[med-svn] [jaligner] branch master updated (a3ab0ed -> 9689d64)

Michael Crusoe misterc-guest at moszumanska.debian.org
Mon Feb 16 06:35:28 UTC 2015


This is an automated email from the git hooks/post-receive script.

misterc-guest pushed a change to branch master
in repository jaligner.

      from  a3ab0ed   add ITP #; relax dependencies; add license info
       new  2b5d5aa   Imported Upstream version 1.0
       new  6485aaa   Imported Upstream version 1.0
       new  4321b41   Merge tag 'upstream/1.0'
       new  9689d64   point to GitHub release

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:
 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 ---
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 api/jaligner/ui/filechooser/package-frame.html     |   51 -
 api/jaligner/ui/filechooser/package-summary.html   |  197 ----
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 api/jaligner/ui/images/ToolbarIcons.html           |  441 -------
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 api/jaligner/ui/logging/DocumentHandler.html       |  310 -----
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 .../ui/logging/class-use/DocumentHandler.html      |  136 ---
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 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 +-
 debian/copyright                                   |    2 +-
 debian/watch                                       |    3 +
 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 -
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 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 -
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 src/NAligner/matrices/PAM160                       |   34 -
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 src/NAligner/matrices/PAM200                       |   34 -
 src/NAligner/matrices/PAM210                       |   34 -
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 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 +-
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 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 +-
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 src/jaligner/matrix/matrices/PAM310                |   68 +-
 src/jaligner/matrix/matrices/PAM320                |   68 +-
 src/jaligner/matrix/matrices/PAM330                |   68 +-
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 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 +++
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 src/jaligner/ui/AlignCommandLine.java              |    6 +-
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 src/jaligner/ui/AlignWindow.java                   |  146 +--
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 src/jaligner/ui/clipboard/ClipboardListener.java   |    4 +-
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 .../ui/filechooser/FileChooserException.java       |    4 +-
 .../ui/filechooser/FileChooserFactory.java         |    4 +-
 src/jaligner/ui/filechooser/FileChooserJNLP.java   |    4 +-
 .../ui/filechooser/FileChooserTrusted.java         |    4 +-
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 src/jaligner/util/SequenceParser.java              |   10 +-
 src/jaligner/util/SequenceParserException.java     |    4 +-
 src/jaligner/util/package.html                     |    4 +-
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