[med-svn] [beast2-mcmc] 03/08: Merge tag 'upstream/2.4.0pre+dfsg'

Andreas Tille tille at debian.org
Wed May 4 08:01:41 UTC 2016


This is an automated email from the git hooks/post-receive script.

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

commit 18a207f766f1e627b482badde79ac8cdd7d8234a
Merge: b9a83f4 e8824d3
Author: Andreas Tille <tille at debian.org>
Date:   Tue Mar 8 16:08:54 2016 +0100

    Merge tag 'upstream/2.4.0pre+dfsg'
    
    Upstream version 2.4.0pre+dfsg

 build.xml                                          |   25 +-
 doc/tutorials/EBSP/Makefile                        |   16 +
 doc/tutorials/EBSP/ebsp2-tut.bib                   |   51 +
 doc/tutorials/EBSP/ebsp2-tut.tex                   |  376 ++++
 doc/tutorials/EBSP/figures/clock_model.png         |  Bin 0 -> 16792 bytes
 doc/tutorials/EBSP/figures/clock_model2.png        |  Bin 0 -> 12830 bytes
 doc/tutorials/EBSP/figures/clock_model3.png        |  Bin 0 -> 12619 bytes
 doc/tutorials/EBSP/figures/clock_model4.png        |  Bin 0 -> 12816 bytes
 doc/tutorials/EBSP/figures/clockrate_prior.png     |  Bin 0 -> 32789 bytes
 doc/tutorials/EBSP/figures/import_alignment.png    |  Bin 0 -> 18962 bytes
 doc/tutorials/EBSP/figures/import_alignment2.png   |  Bin 0 -> 28831 bytes
 doc/tutorials/EBSP/figures/mcmc_panel.png          |  Bin 0 -> 24809 bytes
 doc/tutorials/EBSP/figures/mystery1.pdf            |  Bin 0 -> 6323 bytes
 doc/tutorials/EBSP/figures/mystery2.pdf            |  Bin 0 -> 5929 bytes
 doc/tutorials/EBSP/figures/mystery3.pdf            |  Bin 0 -> 41201 bytes
 doc/tutorials/EBSP/figures/mysteryTimesHist.pdf    |  Bin 0 -> 5382 bytes
 doc/tutorials/EBSP/figures/operators.png           |  Bin 0 -> 68075 bytes
 doc/tutorials/EBSP/figures/ploidy.png              |  Bin 0 -> 66371 bytes
 doc/tutorials/EBSP/figures/popmean.png             |  Bin 0 -> 30859 bytes
 doc/tutorials/EBSP/figures/site_model.png          |  Bin 0 -> 29547 bytes
 doc/tutorials/EBSP/figures/tracer1.png             |  Bin 0 -> 70580 bytes
 doc/tutorials/EBSP/figures/tracer2.png             |  Bin 0 -> 52951 bytes
 doc/tutorials/EBSP/figures/tree_prior.png          |  Bin 0 -> 47827 bytes
 doc/tutorials/EBSP/figures/view_operators.png      |  Bin 0 -> 34745 bytes
 doc/tutorials/EBSP/mystery-mammal/X.nex.nex        |   40 +
 doc/tutorials/EBSP/mystery-mammal/mt.nex.nex       |   40 +
 doc/tutorials/EBSP/mystery-mammal/nuclear.nex.nex  |   40 +
 doc/tutorials/EBSP/scripts/plotEBSP.R              |  224 +++
 examples/testHKY.json                              |   14 +-
 examples/testTipDates.xml                          |    2 +-
 examples/testUCLNclock.json                        |  135 ++
 packages.xml                                       |   71 -
 release/Linux/bin/beast                            |    2 +-
 release/common/VERSION HISTORY.txt                 |    2 +-
 release/common/tools/DensiTree_launch4j.xml        |    2 +-
 src/beast/app/BEASTVersion.java                    |   21 +-
 src/beast/app/BeastMCMC.java                       |  121 +-
 src/beast/app/DocMaker.java                        |  213 ++-
 src/beast/app/ModelBuilder.java                    |   15 +-
 src/beast/app/beastapp/BeastDialog.java            |   45 +-
 src/beast/app/beastapp/BeastLauncher.java          |   91 +-
 src/beast/app/beastapp/BeastMain.java              |  116 +-
 src/beast/app/beastapp/WholeNumberField.java       |   43 +-
 src/beast/app/beauti/AlignmentListInputEditor.java |  494 ++---
 src/beast/app/beauti/AlignmentViewer.java          |  140 +-
 src/beast/app/beauti/Beauti.java                   |  357 ++--
 src/beast/app/beauti/BeautiAlignmentProvider.java  |  145 +-
 src/beast/app/beauti/BeautiConfig.java             |  195 +-
 src/beast/app/beauti/BeautiConnector.java          |  178 +-
 src/beast/app/beauti/BeautiDoc.java                | 1298 ++++++-------
 src/beast/app/beauti/BeautiLauncher.java           |    5 +-
 src/beast/app/beauti/BeautiPanel.java              |  150 +-
 src/beast/app/beauti/BeautiPanelConfig.java        |  254 +--
 src/beast/app/beauti/BeautiSubTemplate.java        |  224 +--
 .../app/beauti/ClockModelListInputEditor.java      |   42 +-
 src/beast/app/beauti/ClonePartitionPanel.java      |   30 +-
 src/beast/app/beauti/Fragment.java                 |    6 +-
 src/beast/app/beauti/FrequenciesInputEditor.java   |   40 +-
 ...eTreeForSpeciesTreeDistributionInputEditor.java |   70 +-
 src/beast/app/beauti/GuessPatternDialog.java       |  224 ++-
 src/beast/app/beauti/JPackageDialog.java           |  399 ++--
 src/beast/app/beauti/JPackageRepositoryDialog.java |  155 +-
 src/beast/app/beauti/LoggerListInputEditor.java    |   17 +-
 src/beast/app/beauti/MRCAPriorInputEditor.java     |   89 +-
 src/beast/app/beauti/OperatorListInputEditor.java  |   46 +-
 .../beauti/ParametricDistributionInputEditor.java  |  167 +-
 src/beast/app/beauti/PartitionContext.java         |   25 +-
 src/beast/app/beauti/PriorInputEditor.java         |   49 +-
 src/beast/app/beauti/PriorListInputEditor.java     |   89 +-
 src/beast/app/beauti/SiteModelInputEditor.java     |   59 +-
 .../app/beauti/SpeciesTreePriorInputEditor.java    |   10 +-
 src/beast/app/beauti/StateNodeListInputEditor.java |    7 +-
 src/beast/app/beauti/TaxonSetDialog.java           |   79 +-
 src/beast/app/beauti/TaxonSetInputEditor.java      |  199 +-
 src/beast/app/beauti/TipDatesInputEditor.java      |  274 ++-
 .../app/beauti/TreeDistributionInputEditor.java    |   75 +-
 .../app/beauti/guiutil/S11InitialSelection.java    |   40 +-
 src/beast/app/draw/Arrow.java                      |   43 +-
 src/beast/app/draw/BEASTObjectDialog.java          |   74 +-
 src/beast/app/draw/BEASTObjectInputEditor.java     |  464 +++--
 src/beast/app/draw/BEASTObjectPanel.java           |  298 +--
 src/beast/app/draw/BEASTObjectSet.java             |    8 +-
 src/beast/app/draw/BEASTObjectShape.java           |  102 +-
 src/beast/app/draw/BooleanInputEditor.java         |   24 +-
 src/beast/app/draw/Document.java                   |  941 +++++-----
 src/beast/app/draw/DoubleListInputEditor.java      |  127 +-
 src/beast/app/draw/EnumInputEditor.java            |   38 +-
 src/beast/app/draw/ExtensionFileFilter.java        |   11 +-
 src/beast/app/draw/HelpBrowser.java                |   48 +-
 src/beast/app/draw/InputEditor.java                |  126 +-
 src/beast/app/draw/InputEditorFactory.java         |  202 +-
 src/beast/app/draw/InputShape.java                 |   75 +-
 src/beast/app/draw/IntegerListInputEditor.java     |  157 +-
 src/beast/app/draw/ListInputEditor.java            |  209 ++-
 src/beast/app/draw/ModelBuilder.java               |  657 ++++---
 src/beast/app/draw/MyAction.java                   |   25 +-
 src/beast/app/draw/ParameterInputEditor.java       |  110 +-
 src/beast/app/draw/Selection.java                  |   74 +-
 src/beast/app/draw/Shape.java                      |  197 +-
 src/beast/app/draw/SmallButton.java                |   15 +-
 src/beast/app/draw/SmallButtonOld.java             |    7 +-
 src/beast/app/draw/SmallLabel.java                 |    7 +-
 src/beast/app/draw/TrackPoint.java                 |    8 +-
 src/beast/app/seqgen/MergeDataWith.java            |   34 +-
 src/beast/app/seqgen/SequenceSimulator.java        |   89 +-
 src/beast/app/seqgen/SimulatedAlignment.java       |   57 +-
 src/beast/app/tools/AppStore.java                  |  110 +-
 src/beast/app/tools/AppStoreLauncher.java          |   12 +-
 src/beast/app/tools/EBSPAnalyser.java              |  136 +-
 src/beast/app/tools/LogCombiner.java               |  254 +--
 src/beast/app/tools/LogCombinerDialog.java         |  111 +-
 src/beast/app/tools/LogCombinerLauncher.java       |    6 +-
 src/beast/app/tools/TableEditorStopper.java        |    7 +-
 src/beast/app/treeannotator/CladeSystem.java       |    9 +-
 src/beast/app/treeannotator/ContourAttrib.java     |    1 +
 src/beast/app/treeannotator/ContourGenerator.java  |   53 +-
 src/beast/app/treeannotator/ContourPath.java       |    1 +
 src/beast/app/treeannotator/ContourWithSynder.java |    9 +-
 src/beast/app/treeannotator/FileDrop.java          |   35 +-
 .../treeannotator/KernelDensityEstimator2D.java    |    9 +-
 src/beast/app/treeannotator/RealNumberField.java   |   35 +-
 src/beast/app/treeannotator/SnyderContour.java     |   10 +-
 src/beast/app/treeannotator/TreeAnnotator.java     |  200 +-
 .../app/treeannotator/TreeAnnotatorDialog.java     |   54 +-
 .../app/treeannotator/TreeAnnotatorLauncher.java   |    5 +-
 src/beast/app/treeannotator/TreeSetParser.java     |  329 ++--
 src/beast/app/util/Arguments.java                  |    5 +-
 src/beast/app/util/ErrorLogHandler.java            |    9 +-
 src/beast/app/util/FileDrop.java                   |   48 +-
 src/beast/app/util/MessageLogHandler.java          |   13 +-
 src/beast/app/util/Utils.java                      |   69 +-
 src/beast/app/util/Utils6.java                     |   21 +-
 src/beast/app/util/Version.java                    |   10 +-
 src/beast/app/util/WholeNumberField.java           |   42 +-
 src/beast/core/BEASTInterface.java                 |  262 +--
 src/beast/core/BEASTObject.java                    |   41 +-
 src/beast/core/BEASTObjectAnnotation.java          |   12 -
 src/beast/core/CalculationNode.java                |   16 +-
 src/beast/core/Citation.java                       |    6 +-
 src/beast/core/Distribution.java                   |   17 +-
 src/beast/core/Function.java                       |   23 +-
 src/beast/core/Input.java                          |  266 +--
 src/beast/core/InputForAnnotatedConstructor.java   |  277 +++
 src/beast/core/Loggable.java                       |    7 +-
 src/beast/core/Logger.java                         |  230 +--
 src/beast/core/MCMC.java                           |  244 ++-
 src/beast/core/Operator.java                       |  127 +-
 src/beast/core/OperatorSchedule.java               |   76 +-
 src/beast/core/Param.java                          |   40 +-
 src/beast/core/Runnable.java                       |   12 +-
 src/beast/core/State.java                          |  236 +--
 src/beast/core/StateNode.java                      |   24 +-
 src/beast/core/StateNodeInitialiser.java           |    6 +-
 src/beast/core/parameter/BooleanParameter.java     |   37 +-
 src/beast/core/parameter/BooleanParameterList.java |    4 +-
 src/beast/core/parameter/CompoundValuable.java     |   38 +-
 src/beast/core/parameter/GeneralParameterList.java |   76 +-
 src/beast/core/parameter/IntegerParameter.java     |   59 +-
 src/beast/core/parameter/IntegerParameterList.java |    7 +-
 src/beast/core/parameter/Map.java                  |   40 +-
 src/beast/core/parameter/Parameter.java            |  172 +-
 src/beast/core/parameter/RealParameter.java        |   48 +-
 src/beast/core/parameter/RealParameterList.java    |    7 +-
 src/beast/core/util/CompoundDistribution.java      |   50 +-
 src/beast/core/util/ESS.java                       |  223 ++-
 src/beast/core/util/Log.java                       |   13 +
 src/beast/core/util/Sum.java                       |   26 +-
 src/beast/evolution/alignment/Alignment.java       |  267 +--
 .../evolution/alignment/AscertainedAlignment.java  |   56 +-
 .../evolution/alignment/FilteredAlignment.java     |   24 +-
 src/beast/evolution/alignment/Sequence.java        |   30 +-
 src/beast/evolution/alignment/Taxon.java           |   18 +-
 src/beast/evolution/alignment/TaxonSet.java        |   28 +-
 .../evolution/alignment/distance/Distance.java     |    6 +-
 .../alignment/distance/HammingDistance.java        |    6 +-
 .../evolution/branchratemodel/BranchRateModel.java |    2 +-
 .../branchratemodel/RandomLocalClockModel.java     |   33 +-
 .../evolution/branchratemodel/RateStatistic.java   |   34 +-
 .../branchratemodel/StrictClockModel.java          |    4 +-
 .../branchratemodel/UCRelaxedClockModel.java       |   48 +-
 src/beast/evolution/datatype/DataType.java         |   56 +-
 src/beast/evolution/datatype/StandardData.java     |   32 +-
 src/beast/evolution/datatype/UserDataType.java     |   42 +-
 .../evolution/likelihood/BeagleTreeLikelihood.java |  149 +-
 .../evolution/likelihood/BeerLikelihoodCore.java   |  448 ++---
 .../evolution/likelihood/BeerLikelihoodCore4.java  |  271 +--
 .../likelihood/GenericTreeLikelihood.java          |   10 +-
 src/beast/evolution/likelihood/LikelihoodCore.java |   81 +-
 .../likelihood/ThreadedBeerLikelihoodCore.java     |  984 ++++++++++
 .../likelihood/ThreadedBeerLikelihoodCore4.java    |  293 +++
 .../likelihood/ThreadedLikelihoodCore.java         |  152 ++
 .../likelihood/ThreadedTreeLikelihood.java         |  363 ++++
 src/beast/evolution/likelihood/TreeLikelihood.java |  123 +-
 src/beast/evolution/operators/BitFlipOperator.java |    9 +-
 .../operators/CompoundParameterHelper.java         |   40 +-
 .../evolution/operators/DeltaExchangeOperator.java |  111 +-
 src/beast/evolution/operators/Exchange.java        |   90 +-
 .../evolution/operators/IntRandomWalkOperator.java |   13 +-
 .../evolution/operators/IntUniformOperator.java    |   10 +-
 src/beast/evolution/operators/JointOperator.java   |   18 +-
 src/beast/evolution/operators/NodeReheight.java    |  204 +--
 .../operators/RealRandomWalkOperator.java          |   27 +-
 src/beast/evolution/operators/ScaleOperator.java   |   90 +-
 src/beast/evolution/operators/SliceOperator.java   |   37 +-
 src/beast/evolution/operators/SubtreeSlide.java    |  100 +-
 src/beast/evolution/operators/SwapOperator.java    |   16 +-
 .../evolution/operators/TipDatesRandomWalker.java  |   44 +-
 src/beast/evolution/operators/TipDatesScaler.java  |   52 +-
 src/beast/evolution/operators/TreeOperator.java    |    6 +-
 src/beast/evolution/operators/Uniform.java         |   12 +-
 src/beast/evolution/operators/UniformOperator.java |   28 +-
 src/beast/evolution/operators/UpDownOperator.java  |   39 +-
 src/beast/evolution/operators/WilsonBalding.java   |   70 +-
 src/beast/evolution/sitemodel/SiteModel.java       |   54 +-
 .../evolution/sitemodel/SiteModelInterface.java    |   22 +-
 .../speciation/BirthDeathGernhard08Model.java      |   37 +-
 .../speciation/CalibratedBirthDeathModel.java      |  217 +--
 .../speciation/CalibratedYuleInitialTree.java      |   25 +-
 .../evolution/speciation/CalibratedYuleModel.java  |  193 +-
 .../speciation/CalibrationLineagesIterator.java    |   70 +-
 .../evolution/speciation/CalibrationPoint.java     |   13 +-
 .../GeneTreeForSpeciesTreeDistribution.java        |  223 +--
 src/beast/evolution/speciation/RandomGeneTree.java |    8 +-
 .../speciation/SpeciesTreeDistribution.java        |    1 -
 .../evolution/speciation/SpeciesTreeLogger.java    |   24 +-
 .../evolution/speciation/SpeciesTreePrior.java     |   84 +-
 .../evolution/speciation/StarBeastStartState.java  |  151 +-
 src/beast/evolution/speciation/TreeTopFinder.java  |   17 +-
 src/beast/evolution/speciation/YuleModel.java      |   18 +-
 .../substitutionmodel/BinaryCovarion.java          |   63 +-
 .../evolution/substitutionmodel/Blosum62.java      |   10 +-
 src/beast/evolution/substitutionmodel/CPREV.java   |   10 +-
 src/beast/evolution/substitutionmodel/Dayhoff.java |   10 +-
 .../substitutionmodel/DefaultEigenSystem.java      |    8 +-
 .../EmpiricalSubstitutionModel.java                |   73 +-
 .../evolution/substitutionmodel/Frequencies.java   |   87 +-
 src/beast/evolution/substitutionmodel/GTR.java     |   29 +-
 .../GeneralSubstitutionModel.java                  |   50 +-
 src/beast/evolution/substitutionmodel/HKY.java     |   14 +-
 src/beast/evolution/substitutionmodel/JTT.java     |   10 +-
 .../evolution/substitutionmodel/JukesCantor.java   |   18 +-
 src/beast/evolution/substitutionmodel/MTREV.java   |   10 +-
 .../substitutionmodel/MutationDeathModel.java      |   16 +-
 src/beast/evolution/substitutionmodel/SYM.java     |   27 +-
 .../substitutionmodel/SubstitutionModel.java       |   16 +-
 src/beast/evolution/substitutionmodel/TIM.java     |   25 +-
 src/beast/evolution/substitutionmodel/TN93.java    |   14 +-
 src/beast/evolution/substitutionmodel/TVM.java     |   27 +-
 src/beast/evolution/substitutionmodel/WAG.java     |   12 +-
 src/beast/evolution/tree/CladeSet.java             |   12 +-
 src/beast/evolution/tree/Node.java                 |  173 +-
 src/beast/evolution/tree/RandomTree.java           |  265 +--
 src/beast/evolution/tree/TraitSet.java             |   88 +-
 src/beast/evolution/tree/Tree.java                 |  253 +--
 src/beast/evolution/tree/TreeDistribution.java     |    6 +-
 src/beast/evolution/tree/TreeHeightLogger.java     |   10 +-
 src/beast/evolution/tree/TreeInterface.java        |    5 +-
 src/beast/evolution/tree/TreeTraceAnalysis.java    |   23 +-
 src/beast/evolution/tree/TreeUtils.java            |   30 +-
 .../evolution/tree/TreeWithMetaDataLogger.java     |   26 +-
 .../evolution/tree/coalescent/BayesianSkyline.java |   30 +-
 .../evolution/tree/coalescent/Coalescent.java      |   10 +-
 .../coalescent/CompoundPopulationFunction.java     |   63 +-
 .../tree/coalescent/ConstantPopulation.java        |   14 +-
 .../tree/coalescent/ExponentialGrowth.java         |   19 +-
 .../evolution/tree/coalescent/IntervalType.java    |    3 +-
 .../tree/coalescent/PopulationFunction.java        |   26 +-
 .../evolution/tree/coalescent/SampleOffValues.java |   21 +-
 .../tree/coalescent/ScaledPopulationFunction.java  |   23 +-
 .../evolution/tree/coalescent/TreeIntervals.java   |   37 +-
 src/beast/math/Binomial.java                       |    2 +-
 src/beast/math/distributions/Beta.java             |   27 +-
 src/beast/math/distributions/ChiSquare.java        |   17 +-
 src/beast/math/distributions/Dirichlet.java        |   30 +-
 src/beast/math/distributions/Exponential.java      |   22 +-
 src/beast/math/distributions/Gamma.java            |   29 +-
 src/beast/math/distributions/InverseGamma.java     |   45 +-
 .../math/distributions/LaplaceDistribution.java    |   21 +-
 .../distributions/LogNormalDistributionModel.java  |   57 +-
 src/beast/math/distributions/MRCAPrior.java        |  197 +-
 .../distributions/MarkovChainDistribution.java     |   21 +-
 src/beast/math/distributions/Normal.java           |   27 +-
 .../math/distributions/ParametricDistribution.java |   35 +-
 src/beast/math/distributions/Poisson.java          |   14 +-
 src/beast/math/distributions/Prior.java            |   15 +-
 src/beast/math/distributions/Uniform.java          |    8 +-
 src/beast/math/statistic/DiscreteStatistics.java   |   12 +-
 src/beast/math/statistic/RPNcalculator.java        |   51 +-
 .../math/statistic/RPNexpressionCalculator.java    |    2 +-
 src/beast/util/AddOnManager.java                   | 1019 +++++++----
 src/beast/util/ClusterTree.java                    |  486 ++---
 src/beast/util/CollectionUtils.java                |    4 +-
 src/beast/util/CredibleSet.java                    |    2 +-
 src/beast/util/FrequencySet.java                   |   18 +-
 src/beast/util/InputType.java                      |   66 +
 src/beast/util/JSONParser.java                     | 1258 ++++++++-----
 src/beast/util/JSONParserException.java            |   48 +-
 src/beast/util/JSONProducer.java                   |  407 ++---
 src/beast/util/LogAnalyser.java                    |  340 ++--
 src/beast/util/LogComparator.java                  |   26 +-
 src/beast/util/MersenneTwisterFast.java            |   56 +-
 src/beast/util/NexusParser.java                    |  658 +++----
 src/beast/util/OutputUtils.java                    |   28 +-
 src/beast/util/Package.java                        |  238 ++-
 src/beast/util/PackageDependency.java              |   61 +-
 src/beast/util/PackageVersion.java                 |  128 ++
 src/beast/util/Randomizer.java                     |    6 +-
 src/beast/util/TreeParser.java                     |  138 +-
 src/beast/util/XMLParser.java                      |  960 ++++++----
 src/beast/util/XMLParserException.java             |   72 +-
 src/beast/util/XMLParserUtils.java                 |  252 ++-
 src/beast/util/XMLProducer.java                    |  596 +++---
 src/beast/util/treeparser/Newick.g4                |    2 +-
 src/beast/util/treeparser/NewickBaseVisitor.java   |    2 +-
 src/beast/util/treeparser/NewickLexer.java         |   48 +-
 src/beast/util/treeparser/NewickParser.java        |    2 +-
 src/beast/util/treeparser/NewickVisitor.java       |    2 +-
 .../commons/math/ConvergingAlgorithmImpl.java      |   30 +-
 .../math/MaxEvaluationsExceededException.java      |    2 -
 .../math/MaxIterationsExceededException.java       |    2 -
 .../commons/math/analysis/BinaryFunction.java      |    3 +-
 .../commons/math/analysis/ComposableFunction.java  |    6 +-
 .../analysis/integration/RombergIntegrator.java    |    6 +-
 .../analysis/integration/TrapezoidIntegrator.java  |    6 +-
 .../integration/UnivariateRealIntegratorImpl.java  |   14 +-
 .../math/analysis/solvers/BisectionSolver.java     |   12 +-
 .../commons/math/analysis/solvers/BrentSolver.java |   14 +-
 .../math/analysis/solvers/MullerSolver.java        |   12 +-
 .../math/analysis/solvers/NewtonSolver.java        |   12 +-
 .../math/analysis/solvers/RiddersSolver.java       |   12 +-
 .../math/analysis/solvers/SecantSolver.java        |   12 +-
 .../analysis/solvers/UnivariateRealSolverImpl.java |   15 +-
 .../solvers/UnivariateRealSolverUtils.java         |    2 +-
 .../AbstractContinuousDistribution.java            |   10 +-
 .../math/distribution/AbstractDistribution.java    |    3 +-
 .../distribution/AbstractIntegerDistribution.java  |   15 +-
 .../math/distribution/BetaDistribution.java        |    2 +-
 .../math/distribution/BetaDistributionImpl.java    |   24 +-
 .../distribution/BinomialDistributionImpl.java     |   15 +-
 .../math/distribution/CauchyDistributionImpl.java  |   15 +-
 .../math/distribution/ChiSquaredDistribution.java  |    2 +-
 .../distribution/ChiSquaredDistributionImpl.java   |   16 +-
 .../math/distribution/ExponentialDistribution.java |    2 +-
 .../distribution/ExponentialDistributionImpl.java  |   13 +-
 .../math/distribution/FDistributionImpl.java       |   15 +-
 .../math/distribution/GammaDistribution.java       |    2 +-
 .../math/distribution/GammaDistributionImpl.java   |   19 +-
 .../commons/math/distribution/HasDensity.java      |    1 +
 .../HypergeometricDistributionImpl.java            |   21 +-
 .../math/distribution/NormalDistribution.java      |    2 +-
 .../math/distribution/NormalDistributionImpl.java  |   19 +-
 .../math/distribution/PascalDistributionImpl.java  |   15 +-
 .../math/distribution/PoissonDistributionImpl.java |   15 +-
 .../math/distribution/TDistributionImpl.java       |   15 +-
 .../math/distribution/WeibullDistributionImpl.java |   15 +-
 .../math/distribution/ZipfDistributionImpl.java    |   15 +-
 src/org/json/CDL.java                              |  279 ---
 src/org/json/Cookie.java                           |  169 --
 src/org/json/CookieList.java                       |   90 -
 src/org/json/HTTP.java                             |  163 --
 src/org/json/HTTPTokener.java                      |   77 -
 src/org/json/JSON.java                             |  117 ++
 src/org/json/JSONArray.java                        | 1170 +++++-------
 src/org/json/JSONException.java                    |   74 +-
 src/org/json/JSONML.java                           |  467 -----
 src/org/json/JSONObject.java                       | 1922 ++++++--------------
 src/org/json/JSONString.java                       |   18 -
 src/org/json/JSONStringer.java                     |  510 +++++-
 src/org/json/JSONTokener.java                      |  849 +++++----
 src/org/json/JSONWriter.java                       |  327 ----
 src/org/json/Kim.java                              |  373 ----
 src/org/json/Property.java                         |   74 -
 src/org/json/README                                |   68 -
 src/org/json/XML.java                              |  508 ------
 src/org/json/XMLTokener.java                       |  365 ----
 src/org/json/zip/BitInputStream.java               |  169 --
 src/org/json/zip/BitOutputStream.java              |  154 --
 src/org/json/zip/BitReader.java                    |   41 -
 src/org/json/zip/BitWriter.java                    |   51 -
 src/org/json/zip/Compressor.java                   |  575 ------
 src/org/json/zip/Decompressor.java                 |  325 ----
 src/org/json/zip/Huff.java                         |  406 -----
 src/org/json/zip/JSONzip.java                      |  281 ---
 src/org/json/zip/Keep.java                         |   84 -
 src/org/json/zip/MapKeep.java                      |  160 --
 src/org/json/zip/None.java                         |   15 -
 src/org/json/zip/PostMortem.java                   |   47 -
 src/org/json/zip/README                            |    2 -
 src/org/json/zip/TrieKeep.java                     |  396 ----
 src/test/beast/BEASTTestCase.java                  |    3 +-
 src/test/beast/app/BeautiSubTemplateTest.java      |  184 +-
 src/test/beast/app/BeautiTest.java                 |   32 +-
 src/test/beast/app/beauti/BeautiBase.java          |   22 +-
 .../app/beauti/BeautiDivergenceDatingTest.java     |   43 +-
 .../beast/app/beauti/BeautiRateTutorialTest.java   |   22 +-
 src/test/beast/app/beauti/BeautiSimpleTest.java    |   16 +-
 src/test/beast/app/beauti/BeautiStarBeastTest.java |    5 +-
 src/test/beast/app/beauti/CloneTest.java           |    1 -
 src/test/beast/app/beauti/FixedMeanRateTest.java   |   24 +-
 src/test/beast/app/beauti/LinkUnlinkTest.java      |    2 +-
 src/test/beast/beast2vs1/ClockModelTest.java       |    3 +-
 src/test/beast/beast2vs1/StarBEASTTest.java        |    3 +-
 .../beast/beast2vs1/SubstitutionModelTest.java     |    3 +-
 src/test/beast/beast2vs1/TaxonOrderTest.java       |    3 +-
 src/test/beast/beast2vs1/TestFramework.java        |   26 +-
 src/test/beast/beast2vs1/TipTimeTest.java          |    3 +-
 src/test/beast/beast2vs1/TreePriorTest.java        |    3 +-
 src/test/beast/beast2vs1/TreeTest.java             |    3 +-
 .../beast/beast2vs1/trace/DiscreteStatistics.java  |   13 +-
 src/test/beast/beast2vs1/trace/Expectation.java    |   13 +-
 src/test/beast/beast2vs1/trace/LogAnalyser.java    |   25 +-
 src/test/beast/beast2vs1/trace/LogFileTraces.java  |    4 +
 .../beast/beast2vs1/trace/NumberFormatter.java     |    2 +-
 src/test/beast/beast2vs1/trace/TraceException.java |    4 +-
 .../beast/beast2vs1/trace/TraceStatistics.java     |    4 +-
 src/test/beast/beast2vs1/trace/TraceType.java      |    9 +-
 src/test/beast/beast2vs1/trace/TrimLineReader.java |    3 +-
 src/test/beast/core/BEASTInterfaceTest.java        |   36 +-
 src/test/beast/core/StateNodeInitialiserTest.java  |    5 +-
 .../core/parameter/BooleanParameterListTest.java   |   18 +-
 .../core/parameter/IntegerParameterListTest.java   |   18 +-
 src/test/beast/core/parameter/ParameterTest.java   |    2 -
 .../core/parameter/RealParameterListTest.java      |   18 +-
 .../evolution/alignment/FilteredAlignmentTest.java |   17 +-
 .../alignment/UncertainAlignmentTest.java          |    8 +-
 .../alignment/UnorderedAlignmentsTest.java         |   13 +-
 .../evolution/likelihood/TreeLikelihoodTest.java   |  159 +-
 .../evolution/operator/ExchangeOperatorTest.java   |    2 -
 .../operator/IntRandomWalkOperatorTest.java        |    4 +-
 .../operator/UniformIntegerOperatorTest.java       |    4 +-
 .../speciation/BirthDeathGernhard08ModelTest.java  |   24 +-
 src/test/beast/evolution/substmodel/GTRTest.java   |   60 +-
 src/test/beast/evolution/substmodel/HKYTest.java   |   37 +-
 src/test/beast/evolution/tree/RandomTreeTest.java  |    8 +-
 .../beast/evolution/tree/TreeAnnotatorTest.java    |   13 +-
 .../tree/coalescent/BayesianSkylineTest.java       |    2 +-
 src/test/beast/integration/DocumentationTest.java  |   63 +-
 .../beast/integration/ExampleJSONParsingTest.java  |   46 +-
 .../beast/integration/ExampleXmlParsingTest.java   |   46 +-
 src/test/beast/integration/InputTypeTest.java      |  172 +-
 src/test/beast/integration/ResumeTest.java         |    7 +-
 src/test/beast/integration/XMLElementNameTest.java |   81 +-
 src/test/beast/integration/XMLProducerTest.java    |   33 +-
 .../LogNormalDistributionModelTest.java            |    7 +-
 .../beast/math/distributions/MRCAPriorTest.java    |   35 +-
 .../MeanOfParametricDistributionTest.java          |   11 +-
 .../beast/util/AnnotatedRunnableTestClass.java     |   97 +
 src/test/beast/util/JSONTest.java                  |  109 +-
 src/test/beast/util/NexusParserTest.java           |   54 +-
 src/test/beast/util/TreeParserTest.java            |   43 +-
 src/test/beast/util/XMLTest.java                   |   43 +
 templates/Standard.xml                             |    4 +-
 templates/StarBeast.xml                            |    7 +-
 templates/TreePriors.xml                           |    2 +-
 version.xml                                        |    1 +
 455 files changed, 21656 insertions(+), 21730 deletions(-)

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