Package pal.eval

Interface MolecularClockLikelihoodModel.Internal

  • Enclosing interface:
    MolecularClockLikelihoodModel

    public static interface MolecularClockLikelihoodModel.Internal
    The Internal calculator may maintain state and is approapriate permanent attachment to internal nodes of the tree structure
    • Method Detail

      • calculateExtendedConditionals

        ConditionalProbabilityStore calculateExtendedConditionals​(double topBaseHeight,
                                                                  double bottomBaseHeight,
                                                                  PatternInfo centerPattern,
                                                                  ConditionalProbabilityStore leftConditionalProbabilityProbabilties,
                                                                  ConditionalProbabilityStore rightConditionalProbabilityProbabilties)
        Parameters:
        patternLookup -
        numberOfPatterns -
        leftConditionalProbabilityProbabilties - Implementations should be allowed to overwrite in certain cases
        rightConditionalProbabilityProbabilties - Implementations should be allowed to overwrite in certain cases
        Returns:
        true if result build on cached information
      • calculatePostExtendedFlatConditionals

        ConditionalProbabilityStore calculatePostExtendedFlatConditionals​(double topBaseHeight,
                                                                          double bottomBaseHeight,
                                                                          PatternInfo centerPattern,
                                                                          ConditionalProbabilityStore leftConditionalProbabilityProbabilties,
                                                                          ConditionalProbabilityStore rightConditionalProbabilityProbabilties)
        Extends left and right conditionals by type and then calculates flat conditionals
        Parameters:
        patternLookup -
        numberOfPatterns -
        leftConditionalProbabilityProbabilties - Implementations should be allowed to overwrite in certain cases
        rightConditionalProbabilityProbabilties - Implementations should be allowed to overwrite in certain cases
        Returns:
        true if result build on cached information
      • calculateFlatConditionals

        ConditionalProbabilityStore calculateFlatConditionals​(PatternInfo centerPattern,
                                                              ConditionalProbabilityStore leftConditionalProbabilityProbabilties,
                                                              ConditionalProbabilityStore rightConditionalProbabilityProbabilties)
        Parameters:
        centerPattern - the center pattern info
        leftConditionalProbabilityProbabilties - Implementations should be allowed to overwrite in certain cases
        rightConditionalProbabilityProbabilties - Implementations should be allowed to overwrite in certain cases
        Returns:
        true if result build on cached information