Package org.biojava.nbio.alignment

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

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

  • Constructor Details

    • FractionalIdentityInProfileScorer

      public FractionalIdentityInProfileScorer(Profile<S,C> profile, int query, int target)
      Creates a fractional identity scorer for an aligned pair of sequences in the given alignment profile.
      Parameters:
      profile - alignment profile containing pair of sequences
      query - index in the profile of the first sequence of the pair
      target - index in the profile of the second sequence of the pair

  • Method Details