[med-svn] [beast2-mcmc] branch master updated (7975391 -> 50ded24)

[Andreas Tille]

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

      from  7975391   d/watch: stop reporting pre-releases
       new  37327ec   Imported Upstream version 2.4.3+dfsg
       new  7d77a98   Merge tag 'upstream/2.4.3+dfsg'
       new  450ebc2   New upstream version
       new  50ded24   Upload to unstable

The 4 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 +-
 debian/changelog                                   |   5 +-
 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 ++++++
 69 files changed, 1957 insertions(+), 552 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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