Package org.forester.pccx
Interface ScoringMethodForExternalNode
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- All Known Implementing Classes:
BranchCountingBasedScoringMethod
,BranchLengthBasedScoringMethod
,LogBranchLengthBasedScoringMethod
public interface ScoringMethodForExternalNode
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description void
calculateScoreForExternalNode(java.util.SortedMap<PhylogenyNode,java.lang.Double> external_node_scores, Phylogeny phylogeny, PhylogenyNode external_node, CoverageCalculationOptions options)
This calculates the coverage score for one external node.java.lang.String
getDesciption()
This returns a short description of this scoring methoddouble
getNormalizationFactor(Phylogeny phylogeny)
This calculates a normalization factor, so that a normalized score of 1.0 means complete coverage.
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Method Detail
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calculateScoreForExternalNode
void calculateScoreForExternalNode(java.util.SortedMap<PhylogenyNode,java.lang.Double> external_node_scores, Phylogeny phylogeny, PhylogenyNode external_node, CoverageCalculationOptions options)
This calculates the coverage score for one external node.- Parameters:
external_node_scores
- SortedMapin 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
- CoverageCalculationOptionsannotate_phylogeny
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getDesciption
java.lang.String getDesciption()
This returns a short description of this scoring method- Returns:
- short description of this scoring method
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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
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