public static interface MolecularClockLikelihoodModel.External
Modifier and Type | Method and 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 probabilities
|
double |
calculateLogLikelihoodNonRoot(double nodeHeight,
PatternInfo centerPattern,
ConditionalProbabilityStore ascendentConditionalProbabilitiesStore,
ConditionalProbabilityStore descendentConditionalProbabilitiesStore)
Calculate the likelihood given a non root node
|
double |
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) |
void calculateSingleDescendentExtendedConditionals(double topBaseHeight, double bottomBaseHeight, PatternInfo centerPattern, ConditionalProbabilityStore descendentConditionalProbabilities)
void calculateSingleAscendentExtendedConditionalsDirect(double topBaseHeight, double bottomBaseHeight, PatternInfo centerPattern, ConditionalProbabilityStore ascendentConditionalProbabilityProbabilties)
void calculateSingleAscendentExtendedConditionalsIndirect(double topBaseHeight, double bottomBaseHeight, PatternInfo centerPattern, ConditionalProbabilityStore baseAscendentConditionalProbabilityProbabilties, ConditionalProbabilityStore resultConditionalProbabilityProbabilties)
void calculateExtendedConditionals(double topBaseHeight, double bottomBaseHeight, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities, ConditionalProbabilityStore resultStore)
distance
- model
- patternLookup
- numberOfPatterns
- leftConditionalProbabilityProbabilties
- Implementations must not overwrite or changerightConditionalProbabilityProbabilties
- Implementations must not overwrite or changeresultStore
- Where to stick the created categoryPatternState informationdouble calculateLogLikelihood(double rootHeight, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilitiesStore, ConditionalProbabilityStore rightConditionalProbabilitiesStore)
rootHeight
- the height of the likelihood calculationleftConditionalProbabilities
- Assumed to be extended to the rootHeightrightConditionalProbabilities
- Assumed to be extended to the rootHeightdouble calculateLogLikelihoodNonRoot(double nodeHeight, PatternInfo centerPattern, ConditionalProbabilityStore ascendentConditionalProbabilitiesStore, ConditionalProbabilityStore descendentConditionalProbabilitiesStore)
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 nodeHeightdouble calculateLogLikelihoodSingle(double rootHeight, PatternInfo centerPattern, ConditionalProbabilityStore conditionalProbabilitiesStore)
SiteDetails calculateSiteDetails(double rootHeight, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilitiesStore, ConditionalProbabilityStore rightConditionalProbabilitiesStore)
void calculateFlatConditionals(double rootHeight, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilitiesStore, ConditionalProbabilityStore rightConditionalProbabilitiesStore, ConditionalProbabilityStore resultConditionalProbabilitiesStore)