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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void |
LHCalculator.External.calculateExtended(double distance,
SubstitutionModel model,
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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ConditionalProbabilityStore |
SimpleUnconstrainedLikelihoodModel.InternalImpl.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 |
UnconstrainedLikelihoodModel.Internal.calculateExtended(double distance,
PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilities,
ConditionalProbabilityStore rightConditionalProbabilities) |
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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 |
MolecularClockLikelihoodModel.Internal.calculateExtendedConditionals(double topBaseHeight,
double bottomBaseHeight,
PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilityProbabilties,
ConditionalProbabilityStore rightConditionalProbabilityProbabilties) |
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void |
LHCalculator.External.calculateFlat(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).
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ConditionalProbabilityStore |
SimpleUnconstrainedLikelihoodModel.InternalImpl.calculateFlat(PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilities,
ConditionalProbabilityStore rightConditionalProbabilities) |
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void |
UnconstrainedLikelihoodModel.External.calculateFlat(PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilities,
ConditionalProbabilityStore rightConditionalProbabilities,
ConditionalProbabilityStore resultStore) |
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ConditionalProbabilityStore |
UnconstrainedLikelihoodModel.Internal.calculateFlat(PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilities,
ConditionalProbabilityStore rightConditionalProbabilities) |
calculate flat probability information (not extended over a branch).
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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 |
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
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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
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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
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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
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double |
UnconstrainedLikelihoodModel.External.calculateLogLikelihood(PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilities,
ConditionalProbabilityStore rightConditionalProbabilities) |
Calculate the likelihood given two sub trees (left, right) and their extended likeihood probabilities
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double |
MolecularClockLikelihoodModel.External.calculateLogLikelihoodNonRoot(double nodeHeight,
PatternInfo centerPattern,
ConditionalProbabilityStore ascendentConditionalProbabilitiesStore,
ConditionalProbabilityStore descendentConditionalProbabilitiesStore) |
Calculate the likelihood given a non root node
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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
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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 |
LHCalculator.AbstractExternal.calculateSiteDetailsRooted(SubstitutionModel model,
PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilitiesStore,
ConditionalProbabilityStore rightConditionalProbabilitiesStore) |
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SiteDetails |
LHCalculator.External.calculateSiteDetailsRooted(SubstitutionModel model,
PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilitiesStore,
ConditionalProbabilityStore rightConditionalProbabilitiesStore) |
Calculate the conditional probabilities of each pattern for each category
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SiteDetails |
UnconstrainedLikelihoodModel.External.calculateSiteDetailsRooted(PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilitiesStore,
ConditionalProbabilityStore rightConditionalProbabilitiesStore) |
Calculate the conditional probabilities of each pattern for each category
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SiteDetails |
LHCalculator.AbstractExternal.calculateSiteDetailsUnrooted(double distance,
SubstitutionModel model,
PatternInfo centerPattern,
ConditionalProbabilityStore leftFlatConditionalProbabilities,
ConditionalProbabilityStore rightFlatConditionalProbabilities,
ConditionalProbabilityStore tempStore) |
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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
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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
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MolecularClockLikelihoodModel.Leaf |
MolecularClockLikelihoodModel.Instance.createNewLeaf(MolecularClockLikelihoodModel.HeightConverter converter,
PatternInfo pattern,
int[] patternStateMatchup) |
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