Uses of Class
pal.eval.ConditionalProbabilityStore

Packages that use ConditionalProbabilityStore
pal.eval Classes for evaluating evolutionary hypothesis (chi-square and likelihood criteria) and estimating model parameters. 
pal.treesearch   
 

Uses of ConditionalProbabilityStore in pal.eval
 

Methods in pal.eval that return ConditionalProbabilityStore
 ConditionalProbabilityStore MolecularClockLikelihoodModel.Internal.calculateAscendentExtendedConditionals(double topBaseHeight, double bottomBaseHeight, PatternInfo centerPattern, ConditionalProbabilityStore ascendentConditionalProbabilityProbabilties, ConditionalProbabilityStore otherConditionalProbabilityProbabilties)
           
 ConditionalProbabilityStore MolecularClockLikelihoodModel.Internal.calculateAscendentFlatConditionals(PatternInfo centerPattern, ConditionalProbabilityStore ascenedentConditionalProbabilityProbabilties, ConditionalProbabilityStore otherConditionalProbabilityProbabilties)
           
 ConditionalProbabilityStore SimpleUnconstrainedLikelihoodModel.InternalImpl.calculateExtended(double distance, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities)
           
 ConditionalProbabilityStore UnconstrainedLikelihoodModel.Internal.calculateExtended(double distance, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities)
           
 ConditionalProbabilityStore LHCalculator.Internal.calculateExtended(double distance, SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities, boolean modelChangedSinceLastCall)
           
 ConditionalProbabilityStore MolecularClockLikelihoodModel.Leaf.calculateExtendedConditionals(double topHeight, double bottomHeight)
           
 ConditionalProbabilityStore MolecularClockLikelihoodModel.Internal.calculateExtendedConditionals(double topBaseHeight, double bottomBaseHeight, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilityProbabilties, ConditionalProbabilityStore rightConditionalProbabilityProbabilties)
           
 ConditionalProbabilityStore LHCalculator.Internal.calculateFlat(PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities)
          calculate flat probability information (not extended over a branch).
 ConditionalProbabilityStore SimpleUnconstrainedLikelihoodModel.InternalImpl.calculateFlat(PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities)
           
 ConditionalProbabilityStore UnconstrainedLikelihoodModel.Internal.calculateFlat(PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities)
          calculate flat probability information (not extended over a branch).
 ConditionalProbabilityStore MolecularClockLikelihoodModel.Leaf.calculateFlatConditionals(double height)
           
 ConditionalProbabilityStore MolecularClockLikelihoodModel.Internal.calculateFlatConditionals(PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilityProbabilties, ConditionalProbabilityStore rightConditionalProbabilityProbabilties)
           
 ConditionalProbabilityStore LHCalculator.Internal.calculatePostExtendedFlat(double distance, SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities, boolean modelChangedSinceLastCall)
           
 ConditionalProbabilityStore MolecularClockLikelihoodModel.Internal.calculatePostExtendedFlatConditionals(double topBaseHeight, double bottomBaseHeight, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilityProbabilties, ConditionalProbabilityStore rightConditionalProbabilityProbabilties)
          Extends left and right conditionals by type and then calculates flat conditionals
 ConditionalProbabilityStore MolecularClockLikelihoodModel.Instance.createAppropriateConditionalProbabilityStore(boolean isForLeaf)
           
 ConditionalProbabilityStore LHCalculator.Generator.createAppropriateConditionalProbabilityStore(boolean isForLeaf)
           
 ConditionalProbabilityStore UnconstrainedLikelihoodModel.Instance.createAppropriateConditionalProbabilityStore(boolean isForLeaf)
           
 ConditionalProbabilityStore ConditionalProbabilityStore.getCopy()
          Cloning
 ConditionalProbabilityStore SimpleUnconstrainedLikelihoodModel.LeafImpl.getExtendedConditionalProbabilities(double distance)
           
 ConditionalProbabilityStore UnconstrainedLikelihoodModel.Leaf.getExtendedConditionalProbabilities(double distance)
           
 ConditionalProbabilityStore LHCalculator.Leaf.getExtendedConditionalProbabilities(double distance, SubstitutionModel model, boolean modelChanged)
           
 ConditionalProbabilityStore SimpleLeafCalculator.getExtendedConditionalProbabilities(double distance, SubstitutionModel model, boolean modelChanged)
           
 ConditionalProbabilityStore LHCalculator.Leaf.getFlatConditionalProbabilities()
           
 ConditionalProbabilityStore SimpleLeafCalculator.getFlatConditionalProbabilities()
           
 ConditionalProbabilityStore SimpleUnconstrainedLikelihoodModel.LeafImpl.getFlatConditionalProbabilities()
           
 ConditionalProbabilityStore UnconstrainedLikelihoodModel.Leaf.getFlatConditionalProbabilities()
           
 

Methods in pal.eval with parameters of type ConditionalProbabilityStore
 ConditionalProbabilityStore MolecularClockLikelihoodModel.Internal.calculateAscendentExtendedConditionals(double topBaseHeight, double bottomBaseHeight, PatternInfo centerPattern, ConditionalProbabilityStore ascendentConditionalProbabilityProbabilties, ConditionalProbabilityStore otherConditionalProbabilityProbabilties)
           
 ConditionalProbabilityStore 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)
           
 ConditionalProbabilityStore SimpleUnconstrainedLikelihoodModel.InternalImpl.calculateExtended(double distance, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities)
           
 ConditionalProbabilityStore UnconstrainedLikelihoodModel.Internal.calculateExtended(double distance, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities)
           
 void UnconstrainedLikelihoodModel.External.calculateExtended(double distance, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities, ConditionalProbabilityStore resultStore)
           
 ConditionalProbabilityStore LHCalculator.Internal.calculateExtended(double distance, SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities, boolean modelChangedSinceLastCall)
           
 void LHCalculator.External.calculateExtended(double distance, SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities, ConditionalProbabilityStore resultStore)
           
 ConditionalProbabilityStore MolecularClockLikelihoodModel.Internal.calculateExtendedConditionals(double topBaseHeight, double bottomBaseHeight, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilityProbabilties, ConditionalProbabilityStore rightConditionalProbabilityProbabilties)
           
 void MolecularClockLikelihoodModel.External.calculateExtendedConditionals(double topBaseHeight, double bottomBaseHeight, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities, ConditionalProbabilityStore resultStore)
           
 ConditionalProbabilityStore LHCalculator.Internal.calculateFlat(PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities)
          calculate flat probability information (not extended over a branch).
 ConditionalProbabilityStore SimpleUnconstrainedLikelihoodModel.InternalImpl.calculateFlat(PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities)
           
 ConditionalProbabilityStore UnconstrainedLikelihoodModel.Internal.calculateFlat(PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities)
          calculate flat probability information (not extended over a branch).
 void LHCalculator.External.calculateFlat(PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities, ConditionalProbabilityStore resultStore)
           
 void UnconstrainedLikelihoodModel.External.calculateFlat(PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities, ConditionalProbabilityStore resultStore)
           
 void MolecularClockLikelihoodModel.External.calculateFlatConditionals(double rootHeight, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilitiesStore, ConditionalProbabilityStore rightConditionalProbabilitiesStore, ConditionalProbabilityStore resultConditionalProbabilitiesStore)
           
 ConditionalProbabilityStore MolecularClockLikelihoodModel.Internal.calculateFlatConditionals(PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilityProbabilties, ConditionalProbabilityStore rightConditionalProbabilityProbabilties)
           
 double MolecularClockLikelihoodModel.External.calculateLogLikelihood(double rootHeight, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilitiesStore, ConditionalProbabilityStore rightConditionalProbabilitiesStore)
          Calculate the likelihood given two sub trees (left, right) and their extended likeihood probabilities
 double 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 probabilities
 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 probabilities
 double UnconstrainedLikelihoodModel.External.calculateLogLikelihood(PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities)
          Calculate the likelihood given two sub trees (left, right) and their extended likeihood probabilities
 double LHCalculator.External.calculateLogLikelihood(SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities)
          Calculate the likelihood given two sub trees (left, right) and their extended likeihood probabilities
 double MolecularClockLikelihoodModel.External.calculateLogLikelihoodNonRoot(double nodeHeight, PatternInfo centerPattern, ConditionalProbabilityStore ascendentConditionalProbabilitiesStore, ConditionalProbabilityStore descendentConditionalProbabilitiesStore)
          Calculate the likelihood given a non root node
 double 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 root
 double LHCalculator.External.calculateLogLikelihoodSingle(SubstitutionModel model, int[] patternWeights, int numberOfPatterns, ConditionalProbabilityStore conditionalProbabilityStore)
          Calculate the likelihood given the conditional probabilites at the root
 ConditionalProbabilityStore LHCalculator.Internal.calculatePostExtendedFlat(double distance, SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities, boolean modelChangedSinceLastCall)
           
 ConditionalProbabilityStore MolecularClockLikelihoodModel.Internal.calculatePostExtendedFlatConditionals(double topBaseHeight, double bottomBaseHeight, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilityProbabilties, ConditionalProbabilityStore rightConditionalProbabilityProbabilties)
          Extends left and right conditionals by type and then calculates flat conditionals
 void 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 UnconstrainedLikelihoodModel.External.calculateSingleExtendedDirect(double distance, int numberOfPatterns, ConditionalProbabilityStore conditionalProbabilities)
          Extend the conditionals back in time by some distance
 void LHCalculator.External.calculateSingleExtendedDirect(double distance, SubstitutionModel model, int numberOfPatterns, ConditionalProbabilityStore conditionalProbabilities)
          Extend the conditionals back in time by some distance, with some model
 void UnconstrainedLikelihoodModel.External.calculateSingleExtendedIndirect(double distance, int numberOfPatterns, ConditionalProbabilityStore baseConditionalProbabilities, ConditionalProbabilityStore resultConditionalProbabilities)
          Extend the conditionals back in time by some distance
 void LHCalculator.External.calculateSingleExtendedIndirect(double distance, SubstitutionModel model, int numberOfPatterns, ConditionalProbabilityStore baseConditionalProbabilities, ConditionalProbabilityStore resultConditionalProbabilities)
          Extend the conditionals back in time by some distance, with some model
 SiteDetails MolecularClockLikelihoodModel.External.calculateSiteDetails(double rootHeight, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilitiesStore, ConditionalProbabilityStore rightConditionalProbabilitiesStore)
           
 SiteDetails UnconstrainedLikelihoodModel.External.calculateSiteDetailsRooted(PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilitiesStore, ConditionalProbabilityStore rightConditionalProbabilitiesStore)
          Calculate the conditional probabilities of each pattern for each category
 SiteDetails LHCalculator.External.calculateSiteDetailsRooted(SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilitiesStore, ConditionalProbabilityStore rightConditionalProbabilitiesStore)
          Calculate the conditional probabilities of each pattern for each category
 SiteDetails LHCalculator.AbstractExternal.calculateSiteDetailsRooted(SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilitiesStore, ConditionalProbabilityStore rightConditionalProbabilitiesStore)
           
 SiteDetails UnconstrainedLikelihoodModel.External.calculateSiteDetailsUnrooted(double distance, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilitiesStore, ConditionalProbabilityStore rightConditionalProbabilitiesStore, ConditionalProbabilityStore tempStore)
          Calculate the conditional probabilities of each pattern for each category
 SiteDetails LHCalculator.External.calculateSiteDetailsUnrooted(double distance, SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilitiesStore, ConditionalProbabilityStore rightConditionalProbabilitiesStore, ConditionalProbabilityStore tempStore)
          Calculate the conditional probabilities of each pattern for each category
 SiteDetails LHCalculator.AbstractExternal.calculateSiteDetailsUnrooted(double distance, SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftFlatConditionalProbabilities, ConditionalProbabilityStore rightFlatConditionalProbabilities, ConditionalProbabilityStore tempStore)
           
 void ConditionalProbabilityStore.ExtraProcessor.setParent(ConditionalProbabilityStore parent)
           
 

Uses of ConditionalProbabilityStore in pal.treesearch
 

Methods in pal.treesearch that return ConditionalProbabilityStore
 ConditionalProbabilityStore MRDTGlobalClockModel.createAppropriateConditionalProbabilityStore(boolean isForLeaf)
           
 ConditionalProbabilityStore ConstraintModel.createAppropriateConditionalProbabilityStore(boolean isForLeaf)
           
 ConditionalProbabilityStore SRDTGlobalClockModel.createAppropriateConditionalProbabilityStore(boolean isForLeaf)
           
 ConditionalProbabilityStore FixedBSRDTGlobalClockModel.createAppropriateConditionalProbabilityStore(boolean isForLeaf)
           
 ConditionalProbabilityStore FixedSRDTGlobalClockModel.createAppropriateConditionalProbabilityStore(boolean isForLeaf)
           
 ConditionalProbabilityStore GlobalClockModel.createAppropriateConditionalProbabilityStore(boolean isForLeaf)
           
 ConditionalProbabilityStore UnconstrainedModel.createAppropriateConditionalProbabilityStore(boolean isForLeaf)
           
 ConditionalProbabilityStore PivotNode.getAscendentExtended(double baseHeight, ConstrainedNode childCaller, GeneralConstructionTool tool, boolean allowCaching)
           
 ConditionalProbabilityStore ParentableConstrainedNode.getAscendentExtended(double baseHeight, ConstrainedNode childCaller, GeneralConstructionTool tool, boolean allowCaching)
           
 ConditionalProbabilityStore ConstrainedInternalNode.getAscendentExtended(double baseHeight, ConstrainedNode childCaller, GeneralConstructionTool tool, boolean allowCaching)
           
 ConditionalProbabilityStore PivotNode.getAscendentFlat(ConstrainedNode childCaller, GeneralConstructionTool tool, boolean allowCaching)
           
 ConditionalProbabilityStore ParentableConstrainedNode.getAscendentFlat(ConstrainedNode childCaller, GeneralConstructionTool tool, boolean allowCaching)
           
 ConditionalProbabilityStore ConstrainedInternalNode.getAscendentFlat(ConstrainedNode childCaller, GeneralConstructionTool tool, boolean allowCaching)
           
 ConditionalProbabilityStore ConstrainedLeafNode.getDescendentExtendedConditionals(double extensionHeight, GeneralConstructionTool tool, boolean allowCaching)
           
 ConditionalProbabilityStore ConstrainedNode.getDescendentExtendedConditionals(double extensionHeight, GeneralConstructionTool tool, boolean allowCaching)
           
 ConditionalProbabilityStore AbstractParentableConstrainedNode.getDescendentExtendedConditionals(double extensionHeight, GeneralConstructionTool tool, boolean allowCaching)
           
 ConditionalProbabilityStore ConstrainedLeafNode.getDescendentExtendedConditionalsWithAdjustedInternalHeights(double extensionHeight, GeneralConstructionTool tool, ConstrainedNode.HeightAdjustment internalNodeHeightAdjuster, boolean allowCaching)
           
 ConditionalProbabilityStore ConstrainedNode.getDescendentExtendedConditionalsWithAdjustedInternalHeights(double adjustedExtensionHeight, GeneralConstructionTool tool, ConstrainedNode.HeightAdjustment internalNodeHeightAdjuster, boolean allowCaching)
           
 ConditionalProbabilityStore AbstractParentableConstrainedNode.getDescendentExtendedConditionalsWithAdjustedInternalHeights(double adjustedExtensionHeight, GeneralConstructionTool tool, ConstrainedNode.HeightAdjustment internalNodeHeightAdjuster, boolean allowCaching)
           
 ConditionalProbabilityStore ConstrainedLeafNode.getDescendentFlatConditionals(GeneralConstructionTool tool, boolean allowCaching)
           
 ConditionalProbabilityStore ConstrainedNode.getDescendentFlatConditionals(GeneralConstructionTool tool, boolean allowCaching)
           
 ConditionalProbabilityStore AbstractParentableConstrainedNode.getDescendentFlatConditionals(GeneralConstructionTool tool, boolean allowCaching)
           
 ConditionalProbabilityStore FreeNode.getExtendedConditionalProbabilities(double distance, FreeBranch callingConnection, GeneralConstructionTool tool)
           
 ConditionalProbabilityStore PivotNode.getExtendedConditionalProbabilities(double distance, FreeBranch caller, GeneralConstructionTool tool)
           
 ConditionalProbabilityStore FreeLeafNode.getExtendedConditionalProbabilities(double distance, FreeBranch callingBranch, GeneralConstructionTool tool)
           
 ConditionalProbabilityStore FreeInternalNode.getExtendedConditionalProbabilities(double distance, FreeBranch callerConnection, GeneralConstructionTool tool)
           
 ConditionalProbabilityStore FreeNode.getExtendedConditionalProbabilities(double distance, FreeBranch callingConnection, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool)
           
 ConditionalProbabilityStore PivotNode.getExtendedConditionalProbabilities(double distance, FreeBranch caller, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool)
           
 ConditionalProbabilityStore FreeLeafNode.getExtendedConditionalProbabilities(double distance, FreeBranch callingBranch, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool)
           
 ConditionalProbabilityStore FreeInternalNode.getExtendedConditionalProbabilities(double distance, FreeBranch callerConnection, UnconstrainedLikelihoodModel.External externalCalculator, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool)
           
 ConditionalProbabilityStore FreeBranch.getExtendedConditionalProbabilities(FreeNode caller, GeneralConstructionTool tool)
           
 ConditionalProbabilityStore FreeBranch.getExtendedConditionalProbabilities(FreeNode caller, UnconstrainedLikelihoodModel.External externalCalculator, ConditionalProbabilityStore extendedStore, GeneralConstructionTool tool)
           
 ConditionalProbabilityStore FreeNode.getFlatConditionalProbabilities(FreeBranch caller, GeneralConstructionTool tool)
           
 ConditionalProbabilityStore PivotNode.getFlatConditionalProbabilities(FreeBranch caller, GeneralConstructionTool tool)
           
 ConditionalProbabilityStore FreeLeafNode.getFlatConditionalProbabilities(FreeBranch caller, GeneralConstructionTool tool)
           
 ConditionalProbabilityStore FreeInternalNode.getFlatConditionalProbabilities(FreeBranch callerConnection, GeneralConstructionTool tool)
           
 ConditionalProbabilityStore FreeLeafNode.getFlatConditionalProbabilities(FreeBranch callingBranch, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool)
           
 ConditionalProbabilityStore FreeInternalNode.getFlatConditionalProbabilities(FreeBranch callerConnection, UnconstrainedLikelihoodModel.External externalCalculator, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool)
           
protected  ConditionalProbabilityStore AbstractParentableConstrainedNode.getLeftDescendentExtendedConditionals(double specifiedHeight, GeneralConstructionTool tool, boolean allowCaching)
          Obtain conditionals by extended left child conditionals to a particular height
protected  ConditionalProbabilityStore AbstractParentableConstrainedNode.getLeftDescendentExtendedConditionals(GeneralConstructionTool tool, boolean allowCaching)
          Obtain conditionals by extended left child conditionals to height of this node
 ConditionalProbabilityStore FreeLeafNode.getLeftExtendedConditionalProbabilities(FreeBranch caller, UnconstrainedLikelihoodModel.External externalCalculator, ConditionalProbabilityStore resultStore)
           
 ConditionalProbabilityStore FreeInternalNode.getLeftExtendedConditionalProbabilities(FreeBranch callingConnection, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool)
           
 ConditionalProbabilityStore FreeBranch.getLeftFlatConditionalProbabilities(GeneralConstructionTool tool)
           
protected  ConditionalProbabilityStore AbstractParentableConstrainedNode.getRightDescendentExtendedConditionals(double specifiedHeight, GeneralConstructionTool tool, boolean allowCaching)
          Obtain conditionals by extended left child conditionals to a particular height
protected  ConditionalProbabilityStore AbstractParentableConstrainedNode.getRightDescendentExtendedConditionals(GeneralConstructionTool tool, boolean allowCaching)
          Obtain conditionals by extended right child conditionals to height of this node
 ConditionalProbabilityStore FreeLeafNode.getRightExtendedConditionalProbabilities(FreeBranch caller, UnconstrainedLikelihoodModel.External externalCalculator, ConditionalProbabilityStore resultStore)
           
 ConditionalProbabilityStore FreeInternalNode.getRightExtendedConditionalProbabilities(FreeBranch callingConnection, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool)
           
 ConditionalProbabilityStore FreeBranch.getRightFlatConditionalProbabilities(GeneralConstructionTool tool)
           
 ConditionalProbabilityStore GeneralConstructionTool.newConditionalProbabilityStore(boolean isForLeaf)
           
 ConditionalProbabilityStore GeneralConstructionTool.obtainTempConditionalProbabilityStore()
           
 

Methods in pal.treesearch with parameters of type ConditionalProbabilityStore
 ConditionalProbabilityStore FreeNode.getExtendedConditionalProbabilities(double distance, FreeBranch callingConnection, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool)
           
 ConditionalProbabilityStore PivotNode.getExtendedConditionalProbabilities(double distance, FreeBranch caller, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool)
           
 ConditionalProbabilityStore FreeLeafNode.getExtendedConditionalProbabilities(double distance, FreeBranch callingBranch, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool)
           
 ConditionalProbabilityStore FreeInternalNode.getExtendedConditionalProbabilities(double distance, FreeBranch callerConnection, UnconstrainedLikelihoodModel.External externalCalculator, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool)
           
 ConditionalProbabilityStore FreeBranch.getExtendedConditionalProbabilities(FreeNode caller, UnconstrainedLikelihoodModel.External externalCalculator, ConditionalProbabilityStore extendedStore, GeneralConstructionTool tool)
           
 ConditionalProbabilityStore FreeLeafNode.getFlatConditionalProbabilities(FreeBranch callingBranch, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool)
           
 ConditionalProbabilityStore FreeInternalNode.getFlatConditionalProbabilities(FreeBranch callerConnection, UnconstrainedLikelihoodModel.External externalCalculator, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool)
           
 ConditionalProbabilityStore FreeLeafNode.getLeftExtendedConditionalProbabilities(FreeBranch caller, UnconstrainedLikelihoodModel.External externalCalculator, ConditionalProbabilityStore resultStore)
           
 ConditionalProbabilityStore FreeInternalNode.getLeftExtendedConditionalProbabilities(FreeBranch callingConnection, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool)
           
 ConditionalProbabilityStore FreeLeafNode.getRightExtendedConditionalProbabilities(FreeBranch caller, UnconstrainedLikelihoodModel.External externalCalculator, ConditionalProbabilityStore resultStore)
           
 ConditionalProbabilityStore FreeInternalNode.getRightExtendedConditionalProbabilities(FreeBranch callingConnection, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool)