ScoringMethodForExternalNode

All Known Implementing Classes:: BranchCountingBasedScoringMethod, BranchLengthBasedScoringMethod, LogBranchLengthBasedScoringMethod

public interface ScoringMethodForExternalNode

Method Summary

Modifier and Type

Method

Description

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 Details
- 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<PhylogenyNode, Double> 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