Package org.biojava.nbio.alignment.template

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

Type Parameters:
S - each Sequence in the pair of alignment Profiles is of type S
C - each element of an AlignedSequence is a Compound of type C
All Superinterfaces:
Scorer
All Known Subinterfaces:
PartitionRefiner<S,C>, ProfileProfileAligner<S,C>
All Known Implementing Classes:
AbstractProfileProfileAligner, SimpleProfileProfileAligner
public interface ProfileProfileScorer<S extends Sequence<C>,C extends Compound> extends Scorer
Defines an algorithm which computes a score for a pairing of alignment profiles.
Author:
Mark Chapman

  • Method Details

    • getQuery

      Profile<S,C> getQuery()
      Returns the first profile of the pair.
      Returns:
      the first profile of the pair

    • getTarget

      Profile<S,C> getTarget()
      Returns the second profile of the pair.
      Returns:
      the second profile of the pair