Package pal.eval
Interface MolecularClockLikelihoodModel.External
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- Enclosing interface:
- MolecularClockLikelihoodModel
public static interface MolecularClockLikelihoodModel.External
The External calculator does not maintain any state and is approapriate for calculation where a store is provided
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description void
calculateExtendedConditionals(double topBaseHeight, double bottomBaseHeight, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities, ConditionalProbabilityStore resultStore)
void
calculateFlatConditionals(double rootHeight, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilitiesStore, ConditionalProbabilityStore rightConditionalProbabilitiesStore, ConditionalProbabilityStore resultConditionalProbabilitiesStore)
double
calculateLogLikelihood(double rootHeight, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilitiesStore, ConditionalProbabilityStore rightConditionalProbabilitiesStore)
Calculate the likelihood given two sub trees (left, right) and their extended likeihood probabilitiesdouble
calculateLogLikelihoodNonRoot(double nodeHeight, PatternInfo centerPattern, ConditionalProbabilityStore ascendentConditionalProbabilitiesStore, ConditionalProbabilityStore descendentConditionalProbabilitiesStore)
Calculate the likelihood given a non root nodedouble
calculateLogLikelihoodSingle(double rootHeight, PatternInfo centerPattern, ConditionalProbabilityStore conditionalProbabilitiesStore)
void
calculateSingleAscendentExtendedConditionalsDirect(double topBaseHeight, double bottomBaseHeight, PatternInfo centerPattern, ConditionalProbabilityStore ascendentConditionalProbabilityProbabilties)
void
calculateSingleAscendentExtendedConditionalsIndirect(double topBaseHeight, double bottomBaseHeight, PatternInfo centerPattern, ConditionalProbabilityStore baseAscendentConditionalProbabilityProbabilties, ConditionalProbabilityStore resultConditionalProbabilityProbabilties)
void
calculateSingleDescendentExtendedConditionals(double topBaseHeight, double bottomBaseHeight, PatternInfo centerPattern, ConditionalProbabilityStore descendentConditionalProbabilities)
SiteDetails
calculateSiteDetails(double rootHeight, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilitiesStore, ConditionalProbabilityStore rightConditionalProbabilitiesStore)
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Method Detail
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calculateSingleDescendentExtendedConditionals
void calculateSingleDescendentExtendedConditionals(double topBaseHeight, double bottomBaseHeight, PatternInfo centerPattern, ConditionalProbabilityStore descendentConditionalProbabilities)
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calculateSingleAscendentExtendedConditionalsDirect
void calculateSingleAscendentExtendedConditionalsDirect(double topBaseHeight, double bottomBaseHeight, PatternInfo centerPattern, ConditionalProbabilityStore ascendentConditionalProbabilityProbabilties)
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calculateSingleAscendentExtendedConditionalsIndirect
void calculateSingleAscendentExtendedConditionalsIndirect(double topBaseHeight, double bottomBaseHeight, PatternInfo centerPattern, ConditionalProbabilityStore baseAscendentConditionalProbabilityProbabilties, ConditionalProbabilityStore resultConditionalProbabilityProbabilties)
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calculateExtendedConditionals
void calculateExtendedConditionals(double topBaseHeight, double bottomBaseHeight, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities, ConditionalProbabilityStore resultStore)
- Parameters:
distance
-model
-patternLookup
-numberOfPatterns
-leftConditionalProbabilityProbabilties
- Implementations must not overwrite or changerightConditionalProbabilityProbabilties
- Implementations must not overwrite or changeresultStore
- Where to stick the created categoryPatternState information
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calculateLogLikelihood
double calculateLogLikelihood(double rootHeight, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilitiesStore, ConditionalProbabilityStore rightConditionalProbabilitiesStore)
Calculate the likelihood given two sub trees (left, right) and their extended likeihood probabilities- Parameters:
rootHeight
- the height of the likelihood calculationleftConditionalProbabilities
- Assumed to be extended to the rootHeightrightConditionalProbabilities
- Assumed to be extended to the rootHeight- Returns:
- the Log likelihood
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calculateLogLikelihoodNonRoot
double calculateLogLikelihoodNonRoot(double nodeHeight, PatternInfo centerPattern, ConditionalProbabilityStore ascendentConditionalProbabilitiesStore, ConditionalProbabilityStore descendentConditionalProbabilitiesStore)
Calculate the likelihood given a non root node- Parameters:
nodeHeight
- the height of node doing the likelihood calculationcenterPatter
- assumed left is ascendent component, right is descendentascendentConditionalProbabilities
- Assumed to be extended (downwards) to the nodeHeightdescendentConditionalProbabilities
- Assumed to be extended (upwards) to the nodeHeight- Returns:
- the Log likelihood
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calculateLogLikelihoodSingle
double calculateLogLikelihoodSingle(double rootHeight, PatternInfo centerPattern, ConditionalProbabilityStore conditionalProbabilitiesStore)
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calculateSiteDetails
SiteDetails calculateSiteDetails(double rootHeight, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilitiesStore, ConditionalProbabilityStore rightConditionalProbabilitiesStore)
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calculateFlatConditionals
void calculateFlatConditionals(double rootHeight, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilitiesStore, ConditionalProbabilityStore rightConditionalProbabilitiesStore, ConditionalProbabilityStore resultConditionalProbabilitiesStore)
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