Package org.biojava.nbio.alignment

Class FractionalIdentityScorer<S extends Sequence<C>,C extends Compound>

java.lang.Object
org.biojava.nbio.alignment.template.AbstractScorer
org.biojava.nbio.alignment.FractionalIdentityScorer<S,C>
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 Implemented Interfaces:
PairwiseSequenceScorer<S,C>, Scorer
Direct Known Subclasses:
FractionalIdentityInProfileScorer
public class FractionalIdentityScorer<S extends Sequence<C>,C extends Compound> extends AbstractScorer implements PairwiseSequenceScorer<S,C>
Implements an algorithm which computes a score for a sequence alignment pair. The reported score is the number of alignment columns which have identical Compounds.
Author:
Mark Chapman

  • Constructor Details

    • FractionalIdentityScorer

      public FractionalIdentityScorer(PairwiseSequenceAligner<S,C> aligner)
      Creates a fractional identity scorer for a pair of sequences aligned by the given pairwise sequence aligner.
      Parameters:
      aligner - a pairwise sequence aligner

    • FractionalIdentityScorer

      public FractionalIdentityScorer(SequencePair<S,C> pair)
      Creates a fractional identity scorer for an aligned pair of sequences.
      Parameters:
      pair - an aligned pair of sequences

  • Method Details