org.forester.pccx

Interface ScoringMethodForExternalNode

All Known Implementing Classes:

BranchCountingBasedScoringMethod, BranchLengthBasedScoringMethod, LogBranchLengthBasedScoringMethod

public interface ScoringMethodForExternalNode

Method Summary

Modifier and Type	Method and Description
void	calculateScoreForExternalNode(SortedMap<PhylogenyNode,Double> external_node_scores, Phylogeny phylogeny, PhylogenyNode external_node, CoverageCalculationOptions options) This calculates the coverage score for one external node.
String	getDesciption() This returns a short description of this scoring method
double	getNormalizationFactor(Phylogeny phylogeny) This calculates a normalization factor, so that a normalized score of 1.0 means complete coverage.

Method Detail

calculateScoreForExternalNode

void calculateScoreForExternalNode(SortedMap<PhylogenyNode,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

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