Interface ScoringMethodForExternalNode

    • Method Detail

      • calculateScoreForExternalNode

        void calculateScoreForExternalNode​(java.util.SortedMap<PhylogenyNode,​java.lang.Double> external_node_scores,
                                           Phylogeny phylogeny,
                                           PhylogenyNode external_node,
                                           CoverageCalculationOptions options)
        This calculates the coverage score for one external node.
        Parameters:
        external_node_scores - SortedMap in which the external node scores are stored (node->score)
        phylogeny - Phylogeny containing the external nodes to score
        external_node - PhylogenyNod for which to calculate the score
        options - CoverageCalculationOptions
        annotate_phylogeny -
      • getDesciption

        java.lang.String getDesciption()
        This returns a short description of this scoring method
        Returns:
        short description of this scoring method
      • getNormalizationFactor

        double getNormalizationFactor​(Phylogeny phylogeny)
        This calculates a normalization factor, so that a normalized score of 1.0 means complete coverage.
        Parameters:
        phylogeny - Phylogeny containing the external nodes to score
        Returns:
        normalization factor