public static interface LHCalculator.Internal
Modifier and Type | Method and Description |
---|---|
ConditionalProbabilityStore |
calculateExtended(double distance,
SubstitutionModel model,
PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilities,
ConditionalProbabilityStore rightConditionalProbabilities,
boolean modelChangedSinceLastCall) |
ConditionalProbabilityStore |
calculateFlat(PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilities,
ConditionalProbabilityStore rightConditionalProbabilities)
calculate flat probability information (not extended over a branch).
|
ConditionalProbabilityStore |
calculatePostExtendedFlat(double distance,
SubstitutionModel model,
PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilities,
ConditionalProbabilityStore rightConditionalProbabilities,
boolean modelChangedSinceLastCall) |
ConditionalProbabilityStore calculateFlat(PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities)
centerPattern
- the pattern informationleftConditionalProbabilities
- Implementations should be allowed to overwrite in certain casesrightConditionalProbabilities
- Implementations should be allowed to overwrite in certain casesConditionalProbabilityStore calculateExtended(double distance, SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities, boolean modelChangedSinceLastCall)
distance
- model
- centerPattern
- the pattern informationleftConditionalProbabilities
- rightConditionalProbabilities
- modelChangedSinceLastCall
- this should be true if the substituion model has altered since the last call to this method on this particular object, false otherwiseConditionalProbabilityStore calculatePostExtendedFlat(double distance, SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities, boolean modelChangedSinceLastCall)