[med-svn] [beast2-mcmc] 02/04: Merge tag 'upstream/2.4.2+dfsg'

[Andreas Tille]

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

commit 8926a1b42997385d9df931de4c92fa615d24180b
Merge: f34014e 4a468e4
Author: Andreas Tille <tille at debian.org>
Date:   Mon Jul 18 13:55:51 2016 +0200

    Merge tag 'upstream/2.4.2+dfsg'
    
    Upstream version 2.4.2+dfsg

 build.xml                                          |   2 +-
 release/common/README.txt                          |   4 +-
 release/common/VERSION HISTORY.txt                 |  17 +-
 src/beast/app/BEASTVersion.java                    |   4 +-
 src/beast/app/BEASTVersion2.java                   |   4 +-
 src/beast/app/BeastMCMC.java                       |   4 +-
 src/beast/app/ModelBuilder.java                    |   4 +-
 src/beast/app/beastapp/BeastDialog.java            |   4 +-
 src/beast/app/beastapp/BeastLauncher.java          |   2 +-
 src/beast/app/beastapp/BeastMain.java              |  78 +++++---
 src/beast/app/beauti/AlignmentListInputEditor.java |   4 +-
 src/beast/app/beauti/AlignmentViewer.java          |   6 +-
 src/beast/app/beauti/Beauti.java                   |  47 ++++-
 src/beast/app/beauti/BeautiDoc.java                |   3 +
 src/beast/app/beauti/BeautiSubTemplate.java        |   2 +-
 src/beast/app/beauti/JPackageDialog.java           |   3 +-
 src/beast/app/beauti/MRCAPriorInputEditor.java     |   4 +-
 .../beauti/ParametricDistributionInputEditor.java  |   8 +-
 src/beast/app/beauti/PriorInputEditor.java         |  15 +-
 src/beast/app/beauti/TaxonSetDialog.java           |   4 +-
 src/beast/app/beauti/TipDatesInputEditor.java      |   5 +-
 .../app/beauti/TreeDistributionInputEditor.java    |   8 +-
 src/beast/app/draw/BEASTObjectShape.java           |   3 +-
 src/beast/app/draw/HelpBrowser.java                |   4 +-
 src/beast/app/draw/InputEditor.java                |  15 +-
 src/beast/app/draw/IntegerListInputEditor.java     |   9 +-
 src/beast/app/draw/ModelBuilder.java               |   7 +-
 src/beast/app/tools/AppStore.java                  |   5 +-
 src/beast/app/tools/EBSPAnalyser.java              |   8 +-
 src/beast/app/tools/LogCombiner.java               | 218 +++++++++++++++------
 src/beast/app/tools/LogCombinerDialog.java         |   3 +-
 src/beast/app/treeannotator/TreeAnnotator.java     |  36 ++--
 src/beast/app/util/Utils.java                      |  99 +++++++++-
 src/beast/core/BEASTInterface.java                 |   6 +
 src/beast/core/BEASTObject.java                    |   5 +-
 src/beast/core/Logger.java                         |  57 +++---
 src/beast/core/MCMC.java                           |  18 +-
 .../evolution/speciation/CalibratedYuleModel.java  |  22 ++-
 .../evolution/speciation/SpeciesTreePrior.java     |   4 +-
 .../substitutionmodel/BinaryCovarion.java          |  23 ++-
 src/beast/evolution/tree/Node.java                 |   2 +-
 src/beast/evolution/tree/RandomTree.java           |  21 +-
 src/beast/evolution/tree/Tree.java                 |   3 +
 src/beast/util/AddOnManager.java                   |  62 ++----
 src/beast/util/FrequencySet.java                   |   3 +
 src/beast/util/NexusParser.java                    |   2 +-
 src/beast/util/XMLProducer.java                    |  24 ++-
 src/test/beast/app/tools/LogCombinerTest.java      | 197 +++++++++++++++++++
 src/test/beast/core/LoggerTest.java                | 129 ++++++++++++
 .../substmodel/BinaryCovarionModelTest.java        | 125 ++++++++++++
 templates/ClockModels.xml                          |   5 +-
 version.xml                                        |   2 +-
 52 files changed, 1076 insertions(+), 273 deletions(-)

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