[med-svn] [beast2-mcmc] 02/04: Merge tag 'upstream/2.4.3+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 7d77a988a27d9b8a4fadf83bddac0f4876eceba3
Merge: 7975391 37327ec
Author: Andreas Tille <tille at debian.org>
Date:   Tue Aug 30 08:31:11 2016 +0200

    Merge tag 'upstream/2.4.3+dfsg'
    
    Upstream version 2.4.3+dfsg

 build.xml                                          |   4 +-
 release/common/README.txt                          |   4 +-
 release/common/VERSION HISTORY.txt                 |  27 +-
 src/beast/app/BEASTVersion.java                    |   2 +-
 src/beast/app/BEASTVersion2.java                   |   2 +-
 src/beast/app/BeastMCMC.java                       |   8 +-
 src/beast/app/DocMaker.java                        |   3 +-
 src/beast/app/beastapp/BeastLauncher.java          |   2 +-
 src/beast/app/beastapp/BeastMain.java              |   2 +
 src/beast/app/beauti/AlignmentImporter.java        |  54 +++
 src/beast/app/beauti/AlignmentListInputEditor.java |   8 +-
 src/beast/app/beauti/Beauti.java                   |  12 +-
 src/beast/app/beauti/BeautiAlignmentProvider.java  | 468 ++++++++++++---------
 src/beast/app/beauti/BeautiDoc.java                |   1 +
 src/beast/app/beauti/GuessPatternDialog.java       |   5 +-
 src/beast/app/beauti/JPackageDialog.java           | 166 +++++++-
 src/beast/app/beauti/JPackageRepositoryDialog.java |   2 +
 src/beast/app/beauti/MRCAPriorInputEditor.java     | 101 +++++
 src/beast/app/beauti/OperatorListInputEditor.java  |   3 +-
 .../beauti/ParametricDistributionInputEditor.java  |  19 +-
 src/beast/app/beauti/PriorInputEditor.java         |   4 +-
 src/beast/app/beauti/PriorListInputEditor.java     | 173 +++++---
 src/beast/app/beauti/PriorProvider.java            |  24 ++
 src/beast/app/beauti/TaxonSetDialog.java           |   6 +-
 src/beast/app/beauti/TaxonSetInputEditor.java      |   9 +-
 src/beast/app/beauti/TipDatesInputEditor.java      | 159 -------
 src/beast/app/draw/BEASTObjectInputEditor.java     |   3 +-
 src/beast/app/draw/DoubleListInputEditor.java      |   7 +-
 src/beast/app/draw/EnumInputEditor.java            |   4 +
 src/beast/app/draw/InputEditor.java                |   2 +-
 src/beast/app/draw/IntegerListInputEditor.java     |   3 +-
 src/beast/app/tools/LogCombiner.java               |   8 +-
 src/beast/app/treeannotator/TreeAnnotator.java     |   2 +
 src/beast/app/util/Utils.java                      |   2 +-
 src/beast/core/BEASTInterface.java                 |  38 +-
 src/beast/core/Citation.java                       |  18 +-
 src/beast/core/Logger.java                         |   2 +-
 src/beast/core/parameter/Parameter.java            |   2 +-
 src/beast/core/util/Sum.java                       |  32 +-
 src/beast/evolution/alignment/TaxonSet.java        |   4 +-
 src/beast/evolution/datatype/IntegerData.java      |   7 +
 .../likelihood/ThreadedTreeLikelihood.java         |   8 +-
 .../evolution/speciation/CalibratedYuleModel.java  |   1 +
 src/beast/evolution/tree/RandomTree.java           |  16 +-
 src/beast/evolution/tree/TraitSet.java             |   3 +-
 src/beast/evolution/tree/Tree.java                 |   1 +
 src/beast/evolution/tree/TreeHeightLogger.java     |   7 +-
 src/beast/evolution/tree/TreeStatLogger.java       |  80 ++++
 .../tree/coalescent/ExponentialGrowth.java         |   5 +-
 .../evolution/tree/coalescent/TreeIntervals.java   |  21 +-
 src/beast/math/distributions/Gamma.java            |  42 +-
 src/beast/math/distributions/MRCAPrior.java        |   2 +-
 src/beast/util/AddOnManager.java                   |  89 +++-
 src/beast/util/Package.java                        |  16 +-
 src/beast/util/TreeParser.java                     |  15 +-
 src/beast/util/XMLParser.java                      |  37 +-
 src/beast/util/XMLParserUtils.java                 |  19 +-
 src/beast/util/XMLProducer.java                    |  26 +-
 .../beast/app/beauti/BeautiRateTutorialTest.java   |   5 +-
 src/test/beast/core/BEASTInterfaceTest.java        |  16 +
 src/test/beast/core/util/SumTest.java              |  63 +++
 .../beast/evolution/datatype/IntegerDataTest.java  |  32 ++
 src/test/beast/evolution/tree/TraitSetTest.java    |  78 ++++
 src/test/beast/math/distributions/GammaTest.java   | 101 +++++
 .../beast/math/distributions/InvGammaTest.java     | 128 ++++++
 .../LogNormalDistributionModelTest.java            | 140 +++++-
 .../beast/math/distributions/MRCAPriorTest.java    |  19 +
 .../math/distributions/NormalDistributionTest.java | 132 ++++++
 68 files changed, 1954 insertions(+), 550 deletions(-)

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