[med-svn] [beast2-mcmc] branch upstream updated (4a468e4 -> 37327ec)

[Andreas Tille]

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

      from  4a468e4   Imported Upstream version 2.4.2+dfsg
       new  37327ec   Imported Upstream version 2.4.3+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 +-
 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(-)
 create mode 100644 src/beast/app/beauti/AlignmentImporter.java
 create mode 100644 src/beast/app/beauti/PriorProvider.java
 create mode 100644 src/beast/evolution/tree/TreeStatLogger.java
 create mode 100644 src/test/beast/core/util/SumTest.java
 create mode 100644 src/test/beast/evolution/datatype/IntegerDataTest.java
 create mode 100644 src/test/beast/evolution/tree/TraitSetTest.java
 create mode 100644 src/test/beast/math/distributions/InvGammaTest.java
 create mode 100644 src/test/beast/math/distributions/NormalDistributionTest.java

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