org.forester.pccx

Class BranchCountingBasedScoringMethod

java.lang.Object

org.forester.pccx.BranchCountingBasedScoringMethod

All Implemented Interfaces:

ScoringMethodForExternalNode

Direct Known Subclasses:

BranchLengthBasedScoringMethod, LogBranchLengthBasedScoringMethod

public class BranchCountingBasedScoringMethod
extends Object
implements ScoringMethodForExternalNode

Constructor Summary

Constructors

Constructor and Description
BranchCountingBasedScoringMethod()

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.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

BranchCountingBasedScoringMethod

public BranchCountingBasedScoringMethod()

Method Detail

calculateScoreForExternalNode

public void calculateScoreForExternalNode(SortedMap<PhylogenyNode,Double> external_node_scores,
                                          Phylogeny phylogeny,
                                          PhylogenyNode external_node,
                                          CoverageCalculationOptions options)

Description copied from interface: ScoringMethodForExternalNode

This calculates the coverage score for one external node.

Specified by:

calculateScoreForExternalNode in interface ScoringMethodForExternalNode

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

getDesciption

public String getDesciption()

Description copied from interface: ScoringMethodForExternalNode

This returns a short description of this scoring method

Specified by:

getDesciption in interface ScoringMethodForExternalNode

Returns:

short description of this scoring method

getNormalizationFactor

public double getNormalizationFactor(Phylogeny phylogeny)

Description copied from interface: ScoringMethodForExternalNode

This calculates a normalization factor, so that a normalized score of 1.0 means complete coverage.

Specified by:

getNormalizationFactor in interface ScoringMethodForExternalNode

Parameters:

phylogeny - Phylogeny containing the external nodes to score

Returns:

normalization factor