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