[med-svn] [proalign] 07/10: Updated version 0.603 from 'upstream/0.603'

[Andreas Tille]

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tille pushed a commit to branch master
in repository proalign.

commit 0cc0c45a39d40f24b6c201b4cdc064ad4ded9143
Merge: 3f34d9c 6f89e7c
Author: Andreas Tille <tille at debian.org>
Date:   Thu Nov 16 14:24:55 2017 +0100

    Updated version 0.603 from 'upstream/0.603'
    
    with Debian dir 31484bae0befdaba7162d6aab392d580a0796ffd

 AlignmentLoop.java        |  355 ++++++++++++
 AlignmentNode.java        | 1026 +++++++++++++++++++++++++++++++++
 CheckSequence.java        |   81 +++
 CheckTrailing.java        |   55 ++
 CheckTreeAndData.java     |   46 ++
 EstimateFrequencies.java  |   61 ++
 InFile.java               |   16 +
 MinimumProbWindow.java    |   87 +++
 NeighborJoining.java      |  178 ++++++
 NicePrint.java            |   50 ++
 OpenDialog.java           |   53 ++
 OpenFileChooser.java      |   55 ++
 OpenFolderChooser.java    |   52 ++
 OutFile.java              |   20 +
 OutOfMemoryException.java |   19 +
 PAFileFilter.java         |   46 ++
 ParameterEstimates.java   |  195 +++++++
 PixelRule.java            |  102 ++++
 PrintCurve.java           |   76 +++
 PrintData.java            |  382 +++++++++++++
 PrintMinimumCurve.java    |   73 +++
 PrintNames.java           |  250 +++++++++
 PrintTree.java            |  194 +++++++
 ProAlign.java             |  231 ++++++++
 PwAlignment.java          |  345 ++++++++++++
 PwAlignmentLoop.java      |  273 +++++++++
 PwSubstitutionMatrix.java |  143 +++++
 QualityWindow.java        |   96 ++++
 ReadArguments.java        |  232 ++++++++
 ResultWindow.java         | 1374 +++++++++++++++++++++++++++++++++++++++++++++
 Rule.java                 |  117 ++++
 RunClustalw.java          |  186 ++++++
 RunCommandLine.java       |  209 +++++++
 RunMultiple.java          |  103 ++++
 SampleAlignments.java     |  446 +++++++++++++++
 SampleLoop.java           |  146 +++++
 SaveData.java             |  854 ++++++++++++++++++++++++++++
 SequenceReader.java       |  641 +++++++++++++++++++++
 SetParameters.java        |  881 +++++++++++++++++++++++++++++
 SubstitutionModel.java    |  511 +++++++++++++++++
 TraceBackPath.java        |  518 +++++++++++++++++
 TransformLog.java         |   36 ++
 TreeNode.java             |  317 +++++++++++
 TreeReader.java           |  226 ++++++++
 UserSettings.java         |   85 +++
 Viterbi.java              |  354 ++++++++++++
 WinClustalw.java          |   55 ++
 47 files changed, 11851 insertions(+)

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