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)

Method Detail

calculateFlat

ConditionalProbabilityStore calculateFlat(PatternInfo centerPattern,
                                          ConditionalProbabilityStore leftConditionalProbabilities,
                                          ConditionalProbabilityStore rightConditionalProbabilities)

calculate flat probability information (not extended over a branch).

Parameters:

centerPattern - the pattern information

leftConditionalProbabilities - Implementations should be allowed to overwrite in certain cases

rightConditionalProbabilities - 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 information

leftConditionalProbabilities -

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)