[med-svn] [beast2-mcmc] branch upstream updated (8233c32 -> 5067c09)

[Andreas Tille]

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

      from  8233c32   Imported Upstream version 2.3.1+dfsg
       new  5067c09   Imported Upstream version 2.3.2+dfsg

The 1 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:
 build.xml                                          |   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
 lib/antlr-runtime-4.5.jar                          | Bin 374042 -> 0 bytes
 release/Linux/bin/{densitree => loganalyser}       |   2 +-
 release/common/README.txt                          |  16 +-
 release/common/VERSION HISTORY.txt                 |  32 +++-
 release/common/tools/DensiTree.jar                 | Bin 2325714 -> 0 bytes
 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 +-
 40 files changed, 788 insertions(+), 233 deletions(-)
 delete mode 100644 lib/antlr-runtime-4.5.jar
 copy release/Linux/bin/{densitree => loganalyser} (93%)
 delete mode 100644 release/common/tools/DensiTree.jar
 copy src/beast/app/draw/{DoubleListInputEditor.java => IntegerListInputEditor.java} (93%)

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