org.forester.pccx

Class BranchLengthBasedScoringMethod

java.lang.Object

org.forester.pccx.BranchCountingBasedScoringMethod

org.forester.pccx.BranchLengthBasedScoringMethod

All Implemented Interfaces:

ScoringMethodForExternalNode

public class BranchLengthBasedScoringMethod
extends BranchCountingBasedScoringMethod

Field Summary

Fields

Modifier and Type	Field and Description
static double	MIN_ALLOWED_BL_VALUE

Constructor Summary

Constructors

Constructor and Description
BranchLengthBasedScoringMethod()

Method Summary

Modifier and Type	Method and Description
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 org.forester.pccx.BranchCountingBasedScoringMethod

calculateScoreForExternalNode

Methods inherited from class java.lang.Object

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

Field Detail

MIN_ALLOWED_BL_VALUE

public static final double MIN_ALLOWED_BL_VALUE

See Also:

Constant Field Values

Constructor Detail

BranchLengthBasedScoringMethod

public BranchLengthBasedScoringMethod()

Method Detail

getDesciption

public String getDesciption()

Description copied from interface: ScoringMethodForExternalNode

This returns a short description of this scoring method

Specified by:

getDesciption in interface ScoringMethodForExternalNode

Overrides:

getDesciption in class BranchCountingBasedScoringMethod

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

Overrides:

getNormalizationFactor in class BranchCountingBasedScoringMethod

Parameters:

phylogeny - Phylogeny containing the external nodes to score

Returns:

normalization factor