org.biojava3.alignment.template
Interface PairInProfileScorer<S extends Sequence<C>,C extends Compound>

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 Superinterfaces:
PairwiseSequenceScorer<S,C>, Scorer
All Known Implementing Classes:
FractionalIdentityInProfileScorer, FractionalSimilarityInProfileScorer

public interface PairInProfileScorer<S extends Sequence<C>,C extends Compound>
extends PairwiseSequenceScorer<S,C>

Defines an algorithm which computes a score for a sequence alignment pair picked from an alignment Profile.

Author:
Mark Chapman

Method Summary
 Profile<S,C> getProfile()
          Returns the Profile from which the aligned pair originated.
 
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
 

Method Detail

getProfile

Profile<S,C> getProfile()
Returns the Profile from which the aligned pair originated.

Returns:
the original profile