Package org.biojava.nbio.alignment

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

java.lang.Object
org.biojava.nbio.alignment.template.AbstractScorer
org.biojava.nbio.alignment.FractionalSimilarityScorer<S,C>
org.biojava.nbio.alignment.FractionalSimilarityInProfileScorer<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 FractionalSimilarityInProfileScorer<S extends Sequence<C>,C extends Compound> extends FractionalSimilarityScorer<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 similar Compounds.
Author:
Mark Chapman

  • Constructor Details

    • FractionalSimilarityInProfileScorer

      public FractionalSimilarityInProfileScorer(Profile<S,C> profile, int query, int target)
      Creates a fractional similarity 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