Package org.biojava.nbio.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, SubstitutionMatrixScorer
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 Details

    • 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