Package org.forester.pccx
Class BranchCountingBasedScoringMethod
- java.lang.Object
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- org.forester.pccx.BranchCountingBasedScoringMethod
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- All Implemented Interfaces:
ScoringMethodForExternalNode
- Direct Known Subclasses:
BranchLengthBasedScoringMethod
,LogBranchLengthBasedScoringMethod
public class BranchCountingBasedScoringMethod extends java.lang.Object implements ScoringMethodForExternalNode
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Constructor Summary
Constructors Constructor Description BranchCountingBasedScoringMethod()
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Method Summary
All Methods Instance Methods Concrete 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
public void calculateScoreForExternalNode(java.util.SortedMap<PhylogenyNode,java.lang.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 interfaceScoringMethodForExternalNode
- 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
- CoverageCalculationOptions
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getDesciption
public java.lang.String getDesciption()
Description copied from interface:ScoringMethodForExternalNode
This returns a short description of this scoring method- Specified by:
getDesciption
in interfaceScoringMethodForExternalNode
- Returns:
- short description of this scoring method
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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 interfaceScoringMethodForExternalNode
- Parameters:
phylogeny
- Phylogeny containing the external nodes to score- Returns:
- normalization factor
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