Uses of Class
pal.eval.PatternInfo

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

Uses of PatternInfo in pal.eval
 

Methods in pal.eval that return PatternInfo
 PatternInfo PatternInfo.getCopy()
          Obtain an exact copy of this pattern info
 

Methods in pal.eval with parameters of type PatternInfo
 int PatternInfo.build(PatternInfo leftPattern, PatternInfo rightPattern, int numberOfSites)
           
 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)
           
 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)
           
 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)
           
 MolecularClockLikelihoodModel.Leaf MolecularClockLikelihoodModel.Instance.createNewLeaf(MolecularClockLikelihoodModel.HeightConverter converter, PatternInfo pattern, int[] patternStateMatchup)
           
 

Uses of PatternInfo in pal.treesearch
 

Methods in pal.treesearch that return PatternInfo
 PatternInfo GeneralConstructionTool.constructFreshPatternInfo(boolean binaryPattern)
           
 PatternInfo PivotNode.getAscendentPatternInfo(ConstrainedNode childCaller, GeneralConstructionTool tool)
           
 PatternInfo ParentableConstrainedNode.getAscendentPatternInfo(ConstrainedNode childCaller, GeneralConstructionTool tool)
           
 PatternInfo ConstrainedInternalNode.getAscendentPatternInfo(ConstrainedNode childCaller, GeneralConstructionTool tool)
           
 PatternInfo ConstrainedInternalNode.getCenterPattern(GeneralConstructionTool tool)
          For center pattern, left is ascendent component, right is descendent component
 PatternInfo FreeBranch.getCenterPatternInfo(GeneralConstructionTool tool)
           
 PatternInfo ConstrainedLeafNode.getDescendentPatternInfo(GeneralConstructionTool tool)
           
 PatternInfo ConstrainedNode.getDescendentPatternInfo(GeneralConstructionTool tool)
           
 PatternInfo AbstractParentableConstrainedNode.getDescendentPatternInfo(GeneralConstructionTool tool)
           
protected  PatternInfo AbstractParentableConstrainedNode.getLeftChildPatternInfo(GeneralConstructionTool tool)
           
 PatternInfo FreeBranch.getLeftPatternInfo(GeneralConstructionTool tool)
           
 PatternInfo FreeNode.getLeftPatternInfo(GeneralConstructionTool tool, FreeBranch caller)
           
 PatternInfo PivotNode.getLeftPatternInfo(GeneralConstructionTool tool, FreeBranch caller)
           
 PatternInfo FreeLeafNode.getLeftPatternInfo(GeneralConstructionTool tool, FreeBranch caller)
           
 PatternInfo FreeInternalNode.getLeftPatternInfo(GeneralConstructionTool tool, FreeBranch caller)
           
 PatternInfo AbstractLeafNode.getPatternInfo()
           
 PatternInfo FreeNode.getPatternInfo(GeneralConstructionTool tool, FreeBranch caller)
           
 PatternInfo PivotNode.getPatternInfo(GeneralConstructionTool tool, FreeBranch caller)
           
 PatternInfo FreeLeafNode.getPatternInfo(GeneralConstructionTool tool, FreeBranch caller)
           
 PatternInfo FreeInternalNode.getPatternInfo(GeneralConstructionTool tool, FreeBranch caller)
           
 PatternInfo FreeBranch.getPatternInfo(GeneralConstructionTool tool, FreeNode caller)
           
protected  PatternInfo AbstractParentableConstrainedNode.getRightChildPatternInfo(GeneralConstructionTool tool)
           
 PatternInfo FreeBranch.getRightPatternInfo(GeneralConstructionTool tool)
           
 PatternInfo FreeNode.getRightPatternInfo(GeneralConstructionTool tool, FreeBranch caller)
           
 PatternInfo PivotNode.getRightPatternInfo(GeneralConstructionTool tool, FreeBranch caller)
           
 PatternInfo FreeLeafNode.getRightPatternInfo(GeneralConstructionTool tool, FreeBranch caller)
           
 PatternInfo FreeInternalNode.getRightPatternInfo(GeneralConstructionTool tool, FreeBranch caller)
           
 

Methods in pal.treesearch with parameters of type PatternInfo
 int GeneralConstructionTool.build(PatternInfo beingBuilt, PatternInfo left, PatternInfo right)
           
 MolecularClockLikelihoodModel.Leaf MRDTGlobalClockModel.createNewClockLeaf(PatternInfo pattern, int[] patternStateMatchup)
           
 MolecularClockLikelihoodModel.Leaf ConstraintModel.GroupManager.createNewClockLeaf(PatternInfo pattern, int[] patternStateMatchup)
           
 MolecularClockLikelihoodModel.Leaf SRDTGlobalClockModel.createNewClockLeaf(PatternInfo pattern, int[] patternStateMatchup)
           
 MolecularClockLikelihoodModel.Leaf FixedBSRDTGlobalClockModel.createNewClockLeaf(PatternInfo pattern, int[] patternStateMatchup)
           
 MolecularClockLikelihoodModel.Leaf FixedSRDTGlobalClockModel.createNewClockLeaf(PatternInfo pattern, int[] patternStateMatchup)
           
 MolecularClockLikelihoodModel.Leaf GlobalClockModel.createNewClockLeaf(PatternInfo pattern, int[] patternStateMatchup)
           
 void FreeBranch.getCenterPatternInfo(GeneralConstructionTool tool, PatternInfo store)