[med-svn] [beast2-mcmc] branch upstream updated (37327ec -> ef83e24)

[Andreas Tille]

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

      from  37327ec   Imported Upstream version 2.4.3+dfsg
       new  ef83e24   Imported Upstream version 2.4.4+dfsg

The 1 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 +-
 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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