[med-svn] [jaligner] 03/04: Merge tag 'upstream/1.0'
Michael Crusoe
misterc-guest at moszumanska.debian.org
Mon Feb 16 06:35:36 UTC 2015
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to branch master
in repository jaligner.
commit 4321b4159c83964aabd9a883635079bd7b0c8f3e
Merge: a3ab0ed 6485aaa
Author: Michael R. Crusoe <mcrusoe at msu.edu>
Date: Mon Feb 16 01:23:33 2015 -0500
Merge tag 'upstream/1.0'
Upstream version 1.0 (from GitHub)
README | 4 +-
README.md | 2 +
api/allclasses-frame.html | 110 --
api/allclasses-noframe.html | 110 --
api/constant-values.html | 298 -----
api/deprecated-list.html | 134 ---
api/help-doc.html | 193 ---
api/index-all.html | 798 -------------
api/index.html | 26 -
api/jaligner.css | 38 -
api/jaligner/Alignment.html | 891 --------------
api/jaligner/Cell.html | 385 ------
api/jaligner/Directions.html | 321 -----
api/jaligner/Markups.html | 321 -----
api/jaligner/Sequence.html | 635 ----------
api/jaligner/SmithWatermanGotoh.html | 247 ----
api/jaligner/class-use/Alignment.html | 229 ----
api/jaligner/class-use/Cell.html | 136 ---
api/jaligner/class-use/Directions.html | 136 ---
api/jaligner/class-use/Markups.html | 136 ---
api/jaligner/class-use/Sequence.html | 242 ----
api/jaligner/class-use/SmithWatermanGotoh.html | 136 ---
api/jaligner/example/Example.html | 307 -----
api/jaligner/example/class-use/Example.html | 136 ---
api/jaligner/example/package-frame.html | 32 -
api/jaligner/example/package-summary.html | 168 ---
api/jaligner/example/package-tree.html | 145 ---
api/jaligner/example/package-use.html | 136 ---
api/jaligner/formats/CLUSTAL.html | 322 -----
api/jaligner/formats/FASTA.html | 302 -----
api/jaligner/formats/Format.html | 309 -----
api/jaligner/formats/FormatFactory.html | 301 -----
api/jaligner/formats/Pair.html | 278 -----
api/jaligner/formats/class-use/CLUSTAL.html | 136 ---
api/jaligner/formats/class-use/FASTA.html | 136 ---
api/jaligner/formats/class-use/Format.html | 220 ----
api/jaligner/formats/class-use/FormatFactory.html | 172 ---
api/jaligner/formats/class-use/Pair.html | 136 ---
api/jaligner/formats/package-frame.html | 40 -
api/jaligner/formats/package-summary.html | 183 ---
api/jaligner/formats/package-tree.html | 147 ---
api/jaligner/formats/package-use.html | 168 ---
api/jaligner/matrix/MatricesCompartor.html | 277 -----
api/jaligner/matrix/Matrix.html | 317 -----
api/jaligner/matrix/MatrixLoader.html | 342 ------
api/jaligner/matrix/MatrixLoaderException.html | 238 ----
.../matrix/class-use/MatricesCompartor.html | 136 ---
api/jaligner/matrix/class-use/Matrix.html | 237 ----
api/jaligner/matrix/class-use/MatrixLoader.html | 136 ---
.../matrix/class-use/MatrixLoaderException.html | 196 ----
api/jaligner/matrix/package-frame.html | 47 -
api/jaligner/matrix/package-summary.html | 189 ---
api/jaligner/matrix/package-tree.html | 152 ---
api/jaligner/matrix/package-use.html | 187 ---
api/jaligner/package-frame.html | 42 -
api/jaligner/package-summary.html | 188 ---
api/jaligner/package-tree.html | 146 ---
api/jaligner/package-use.html | 212 ----
api/jaligner/test/AlignmentScoreChecker.html | 260 -----
api/jaligner/test/RandomSequenceGenerator.html | 284 -----
.../test/class-use/AlignmentScoreChecker.html | 136 ---
.../test/class-use/RandomSequenceGenerator.html | 136 ---
api/jaligner/test/package-frame.html | 34 -
api/jaligner/test/package-summary.html | 171 ---
api/jaligner/test/package-tree.html | 145 ---
api/jaligner/test/package-use.html | 136 ---
api/jaligner/ui/AlignCommandLine.html | 260 -----
api/jaligner/ui/AlignWindow.html | 569 ---------
api/jaligner/ui/class-use/AlignCommandLine.html | 136 ---
api/jaligner/ui/class-use/AlignWindow.html | 136 ---
api/jaligner/ui/clipboard/ClipboardHandler.html | 248 ----
api/jaligner/ui/clipboard/ClipboardHandlerAWT.html | 293 -----
.../ui/clipboard/ClipboardHandlerFactory.html | 236 ----
.../ui/clipboard/ClipboardHandlerJNLP.html | 293 -----
api/jaligner/ui/clipboard/ClipboardListener.html | 225 ----
api/jaligner/ui/clipboard/ClipboardPoller.html | 314 -----
.../ui/clipboard/class-use/ClipboardHandler.html | 196 ----
.../clipboard/class-use/ClipboardHandlerAWT.html | 136 ---
.../class-use/ClipboardHandlerFactory.html | 136 ---
.../clipboard/class-use/ClipboardHandlerJNLP.html | 136 ---
.../ui/clipboard/class-use/ClipboardListener.html | 199 ----
.../ui/clipboard/class-use/ClipboardPoller.html | 136 ---
api/jaligner/ui/clipboard/package-frame.html | 51 -
api/jaligner/ui/clipboard/package-summary.html | 198 ----
api/jaligner/ui/clipboard/package-tree.html | 155 ---
api/jaligner/ui/clipboard/package-use.html | 188 ---
api/jaligner/ui/filechooser/FileChooser.html | 372 ------
.../ui/filechooser/FileChooserException.html | 242 ----
.../ui/filechooser/FileChooserFactory.html | 236 ----
api/jaligner/ui/filechooser/FileChooserJNLP.html | 325 ------
.../ui/filechooser/FileChooserTrusted.html | 325 ------
api/jaligner/ui/filechooser/NamedInputStream.html | 288 -----
.../ui/filechooser/class-use/FileChooser.html | 196 ----
.../class-use/FileChooserException.html | 215 ----
.../filechooser/class-use/FileChooserFactory.html | 136 ---
.../ui/filechooser/class-use/FileChooserJNLP.html | 136 ---
.../filechooser/class-use/FileChooserTrusted.html | 136 ---
.../ui/filechooser/class-use/NamedInputStream.html | 217 ----
api/jaligner/ui/filechooser/package-frame.html | 51 -
api/jaligner/ui/filechooser/package-summary.html | 197 ----
api/jaligner/ui/filechooser/package-tree.html | 153 ---
api/jaligner/ui/filechooser/package-use.html | 193 ---
api/jaligner/ui/images/ToolbarIcons.html | 441 -------
api/jaligner/ui/images/class-use/ToolbarIcons.html | 136 ---
api/jaligner/ui/images/package-frame.html | 32 -
api/jaligner/ui/images/package-summary.html | 167 ---
api/jaligner/ui/images/package-tree.html | 145 ---
api/jaligner/ui/images/package-use.html | 136 ---
api/jaligner/ui/logging/DocumentHandler.html | 310 -----
api/jaligner/ui/logging/RecordFormatter.html | 318 -----
.../ui/logging/class-use/DocumentHandler.html | 136 ---
.../ui/logging/class-use/RecordFormatter.html | 136 ---
api/jaligner/ui/logging/package-frame.html | 34 -
api/jaligner/ui/logging/package-summary.html | 171 ---
api/jaligner/ui/logging/package-tree.html | 149 ---
api/jaligner/ui/logging/package-use.html | 136 ---
api/jaligner/ui/package-frame.html | 34 -
api/jaligner/ui/package-summary.html | 171 ---
api/jaligner/ui/package-tree.html | 160 ---
api/jaligner/ui/package-use.html | 136 ---
api/jaligner/ui/util/PrintJobMointor.html | 235 ----
api/jaligner/ui/util/TextComponentUtil.html | 449 -------
.../ui/util/TextComponentUtilException.html | 238 ----
.../ui/util/class-use/PrintJobMointor.html | 136 ---
.../ui/util/class-use/TextComponentUtil.html | 136 ---
.../util/class-use/TextComponentUtilException.html | 197 ----
api/jaligner/ui/util/package-frame.html | 45 -
api/jaligner/ui/util/package-summary.html | 185 ---
api/jaligner/ui/util/package-tree.html | 150 ---
api/jaligner/ui/util/package-use.html | 162 ---
api/jaligner/util/Commons.html | 394 -------
api/jaligner/util/SequenceParser.html | 297 -----
api/jaligner/util/SequenceParserException.html | 238 ----
api/jaligner/util/class-use/Commons.html | 136 ---
api/jaligner/util/class-use/SequenceParser.html | 136 ---
.../util/class-use/SequenceParserException.html | 180 ---
api/jaligner/util/package-frame.html | 45 -
api/jaligner/util/package-summary.html | 185 ---
api/jaligner/util/package-tree.html | 150 ---
api/jaligner/util/package-use.html | 162 ---
api/overview-frame.html | 64 -
api/overview-summary.html | 193 ---
api/overview-tree.html | 186 ---
api/package-list | 12 -
api/packages.html | 37 -
api/resources/inherit.gif | Bin 57 -> 0 bytes
api/serialized-form.html | 1232 --------------------
build.properties | 16 +-
build.xml | 111 +-
jaligner.bat | 1 -
jaligner.css | 38 -
jaligner.jar | Bin 0 -> 182588 bytes
jaligner.sh | 1 -
src/NAligner/.cvsignore | 13 -
src/NAligner/Alignment.cs | 244 ----
src/NAligner/AssemblyInfo.cs | 79 --
src/NAligner/Cell.cs | 75 --
src/NAligner/Directions.cs | 38 -
src/NAligner/Markups.cs | 39 -
src/NAligner/Matrix.cs | 117 --
src/NAligner/NAligner.csproj | 189 ---
src/NAligner/NAligner.ndoc | 296 -----
src/NAligner/NamespaceDoc.cs | 36 -
src/NAligner/Sequence.cs | 283 -----
src/NAligner/SmithWatermanGotoh.cs | 416 -------
src/NAligner/formats/AlignmentFormatter.cs | 44 -
src/NAligner/formats/CLUSTAL.cs | 117 --
src/NAligner/formats/FASTA.cs | 70 --
src/NAligner/formats/FormatterFactory.cs | 72 --
src/NAligner/formats/NamespaceDoc.cs | 29 -
src/NAligner/formats/Pair.cs | 189 ---
src/NAligner/matrices/BLOSUM100 | 31 -
src/NAligner/matrices/BLOSUM30 | 31 -
src/NAligner/matrices/BLOSUM35 | 31 -
src/NAligner/matrices/BLOSUM40 | 31 -
src/NAligner/matrices/BLOSUM45 | 31 -
src/NAligner/matrices/BLOSUM50 | 31 -
src/NAligner/matrices/BLOSUM55 | 31 -
src/NAligner/matrices/BLOSUM60 | 31 -
src/NAligner/matrices/BLOSUM62 | 31 -
src/NAligner/matrices/BLOSUM65 | 31 -
src/NAligner/matrices/BLOSUM70 | 31 -
src/NAligner/matrices/BLOSUM75 | 31 -
src/NAligner/matrices/BLOSUM80 | 31 -
src/NAligner/matrices/BLOSUM85 | 31 -
src/NAligner/matrices/BLOSUM90 | 31 -
src/NAligner/matrices/BLOSUMN | 31 -
src/NAligner/matrices/DAYHOFF | 32 -
src/NAligner/matrices/EDNAFULL | 25 -
src/NAligner/matrices/GONNET | 26 -
src/NAligner/matrices/IDENTITY | 25 -
src/NAligner/matrices/MATCH | 25 -
src/NAligner/matrices/PAM10 | 34 -
src/NAligner/matrices/PAM100 | 34 -
src/NAligner/matrices/PAM110 | 34 -
src/NAligner/matrices/PAM120 | 34 -
src/NAligner/matrices/PAM130 | 34 -
src/NAligner/matrices/PAM140 | 34 -
src/NAligner/matrices/PAM150 | 34 -
src/NAligner/matrices/PAM160 | 34 -
src/NAligner/matrices/PAM170 | 34 -
src/NAligner/matrices/PAM180 | 34 -
src/NAligner/matrices/PAM190 | 34 -
src/NAligner/matrices/PAM20 | 34 -
src/NAligner/matrices/PAM200 | 34 -
src/NAligner/matrices/PAM210 | 34 -
src/NAligner/matrices/PAM220 | 34 -
src/NAligner/matrices/PAM230 | 34 -
src/NAligner/matrices/PAM240 | 34 -
src/NAligner/matrices/PAM250 | 34 -
src/NAligner/matrices/PAM260 | 34 -
src/NAligner/matrices/PAM270 | 34 -
src/NAligner/matrices/PAM280 | 34 -
src/NAligner/matrices/PAM290 | 34 -
src/NAligner/matrices/PAM30 | 34 -
src/NAligner/matrices/PAM300 | 34 -
src/NAligner/matrices/PAM310 | 34 -
src/NAligner/matrices/PAM320 | 34 -
src/NAligner/matrices/PAM330 | 34 -
src/NAligner/matrices/PAM340 | 34 -
src/NAligner/matrices/PAM350 | 34 -
src/NAligner/matrices/PAM360 | 34 -
src/NAligner/matrices/PAM370 | 34 -
src/NAligner/matrices/PAM380 | 34 -
src/NAligner/matrices/PAM390 | 34 -
src/NAligner/matrices/PAM40 | 34 -
src/NAligner/matrices/PAM400 | 34 -
src/NAligner/matrices/PAM410 | 34 -
src/NAligner/matrices/PAM420 | 34 -
src/NAligner/matrices/PAM430 | 34 -
src/NAligner/matrices/PAM440 | 34 -
src/NAligner/matrices/PAM450 | 34 -
src/NAligner/matrices/PAM460 | 34 -
src/NAligner/matrices/PAM470 | 34 -
src/NAligner/matrices/PAM480 | 34 -
src/NAligner/matrices/PAM490 | 34 -
src/NAligner/matrices/PAM50 | 34 -
src/NAligner/matrices/PAM500 | 34 -
src/NAligner/matrices/PAM60 | 34 -
src/NAligner/matrices/PAM70 | 34 -
src/NAligner/matrices/PAM80 | 34 -
src/NAligner/matrices/PAM90 | 34 -
src/NAligner/matrices/TEST1 | 25 -
src/NAligner/naligner.sln | 21 -
src/NAligner/util/AlphanumericComparator.cs | 71 --
src/NAligner/util/Commons.cs | 115 --
src/NAligner/util/NAlignerException.cs | 38 -
src/NAligner/util/Tokenizer.cs | 195 ----
src/jaligner/Alignment.java | 292 ++++-
src/jaligner/Cell.java | 4 +-
src/jaligner/Directions.java | 4 +-
src/jaligner/Markups.java | 4 +-
src/jaligner/NeedlemanWunsch.java | 302 +++++
src/jaligner/NeedlemanWunschGotoh.java | 427 +++++++
src/jaligner/Sequence.java | 272 +++--
src/jaligner/SmithWatermanGotoh.java | 79 +-
src/jaligner/TracebackNode.java | 97 ++
src/jaligner/example/NeedlemanWunschExample.java | 72 ++
.../example/NeedlemanWunschGotohExample.java | 91 ++
...Example.java => SmithWatermanGotohExample.java} | 10 +-
src/jaligner/example/package.html | 4 +-
src/jaligner/example/sequences/p53_human.fasta | 12 +-
src/jaligner/example/sequences/p53_mouse.fasta | 14 +-
src/jaligner/formats/CLUSTAL.java | 4 +-
src/jaligner/formats/FASTA.java | 4 +-
src/jaligner/formats/Format.java | 4 +-
src/jaligner/formats/FormatFactory.java | 8 +-
src/jaligner/formats/Pair.java | 6 +-
src/jaligner/formats/package.html | 4 +-
src/jaligner/matrix/MatricesCompartor.java | 11 +-
src/jaligner/matrix/Matrix.java | 95 +-
src/jaligner/matrix/MatrixGenerator.java | 59 +
src/jaligner/matrix/MatrixLoader.java | 170 +--
src/jaligner/matrix/MatrixLoaderException.java | 4 +-
src/jaligner/matrix/matrices/BLOSUM100 | 62 +-
src/jaligner/matrix/matrices/BLOSUM30 | 62 +-
src/jaligner/matrix/matrices/BLOSUM35 | 62 +-
src/jaligner/matrix/matrices/BLOSUM40 | 62 +-
src/jaligner/matrix/matrices/BLOSUM45 | 62 +-
src/jaligner/matrix/matrices/BLOSUM50 | 62 +-
src/jaligner/matrix/matrices/BLOSUM55 | 62 +-
src/jaligner/matrix/matrices/BLOSUM60 | 62 +-
src/jaligner/matrix/matrices/BLOSUM62 | 62 +-
src/jaligner/matrix/matrices/BLOSUM65 | 62 +-
src/jaligner/matrix/matrices/BLOSUM70 | 62 +-
src/jaligner/matrix/matrices/BLOSUM75 | 62 +-
src/jaligner/matrix/matrices/BLOSUM80 | 62 +-
src/jaligner/matrix/matrices/BLOSUM85 | 62 +-
src/jaligner/matrix/matrices/BLOSUM90 | 62 +-
src/jaligner/matrix/matrices/BLOSUMN | 62 +-
src/jaligner/matrix/matrices/DAYHOFF | 64 +-
src/jaligner/matrix/matrices/EDNAFULL | 50 +-
src/jaligner/matrix/matrices/GONNET | 52 +-
src/jaligner/matrix/matrices/IDENTITY | 50 +-
src/jaligner/matrix/matrices/MATCH | 50 +-
src/jaligner/matrix/matrices/PAM10 | 68 +-
src/jaligner/matrix/matrices/PAM100 | 68 +-
src/jaligner/matrix/matrices/PAM110 | 68 +-
src/jaligner/matrix/matrices/PAM120 | 68 +-
src/jaligner/matrix/matrices/PAM130 | 68 +-
src/jaligner/matrix/matrices/PAM140 | 68 +-
src/jaligner/matrix/matrices/PAM150 | 68 +-
src/jaligner/matrix/matrices/PAM160 | 68 +-
src/jaligner/matrix/matrices/PAM170 | 68 +-
src/jaligner/matrix/matrices/PAM180 | 68 +-
src/jaligner/matrix/matrices/PAM190 | 68 +-
src/jaligner/matrix/matrices/PAM20 | 68 +-
src/jaligner/matrix/matrices/PAM200 | 68 +-
src/jaligner/matrix/matrices/PAM210 | 68 +-
src/jaligner/matrix/matrices/PAM220 | 68 +-
src/jaligner/matrix/matrices/PAM230 | 68 +-
src/jaligner/matrix/matrices/PAM240 | 68 +-
src/jaligner/matrix/matrices/PAM250 | 68 +-
src/jaligner/matrix/matrices/PAM260 | 68 +-
src/jaligner/matrix/matrices/PAM270 | 68 +-
src/jaligner/matrix/matrices/PAM280 | 68 +-
src/jaligner/matrix/matrices/PAM290 | 68 +-
src/jaligner/matrix/matrices/PAM30 | 68 +-
src/jaligner/matrix/matrices/PAM300 | 68 +-
src/jaligner/matrix/matrices/PAM310 | 68 +-
src/jaligner/matrix/matrices/PAM320 | 68 +-
src/jaligner/matrix/matrices/PAM330 | 68 +-
src/jaligner/matrix/matrices/PAM340 | 68 +-
src/jaligner/matrix/matrices/PAM350 | 68 +-
src/jaligner/matrix/matrices/PAM360 | 68 +-
src/jaligner/matrix/matrices/PAM370 | 68 +-
src/jaligner/matrix/matrices/PAM380 | 68 +-
src/jaligner/matrix/matrices/PAM390 | 68 +-
src/jaligner/matrix/matrices/PAM40 | 68 +-
src/jaligner/matrix/matrices/PAM400 | 68 +-
src/jaligner/matrix/matrices/PAM410 | 68 +-
src/jaligner/matrix/matrices/PAM420 | 68 +-
src/jaligner/matrix/matrices/PAM430 | 68 +-
src/jaligner/matrix/matrices/PAM440 | 68 +-
src/jaligner/matrix/matrices/PAM450 | 68 +-
src/jaligner/matrix/matrices/PAM460 | 68 +-
src/jaligner/matrix/matrices/PAM470 | 68 +-
src/jaligner/matrix/matrices/PAM480 | 68 +-
src/jaligner/matrix/matrices/PAM490 | 68 +-
src/jaligner/matrix/matrices/PAM50 | 68 +-
src/jaligner/matrix/matrices/PAM500 | 68 +-
src/jaligner/matrix/matrices/PAM60 | 68 +-
src/jaligner/matrix/matrices/PAM70 | 68 +-
src/jaligner/matrix/matrices/PAM80 | 68 +-
src/jaligner/matrix/matrices/PAM90 | 68 +-
src/jaligner/matrix/package.html | 4 +-
src/jaligner/package.html | 4 +-
src/jaligner/test/AlignmentScoreChecker.java | 131 ---
src/jaligner/test/NeedlemanWunschGotohTester.java | 130 +++
src/jaligner/test/NeedlemanWunschTester.java | 128 ++
src/jaligner/test/RandomSequenceGenerator.java | 30 +-
src/jaligner/test/SmithWatermanGotohTester.java | 130 +++
src/jaligner/test/package.html | 2 +-
src/jaligner/ui/AlignCommandLine.java | 6 +-
src/jaligner/ui/AlignWindow.form | 51 +-
src/jaligner/ui/AlignWindow.java | 146 +--
src/jaligner/ui/clipboard/ClipboardHandler.java | 4 +-
src/jaligner/ui/clipboard/ClipboardHandlerAWT.java | 4 +-
.../ui/clipboard/ClipboardHandlerFactory.java | 4 +-
.../ui/clipboard/ClipboardHandlerJNLP.java | 4 +-
src/jaligner/ui/clipboard/ClipboardListener.java | 4 +-
src/jaligner/ui/clipboard/ClipboardPoller.java | 4 +-
src/jaligner/ui/clipboard/package.html | 4 +-
src/jaligner/ui/filechooser/FileChooser.java | 4 +-
.../ui/filechooser/FileChooserException.java | 4 +-
.../ui/filechooser/FileChooserFactory.java | 4 +-
src/jaligner/ui/filechooser/FileChooserJNLP.java | 4 +-
.../ui/filechooser/FileChooserTrusted.java | 4 +-
src/jaligner/ui/filechooser/NamedInputStream.java | 4 +-
src/jaligner/ui/filechooser/package.html | 4 +-
src/jaligner/ui/images/ToolbarIcons.java | 5 +-
src/jaligner/ui/images/package.html | 4 +-
src/jaligner/ui/logging/DocumentHandler.java | 4 +-
src/jaligner/ui/logging/RecordFormatter.java | 4 +-
src/jaligner/ui/logging/package.html | 4 +-
src/jaligner/ui/package.html | 4 +-
src/jaligner/ui/util/PrintJobMointor.java | 4 +-
src/jaligner/ui/util/TextComponentUtil.java | 4 +-
.../ui/util/TextComponentUtilException.java | 4 +-
src/jaligner/ui/util/package.html | 4 +-
src/jaligner/util/Commons.java | 14 +-
src/jaligner/util/SequenceParser.java | 10 +-
src/jaligner/util/SequenceParserException.java | 4 +-
src/jaligner/util/package.html | 4 +-
384 files changed, 4649 insertions(+), 38093 deletions(-)
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