[med-svn] [beast2-mcmc] branch master updated (50ded24 -> 3e5c35b)

[Andreas Tille]

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

      from  50ded24   Upload to unstable
       new  ef83e24   Imported Upstream version 2.4.4+dfsg
       new  6c9151a   Merge tag 'upstream/2.4.4+dfsg'
       new  b3560c8   New upstream version
       new  e0d9849   debhelper 10
       new  134a580   d/watch: version=4
       new  3e5c35b   Upload to unstable

The 6 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                                   |   8 +
 debian/compat                                      |   2 +-
 debian/control                                     |   2 +-
 debian/watch                                       |   2 +-
 release/common/README.txt                          |   4 +-
 release/common/VERSION HISTORY.txt                 |  15 +-
 src/beast/app/BEASTVersion.java                    |   2 +-
 src/beast/app/BEASTVersion2.java                   |   2 +-
 src/beast/app/beastapp/BeastLauncher.java          |   2 +-
 src/beast/app/beauti/AlignmentListInputEditor.java |  50 +----
 src/beast/app/beauti/BeautiAlignmentProvider.java  |   4 +
 src/beast/app/beauti/BeautiConfig.java             |   7 +-
 src/beast/app/beauti/BeautiDoc.java                |  77 +++++---
 src/beast/app/beauti/GuessPatternDialog.java       |  52 ++++--
 src/beast/app/beauti/MRCAPriorInputEditor.java     |   3 +
 src/beast/app/treeannotator/TreeAnnotator.java     | 201 ++++++++++++---------
 src/beast/app/treeannotator/TreeSetParser.java     |   3 +-
 src/beast/app/util/Utils6.java                     |  12 +-
 src/beast/evolution/operators/NodeReheight.java    |   2 +-
 src/beast/evolution/tree/Tree.java                 |  56 +++---
 .../evolution/tree/TreeWithMetaDataLogger.java     |  36 ++--
 src/beast/util/AddOnManager.java                   | 116 ++++++------
 src/beast/util/NexusParser.java                    |  32 ++--
 src/beast/util/TreeParser.java                     |  34 ++--
 src/beast/util/treeparser/Newick.g4                |   5 +-
 src/beast/util/treeparser/NewickBaseVisitor.java   |   2 +-
 src/beast/util/treeparser/NewickLexer.java         |  92 ++++++----
 src/beast/util/treeparser/NewickParser.java        |  27 +--
 src/beast/util/treeparser/NewickVisitor.java       |   2 +-
 .../evolution/alignment/FilteredAlignmentTest.java |  68 ++++++-
 src/test/beast/util/TreeParserTest.java            |  14 ++
 version.xml                                        |   2 +-
 33 files changed, 561 insertions(+), 379 deletions(-)

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