Class AbstractScorer
java.lang.Object
org.biojava.nbio.alignment.template.AbstractScorer
- All Implemented Interfaces:
Scorer
- Direct Known Subclasses:
AbstractMatrixAligner,FractionalIdentityScorer,FractionalSimilarityScorer,StandardRescoreRefiner,SubstitutionMatrixScorer
Implements common code for algorithms which compute a score.
- Author:
- Mark Chapman
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptiondoubleReturns score as a distance between 0.0 and 1.0.doublegetDistance(double scale) Returns score as a distance between 0.0 and scale.doubleReturns score as a similarity between 0.0 and 1.0.doublegetSimilarity(double scale) Returns score as a similarity between 0.0 and scale.Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, waitMethods inherited from interface org.biojava.nbio.alignment.template.Scorer
getMaxScore, getMinScore, getScore
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Constructor Details
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AbstractScorer
public AbstractScorer()
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Method Details
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getDistance
public double getDistance()Description copied from interface:ScorerReturns score as a distance between 0.0 and 1.0. This equals (Scorer.getMaxScore()-Scorer.getScore()) / (Scorer.getMaxScore()-Scorer.getMinScore()).- Specified by:
getDistancein interfaceScorer- Returns:
- score as a distance between 0.0 and 1.0
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getDistance
public double getDistance(double scale) Description copied from interface:ScorerReturns score as a distance between 0.0 and scale. This equals scale * (Scorer.getMaxScore()-Scorer.getScore()) / (Scorer.getMaxScore()-Scorer.getMinScore()).- Specified by:
getDistancein interfaceScorer- Parameters:
scale- maximum distance- Returns:
- score as a distance between 0.0 and scale
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getSimilarity
public double getSimilarity()Description copied from interface:ScorerReturns score as a similarity between 0.0 and 1.0. This equals (Scorer.getScore()-Scorer.getMinScore()) / (Scorer.getMaxScore()-Scorer.getMinScore()).- Specified by:
getSimilarityin interfaceScorer- Returns:
- score as a similarity between 0.0 and 1.0
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getSimilarity
public double getSimilarity(double scale) Description copied from interface:ScorerReturns score as a similarity between 0.0 and scale. This equals scale * (Scorer.getScore()-Scorer.getMinScore()) / (Scorer.getMaxScore()-Scorer.getMinScore()).- Specified by:
getSimilarityin interfaceScorer- Parameters:
scale- maximum similarity- Returns:
- score as a similarity between 0.0 and scale
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