Package org.biojava.nbio.alignment.template

Interface PairInProfileScorer<S extends org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.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 org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.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

Modifier and Type	Method	Description
org.biojava.nbio.core.alignment.template.Profile<S,C>	getProfile()	Returns the Profile from which the aligned pair originated.

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

getQuery, getTarget

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

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

Method Detail

getProfile

org.biojava.nbio.core.alignment.template.Profile<S,C> getProfile()

Returns the Profile from which the aligned pair originated.

Returns:

the original profile