S - each Sequence of the alignment pair is of type SC - each element of an AlignedSequence is a Compound of type CPairwiseSequenceScorer<S,C>, ScorerFractionalIdentityInProfileScorerpublic class FractionalIdentityScorer<S extends Sequence<C>,C extends Compound> extends AbstractScorer implements PairwiseSequenceScorer<S,C>
Compounds.| Constructor | Description |
|---|---|
FractionalIdentityScorer(PairwiseSequenceAligner<S,C> aligner) |
Creates a fractional identity scorer for a pair of sequences aligned by the given pairwise sequence aligner.
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FractionalIdentityScorer(SequencePair<S,C> pair) |
Creates a fractional identity scorer for an aligned pair of sequences.
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| Modifier and Type | Method | Description |
|---|---|---|
double |
getMaxScore() |
Returns maximum possible score.
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double |
getMinScore() |
Returns minimum possible score.
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S |
getQuery() |
Returns the first sequence of the pair.
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double |
getScore() |
Returns score resulting from algorithm.
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S |
getTarget() |
Returns the second sequence of the pair.
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getDistance, getDistance, getSimilarity, getSimilarityclone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, waitgetDistance, getDistance, getSimilarity, getSimilaritypublic FractionalIdentityScorer(PairwiseSequenceAligner<S,C> aligner)
aligner - a pairwise sequence alignerpublic FractionalIdentityScorer(SequencePair<S,C> pair)
pair - an aligned pair of sequencespublic S getQuery()
PairwiseSequenceScorerpublic S getTarget()
PairwiseSequenceScorerpublic double getMaxScore()
ScorergetMaxScore in interface Scorerpublic double getMinScore()
ScorergetMinScore in interface Scorerpublic double getScore()
ScorerScorer.getScore() - Scorer.getMinScore()) / (Scorer.getMaxScore() - Scorer.getMinScore()).