org.forester.pccx
Class LogBranchLengthBasedScoringMethod
java.lang.Object
org.forester.pccx.BranchCountingBasedScoringMethod
org.forester.pccx.LogBranchLengthBasedScoringMethod
- All Implemented Interfaces:
- ScoringMethodForExternalNode
public class LogBranchLengthBasedScoringMethod
- extends BranchCountingBasedScoringMethod
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
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
LogBranchLengthBasedScoringMethod
public LogBranchLengthBasedScoringMethod()
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