[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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