Package org.biojava.nbio.alignment.template

Interface ProfileProfileAligner<S extends org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.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 org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.Compound>
extends Aligner<S,C>, ProfileProfileScorer<S,C>

Defines an Aligner for a pair of Profiles.

Author:

Mark Chapman

Method Summary

Modifier and Type	Method	Description
org.biojava.nbio.core.alignment.template.ProfilePair<S,C>	getPair()	Returns alignment profile pair.

Methods inherited from interface org.biojava.nbio.alignment.template.Aligner

getComputationTime, getProfile

Methods inherited from interface org.biojava.nbio.alignment.template.ProfileProfileScorer

getQuery, getTarget

Methods inherited from interface org.biojava.nbio.alignment.template.Scorer

getDistance, getDistance, getMaxScore, getMinScore, getScore, getSimilarity, getSimilarity

Method Detail

getPair

org.biojava.nbio.core.alignment.template.ProfilePair<S,C> getPair()

Returns alignment profile pair.

Returns:

alignment profile pair