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 Details

    • 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
    • calculateAscendentExtendedConditionals

      ConditionalProbabilityStore calculateAscendentExtendedConditionals(double topBaseHeight, double bottomBaseHeight, PatternInfo centerPattern, ConditionalProbabilityStore ascendentConditionalProbabilityProbabilties, ConditionalProbabilityStore otherConditionalProbabilityProbabilties)
    • calculateAscendentFlatConditionals

      ConditionalProbabilityStore calculateAscendentFlatConditionals(PatternInfo centerPattern, ConditionalProbabilityStore ascenedentConditionalProbabilityProbabilties, ConditionalProbabilityStore otherConditionalProbabilityProbabilties)
    • 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