Package org.biojava.nbio.alignment.template

Interface PairInProfileScorer<S extends Sequence<C>,C extends Compound>

Type Parameters:
S - each Sequence of the alignment pair is of type S
C - each element of an AlignedSequence is a Compound of type C
All Superinterfaces:
PairwiseSequenceScorer<S,C>, Scorer
All Known Implementing Classes:
FractionalIdentityInProfileScorer, FractionalSimilarityInProfileScorer
public interface PairInProfileScorer<S extends Sequence<C>,C extends Compound> extends PairwiseSequenceScorer<S,C>
Defines an algorithm which computes a score for a sequence alignment pair picked from an alignment Profile.
Author:
Mark Chapman

  • Method Details

    • getProfile

      Profile<S,C> getProfile()
      Returns the Profile from which the aligned pair originated.
      Returns:
      the original profile