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commit 0924a2a7bf928b66b9f939705ef0e49d633b51c6 Merge: b2b36b7 0110375 Author: Andreas Tille <[email protected]> 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(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/beast2-mcmc.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
