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 void
LHCalculator.AbstractExternal.calculateCategoryPatternProbabilities
(double distance, SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftFlatConditionalProbabilities, ConditionalProbabilityStore rightFlatConditionalProbabilities, ConditionalProbabilityStore tempStore, double[][] categoryPatternLogLikelihoodStore) protected abstract void
LHCalculator.AbstractExternal.calculateCategoryPatternProbabilities
(SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities, double[][] categoryPatternLikelihoodStore) void
LHCalculator.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) void
UnconstrainedLikelihoodModel.External.calculateExtended
(double distance, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities, ConditionalProbabilityStore resultStore) UnconstrainedLikelihoodModel.Internal.calculateExtended
(double distance, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities) void
MolecularClockLikelihoodModel.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) void
LHCalculator.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) void
UnconstrainedLikelihoodModel.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).void
MolecularClockLikelihoodModel.External.calculateFlatConditionals
(double rootHeight, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilitiesStore, ConditionalProbabilityStore rightConditionalProbabilitiesStore, ConditionalProbabilityStore resultConditionalProbabilitiesStore) MolecularClockLikelihoodModel.Internal.calculateFlatConditionals
(PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilityProbabilties, ConditionalProbabilityStore rightConditionalProbabilityProbabilties) double
LHCalculator.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 probabilitiesdouble
LHCalculator.External.calculateLogLikelihood
(SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities) Calculate the likelihood given two sub trees (left, right) and their extended likeihood probabilitiesdouble
MolecularClockLikelihoodModel.External.calculateLogLikelihood
(double rootHeight, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilitiesStore, ConditionalProbabilityStore rightConditionalProbabilitiesStore) Calculate the likelihood given two sub trees (left, right) and their extended likeihood probabilitiesdouble
UnconstrainedLikelihoodModel.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 probabilitiesdouble
UnconstrainedLikelihoodModel.External.calculateLogLikelihood
(PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities) Calculate the likelihood given two sub trees (left, right) and their extended likeihood probabilitiesdouble
MolecularClockLikelihoodModel.External.calculateLogLikelihoodNonRoot
(double nodeHeight, PatternInfo centerPattern, ConditionalProbabilityStore ascendentConditionalProbabilitiesStore, ConditionalProbabilityStore descendentConditionalProbabilitiesStore) Calculate the likelihood given a non root nodedouble
LHCalculator.External.calculateLogLikelihoodSingle
(SubstitutionModel model, int[] patternWeights, int numberOfPatterns, ConditionalProbabilityStore conditionalProbabilityStore) Calculate the likelihood given the conditional probabilites at the rootdouble
MolecularClockLikelihoodModel.External.calculateLogLikelihoodSingle
(double rootHeight, PatternInfo centerPattern, ConditionalProbabilityStore conditionalProbabilitiesStore) double
UnconstrainedLikelihoodModel.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 conditionalsvoid
MolecularClockLikelihoodModel.External.calculateSingleAscendentExtendedConditionalsDirect
(double topBaseHeight, double bottomBaseHeight, PatternInfo centerPattern, ConditionalProbabilityStore ascendentConditionalProbabilityProbabilties) void
MolecularClockLikelihoodModel.External.calculateSingleAscendentExtendedConditionalsIndirect
(double topBaseHeight, double bottomBaseHeight, PatternInfo centerPattern, ConditionalProbabilityStore baseAscendentConditionalProbabilityProbabilties, ConditionalProbabilityStore resultConditionalProbabilityProbabilties) void
MolecularClockLikelihoodModel.External.calculateSingleDescendentExtendedConditionals
(double topBaseHeight, double bottomBaseHeight, PatternInfo centerPattern, ConditionalProbabilityStore descendentConditionalProbabilities) void
LHCalculator.External.calculateSingleExtendedDirect
(double distance, SubstitutionModel model, int numberOfPatterns, ConditionalProbabilityStore conditionalProbabilities) Extend the conditionals back in time by some distance, with some modelvoid
UnconstrainedLikelihoodModel.External.calculateSingleExtendedDirect
(double distance, int numberOfPatterns, ConditionalProbabilityStore conditionalProbabilities) Extend the conditionals back in time by some distancevoid
LHCalculator.External.calculateSingleExtendedIndirect
(double distance, SubstitutionModel model, int numberOfPatterns, ConditionalProbabilityStore baseConditionalProbabilities, ConditionalProbabilityStore resultConditionalProbabilities) Extend the conditionals back in time by some distance, with some modelvoid
UnconstrainedLikelihoodModel.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 SiteDetails
LHCalculator.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 SiteDetails
LHCalculator.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 categoryvoid
ConditionalProbabilityStore.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 ConditionalProbabilityStore
AbstractParentableConstrainedNode.getLeftDescendentExtendedConditionals
(double specifiedHeight, GeneralConstructionTool tool, boolean allowCaching) Obtain conditionals by extended left child conditionals to a particular heightprotected final ConditionalProbabilityStore
AbstractParentableConstrainedNode.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 ConditionalProbabilityStore
AbstractParentableConstrainedNode.getRightDescendentExtendedConditionals
(double specifiedHeight, GeneralConstructionTool tool, boolean allowCaching) Obtain conditionals by extended left child conditionals to a particular heightprotected final ConditionalProbabilityStore
AbstractParentableConstrainedNode.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)