org.biojava3.alignment.template
Interface PairwiseSequenceScorer<S extends Sequence<C>,C extends 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

public interface PairwiseSequenceScorer<S extends Sequence<C>,C extends Compound>
extends Scorer

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

Author:
Mark Chapman

Method Summary
 S getQuery()
          Returns the first sequence of the pair.
 S getTarget()
          Returns the second sequence of the pair.
 
Methods inherited from interface org.biojava3.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