Package pal.eval

Interface UnconstrainedLikelihoodModel.Internal

    • 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,
                                                      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