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Cleaning up old stuff - including old likelihood native libraries #1189

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7e163fd
Cleaning up old stuff - including old likelihood native libraries
rambaut Jun 28, 2024
c073163
Merge remote-tracking branch 'origin/master' into cleanup
rambaut Jul 5, 2024
d1f72a2
Merge branch 'main' into cleanup
rambaut Nov 12, 2025
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3 changes: 0 additions & 3 deletions src/dr/app/beast/development_parsers.properties
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Expand Up @@ -147,9 +147,6 @@ dr.inference.operators.factorAnalysis.LoadingsRotationOperator
dr.inference.model.SVDStatistic
dr.inferencexml.operators.factorAnalysis.IntegratedFactorsParser

# SEQUENCE SIMULATOR
dr.app.seqgen.RecomboGen

# POPULATION MODELS
dr.evomodel.epidemiology.LogisticGrowthN0ModelParser
dr.evomodelxml.coalescent.demographicmodel.ExponentialConstantModelParser
Expand Down
105 changes: 29 additions & 76 deletions src/dr/app/beast/release_parsers.properties
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Expand Up @@ -45,10 +45,6 @@ dr.evoxml.GeneralDataTypeParser
dr.evoxml.CompositeDataTypeParser
dr.evoxml.DateParser
dr.evoxml.LocationParser
dr.evoxml.OldHiddenNucleotideParser
dr.evoxml.MicrosatelliteParser
dr.evoxml.MicrosatellitePatternParser
dr.evoxml.MicrosatelliteSimulatorParser
dr.evoxml.KStateDataTypeParser
dr.evoxml.MutationDeathTypeParser
dr.evoxml.MetagenomeDataParser
Expand Down Expand Up @@ -286,7 +282,6 @@ dr.evoxml.MultiLociDistanceParser

# TREE MODELS
dr.evomodelxml.tree.TreeModelParser
dr.evomodelxml.tree.MicrosatelliteSamplerTreeModelParser
dr.evomodelxml.tree.TipHeightLikelihoodParser
dr.evomodelxml.tree.TreeMetricStatisticParser
dr.evomodelxml.tree.TreeLengthStatisticParser
Expand Down Expand Up @@ -327,14 +322,8 @@ dr.evomodelxml.operators.GibbsPruneAndRegraftParser
dr.evomodelxml.operators.RateExchangeOperatorParser
dr.evomodelxml.operators.TreeBitMoveOperatorParser
dr.evomodelxml.operators.TreeBitRandomWalkOperatorParser
dr.evomodelxml.operators.TreeNodeSlideParser
dr.evomodel.continuous.GibbsIndependentCoalescentOperator
dr.evomodel.continuous.CoalescentTreeRejectionSampler
dr.evomodelxml.operators.MicrosatelliteUpDownOperatorParser
dr.evomodelxml.operators.MicrosatelliteBitFlipOperatorParser
dr.evomodelxml.operators.MicrosatelliteModelSelectOperatorParser
dr.evomodelxml.operators.MicrosatelliteFullAncestryImportanceSamplingOperatorParser
dr.evomodelxml.operators.MicrosatelliteSingleAncestralStateGibbsOperatorParser
dr.evomodelxml.operators.RandomWalkIntegerNodeHeightWeightedOperatorParser
dr.evomodelxml.operators.RandomWalkIntegerSetSizeWeightedOperatorParser

Expand All @@ -350,7 +339,7 @@ dr.evomodelxml.tree.CTMCScalePriorParser
# RATE OPERATORS
dr.evomodelxml.operators.RateScaleOperatorParser
dr.evomodelxml.operators.RateVarianceScaleOperatorParser
dr.evomodelxml.operators.RateSampleOperatorParser
#dr.evomodelxml.operators.RateSampleOperatorParser

# LIKELIHOODS
dr.inferencexml.model.CompoundLikelihoodParser
Expand Down Expand Up @@ -546,19 +535,16 @@ dr.inferencexml.model.DiagonalMatrixParser
dr.inferencexml.model.CompoundSymmetricMatrixParser
dr.inferencexml.model.CorrelationSymmetricMatrixParser
dr.inferencexml.model.MarkovRandomFieldMatrixParser
dr.inferencexml.distribution.MultivariateOUModelParser
#dr.inferencexml.distribution.MultivariateOUModelParser
dr.inferencexml.model.CachedMatrixInverseParser

dr.oldevomodelxml.substmodel.PositiveDefiniteSubstitutionModelParser
dr.evomodelxml.substmodel.PositiveDefiniteSubstitutionModelParser

# STOCHASTIC VARIABLE SELECTION
dr.evomodel.operators.BitFlipInSubstitutionModelOperator
dr.inference.operators.RateBitExchangeOperator
dr.inferencexml.distribution.CachedDistributionLikelihoodParser

# SEQUENCE SIMULATOR
dr.app.seqgen.SequenceSimulator

# SPECIAL STATISTICS
dr.inference.model.MonotonicStatistic
dr.inference.model.MatrixInverseStatistic
Expand All @@ -580,34 +566,32 @@ dr.inferencexml.model.LikelihoodBenchmarkerParser
dr.inferencexml.distribution.EmpiricalDistributionLikelihoodParser

# ANCESTRAL RECOMBINATION GRAPHS
dr.evomodel.arg.coalescent.ARGCoalescentLikelihood
dr.evomodel.arg.coalescent.ARGUniformPrior
dr.evomodel.arg.likelihood.ARGLikelihood
dr.evomodel.arg.operators.SlidingPatternsOperator
dr.evomodel.arg.branchratemodel.ARGDiscretizedBranchRates
dr.evomodel.arg.ARGModel
dr.evomodel.arg.UniformPartitionLikelihood
dr.evomodel.arg.operators.ARGSubtreeSlideOperator
dr.evomodel.arg.operators.ARGExchangeOperator
dr.evomodel.arg.operators.ObsoleteARGAddRemoveEventOperator
dr.evomodel.arg.operators.ARGPartitioningOperator
dr.evomodel.arg.operators.ObsoleteARGNewEventOperator
dr.evomodel.arg.operators.ARGAddRemoveEventOperator
dr.evomodel.arg.operators.ARGSwapOperator
dr.evomodel.arg.ARGReassortmentNodeCountStatistic
dr.evomodel.arg.ARGTraceAnalysisParser
dr.evomodel.arg.ARGReassortmentTimingStatistic
dr.evomodel.arg.PoissonPartitionLikelihood
dr.evomodel.arg.RecombinationPartitionStatistic
dr.evomodel.arg.ARGTotalLengthStatistic
dr.evomodel.arg.ARGDistinctTreeCountStatistic
dr.evomodel.arg.HierarchicalPartitionLikelihood
dr.evomodel.arg.ARGRelaxedClock
dr.evomodel.arg.ARGRatePrior
dr.evomodel.arg.ARGTreeLogger
dr.evomodel.arg.ARGLogger

dr.evoxml.MicrosatellitePatternStatisticParser
#dr.evomodel.arg.coalescent.ARGCoalescentLikelihood
#dr.evomodel.arg.coalescent.ARGUniformPrior
#dr.evomodel.arg.likelihood.ARGLikelihood
#dr.evomodel.arg.operators.SlidingPatternsOperator
#dr.evomodel.arg.branchratemodel.ARGDiscretizedBranchRates
#dr.evomodel.arg.ARGModel
#dr.evomodel.arg.UniformPartitionLikelihood
#dr.evomodel.arg.operators.ARGSubtreeSlideOperator
#dr.evomodel.arg.operators.ARGExchangeOperator
#dr.evomodel.arg.operators.ObsoleteARGAddRemoveEventOperator
#dr.evomodel.arg.operators.ARGPartitioningOperator
#dr.evomodel.arg.operators.ObsoleteARGNewEventOperator
#dr.evomodel.arg.operators.ARGAddRemoveEventOperator
#dr.evomodel.arg.operators.ARGSwapOperator
#dr.evomodel.arg.ARGReassortmentNodeCountStatistic
#dr.evomodel.arg.ARGTraceAnalysisParser
#dr.evomodel.arg.ARGReassortmentTimingStatistic
#dr.evomodel.arg.PoissonPartitionLikelihood
#dr.evomodel.arg.RecombinationPartitionStatistic
#dr.evomodel.arg.ARGTotalLengthStatistic
#dr.evomodel.arg.ARGDistinctTreeCountStatistic
#dr.evomodel.arg.HierarchicalPartitionLikelihood
#dr.evomodel.arg.ARGRelaxedClock
#dr.evomodel.arg.ARGRatePrior
#dr.evomodel.arg.ARGTreeLogger
#dr.evomodel.arg.ARGLogger

# N & S counting
dr.evomodel.trace.DnDsPerSiteAnalysis
Expand Down Expand Up @@ -728,34 +712,3 @@ dr.evomodel.antigenic.NPAntigenicLikelihood
# NEW ANTIGENIC EVOLUTION/EVOLUTIONARY CARTOGRAPHY
dr.evomodelxml.antigenic.AntigenicLikelihoodParser
dr.evomodelxml.antigenic.AntigenicLikelihoodGradientParser

## AlloppNet by Graham Jones
# ALLOPOLYPLOID NETWORKS
dr.evomodel.alloppnet.parsers.AlloppMSCoalescentParser
dr.evomodel.alloppnet.parsers.AlloppNetworkPriorModelParser
dr.evomodel.alloppnet.parsers.AlloppNetworkPriorParser
dr.evomodel.alloppnet.parsers.AlloppSpeciesBindingsApSpInfoParser
dr.evomodel.alloppnet.parsers.AlloppSpeciesBindingsIndividualParser
dr.evomodel.alloppnet.parsers.AlloppSpeciesBindingsParser
dr.evomodel.alloppnet.parsers.AlloppSpeciesNetworkModelParser
dr.evomodel.alloppnet.parsers.AlloppNumHybsStatisticParser

# MULTIPLY LABELLED TREES
dr.evomodel.alloppnet.parsers.MulMSCoalescentParser
dr.evomodel.alloppnet.parsers.MulSpeciesBindingsParser
dr.evomodel.alloppnet.parsers.MulSpeciesTreeModelParser
dr.evomodel.alloppnet.parsers.MulSpeciesTreePriorParser

# OPERATORS
dr.evomodel.alloppnet.parsers.AlloppNetworkNodeSlideParser
dr.evomodel.alloppnet.parsers.AlloppSequenceReassignmentParser
dr.evomodel.alloppnet.parsers.AlloppMoveLegsParser
dr.evomodel.alloppnet.parsers.AlloppChangeNumHybridizationsParser
dr.evomodel.alloppnet.parsers.AlloppHybPopSizesScaleParser
dr.evomodel.alloppnet.parsers.MulTreeNodeSlideParser
dr.evomodel.alloppnet.parsers.MulTreeSequenceReassignmentParser

## DISSECT by Graham Jones
# SPECIES DELIMITATION
dr.evomodel.alloppnet.parsers.BirthDeathCollapseModelParser
dr.evomodel.alloppnet.parsers.BirthDeathCollapseNClustersStatisticParser
2 changes: 1 addition & 1 deletion src/dr/app/beauti/components/ancestralstates/AncestralStatesComponentGenerator.java
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Expand Up @@ -37,8 +37,8 @@
import dr.evomodel.tree.DefaultTreeModel;
import dr.evomodel.tree.TreeModel;
import dr.evomodelxml.tree.TreeLoggerParser;
import dr.evomodelxml.treelikelihood.AncestralStateTreeLikelihoodParser;
import dr.evomodelxml.treelikelihood.MarkovJumpsTreeLikelihoodParser;
import dr.oldevomodelxml.treelikelihood.AncestralStateTreeLikelihoodParser;
import dr.util.Attribute;

import java.util.ArrayList;
Expand Down
57 changes: 29 additions & 28 deletions src/dr/app/beauti/components/discrete/DiscreteTraitsComponentGenerator.java
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Expand Up @@ -28,7 +28,11 @@
package dr.app.beauti.components.discrete;

import dr.evomodel.tree.DefaultTreeModel;
import dr.evomodelxml.substmodel.ComplexSubstitutionModelParser;
import dr.evomodelxml.substmodel.FrequencyModelParser;
import dr.evomodelxml.substmodel.GeneralSubstitutionModelParser;
import dr.evomodelxml.substmodel.GlmSubstitutionModelParser;
import dr.evomodelxml.treelikelihood.AncestralStateTreeLikelihoodParser;
import dr.evomodelxml.treelikelihood.MarkovJumpsTreeLikelihoodParser;
import dr.app.beauti.components.ancestralstates.AncestralStatesComponentOptions;
import dr.app.beauti.generator.BaseComponentGenerator;
Expand All @@ -42,14 +46,6 @@
import dr.inference.operators.MultivariateNormalOperator;
import dr.inferencexml.distribution.BinomialLikelihoodParser;
import dr.inferencexml.distribution.GeneralizedLinearModelParser;
import dr.oldevomodel.sitemodel.SiteModel;
import dr.oldevomodel.substmodel.AbstractSubstitutionModel;
import dr.oldevomodelxml.sitemodel.GammaSiteModelParser;
import dr.oldevomodelxml.substmodel.ComplexSubstitutionModelParser;
import dr.oldevomodelxml.substmodel.FrequencyModelParser;
import dr.oldevomodelxml.substmodel.GeneralSubstitutionModelParser;
import dr.oldevomodelxml.treelikelihood.AncestralStateTreeLikelihoodParser;
import dr.oldevomodelxml.treelikelihood.TreeLikelihoodParser;
import dr.evoxml.AttributePatternsParser;
import dr.evoxml.GeneralDataTypeParser;
import dr.evoxml.TaxaParser;
Expand All @@ -63,7 +59,12 @@

import java.util.Set;

import static dr.app.phylogeography.tools.DiscreteRatePriorGenerator.MODEL;
import static dr.evomodelxml.siteratemodel.SiteModelParser.SITE_MODEL;
import static dr.evomodelxml.siteratemodel.SiteModelParser.SUBSTITUTION_MODEL;
import static dr.evomodelxml.substmodel.ComplexSubstitutionModelParser.ROOT_FREQUENCIES;
import static dr.evomodelxml.treelikelihood.AncestralStateTreeLikelihoodParser.RECONSTRUCTING_TREE_LIKELIHOOD;
import static dr.evomodelxml.treelikelihood.BeagleTreeLikelihoodParser.TREE_LIKELIHOOD;

/**
* @author Andrew Rambaut
Expand Down Expand Up @@ -274,7 +275,7 @@ private void writeDiscreteTraitsSubstitutionModel(PartitionSubstitutionModel mod
writer.writeComment("symmetric CTMC model for discrete state reconstructions");

writer.writeOpenTag(GeneralSubstitutionModelParser.GENERAL_SUBSTITUTION_MODEL, new Attribute[]{
new Attribute.Default<String>(XMLParser.ID, prefix + AbstractSubstitutionModel.MODEL)});
new Attribute.Default<String>(XMLParser.ID, prefix + MODEL)});

writer.writeIDref(GeneralDataTypeParser.GENERAL_DATA_TYPE, prefix + "dataType");

Expand All @@ -292,7 +293,7 @@ private void writeDiscreteTraitsSubstitutionModel(PartitionSubstitutionModel mod
writer.writeComment("asymmetric CTMC model for discrete state reconstructions");

writer.writeOpenTag(GeneralSubstitutionModelParser.GENERAL_SUBSTITUTION_MODEL, new Attribute[]{
new Attribute.Default<String>(XMLParser.ID, prefix + AbstractSubstitutionModel.MODEL),
new Attribute.Default<String>(XMLParser.ID, prefix + MODEL),
new Attribute.Default<Boolean>(ComplexSubstitutionModelParser.RANDOMIZE, false)});

writer.writeIDref(GeneralDataTypeParser.GENERAL_DATA_TYPE, prefix + "dataType");
Expand All @@ -311,7 +312,7 @@ private void writeDiscreteTraitsSubstitutionModel(PartitionSubstitutionModel mod
writer.writeComment("GLM substitution model");

writer.writeOpenTag(GlmSubstitutionModelParser.GLM_SUBSTITUTION_MODEL, new Attribute[] {
new Attribute.Default<String>(XMLParser.ID, prefix + AbstractSubstitutionModel.MODEL)
new Attribute.Default<String>(XMLParser.ID, prefix + MODEL)
});

writer.writeIDref(GeneralDataTypeParser.GENERAL_DATA_TYPE, prefix + "dataType");
Expand Down Expand Up @@ -398,9 +399,9 @@ private void writeDiscreteTraitsSubstitutionModelReferences(XMLWriter writer) {
for (PartitionSubstitutionModel model : options.getPartitionSubstitutionModels(GeneralDataType.INSTANCE)) {
if (model.getDiscreteSubstType() == DiscreteSubstModelType.GLM_SUBST) {
// not strictly necessary but makes the XML consistent
writer.writeIDref(GlmSubstitutionModelParser.GLM_SUBSTITUTION_MODEL, model.getName() + "." + AbstractSubstitutionModel.MODEL);
writer.writeIDref(GlmSubstitutionModelParser.GLM_SUBSTITUTION_MODEL, model.getName() + "." + MODEL);
} else {
writer.writeIDref(GeneralSubstitutionModelParser.GENERAL_SUBSTITUTION_MODEL, model.getName() + "." + AbstractSubstitutionModel.MODEL);
writer.writeIDref(GeneralSubstitutionModelParser.GENERAL_SUBSTITUTION_MODEL, model.getName() + "." + MODEL);
}
}
}
Expand Down Expand Up @@ -434,19 +435,19 @@ private void writeDiscreteFrequencyModel(String prefix, String dataTypePrefix, i

private void writeDiscreteTraitsSiteModel(PartitionSubstitutionModel model, XMLWriter writer) {
String prefix = model.getName() + ".";
writer.writeOpenTag(SiteModel.SITE_MODEL, new Attribute[]{
new Attribute.Default<String>(XMLParser.ID, prefix + SiteModel.SITE_MODEL)});
writer.writeOpenTag(SITE_MODEL, new Attribute[]{
new Attribute.Default<String>(XMLParser.ID, prefix + SITE_MODEL)});

writer.writeOpenTag(GammaSiteModelParser.SUBSTITUTION_MODEL);
writer.writeOpenTag(SUBSTITUTION_MODEL);
if (model.getDiscreteSubstType() == DiscreteSubstModelType.GLM_SUBST) {
// not strictly necessary but makes the XML consistent
writer.writeIDref(GlmSubstitutionModelParser.GLM_SUBSTITUTION_MODEL, prefix + AbstractSubstitutionModel.MODEL);
writer.writeIDref(GlmSubstitutionModelParser.GLM_SUBSTITUTION_MODEL, prefix + MODEL);
} else {
writer.writeIDref(GeneralSubstitutionModelParser.GENERAL_SUBSTITUTION_MODEL, prefix + AbstractSubstitutionModel.MODEL);
writer.writeIDref(GeneralSubstitutionModelParser.GENERAL_SUBSTITUTION_MODEL, prefix + MODEL);
}
writer.writeCloseTag(GammaSiteModelParser.SUBSTITUTION_MODEL);
writer.writeCloseTag(SUBSTITUTION_MODEL);

writer.writeCloseTag(SiteModel.SITE_MODEL);
writer.writeCloseTag(SITE_MODEL);
}

private void writeRatesAndIndicators(PartitionSubstitutionModel model, int dimension, Integer relativeTo, XMLWriter writer) {
Expand Down Expand Up @@ -518,15 +519,15 @@ public void writeTreeLikelihood(AbstractPartitionData partition, XMLWriter write
PartitionClockModel clockModel = partition.getPartitionClockModel();

AncestralStatesComponentOptions ancestralStatesOptions = (AncestralStatesComponentOptions)options.getComponentOptions(AncestralStatesComponentOptions.class);
String treeLikelihoodTag = TreeLikelihoodParser.ANCESTRAL_TREE_LIKELIHOOD;
String treeLikelihoodTag = RECONSTRUCTING_TREE_LIKELIHOOD;
if (ancestralStatesOptions.isCountingStates(partition)) {
treeLikelihoodTag = MarkovJumpsTreeLikelihoodParser.MARKOV_JUMP_TREE_LIKELIHOOD;
}

boolean saveCompleteHistory = ancestralStatesOptions.isCompleteHistoryLogging(partition);

writer.writeOpenTag(treeLikelihoodTag, new Attribute[]{
new Attribute.Default<String>(XMLParser.ID, prefix + TreeLikelihoodParser.TREE_LIKELIHOOD),
new Attribute.Default<String>(XMLParser.ID, prefix + TREE_LIKELIHOOD),
new Attribute.Default<String>(AncestralStateTreeLikelihoodParser.RECONSTRUCTION_TAG_NAME, prefix + AncestralStateTreeLikelihoodParser.RECONSTRUCTION_TAG),
new Attribute.Default<Boolean>(MarkovJumpsTreeLikelihoodParser.USE_UNIFORMIZATION, true),
new Attribute.Default<String>(MarkovJumpsTreeLikelihoodParser.SAVE_HISTORY, saveCompleteHistory ? "true" : "false"),
Expand All @@ -535,16 +536,16 @@ public void writeTreeLikelihood(AbstractPartitionData partition, XMLWriter write

writer.writeIDref(AttributePatternsParser.ATTRIBUTE_PATTERNS, prefix + "pattern");
writer.writeIDref(DefaultTreeModel.TREE_MODEL, treeModel.getPrefix() + DefaultTreeModel.TREE_MODEL);
writer.writeIDref(SiteModel.SITE_MODEL, substModel.getName() + "." + SiteModel.SITE_MODEL);
writer.writeIDref(SITE_MODEL, substModel.getName() + "." + SITE_MODEL);

if (partition.getPartitionSubstitutionModel().getDiscreteSubstType() == DiscreteSubstModelType.GLM_SUBST) {
// not strictly necessary but makes the XML consistent
writer.writeIDref(GlmSubstitutionModelParser.GLM_SUBSTITUTION_MODEL, prefix + AbstractSubstitutionModel.MODEL);
writer.writeIDref(GlmSubstitutionModelParser.GLM_SUBSTITUTION_MODEL, prefix + MODEL);
} else {
writer.writeIDref(GeneralSubstitutionModelParser.GENERAL_SUBSTITUTION_MODEL, prefix + AbstractSubstitutionModel.MODEL);
writer.writeIDref(GeneralSubstitutionModelParser.GENERAL_SUBSTITUTION_MODEL, prefix + MODEL);
}

writer.writeIDref(GeneralSubstitutionModelParser.GENERAL_SUBSTITUTION_MODEL, substModel.getName() + "." + AbstractSubstitutionModel.MODEL);
writer.writeIDref(GeneralSubstitutionModelParser.GENERAL_SUBSTITUTION_MODEL, substModel.getName() + "." + MODEL);

ClockModelGenerator.writeBranchRatesModelRef(clockModel, writer);

Expand All @@ -563,7 +564,7 @@ private void writeTreeLikelihoodReferences(XMLWriter writer) {
for (AbstractPartitionData partition : options.dataPartitions) {
if (partition.getTraits() != null) {
AncestralStatesComponentOptions ancestralStatesOptions = (AncestralStatesComponentOptions)options.getComponentOptions(AncestralStatesComponentOptions.class);
String treeLikelihoodTag = TreeLikelihoodParser.ANCESTRAL_TREE_LIKELIHOOD;
String treeLikelihoodTag = RECONSTRUCTING_TREE_LIKELIHOOD;
if (ancestralStatesOptions.isCountingStates(partition)) {
treeLikelihoodTag = MarkovJumpsTreeLikelihoodParser.MARKOV_JUMP_TREE_LIKELIHOOD;
}
Expand All @@ -572,7 +573,7 @@ private void writeTreeLikelihoodReferences(XMLWriter writer) {
String prefix = partition.getName() + ".";
if (trait.getTraitType() == TraitData.TraitType.DISCRETE) {
writer.writeIDref(treeLikelihoodTag,
prefix + TreeLikelihoodParser.TREE_LIKELIHOOD);
prefix + TREE_LIKELIHOOD);
}
}
}
Expand Down
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