Package org.biojava.nbio.alignment
Class StandardRescoreRefiner<S extends Sequence<C>,C extends Compound>
- java.lang.Object
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- org.biojava.nbio.alignment.template.AbstractScorer
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- org.biojava.nbio.alignment.StandardRescoreRefiner<S,C>
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- All Implemented Interfaces:
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
Constructors Constructor Description StandardRescoreRefiner(Alignments.PairInProfileScorerType pips, Alignments.ProfileProfileAlignerType ppa)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description long
getComputationTime()
Returns the computation time needed for an alignment computed in nanoseconds.double
getMaxScore()
Returns maximum possible score.double
getMinScore()
Returns minimum possible score.Alignments.PairInProfileScorerType
getPairInProfileScorer()
Returns class type of pairwise scoring subroutine.Profile<S,C>
getProfile()
Returns the alignmentProfile
produced by this alignment algorithm.Alignments.ProfileProfileAlignerType
getProfileProfileAligner()
Returns class type of profile-profile alignment subroutine.double
getScore()
Returns score resulting from algorithm.-
Methods inherited from class org.biojava.nbio.alignment.template.AbstractScorer
getDistance, getDistance, getSimilarity, getSimilarity
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Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Methods inherited from interface org.biojava.nbio.alignment.template.Scorer
getDistance, getDistance, getSimilarity, getSimilarity
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Constructor Detail
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StandardRescoreRefiner
public StandardRescoreRefiner(Alignments.PairInProfileScorerType pips, Alignments.ProfileProfileAlignerType ppa)
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Method Detail
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getPairInProfileScorer
public Alignments.PairInProfileScorerType getPairInProfileScorer()
Description copied from interface:RescoreRefiner
Returns class type of pairwise scoring subroutine.- Specified by:
getPairInProfileScorer
in interfaceRescoreRefiner<S extends Sequence<C>,C extends Compound>
- Returns:
- class type of pairwise scoring subroutine
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getProfileProfileAligner
public Alignments.ProfileProfileAlignerType getProfileProfileAligner()
Description copied from interface:RescoreRefiner
Returns class type of profile-profile alignment subroutine.- Specified by:
getProfileProfileAligner
in 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:Aligner
Returns the computation time needed for an alignment computed in nanoseconds.
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getProfile
public Profile<S,C> getProfile()
Description copied from interface:Aligner
Returns the alignmentProfile
produced by this alignment algorithm.
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getMaxScore
public double getMaxScore()
Description copied from interface:Scorer
Returns maximum possible score.- Specified by:
getMaxScore
in interfaceScorer
- Returns:
- maximum possible score
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getMinScore
public double getMinScore()
Description copied from interface:Scorer
Returns minimum possible score.- Specified by:
getMinScore
in interfaceScorer
- Returns:
- minimum possible score
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getScore
public double getScore()
Description copied from interface:Scorer
Returns 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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