[med-svn] [beast2-mcmc] 07/08: Merge tag 'upstream/2.4.1pre+dfsg'

[Andreas Tille]

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

commit 0924a2a7bf928b66b9f939705ef0e49d633b51c6
Merge: b2b36b7 0110375
Author: Andreas Tille <tille at debian.org>
Date:   Wed May 4 09:44:13 2016 +0200

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

 build.xml                                          |  23 +++--
 examples/testUCLNclock.json                        |   2 +-
 release/Linux/bin/beast                            |  19 +++-
 release/Mac/install.png                            | Bin 17518 -> 17128 bytes
 release/Windows/AppStore_launch4j.xml              |   2 +-
 release/Windows/BEAST_launch4j.xml                 |   2 +-
 release/Windows/BEAUti_launch4j.xml                |   2 +-
 release/Windows/LogCombiner_launch4j.xml           |   2 +-
 release/Windows/TreeAnnotator_launch4j.xml         |   2 +-
 release/common/README.txt                          |   6 +-
 release/common/VERSION HISTORY.txt                 |  29 +++++-
 src/beast/app/BEASTVersion.java                    |   4 +-
 src/beast/app/beastapp/BeastLauncher.java          |  56 ++++++++---
 src/beast/app/beastapp/BeastMain.java              |  10 +-
 src/beast/app/beauti/AlignmentListInputEditor.java |  52 +++++-----
 src/beast/app/beauti/Beauti.java                   |  47 ++++++---
 src/beast/app/beauti/BeautiAlignmentProvider.java  |  12 ++-
 src/beast/app/beauti/BeautiDoc.java                | 101 +++++++++----------
 src/beast/app/beauti/BeautiLauncher.java           |   2 +
 src/beast/app/beauti/BeautiPanelConfig.java        |   2 +-
 src/beast/app/beauti/GuessPatternDialog.java       |  12 ++-
 src/beast/app/beauti/JPackageDialog.java           |   6 +-
 src/beast/app/beauti/TaxonSetInputEditor.java      |  36 ++++---
 src/beast/app/beauti/TipDatesInputEditor.java      |   2 +-
 src/beast/app/draw/InputEditorFactory.java         |   2 +-
 src/beast/app/draw/ListInputEditor.java            |   5 +-
 .../treeannotator/KernelDensityEstimator2D.java    |   2 +-
 src/beast/app/treeannotator/RealNumberField.java   |   2 +-
 src/beast/app/util/Utils.java                      | 107 +++++++++++++++++++++
 src/beast/app/util/Utils6.java                     |  12 +++
 src/beast/core/Input.java                          |   4 +
 src/beast/core/Logger.java                         |   7 +-
 src/beast/core/OperatorSchedule.java               |   2 -
 .../evolution/likelihood/BeagleTreeLikelihood.java |  80 ++++++++++++---
 .../likelihood/ThreadedTreeLikelihood.java         |   4 +-
 src/beast/evolution/likelihood/TreeLikelihood.java |   2 +-
 .../evolution/operators/DeltaExchangeOperator.java |  72 ++++++++------
 src/beast/evolution/operators/SubtreeSlide.java    |   2 +-
 .../evolution/sitemodel/SiteModelInterface.java    |   2 +-
 .../substitutionmodel/DefaultEigenSystem.java      |   6 +-
 .../evolution/substitutionmodel/Frequencies.java   |   9 +-
 src/beast/evolution/tree/RandomTree.java           |   6 +-
 src/beast/util/AddOnManager.java                   |  78 ++++++++++-----
 src/beast/util/ClusterTree.java                    |   3 +-
 src/beast/util/JSONProducer.java                   |  25 +++--
 src/beast/util/MersenneTwisterFast.java            |   4 +-
 src/beast/util/NexusParser.java                    |   2 +-
 src/beast/util/Package.java                        |   2 +-
 src/beast/util/PackageDependency.java              |   2 +-
 src/beast/util/Randomizer.java                     |   2 +-
 src/beast/util/TreeParser.java                     |   3 +-
 src/beast/util/XMLProducer.java                    |   4 +
 .../operator/DeltaExchangeOperatorTest.java        |  64 ++++++++++++
 .../beast/evolution/operator/TestOperator.java     |  52 ++++++++++
 src/test/beast/util/JSONTest.java                  |   6 +-
 templates/ClockModels.xml                          |  14 +--
 templates/Standard.xml                             |   2 +-
 templates/StarBeast.xml                            |   4 +-
 version.xml                                        |   2 +-
 59 files changed, 750 insertions(+), 276 deletions(-)

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