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Packages that use PatternInfo | |
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pal.eval | Classes for evaluating evolutionary hypothesis (chi-square and likelihood criteria) and estimating model parameters. |
pal.treesearch |
Uses of PatternInfo in pal.eval |
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Methods in pal.eval that return PatternInfo | |
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PatternInfo |
PatternInfo.getCopy()
Obtain an exact copy of this pattern info |
Methods in pal.eval with parameters of type PatternInfo | |
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int |
PatternInfo.build(PatternInfo leftPattern,
PatternInfo rightPattern,
int numberOfSites)
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ConditionalProbabilityStore |
MolecularClockLikelihoodModel.Internal.calculateAscendentExtendedConditionals(double topBaseHeight,
double bottomBaseHeight,
PatternInfo centerPattern,
ConditionalProbabilityStore ascendentConditionalProbabilityProbabilties,
ConditionalProbabilityStore otherConditionalProbabilityProbabilties)
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ConditionalProbabilityStore |
MolecularClockLikelihoodModel.Internal.calculateAscendentFlatConditionals(PatternInfo centerPattern,
ConditionalProbabilityStore ascenedentConditionalProbabilityProbabilties,
ConditionalProbabilityStore otherConditionalProbabilityProbabilties)
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protected abstract void |
LHCalculator.AbstractExternal.calculateCategoryPatternProbabilities(double distance,
SubstitutionModel model,
PatternInfo centerPattern,
ConditionalProbabilityStore leftFlatConditionalProbabilities,
ConditionalProbabilityStore rightFlatConditionalProbabilities,
ConditionalProbabilityStore tempStore,
double[][] categoryPatternLogLikelihoodStore)
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protected abstract void |
LHCalculator.AbstractExternal.calculateCategoryPatternProbabilities(SubstitutionModel model,
PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilities,
ConditionalProbabilityStore rightConditionalProbabilities,
double[][] categoryPatternLikelihoodStore)
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ConditionalProbabilityStore |
SimpleUnconstrainedLikelihoodModel.InternalImpl.calculateExtended(double distance,
PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilities,
ConditionalProbabilityStore rightConditionalProbabilities)
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ConditionalProbabilityStore |
UnconstrainedLikelihoodModel.Internal.calculateExtended(double distance,
PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilities,
ConditionalProbabilityStore rightConditionalProbabilities)
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void |
UnconstrainedLikelihoodModel.External.calculateExtended(double distance,
PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilities,
ConditionalProbabilityStore rightConditionalProbabilities,
ConditionalProbabilityStore resultStore)
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ConditionalProbabilityStore |
LHCalculator.Internal.calculateExtended(double distance,
SubstitutionModel model,
PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilities,
ConditionalProbabilityStore rightConditionalProbabilities,
boolean modelChangedSinceLastCall)
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void |
LHCalculator.External.calculateExtended(double distance,
SubstitutionModel model,
PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilities,
ConditionalProbabilityStore rightConditionalProbabilities,
ConditionalProbabilityStore resultStore)
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ConditionalProbabilityStore |
MolecularClockLikelihoodModel.Internal.calculateExtendedConditionals(double topBaseHeight,
double bottomBaseHeight,
PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilityProbabilties,
ConditionalProbabilityStore rightConditionalProbabilityProbabilties)
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void |
MolecularClockLikelihoodModel.External.calculateExtendedConditionals(double topBaseHeight,
double bottomBaseHeight,
PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilities,
ConditionalProbabilityStore rightConditionalProbabilities,
ConditionalProbabilityStore resultStore)
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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)
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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)
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void |
UnconstrainedLikelihoodModel.External.calculateFlat(PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilities,
ConditionalProbabilityStore rightConditionalProbabilities,
ConditionalProbabilityStore resultStore)
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void |
MolecularClockLikelihoodModel.External.calculateFlatConditionals(double rootHeight,
PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilitiesStore,
ConditionalProbabilityStore rightConditionalProbabilitiesStore,
ConditionalProbabilityStore resultConditionalProbabilitiesStore)
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ConditionalProbabilityStore |
MolecularClockLikelihoodModel.Internal.calculateFlatConditionals(PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilityProbabilties,
ConditionalProbabilityStore rightConditionalProbabilityProbabilties)
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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)
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ConditionalProbabilityStore |
LHCalculator.Internal.calculatePostExtendedFlat(double distance,
SubstitutionModel model,
PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilities,
ConditionalProbabilityStore rightConditionalProbabilities,
boolean modelChangedSinceLastCall)
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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)
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void |
MolecularClockLikelihoodModel.External.calculateSingleAscendentExtendedConditionalsIndirect(double topBaseHeight,
double bottomBaseHeight,
PatternInfo centerPattern,
ConditionalProbabilityStore baseAscendentConditionalProbabilityProbabilties,
ConditionalProbabilityStore resultConditionalProbabilityProbabilties)
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void |
MolecularClockLikelihoodModel.External.calculateSingleDescendentExtendedConditionals(double topBaseHeight,
double bottomBaseHeight,
PatternInfo centerPattern,
ConditionalProbabilityStore descendentConditionalProbabilities)
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SiteDetails |
MolecularClockLikelihoodModel.External.calculateSiteDetails(double rootHeight,
PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilitiesStore,
ConditionalProbabilityStore rightConditionalProbabilitiesStore)
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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)
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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)
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MolecularClockLikelihoodModel.Leaf |
MolecularClockLikelihoodModel.Instance.createNewLeaf(MolecularClockLikelihoodModel.HeightConverter converter,
PatternInfo pattern,
int[] patternStateMatchup)
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Uses of PatternInfo in pal.treesearch |
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Methods in pal.treesearch with parameters of type PatternInfo | |
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int |
GeneralConstructionTool.build(PatternInfo beingBuilt,
PatternInfo left,
PatternInfo right)
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MolecularClockLikelihoodModel.Leaf |
MRDTGlobalClockModel.createNewClockLeaf(PatternInfo pattern,
int[] patternStateMatchup)
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MolecularClockLikelihoodModel.Leaf |
ConstraintModel.GroupManager.createNewClockLeaf(PatternInfo pattern,
int[] patternStateMatchup)
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MolecularClockLikelihoodModel.Leaf |
SRDTGlobalClockModel.createNewClockLeaf(PatternInfo pattern,
int[] patternStateMatchup)
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MolecularClockLikelihoodModel.Leaf |
FixedBSRDTGlobalClockModel.createNewClockLeaf(PatternInfo pattern,
int[] patternStateMatchup)
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MolecularClockLikelihoodModel.Leaf |
FixedSRDTGlobalClockModel.createNewClockLeaf(PatternInfo pattern,
int[] patternStateMatchup)
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MolecularClockLikelihoodModel.Leaf |
GlobalClockModel.createNewClockLeaf(PatternInfo pattern,
int[] patternStateMatchup)
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void |
FreeBranch.getCenterPatternInfo(GeneralConstructionTool tool,
PatternInfo store)
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