[med-svn] [beast2-mcmc] branch master updated (6a219ca -> a8f0d6f)

[Andreas Tille]

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tille pushed a change to branch master
in repository beast2-mcmc.

      from  6a219ca   Package builds without binary jars
      adds  8233c32   Imported Upstream version 2.3.1+dfsg
       new  5067c09   Imported Upstream version 2.3.2+dfsg
       new  87e54a0   Merge tag 'upstream/2.3.2+dfsg'
       new  a8f0d6f   New upstream version

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Summary of changes:
 build.xml                                          |   4 +-
 debian/changelog                                   |   4 +-
 .../figures/BEAUti_DataPartitions.png              | Bin 85593 -> 44401 bytes
 doc/tutorials/STARBEAST/StarBEAST_tutorial.bib     |  20 +++
 doc/tutorials/STARBEAST/StarBEAST_tutorial.tex     |  72 +++++++-
 doc/tutorials/STARBEAST/figures/BEAST.png          | Bin 98804 -> 101788 bytes
 release/Linux/bin/{densitree => loganalyser}       |   2 +-
 release/common/README.txt                          |  16 +-
 release/common/VERSION HISTORY.txt                 |  32 +++-
 src/beast/app/BEASTVersion.java                    |   4 +-
 src/beast/app/beastapp/BeastMain.java              |   9 +-
 src/beast/app/beauti/BeautiAlignmentProvider.java  |   9 +-
 src/beast/app/beauti/BeautiDoc.java                |  13 +-
 src/beast/app/beauti/BeautiSubTemplate.java        |  22 +++
 src/beast/app/beauti/PriorInputEditor.java         |  52 ++++--
 src/beast/app/beauti/SiteModelInputEditor.java     |   3 +
 src/beast/app/beauti/TaxonSetInputEditor.java      |   4 +
 src/beast/app/beauti/TipDatesInputEditor.java      |  52 ++++--
 ...nputEditor.java => IntegerListInputEditor.java} |  51 ++++--
 src/beast/app/draw/ParameterInputEditor.java       |  27 +--
 src/beast/app/tools/LogCombiner.java               |  10 ++
 src/beast/app/tools/LogCombinerDialog.java         |   2 +-
 src/beast/core/Logger.java                         |   2 +
 src/beast/core/MCMC.java                           |   4 +-
 src/beast/core/State.java                          |   2 +-
 src/beast/evolution/operators/NodeReheight.java    |   9 +
 src/beast/evolution/operators/SubtreeSlide.java    |  23 ++-
 src/beast/evolution/operators/TreeOperator.java    |   4 +-
 src/beast/evolution/speciation/RandomGeneTree.java |   5 +-
 .../GeneralSubstitutionModel.java                  |  13 +-
 src/beast/evolution/tree/RandomTree.java           | 192 +++++++++++++++------
 src/beast/evolution/tree/TreeInterface.java        |   2 +-
 src/beast/math/distributions/MRCAPrior.java        | 121 ++++++++++---
 src/beast/math/statistic/RPNcalculator.java        |  13 ++
 src/beast/util/AddOnManager.java                   |  80 ++++++---
 src/beast/util/LogAnalyser.java                    | 120 +++++++++++--
 src/beast/util/TreeParser.java                     |  22 ++-
 src/beast/util/XMLProducer.java                    |   2 +-
 src/test/beast/util/TreeParserTest.java            |   3 +-
 39 files changed, 790 insertions(+), 235 deletions(-)
 copy release/Linux/bin/{densitree => loganalyser} (93%)
 copy src/beast/app/draw/{DoubleListInputEditor.java => IntegerListInputEditor.java} (93%)

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