[med-svn] [beast2-mcmc] 02/06: Merge tag 'upstream/2.4.4+dfsg'

[Andreas Tille]

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

commit 6c9151abe0b5c049fdb1ec2643559ae0d198a62b
Merge: 50ded24 ef83e24
Author: Andreas Tille <tille at debian.org>
Date:   Fri Dec 2 11:17:00 2016 +0100

    Merge tag 'upstream/2.4.4+dfsg'
    
    Upstream version 2.4.4+dfsg

 build.xml                                          |   4 +-
 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 +-
 29 files changed, 550 insertions(+), 376 deletions(-)

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