org.biojava3.alignment.template
Interface ProfileProfileScorer<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:
Scorer
All Known Subinterfaces:
PartitionRefiner<S,C>, ProfileProfileAligner<S,C>
All Known Implementing Classes:
AbstractProfileProfileAligner, SimpleProfileProfileAligner

public interface ProfileProfileScorer<S extends Sequence<C>,C extends Compound>
extends Scorer

Defines an algorithm which computes a score for a pairing of alignment profiles.

Author:
Mark Chapman

Method Summary
 Profile<S,C> getQuery()
          Returns the first profile of the pair.
 Profile<S,C> getTarget()
          Returns the second profile of the pair.
 
Methods inherited from interface org.biojava3.alignment.template.Scorer
getDistance, getDistance, getMaxScore, getMinScore, getScore, getSimilarity, getSimilarity
 

Method Detail

getQuery

Profile<S,C> getQuery()
Returns the first profile of the pair.

Returns:
the first profile of the pair

getTarget

Profile<S,C> getTarget()
Returns the second profile of the pair.

Returns:
the second profile of the pair