Uses of Class
pal.eval.PatternInfo
Packages that use PatternInfo
Package
Description
Classes for evaluating evolutionary hypothesis (chi-square and likelihood
criteria) and estimating model parameters.
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Uses of PatternInfo in pal.eval
Methods in pal.eval that return PatternInfoModifier and TypeMethodDescriptionPatternInfo.getCopy()Obtain an exact copy of this pattern infoMethods in pal.eval with parameters of type PatternInfoModifier and TypeMethodDescriptionintPatternInfo.build(PatternInfo leftPattern, PatternInfo rightPattern, int numberOfSites) MolecularClockLikelihoodModel.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 nodedoubleMolecularClockLikelihoodModel.External.calculateLogLikelihoodSingle(double rootHeight, PatternInfo centerPattern, ConditionalProbabilityStore conditionalProbabilitiesStore) 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 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) MolecularClockLikelihoodModel.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 categoryMolecularClockLikelihoodModel.Instance.createNewLeaf(MolecularClockLikelihoodModel.HeightConverter converter, PatternInfo pattern, int[] patternStateMatchup) -
Uses of PatternInfo in pal.treesearch
Methods in pal.treesearch that return PatternInfoModifier and TypeMethodDescriptionGeneralConstructionTool.constructFreshPatternInfo(boolean binaryPattern) ConstrainedInternalNode.getAscendentPatternInfo(ConstrainedNode childCaller, GeneralConstructionTool tool) ParentableConstrainedNode.getAscendentPatternInfo(ConstrainedNode childCaller, GeneralConstructionTool tool) PivotNode.getAscendentPatternInfo(ConstrainedNode childCaller, GeneralConstructionTool tool) ConstrainedInternalNode.getCenterPattern(GeneralConstructionTool tool) For center pattern, left is ascendent component, right is descendent componentfinal PatternInfoFreeBranch.getCenterPatternInfo(GeneralConstructionTool tool) final PatternInfoAbstractParentableConstrainedNode.getDescendentPatternInfo(GeneralConstructionTool tool) ConstrainedLeafNode.getDescendentPatternInfo(GeneralConstructionTool tool) ConstrainedNode.getDescendentPatternInfo(GeneralConstructionTool tool) protected final PatternInfoAbstractParentableConstrainedNode.getLeftChildPatternInfo(GeneralConstructionTool tool) final PatternInfoFreeBranch.getLeftPatternInfo(GeneralConstructionTool tool) FreeInternalNode.getLeftPatternInfo(GeneralConstructionTool tool, FreeBranch caller) FreeLeafNode.getLeftPatternInfo(GeneralConstructionTool tool, FreeBranch caller) FreeNode.getLeftPatternInfo(GeneralConstructionTool tool, FreeBranch caller) PivotNode.getLeftPatternInfo(GeneralConstructionTool tool, FreeBranch caller) final PatternInfoAbstractLeafNode.getPatternInfo()final PatternInfoFreeBranch.getPatternInfo(GeneralConstructionTool tool, FreeNode caller) FreeInternalNode.getPatternInfo(GeneralConstructionTool tool, FreeBranch caller) FreeLeafNode.getPatternInfo(GeneralConstructionTool tool, FreeBranch caller) FreeNode.getPatternInfo(GeneralConstructionTool tool, FreeBranch caller) PivotNode.getPatternInfo(GeneralConstructionTool tool, FreeBranch caller) protected final PatternInfoAbstractParentableConstrainedNode.getRightChildPatternInfo(GeneralConstructionTool tool) final PatternInfoFreeBranch.getRightPatternInfo(GeneralConstructionTool tool) FreeInternalNode.getRightPatternInfo(GeneralConstructionTool tool, FreeBranch caller) FreeLeafNode.getRightPatternInfo(GeneralConstructionTool tool, FreeBranch caller) FreeNode.getRightPatternInfo(GeneralConstructionTool tool, FreeBranch caller) PivotNode.getRightPatternInfo(GeneralConstructionTool tool, FreeBranch caller) Methods in pal.treesearch with parameters of type PatternInfoModifier and TypeMethodDescriptionintGeneralConstructionTool.build(PatternInfo beingBuilt, PatternInfo left, PatternInfo right) ConstraintModel.GroupManager.createNewClockLeaf(PatternInfo pattern, int[] patternStateMatchup) FixedBSRDTGlobalClockModel.createNewClockLeaf(PatternInfo pattern, int[] patternStateMatchup) FixedSRDTGlobalClockModel.createNewClockLeaf(PatternInfo pattern, int[] patternStateMatchup) GlobalClockModel.createNewClockLeaf(PatternInfo pattern, int[] patternStateMatchup) MRDTGlobalClockModel.createNewClockLeaf(PatternInfo pattern, int[] patternStateMatchup) SRDTGlobalClockModel.createNewClockLeaf(PatternInfo pattern, int[] patternStateMatchup) voidFreeBranch.getCenterPatternInfo(GeneralConstructionTool tool, PatternInfo store)