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