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 Details

    • 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:
      resultStore - Where to stick the created categoryPatternState information
      distance -
      model -
      patternLookup -
      numberOfPatterns -
      leftConditionalProbabilityProbabilties - Implementations must not overwrite or change
      rightConditionalProbabilityProbabilties - Implementations must not overwrite or change
    • 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
    • calculateLogLikelihoodSingle

      double calculateLogLikelihoodSingle(double rootHeight, PatternInfo centerPattern, ConditionalProbabilityStore conditionalProbabilitiesStore)
    • calculateSiteDetails

      SiteDetails calculateSiteDetails(double rootHeight, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilitiesStore, ConditionalProbabilityStore rightConditionalProbabilitiesStore)
    • calculateFlatConditionals

      void calculateFlatConditionals(double rootHeight, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilitiesStore, ConditionalProbabilityStore rightConditionalProbabilitiesStore, ConditionalProbabilityStore resultConditionalProbabilitiesStore)