[med-svn] [beast2-mcmc] branch master updated (f34014e -> 1cca84e)

[Andreas Tille]

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

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

      from  f34014e   Respect proxy settings in beauti2 script
       new  4a468e4   Imported Upstream version 2.4.2+dfsg
       new  8926a1b   Merge tag 'upstream/2.4.2+dfsg'
       new  7285835   New upstream version
       new  1cca84e   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                                          |   2 +-
 debian/changelog                                   |   5 +-
 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 +-
 53 files changed, 1079 insertions(+), 275 deletions(-)
 create mode 100644 src/test/beast/app/tools/LogCombinerTest.java
 create mode 100644 src/test/beast/core/LoggerTest.java
 create mode 100644 src/test/beast/evolution/substmodel/BinaryCovarionModelTest.java

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