org.forester.pccx
Class LogBranchLengthBasedScoringMethod

java.lang.Object
  extended by org.forester.pccx.BranchCountingBasedScoringMethod
      extended by org.forester.pccx.LogBranchLengthBasedScoringMethod
All Implemented Interfaces:
ScoringMethodForExternalNode

public class LogBranchLengthBasedScoringMethod
extends BranchCountingBasedScoringMethod


Field Summary
static double MAX_ALLOWED_BL_VALUE
           
static double MIN_ALLOWED_BL_VALUE
           
 
Constructor Summary
LogBranchLengthBasedScoringMethod()
           
 
Method Summary
 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

MAX_ALLOWED_BL_VALUE

public static final double MAX_ALLOWED_BL_VALUE
See Also:
Constant Field Values
Constructor Detail

LogBranchLengthBasedScoringMethod

public LogBranchLengthBasedScoringMethod()
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