[med-svn] [beast2-mcmc] branch master updated (79965b3 -> e207f5f)

[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  79965b3   New upstream version
       new  c4a077c   Fix watch file
       new  531b3f5   Imported Upstream version 2.4.1+dfsg
       new  68894e9   Merge tag 'upstream/2.4.1+dfsg'
       new  cd58440   cme fix dpkg-control
       new  f283606   Revert wrong change in build.xml (due to remaining quilt patches)
       new  d921772   Refresh patches
       new  206e8ff   json lib issue is fixed
       new  e207f5f   Add ITP

The 8 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                                          |  56 +++--
 debian/changelog                                   |   7 +-
 debian/control                                     |   4 +-
 debian/patches/fix_classpath_in_build_xml.patch    |   2 +-
 debian/patches/remove_appbundler.patch             |   2 +-
 debian/watch                                       |   2 +-
 examples/nexus/primate-mtDNA.nex                   |   2 +-
 release/Linux/bin/beast                            |  11 +-
 release/common/README.txt                          |   6 +-
 release/common/VERSION HISTORY.txt                 |  18 +-
 src/beast/app/BEASTVersion.java                    |   4 +-
 src/beast/app/BEASTVersion2.java                   |  36 ++++
 src/beast/app/BeastMCMC.java                       |   2 +-
 src/beast/app/DocMaker.java                        |   2 +-
 src/beast/app/beastapp/BeastLauncher.java          | 121 +++++++++--
 src/beast/app/beastapp/BeastMain.java              |  46 ++---
 src/beast/app/beauti/Beauti.java                   |  79 +++++---
 src/beast/app/beauti/BeautiAlignmentProvider.java  |  20 +-
 src/beast/app/beauti/BeautiConfig.java             |   9 +
 src/beast/app/beauti/BeautiDoc.java                |  61 ++++++
 src/beast/app/beauti/BeautiLauncher.java           |   3 +-
 src/beast/app/beauti/MRCAPriorInputEditor.java     |  11 +-
 src/beast/app/beauti/PriorListInputEditor.java     |  13 ++
 src/beast/app/beauti/TaxonSetInputEditor.java      |  93 +++++----
 src/beast/app/tools/EBSPAnalyser.java              |   4 +-
 src/beast/app/tools/LogCombiner.java               |   4 +-
 src/beast/app/treeannotator/TreeAnnotator.java     |  10 +-
 src/beast/app/util/Utils.java                      |  62 ------
 src/beast/app/util/Utils6.java                     |  68 +++++++
 src/beast/core/MCMC.java                           |   7 +-
 .../evolution/alignment/FilteredAlignment.java     |  27 ++-
 .../evolution/likelihood/BeagleTreeLikelihood.java |  44 ++--
 src/beast/evolution/operators/Exchange.java        |  95 +++------
 .../evolution/substitutionmodel/Frequencies.java   |   2 +-
 src/beast/evolution/tree/Node.java                 |   2 +-
 src/beast/util/AddOnManager.java                   |   4 +-
 src/beast/util/JSONProducer.java                   |   4 +-
 src/beast/util/LogAnalyser.java                    |  39 ++--
 src/beast/util/LogComparator.java                  |   4 +-
 src/beast/util/NexusParser.java                    | 225 ++++++++++++++++++---
 .../evolution/alignment/FilteredAlignmentTest.java |  20 ++
 src/test/beast/integration/XMLProducerTest.java    |  84 +++++++-
 version.xml                                        |   2 +-
 43 files changed, 965 insertions(+), 352 deletions(-)
 create mode 100644 src/beast/app/BEASTVersion2.java

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