------------
+# 24-Mar-2003 : Translated into Dutch
+# 31-Aug-2003 : Initial version (AL);
+#
+
+Auto_Range=Automatisch bereik
+All_Axes=Beide assen
+Chart_Properties=Eigenschappen
+Copy=Kopie\u00EBren
+Domain_Axis=Horizontale As
+PNG_Image_Files=PNG afbeelding
+Print...=Afdrukken...
+Properties...=Eigenschappen...
+Save_as...=Opslaan als...
+Range_Axis=Verticale As
+Zoom_In=Inzoomen
+Zoom_Out=Uitzoomen
diff --git a/org/jfree/chart/LocalizationBundle_pl.properties b/org/jfree/chart/LocalizationBundle_pl.properties
new file mode 100644
index 0000000..304418d
--- /dev/null
+++ b/org/jfree/chart/LocalizationBundle_pl.properties
@@ -0,0 +1,19 @@
+# org.jfree.chart.ChartPanel ResourceBundle properties file
+#
+# Changes (from 15-Mar-2004)
+# --------------------------
+# 15-Mar-2004 : Initial version (Kuba Duda);
+#
+
+Auto_Range=Automatyczny zakres
+All_Axes=Obie osie
+Chart_Properties=W\u0142a\u015bciwo\u015bci wykresu
+Copy=Kopiuj
+Domain_Axis=O\u015b pozioma
+PNG_Image_Files=Pliki graficzne PNG
+Print...=Drukuj...
+Properties...=W\u0142a\u015bciwo\u015bci...
+Save_as...=Zapisz jako...
+Range_Axis=O\u015b pionowa
+Zoom_In=Powi\u0119ksz
+Zoom_Out=Pomniejsz
diff --git a/org/jfree/chart/LocalizationBundle_pt_BR.properties b/org/jfree/chart/LocalizationBundle_pt_BR.properties
new file mode 100644
index 0000000..2a32afe
--- /dev/null
+++ b/org/jfree/chart/LocalizationBundle_pt_BR.properties
@@ -0,0 +1,19 @@
+# org.jfree.chart.ChartPanel ResourceBundle properties file - portuguese version
+#
+# Changes (from 24-May-2007)
+# --------------------------
+# 24-May-2007 : Initial version (Leonardo Alves Machado);
+#
+
+Auto_Range=Escala autom\u00E1tica
+All_Axes=Todos os eixos
+Chart_Properties=Propriedades do gr\u00E1fico
+Copy=Copiar
+Domain_Axis=Eixo horizontal
+PNG_Image_Files=Formato PNG (Portable Network Graphics) (*.png)
+Print...=Imprimir...
+Properties...=Propriedades...
+Save_as...=Salvar como...
+Range_Axis=Eixo vertical
+Zoom_In=Ampliar
+Zoom_Out=Reduzir
diff --git a/org/jfree/chart/LocalizationBundle_pt_PT.properties b/org/jfree/chart/LocalizationBundle_pt_PT.properties
new file mode 100644
index 0000000..33ae0d0
--- /dev/null
+++ b/org/jfree/chart/LocalizationBundle_pt_PT.properties
@@ -0,0 +1,19 @@
+# org.jfree.chart.ChartPanel ResourceBundle properties file - portuguese version
+#
+# Changes (from 09-Set-2003)
+# --------------------------
+# 09-Set-2003 : Initial version (ER);
+#
+
+Auto_Range=Escala autom\u00E1tica
+All_Axes=Todos os eixos
+Chart_Properties=Propriedades do gr\u00E1fico
+Copy=Copiar
+Domain_Axis=Eixo horizontal
+PNG_Image_Files=Formato PNG (Portable Network Graphics) (*.png)
+Print...=Imprimir...
+Properties...=Propriedades...
+Save_as...=Gravar como...
+Range_Axis=Eixo vertical
+Zoom_In=Aproximar
+Zoom_Out=Afastar
diff --git a/org/jfree/chart/LocalizationBundle_ru.properties b/org/jfree/chart/LocalizationBundle_ru.properties
new file mode 100644
index 0000000..4380965
--- /dev/null
+++ b/org/jfree/chart/LocalizationBundle_ru.properties
@@ -0,0 +1,19 @@
+# org.jfree.chart.ChartPanel ResourceBundle properties file
+#
+# Changes (from 10-Nov-2003)
+# --------------------------
+# 10-Nov-2003 : Initial version (AL);
+#
+
+Auto_Range=\u0410\u0432\u0442\u043e\u043c\u0430\u0441\u0448\u0442\u0430\u0431\u0438\u0440\u043e\u0432\u0430\u043d\u0438\u0435
+All_Axes=\u041f\u043e \u0432\u0441\u0435\u043c \u043e\u0441\u044f\u043c
+Chart_Properties=\u041d\u0430\u0441\u0442\u0440\u043e\u0439\u043a\u0438 \u0433\u0440\u0430\u0444\u0438\u043a\u0430
+Copy=\u041a\u043e\u043f\u0438\u0440\u043e\u0432\u0430\u0442\u044c
+Domain_Axis=\u041f\u043e \u0433\u043e\u0440\u0438\u0437\u043e\u043d\u0442\u0430\u043b\u044c\u043d\u043e\u0439 \u043e\u0441\u0438
+PNG_Image_Files=PNG \u0444\u0430\u0439\u043b
+Print...=\u041f\u0435\u0447\u0430\u0442\u044c...
+Properties...=\u041d\u0430\u0441\u0442\u0440\u043e\u0439\u043a\u0438...
+Save_as...=\u0421\u043e\u0445\u0440\u0430\u043d\u0438\u0442\u044c \u043a\u0430\u043a...
+Range_Axis=\u041f\u043e \u0432\u0435\u0440\u0442\u0438\u043a\u0430\u043b\u044c\u043d\u043e\u0439 \u043e\u0441\u0438
+Zoom_In=\u041f\u0440\u0438\u0431\u043b\u0438\u0437\u0438\u0442\u044c
+Zoom_Out=\u041e\u0442\u0434\u0430\u043b\u0438\u0442\u044c
diff --git a/org/jfree/chart/LocalizationBundle_zh_CN.properties b/org/jfree/chart/LocalizationBundle_zh_CN.properties
new file mode 100644
index 0000000..6b98699
--- /dev/null
+++ b/org/jfree/chart/LocalizationBundle_zh_CN.properties
@@ -0,0 +1,19 @@
+# org.jfree.chart.ChartPanel ResourceBundle properties file
+#
+# Changes
+# -------
+# 29-Jun-2005 : Initial version, see: http://www.jfree.org/phpBB2/viewtopic.php?t=13495;
+#
+
+Auto_Range=\u81ea\u52a8\u8c03\u6574
+All_Axes=\u6240\u6709\u8f74
+Chart_Properties=\u56fe\u8868\u5c5e\u6027
+Copy=\u590d\u5236
+Domain_Axis=\u6c34\u5e73\u8f74
+PNG_Image_Files=PNG \u683c\u5f0f\u7684\u56fe\u50cf
+Print...=\u6253\u5370
+Properties...=\u5c5e\u6027
+Save_as...=\u53e6\u5b58\u4e3a
+Range_Axis=\u5782\u76f4\u8f74
+Zoom_In=\u653e\u5927
+Zoom_Out=\u7f29\u5c0f
diff --git a/org/jfree/chart/LocalizationBundle_zh_TW.properties b/org/jfree/chart/LocalizationBundle_zh_TW.properties
new file mode 100644
index 0000000..e115e02
--- /dev/null
+++ b/org/jfree/chart/LocalizationBundle_zh_TW.properties
@@ -0,0 +1,19 @@
+# org.jfree.chart.ChartPanel ResourceBundle properties file
+#
+# Changes (from 31-Aug-2003)
+# --------------------------
+# 31-Aug-2003 : Initial version (AL);
+#
+
+Auto_Range=\u81ea\u52d5\u8abf\u6574
+All_Axes=\u6240\u6709\u8ef8
+Chart_Properties=\u5716\u8868\u5167\u5bb9
+Copy=\u8907\u88fd
+Domain_Axis=\u6a6b\u8ef8
+PNG_Image_Files=PNG\u5716\u6a94
+Print...=\u5217\u5370
+Properties...=\u5167\u5bb9
+Save_as...=\u53e6\u5b58\u65b0\u6a94
+Range_Axis=\u7e31\u8ef8
+Zoom_In=\u653e\u5927
+Zoom_Out=\u7e2e\u5c0f
diff --git a/org/jfree/chart/MouseWheelHandler.class b/org/jfree/chart/MouseWheelHandler.class
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index 0000000..f17c56c
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diff --git a/org/jfree/chart/editor/LocalizationBundle.properties b/org/jfree/chart/editor/LocalizationBundle.properties
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index 0000000..64996bf
--- /dev/null
+++ b/org/jfree/chart/editor/LocalizationBundle.properties
@@ -0,0 +1,68 @@
+# org.jfree.chart.ui.ui ResourceBundle properties file
+#
+# Changes (from 31-Aug-2003)
+# --------------------------
+# 31-Aug-2003 : Initial version (AL);
+#
+
+\:=:
+Appearance=Appearance
+Auto-adjust_range=Auto-adjust range:
+Background=Background:
+Background_Color=Background Color
+Background_paint=Background paint:
+Color=Color:
+Color_Bar=Color Bar
+Domain_Axis=Domain Axis
+Draw_anti-aliased=Draw anti-aliased
+Draw_lines=Draw Lines:
+Draw_shapes=Draw Shapes:
+Edit...=Edit...
+Edit_Insets=Edit Insets
+Font=Font:
+Font_Selection=Font Selection
+General=General:
+Grid_Color=Grid Color
+Insets=Insets:
+Invert_Palette=Invert Palette:
+Label=Label:
+Label_Color=Label Color
+Label_Insets=Label Insets:
+Legend=Legend
+Maximum_range_value=Maximum range value:
+Minimum_range_value=Minimum range value:
+No_editor_implemented=No editor implemented
+Orientation=Orientation:
+Other=Other
+Outline=Outline:
+Outline_Color=Outline Color
+Outline_stroke=Outline stroke:
+Outline_Paint=Outline paint:
+Paint=Paint:
+Palette_Selection=Palette Selection
+Palette=Palette:
+Pen_Stroke_Selection=Pen/Stroke Selection
+Plot=Plot
+Range=Range
+Range_Axis=Range Axis
+Select...=Select...
+Series_Label_Color=Series Label Color
+Series_label_font=Series label font:
+Series_label_paint=Series label paint:
+Series_Outline_Paint=Series Outline Paint:
+Series_Outline_Stroke=Series Outline Stroke:
+Series_Paint=Series Paint:
+Series_Stroke=Series Stroke:
+Show_Legend=Show Legend:
+Show_tick_labels=Show tick labels
+Show_tick_marks=Show tick marks
+Show_Title=Show Title:
+Set_palette...=Set palette...
+Step_Palette=Step Palette:
+Stroke_Selection=Stroke Selection
+Text=Text:
+Ticks=Ticks
+Tick_label_font=Tick label font:
+Tick_Label_Insets=Tick Label Insets:
+Title=Title
+Title_Color=Title Color
diff --git a/org/jfree/chart/editor/LocalizationBundle_de.properties b/org/jfree/chart/editor/LocalizationBundle_de.properties
new file mode 100644
index 0000000..6097039
--- /dev/null
+++ b/org/jfree/chart/editor/LocalizationBundle_de.properties
@@ -0,0 +1,69 @@
+# org.jfree.chart.ui.ui ResourceBundle properties file - german version
+#
+# Changes (from 31-Aug-2003)
+# --------------------------
+# 31-Aug-2003 : Initial version (AL);
+# 15-Mar-2004 : Revised version (Christian W. Zuckschwerdt);
+#
+
+\:=:
+Appearance=Darstellung
+Auto-adjust_range=Autojustage des Wertebereichs:
+Background=Hintergrund:
+Background_Color=Hintergrundfarbe
+Background_paint=Hintergrundfarbe:
+Color=Farbe:
+Color_Bar=Farbleiste
+Domain_Axis=Rubrikenachse
+Draw_anti-aliased=Zeichnung gl\u00e4tten
+Draw_lines=Zeichne Linien:
+Draw_shapes=Zeichne Formen:
+Edit...=Bearbeiten...
+Edit_Insets=Seitenr\u00e4nder bearbeiten
+Font=Schrift:
+Font_Selection=Schriftwahl
+General=Allgemein:
+Grid_Color=Gitterfarbe
+Insets=R\u00e4nder:
+Invert_Palette=Palette invertieren:
+Label=Beschriftung:
+Label_Color=Beschriftungsfarbe
+Label_Insets=Beschriftungsr\u00e4nder:
+Legend=Legende
+Maximum_range_value=Maximalwert:
+Minimum_range_value=Minimalwert:
+No_editor_implemented=Kein Editor verf\u00fcgbar
+Orientation=Orientierung:
+Other=Sonstiges
+Outline=Rahmenlinien:
+Outline_Color=Rahmenfarbe
+Outline_stroke=Rahmenart:
+Outline_Paint=Rahmenfarbe:
+Paint=Farbe:
+Palette_Selection=Farbauswahl
+Palette=Palette:
+Pen_Stroke_Selection=Linienst\u00e4rke w\u00e4hlen
+Plot=Diagramm
+Range=Wertebereich
+Range_Axis=Werteachse
+Select...=Ausw\u00e4hlen...
+Series_Label_Color=Farbe der Datenreihenbeschriftung
+Series_label_font=Schrift der Datenreihenbeschriftung:
+Series_label_paint=Farbe der Datenreihenbeschriftung:
+Series_Outline_Paint=Farbe der Datenreihenrahmen:
+Series_Outline_Stroke=Art der Datenreihenrahmen:
+Series_Paint=Datenreihenfarbe:
+Series_Stroke=Datenreihenrahmen:
+Show_Legend=Legende anzeigen:
+Show_tick_labels=Beschriftungen zeichnen
+Show_tick_marks=Markierungen zeichnen
+Show_Title=\u00dcberschrift anzeigen:
+Set_palette...=Palette w\u00e4hlen...
+Step_Palette=Step Palette:
+Stroke_Selection=Linienauswahl
+Text=Text:
+Ticks=Markierungen
+Tick_label_font=Markierungsschift:
+Tick_Label_Insets=Markierungsr\u00e4nder:
+Title=\u00dcberschrift
+Title_Color=Titelfarbe
diff --git a/org/jfree/chart/editor/LocalizationBundle_es.properties b/org/jfree/chart/editor/LocalizationBundle_es.properties
new file mode 100644
index 0000000..d25c642
--- /dev/null
+++ b/org/jfree/chart/editor/LocalizationBundle_es.properties
@@ -0,0 +1,69 @@
+# org.jfree.chart.ui.ui ResourceBundle properties file - spanish version
+#
+# Changes (from 16-Dec-2003)
+# --------------------------
+# 16-Dec-2003 : Initial Version: Complejo Hospitalario Universitario Juan Canalejo
+# 14-Oct-2004 : Revised by: Leopoldo Federico P�rtile (Grupo de Procesamiento Digital de Im�genes)
+# Universidad Tecnol�gica Nacional - Facultad Regional Resistencia, Argentina
+
+\:=\ :
+Appearance=Apariencia
+Auto-adjust_range=Ejes auto-ajustables :
+Background=Fondo :
+Background_Color=Color de fondo
+Background_paint=Color de fondo :
+Color=Color :
+Color_Bar=Color de la barra
+Domain_Axis=Eje de las abcisas
+Draw_anti-aliased=Anti-aliasing
+Draw_lines=Dibujar l\u00edneas:
+Draw_shapes=Draw figuras:
+Edit...=Editar...
+Edit_Insets=Regular la posici\u00F3n
+Font=Fuente :
+Font_Selection=Selecci\u00F3n de fuente
+General=General :
+Grid_Color=Color de la rejilla
+Insets=Posici\u00F3n :
+Invert_Palette=Invertir la paleta :
+Label=Etiqueta :
+Label_Color=Color de la etiqueta
+Label_Insets=Posici\u00F3n de la etiqueta :
+Legend=Leyenda
+Maximum_range_value=Valor m\u00E3ximo del eje :
+Minimum_range_value=Valor m\u00EDnimo del eje :
+No_editor_implemented=Editor no disponble
+Orientation=Orientaci\u00F3n:
+Other=Otro
+Outline=Borde :
+Outline_Paint=Color del borde :
+Outline_Color=Color del borde
+Outline_stroke=Estilo del trazo del borde :
+Paint=Color :
+Palette=Paleta :
+Palette_Selection=Selecci\u00F3n de la paleta
+Pen_Stroke_Selection=Selecci\u00F3n del trazo
+Plot=Trazo
+Range=Intervalo
+Range_Axis=Eje de ordenadas
+Select...=Seleccionar...
+Series_Label_Color=Color de la etiqueta de las series
+Series_label_font=Fuente de la etiqueta de las series :
+Series_label_paint=Color de la etiqueta de las series :
+Series_Outline_Paint=Color del borde de las series :
+Series_Outline_Stroke=Estilo del trazo del borde :
+Series_Paint=Color de las series :
+Series_Stroke=Estilo del trazo de las series :
+Show_Legend=Mostrar leyenda:
+Show_tick_labels=Visualizar etiquetas de graduaci\u00F3n de escala
+Show_tick_marks=Visualizar marcas de graduaci\u00F3n de escala
+Show_Title=Mostrar t\u00EDtulo
+Set_palette...=Escoja la paleta...
+Step_Palette=Paso de paleta :
+Stroke_Selection=Selecci\u00F3n del trazo
+Text=Texto :
+Tick_label_font=Fuente de las etiquetas de graduaci\u00F3n de escala :
+Tick_Label_Insets=Posici\u00F3n de las etiquetas de graduaci\u00F3n de escala :
+Ticks=Etiquetas de graduaci\u00F3n de escala
+Title=T\u00EDtulo
+Title_Color=Color del t\u00EDtulo
diff --git a/org/jfree/chart/editor/LocalizationBundle_fr.properties b/org/jfree/chart/editor/LocalizationBundle_fr.properties
new file mode 100644
index 0000000..9cb6429
--- /dev/null
+++ b/org/jfree/chart/editor/LocalizationBundle_fr.properties
@@ -0,0 +1,62 @@
+# org.jfree.chart.ui.ui ResourceBundle properties file - french version
+#
+# Changes (from 31-Aug-2003)
+# --------------------------
+# 31-Aug-2003 : Initial version (AL);
+#
+
+\:=\ :
+Appearance=G\u00E9n\u00E9ral
+Auto-adjust_range=R\u00E9glage automatique de l'\u00E9chelle :
+Background=Fond :
+Background_Color=Couleur du fond
+Background_paint=Couleur du fond :
+Color=Couleur :
+Color_Bar=Couleur de la barre
+Domain_Axis=Axe des abcisses
+Draw_anti-aliased=Anti-aliasing
+Edit...=Edition...
+Edit_Insets=R\u00E9gler la position
+Font=Police :
+Font_Selection=S\u00E9lection de la police
+General=G\u00E9n\u00E9ral :
+Grid_Color=Couleur de la grille
+Insets=Position :
+Invert_Palette=Inversion de la palette :
+Label=Etiquette :
+Label_Color=Couleur de l'\u00E9tiquette
+Label_Insets=Position de l'\u00E9tiquette :
+Legend=L\u00E9gende
+Maximum_range_value=Valeur maximum de l'axe :
+Minimum_range_value=Valeur minimum de l'axe :
+No_editor_implemented=Aucun \u00E9diteur disponible
+Other=Autre
+Outline=Bordure :
+Outline_Paint=Couleur de la bordure :
+Outline_Color=Outline Color
+Outline_stroke=Bordure :
+Paint=Couleur :
+Palette=Palette :
+Palette_Selection=Selection de la palette
+Pen_Stroke_Selection=S\u00E9lection du style de trait
+Plot=Trac\u00E9
+Range=Echelle
+Range_Axis=Axe des ordonn\u00E9es
+Select...=S\u00E9lectionner...
+Series_Label_Color=S\u00E9lection de la couleur de l'\u00E9tiquette
+Series_label_font=Police de l'\u00E9tiquette de s\u00E9rie :
+Series_label_paint=Couleur de l'\u00E9tiquette de s\u00E9rie :
+Series_Outline_Paint=Couleur de bordure de la s\u00E9rie :
+Series_Outline_Stroke=Style du trait de bordure de la s\u00E9rie :
+Series_Paint=Couleur de la s\u00E9rie :
+Series_Stroke=Style du trait de la s\u00E9rie :
+Show_tick_labels=Afficher les \u00E9tiquettes de graduation
+Show_tick_marks=Afficher les rep\u00E8res de graduation
+Set_palette...=Choix de palette...
+Step_Palette=Changement de palette :
+Stroke_Selection=S\u00E9lection du style de trait
+Text=Texte :
+Tick_label_font=Police des \u00E9tiquettes de graduation :
+Tick_Label_Insets=Position des \u00E9tiquettes de graduation :
+Ticks=Etiquettes de graduation
+Title_Color=Couleur du titre
diff --git a/org/jfree/chart/editor/LocalizationBundle_nl.properties b/org/jfree/chart/editor/LocalizationBundle_nl.properties
new file mode 100644
index 0000000..be119ce
--- /dev/null
+++ b/org/jfree/chart/editor/LocalizationBundle_nl.properties
@@ -0,0 +1,67 @@
+# org.jfree.chart.ui.ui ResourceBundle properties file
+#
+# Changes (from 31-Aug-2003)
+# --------------------------
+# 24-Mar-2003 : Translated into Dutch
+# 31-Aug-2003 : Initial version (AL);
+#
+
+\:=:
+Appearance=Uiterlijk
+Auto-adjust_range=Bereik automatisch bepalen
+Background=Achtergrond
+Background_Color=Achtergrondkleur
+
+# "Paint" translated sounds a bit silly IMHO. Since at present only single,
+# opaque colors are selectable anyway, lets just call it that -- color.
+Background_paint=Achtergrondkleur:
+
+Color=Kleur:
+Color_Bar=Kleurbalk
+Domain_Axis=Domein as
+Draw_anti-aliased=Kartelrandjes maskeren (anti-aliasing)
+Edit...=Wijzig...
+Edit_Insets=Wijzig marges
+Font=Lettertype:
+Font_Selection=Lettertype keuze
+General=Algemeen:
+Grid_Color=Rasterkleur
+Insets=Marges:
+Invert_Palette=Palet inverteren:
+Label=Label:
+Label_Color=Labelkleur
+Label_Insets=Labelmarges:
+Legend=Legenda
+Maximum_range_value=Hoogste waarde:
+Minimum_range_value=Laagste waarde:
+No_editor_implemented=Geen editor beschikbaar
+Other=Overig
+Outline=Rand:
+Outline_Color=Randkleur
+Outline_stroke=Rand stijl:
+Outline_Paint=Randkleur:
+Paint=Kleur:
+Palette_Selection=Paletkleuze
+Palette=Palet:
+Pen_Stroke_Selection=Pen/Stijl Keuze
+Plot=Diagram
+Range=Bereik
+Range_Axis=Gegevens as
+Select...=Selecteer...
+Series_Label_Color=Kleur serienaam
+Series_label_font=Lettertype serienaam:
+Series_label_paint=Kleur serienaam:
+Series_Outline_Paint=Kleur serie-rand:
+Series_Outline_Stroke=Stijl serie-rand:
+Series_Paint=Kleur v.d. serie:
+Series_Stroke=Stijl v.d. serie:
+Show_tick_labels=Toon waarde-labels
+Show_tick_marks=Toon waarde-streepjes
+Set_palette...=Kies palet...
+Step_Palette=Stap palet:
+Stroke_Selection=Stijlkeuze
+Text=Tekst:
+Ticks=Waarde-streepjes
+Tick_label_font=Lettertype waarde-labes:
+Tick_Label_Insets=Waarde-label marges:
+Title_Color=Kleur titel
diff --git a/org/jfree/chart/editor/LocalizationBundle_pl.properties b/org/jfree/chart/editor/LocalizationBundle_pl.properties
new file mode 100644
index 0000000..8fba33c
--- /dev/null
+++ b/org/jfree/chart/editor/LocalizationBundle_pl.properties
@@ -0,0 +1,62 @@
+# org.jfree.chart.ui.ui ResourceBundle properties file
+#
+# Changes (from 15-Mar-2004)
+# --------------------------
+# 15-Mar-2004 : Initial version (Kuba Duda);
+#
+
+\:=:
+Appearance=Wygl\u0105d
+Auto-adjust_range=Automatycznie dostosuj zakres:
+Background=T\u0142o:
+Background_Color=Kolor t\u0142a
+Background_paint=Wype\u0142nienie t\u0142a:
+Color=Kolor:
+Color_Bar=Pasek kolor\u00f3w
+Domain_Axis=O\u015b domeny
+Draw_anti-aliased=Wyg\u0142adzaj kraw\u0119dzie
+Edit...=Edytuj...
+Edit_Insets=Edytuj wstawki
+Font=Czcionka:
+Font_Selection=Wyb\u00f3r czcionki
+General=Og\u00f3lne:
+Grid_Color=Kolor siatki
+Insets=Wstawki:
+Invert_Palette=Odwr\u00f3\u0107 palet\u0119:
+Label=Etykieta:
+Label_Color=Kolor etykiet
+Label_Insets=Wstawki etykiet:
+Legend=Legenda
+Maximum_range_value=Maksymalna warto\u015b\u0107 zakresu:
+Minimum_range_value=Minimalna warto\u015b\u0107 zakresu:
+No_editor_implemented=Edytor nie zaimplementowany
+Other=Inne
+Outline=Obrys:
+Outline_Color=Kolor konturu
+Outline_stroke=Obrys konturu:
+Outline_Paint=wype\u0142nienie konturu:
+Paint=Wype\u0142nienie:
+Palette_Selection=Wyb\u00f3r palety
+Palette=Paleta:
+Pen_Stroke_Selection=Wyb\u00f3r pi\u00f3ra/obrysu
+Plot=Wykres
+Range=Zakres
+Range_Axis=O\u015b zakresu
+Select...=Wybierz...
+Series_Label_Color=Kolor etykiety serii
+Series_label_font=Czcionka etykiety serii:
+Series_label_paint=Wype\u0142nienie etykiety serii:
+Series_Outline_Paint=Wype\u0142nienie obrysu serii:
+Series_Outline_Stroke=Kolor obrysu serii:
+Series_Paint=Wype\u0142nienie serii:
+Series_Stroke=Kolor serii:
+Show_tick_labels=Pokazuj etykiety skali
+Show_tick_marks=Pokazuj znaczniki skali
+Set_palette...=Wybierz palet\u0119...
+Step_Palette=Paleta krokowa:
+Stroke_Selection=Wyb\u00f3r obrysu
+Text=Tekst:
+Ticks=Podzia\u0142ka
+Tick_label_font=Czcionka etykiet podzia\u0142ki:
+Tick_Label_Insets=Wstawki etykiet podzia\u0142ki:
+Title_Color=Kolor tytu\u0142u
diff --git a/org/jfree/chart/editor/LocalizationBundle_pt_BR.properties b/org/jfree/chart/editor/LocalizationBundle_pt_BR.properties
new file mode 100644
index 0000000..b42ccd3
--- /dev/null
+++ b/org/jfree/chart/editor/LocalizationBundle_pt_BR.properties
@@ -0,0 +1,62 @@
+# org.jfree.chart.ChartPanel ResourceBundle properties file - portuguese version
+#
+# Changes (from 24-May-2007)
+# --------------------------
+# 24-May-2007 : Initial version (Leonardo Alves Machado)
+#
+
+\:=\ :
+Appearance=Geral
+Auto-adjust_range=Eixos auto-ajust\u00E1veis :
+Background=Fundo :
+Background_Color=Cor de fundo
+Background_paint=Cor de fundo :
+Color=Cor :
+Color_Bar=Cor da barra
+Domain_Axis=Eixo das abcissas
+Draw_anti-aliased=Anti-aliasing
+Edit...=Editar...
+Edit_Insets=Regular a posi\u00E7\u00E3o
+Font=Fonte :
+Font_Selection=Sele\u00E7\u00E3o da fonte
+General=Geral :
+Grid_Color=Cor da grade
+Insets=Posi\u00E7\u00E3o :
+Invert_Palette=Inverter o palete :
+Label=R\u00F3tulo :
+Label_Color=Cor do r\u00F3tulo
+Label_Insets=Posi\u00E7\u00E3o do r\u00F3tulo :
+Legend=Legenda
+Maximum_range_value=Valor m\u00E1ximo do eixo :
+Minimum_range_value=Valor m\u00EDnimo do eixo :
+No_editor_implemented=Editor n\u00E3o dispon\u00EDvel
+Other=Outro
+Outline=Borda :
+Outline_Paint=Cor da borda :
+Outline_Color=Cor da borda
+Outline_stroke=Estilo do tra\u00E7o da borda :
+Paint=Cor :
+Palette=Palete :
+Palette_Selection=Sele\u00E7\u00E3o do palete
+Pen_Stroke_Selection=Sele\u00E7\u00E3o de tra\u00E7o
+Plot=Tra\u00E7o
+Range=Intervalo
+Range_Axis=Eixo das ordenadas
+Select...=Selecionar...
+Series_Label_Color=Cor do r\u00F3tulo das s\u00E9ries
+Series_label_font=Fonte do r\u00F3tulo das s\u00E9ries :
+Series_label_paint=Cor do r\u00F3tulo das s\u00E9ries :
+Series_Outline_Paint=Cor da borda das s\u00E9ries :
+Series_Outline_Stroke=Estilo do tra\u00E7o da borda :
+Series_Paint=Cor da s\u00E9ries :
+Series_Stroke=Estilo do tra\u00E7o das s\u00E9ries :
+Show_tick_labels=Visualizar r\u00F3tulos de gradua\u00E7\u00E3o de escala
+Show_tick_marks=Visualizar marcas de gradua\u00E7\u00E3o de escala
+Set_palette...=Escolha do palete...
+Step_Palette=Espaçamento do palete :
+Stroke_Selection=Sele\u00E7\u00E3o do tra\u00E7o
+Text=Texto :
+Tick_label_font=Fonte dos r\u00F3tulos de gradua\u00E7\u00E3o de escala :
+Tick_Label_Insets=Posi\u00E7\u00E3o dos r\u00F3tulos de gradua\u00E7\u00E3o de escala :
+Ticks=R\u00F3tulos de gradua\u00E7\u00E3o de escala
+Title_Color=Cor do t\u00EDtulo
diff --git a/org/jfree/chart/editor/LocalizationBundle_pt_PT.properties b/org/jfree/chart/editor/LocalizationBundle_pt_PT.properties
new file mode 100644
index 0000000..46b3da2
--- /dev/null
+++ b/org/jfree/chart/editor/LocalizationBundle_pt_PT.properties
@@ -0,0 +1,62 @@
+# org.jfree.chart.ChartPanel ResourceBundle properties file - portuguese version
+#
+# Changes (from 09-Set-2003)
+# --------------------------
+# 09-Set-2003 : Initial version (Eduardo Ramalho);
+#
+
+\:=\ :
+Appearance=Geral
+Auto-adjust_range=Eixos auto-ajust\u00E1veis :
+Background=Fundo :
+Background_Color=Cor de fundo
+Background_paint=Cor de fundo :
+Color=Cor :
+Color_Bar=Cor da barra
+Domain_Axis=Eixo das abcissas
+Draw_anti-aliased=Anti-aliasing
+Edit...=Editar...
+Edit_Insets=Regular a posi\u00E7\u00E3o
+Font=Fonte :
+Font_Selection=Selec\u00E7\u00E3o da fonte
+General=Geral :
+Grid_Color=Cor da grelha
+Insets=Posi\u00E7\u00E3o :
+Invert_Palette=Inverter a paleta :
+Label=Etiqueta :
+Label_Color=Cor da etiqueta
+Label_Insets=Posi\u00E7\u00E3o da etiqueta :
+Legend=Legenda
+Maximum_range_value=Valor m\u00E1ximo do eixo :
+Minimum_range_value=Valor m\u00EDnimo do eixo :
+No_editor_implemented=Editor n\u00E3o dispon\u00EDvel
+Other=Outro
+Outline=Borda :
+Outline_Paint=Cor da borda :
+Outline_Color=Cor da borda
+Outline_stroke=Estilo do tra\u00E7o da borda :
+Paint=Cor :
+Palette=Palete :
+Palette_Selection=Selec\u00E7\u00E3o da palete
+Pen_Stroke_Selection=Selec\u00E7\u00E3o de tra\u00E7o
+Plot=Tra\u00E7o
+Range=Intervalo
+Range_Axis=Eixo das ordenadas
+Select...=Seleccionar...
+Series_Label_Color=Cor da etiqueta das s\u00E9ries
+Series_label_font=Fonte da etiqueta das s\u00E9ries :
+Series_label_paint=Cor da etiqueta das s\u00E9ries :
+Series_Outline_Paint=Cor da borda das s\u00E9ries :
+Series_Outline_Stroke=Estilo do tra\u00E7o da borda :
+Series_Paint=Cor da s\u00E9ries :
+Series_Stroke=Estilo do tra\u00E7o das s\u00E9ries :
+Show_tick_labels=Visualizar etiquetas de gradua\u00E7\u00E3o de escala
+Show_tick_marks=Visualizar marcas de gradua\u00E7\u00E3o de escala
+Set_palette...=Escolha de palete...
+Step_Palette=Changement de palette :
+Stroke_Selection=Selec\u00E7\u00E3o do tra\u00E7o
+Text=Texto :
+Tick_label_font=Fonte das etiquetas de gradua\u00E7\u00E3o de escala :
+Tick_Label_Insets=Posi\u00E7\u00E3o das etiquetas de gradua\u00E7\u00E3o de escala :
+Ticks=Etiquetas de gradua\u00E7\u00E3o de escala
+Title_Color=Cor do t\u00EDtulo
diff --git a/org/jfree/chart/editor/LocalizationBundle_ru.properties b/org/jfree/chart/editor/LocalizationBundle_ru.properties
new file mode 100644
index 0000000..75ca34d
--- /dev/null
+++ b/org/jfree/chart/editor/LocalizationBundle_ru.properties
@@ -0,0 +1,62 @@
+# org.jfree.chart.ui.ui ResourceBundle properties file
+#
+# Changes (from 10-Nov-2003)
+# --------------------------
+# 10-Nov-2003 : Initial version (AL);
+#
+
+\:=:
+Appearance=\u0412\u0438\u0434
+Auto-adjust_range=\u0410\u0432\u0442\u0440\u043e\u0440\u0435\u0433\u0443\u043b\u0438\u0440\u043e\u0432\u043a\u0430:
+Background=\u0424\u043e\u043d:
+Background_Color=\u0426\u0432\u0435\u0442 \u0444\u043e\u043d\u0430
+Background_paint=\u0424\u043e\u043d\u043e\u0432\u044b\u0439 \u0440\u0438\u0441\u0443\u043d\u043e\u043a:
+Color=\u0426\u0432\u0435\u0442:
+Color_Bar=\u0426\u0432\u0435\u0442\u043e\u0432\u043e\u0439 \u0433\u0440\u0443\u0433
+Domain_Axis=\u041e\u0441\u044c \u043f\u0430\u0440\u0430\u043c\u0435\u0442\u0440\u043e\u0432
+Draw_anti-aliased=\u0410\u043d\u0442\u0438-\u0430\u043b\u0438\u0430\u0441\u0438\u043d\u0433
+Edit...=\u0420\u0435\u0434\u0430\u043a\u0442\u0438\u0440\u043e\u0432\u0430\u0442\u044c...
+Edit_Insets=\u041d\u0430\u0441\u0442\u0440\u043e\u0439\u043a\u0430 \u043e\u0442\u0441\u0442\u0443\u043f\u043e\u0432
+Font=\u0428\u0440\u0438\u0444\u0442:
+Font_Selection=\u0412\u044b\u0431\u043e\u0440 \u0448\u0440\u0438\u0444\u0442\u0430
+General=\u041e\u0441\u043d\u043e\u0432\u043d\u044b\u0435:
+Grid_Color=\u0426\u0432\u0435\u0442 \u0441\u0435\u0442\u043a\u0438
+Insets=\u041e\u0442\u0441\u0442\u0443\u043f\u044b:
+Invert_Palette=\u0418\u043d\u0432\u0435\u0440\u0442\u0438\u0440\u043e\u0432\u0430\u0442\u044c \u043f\u0430\u043b\u0438\u0442\u0440\u0443:
+Label=\u041c\u0435\u0442\u043a\u0430:
+Label_Color=\u0426\u0432\u0435\u0442 \u043c\u0435\u0442\u043a\u0438
+Label_Insets=\u041e\u0442\u0441\u0442\u0443\u043f\u044b \u043c\u0435\u0442\u043a\u0438:
+Legend=\u041b\u0435\u0433\u0435\u043d\u0434\u0430
+Maximum_range_value=\u041c\u0430\u043a\u0441\u0438\u043c\u0430\u043b\u044c\u043d\u043e\u0435 \u0437\u043d\u0430\u0447\u0435\u043d\u0438\u0435:
+Minimum_range_value=\u041c\u0438\u043d\u0438\u043c\u0430\u043b\u044c\u043d\u043e\u0435 \u0437\u043d\u0430\u0447\u0435\u043d\u0438\u0435:
+No_editor_implemented=\u041d\u0435 \u0443\u0441\u0442\u0430\u043d\u043e\u0432\u043b\u0435\u043d \u0440\u0435\u0434\u0430\u043a\u0442\u043e\u0440
+Other=\u0414\u043e\u043f\u043e\u043b\u043d\u0438\u0442\u0435\u043b\u044c\u043d\u043e
+Outline=\u0420\u0430\u043c\u043a\u0430:
+Outline_Color=\u0426\u0432\u0435\u0442 \u0440\u0430\u043c\u043a\u0438
+Outline_stroke=\u0421\u0442\u0438\u043b\u044c \u0440\u0430\u043c\u043a\u0438:
+Outline_Paint=\u041e\u043a\u0440\u0430\u0441\u043a\u0430 \u0440\u0430\u043c\u043a\u0438:
+Paint=\u041e\u043a\u0440\u0430\u0441\u043a\u0430:
+Palette_Selection=\u0412\u044b\u0431\u043e\u0440 \u043f\u0430\u043b\u0438\u0442\u0440\u044b
+Palette=\u041f\u0430\u043b\u0438\u0442\u0440\u0430:
+Pen_Stroke_Selection=\u0412\u044b\u0431\u043e\u0440 \u041a\u0430\u0440\u0430\u043d\u0434\u0430\u0448/\u0428\u0442\u0440\u0438\u0445
+Plot=\u0413\u0440\u0430\u0444\u0438\u043a
+Range=\u041e\u0431\u043b\u0430\u0441\u0442\u044c
+Range_Axis=\u041e\u0441\u044c \u0437\u043d\u0430\u0447\u0435\u043d\u0438\u0439
+Select...=\u0412\u044b\u0431\u043e\u0440...
+Series_Label_Color=\u0426\u0432\u0435\u0442 \u043c\u0435\u0442\u043a\u0438 \u0441\u0435\u0440\u0438\u0438
+Series_label_font=\u0428\u0440\u0438\u0444\u0442 \u043c\u0435\u0442\u043a\u0438 \u0441\u0435\u0440\u0438\u0438:
+Series_label_paint=\u041e\u0442\u043e\u0431\u0440\u0430\u0436\u0435\u043d\u0438\u0435 \u043c\u0435\u0442\u043a\u0438 \u0441\u0435\u0440\u0438\u0438:
+Series_Outline_Paint=\u041e\u043a\u0440\u0430\u0441\u043a\u0430 \u0440\u0430\u043c\u043a\u0438 \u0441\u0435\u0440\u0438\u0438:
+Series_Outline_Stroke=\u0428\u0442\u0440\u0438\u0445\u043e\u0432\u0430\u044f \u0440\u0430\u043c\u043a\u0430 \u0441\u0435\u0440\u0438\u0438:
+Series_Paint=\u041e\u043a\u0440\u0430\u0441\u043a\u0430 \u0441\u0435\u0440\u0438\u0438:
+Series_Stroke=\u0428\u0442\u0440\u0438\u0445\u0438 \u0441\u0435\u0440\u0438\u0438:
+Show_tick_labels=\u041f\u043e\u043a\u0430\u0437\u044b\u0432\u0430\u0442\u044c \u043e\u0441\u0435\u0432\u044b\u0435 \u043e\u0442\u043c\u0435\u0442\u043a\u0438
+Show_tick_marks=\u041f\u043e\u043a\u0430\u0437\u044b\u0432\u0430\u0442\u044c \u043e\u0441\u0435\u0432\u044b\u0435 \u0448\u0442\u0440\u0438\u0445\u0438
+Set_palette...=\u0423\u0441\u0442\u0430\u043d\u043e\u0432\u0438\u0442\u044c \u043f\u0430\u043b\u0438\u0442\u0440\u0443...
+Step_Palette=\u0428\u0430\u0433 \u043f\u0430\u043b\u0438\u0442\u0440\u044b:
+Stroke_Selection=\u0412\u044b\u0431\u043e\u0440 \u0448\u0442\u0440\u0438\u0445\u0430
+Text=\u0422\u0435\u043a\u0441\u0442:
+Ticks=\u041e\u0442\u043c\u0435\u0442\u043a\u0438
+Tick_label_font=\u0428\u0440\u0438\u0444\u0442 \u043e\u0442\u043c\u0435\u0442\u043a\u0438:
+Tick_Label_Insets=\u041e\u0442\u0441\u0442\u0443\u043f\u044b \u043e\u0442\u043c\u0435\u0442\u043e\u043a:
+Title_Color=\u0426\u0432\u0435\u0442 \u0437\u0430\u0433\u043e\u043b\u043e\u0432\u043a\u0430
diff --git a/org/jfree/chart/editor/LocalizationBundle_zh_CN.properties b/org/jfree/chart/editor/LocalizationBundle_zh_CN.properties
new file mode 100644
index 0000000..ea2ade2
--- /dev/null
+++ b/org/jfree/chart/editor/LocalizationBundle_zh_CN.properties
@@ -0,0 +1,68 @@
+# org.jfree.chart.ui.ui ResourceBundle properties file
+#
+# Changes
+# -------
+# 29-Jun-2005 : Initial version, see: http://www.jfree.org/phpBB2/viewtopic.php?t=13495;
+#
+
+\:=:
+Appearance=\u5916\u89c2
+Auto-adjust_range=\u81ea\u52a8\u8c03\u8282\u8303\u56f4:
+Background=\u80cc\u666f:
+Background_Color=\u80cc\u666f\u8272
+Background_paint=\u80cc\u666f\u586b\u5145:
+Color=\u989c\u8272:
+Color_Bar=\u8272\u5f69\u6761
+Domain_Axis=\u9879\u76ee\u8f74
+Draw_anti-aliased=\u7ed8\u5236\u53cd\u6df7\u6dc6
+Draw_lines=\u753b\u7ebf:
+Draw_shapes=\u753b\u5f62\u72b6:
+Edit...=\u7f16\u8f91...
+Edit_Insets=\u7f16\u8f91\u5d4c\u5165
+Font=\u5b57\u4f53:
+Font_Selection=\u5b57\u4f53\u9009\u62e9
+General=\u7efc\u5408:
+Grid_Color=\u7f51\u683c\u989c\u8272
+Insets=\u63d2\u56fe:
+Invert_Palette=\u53cd\u8f6c\u8c03\u8272\u677f:
+Label=\u6807\u7b7e:
+Label_Color=\u6807\u7b7e\u989c\u8272
+Label_Insets=\u6807\u7b7e\u63d2\u56fe:
+Legend=\u56fe\u4f8b
+Maximum_range_value=\u6700\u5927\u503c:
+Minimum_range_value=\u6700\u5c0f\u503c:
+No_editor_implemented=\u6ca1\u6709\u53ef\u6267\u884c\u7684\u7f16\u8f91\u5668
+Orientation=\u65b9\u5411:
+Other=\u5176\u4ed6
+Outline=\u8f6e\u5ed3:
+Outline_Color=\u8f6e\u5ed3\u989c\u8272
+Outline_stroke=\u8f6e\u5ed3\u7ebf\u6761:
+Outline_Paint=\u8f6e\u5ed3\u586b\u5145:
+Paint=\u586b\u5145:
+Palette_Selection=\u8c03\u8272\u677f\u9009\u62e9
+Palette=\u8c03\u8272\u677f:
+Pen_Stroke_Selection=\u753b\u7b14/\u7ebf\u578b \u9009\u62e9
+Plot=\u56fe
+Range=\u8303\u56f4
+Range_Axis=\u8303\u56f4\u8f74
+Select...=\u9009\u62e9...
+Series_Label_Color=\u5e8f\u5217\u6807\u7b7e\u8272
+Series_label_font=\u5e8f\u5217\u6807\u7b7e\u5b57\u4f53:
+Series_label_paint=\u5e8f\u5217\u6807\u7b7e\u586b\u5145:
+Series_Outline_Paint=\u5e8f\u5217\u8f6e\u5ed3\u586b\u5145:
+Series_Outline_Stroke=\u5e8f\u5217\u8f6e\u5ed3\u7ebf\u578b:
+Series_Paint=\u5e8f\u5217\u586b\u5145:
+Series_Stroke=\u5e8f\u5217\u7ebf\u578b:
+Show_Legend=\u663e\u793a\u56fe\u4f8b:
+Show_tick_labels=\u663e\u793a\u523b\u5ea6\u6807\u7b7e
+Show_tick_marks=\u663e\u793a\u6807\u7b7e\u8bb0\u53f7
+Show_Title=\u663e\u793a\u6807\u9898:
+Set_palette...=\u8bbe\u7f6e\u8c03\u8272\u677f...
+Step_Palette=Step \u8c03\u8272\u677f:
+Stroke_Selection=\u7ebf\u578b\u9009\u62e9
+Text=\u6b63\u6587:
+Ticks=\u523b\u5ea6\u7ebf
+Tick_label_font=\u523b\u5ea6\u6807\u7b7e\u5b57\u4f53:
+Tick_Label_Insets=\u523b\u5ea6\u6807\u7b7e\u63d2\u56fe:
+Title=\u6807\u9898
+Title_Color=\u6807\u9898\u989c\u8272
diff --git a/org/jfree/chart/editor/PaletteChooserPanel.class b/org/jfree/chart/editor/PaletteChooserPanel.class
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diff --git a/org/jfree/chart/editor/PaletteSample.class b/org/jfree/chart/editor/PaletteSample.class
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index 0000000..37bfff9
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diff --git a/org/jfree/chart/encoders/EncoderUtil.class b/org/jfree/chart/encoders/EncoderUtil.class
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diff --git a/org/jfree/chart/encoders/ImageEncoder.class b/org/jfree/chart/encoders/ImageEncoder.class
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diff --git a/org/jfree/chart/encoders/ImageEncoderFactory.class b/org/jfree/chart/encoders/ImageEncoderFactory.class
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diff --git a/org/jfree/chart/encoders/ImageFormat.class b/org/jfree/chart/encoders/ImageFormat.class
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diff --git a/org/jfree/chart/encoders/KeypointPNGEncoderAdapter.class b/org/jfree/chart/encoders/KeypointPNGEncoderAdapter.class
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index 0000000..e39d7bc
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diff --git a/org/jfree/chart/encoders/SunJPEGEncoderAdapter.class b/org/jfree/chart/encoders/SunJPEGEncoderAdapter.class
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diff --git a/org/jfree/chart/encoders/SunPNGEncoderAdapter.class b/org/jfree/chart/encoders/SunPNGEncoderAdapter.class
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diff --git a/org/jfree/chart/entity/AxisEntity.class b/org/jfree/chart/entity/AxisEntity.class
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diff --git a/org/jfree/chart/entity/CategoryItemEntity.class b/org/jfree/chart/entity/CategoryItemEntity.class
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diff --git a/org/jfree/chart/entity/CategoryLabelEntity.class b/org/jfree/chart/entity/CategoryLabelEntity.class
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diff --git a/org/jfree/chart/entity/ChartEntity.class b/org/jfree/chart/entity/ChartEntity.class
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diff --git a/org/jfree/chart/entity/ContourEntity.class b/org/jfree/chart/entity/ContourEntity.class
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diff --git a/org/jfree/chart/entity/EntityCollection.class b/org/jfree/chart/entity/EntityCollection.class
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diff --git a/org/jfree/chart/entity/JFreeChartEntity.class b/org/jfree/chart/entity/JFreeChartEntity.class
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index 0000000..13953b4
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diff --git a/org/jfree/chart/entity/LegendItemEntity.class b/org/jfree/chart/entity/LegendItemEntity.class
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index 0000000..d9006ad
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diff --git a/org/jfree/chart/entity/PieSectionEntity.class b/org/jfree/chart/entity/PieSectionEntity.class
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index 0000000..bf355ab
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diff --git a/org/jfree/chart/entity/PlotEntity.class b/org/jfree/chart/entity/PlotEntity.class
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index 0000000..3fd8f22
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diff --git a/org/jfree/chart/entity/StandardEntityCollection.class b/org/jfree/chart/entity/StandardEntityCollection.class
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diff --git a/org/jfree/chart/entity/TickLabelEntity.class b/org/jfree/chart/entity/TickLabelEntity.class
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diff --git a/org/jfree/chart/entity/TitleEntity.class b/org/jfree/chart/entity/TitleEntity.class
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index 0000000..303f6d0
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diff --git a/org/jfree/chart/entity/XYAnnotationEntity.class b/org/jfree/chart/entity/XYAnnotationEntity.class
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index 0000000..e304b20
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diff --git a/org/jfree/chart/entity/XYItemEntity.class b/org/jfree/chart/entity/XYItemEntity.class
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index 0000000..8629b11
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diff --git a/org/jfree/chart/event/AxisChangeEvent.class b/org/jfree/chart/event/AxisChangeEvent.class
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index 0000000..3e69ccb
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diff --git a/org/jfree/chart/event/AxisChangeListener.class b/org/jfree/chart/event/AxisChangeListener.class
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index 0000000..049ab4c
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diff --git a/org/jfree/chart/event/ChartChangeEvent.class b/org/jfree/chart/event/ChartChangeEvent.class
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index 0000000..ef11529
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diff --git a/org/jfree/chart/event/ChartChangeListener.class b/org/jfree/chart/event/ChartChangeListener.class
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diff --git a/org/jfree/chart/event/ChartProgressEvent.class b/org/jfree/chart/event/ChartProgressEvent.class
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index 0000000..894cbda
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diff --git a/org/jfree/chart/event/ChartProgressListener.class b/org/jfree/chart/event/ChartProgressListener.class
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index 0000000..9cdb1a7
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diff --git a/org/jfree/chart/event/MarkerChangeEvent.class b/org/jfree/chart/event/MarkerChangeEvent.class
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index 0000000..eed21d8
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diff --git a/org/jfree/chart/event/MarkerChangeListener.class b/org/jfree/chart/event/MarkerChangeListener.class
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index 0000000..b7df08e
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diff --git a/org/jfree/chart/event/OverlayChangeEvent.class b/org/jfree/chart/event/OverlayChangeEvent.class
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diff --git a/org/jfree/chart/event/OverlayChangeListener.class b/org/jfree/chart/event/OverlayChangeListener.class
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index 0000000..574fe51
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diff --git a/org/jfree/chart/event/PlotChangeEvent.class b/org/jfree/chart/event/PlotChangeEvent.class
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index 0000000..432e118
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diff --git a/org/jfree/chart/event/PlotChangeListener.class b/org/jfree/chart/event/PlotChangeListener.class
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diff --git a/org/jfree/chart/event/RendererChangeEvent.class b/org/jfree/chart/event/RendererChangeEvent.class
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diff --git a/org/jfree/chart/event/RendererChangeListener.class b/org/jfree/chart/event/RendererChangeListener.class
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index 0000000..255b340
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diff --git a/org/jfree/chart/event/TitleChangeEvent.class b/org/jfree/chart/event/TitleChangeEvent.class
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index 0000000..657f3ff
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diff --git a/org/jfree/chart/event/TitleChangeListener.class b/org/jfree/chart/event/TitleChangeListener.class
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index 0000000..9b70ba6
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diff --git a/org/jfree/chart/gorilla.jpg b/org/jfree/chart/gorilla.jpg
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diff --git a/org/jfree/chart/imagemap/DynamicDriveToolTipTagFragmentGenerator.class b/org/jfree/chart/imagemap/DynamicDriveToolTipTagFragmentGenerator.class
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index 0000000..74b174a
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diff --git a/org/jfree/chart/imagemap/OverLIBToolTipTagFragmentGenerator.class b/org/jfree/chart/imagemap/OverLIBToolTipTagFragmentGenerator.class
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diff --git a/org/jfree/chart/imagemap/StandardToolTipTagFragmentGenerator.class b/org/jfree/chart/imagemap/StandardToolTipTagFragmentGenerator.class
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index 0000000..45ef27c
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diff --git a/org/jfree/chart/imagemap/StandardURLTagFragmentGenerator.class b/org/jfree/chart/imagemap/StandardURLTagFragmentGenerator.class
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index 0000000..d939fdf
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diff --git a/org/jfree/chart/imagemap/ToolTipTagFragmentGenerator.class b/org/jfree/chart/imagemap/ToolTipTagFragmentGenerator.class
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diff --git a/org/jfree/chart/imagemap/URLTagFragmentGenerator.class b/org/jfree/chart/imagemap/URLTagFragmentGenerator.class
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diff --git a/org/jfree/chart/labels/AbstractCategoryItemLabelGenerator.class b/org/jfree/chart/labels/AbstractCategoryItemLabelGenerator.class
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index 0000000..5463792
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diff --git a/org/jfree/chart/labels/AbstractPieItemLabelGenerator.class b/org/jfree/chart/labels/AbstractPieItemLabelGenerator.class
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index 0000000..33902a9
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diff --git a/org/jfree/chart/labels/AbstractXYItemLabelGenerator.class b/org/jfree/chart/labels/AbstractXYItemLabelGenerator.class
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index 0000000..f2c3c33
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diff --git a/org/jfree/chart/labels/BoxAndWhiskerToolTipGenerator.class b/org/jfree/chart/labels/BoxAndWhiskerToolTipGenerator.class
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index 0000000..26e2dca
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diff --git a/org/jfree/chart/labels/BoxAndWhiskerXYToolTipGenerator.class b/org/jfree/chart/labels/BoxAndWhiskerXYToolTipGenerator.class
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index 0000000..0001f8f
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diff --git a/org/jfree/chart/plot/LocalizationBundle.properties b/org/jfree/chart/plot/LocalizationBundle.properties
new file mode 100644
index 0000000..6c7ff47
--- /dev/null
+++ b/org/jfree/chart/plot/LocalizationBundle.properties
@@ -0,0 +1,23 @@
+# org.jfree.chart.plot.plot ResourceBundle properties file
+#
+# Changes (from 31-Aug-2003)
+# --------------------------
+# 31-Aug-2003 : Initial version (AL);
+# 19-Jan-2004 : Added Polar_Plot (DG);
+#
+
+Category_Plot=Category Plot
+Combined_Domain_XYPlot=Combined Domain XYPlot
+Combined_Range_XYPlot=Combined Range XYPlot
+Compass_Plot=Compass Plot
+Contour_Plot=Contour Plot
+Fast_Scatter_Plot=Fast Scatter Plot
+Meter_Plot=Meter Plot
+Period_Marker_Plot=Period Marker Plot
+Pie_Plot=Pie Plot
+Thermometer_Plot=Thermometer Plot
+XY_Plot=XY Plot
+Polar_Plot=Polar Plot
+
+#Secteurs 3D
+Pie_3D_Plot=Pie 3D Plot
diff --git a/org/jfree/chart/plot/LocalizationBundle_de.properties b/org/jfree/chart/plot/LocalizationBundle_de.properties
new file mode 100644
index 0000000..8c889f0
--- /dev/null
+++ b/org/jfree/chart/plot/LocalizationBundle_de.properties
@@ -0,0 +1,22 @@
+# org.jfree.chart.plot.plot ResourceBundle properties file - german version
+#
+# Changes (from 31-Aug-2003)
+# --------------------------
+# 31-Aug-2003 : Initial version (AL);
+# 15-Mar-2004 : Revised version (Christian W. Zuckschwerdt);
+#
+
+Category_Plot=Kategoriediagramm
+Combined_Domain_XYPlot=Rubriken-kombiniertes XY-Diagramm
+Combined_Range_XYPlot=Werte-kombiniertes XY-Diagramm
+Compass_Plot=Kompass-Diagramm
+Contour_Plot=Liniendiagramm
+Fast_Scatter_Plot=Streudiagramm
+Meter_Plot=Tachometer-Diagramm
+Period_Marker_Plot=Zeitreihe
+Pie_Plot=Kreisdiagramm
+Thermometer_Plot=Thermometer-Diagramm
+XY_Plot=XY-Diagramm
+
+#Secteurs 3D
+Pie_3D_Plot=3D-Kreisdiagramm
diff --git a/org/jfree/chart/plot/LocalizationBundle_es.properties b/org/jfree/chart/plot/LocalizationBundle_es.properties
new file mode 100644
index 0000000..caaf74b
--- /dev/null
+++ b/org/jfree/chart/plot/LocalizationBundle_es.properties
@@ -0,0 +1,19 @@
+# org.jfree.chart.plot.plot ResourceBundle properties file - spanish version
+#
+# Changes (from 16-Dec-2003)
+# --------------------------
+# 16-Dec-2003 : Initial Version: Complejo Hospitalario Universitario Juan Canalejo
+#
+
+Category_Plot=Barras
+Combined_Domain_XYPlot=Curvas combinadas por la abcisa
+Combined_Range_XYPlot=Curvas combinadas por la ordenada
+Compass_Plot=Diagrama del comp\u00a3s
+Contour_Plot=Contorno del comp\u00a3s
+Fast_Scatter_Plot=Dispersi\u00f3n
+Meter_Plot=Diagrama del metro
+Period_Marker_Plot=Diagrama del marcador del per�odo
+Pie_Plot=Sectores
+Thermometer_Plot=Term\u00f3metro
+XY_Plot=Curvas
+Pie_3D_Plot=Sectores 3D
diff --git a/org/jfree/chart/plot/LocalizationBundle_fr.properties b/org/jfree/chart/plot/LocalizationBundle_fr.properties
new file mode 100644
index 0000000..b544d6f
--- /dev/null
+++ b/org/jfree/chart/plot/LocalizationBundle_fr.properties
@@ -0,0 +1,19 @@
+# org.jfree.chart.plot.plot ResourceBundle properties file - French version
+#
+# Changes (from 31-Aug-2003)
+# --------------------------
+# 31-Aug-2003 : Initial version (AL);
+#
+
+Category_Plot=Barres
+Combined_Domain_XYPlot=Courbes combin\u00E9es sur l'abcisse
+Combined_Range_XYPlot=Courbes combin\u00E9es sur l'ordonn\u00E9e
+Compass_Plot=Compas
+Contour_Plot=Contours
+Fast_Scatter_Plot=Nuage de points
+Meter_Plot=Niveaux
+Period_Marker_Plot=Period Marker Plot
+Pie_Plot=Secteurs
+Thermometer_Plot=Thermom\u00E8tre
+XY_Plot=Courbes
+Pie_3D_Plot=Secteurs 3D
diff --git a/org/jfree/chart/plot/LocalizationBundle_nl.properties b/org/jfree/chart/plot/LocalizationBundle_nl.properties
new file mode 100644
index 0000000..1b73640
--- /dev/null
+++ b/org/jfree/chart/plot/LocalizationBundle_nl.properties
@@ -0,0 +1,22 @@
+# org.jfree.chart.plot.plot ResourceBundle properties file
+#
+# Changes (from 31-Aug-2003)
+# --------------------------
+# 24-Mar-2003 : Translated into Dutch
+# 31-Aug-2003 : Initial version (AL);
+#
+
+Category_Plot=Categorie diagram
+Combined_Domain_XYPlot=Diagrammen met gecombineerd domein
+Combined_Range_XYPlot=Diagrammen met gecombineerd bereik
+Compass_Plot=Kompas diagram
+Contour_Plot=Contour diagram
+Fast_Scatter_Plot=Spreidingsdiagram
+Meter_Plot=Wijzerplaat-diagram
+Period_Marker_Plot=Periodemarker-diagram
+Pie_Plot=Taartdiagram
+Thermometer_Plot=Thermometer-diagram
+XY_Plot=XY Diagram
+
+#Secteurs 3D
+Pie_3D_Plot=3D Taartdiagram
diff --git a/org/jfree/chart/plot/LocalizationBundle_pl.properties b/org/jfree/chart/plot/LocalizationBundle_pl.properties
new file mode 100644
index 0000000..d74ab86
--- /dev/null
+++ b/org/jfree/chart/plot/LocalizationBundle_pl.properties
@@ -0,0 +1,22 @@
+# org.jfree.chart.plot.plot ResourceBundle properties file
+#
+# Changes (from 15-Mar-2004)
+# --------------------------
+# 15-Mar-2004 : Initial version (Kuba Duda);
+#
+
+Category_Plot=Wykres kategorii
+Combined_Domain_XYPlot=Wykres kombinowany z dzielon\u0105 osi\u0105 domeny
+Combined_Range_XYPlot=Wykres kombinowany z dzielon\u0105 osi\u0105 zasi\u0119gu
+Compass_Plot=wykres kompasowy
+Contour_Plot=Wykres konturowy
+Fast_Scatter_Plot=Szybki wykres rozproszony punktowy
+Meter_Plot=Wykres miernikowy
+Period_Marker_Plot=Wykres zaznaczaj\u0105cy okresy czasu
+Pie_Plot=Wykres ko\u0142owy
+Thermometer_Plot=Wykres temperatury
+XY_Plot=Wykres XY
+Polar_Plot=Wykres dwuwymiarowy o wsp\u00f3\u0142rz\u0119dnych biegunowych
+
+#Secteurs 3D
+Pie_3D_Plot=Wykres ko\u0142owy 3D
diff --git a/org/jfree/chart/plot/LocalizationBundle_pt_PT.properties b/org/jfree/chart/plot/LocalizationBundle_pt_PT.properties
new file mode 100644
index 0000000..c54561e
--- /dev/null
+++ b/org/jfree/chart/plot/LocalizationBundle_pt_PT.properties
@@ -0,0 +1,19 @@
+# org.jfree.chart.ChartPanel ResourceBundle properties file - portuguese version
+#
+# Changes (from 09-Set-2003)
+# --------------------------
+# 09-Set-2003 : Initial version (Eduardo Ramalho);
+#
+
+Category_Plot=Barras
+Combined_Domain_XYPlot=Curvas combinadas pela abcissa
+Combined_Range_XYPlot=Curvas combinadas pela ordenada
+Compass_Plot=Compasso
+Contour_Plot=Contours
+Fast_Scatter_Plot=Dispers\u00E3o
+Meter_Plot=N\u00EDvel
+Period_Marker_Plot=Period Marker Plot
+Pie_Plot=Sectores
+Thermometer_Plot=Term\u00a2metro
+XY_Plot=Curvas
+Pie_3D_Plot=Sectores 3D
diff --git a/org/jfree/chart/plot/LocalizationBundle_ru.properties b/org/jfree/chart/plot/LocalizationBundle_ru.properties
new file mode 100644
index 0000000..2d5d536
--- /dev/null
+++ b/org/jfree/chart/plot/LocalizationBundle_ru.properties
@@ -0,0 +1,21 @@
+# org.jfree.chart.plot.plot ResourceBundle properties file
+#
+# Changes (from 10-Nov-2003)
+# --------------------------
+# 10-Nov-2003 : Initial version (AL);
+#
+
+Category_Plot=\u041a\u0430\u0442\u0435\u0433\u043e\u0440\u0438\u044f
+Combined_Domain_XYPlot=\u0421\u043e\u0432\u043c\u0435\u0449\u0435\u043d\u0438\u0435 \u043f\u043e \u043e\u0441\u0438 \u043f\u0430\u0440\u0430\u043c\u0435\u0442\u0440\u043e\u0432
+Combined_Range_XYPlot=\u0421\u043e\u0432\u043c\u0435\u0449\u0435\u043d\u0438\u0435 \u043f\u043e \u043e\u0441\u0438 \u0437\u043d\u0430\u0447\u0435\u043d\u0438\u0439
+Compass_Plot=\u041a\u043e\u043c\u043f\u0430\u0441
+Contour_Plot=\u041a\u043e\u043d\u0442\u0443\u0440
+Fast_Scatter_Plot=\u0420\u043e\u0441\u0441\u044b\u043f\u044c
+Meter_Plot=\u041c\u0435\u0442\u0440\u0438\u043a\u0430
+Period_Marker_Plot=\u041f\u0435\u0440\u0438\u043e\u0434
+Pie_Plot=\u041a\u0440\u0443\u0433
+Thermometer_Plot=\u0422\u0435\u0440\u043c\u043e\u043c\u0435\u0442\u0440
+XY_Plot=XY
+
+#Secteurs 3D
+Pie_3D_Plot=\u0422\u0440\u0435\u0445\u043c\u0435\u0440\u043d\u044b\u0439 \u043a\u0440\u0443\u0433
diff --git a/org/jfree/chart/plot/LocalizationBundle_zh_CN.properties b/org/jfree/chart/plot/LocalizationBundle_zh_CN.properties
new file mode 100644
index 0000000..4ce0105
--- /dev/null
+++ b/org/jfree/chart/plot/LocalizationBundle_zh_CN.properties
@@ -0,0 +1,22 @@
+# org.jfree.chart.plot.plot ResourceBundle properties file
+#
+# Changes
+# -------
+# 29-Jun-2005 : Initial version, see: http://www.jfree.org/phpBB2/viewtopic.php?t=13495;
+#
+
+Category_Plot=\u7c7b\u6bd4\u56fe
+Combined_Domain_XYPlot=\u7ec4\u5408\u7684\u9879\u76ee XY \u56fe
+Combined_Range_XYPlot=\u7ec4\u5408\u7684\u8303\u56f4 XY \u56fe
+Compass_Plot=\u7f57\u76d8\u56fe
+Contour_Plot=\u8f6e\u5ed3\u56fe
+Fast_Scatter_Plot=\u5feb\u901f\u5206\u6563\u56fe
+Meter_Plot=\u4eea\u8868\u56fe
+Period_Marker_Plot=\u5468\u671f\u6807\u8bb0\u56fe
+Pie_Plot=\u997c\u56fe
+Thermometer_Plot=\u6e29\u5ea6\u8ba1\u56fe
+XY_Plot=XY \u56fe
+Polar_Plot=\u6781\u5750\u6807\u56fe
+
+#Secteurs 3D
+Pie_3D_Plot=\u4e09\u7ef4\u997c\u56fe
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index 0000000..2e12b0a
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index 0000000..367e95c
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diff --git a/org/jfree/ui/LocalizationBundle.properties b/org/jfree/ui/LocalizationBundle.properties
new file mode 100644
index 0000000..7db6544
--- /dev/null
+++ b/org/jfree/ui/LocalizationBundle.properties
@@ -0,0 +1,25 @@
+# org.jfree.ui.ui ResourceBundle properties file
+#
+# Changes (from 31-Aug-2003)
+# --------------------------
+# 31-Aug-2003 : Initial version (AL);
+#
+
+Attributes=Attributes:
+B=B:
+Bold=Bold
+Bottom=Bottom
+Font=Font:
+Insets=Insets:
+Italic=Italic
+L=L:
+Left=Left
+No_Font_Selected=No font selected.
+R=R:
+Right=Right
+Size=Size:
+T=T:
+Top=Top
+Help=Help
+OK=OK
+Cancel=Cancel
diff --git a/org/jfree/ui/LocalizationBundle_de.properties b/org/jfree/ui/LocalizationBundle_de.properties
new file mode 100644
index 0000000..a916c30
--- /dev/null
+++ b/org/jfree/ui/LocalizationBundle_de.properties
@@ -0,0 +1,25 @@
+# org.jfree.ui.ui ResourceBundle properties file - german version
+#
+# Changes (from 31-Aug-2003)
+# --------------------------
+# 15-Mar-2004 : Initial version (Christian W. Zuckschwerdt);
+#
+
+Attributes=Attribute:
+B=U:
+Bold=Fett
+Bottom=Unten
+Font=Schrift:
+Insets=R\u00e4nder:
+Italic=Kursiv
+L=L:
+Left=Links
+No_Font_Selected=Keine Schrift gew\u00e4hlt.
+R=R:
+Right=Rechts
+Size=Gr\u00f6\u00dfe:
+T=O:
+Top=Oben
+Help=Hilfe
+OK=OK
+Cancel=Abbrechen
diff --git a/org/jfree/ui/LocalizationBundle_es.properties b/org/jfree/ui/LocalizationBundle_es.properties
new file mode 100644
index 0000000..49053c6
--- /dev/null
+++ b/org/jfree/ui/LocalizationBundle_es.properties
@@ -0,0 +1,25 @@
+# org.jfree.ui.ui ResourceBundle properties file spanish
+#
+# Changes (from 31-Aug-2003)
+# --------------------------
+# 14-Oct-2004 : Initial version: Leopoldo Federico P�rtile (Grupo de Procesamiento Digital de Im�genes)
+# Universidad Tecnol�gica Nacional - Facultad Regional Resistencia, Argentina
+
+Attributes=Atributos:
+B=Inf:
+Bold=Negrita
+Bottom=Inferior
+Font=Fuente:
+Insets=M�rgenes:
+Italic=Cursiva
+L=Izq:
+Left=Izquierda
+No_Font_Selected=No se seleccion\00F3 ninguna fuente.
+R=Der:
+Right=Derecha
+Size=Tama\u00f1o:
+T=Sup:
+Top=Superior
+Help=Ayuda
+OK=Aceptar
+Cancel=Cancelar
diff --git a/org/jfree/ui/LocalizationBundle_fr.properties b/org/jfree/ui/LocalizationBundle_fr.properties
new file mode 100644
index 0000000..01c5595
--- /dev/null
+++ b/org/jfree/ui/LocalizationBundle_fr.properties
@@ -0,0 +1,22 @@
+# org.jfree.ui.ui ResourceBundle properties file - french version
+#
+# Changes (from 31-Aug-2003)
+# --------------------------
+# 31-Aug-2003 : Initial version (AL);
+#
+
+Attributes=Attributs :
+B=B :
+Bold=Gras
+Bottom=Bas
+Font=Police :
+Insets=Position :
+Italic=Italique
+L=G :
+Left=Gauche
+No_Font_Selected=Aucune police n'a \u00E9t\u00E9 s\u00E9lectionn\u00E9e.
+R=D :
+Right=Droite
+Size=Taille :
+T=H :
+Top=Haut
diff --git a/org/jfree/ui/LocalizationBundle_pt_PT.properties b/org/jfree/ui/LocalizationBundle_pt_PT.properties
new file mode 100644
index 0000000..e9641dc
--- /dev/null
+++ b/org/jfree/ui/LocalizationBundle_pt_PT.properties
@@ -0,0 +1,22 @@
+# org.jfree.chart.ChartPanel ResourceBundle properties file - portuguese version
+#
+# Changes (from 09-Set-2003)
+# --------------------------
+# 09-Set-2003 : Initial version (Eduardo Ramalho);
+#
+
+Attributes=Atributos:
+B=B:
+Bold=Negrito
+Bottom=Fundo
+Font=Fonte:
+Insets=Posi\u00e7\u00e3o:
+Italic=It\u00e1lico
+L=E:
+Left=Esquerda
+No_Font_Selected=Nenhuma fonte est\u00e1 seleccionada.
+R=D:
+Right=Direita
+Size=Tamanho:
+T=T:
+Top=Topo
\ No newline at end of file
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index 0000000..e72cb12
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@@ -0,0 +1,68 @@
+JSON in Java [package org.json]
+
+Douglas Crockford
+douglas at crockford.com
+
+2011-02-02
+
+
+JSON is a light-weight, language independent, data interchange format.
+See http://www.JSON.org/
+
+The files in this package implement JSON encoders/decoders in Java.
+It also includes the capability to convert between JSON and XML, HTTP
+headers, Cookies, and CDL.
+
+This is a reference implementation. There is a large number of JSON packages
+in Java. Perhaps someday the Java community will standardize on one. Until
+then, choose carefully.
+
+The license includes this restriction: "The software shall be used for good,
+not evil." If your conscience cannot live with that, then choose a different
+package.
+
+The package compiles on Java 1.2 thru Java 1.4.
+
+
+JSONObject.java: The JSONObject can parse text from a String or a JSONTokener
+to produce a map-like object. The object provides methods for manipulating its
+contents, and for producing a JSON compliant object serialization.
+
+JSONArray.java: The JSONObject can parse text from a String or a JSONTokener
+to produce a vector-like object. The object provides methods for manipulating
+its contents, and for producing a JSON compliant array serialization.
+
+JSONTokener.java: The JSONTokener breaks a text into a sequence of individual
+tokens. It can be constructed from a String, Reader, or InputStream.
+
+JSONException.java: The JSONException is the standard exception type thrown
+by this package.
+
+
+JSONString.java: The JSONString interface requires a toJSONString method,
+allowing an object to provide its own serialization.
+
+JSONStringer.java: The JSONStringer provides a convenient facility for
+building JSON strings.
+
+JSONWriter.java: The JSONWriter provides a convenient facility for building
+JSON text through a writer.
+
+
+CDL.java: CDL provides support for converting between JSON and comma
+delimited lists.
+
+Cookie.java: Cookie provides support for converting between JSON and cookies.
+
+CookieList.java: CookieList provides support for converting between JSON and
+cookie lists.
+
+HTTP.java: HTTP provides support for converting between JSON and HTTP headers.
+
+HTTPTokener.java: HTTPTokener extends JSONTokener for parsing HTTP headers.
+
+XML.java: XML provides support for converting between JSON and XML.
+
+JSONML.java: JSONML provides support for converting between JSONML and XML.
+
+XMLTokener.java: XMLTokener extends JSONTokener for parsing XML text.
\ No newline at end of file
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diff --git a/resources/about.properties b/resources/about.properties
new file mode 100644
index 0000000..652ab76
--- /dev/null
+++ b/resources/about.properties
@@ -0,0 +1,22 @@
+#
+# Copyright (c) 2007-2011 by The Broad Institute of MIT and Harvard. All Rights Reserved.
+#
+# This software is licensed under the terms of the GNU Lesser General Public License (LGPL),
+# Version 2.1 which is available at http://www.opensource.org/licenses/lgpl-2.1.php.
+#
+# THE SOFTWARE IS PROVIDED "AS IS." THE BROAD AND MIT MAKE NO REPRESENTATIONS OR
+# WARRANTES OF ANY KIND CONCERNING THE SOFTWARE, EXPRESS OR IMPLIED, INCLUDING,
+# WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR
+# PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER
+# OR NOT DISCOVERABLE. IN NO EVENT SHALL THE BROAD OR MIT, OR THEIR RESPECTIVE
+# TRUSTEES, DIRECTORS, OFFICERS, EMPLOYEES, AND AFFILIATES BE LIABLE FOR ANY DAMAGES
+# OF ANY KIND, INCLUDING, WITHOUT LIMITATION, INCIDENTAL OR CONSEQUENTIAL DAMAGES,
+# ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER
+# THE BROAD OR MIT SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT
+# SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
+#
+
+version=2.1.18
+build=2530
+timestamp=06/10/2012 09:58 PM
+master-resource-url=@DEFAULT_MASTER_RESOURCE_URL
\ No newline at end of file
diff --git a/resources/codonTable.txt b/resources/codonTable.txt
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index 0000000..b850371
--- /dev/null
+++ b/resources/codonTable.txt
@@ -0,0 +1,66 @@
+TTT Phenylalanine Phe F
+TTC Phenylalanine Phe F
+TTA Leucine Leu L
+TTG Leucine Leu L
+TCT Serine Ser S
+TCC Serine Ser S
+TCA Serine Ser S
+TCG Serine Ser S
+TAT Tyrosine Tyr Y
+TAC Tyrosine Tyr Y
+TAA Termination (ochre) Ter *
+TAG Termination (amber) Ter *
+TGT Cysteine Cys C
+TGC Cysteine Cys C
+TGA Termination (opal or umber) Ter *
+TGG Tryptophan Trp W
+CTT Leucine Leu L
+CTC Leucine Leu L
+CTA Leucine Leu L
+CTG Leucine Leu L
+CCT Proline Pro P
+CCC Proline Pro P
+CCA Proline Pro P
+CCG Proline Pro P
+CAT Histidine His H
+CAC Histidine His H
+CAA Glutamine Gln Q
+CAG Glutamine Gln Q
+CGT Arginine Arg R
+CGC Arginine Arg R
+CGA Arginine Arg R
+CGG Arginine Arg R
+ATT Isoleucine Ile I
+ATC Isoleucine Ile I
+ATA Isoleucine Ile I
+ATG Methionine Met M
+ACT Threonine Thr T
+ACC Threonine Thr T
+ACA Threonine Thr T
+ACG Threonine Thr T
+AAT Asparagine Asn N
+AAC Asparagine Asn N
+AAA Lysine Lys K
+AAG Lysine Lys K
+AGT Serine Ser S
+AGC Serine Ser S
+AGA Arginine Arg R
+AGG Arginine Arg R
+GTT Valine Val V
+GTC Valine Val V
+GTA Valine Val V
+GTG Valine Val V
+GCT Alanine Ala A
+GCC Alanine Ala A
+GCA Alanine Ala A
+GCG Alanine Ala A
+GAT Aspartate Asp D
+GAC Aspartate Asp D
+GAA Glutamate Glu E
+GAG Glutamate Glu E
+GGT Glycine Gly G
+GGC Glycine Gly G
+GGA Glycine Gly G
+GGG Glycine Gly G
+n/a Aspartate or Asparagine n/a B
+n/a Glutamate or Glutamine n/a Z
\ No newline at end of file
diff --git a/slider/LICENSE.txt b/slider/LICENSE.txt
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index 0000000..4ffc503
--- /dev/null
+++ b/slider/LICENSE.txt
@@ -0,0 +1,21 @@
+The MIT License
+
+Copyright (c) 2010 Ernest Yu. All rights reserved.
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.
\ No newline at end of file
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