LogBranchLengthBasedScoringMethod (biojava 5.4.0 API)

java.lang.Object
- org.forester.pccx.BranchCountingBasedScoringMethod
- - org.forester.pccx.LogBranchLengthBasedScoringMethod

All Implemented Interfaces:: ScoringMethodForExternalNode

public class LogBranchLengthBasedScoringMethod
extends BranchCountingBasedScoringMethod

Field Summary

Fields
Modifier and Type Field Description

static double MAX_ALLOWED_BL_VALUE

static double MIN_ALLOWED_BL_VALUE

Constructor Summary

Constructors
Constructor Description

LogBranchLengthBasedScoringMethod()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`java.lang.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 java.lang.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