[med-svn] [beast2-mcmc] branch upstream updated (0110375 -> 531b3f5)

[Andreas Tille]

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

      from  0110375   Imported Upstream version 2.4.1pre+dfsg
       new  531b3f5   Imported Upstream version 2.4.1+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                                          |  26 ++-
 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 +-
 38 files changed, 942 insertions(+), 328 deletions(-)
 create mode 100644 src/beast/app/BEASTVersion2.java

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