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 TypeMethodDescriptionint
PatternInfo.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 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
MolecularClockLikelihoodModel.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 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) MolecularClockLikelihoodModel.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 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 PatternInfo
FreeBranch.getCenterPatternInfo
(GeneralConstructionTool tool) final PatternInfo
AbstractParentableConstrainedNode.getDescendentPatternInfo
(GeneralConstructionTool tool) ConstrainedLeafNode.getDescendentPatternInfo
(GeneralConstructionTool tool) ConstrainedNode.getDescendentPatternInfo
(GeneralConstructionTool tool) protected final PatternInfo
AbstractParentableConstrainedNode.getLeftChildPatternInfo
(GeneralConstructionTool tool) final PatternInfo
FreeBranch.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 PatternInfo
AbstractLeafNode.getPatternInfo()
final PatternInfo
FreeBranch.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 PatternInfo
AbstractParentableConstrainedNode.getRightChildPatternInfo
(GeneralConstructionTool tool) final PatternInfo
FreeBranch.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 TypeMethodDescriptionint
GeneralConstructionTool.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) void
FreeBranch.getCenterPatternInfo
(GeneralConstructionTool tool, PatternInfo store)