Package pal.eval

Interface UnconstrainedLikelihoodModel.Instance

  • All Superinterfaces:
    java.io.Serializable
    Enclosing interface:
    UnconstrainedLikelihoodModel

    public static interface UnconstrainedLikelihoodModel.Instance
    extends java.io.Serializable
    • Method Detail

      • 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
      • 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

        java.lang.String getSubstitutionModelSummary()