org.forester.pccx
Class BranchCountingBasedScoringMethod

java.lang.Object
  extended by org.forester.pccx.BranchCountingBasedScoringMethod
All Implemented Interfaces:
ScoringMethodForExternalNode
Direct Known Subclasses:
BranchLengthBasedScoringMethod, LogBranchLengthBasedScoringMethod

public class BranchCountingBasedScoringMethod
extends Object
implements ScoringMethodForExternalNode


Constructor Summary
BranchCountingBasedScoringMethod()
           
 
Method Summary
 void calculateScoreForExternalNode(SortedMap<PhylogenyNode,Double> external_node_scores, Phylogeny phylogeny, PhylogenyNode external_node, CoverageCalculationOptions options)
          This calculates the coverage score for one external node.
 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 java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

BranchCountingBasedScoringMethod

public BranchCountingBasedScoringMethod()
Method Detail

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 score
external_node - PhylogenyNod for which to calculate the score
options - 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