org.biojava3.alignment
Class FractionalIdentityInProfileScorer<S extends Sequence<C>,C extends Compound>

java.lang.Object
  extended by org.biojava3.alignment.template.AbstractScorer
      extended by org.biojava3.alignment.FractionalIdentityScorer<S,C>
          extended by org.biojava3.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 Summary
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.
 
Method Summary
 Profile<S,C> getProfile()
          Returns the Profile from which the aligned pair originated.
 
Methods inherited from class org.biojava3.alignment.FractionalIdentityScorer
getMaxScore, getMinScore, getQuery, getScore, getTarget
 
Methods inherited from class org.biojava3.alignment.template.AbstractScorer
getDistance, getDistance, getSimilarity, getSimilarity
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 
Methods inherited from interface org.biojava3.alignment.template.PairwiseSequenceScorer
getQuery, getTarget
 
Methods inherited from interface org.biojava3.alignment.template.Scorer
getDistance, getDistance, getMaxScore, getMinScore, getScore, getSimilarity, getSimilarity
 

Constructor Detail

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 Detail

getProfile

public Profile<S,C> getProfile()
Description copied from interface: PairInProfileScorer
Returns the Profile from which the aligned pair originated.

Specified by:
getProfile in interface PairInProfileScorer<S extends Sequence<C>,C extends Compound>
Returns:
the original profile