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java.lang.Objectorg.biojava3.alignment.template.AbstractScorer
org.biojava3.alignment.StandardRescoreRefiner<S,C>
public class StandardRescoreRefiner<S extends Sequence<C>,C extends Compound>
Constructor Summary | |
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StandardRescoreRefiner(Alignments.PairInProfileScorerType pips,
Alignments.ProfileProfileAlignerType ppa)
|
Method Summary | |
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long |
getComputationTime()
Returns the computation time needed for an alignment computed in nanoseconds. |
int |
getMaxScore()
Returns maximum possible score. |
int |
getMinScore()
Returns minimum possible score. |
Alignments.PairInProfileScorerType |
getPairInProfileScorer()
Returns class type of pairwise scoring subroutine. |
Profile<S,C> |
getProfile()
Returns the alignment Profile produced by this alignment algorithm. |
Alignments.ProfileProfileAlignerType |
getProfileProfileAligner()
Returns class type of profile-profile alignment subroutine. |
int |
getScore()
Returns score resulting from algorithm. |
Methods inherited from class org.biojava3.alignment.template.AbstractScorer |
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getDistance, getDistance, getSimilarity, getSimilarity |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Methods inherited from interface org.biojava3.alignment.template.Scorer |
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getDistance, getDistance, getSimilarity, getSimilarity |
Constructor Detail |
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public StandardRescoreRefiner(Alignments.PairInProfileScorerType pips, Alignments.ProfileProfileAlignerType ppa)
Method Detail |
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public Alignments.PairInProfileScorerType getPairInProfileScorer()
RescoreRefiner
getPairInProfileScorer
in interface RescoreRefiner<S extends Sequence<C>,C extends Compound>
public Alignments.ProfileProfileAlignerType getProfileProfileAligner()
RescoreRefiner
getProfileProfileAligner
in interface RescoreRefiner<S extends Sequence<C>,C extends Compound>
public long getComputationTime()
Aligner
getComputationTime
in interface Aligner<S extends Sequence<C>,C extends Compound>
public Profile<S,C> getProfile()
Aligner
Profile
produced by this alignment algorithm.
getProfile
in interface Aligner<S extends Sequence<C>,C extends Compound>
public int getMaxScore()
Scorer
getMaxScore
in interface Scorer
public int getMinScore()
Scorer
getMinScore
in interface Scorer
public int getScore()
Scorer
Scorer.getScore()
- Scorer.getMinScore()
) / (Scorer.getMaxScore()
- Scorer.getMinScore()
).
getScore
in interface Scorer
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