org.forester.pccx
Class BranchCountingBasedScoringMethod
java.lang.Object
org.forester.pccx.BranchCountingBasedScoringMethod
- All Implemented Interfaces:
- ScoringMethodForExternalNode
- Direct Known Subclasses:
- BranchLengthBasedScoringMethod, LogBranchLengthBasedScoringMethod
public class BranchCountingBasedScoringMethod
- extends Object
- implements ScoringMethodForExternalNode
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
BranchCountingBasedScoringMethod
public BranchCountingBasedScoringMethod()
calculateScoreForExternalNode
public void calculateScoreForExternalNode(SortedMap<PhylogenyNode,Double> external_node_scores,
Phylogeny phylogeny,
PhylogenyNode external_node,
CoverageCalculationOptions options)
- Description copied from interface:
ScoringMethodForExternalNode
- This calculates the coverage score for one external node.
- Specified by:
calculateScoreForExternalNode
in interface ScoringMethodForExternalNode
- Parameters:
external_node_scores
- SortedMap in which the external node
scores are stored (node->score)phylogeny
- Phylogeny containing the external nodes to scoreexternal_node
- PhylogenyNod for which to calculate the scoreoptions
- CoverageCalculationOptions
getDesciption
public String getDesciption()
- Description copied from interface:
ScoringMethodForExternalNode
- This returns a short description of this scoring method
- Specified by:
getDesciption
in interface ScoringMethodForExternalNode
- 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
- Parameters:
phylogeny
- Phylogeny containing the external nodes to score
- Returns:
- normalization factor