[med-svn] [mauve] branch master updated (0b86d17 -> 0e9ac58)
Andreas Tille
tille at debian.org
Wed Apr 22 12:13:04 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository mauve.
from 0b86d17 Leave wrapper script as example in download archive
new 5e3ea89 Imported Upstream version 2.4.0+4734
new 6503dcd Merge tag 'upstream/2.4.0+4734'
new 9feb509 Re-add debian/ dir that was lost after git-import-orig ( :-( )
new 0e9ac58 Try to use libzeus-jscl-java which was just created in pkg-java Git but this does not seem to work :-(
The 4 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
.classpath | 20 +
.project | 17 +
.settings/org.eclipse.jdt.core.prefs | 12 +
.umlproject | 9 +
COPYING | 340 ++++++
README | 63 ++
TODO | 68 ++
build.xml | 516 +++++++++
build_support/appbundler-1.0.jar | Bin 0 -> 133599 bytes
debian/bin/mauve | 2 +-
debian/control | 2 +-
debian/get-orig-source | 3 +-
debian/patches/debian_classes.patch | 3 +-
debian/rules | 2 +-
doc/overview.txt | 64 ++
ext/core-1.9.2-SNAPSHOT.jar | Bin 0 -> 2471408 bytes
ext/goose.jar | Bin 0 -> 89124 bytes
ext/gui-1.9.2-SNAPSHOT.jar | Bin 0 -> 228711 bytes
ext/jnlp.jar | Bin 0 -> 7042 bytes
ext/jsc.jar | Bin 0 -> 1075447 bytes
ext/unix-0.5.jar | Bin 0 -> 8482 bytes
ext/zeus-jscl.jar | Bin 0 -> 128804 bytes
jarAlignments.xml | 161 +++
jws/deployment.txt | 48 +
jws/index.html | 18 +
jws/mauve.jnlp.template | 29 +
linux-x64/Mauve | 34 +
mauve.dox | 1153 ++++++++++++++++++++
notes/Biojava Renderer Notes.txt | 14 +
notes/Mauve Notes.txt | 95 ++
notes/icon_with_rollover_template.psd | Bin 0 -> 149398 bytes
publish.xml | 77 ++
src/images/Back16.gif | Bin 0 -> 183 bytes
src/images/DarkHand16.gif | Bin 0 -> 636 bytes
src/images/Dcj16.gif | Bin 0 -> 355 bytes
src/images/Down16.gif | Bin 0 -> 185 bytes
src/images/DownRollover16.png | Bin 0 -> 351 bytes
src/images/Forward16.gif | Bin 0 -> 183 bytes
src/images/Grimm16.gif | Bin 0 -> 345 bytes
src/images/Hand16.gif | Bin 0 -> 1072 bytes
src/images/Home16.gif | Bin 0 -> 420 bytes
src/images/ScoreAssembly.png | Bin 0 -> 284 bytes
src/images/Up16.gif | Bin 0 -> 184 bytes
src/images/UpRollover16.png | Bin 0 -> 358 bytes
src/images/Zoom16.gif | Bin 0 -> 303 bytes
src/images/ZoomIn16.gif | Bin 0 -> 304 bytes
src/images/ZoomIn24.gif | Bin 0 -> 484 bytes
src/images/ZoomOut16.gif | Bin 0 -> 304 bytes
src/images/ZoomOut24.gif | Bin 0 -> 477 bytes
src/images/aPlus16.png | Bin 0 -> 357 bytes
src/images/fist_icon.gif | Bin 0 -> 112 bytes
src/images/hand_icon.gif | Bin 0 -> 130 bytes
src/images/mauve_icon.gif | Bin 0 -> 555 bytes
src/images/mauve_logo.png | Bin 0 -> 18351 bytes
src/images/minus16.png | Bin 0 -> 181 bytes
src/images/minusRollover16.png | Bin 0 -> 304 bytes
src/images/plus16.png | Bin 0 -> 202 bytes
src/images/plusRollover16.png | Bin 0 -> 323 bytes
src/images/r16.png | Bin 0 -> 292 bytes
src/images/searchBinoculars16.png | Bin 0 -> 992 bytes
src/images/searchBinoculars24.png | Bin 0 -> 1766 bytes
src/images/searchBinoculars32.png | Bin 0 -> 1735 bytes
src/org/gel/air/util/GroupHelpers.java | 29 +
src/org/gel/air/util/IOUtils.java | 129 +++
src/org/gel/air/util/MathUtils.java | 34 +
src/org/gel/air/util/StatusBox.java | 40 +
src/org/gel/mauve/BaseViewerModel.java | 971 +++++++++++++++++
src/org/gel/mauve/BrowserLauncher.java | 824 ++++++++++++++
src/org/gel/mauve/Chromosome.java | 56 +
src/org/gel/mauve/ColorScheme.java | 25 +
src/org/gel/mauve/DbXrefFactory.java | 155 +++
src/org/gel/mauve/DbXrefHandler.java | 23 +
src/org/gel/mauve/FilterCacheSpec.java | 48 +
src/org/gel/mauve/Genome.java | 204 ++++
src/org/gel/mauve/GenomeBuilder.java | 213 ++++
src/org/gel/mauve/HighlightListener.java | 7 +
src/org/gel/mauve/LCB.java | 172 +++
src/org/gel/mauve/LCBLeftComparator.java | 32 +
src/org/gel/mauve/LCBlist.java | 409 +++++++
src/org/gel/mauve/LcbIdComparator.java | 15 +
src/org/gel/mauve/LcbViewerModel.java | 759 +++++++++++++
src/org/gel/mauve/Match.java | 170 +++
src/org/gel/mauve/MatchStartComparator.java | 41 +
src/org/gel/mauve/MauveConstants.java | 182 +++
src/org/gel/mauve/MauveFormatException.java | 11 +
src/org/gel/mauve/MauveHelperFunctions.java | 303 +++++
src/org/gel/mauve/ModelBuilder.java | 566 ++++++++++
src/org/gel/mauve/ModelEvent.java | 13 +
src/org/gel/mauve/ModelListener.java | 22 +
src/org/gel/mauve/ModelProgressListener.java | 15 +
src/org/gel/mauve/MyConsole.java | 47 +
src/org/gel/mauve/OptionsBuilder.java | 84 ++
src/org/gel/mauve/PreferencesDump.java | 23 +
src/org/gel/mauve/SeqFeatureData.java | 315 ++++++
src/org/gel/mauve/SimilarityIndex.java | 380 +++++++
src/org/gel/mauve/SupportedFormat.java | 90 ++
src/org/gel/mauve/ViewerMode.java | 10 +
src/org/gel/mauve/XMFAAlignment.java | 885 +++++++++++++++
src/org/gel/mauve/XmfaViewerModel.java | 561 ++++++++++
src/org/gel/mauve/analysis/BrokenCDS.java | 208 ++++
src/org/gel/mauve/analysis/CDSErrorExporter.java | 640 +++++++++++
src/org/gel/mauve/analysis/Gap.java | 240 ++++
src/org/gel/mauve/analysis/IdentityMatrix.java | 104 ++
src/org/gel/mauve/analysis/LiteWeightFeature.java | 130 +++
.../mauve/analysis/OneToOneOrthologExporter.java | 1122 +++++++++++++++++++
.../gel/mauve/analysis/PermutationExporter.java | 696 ++++++++++++
src/org/gel/mauve/analysis/SNP.java | 331 ++++++
src/org/gel/mauve/analysis/Segment.java | 169 +++
src/org/gel/mauve/analysis/SegmentComparator.java | 65 ++
src/org/gel/mauve/analysis/SnpExporter.java | 502 +++++++++
src/org/gel/mauve/analysis/TreeAnalysis.java | 58 +
src/org/gel/mauve/assembly/AssemblyScorer.java | 810 ++++++++++++++
src/org/gel/mauve/assembly/ScoreAssembly.java | 427 ++++++++
src/org/gel/mauve/backbone/Backbone.java | 82 ++
src/org/gel/mauve/backbone/BackboneList.java | 150 +++
.../gel/mauve/backbone/BackboneListBuilder.java | 121 ++
src/org/gel/mauve/chado/ChadoDB.java | 79 ++
src/org/gel/mauve/chado/ChadoFeatureLoader.java | 52 +
src/org/gel/mauve/chado/ChadoReader.java | 41 +
src/org/gel/mauve/chado/ChadoWriter.java | 41 +
src/org/gel/mauve/chado/DBUtils.java | 18 +
src/org/gel/mauve/color/BackboneLcbColor.java | 34 +
.../gel/mauve/color/BackboneMultiplicityColor.java | 209 ++++
src/org/gel/mauve/color/ColorMenu.java | 126 +++
src/org/gel/mauve/color/LCBColorScheme.java | 57 +
.../gel/mauve/color/MultiplicityColorScheme.java | 78 ++
.../mauve/color/MultiplicityTypeColorScheme.java | 46 +
.../NormalizedMultiplicityTypeColorScheme.java | 73 ++
.../mauve/color/NormalizedOffsetColorScheme.java | 82 ++
src/org/gel/mauve/color/OffsetColorScheme.java | 57 +
src/org/gel/mauve/contigs/ChangedFastaFormat.java | 25 +
.../gel/mauve/contigs/ChangedFeatureWriter.java | 110 ++
src/org/gel/mauve/contigs/ContigFeatureWriter.java | 129 +++
src/org/gel/mauve/contigs/ContigGrouper.java | 349 ++++++
src/org/gel/mauve/contigs/ContigHandler.java | 37 +
src/org/gel/mauve/contigs/ContigInverter.java | 496 +++++++++
.../gel/mauve/contigs/ContigMauveAlignFrame.java | 168 +++
src/org/gel/mauve/contigs/ContigOrderer.java | 345 ++++++
src/org/gel/mauve/contigs/ContigRenamer.java | 67 ++
src/org/gel/mauve/contigs/ContigReorderer.java | 574 ++++++++++
.../gel/mauve/contigs/DefaultContigHandler.java | 60 +
.../gel/mauve/contigs/FastAContigChangeWriter.java | 175 +++
src/org/gel/mauve/contigs/FeatureFixer.java | 84 ++
.../gel/mauve/contigs/ListSequenceIterator.java | 31 +
src/org/gel/mauve/dcj/DCJ.java | 758 +++++++++++++
src/org/gel/mauve/dcj/DCJWindow.java | 261 +++++
src/org/gel/mauve/dcjx/Adjacency.java | 102 ++
src/org/gel/mauve/dcjx/AdjacencyGraph.java | 255 +++++
src/org/gel/mauve/dcjx/Block.java | 61 ++
src/org/gel/mauve/dcjx/BlockEnd.java | 12 +
src/org/gel/mauve/dcjx/Constants.java | 12 +
src/org/gel/mauve/dcjx/Contig.java | 109 ++
src/org/gel/mauve/dcjx/DCJ.java | 116 ++
src/org/gel/mauve/dcjx/DCJDistance.java | 231 ++++
src/org/gel/mauve/dcjx/FastAccessTable.java | 38 +
src/org/gel/mauve/dcjx/Head.java | 18 +
src/org/gel/mauve/dcjx/Permutation.java | 196 ++++
src/org/gel/mauve/dcjx/Tail.java | 18 +
src/org/gel/mauve/dcjx/VestigialDCJ.java | 96 ++
src/org/gel/mauve/format/BaseFormat.java | 129 +++
src/org/gel/mauve/format/DelegatingSequence.java | 429 ++++++++
src/org/gel/mauve/format/EmblFormat.java | 26 +
src/org/gel/mauve/format/FastaFormat.java | 43 +
src/org/gel/mauve/format/FileFinder.java | 73 ++
src/org/gel/mauve/format/GenbankEmblFormat.java | 248 +++++
src/org/gel/mauve/format/GenbankFileFormat.java | 28 +
src/org/gel/mauve/format/INSDseqFormat.java | 33 +
.../mauve/format/RawFastaBridgeFilterReader.java | 100 ++
src/org/gel/mauve/format/RawFormat.java | 26 +
.../gel/mauve/format/RichDelegatingSequence.java | 171 +++
.../mauve/format/RichStrandedFeatureTemplate.java | 28 +
.../gel/mauve/format/SequenceIteratorCache.java | 116 ++
.../gel/mauve/format/SupportedFormatFactory.java | 83 ++
src/org/gel/mauve/format/TestMain.java | 12 +
src/org/gel/mauve/gaggle/SampleGoose.java | 696 ++++++++++++
src/org/gel/mauve/gui/AlignFrame.java | 717 ++++++++++++
src/org/gel/mauve/gui/AlignWorker.java | 139 +++
.../gel/mauve/gui/AlignmentProcessListener.java | 7 +
src/org/gel/mauve/gui/AnalysisDisplayWindow.java | 278 +++++
src/org/gel/mauve/gui/ConsoleDialog.java | 35 +
src/org/gel/mauve/gui/ExportFrame.java | 464 ++++++++
src/org/gel/mauve/gui/ExportMenu.java | 166 +++
src/org/gel/mauve/gui/FillLayout.java | 85 ++
src/org/gel/mauve/gui/FrameLoader.java | 102 ++
src/org/gel/mauve/gui/GenomeCellRenderer.java | 26 +
src/org/gel/mauve/gui/HintMessageEvent.java | 17 +
src/org/gel/mauve/gui/HintMessageListener.java | 7 +
src/org/gel/mauve/gui/LCBStatusBar.java | 195 ++++
src/org/gel/mauve/gui/LcbLinePanel.java | 283 +++++
src/org/gel/mauve/gui/Mauve.java | 379 +++++++
src/org/gel/mauve/gui/MauveAlignFrame.java | 320 ++++++
src/org/gel/mauve/gui/MauveFrame.java | 766 +++++++++++++
src/org/gel/mauve/gui/MauveRenderingHints.java | 19 +
.../gel/mauve/gui/MySymbolSequenceRenderer.java | 116 ++
src/org/gel/mauve/gui/PrintPreviewCanvas.java | 77 ++
src/org/gel/mauve/gui/PrintPreviewDialog.java | 51 +
src/org/gel/mauve/gui/PrintUtilities.java | 34 +
.../gel/mauve/gui/ProgressiveMauveAlignFrame.java | 602 ++++++++++
src/org/gel/mauve/gui/QualifierPanel.java | 68 ++
src/org/gel/mauve/gui/RearrangementPanel.java | 976 +++++++++++++++++
src/org/gel/mauve/gui/SequenceNavigator.java | 745 +++++++++++++
src/org/gel/mauve/gui/SplashScreen.java | 91 ++
src/org/gel/mauve/gui/StyleMenu.java | 285 +++++
src/org/gel/mauve/gui/SwingWorker.java | 137 +++
src/org/gel/mauve/gui/dnd/DnDList.java | 264 +++++
src/org/gel/mauve/gui/dnd/FileDrop.java | 572 ++++++++++
src/org/gel/mauve/gui/dnd/TransferableObject.java | 262 +++++
.../gui/navigation/AnnotationContainsFilter.java | 120 ++
.../gel/mauve/gui/navigation/NavigationPanel.java | 203 ++++
.../mauve/gui/navigation/SearchResultPanel.java | 524 +++++++++
.../mauve/gui/sequence/AbstractSequencePanel.java | 151 +++
src/org/gel/mauve/gui/sequence/ControlPanel.java | 263 +++++
.../gel/mauve/gui/sequence/FeatureFilterer.java | 329 ++++++
src/org/gel/mauve/gui/sequence/FeaturePanel.java | 505 +++++++++
.../gui/sequence/FlatFileFeatureConstants.java | 68 ++
.../gui/sequence/FlatFileFeatureImporter.java | 318 ++++++
src/org/gel/mauve/gui/sequence/HighlightPanel.java | 99 ++
src/org/gel/mauve/gui/sequence/HistogramPanel.java | 68 ++
src/org/gel/mauve/gui/sequence/MatchPanel.java | 1031 +++++++++++++++++
src/org/gel/mauve/gui/sequence/MatchPopupMenu.java | 94 ++
.../MultiGenomeRectangularBeadRenderer.java | 86 ++
.../gel/mauve/gui/sequence/RRSequencePanel.java | 193 ++++
.../mauve/gui/sequence/RangeHighlightPanel.java | 92 ++
src/org/gel/mauve/gui/sequence/RulerPanel.java | 90 ++
src/org/gel/mauve/gui/sequence/SeqPanel.java | 317 ++++++
.../gui/sequence/ZiggyRectangularBeadRenderer.java | 276 +++++
src/org/gel/mauve/histogram/HistogramBuilder.java | 122 +++
src/org/gel/mauve/histogram/ZoomHistogram.java | 382 +++++++
src/org/gel/mauve/module/MauveModule.java | 22 +
src/org/gel/mauve/module/MauveModuleFrame.java | 23 +
src/org/gel/mauve/module/ModuleListener.java | 9 +
.../gel/mauve/recombination/WeakArgDataModel.java | 18 +
.../mauve/recombination/WeakArgModelBuilder.java | 268 +++++
.../gel/mauve/remote/MauveDisplayCommunicator.java | 17 +
src/org/gel/mauve/remote/MauveInterface.java | 14 +
src/org/gel/mauve/remote/MauveInterfaceImpl.java | 75 ++
src/org/gel/mauve/remote/RemoteApplet.java | 182 +++
src/org/gel/mauve/remote/RemoteControl.java | 9 +
src/org/gel/mauve/remote/RemoteControlImpl.java | 38 +
.../gel/mauve/remote/WargDisplayCommunicator.java | 32 +
src/org/gel/mauve/remote/WargInterface.java | 8 +
src/org/gel/mauve/summary/AnalysisModuleFrame.java | 117 ++
src/org/gel/mauve/summary/MauveInterfacer.java | 60 +
src/org/gel/mauve/summary/ProcessBackboneFile.java | 183 ++++
.../mauve/summary/output/AbstractIslandWriter.java | 22 +
.../summary/output/AbstractMatchDataWriter.java | 185 ++++
.../summary/output/AbstractTabbedDataWriter.java | 198 ++++
.../summary/output/AlignedSequenceWriter.java | 124 +++
.../mauve/summary/output/BackboneCompareFile.java | 37 +
.../summary/output/IslandCoordinateWriter.java | 55 +
.../mauve/summary/output/IslandFeatureWriter.java | 84 ++
.../summary/output/IslandGeneFeatureWriter.java | 208 ++++
.../mauve/summary/output/OverviewFileWriter.java | 238 ++++
.../mauve/summary/output/PartialFastaWriter.java | 68 ++
.../mauve/summary/output/SegmentDataProcessor.java | 285 +++++
.../mauve/summary/output/TroubleMatchWriter.java | 98 ++
src/org/gel/mauve/tree/FileKey.java | 71 ++
src/org/gel/mauve/tree/GISTree.java | 414 +++++++
src/org/gel/mauve/tree/GapKey.java | 45 +
src/org/gel/mauve/tree/IntervalSequenceTree.java | 320 ++++++
src/org/gel/mauve/tree/IstIterator.java | 31 +
src/org/gel/mauve/tree/IstNode.java | 67 ++
src/org/gel/mauve/tree/Key.java | 17 +
src/org/gel/mauve/tree/TreeStore.java | 98 ++
test/org/gel/mauve/LcbViewerModelTest.java | 59 +
test/org/gel/mauve/ModelLoader.java | 44 +
test/org/gel/mauve/XMFAAlignmentTest.java | 95 ++
.../gel/mauve/format/DelegatingSequenceTest.java | 89 ++
test/org/gel/mauve/format/MockFormat.java | 118 ++
test/org/gel/mauve/tree/GistNode.java | 58 +
test/org/gel/mauve/tree/GistTest.java | 194 ++++
testdata/S_bayanus_small.fasta | 12 +
testdata/S_bayanus_small.raw | 9 +
testdata/S_cerevisiae_small.gbk | 207 ++++
testdata/small.alignment | 58 +
testdata/small.mauve | 28 +
testdata/small.mums | 128 +++
testdata/small_raw.alignment | 58 +
278 files changed, 43143 insertions(+), 5 deletions(-)
create mode 100644 .classpath
create mode 100644 .project
create mode 100644 .settings/org.eclipse.jdt.core.prefs
create mode 100644 .umlproject
create mode 100644 COPYING
create mode 100644 README
create mode 100644 TODO
create mode 100644 build.xml
create mode 100644 build_support/appbundler-1.0.jar
create mode 100644 doc/overview.txt
create mode 100644 ext/core-1.9.2-SNAPSHOT.jar
create mode 100644 ext/goose.jar
create mode 100644 ext/gui-1.9.2-SNAPSHOT.jar
create mode 100644 ext/jnlp.jar
create mode 100644 ext/jsc.jar
create mode 100644 ext/unix-0.5.jar
create mode 100644 ext/zeus-jscl.jar
create mode 100644 jarAlignments.xml
create mode 100644 jws/deployment.txt
create mode 100644 jws/index.html
create mode 100644 jws/mauve.jnlp.template
create mode 100755 linux-x64/Mauve
create mode 100644 mauve.dox
create mode 100644 notes/Biojava Renderer Notes.txt
create mode 100644 notes/Mauve Notes.txt
create mode 100644 notes/icon_with_rollover_template.psd
create mode 100644 publish.xml
create mode 100644 src/images/Back16.gif
create mode 100644 src/images/DarkHand16.gif
create mode 100644 src/images/Dcj16.gif
create mode 100644 src/images/Down16.gif
create mode 100644 src/images/DownRollover16.png
create mode 100644 src/images/Forward16.gif
create mode 100644 src/images/Grimm16.gif
create mode 100644 src/images/Hand16.gif
create mode 100644 src/images/Home16.gif
create mode 100644 src/images/ScoreAssembly.png
create mode 100644 src/images/Up16.gif
create mode 100644 src/images/UpRollover16.png
create mode 100644 src/images/Zoom16.gif
create mode 100644 src/images/ZoomIn16.gif
create mode 100644 src/images/ZoomIn24.gif
create mode 100644 src/images/ZoomOut16.gif
create mode 100644 src/images/ZoomOut24.gif
create mode 100644 src/images/aPlus16.png
create mode 100644 src/images/fist_icon.gif
create mode 100644 src/images/hand_icon.gif
create mode 100644 src/images/mauve_icon.gif
create mode 100644 src/images/mauve_logo.png
create mode 100644 src/images/minus16.png
create mode 100644 src/images/minusRollover16.png
create mode 100644 src/images/plus16.png
create mode 100644 src/images/plusRollover16.png
create mode 100644 src/images/r16.png
create mode 100644 src/images/searchBinoculars16.png
create mode 100644 src/images/searchBinoculars24.png
create mode 100644 src/images/searchBinoculars32.png
create mode 100644 src/org/gel/air/util/GroupHelpers.java
create mode 100644 src/org/gel/air/util/IOUtils.java
create mode 100644 src/org/gel/air/util/MathUtils.java
create mode 100644 src/org/gel/air/util/StatusBox.java
create mode 100644 src/org/gel/mauve/BaseViewerModel.java
create mode 100644 src/org/gel/mauve/BrowserLauncher.java
create mode 100644 src/org/gel/mauve/Chromosome.java
create mode 100644 src/org/gel/mauve/ColorScheme.java
create mode 100644 src/org/gel/mauve/DbXrefFactory.java
create mode 100644 src/org/gel/mauve/DbXrefHandler.java
create mode 100644 src/org/gel/mauve/FilterCacheSpec.java
create mode 100644 src/org/gel/mauve/Genome.java
create mode 100644 src/org/gel/mauve/GenomeBuilder.java
create mode 100644 src/org/gel/mauve/HighlightListener.java
create mode 100644 src/org/gel/mauve/LCB.java
create mode 100644 src/org/gel/mauve/LCBLeftComparator.java
create mode 100644 src/org/gel/mauve/LCBlist.java
create mode 100644 src/org/gel/mauve/LcbIdComparator.java
create mode 100644 src/org/gel/mauve/LcbViewerModel.java
create mode 100644 src/org/gel/mauve/Match.java
create mode 100644 src/org/gel/mauve/MatchStartComparator.java
create mode 100644 src/org/gel/mauve/MauveConstants.java
create mode 100644 src/org/gel/mauve/MauveFormatException.java
create mode 100644 src/org/gel/mauve/MauveHelperFunctions.java
create mode 100644 src/org/gel/mauve/ModelBuilder.java
create mode 100644 src/org/gel/mauve/ModelEvent.java
create mode 100644 src/org/gel/mauve/ModelListener.java
create mode 100644 src/org/gel/mauve/ModelProgressListener.java
create mode 100644 src/org/gel/mauve/MyConsole.java
create mode 100644 src/org/gel/mauve/OptionsBuilder.java
create mode 100644 src/org/gel/mauve/PreferencesDump.java
create mode 100644 src/org/gel/mauve/SeqFeatureData.java
create mode 100644 src/org/gel/mauve/SimilarityIndex.java
create mode 100644 src/org/gel/mauve/SupportedFormat.java
create mode 100644 src/org/gel/mauve/ViewerMode.java
create mode 100644 src/org/gel/mauve/XMFAAlignment.java
create mode 100644 src/org/gel/mauve/XmfaViewerModel.java
create mode 100644 src/org/gel/mauve/analysis/BrokenCDS.java
create mode 100644 src/org/gel/mauve/analysis/CDSErrorExporter.java
create mode 100644 src/org/gel/mauve/analysis/Gap.java
create mode 100644 src/org/gel/mauve/analysis/IdentityMatrix.java
create mode 100644 src/org/gel/mauve/analysis/LiteWeightFeature.java
create mode 100644 src/org/gel/mauve/analysis/OneToOneOrthologExporter.java
create mode 100644 src/org/gel/mauve/analysis/PermutationExporter.java
create mode 100644 src/org/gel/mauve/analysis/SNP.java
create mode 100644 src/org/gel/mauve/analysis/Segment.java
create mode 100644 src/org/gel/mauve/analysis/SegmentComparator.java
create mode 100644 src/org/gel/mauve/analysis/SnpExporter.java
create mode 100644 src/org/gel/mauve/analysis/TreeAnalysis.java
create mode 100644 src/org/gel/mauve/assembly/AssemblyScorer.java
create mode 100644 src/org/gel/mauve/assembly/ScoreAssembly.java
create mode 100644 src/org/gel/mauve/backbone/Backbone.java
create mode 100644 src/org/gel/mauve/backbone/BackboneList.java
create mode 100644 src/org/gel/mauve/backbone/BackboneListBuilder.java
create mode 100644 src/org/gel/mauve/chado/ChadoDB.java
create mode 100644 src/org/gel/mauve/chado/ChadoFeatureLoader.java
create mode 100644 src/org/gel/mauve/chado/ChadoReader.java
create mode 100644 src/org/gel/mauve/chado/ChadoWriter.java
create mode 100644 src/org/gel/mauve/chado/DBUtils.java
create mode 100644 src/org/gel/mauve/color/BackboneLcbColor.java
create mode 100644 src/org/gel/mauve/color/BackboneMultiplicityColor.java
create mode 100644 src/org/gel/mauve/color/ColorMenu.java
create mode 100644 src/org/gel/mauve/color/LCBColorScheme.java
create mode 100644 src/org/gel/mauve/color/MultiplicityColorScheme.java
create mode 100644 src/org/gel/mauve/color/MultiplicityTypeColorScheme.java
create mode 100644 src/org/gel/mauve/color/NormalizedMultiplicityTypeColorScheme.java
create mode 100644 src/org/gel/mauve/color/NormalizedOffsetColorScheme.java
create mode 100644 src/org/gel/mauve/color/OffsetColorScheme.java
create mode 100644 src/org/gel/mauve/contigs/ChangedFastaFormat.java
create mode 100644 src/org/gel/mauve/contigs/ChangedFeatureWriter.java
create mode 100644 src/org/gel/mauve/contigs/ContigFeatureWriter.java
create mode 100644 src/org/gel/mauve/contigs/ContigGrouper.java
create mode 100644 src/org/gel/mauve/contigs/ContigHandler.java
create mode 100644 src/org/gel/mauve/contigs/ContigInverter.java
create mode 100644 src/org/gel/mauve/contigs/ContigMauveAlignFrame.java
create mode 100644 src/org/gel/mauve/contigs/ContigOrderer.java
create mode 100644 src/org/gel/mauve/contigs/ContigRenamer.java
create mode 100644 src/org/gel/mauve/contigs/ContigReorderer.java
create mode 100644 src/org/gel/mauve/contigs/DefaultContigHandler.java
create mode 100644 src/org/gel/mauve/contigs/FastAContigChangeWriter.java
create mode 100644 src/org/gel/mauve/contigs/FeatureFixer.java
create mode 100644 src/org/gel/mauve/contigs/ListSequenceIterator.java
create mode 100644 src/org/gel/mauve/dcj/DCJ.java
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create mode 100644 src/org/gel/mauve/dcjx/Adjacency.java
create mode 100644 src/org/gel/mauve/dcjx/AdjacencyGraph.java
create mode 100644 src/org/gel/mauve/dcjx/Block.java
create mode 100644 src/org/gel/mauve/dcjx/BlockEnd.java
create mode 100644 src/org/gel/mauve/dcjx/Constants.java
create mode 100644 src/org/gel/mauve/dcjx/Contig.java
create mode 100644 src/org/gel/mauve/dcjx/DCJ.java
create mode 100644 src/org/gel/mauve/dcjx/DCJDistance.java
create mode 100644 src/org/gel/mauve/dcjx/FastAccessTable.java
create mode 100644 src/org/gel/mauve/dcjx/Head.java
create mode 100644 src/org/gel/mauve/dcjx/Permutation.java
create mode 100644 src/org/gel/mauve/dcjx/Tail.java
create mode 100644 src/org/gel/mauve/dcjx/VestigialDCJ.java
create mode 100644 src/org/gel/mauve/format/BaseFormat.java
create mode 100644 src/org/gel/mauve/format/DelegatingSequence.java
create mode 100644 src/org/gel/mauve/format/EmblFormat.java
create mode 100644 src/org/gel/mauve/format/FastaFormat.java
create mode 100644 src/org/gel/mauve/format/FileFinder.java
create mode 100644 src/org/gel/mauve/format/GenbankEmblFormat.java
create mode 100644 src/org/gel/mauve/format/GenbankFileFormat.java
create mode 100644 src/org/gel/mauve/format/INSDseqFormat.java
create mode 100644 src/org/gel/mauve/format/RawFastaBridgeFilterReader.java
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create mode 100644 src/org/gel/mauve/format/RichDelegatingSequence.java
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create mode 100644 src/org/gel/mauve/format/SupportedFormatFactory.java
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create mode 100644 src/org/gel/mauve/gaggle/SampleGoose.java
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create mode 100644 src/org/gel/mauve/gui/AlignmentProcessListener.java
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create mode 100644 src/org/gel/mauve/gui/HintMessageListener.java
create mode 100644 src/org/gel/mauve/gui/LCBStatusBar.java
create mode 100644 src/org/gel/mauve/gui/LcbLinePanel.java
create mode 100644 src/org/gel/mauve/gui/Mauve.java
create mode 100644 src/org/gel/mauve/gui/MauveAlignFrame.java
create mode 100644 src/org/gel/mauve/gui/MauveFrame.java
create mode 100644 src/org/gel/mauve/gui/MauveRenderingHints.java
create mode 100644 src/org/gel/mauve/gui/MySymbolSequenceRenderer.java
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create mode 100644 src/org/gel/mauve/gui/PrintPreviewDialog.java
create mode 100644 src/org/gel/mauve/gui/PrintUtilities.java
create mode 100644 src/org/gel/mauve/gui/ProgressiveMauveAlignFrame.java
create mode 100644 src/org/gel/mauve/gui/QualifierPanel.java
create mode 100644 src/org/gel/mauve/gui/RearrangementPanel.java
create mode 100644 src/org/gel/mauve/gui/SequenceNavigator.java
create mode 100644 src/org/gel/mauve/gui/SplashScreen.java
create mode 100644 src/org/gel/mauve/gui/StyleMenu.java
create mode 100644 src/org/gel/mauve/gui/SwingWorker.java
create mode 100644 src/org/gel/mauve/gui/dnd/DnDList.java
create mode 100644 src/org/gel/mauve/gui/dnd/FileDrop.java
create mode 100644 src/org/gel/mauve/gui/dnd/TransferableObject.java
create mode 100644 src/org/gel/mauve/gui/navigation/AnnotationContainsFilter.java
create mode 100644 src/org/gel/mauve/gui/navigation/NavigationPanel.java
create mode 100644 src/org/gel/mauve/gui/navigation/SearchResultPanel.java
create mode 100644 src/org/gel/mauve/gui/sequence/AbstractSequencePanel.java
create mode 100644 src/org/gel/mauve/gui/sequence/ControlPanel.java
create mode 100644 src/org/gel/mauve/gui/sequence/FeatureFilterer.java
create mode 100644 src/org/gel/mauve/gui/sequence/FeaturePanel.java
create mode 100644 src/org/gel/mauve/gui/sequence/FlatFileFeatureConstants.java
create mode 100644 src/org/gel/mauve/gui/sequence/FlatFileFeatureImporter.java
create mode 100644 src/org/gel/mauve/gui/sequence/HighlightPanel.java
create mode 100644 src/org/gel/mauve/gui/sequence/HistogramPanel.java
create mode 100644 src/org/gel/mauve/gui/sequence/MatchPanel.java
create mode 100644 src/org/gel/mauve/gui/sequence/MatchPopupMenu.java
create mode 100644 src/org/gel/mauve/gui/sequence/MultiGenomeRectangularBeadRenderer.java
create mode 100644 src/org/gel/mauve/gui/sequence/RRSequencePanel.java
create mode 100644 src/org/gel/mauve/gui/sequence/RangeHighlightPanel.java
create mode 100644 src/org/gel/mauve/gui/sequence/RulerPanel.java
create mode 100644 src/org/gel/mauve/gui/sequence/SeqPanel.java
create mode 100644 src/org/gel/mauve/gui/sequence/ZiggyRectangularBeadRenderer.java
create mode 100644 src/org/gel/mauve/histogram/HistogramBuilder.java
create mode 100644 src/org/gel/mauve/histogram/ZoomHistogram.java
create mode 100644 src/org/gel/mauve/module/MauveModule.java
create mode 100644 src/org/gel/mauve/module/MauveModuleFrame.java
create mode 100644 src/org/gel/mauve/module/ModuleListener.java
create mode 100644 src/org/gel/mauve/recombination/WeakArgDataModel.java
create mode 100644 src/org/gel/mauve/recombination/WeakArgModelBuilder.java
create mode 100644 src/org/gel/mauve/remote/MauveDisplayCommunicator.java
create mode 100644 src/org/gel/mauve/remote/MauveInterface.java
create mode 100644 src/org/gel/mauve/remote/MauveInterfaceImpl.java
create mode 100644 src/org/gel/mauve/remote/RemoteApplet.java
create mode 100644 src/org/gel/mauve/remote/RemoteControl.java
create mode 100644 src/org/gel/mauve/remote/RemoteControlImpl.java
create mode 100644 src/org/gel/mauve/remote/WargDisplayCommunicator.java
create mode 100644 src/org/gel/mauve/remote/WargInterface.java
create mode 100644 src/org/gel/mauve/summary/AnalysisModuleFrame.java
create mode 100644 src/org/gel/mauve/summary/MauveInterfacer.java
create mode 100644 src/org/gel/mauve/summary/ProcessBackboneFile.java
create mode 100644 src/org/gel/mauve/summary/output/AbstractIslandWriter.java
create mode 100644 src/org/gel/mauve/summary/output/AbstractMatchDataWriter.java
create mode 100644 src/org/gel/mauve/summary/output/AbstractTabbedDataWriter.java
create mode 100644 src/org/gel/mauve/summary/output/AlignedSequenceWriter.java
create mode 100644 src/org/gel/mauve/summary/output/BackboneCompareFile.java
create mode 100644 src/org/gel/mauve/summary/output/IslandCoordinateWriter.java
create mode 100644 src/org/gel/mauve/summary/output/IslandFeatureWriter.java
create mode 100644 src/org/gel/mauve/summary/output/IslandGeneFeatureWriter.java
create mode 100644 src/org/gel/mauve/summary/output/OverviewFileWriter.java
create mode 100644 src/org/gel/mauve/summary/output/PartialFastaWriter.java
create mode 100644 src/org/gel/mauve/summary/output/SegmentDataProcessor.java
create mode 100644 src/org/gel/mauve/summary/output/TroubleMatchWriter.java
create mode 100644 src/org/gel/mauve/tree/FileKey.java
create mode 100644 src/org/gel/mauve/tree/GISTree.java
create mode 100644 src/org/gel/mauve/tree/GapKey.java
create mode 100644 src/org/gel/mauve/tree/IntervalSequenceTree.java
create mode 100644 src/org/gel/mauve/tree/IstIterator.java
create mode 100644 src/org/gel/mauve/tree/IstNode.java
create mode 100644 src/org/gel/mauve/tree/Key.java
create mode 100644 src/org/gel/mauve/tree/TreeStore.java
create mode 100644 test/org/gel/mauve/LcbViewerModelTest.java
create mode 100644 test/org/gel/mauve/ModelLoader.java
create mode 100644 test/org/gel/mauve/XMFAAlignmentTest.java
create mode 100644 test/org/gel/mauve/format/DelegatingSequenceTest.java
create mode 100644 test/org/gel/mauve/format/MockFormat.java
create mode 100644 test/org/gel/mauve/tree/GistNode.java
create mode 100644 test/org/gel/mauve/tree/GistTest.java
create mode 100644 testdata/S_bayanus_small.fasta
create mode 100644 testdata/S_bayanus_small.raw
create mode 100644 testdata/S_cerevisiae_small.gbk
create mode 100644 testdata/small.alignment
create mode 100644 testdata/small.mauve
create mode 100644 testdata/small.mums
create mode 100644 testdata/small_raw.alignment
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