org.forester.pccx
Interface ScoringMethodForExternalNode

All Known Implementing Classes:
BranchCountingBasedScoringMethod, BranchLengthBasedScoringMethod, LogBranchLengthBasedScoringMethod

public interface ScoringMethodForExternalNode


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.
 

Method Detail

calculateScoreForExternalNode

void calculateScoreForExternalNode(SortedMap<PhylogenyNode,Double> external_node_scores,
                                   Phylogeny phylogeny,
                                   PhylogenyNode external_node,
                                   CoverageCalculationOptions options)
This calculates the coverage score for one external node.

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
annotate_phylogeny -

getDesciption

String getDesciption()
This returns a short description of this scoring method

Returns:
short description of this scoring method

getNormalizationFactor

double getNormalizationFactor(Phylogeny phylogeny)
This calculates a normalization factor, so that a normalized score of 1.0 means complete coverage.

Parameters:
phylogeny - Phylogeny containing the external nodes to score
Returns:
normalization factor