public class BranchCountingBasedScoringMethod extends java.lang.Object implements ScoringMethodForExternalNode
Constructor and Description |
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BranchCountingBasedScoringMethod() |
Modifier and Type | Method and Description |
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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.
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java.lang.String |
getDesciption()
This returns a short description of this scoring method
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double |
getNormalizationFactor(Phylogeny phylogeny)
This calculates a normalization factor, so that a normalized score of 1.0
means complete coverage.
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public void calculateScoreForExternalNode(java.util.SortedMap<PhylogenyNode,java.lang.Double> external_node_scores, Phylogeny phylogeny, PhylogenyNode external_node, CoverageCalculationOptions options)
ScoringMethodForExternalNode
calculateScoreForExternalNode
in interface ScoringMethodForExternalNode
external_node_scores
- SortedMapphylogeny
- Phylogeny containing the external nodes to scoreexternal_node
- PhylogenyNod for which to calculate the scoreoptions
- CoverageCalculationOptionspublic java.lang.String getDesciption()
ScoringMethodForExternalNode
getDesciption
in interface ScoringMethodForExternalNode
public double getNormalizationFactor(Phylogeny phylogeny)
ScoringMethodForExternalNode
getNormalizationFactor
in interface ScoringMethodForExternalNode
phylogeny
- Phylogeny containing the external nodes to score