Interface RescoreRefiner<S extends Sequence<C>,​C extends Compound>

  • Type Parameters:
    S - each element of the alignment Profile is of type S
    C - each element of an AlignedSequence is a Compound of type C
    All Superinterfaces:
    Aligner<S,​C>, Scorer
    All Known Implementing Classes:
    StandardRescoreRefiner

    public interface RescoreRefiner<S extends Sequence<C>,​C extends Compound>
    extends Aligner<S,​C>
    Defines an algorithm which computes a new alignment Profile by rescoring all pairs in an alignment and realigning.
    Author:
    Mark Chapman
    • Method Detail

      • getPairInProfileScorer

        Alignments.PairInProfileScorerType getPairInProfileScorer()
        Returns class type of pairwise scoring subroutine.
        Returns:
        class type of pairwise scoring subroutine
      • getProfileProfileAligner

        Alignments.ProfileProfileAlignerType getProfileProfileAligner()
        Returns class type of profile-profile alignment subroutine.
        Returns:
        class type of profile-profile alignment subroutine