org.forester.pccx.LogBranchLengthBasedScoringMethod

public class LogBranchLengthBasedScoringMethod extends BranchCountingBasedScoringMethod

Field Details
- 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 Details
- LogBranchLengthBasedScoringMethod
  
  public LogBranchLengthBasedScoringMethod()
Method Details
- 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

Class LogBranchLengthBasedScoringMethod

Field Summary