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
Method Summary |
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)
|
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
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
calculatePostExtendedFlat
ConditionalProbabilityStore calculatePostExtendedFlat(double distance,
SubstitutionModel model,
PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilities,
ConditionalProbabilityStore rightConditionalProbabilities,
boolean modelChangedSinceLastCall)