S - each Sequence of the alignment pair is of type SC - each element of a Sequence is a Compound of type CScorerPairInProfileScorer<S,C>, PairwiseSequenceAligner<S,C>AbstractPairwiseSequenceAligner, AnchoredPairwiseSequenceAligner, FractionalIdentityInProfileScorer, FractionalIdentityScorer, FractionalSimilarityInProfileScorer, FractionalSimilarityScorer, GuanUberbacher, NeedlemanWunsch, SmithWaterman, SubstitutionMatrixScorerpublic interface PairwiseSequenceScorer<S extends Sequence<C>,C extends Compound> extends Scorer
| Modifier and Type | Method | Description |
|---|---|---|
S |
getQuery() |
Returns the first sequence of the pair.
|
S |
getTarget() |
Returns the second sequence of the pair.
|
getDistance, getDistance, getMaxScore, getMinScore, getScore, getSimilarity, getSimilarity