org.biojava.nbio.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

Modifier and Type	Method and Description
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.biojava.nbio.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