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

Type Parameters:
S - each Sequence in the pair of alignment Profiles is of type S
C - each element of an AlignedSequence is a Compound of type C
All Superinterfaces:
Aligner<S,C>, ProfileProfileScorer<S,C>, Scorer
All Known Implementing Classes:
AbstractProfileProfileAligner, SimpleProfileProfileAligner

public interface ProfileProfileAligner<S extends Sequence<C>,C extends Compound>
extends Aligner<S,C>, ProfileProfileScorer<S,C>

Defines an Aligner for a pair of Profiles.

Author:
Mark Chapman

Method Summary
 ProfilePair<S,C> getPair()
          Returns alignment profile pair.
 
Methods inherited from interface org.biojava3.alignment.template.Aligner
getComputationTime, getProfile
 
Methods inherited from interface org.biojava3.alignment.template.ProfileProfileScorer
getQuery, getTarget
 
Methods inherited from interface org.biojava3.alignment.template.Scorer
getDistance, getDistance, getMaxScore, getMinScore, getScore, getSimilarity, getSimilarity
 

Method Detail

getPair

ProfilePair<S,C> getPair()
Returns alignment profile pair.

Returns:
alignment profile pair