Package pal.eval

Interface UnconstrainedLikelihoodModel.Internal

All Known Implementing Classes:
SimpleUnconstrainedLikelihoodModel.InternalImpl
Enclosing interface:
UnconstrainedLikelihoodModel

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

    • calculateFlat

      ConditionalProbabilityStore calculateFlat(PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities)
      calculate flat probability information (not extended over a branch).
      Parameters:
      centerPattern - the pattern information
      leftConditionalProbabilities - Implementations should be allowed to overwrite in certain cases
      rightConditionalProbabilities - Implementations should be allowed to overwrite in certain cases
      Returns:
      true if results built from cached information
    • calculateExtended

      ConditionalProbabilityStore calculateExtended(double distance, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities)
      Parameters:
      distance - The evolutionary distance
      centerPattern - the pattern information
      leftConditionalProbabilities - Implementations should be allowed to overwrite in certain cases
      rightConditionalProbabilities - Implementations should be allowed to overwrite in certain cases
      Returns:
      resulting conditional probabilities