Class SubstitutionMatrixScorer<S extends Sequence<C>,​C extends Compound>

  • Type Parameters:
    S -
    C -
    All Implemented Interfaces:
    PairwiseSequenceScorer<S,​C>, Scorer

    public class SubstitutionMatrixScorer<S extends Sequence<C>,​C extends Compound>
    extends AbstractScorer
    implements PairwiseSequenceScorer<S,​C>
    Scores using a substitution matrix. Specifically, the score is the sum of the substitution matrix entries corresponding to the alignment. Gaps are scored according to the substitution matrix, just as matches and mismatches.
    Author:
    dmyersturnbull