[med-svn] [beast2-mcmc] branch master updated (00dc5ec -> 79965b3)
Andreas Tille
tille at debian.org
Wed May 4 08:01:39 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository beast2-mcmc.
from 00dc5ec Document remaining issue
new b9a83f4 Enable fetching pre-releases; use new uscan options
new e8824d3 Imported Upstream version 2.4.0pre+dfsg
new 18a207f Merge tag 'upstream/2.4.0pre+dfsg'
new b1758c4 Bump version
new b2b36b7 Commit pending changes
new 0110375 Imported Upstream version 2.4.1pre+dfsg
new 0924a2a Merge tag 'upstream/2.4.1pre+dfsg'
new 79965b3 New upstream version
The 8 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
build.xml | 74 +-
debian/changelog | 2 +-
debian/patches/fix_classpath_in_build_xml.patch | 9 +
debian/patches/remove_appbundler.patch | 4 +-
debian/rules | 3 -
debian/watch | 4 +-
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 | 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 | 31 +-
release/common/tools/DensiTree_launch4j.xml | 2 +-
src/beast/app/BEASTVersion.java | 25 +-
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 | 115 +-
src/beast/app/beastapp/BeastMain.java | 126 +-
src/beast/app/beastapp/WholeNumberField.java | 43 +-
src/beast/app/beauti/AlignmentListInputEditor.java | 546 +++---
src/beast/app/beauti/AlignmentViewer.java | 140 +-
src/beast/app/beauti/Beauti.java | 404 ++--
src/beast/app/beauti/BeautiAlignmentProvider.java | 153 +-
src/beast/app/beauti/BeautiConfig.java | 195 +-
src/beast/app/beauti/BeautiConnector.java | 178 +-
src/beast/app/beauti/BeautiDoc.java | 1355 +++++++-------
src/beast/app/beauti/BeautiLauncher.java | 7 +-
src/beast/app/beauti/BeautiPanel.java | 150 +-
src/beast/app/beauti/BeautiPanelConfig.java | 256 +--
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 | 236 +--
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 | 227 +--
src/beast/app/beauti/TipDatesInputEditor.java | 276 ++-
.../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 | 210 ++-
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 | 37 +-
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 | 176 +-
src/beast/app/util/Utils6.java | 33 +-
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 | 270 +--
src/beast/core/InputForAnnotatedConstructor.java | 277 +++
src/beast/core/Loggable.java | 7 +-
src/beast/core/Logger.java | 231 +--
src/beast/core/MCMC.java | 244 ++-
src/beast/core/Operator.java | 127 +-
src/beast/core/OperatorSchedule.java | 74 +-
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 | 219 ++-
.../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 | 125 +-
src/beast/evolution/operators/BitFlipOperator.java | 9 +-
.../operators/CompoundParameterHelper.java | 40 +-
.../evolution/operators/DeltaExchangeOperator.java | 177 +-
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 | 102 +-
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 | 12 +-
.../EmpiricalSubstitutionModel.java | 73 +-
.../evolution/substitutionmodel/Frequencies.java | 96 +-
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 | 271 +--
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 | 1051 +++++++----
src/beast/util/ClusterTree.java | 489 ++---
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 | 418 ++---
src/beast/util/LogAnalyser.java | 340 ++--
src/beast/util/LogComparator.java | 26 +-
src/beast/util/MersenneTwisterFast.java | 60 +-
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 | 8 +-
src/beast/util/TreeParser.java | 141 +-
src/beast/util/XMLParser.java | 960 ++++++----
src/beast/util/XMLParserException.java | 72 +-
src/beast/util/XMLParserUtils.java | 252 ++-
src/beast/util/XMLProducer.java | 600 +++---
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 +-
.../operator/DeltaExchangeOperatorTest.java | 64 +
.../evolution/operator/ExchangeOperatorTest.java | 2 -
.../operator/IntRandomWalkOperatorTest.java | 4 +-
.../beast/evolution/operator/TestOperator.java | 52 +
.../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/ClockModels.xml | 14 +-
templates/Standard.xml | 6 +-
templates/StarBeast.xml | 11 +-
templates/TreePriors.xml | 2 +-
version.xml | 1 +
470 files changed, 22325 insertions(+), 21921 deletions(-)
create mode 100644 doc/tutorials/EBSP/Makefile
create mode 100644 doc/tutorials/EBSP/ebsp2-tut.bib
create mode 100644 doc/tutorials/EBSP/ebsp2-tut.tex
create mode 100644 doc/tutorials/EBSP/figures/clock_model.png
create mode 100644 doc/tutorials/EBSP/figures/clock_model2.png
create mode 100644 doc/tutorials/EBSP/figures/clock_model3.png
create mode 100644 doc/tutorials/EBSP/figures/clock_model4.png
create mode 100644 doc/tutorials/EBSP/figures/clockrate_prior.png
create mode 100644 doc/tutorials/EBSP/figures/import_alignment.png
create mode 100644 doc/tutorials/EBSP/figures/import_alignment2.png
create mode 100644 doc/tutorials/EBSP/figures/mcmc_panel.png
create mode 100644 doc/tutorials/EBSP/figures/mystery1.pdf
create mode 100644 doc/tutorials/EBSP/figures/mystery2.pdf
create mode 100644 doc/tutorials/EBSP/figures/mystery3.pdf
create mode 100644 doc/tutorials/EBSP/figures/mysteryTimesHist.pdf
create mode 100644 doc/tutorials/EBSP/figures/operators.png
create mode 100644 doc/tutorials/EBSP/figures/ploidy.png
create mode 100644 doc/tutorials/EBSP/figures/popmean.png
create mode 100644 doc/tutorials/EBSP/figures/site_model.png
create mode 100644 doc/tutorials/EBSP/figures/tracer1.png
create mode 100644 doc/tutorials/EBSP/figures/tracer2.png
create mode 100644 doc/tutorials/EBSP/figures/tree_prior.png
create mode 100644 doc/tutorials/EBSP/figures/view_operators.png
create mode 100644 doc/tutorials/EBSP/mystery-mammal/X.nex.nex
create mode 100644 doc/tutorials/EBSP/mystery-mammal/mt.nex.nex
create mode 100644 doc/tutorials/EBSP/mystery-mammal/nuclear.nex.nex
create mode 100644 doc/tutorials/EBSP/scripts/plotEBSP.R
create mode 100644 examples/testUCLNclock.json
delete mode 100644 packages.xml
delete mode 100644 src/beast/core/BEASTObjectAnnotation.java
create mode 100644 src/beast/core/InputForAnnotatedConstructor.java
create mode 100644 src/beast/evolution/likelihood/ThreadedBeerLikelihoodCore.java
create mode 100644 src/beast/evolution/likelihood/ThreadedBeerLikelihoodCore4.java
create mode 100644 src/beast/evolution/likelihood/ThreadedLikelihoodCore.java
create mode 100644 src/beast/evolution/likelihood/ThreadedTreeLikelihood.java
create mode 100644 src/beast/util/InputType.java
create mode 100644 src/beast/util/PackageVersion.java
delete mode 100755 src/org/json/CDL.java
delete mode 100755 src/org/json/Cookie.java
delete mode 100755 src/org/json/CookieList.java
delete mode 100755 src/org/json/HTTP.java
delete mode 100755 src/org/json/HTTPTokener.java
create mode 100644 src/org/json/JSON.java
mode change 100755 => 100644 src/org/json/JSONException.java
delete mode 100755 src/org/json/JSONML.java
mode change 100755 => 100644 src/org/json/JSONObject.java
delete mode 100755 src/org/json/JSONString.java
mode change 100755 => 100644 src/org/json/JSONStringer.java
delete mode 100755 src/org/json/JSONWriter.java
delete mode 100644 src/org/json/Kim.java
delete mode 100644 src/org/json/Property.java
delete mode 100755 src/org/json/README
delete mode 100755 src/org/json/XML.java
delete mode 100755 src/org/json/XMLTokener.java
delete mode 100644 src/org/json/zip/BitInputStream.java
delete mode 100644 src/org/json/zip/BitOutputStream.java
delete mode 100644 src/org/json/zip/BitReader.java
delete mode 100644 src/org/json/zip/BitWriter.java
delete mode 100644 src/org/json/zip/Compressor.java
delete mode 100644 src/org/json/zip/Decompressor.java
delete mode 100644 src/org/json/zip/Huff.java
delete mode 100644 src/org/json/zip/JSONzip.java
delete mode 100644 src/org/json/zip/Keep.java
delete mode 100644 src/org/json/zip/MapKeep.java
delete mode 100644 src/org/json/zip/None.java
delete mode 100644 src/org/json/zip/PostMortem.java
delete mode 100644 src/org/json/zip/README
delete mode 100644 src/org/json/zip/TrieKeep.java
create mode 100644 src/test/beast/evolution/operator/DeltaExchangeOperatorTest.java
create mode 100644 src/test/beast/evolution/operator/TestOperator.java
create mode 100644 src/test/beast/util/AnnotatedRunnableTestClass.java
create mode 100644 src/test/beast/util/XMLTest.java
create mode 100644 version.xml
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