Package org.biojava.nbio.alignment.template

Interface PairwiseSequenceScorer<S extends org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.Compound>

Type Parameters:

S - each Sequence of the alignment pair is of type S

C - each element of a Sequence is a Compound of type C

All Superinterfaces:

Scorer

All Known Subinterfaces:

PairInProfileScorer<S,C>, PairwiseSequenceAligner<S,C>

All Known Implementing Classes:

AbstractPairwiseSequenceAligner, AnchoredPairwiseSequenceAligner, FractionalIdentityInProfileScorer, FractionalIdentityScorer, FractionalSimilarityInProfileScorer, FractionalSimilarityScorer, GuanUberbacher, NeedlemanWunsch, SmithWaterman, SubstitutionMatrixScorer

public interface PairwiseSequenceScorer<S extends org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.Compound>
extends Scorer

Defines an algorithm which computes a score for a pair of sequences.

Author:

Mark Chapman

Method Summary

Modifier and Type	Method	Description
S	getQuery()	Returns the first sequence of the pair.
S	getTarget()	Returns the second sequence of the pair.

Methods inherited from interface org.biojava.nbio.alignment.template.Scorer

getDistance, getDistance, getMaxScore, getMinScore, getScore, getSimilarity, getSimilarity

Method Detail

getQuery

S getQuery()

Returns the first sequence of the pair.

Returns:

the first sequence of the pair

getTarget

S getTarget()

Returns the second sequence of the pair.

Returns:

the second sequence of the pair