Package pal.eval

Interface MolecularClockLikelihoodModel.External

  • Enclosing interface:
    MolecularClockLikelihoodModel

    public static interface MolecularClockLikelihoodModel.External
    The External calculator does not maintain any state and is approapriate for calculation where a store is provided
    • Method Detail

      • calculateSingleDescendentExtendedConditionals

        void calculateSingleDescendentExtendedConditionals​(double topBaseHeight,
                                                           double bottomBaseHeight,
                                                           PatternInfo centerPattern,
                                                           ConditionalProbabilityStore descendentConditionalProbabilities)
      • calculateSingleAscendentExtendedConditionalsDirect

        void calculateSingleAscendentExtendedConditionalsDirect​(double topBaseHeight,
                                                                double bottomBaseHeight,
                                                                PatternInfo centerPattern,
                                                                ConditionalProbabilityStore ascendentConditionalProbabilityProbabilties)
      • calculateSingleAscendentExtendedConditionalsIndirect

        void calculateSingleAscendentExtendedConditionalsIndirect​(double topBaseHeight,
                                                                  double bottomBaseHeight,
                                                                  PatternInfo centerPattern,
                                                                  ConditionalProbabilityStore baseAscendentConditionalProbabilityProbabilties,
                                                                  ConditionalProbabilityStore resultConditionalProbabilityProbabilties)
      • calculateExtendedConditionals

        void calculateExtendedConditionals​(double topBaseHeight,
                                           double bottomBaseHeight,
                                           PatternInfo centerPattern,
                                           ConditionalProbabilityStore leftConditionalProbabilities,
                                           ConditionalProbabilityStore rightConditionalProbabilities,
                                           ConditionalProbabilityStore resultStore)
        Parameters:
        distance -
        model -
        patternLookup -
        numberOfPatterns -
        leftConditionalProbabilityProbabilties - Implementations must not overwrite or change
        rightConditionalProbabilityProbabilties - Implementations must not overwrite or change
        resultStore - Where to stick the created categoryPatternState information
      • calculateLogLikelihood

        double calculateLogLikelihood​(double rootHeight,
                                      PatternInfo centerPattern,
                                      ConditionalProbabilityStore leftConditionalProbabilitiesStore,
                                      ConditionalProbabilityStore rightConditionalProbabilitiesStore)
        Calculate the likelihood given two sub trees (left, right) and their extended likeihood probabilities
        Parameters:
        rootHeight - the height of the likelihood calculation
        leftConditionalProbabilities - Assumed to be extended to the rootHeight
        rightConditionalProbabilities - Assumed to be extended to the rootHeight
        Returns:
        the Log likelihood
      • calculateLogLikelihoodNonRoot

        double calculateLogLikelihoodNonRoot​(double nodeHeight,
                                             PatternInfo centerPattern,
                                             ConditionalProbabilityStore ascendentConditionalProbabilitiesStore,
                                             ConditionalProbabilityStore descendentConditionalProbabilitiesStore)
        Calculate the likelihood given a non root node
        Parameters:
        nodeHeight - the height of node doing the likelihood calculation
        centerPatter - assumed left is ascendent component, right is descendent
        ascendentConditionalProbabilities - Assumed to be extended (downwards) to the nodeHeight
        descendentConditionalProbabilities - Assumed to be extended (upwards) to the nodeHeight
        Returns:
        the Log likelihood