Package org.biojava.nbio.alignment
Class StandardRescoreRefiner<S extends Sequence<C>,C extends Compound>
java.lang.Object
org.biojava.nbio.alignment.template.AbstractScorer
org.biojava.nbio.alignment.StandardRescoreRefiner<S,C>
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Aligner<S,,C> RescoreRefiner<S,,C> Scorer
public class StandardRescoreRefiner<S extends Sequence<C>,C extends Compound>
extends AbstractScorer
implements RescoreRefiner<S,C>
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Constructor Summary
ConstructorsConstructorDescriptionStandardRescoreRefiner(Alignments.PairInProfileScorerType pips, Alignments.ProfileProfileAlignerType ppa) -
Method Summary
Modifier and TypeMethodDescriptionlongReturns the computation time needed for an alignment computed in nanoseconds.doubleReturns maximum possible score.doubleReturns minimum possible score.Returns class type of pairwise scoring subroutine.Returns the alignmentProfileproduced by this alignment algorithm.Returns class type of profile-profile alignment subroutine.doublegetScore()Returns score resulting from algorithm.Methods inherited from class org.biojava.nbio.alignment.template.AbstractScorer
getDistance, getDistance, getSimilarity, getSimilarityMethods 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
getDistance, getDistance, getSimilarity, getSimilarity
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Constructor Details
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StandardRescoreRefiner
public StandardRescoreRefiner(Alignments.PairInProfileScorerType pips, Alignments.ProfileProfileAlignerType ppa)
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Method Details
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getPairInProfileScorer
Description copied from interface:RescoreRefinerReturns class type of pairwise scoring subroutine.- Specified by:
getPairInProfileScorerin interfaceRescoreRefiner<S extends Sequence<C>,C extends Compound> - Returns:
- class type of pairwise scoring subroutine
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getProfileProfileAligner
Description copied from interface:RescoreRefinerReturns class type of profile-profile alignment subroutine.- Specified by:
getProfileProfileAlignerin interfaceRescoreRefiner<S extends Sequence<C>,C extends Compound> - Returns:
- class type of profile-profile alignment subroutine
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getComputationTime
public long getComputationTime()Description copied from interface:AlignerReturns the computation time needed for an alignment computed in nanoseconds. -
getProfile
Description copied from interface:AlignerReturns the alignmentProfileproduced by this alignment algorithm. -
getMaxScore
public double getMaxScore()Description copied from interface:ScorerReturns maximum possible score.- Specified by:
getMaxScorein interfaceScorer- Returns:
- maximum possible score
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getMinScore
public double getMinScore()Description copied from interface:ScorerReturns minimum possible score.- Specified by:
getMinScorein interfaceScorer- Returns:
- minimum possible score
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getScore
public double getScore()Description copied from interface:ScorerReturns score resulting from algorithm. This should normalize between 0 and 1 by calculating (Scorer.getScore()-Scorer.getMinScore()) / (Scorer.getMaxScore()-Scorer.getMinScore()).
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