Package org.forester.pccx
Class LogBranchLengthBasedScoringMethod
- java.lang.Object
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- org.forester.pccx.BranchCountingBasedScoringMethod
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- org.forester.pccx.LogBranchLengthBasedScoringMethod
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- All Implemented Interfaces:
ScoringMethodForExternalNode
public class LogBranchLengthBasedScoringMethod extends BranchCountingBasedScoringMethod
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Field Summary
Fields Modifier and Type Field Description static double
MAX_ALLOWED_BL_VALUE
static double
MIN_ALLOWED_BL_VALUE
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Constructor Summary
Constructors Constructor Description LogBranchLengthBasedScoringMethod()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description 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.-
Methods inherited from class org.forester.pccx.BranchCountingBasedScoringMethod
calculateScoreForExternalNode
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Field Detail
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MIN_ALLOWED_BL_VALUE
public static final double MIN_ALLOWED_BL_VALUE
- See Also:
- Constant Field Values
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MAX_ALLOWED_BL_VALUE
public static final double MAX_ALLOWED_BL_VALUE
- See Also:
- Constant Field Values
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Method Detail
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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
- Overrides:
getDesciption
in classBranchCountingBasedScoringMethod
- 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
- Overrides:
getNormalizationFactor
in classBranchCountingBasedScoringMethod
- Parameters:
phylogeny
- Phylogeny containing the external nodes to score- Returns:
- normalization factor
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