Package pal.eval

Interface LHCalculator.External

  • All Superinterfaces:
    java.io.Serializable
    Enclosing interface:
    LHCalculator

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

      • calculateFlat

        void calculateFlat​(PatternInfo centerPattern,
                           ConditionalProbabilityStore leftConditionalProbabilities,
                           ConditionalProbabilityStore rightConditionalProbabilities,
                           ConditionalProbabilityStore resultStore)
        Parameters:
        centerPattern - the pattern information
        leftConditionalProbabilities - Implementations must not overwrite or change
        rightConditionalProbabilities - Implementations must not overwrite or change
        resultStore - Where to stick the created categoryPatternState information
      • calculateExtended

        void calculateExtended​(double distance,
                               SubstitutionModel model,
                               PatternInfo centerPattern,
                               ConditionalProbabilityStore leftConditionalProbabilities,
                               ConditionalProbabilityStore rightConditionalProbabilities,
                               ConditionalProbabilityStore resultStore)
        Parameters:
        distance -
        model -
        centerPattern - the pattern information
        leftConditionalProbabilities - Implementations must not overwrite or change
        rightConditionalProbabilities - Implementations must not overwrite or change
        resultStore - Where to stick the created categoryPatternState information
      • calculateSingleExtendedDirect

        void calculateSingleExtendedDirect​(double distance,
                                           SubstitutionModel model,
                                           int numberOfPatterns,
                                           ConditionalProbabilityStore conditionalProbabilities)
        Extend the conditionals back in time by some distance, with some model
        Parameters:
        distance - The distance to extend by
        model - The model to use
        conditionalProbabilities - The probabilities to extend
      • calculateSingleExtendedIndirect

        void calculateSingleExtendedIndirect​(double distance,
                                             SubstitutionModel model,
                                             int numberOfPatterns,
                                             ConditionalProbabilityStore baseConditionalProbabilities,
                                             ConditionalProbabilityStore resultConditionalProbabilities)
        Extend the conditionals back in time by some distance, with some model
        Parameters:
        distance - The distance to extend by
        model - The model to use
        baseConditionalProbabilities - The probabilities to extend
        resultConditionalProbabilities - The probabilities to extend
      • calculateLogLikelihood

        double calculateLogLikelihood​(double distance,
                                      SubstitutionModel model,
                                      PatternInfo centerPattern,
                                      ConditionalProbabilityStore leftFlatConditionalProbabilities,
                                      ConditionalProbabilityStore rightFlatConditionalProbabilities,
                                      ConditionalProbabilityStore tempStore)
        Calculate the likelihood given two sub trees (left, right) and their flat (unextend) likeihood probabilities
        Parameters:
        distance -
        model -
        centerPattern - the pattern information
        leftFlatConditionalProbabilities -
        rightFlatConditionalProbabilities -
        tempStore - may be used internally to calculate likelihood
        Returns:
        the log likelihood
      • calculateLogLikelihood

        double calculateLogLikelihood​(SubstitutionModel model,
                                      PatternInfo centerPattern,
                                      ConditionalProbabilityStore leftConditionalProbabilities,
                                      ConditionalProbabilityStore rightConditionalProbabilities)
        Calculate the likelihood given two sub trees (left, right) and their extended likeihood probabilities
        Parameters:
        model -
        centerPattern - the pattern information
        leftConditionalProbabilities -
        rightConditionalProbabilities -
        Returns:
        the Log likelihood
      • calculateLogLikelihoodSingle

        double calculateLogLikelihoodSingle​(SubstitutionModel model,
                                            int[] patternWeights,
                                            int numberOfPatterns,
                                            ConditionalProbabilityStore conditionalProbabilityStore)
        Calculate the likelihood given the conditional probabilites at the root
        Parameters:
        model - The substitution model used
        patternWeights - the weights of each pattern
        numberOfPatterns - the number of patterns
        conditionalProbabilities - The conditionals
        Returns:
        the Log likelihood
      • calculateSiteDetailsRooted

        SiteDetails calculateSiteDetailsRooted​(SubstitutionModel model,
                                               PatternInfo centerPattern,
                                               ConditionalProbabilityStore leftConditionalProbabilitiesStore,
                                               ConditionalProbabilityStore rightConditionalProbabilitiesStore)
        Calculate the conditional probabilities of each pattern for each category
        Parameters:
        model -
        centerPattern - the pattern information
        leftConditionalProbabilities -
        rightConditionalProbabilities -
        categoryPatternLogLikelihoodStore - after call will hold a matrix of values in the form [cat][pattern], where [cat][pattern] represents the site probability under a particular category/class, *not* multiplied by the category probability or pattern weights
      • calculateSiteDetailsUnrooted

        SiteDetails calculateSiteDetailsUnrooted​(double distance,
                                                 SubstitutionModel model,
                                                 PatternInfo centerPattern,
                                                 ConditionalProbabilityStore leftConditionalProbabilitiesStore,
                                                 ConditionalProbabilityStore rightConditionalProbabilitiesStore,
                                                 ConditionalProbabilityStore tempStore)
        Calculate the conditional probabilities of each pattern for each category
        Parameters:
        distance - The distance between the two nodes
        model -
        centerPattern - the pattern information
        leftConditionalProbabilities -
        rightConditionalProbabilities -
        categoryPatternLogLikelihoodStore - after call will hold a matrix of values in the form [cat][pattern], where [cat][pattern] represents the site probability under a particular category/class, *not* multiplied by the category probability or pattern weights