pal.eval
Interface UnconstrainedLikelihoodModel.Internal

All Known Implementing Classes:

SimpleUnconstrainedLikelihoodModel.InternalImpl

Enclosing interface:

UnconstrainedLikelihoodModel

public static interface UnconstrainedLikelihoodModel.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, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities)
ConditionalProbabilityStore	calculateFlat(PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities) calculate flat probability information (not extended over a branch).

Method Detail

calculateFlat

public 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

public ConditionalProbabilityStore calculateExtended(double distance,
                                                     PatternInfo centerPattern,
                                                     ConditionalProbabilityStore leftConditionalProbabilities,
                                                     ConditionalProbabilityStore rightConditionalProbabilities)

Parameters:

distance - The evolutionary distance

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:

resulting conditional probabilities