Interface PartitionRefiner<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>, ProfileProfileScorer<S,​C>, Scorer

    public interface PartitionRefiner<S extends Sequence<C>,​C extends Compound>
    extends Aligner<S,​C>, ProfileProfileScorer<S,​C>
    Defines an algorithm which computes a new alignment Profile by splitting a current alignment and realigning.
    Author:
    Mark Chapman
    • Method Detail

      • getProfileProfileAligner

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