Package pal.eval
Interface LHCalculator.Internal
- Enclosing interface:
- LHCalculator
public static interface LHCalculator.Internal
The Internal calculator may maintain state and is approapriate permanent attachment
to internal nodes of the tree structure
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Method Summary
Modifier and TypeMethodDescriptioncalculateExtended(double distance, SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities, boolean modelChangedSinceLastCall) calculateFlat(PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities) calculate flat probability information (not extended over a branch).calculatePostExtendedFlat(double distance, SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities, boolean modelChangedSinceLastCall)
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Method Details
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calculateFlat
ConditionalProbabilityStore calculateFlat(PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities) calculate flat probability information (not extended over a branch).- Parameters:
centerPattern- the pattern informationleftConditionalProbabilities- Implementations should be allowed to overwrite in certain casesrightConditionalProbabilities- Implementations should be allowed to overwrite in certain cases- Returns:
- true if results built from cached information
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calculateExtended
ConditionalProbabilityStore calculateExtended(double distance, SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities, boolean modelChangedSinceLastCall) - Parameters:
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 otherwise- Returns:
- resulting conditional probabilities
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calculatePostExtendedFlat
ConditionalProbabilityStore calculatePostExtendedFlat(double distance, SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities, boolean modelChangedSinceLastCall)
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