Package pal.eval

Interface UnconstrainedLikelihoodModel.Instance

All Superinterfaces:
Serializable
Enclosing interface:
UnconstrainedLikelihoodModel

public static interface UnconstrainedLikelihoodModel.Instance extends Serializable
  • Method Details

    • createNewLeaf

      UnconstrainedLikelihoodModel.Leaf createNewLeaf(int[] patternStateMatchup, int numberOfPatterns)
      Create anew leaf calculator
      Parameters:
      patternStateMatchup - The sequence as reduced to patterns. This should just be one state per pattern. For example given a sequence [ 0, 1,0,1,3,0] a patternMatchup may be [0,1,3] (the first element is the first pattern, which is state 0, the second element is the second pattern which is 1, and the third element is the third pattern (novel pattern) which is state 3)
      numberOfPatterns - The number of patterns in the patternStateMatchup array
      Returns:
      a leaf calculator object
    • createNewExternal

    • createNewInternal

    • isAllowCaching

      boolean isAllowCaching()
      If true, then user can assume that areas of trees that haven't changed, and the model parameters haven't be altered, can have their conditionals cached.
      Returns:
    • createAppropriateConditionalProbabilityStore

      ConditionalProbabilityStore createAppropriateConditionalProbabilityStore(boolean isForLeaf)
    • getSubstitutionModelSummary

      String getSubstitutionModelSummary()
    • getParameterAccess

      NeoParameterized getParameterAccess()