Uses of Class
pal.eval.ConditionalProbabilityStore
Packages that use ConditionalProbabilityStore
Package
Description
Classes for evaluating evolutionary hypothesis (chi-square and likelihood
criteria) and estimating model parameters.
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Uses of ConditionalProbabilityStore in pal.eval
Methods in pal.eval that return ConditionalProbabilityStoreModifier and TypeMethodDescriptionMolecularClockLikelihoodModel.Internal.calculateAscendentExtendedConditionals(double topBaseHeight, double bottomBaseHeight, PatternInfo centerPattern, ConditionalProbabilityStore ascendentConditionalProbabilityProbabilties, ConditionalProbabilityStore otherConditionalProbabilityProbabilties) MolecularClockLikelihoodModel.Internal.calculateAscendentFlatConditionals(PatternInfo centerPattern, ConditionalProbabilityStore ascenedentConditionalProbabilityProbabilties, ConditionalProbabilityStore otherConditionalProbabilityProbabilties) LHCalculator.Internal.calculateExtended(double distance, SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities, boolean modelChangedSinceLastCall) SimpleUnconstrainedLikelihoodModel.InternalImpl.calculateExtended(double distance, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities) UnconstrainedLikelihoodModel.Internal.calculateExtended(double distance, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities) MolecularClockLikelihoodModel.Internal.calculateExtendedConditionals(double topBaseHeight, double bottomBaseHeight, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilityProbabilties, ConditionalProbabilityStore rightConditionalProbabilityProbabilties) MolecularClockLikelihoodModel.Leaf.calculateExtendedConditionals(double topHeight, double bottomHeight) LHCalculator.Internal.calculateFlat(PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities) calculate flat probability information (not extended over a branch).SimpleUnconstrainedLikelihoodModel.InternalImpl.calculateFlat(PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities) UnconstrainedLikelihoodModel.Internal.calculateFlat(PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities) calculate flat probability information (not extended over a branch).MolecularClockLikelihoodModel.Internal.calculateFlatConditionals(PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilityProbabilties, ConditionalProbabilityStore rightConditionalProbabilityProbabilties) MolecularClockLikelihoodModel.Leaf.calculateFlatConditionals(double height) LHCalculator.Internal.calculatePostExtendedFlat(double distance, SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities, boolean modelChangedSinceLastCall) MolecularClockLikelihoodModel.Internal.calculatePostExtendedFlatConditionals(double topBaseHeight, double bottomBaseHeight, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilityProbabilties, ConditionalProbabilityStore rightConditionalProbabilityProbabilties) Extends left and right conditionals by type and then calculates flat conditionalsLHCalculator.Generator.createAppropriateConditionalProbabilityStore(boolean isForLeaf) MolecularClockLikelihoodModel.Instance.createAppropriateConditionalProbabilityStore(boolean isForLeaf) UnconstrainedLikelihoodModel.Instance.createAppropriateConditionalProbabilityStore(boolean isForLeaf) ConditionalProbabilityStore.getCopy()CloningLHCalculator.Leaf.getExtendedConditionalProbabilities(double distance, SubstitutionModel model, boolean modelChanged) SimpleLeafCalculator.getExtendedConditionalProbabilities(double distance, SubstitutionModel model, boolean modelChanged) SimpleUnconstrainedLikelihoodModel.LeafImpl.getExtendedConditionalProbabilities(double distance) UnconstrainedLikelihoodModel.Leaf.getExtendedConditionalProbabilities(double distance) LHCalculator.Leaf.getFlatConditionalProbabilities()SimpleLeafCalculator.getFlatConditionalProbabilities()SimpleUnconstrainedLikelihoodModel.LeafImpl.getFlatConditionalProbabilities()UnconstrainedLikelihoodModel.Leaf.getFlatConditionalProbabilities()Methods in pal.eval with parameters of type ConditionalProbabilityStoreModifier and TypeMethodDescriptionMolecularClockLikelihoodModel.Internal.calculateAscendentExtendedConditionals(double topBaseHeight, double bottomBaseHeight, PatternInfo centerPattern, ConditionalProbabilityStore ascendentConditionalProbabilityProbabilties, ConditionalProbabilityStore otherConditionalProbabilityProbabilties) MolecularClockLikelihoodModel.Internal.calculateAscendentFlatConditionals(PatternInfo centerPattern, ConditionalProbabilityStore ascenedentConditionalProbabilityProbabilties, ConditionalProbabilityStore otherConditionalProbabilityProbabilties) protected abstract voidLHCalculator.AbstractExternal.calculateCategoryPatternProbabilities(double distance, SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftFlatConditionalProbabilities, ConditionalProbabilityStore rightFlatConditionalProbabilities, ConditionalProbabilityStore tempStore, double[][] categoryPatternLogLikelihoodStore) protected abstract voidLHCalculator.AbstractExternal.calculateCategoryPatternProbabilities(SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities, double[][] categoryPatternLikelihoodStore) voidLHCalculator.External.calculateExtended(double distance, SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities, ConditionalProbabilityStore resultStore) LHCalculator.Internal.calculateExtended(double distance, SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities, boolean modelChangedSinceLastCall) SimpleUnconstrainedLikelihoodModel.InternalImpl.calculateExtended(double distance, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities) voidUnconstrainedLikelihoodModel.External.calculateExtended(double distance, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities, ConditionalProbabilityStore resultStore) UnconstrainedLikelihoodModel.Internal.calculateExtended(double distance, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities) voidMolecularClockLikelihoodModel.External.calculateExtendedConditionals(double topBaseHeight, double bottomBaseHeight, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities, ConditionalProbabilityStore resultStore) MolecularClockLikelihoodModel.Internal.calculateExtendedConditionals(double topBaseHeight, double bottomBaseHeight, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilityProbabilties, ConditionalProbabilityStore rightConditionalProbabilityProbabilties) voidLHCalculator.External.calculateFlat(PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities, ConditionalProbabilityStore resultStore) LHCalculator.Internal.calculateFlat(PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities) calculate flat probability information (not extended over a branch).SimpleUnconstrainedLikelihoodModel.InternalImpl.calculateFlat(PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities) voidUnconstrainedLikelihoodModel.External.calculateFlat(PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities, ConditionalProbabilityStore resultStore) UnconstrainedLikelihoodModel.Internal.calculateFlat(PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities) calculate flat probability information (not extended over a branch).voidMolecularClockLikelihoodModel.External.calculateFlatConditionals(double rootHeight, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilitiesStore, ConditionalProbabilityStore rightConditionalProbabilitiesStore, ConditionalProbabilityStore resultConditionalProbabilitiesStore) MolecularClockLikelihoodModel.Internal.calculateFlatConditionals(PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilityProbabilties, ConditionalProbabilityStore rightConditionalProbabilityProbabilties) doubleLHCalculator.External.calculateLogLikelihood(double distance, SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftFlatConditionalProbabilities, ConditionalProbabilityStore rightFlatConditionalProbabilities, ConditionalProbabilityStore tempStore) Calculate the likelihood given two sub trees (left, right) and their flat (unextend) likeihood probabilitiesdoubleLHCalculator.External.calculateLogLikelihood(SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities) Calculate the likelihood given two sub trees (left, right) and their extended likeihood probabilitiesdoubleMolecularClockLikelihoodModel.External.calculateLogLikelihood(double rootHeight, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilitiesStore, ConditionalProbabilityStore rightConditionalProbabilitiesStore) Calculate the likelihood given two sub trees (left, right) and their extended likeihood probabilitiesdoubleUnconstrainedLikelihoodModel.External.calculateLogLikelihood(double distance, PatternInfo centerPattern, ConditionalProbabilityStore leftFlatConditionalProbabilities, ConditionalProbabilityStore rightFlatConditionalProbabilities, ConditionalProbabilityStore tempStore) Calculate the likelihood given two sub trees (left, right) and their flat (unextend) likeihood probabilitiesdoubleUnconstrainedLikelihoodModel.External.calculateLogLikelihood(PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities) Calculate the likelihood given two sub trees (left, right) and their extended likeihood probabilitiesdoubleMolecularClockLikelihoodModel.External.calculateLogLikelihoodNonRoot(double nodeHeight, PatternInfo centerPattern, ConditionalProbabilityStore ascendentConditionalProbabilitiesStore, ConditionalProbabilityStore descendentConditionalProbabilitiesStore) Calculate the likelihood given a non root nodedoubleLHCalculator.External.calculateLogLikelihoodSingle(SubstitutionModel model, int[] patternWeights, int numberOfPatterns, ConditionalProbabilityStore conditionalProbabilityStore) Calculate the likelihood given the conditional probabilites at the rootdoubleMolecularClockLikelihoodModel.External.calculateLogLikelihoodSingle(double rootHeight, PatternInfo centerPattern, ConditionalProbabilityStore conditionalProbabilitiesStore) doubleUnconstrainedLikelihoodModel.External.calculateLogLikelihoodSingle(int[] patternWeights, int numberOfPatterns, ConditionalProbabilityStore conditionalProbabilityStore) Calculate the likelihood given the conditional probabilites at the rootLHCalculator.Internal.calculatePostExtendedFlat(double distance, SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities, boolean modelChangedSinceLastCall) MolecularClockLikelihoodModel.Internal.calculatePostExtendedFlatConditionals(double topBaseHeight, double bottomBaseHeight, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilityProbabilties, ConditionalProbabilityStore rightConditionalProbabilityProbabilties) Extends left and right conditionals by type and then calculates flat conditionalsvoidMolecularClockLikelihoodModel.External.calculateSingleAscendentExtendedConditionalsDirect(double topBaseHeight, double bottomBaseHeight, PatternInfo centerPattern, ConditionalProbabilityStore ascendentConditionalProbabilityProbabilties) voidMolecularClockLikelihoodModel.External.calculateSingleAscendentExtendedConditionalsIndirect(double topBaseHeight, double bottomBaseHeight, PatternInfo centerPattern, ConditionalProbabilityStore baseAscendentConditionalProbabilityProbabilties, ConditionalProbabilityStore resultConditionalProbabilityProbabilties) voidMolecularClockLikelihoodModel.External.calculateSingleDescendentExtendedConditionals(double topBaseHeight, double bottomBaseHeight, PatternInfo centerPattern, ConditionalProbabilityStore descendentConditionalProbabilities) voidLHCalculator.External.calculateSingleExtendedDirect(double distance, SubstitutionModel model, int numberOfPatterns, ConditionalProbabilityStore conditionalProbabilities) Extend the conditionals back in time by some distance, with some modelvoidUnconstrainedLikelihoodModel.External.calculateSingleExtendedDirect(double distance, int numberOfPatterns, ConditionalProbabilityStore conditionalProbabilities) Extend the conditionals back in time by some distancevoidLHCalculator.External.calculateSingleExtendedIndirect(double distance, SubstitutionModel model, int numberOfPatterns, ConditionalProbabilityStore baseConditionalProbabilities, ConditionalProbabilityStore resultConditionalProbabilities) Extend the conditionals back in time by some distance, with some modelvoidUnconstrainedLikelihoodModel.External.calculateSingleExtendedIndirect(double distance, int numberOfPatterns, ConditionalProbabilityStore baseConditionalProbabilities, ConditionalProbabilityStore resultConditionalProbabilities) Extend the conditionals back in time by some distanceMolecularClockLikelihoodModel.External.calculateSiteDetails(double rootHeight, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilitiesStore, ConditionalProbabilityStore rightConditionalProbabilitiesStore) final SiteDetailsLHCalculator.AbstractExternal.calculateSiteDetailsRooted(SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilitiesStore, ConditionalProbabilityStore rightConditionalProbabilitiesStore) LHCalculator.External.calculateSiteDetailsRooted(SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilitiesStore, ConditionalProbabilityStore rightConditionalProbabilitiesStore) Calculate the conditional probabilities of each pattern for each categoryUnconstrainedLikelihoodModel.External.calculateSiteDetailsRooted(PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilitiesStore, ConditionalProbabilityStore rightConditionalProbabilitiesStore) Calculate the conditional probabilities of each pattern for each categoryfinal SiteDetailsLHCalculator.AbstractExternal.calculateSiteDetailsUnrooted(double distance, SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftFlatConditionalProbabilities, ConditionalProbabilityStore rightFlatConditionalProbabilities, ConditionalProbabilityStore tempStore) LHCalculator.External.calculateSiteDetailsUnrooted(double distance, SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilitiesStore, ConditionalProbabilityStore rightConditionalProbabilitiesStore, ConditionalProbabilityStore tempStore) Calculate the conditional probabilities of each pattern for each categoryUnconstrainedLikelihoodModel.External.calculateSiteDetailsUnrooted(double distance, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilitiesStore, ConditionalProbabilityStore rightConditionalProbabilitiesStore, ConditionalProbabilityStore tempStore) Calculate the conditional probabilities of each pattern for each categoryvoidConditionalProbabilityStore.ExtraProcessor.setParent(ConditionalProbabilityStore parent) -
Uses of ConditionalProbabilityStore in pal.treesearch
Methods in pal.treesearch that return ConditionalProbabilityStoreModifier and TypeMethodDescriptionConstraintModel.createAppropriateConditionalProbabilityStore(boolean isForLeaf) FixedBSRDTGlobalClockModel.createAppropriateConditionalProbabilityStore(boolean isForLeaf) FixedSRDTGlobalClockModel.createAppropriateConditionalProbabilityStore(boolean isForLeaf) GlobalClockModel.createAppropriateConditionalProbabilityStore(boolean isForLeaf) MRDTGlobalClockModel.createAppropriateConditionalProbabilityStore(boolean isForLeaf) SRDTGlobalClockModel.createAppropriateConditionalProbabilityStore(boolean isForLeaf) UnconstrainedModel.createAppropriateConditionalProbabilityStore(boolean isForLeaf) ConstrainedInternalNode.getAscendentExtended(double baseHeight, ConstrainedNode childCaller, GeneralConstructionTool tool, boolean allowCaching) ParentableConstrainedNode.getAscendentExtended(double baseHeight, ConstrainedNode childCaller, GeneralConstructionTool tool, boolean allowCaching) PivotNode.getAscendentExtended(double baseHeight, ConstrainedNode childCaller, GeneralConstructionTool tool, boolean allowCaching) ConstrainedInternalNode.getAscendentFlat(ConstrainedNode childCaller, GeneralConstructionTool tool, boolean allowCaching) ParentableConstrainedNode.getAscendentFlat(ConstrainedNode childCaller, GeneralConstructionTool tool, boolean allowCaching) PivotNode.getAscendentFlat(ConstrainedNode childCaller, GeneralConstructionTool tool, boolean allowCaching) AbstractParentableConstrainedNode.getDescendentExtendedConditionals(double extensionHeight, GeneralConstructionTool tool, boolean allowCaching) ConstrainedLeafNode.getDescendentExtendedConditionals(double extensionHeight, GeneralConstructionTool tool, boolean allowCaching) ConstrainedNode.getDescendentExtendedConditionals(double extensionHeight, GeneralConstructionTool tool, boolean allowCaching) AbstractParentableConstrainedNode.getDescendentExtendedConditionalsWithAdjustedInternalHeights(double adjustedExtensionHeight, GeneralConstructionTool tool, ConstrainedNode.HeightAdjustment internalNodeHeightAdjuster, boolean allowCaching) ConstrainedLeafNode.getDescendentExtendedConditionalsWithAdjustedInternalHeights(double extensionHeight, GeneralConstructionTool tool, ConstrainedNode.HeightAdjustment internalNodeHeightAdjuster, boolean allowCaching) ConstrainedNode.getDescendentExtendedConditionalsWithAdjustedInternalHeights(double adjustedExtensionHeight, GeneralConstructionTool tool, ConstrainedNode.HeightAdjustment internalNodeHeightAdjuster, boolean allowCaching) AbstractParentableConstrainedNode.getDescendentFlatConditionals(GeneralConstructionTool tool, boolean allowCaching) ConstrainedLeafNode.getDescendentFlatConditionals(GeneralConstructionTool tool, boolean allowCaching) ConstrainedNode.getDescendentFlatConditionals(GeneralConstructionTool tool, boolean allowCaching) FreeBranch.getExtendedConditionalProbabilities(FreeNode caller, UnconstrainedLikelihoodModel.External externalCalculator, ConditionalProbabilityStore extendedStore, GeneralConstructionTool tool) FreeBranch.getExtendedConditionalProbabilities(FreeNode caller, GeneralConstructionTool tool) FreeInternalNode.getExtendedConditionalProbabilities(double distance, FreeBranch callerConnection, UnconstrainedLikelihoodModel.External externalCalculator, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool) FreeInternalNode.getExtendedConditionalProbabilities(double distance, FreeBranch callerConnection, GeneralConstructionTool tool) FreeLeafNode.getExtendedConditionalProbabilities(double distance, FreeBranch callingBranch, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool) FreeLeafNode.getExtendedConditionalProbabilities(double distance, FreeBranch callingBranch, GeneralConstructionTool tool) FreeNode.getExtendedConditionalProbabilities(double distance, FreeBranch callingConnection, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool) FreeNode.getExtendedConditionalProbabilities(double distance, FreeBranch callingConnection, GeneralConstructionTool tool) PivotNode.getExtendedConditionalProbabilities(double distance, FreeBranch caller, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool) PivotNode.getExtendedConditionalProbabilities(double distance, FreeBranch caller, GeneralConstructionTool tool) FreeInternalNode.getFlatConditionalProbabilities(FreeBranch callerConnection, UnconstrainedLikelihoodModel.External externalCalculator, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool) FreeInternalNode.getFlatConditionalProbabilities(FreeBranch callerConnection, GeneralConstructionTool tool) FreeLeafNode.getFlatConditionalProbabilities(FreeBranch callingBranch, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool) FreeLeafNode.getFlatConditionalProbabilities(FreeBranch caller, GeneralConstructionTool tool) FreeNode.getFlatConditionalProbabilities(FreeBranch caller, GeneralConstructionTool tool) PivotNode.getFlatConditionalProbabilities(FreeBranch caller, GeneralConstructionTool tool) protected final ConditionalProbabilityStoreAbstractParentableConstrainedNode.getLeftDescendentExtendedConditionals(double specifiedHeight, GeneralConstructionTool tool, boolean allowCaching) Obtain conditionals by extended left child conditionals to a particular heightprotected final ConditionalProbabilityStoreAbstractParentableConstrainedNode.getLeftDescendentExtendedConditionals(GeneralConstructionTool tool, boolean allowCaching) Obtain conditionals by extended left child conditionals to height of this nodeFreeInternalNode.getLeftExtendedConditionalProbabilities(FreeBranch callingConnection, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool) FreeLeafNode.getLeftExtendedConditionalProbabilities(FreeBranch caller, UnconstrainedLikelihoodModel.External externalCalculator, ConditionalProbabilityStore resultStore) FreeBranch.getLeftFlatConditionalProbabilities(GeneralConstructionTool tool) protected final ConditionalProbabilityStoreAbstractParentableConstrainedNode.getRightDescendentExtendedConditionals(double specifiedHeight, GeneralConstructionTool tool, boolean allowCaching) Obtain conditionals by extended left child conditionals to a particular heightprotected final ConditionalProbabilityStoreAbstractParentableConstrainedNode.getRightDescendentExtendedConditionals(GeneralConstructionTool tool, boolean allowCaching) Obtain conditionals by extended right child conditionals to height of this nodeFreeInternalNode.getRightExtendedConditionalProbabilities(FreeBranch callingConnection, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool) FreeLeafNode.getRightExtendedConditionalProbabilities(FreeBranch caller, UnconstrainedLikelihoodModel.External externalCalculator, ConditionalProbabilityStore resultStore) FreeBranch.getRightFlatConditionalProbabilities(GeneralConstructionTool tool) GeneralConstructionTool.newConditionalProbabilityStore(boolean isForLeaf) GeneralConstructionTool.obtainTempConditionalProbabilityStore()Methods in pal.treesearch with parameters of type ConditionalProbabilityStoreModifier and TypeMethodDescriptionFreeBranch.getExtendedConditionalProbabilities(FreeNode caller, UnconstrainedLikelihoodModel.External externalCalculator, ConditionalProbabilityStore extendedStore, GeneralConstructionTool tool) FreeInternalNode.getExtendedConditionalProbabilities(double distance, FreeBranch callerConnection, UnconstrainedLikelihoodModel.External externalCalculator, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool) FreeLeafNode.getExtendedConditionalProbabilities(double distance, FreeBranch callingBranch, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool) FreeNode.getExtendedConditionalProbabilities(double distance, FreeBranch callingConnection, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool) PivotNode.getExtendedConditionalProbabilities(double distance, FreeBranch caller, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool) FreeInternalNode.getFlatConditionalProbabilities(FreeBranch callerConnection, UnconstrainedLikelihoodModel.External externalCalculator, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool) FreeLeafNode.getFlatConditionalProbabilities(FreeBranch callingBranch, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool) FreeInternalNode.getLeftExtendedConditionalProbabilities(FreeBranch callingConnection, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool) FreeLeafNode.getLeftExtendedConditionalProbabilities(FreeBranch caller, UnconstrainedLikelihoodModel.External externalCalculator, ConditionalProbabilityStore resultStore) FreeInternalNode.getRightExtendedConditionalProbabilities(FreeBranch callingConnection, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool) FreeLeafNode.getRightExtendedConditionalProbabilities(FreeBranch caller, UnconstrainedLikelihoodModel.External externalCalculator, ConditionalProbabilityStore resultStore)