[med-svn] [beast-mcmc] 02/05: Merge tag 'upstream/1.8.4+dfsg'

Andreas Tille tille at debian.org
Tue Jun 28 08:03:40 UTC 2016


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

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

commit 079f0267b4ad76ce51cb9eebab98a12e10671ec1
Merge: 69ceacf b477f08
Author: Andreas Tille <tille at debian.org>
Date:   Tue Jun 28 09:24:17 2016 +0200

    Merge tag 'upstream/1.8.4+dfsg'
    
    Upstream version 1.8.4+dfsg

 .idea/uiDesigner.xml                               | 124 ++++
 README.md                                          |   2 +-
 build.xml                                          |   7 +-
 build_tempest.xml                                  |  18 +-
 release/common/README.txt                          |   4 +-
 release/common/VERSION HISTORY.txt                 |  28 +-
 release_tempest/Linux/icons/pathogen.png           | Bin 34709 -> 0 bytes
 release_tempest/Linux/scripts/pathogen             |  27 -
 release_tempest/common/README.txt                  |  71 ++-
 .../evomodel/branchmodel/EpochBranchModel.java     |  24 +-
 .../branchmodel/ExternalInternalBranchModel.java   |  23 +-
 .../lineagespecific/BeagleBranchLikelihood.java    |   2 +-
 .../LineageSpecificBranchModel.java                |  25 +-
 .../NewBeagleSequenceLikelihood.java               |   4 +-
 .../evomodel/parsers/ALSTreeLikelihoodParser.java  |   2 +
 .../AncestralStateTreeLikelihoodParser.java        |   7 +-
 .../BalancedBeagleTreeLikelihoodParser.java        |  21 +-
 .../parsers/BeagleTreeLikelihoodParser.java        |   9 +
 .../parsers/MarkovJumpsTreeLikelihoodParser.java   |   2 +
 .../OptimizedBeagleTreeLikelihoodParser.java       | 103 +++-
 .../sitemodel/EpochBranchSubstitutionModel.java    |  21 +-
 .../ExternalInternalBranchSubstitutionModel.java   |  19 +-
 .../evomodel/sitemodel/GammaSiteRateModel.java     |  41 +-
 .../substmodel/ComplexSubstitutionModel.java       |  21 +-
 .../evomodel/substmodel/GLMSubstitutionModel.java  |  15 +
 src/dr/app/beagle/evomodel/substmodel/GTR.java     |  33 +-
 .../beagle/evomodel/substmodel/GY94CodonModel.java |  35 +-
 src/dr/app/beagle/evomodel/substmodel/HKY.java     |  38 +-
 .../beagle/evomodel/substmodel/MG94CodonModel.java |  34 +-
 .../MarkovModulatedSubstitutionModel.java          |  20 +-
 .../substmodel/ProductChainSubstitutionModel.java  |  19 +-
 .../substmodel/SVSComplexSubstitutionModel.java    |   2 +-
 .../substmodel/SVSGeneralSubstitutionModel.java    |  31 +-
 src/dr/app/beagle/evomodel/substmodel/TN93.java    |  34 +-
 .../treelikelihood/ALSBeagleTreeLikelihood.java    |   3 +-
 .../AncestralStateBeagleTreeLikelihood.java        |  28 +-
 .../treelikelihood/BeagleTreeLikelihood.java       | 142 +++--
 .../MarkovJumpsBeagleTreeLikelihood.java           |  16 +-
 .../treelikelihood/OldBeagleTreeLikelihood.java    |  12 +-
 .../treelikelihood/SplitBySiteTraitLogger.java     |  22 +-
 .../evomodel/utilities/CompleteHistoryLogger.java  |  22 +-
 src/dr/app/beagle/mm/MMAlgorithm.java              | 125 ++++
 .../app/beagle/mm/MultiDimensionalScalingMM.java   | 269 ++++++++
 .../MassivelyParallelMDSImpl.java                  |  21 +-
 .../MultiDimensionalScalingCore.java               |   5 +
 .../MultiDimensionalScalingCoreImpl2.java          | 294 +++------
 .../MultiDimensionalScalingLikelihood.java         |  34 +-
 .../NativeMDSSingleton.java                        |  15 +-
 src/dr/app/beast/BeastMain.java                    |  29 +-
 src/dr/app/beast/BeastParser.java                  |  47 +-
 src/dr/app/beast/BeastVersion.java                 |  43 +-
 src/dr/app/beast/beast.properties                  |   4 +-
 src/dr/app/beast/development_parsers.properties    |  24 +-
 src/dr/app/beast/release_parsers.properties        |  11 +-
 src/dr/app/beauti/BeautiApp.java                   |  33 +-
 src/dr/app/beauti/BeautiFrame.java                 |   2 -
 .../clockModelsPanel/OldClockModelsPanel.java      | 681 ---------------------
 .../AncestralStatesComponentGenerator.java         |   2 +-
 .../continuous/ContinuousComponentOptions.java     |   3 +-
 .../discrete/DiscreteTraitsComponentGenerator.java |  12 +-
 .../components/dollo/DolloComponentGenerator.java  |   2 +-
 .../hpm/HierarchicalModelComponentGenerator.java   |   4 +-
 .../MarginalLikelihoodEstimationGenerator.java     |   4 +-
 src/dr/app/beauti/datapanel/DataPanel.java         |  12 +-
 src/dr/app/beauti/generator/BeastGenerator.java    |  56 +-
 ...odelGenerator.java => ClockModelGenerator.java} |  52 +-
 src/dr/app/beauti/generator/Generator.java         |  12 +-
 .../app/beauti/generator/InitialTreeGenerator.java |   2 +-
 src/dr/app/beauti/generator/LogGenerator.java      | 142 ++---
 .../app/beauti/generator/OperatorsGenerator.java   | 230 ++++---
 .../beauti/generator/ParameterPriorGenerator.java  |  10 +-
 .../app/beauti/generator/STARBEASTGenerator.java   |   4 +-
 .../generator/SubstitutionModelGenerator.java      |  49 +-
 .../beauti/generator/TreeLikelihoodGenerator.java  |   6 +-
 .../app/beauti/generator/TreePriorGenerator.java   |  12 +-
 src/dr/app/beauti/mcmcpanel/MCMCPanel.java         |   2 +
 .../app/beauti/operatorspanel/OperatorsPanel.java  |  33 +-
 .../app/beauti/options/AbstractPartitionData.java  |   2 +-
 src/dr/app/beauti/options/BeautiOptions.java       |  84 +--
 src/dr/app/beauti/options/ClockModelGroup.java     |  96 ---
 src/dr/app/beauti/options/ClockModelOptions.java   | 622 +------------------
 src/dr/app/beauti/options/ModelOptions.java        |  20 +-
 src/dr/app/beauti/options/Operator.java            | 111 +++-
 src/dr/app/beauti/options/Parameter.java           |  64 +-
 src/dr/app/beauti/options/PartitionClockModel.java | 243 +++-----
 .../options/PartitionClockModelTreeModelLink.java  |  78 +--
 src/dr/app/beauti/options/PartitionData.java       |   5 +-
 src/dr/app/beauti/options/PartitionOptions.java    | 294 ++++-----
 .../beauti/options/PartitionSubstitutionModel.java |  83 +--
 src/dr/app/beauti/options/PartitionTreeModel.java  |  54 +-
 src/dr/app/beauti/options/PartitionTreePrior.java  |   6 +-
 src/dr/app/beauti/options/TraitGuesser.java        |   2 +-
 src/dr/app/beauti/options/TreeModelOptions.java    |  22 +-
 .../priorsPanel/HierarchicalPriorDialog.java       |   6 +-
 .../app/beauti/priorsPanel/PriorOptionsPanel.java  |  12 +-
 .../app/beauti/priorsPanel/PriorSettingsPanel.java |   8 +-
 src/dr/app/beauti/priorsPanel/PriorsPanel.java     |  24 +-
 .../siteModelsPanel/PartitionModelPanel.java       |   2 +-
 src/dr/app/beauti/tipdatepanel/TipDatesPanel.java  |   5 +-
 .../beauti/treespanel/PartitionTreeModelPanel.java |  11 -
 src/dr/app/beauti/treespanel/TreesPanel.java       |   5 -
 src/dr/app/beauti/types/FixRateType.java           |   2 +-
 src/dr/app/beauti/types/OldClockType.java          |  95 ---
 src/dr/app/beauti/types/PriorType.java             |  18 +-
 src/dr/app/beauti/util/BEAUTiImporter.java         |   2 +-
 src/dr/app/beauti/util/BeautiTemplate.java         | 434 -------------
 src/dr/app/beauti/util/CommandLineBeauti.java      | 267 --------
 src/dr/app/beauti/util/XMLWriter.java              |  24 +-
 src/dr/app/bss/test/BeagleSeqSimTest.java          |   2 +-
 src/dr/app/tempest/TempEstApp.java                 |   5 +-
 src/dr/app/tempest/TempestFrame.java               |  19 +-
 src/dr/app/tools/AncestralSequenceAnnotator.java   |   1 +
 src/dr/app/tools/TreeAnnotatorDialog.java          |   2 +-
 .../alignment/AscertainedSitePatterns.java         |  19 +-
 src/dr/evolution/alignment/UncertainSiteList.java  | 101 +++
 .../coalescent/MultiEpochExponential.java          |  16 +-
 src/dr/evomodel/MSSD/CTMCScalePrior.java           |  37 +-
 src/dr/evomodel/antigenic/AntigenicDriftPrior.java |  45 +-
 src/dr/evomodel/antigenic/AntigenicLikelihood.java |  30 +-
 src/dr/evomodel/antigenic/AntigenicSplitPrior.java |  30 +-
 .../ContinuousAntigenicTraitLikelihood.java        |  24 +-
 .../DiscreteAntigenicTraitLikelihood.java          |  24 +-
 .../misc/obsolete/AGLikelihoodCluster.java         | 435 ++++++-------
 .../misc/obsolete/AGLikelihoodTreeCluster.java     |  43 +-
 .../branchratemodel/CompoundBranchRateModel.java   |   6 +-
 .../CountableBranchCategoryProvider.java           |  59 +-
 .../branchratemodel/DiscretizedBranchRates.java    |  37 +-
 .../evomodel/branchratemodel/LocalClockModel.java  |  31 +-
 .../branchratemodel/RandomLocalClockModel.java     |  34 +-
 .../coalescent/BayesianSkylineLikelihood.java      |  34 +-
 .../coalescent/CataclysmicDemographicModel.java    |  34 +-
 src/dr/evomodel/coalescent/ConstExpConstModel.java |  35 +-
 .../coalescent/ConstantExponentialModel.java       |  34 +-
 .../evomodel/coalescent/ConstantLogisticModel.java |  34 +-
 .../coalescent/ExpConstExpDemographicModel.java    |  34 +-
 src/dr/evomodel/coalescent/ExpansionModel.java     |  34 +-
 .../coalescent/ExponentialConstantModel.java       |  34 +-
 .../coalescent/ExponentialLogisticModel.java       |  34 +-
 .../GMRFMultilocusSkyrideLikelihood.java           | 402 ++++++++++--
 .../evomodel/coalescent/GMRFSkyrideLikelihood.java |  78 ++-
 .../evomodel/coalescent/LogisticGrowthModel.java   |  34 +-
 src/dr/evomodel/coalescent/SkylineLikelihood.java  |  36 +-
 .../coalescent/VariableDemographicModel.java       |  35 +-
 .../coalescent/VariableSkylineLikelihood.java      |  33 +-
 .../GMRFMultilocusSkyrideBlockUpdateOperator.java  |  64 +-
 .../AbstractMultivariateTraitLikelihood.java       | 258 ++++----
 .../BinaryLatentLiabilityLikelihood.java           |  17 +-
 .../continuous/ContinuousDiffusionStatistic.java   | 119 +++-
 .../FullyConjugateMultivariateTraitLikelihood.java | 264 ++++++--
 .../continuous/GaussianProcessFromTree.java        |  55 ++
 .../IntegratedMultivariateTraitLikelihood.java     | 229 +++----
 .../IntervalLatentLiabilityLikelihood.java         |  17 +-
 .../MultinomialLatentLiabilityLikelihood.java      |  17 +-
 ...NonPhylogeneticMultivariateTraitLikelihood.java |  17 +-
 .../OrderedLatentLiabilityLikelihood.java          |  17 +-
 .../SampledMultivariateTraitLikelihood.java        |   5 +-
 .../SemiConjugateMultivariateTraitLikelihood.java  |   4 +-
 .../evomodel/continuous/plink/PlinkImporter.java   |  15 +-
 .../epidemiology/casetocase/AbstractCase.java      |  13 +-
 .../epidemiology/casetocase/AbstractOutbreak.java  |  10 +-
 .../epidemiology/casetocase/BranchMapModel.java    |   2 +-
 .../CaseToCaseTransmissionLikelihood.java          |  49 +-
 .../casetocase/CaseToCaseTreeLikelihood.java       | 514 +++++-----------
 .../epidemiology/casetocase/CategoryOutbreak.java  |  90 ++-
 .../casetocase/PartitionedTreeLogger.java          |   5 +-
 .../casetocase/PartitionedTreeModel.java           | 493 +++++++++++++--
 .../casetocase/PartitionedTreeModelParser.java     |  21 +-
 .../casetocase/WithinCaseCoalescent.java           | 164 +----
 .../operators/InfectionBranchMovementOperator.java | 105 ++--
 .../operators/TransmissionSubtreeSlideA.java       |  15 +-
 .../operators/TransmissionSubtreeSlideB.java       |  11 +-
 .../operators/TransmissionWilsonBaldingA.java      |  21 +-
 .../operators/TransmissionWilsonBaldingB.java      |  10 +-
 .../operators/LatentFactorHamiltonianMC.java       | 102 +--
 .../evomodel/operators/LoadingsHamiltonianMC.java  | 155 +++++
 src/dr/evomodel/operators/SubtreeLeapOperator.java |   6 +-
 .../speciation/AlloppSpeciesNetworkModel.java      |  57 +-
 .../speciation/BirthDeathCollapseModel.java        |  45 +-
 .../speciation/BirthDeathGernhard08Model.java      |  52 +-
 .../speciation/BirthDeathSerialSamplingModel.java  |  32 +-
 .../evomodel/speciation/MulSpeciesTreeModel.java   | 210 ++++---
 .../speciation/PopsIOSpeciesTreeModel.java         |  13 +-
 src/dr/evomodel/speciation/SpeciesTreeModel.java   |  33 +-
 src/dr/evomodel/substmodel/Blosum62.java           |  22 +-
 src/dr/evomodel/substmodel/CPREV.java              |  20 +-
 .../substmodel/ComplexSubstitutionModel.java       |  24 +-
 src/dr/evomodel/substmodel/Dayhoff.java            |  22 +-
 src/dr/evomodel/substmodel/FLU.java                |  25 +-
 .../evomodel/substmodel/GLMSubstitutionModel.java  |  18 +-
 src/dr/evomodel/substmodel/GTR.java                |  34 +-
 src/dr/evomodel/substmodel/HKY.java                |  40 +-
 src/dr/evomodel/substmodel/JTT.java                |  21 +-
 src/dr/evomodel/substmodel/LG.java                 |  23 +-
 src/dr/evomodel/substmodel/MTREV.java              |  28 +-
 .../substmodel/MarginalVarianceStatistic.java      |   2 +-
 .../substmodel/SVSGeneralSubstitutionModel.java    |  28 +-
 src/dr/evomodel/substmodel/TN93.java               |  34 +-
 src/dr/evomodel/substmodel/WAG.java                |  22 +-
 .../tree}/ConditionalCladeProbability.java         |   4 +-
 .../tree/ProgressiveScalarTreeTransform.java       |   7 +
 src/dr/evomodel/tree/TerminalBranchStatistic.java  |  73 +++
 src/dr/evomodel/tree/TransformedTreeModel.java     |  30 +-
 src/dr/evomodel/tree/TreeModel.java                |  56 +-
 src/dr/evomodel/tree/TreeTransform.java            |  28 +-
 .../treelikelihood/HypermutantErrorModel.java      |  44 +-
 .../treelikelihood/SequenceErrorModel.java         |  46 +-
 src/dr/evomodelxml/MSSD/CTMCScalePriorParser.java  |   4 +-
 src/dr/evomodelxml/TreeWorkingPriorParsers.java    |   2 +-
 .../branchratemodel/LocalClockModelParser.java     |   4 +-
 .../coalescent/GMRFSkyrideLikelihoodParser.java    |  84 ++-
 .../operators/LoadingsHamiltonianMCParser.java     |  65 ++
 .../operators/SubtreeLeapOperatorParser.java       |  12 +-
 .../substmodel/MultivariateOUModelParser.java      |   2 +-
 .../evomodelxml/tree/MonophylyStatisticParser.java |   6 +-
 .../tree/TerminalBranchStatisticParser.java        |  73 +++
 src/dr/evoxml/NewickParser.java                    |  10 +-
 .../evoxml/UncertainAttributePatternsParser.java   | 230 +++++++
 .../distribution/GeneralizedLinearModel.java       |  16 +-
 .../distribution/MomentDistributionModel.java      |  27 +-
 .../MultivariateDistributionLikelihood.java        |   1 -
 .../MultivariateNormalDistributionModel.java       |  10 +
 .../distribution}/MultivariateOUModel.java         |   6 +-
 .../distribution/NormalDistributionModel.java      |  12 +-
 .../mcmc/MarginalLikelihoodEstimator.java          |  85 ++-
 src/dr/inference/mcmcmc/MCMCMC.java                |  15 -
 src/dr/inference/model/ComplementParameter.java    | 112 ++++
 src/dr/inference/model/CompoundLikelihood.java     |  23 +-
 .../ElementWiseMatrixMultiplicationParameter.java  |  69 +++
 .../model/EqualityConstrainedParameter.java        |  17 +-
 src/dr/inference/model/FastBUTMP.java              | 226 +++++++
 src/dr/inference/model/FastMatrixParameter.java    |   7 +
 src/dr/inference/model/FastTransposedBUTMP.java    | 125 ++++
 .../inference/model/IndianBuffetProcessPrior.java  |   4 +-
 src/dr/inference/model/LatentFactorModel.java      |  93 ++-
 src/dr/inference/model/MaskedParameter.java        |  34 +-
 .../inference/model/MatrixParameterInterface.java  |   2 +-
 src/dr/inference/model/MixtureModelLikelihood.java |  19 +-
 src/dr/inference/model/Parameter.java              |   4 +-
 .../inference/model/TransposedMatrixParameter.java |   5 +
 src/dr/inference/model/WeightedMixtureModel.java   |  18 +-
 .../operators/EllipticalSliceOperator.java         |   8 +-
 .../inference/operators/FactorGibbsOperator.java   |  13 +-
 .../operators/FactorIndependenceOperator.java      |  13 +-
 src/dr/inference/operators/FactorOperator.java     |  13 +-
 src/dr/inference/operators/GibbsOperator.java      |   4 +-
 .../LatentFactorModelPrecisionGibbsOperator.java   |   7 +-
 .../inference/operators/LoadingsGibbsOperator.java |   9 +-
 ...or.java => LoadingsGibbsTruncatedOperator.java} | 131 ++--
 .../operators/LoadingsIndependenceOperator.java    |   7 +-
 src/dr/inference/operators/MaskMoveOperator.java   | 182 ++++++
 .../operators/ModeIndependenceOperator.java        | 258 ++++++++
 .../operators/PathDependentOperator.java}          |  23 +-
 src/dr/inference/trace/CnCsPerSiteAnalysis.java    |  87 ++-
 .../inference/trace/CnCsToDnDsPerSiteAnalysis.java |  28 +-
 src/dr/inference/trace/DnDsPerSiteAnalysis.java    |  29 +-
 .../distribution/GammaDistributionModelParser.java |  44 +-
 .../distribution/GeneralizedLinearModelParser.java |  15 +-
 .../MomentDistributionModelParser.java             |   8 +-
 .../model/ComplementParameterParser.java           |  67 ++
 .../model/CompoundLikelihoodParser.java            |   6 +-
 .../ElementWiseMatrixMultiplicationParser.java     |  48 ++
 src/dr/inferencexml/model/FastBUTMPParser.java     | 108 ++++
 .../model/ImmutableParameterParser.java            |   5 +
 .../model/IndianBuffetProcessPriorParser.java      |   2 +-
 .../model/LatentFactorModelParser.java             |  23 +-
 .../operators/LoadingsGibbsOperatorParser.java     |  15 +
 .../operators/MaskMoveOperatorParser.java          | 129 ++++
 .../distributions/CompoundGaussianProcess.java     | 154 ++++-
 .../math/distributions/DirichletDistribution.java  |  33 +-
 .../GaussianProcessRandomGenerator.java            |   4 +
 .../MultivariateNormalDistribution.java            |   9 +
 src/dr/math/distributions/NormalDistribution.java  |   1 +
 src/dr/util/Citable.java                           |  14 +-
 src/dr/util/Citation.java                          | 168 ++++-
 src/dr/util/CommonCitations.java                   | 201 +++++-
 src/dr/util/MessageLogHandler.java                 |   8 +-
 .../RelativeRatesType.java => util/Pair.java}      |  37 +-
 src/dr/util/Transform.java                         |  30 +-
 src/dr/xml/AbstractXMLObjectParser.java            |   7 +-
 src/dr/xml/XMLObjectParser.java                    |   4 +-
 src/dr/xml/XMLParser.java                          | 126 ++--
 .../AncestralStateBeagleTreeLikelihoodTest.java    |   1 +
 src/test/dr/app/beagle/MarkovJumpsTest.java        |   1 +
 283 files changed, 9422 insertions(+), 6080 deletions(-)

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/beast-mcmc.git



More information about the debian-med-commit mailing list