[med-svn] [beast2-mcmc] 03/08: Merge tag 'upstream/2.4.1+dfsg'

[Andreas Tille]

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

commit 68894e9791149ce2b57e74f897392107a178bb63
Merge: c4a077c 531b3f5
Author: Andreas Tille <tille at debian.org>
Date:   Wed May 4 11:09:49 2016 +0200

    Merge tag 'upstream/2.4.1+dfsg'
    
    Upstream version 2.4.1+dfsg

 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(-)

diff --cc build.xml
index 2a42ff8,ba0e4f1..ee3e7b9
--- a/build.xml
+++ b/build.xml
@@@ -162,9 -161,9 +162,9 @@@
          <mkdir dir="${release_dir}/package/lib" />
          <copy file="${dist}/beast.src.jar" todir="${release_dir}/package/"/>
          <copy file="${dist}/beast.jar" todir="${release_dir}/package/lib/"/>
 -        <copy file="../beast2/version.xml" todir="${release_dir}/package/"/>
 +        <copy file="version.xml" todir="${release_dir}/package/"/>
  
-         <jar jarfile="${release_dir}/package/beast.package.${version}.zip">
+         <jar jarfile="${release_dir}/package/BEAST.addon.v${version}.zip">
              <fileset dir="${release_dir}/package">
                  <include name="version.xml" />
                  <include name="lib/beast.jar" />

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