[med-svn] [beast2-mcmc] 02/03: Merge tag 'upstream/2.3.2+dfsg'

[Andreas Tille]

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

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

commit 87e54a07cfc76788ef37ae20c6e7aab010513faa
Merge: 6a219ca 5067c09
Author: Andreas Tille <tille at debian.org>
Date:   Mon Nov 30 22:06:28 2015 +0100

    Merge tag 'upstream/2.3.2+dfsg'
    
    Upstream version 2.3.2+dfsg

 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
 release/Linux/bin/loganalyser                      |  33 ++
 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 ++-
 src/beast/app/draw/IntegerListInputEditor.java     | 419 +++++++++++++++++++++
 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 +-
 38 files changed, 1207 insertions(+), 213 deletions(-)

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/beast2-mcmc.git