Package pal.eval
Interface LHCalculator.Internal
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- 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
All Methods Instance Methods Abstract Methods Modifier and Type Method 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)
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Method Detail
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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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