Package org.forester.pccx
Class BranchCountingBasedScoringMethod
java.lang.Object
org.forester.pccx.BranchCountingBasedScoringMethod
- All Implemented Interfaces:
ScoringMethodForExternalNode
- Direct Known Subclasses:
BranchLengthBasedScoringMethod,LogBranchLengthBasedScoringMethod
public class BranchCountingBasedScoringMethod
extends Object
implements ScoringMethodForExternalNode
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoidcalculateScoreForExternalNode(SortedMap<PhylogenyNode, Double> external_node_scores, Phylogeny phylogeny, PhylogenyNode external_node, CoverageCalculationOptions options) This calculates the coverage score for one external node.This returns a short description of this scoring methoddoublegetNormalizationFactor(Phylogeny phylogeny) This calculates a normalization factor, so that a normalized score of 1.0 means complete coverage.
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Constructor Details
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BranchCountingBasedScoringMethod
public BranchCountingBasedScoringMethod()
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Method Details
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calculateScoreForExternalNode
public void calculateScoreForExternalNode(SortedMap<PhylogenyNode, Double> external_node_scores, Phylogeny phylogeny, PhylogenyNode external_node, CoverageCalculationOptions options) Description copied from interface:ScoringMethodForExternalNodeThis calculates the coverage score for one external node.- Specified by:
calculateScoreForExternalNodein interfaceScoringMethodForExternalNode- Parameters:
external_node_scores- SortedMap<PhylogenyNode, Double> in 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
Description copied from interface:ScoringMethodForExternalNodeThis returns a short description of this scoring method- Specified by:
getDesciptionin interfaceScoringMethodForExternalNode- Returns:
- short description of this scoring method
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getNormalizationFactor
Description copied from interface:ScoringMethodForExternalNodeThis calculates a normalization factor, so that a normalized score of 1.0 means complete coverage.- Specified by:
getNormalizationFactorin interfaceScoringMethodForExternalNode- Parameters:
phylogeny- Phylogeny containing the external nodes to score- Returns:
- normalization factor
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