org.biojava.nbio.core.alignment.template

Interface ProfilePair<S extends Sequence<C>,C extends Compound>

Type Parameters:

S - each element of an alignment Profile is of type S

C - each element of an AlignedSequence is a Compound of type C

All Superinterfaces:

Iterable<AlignedSequence<S,C>>, Profile<S,C>

All Known Subinterfaces:

MutableProfilePair<S,C>

All Known Implementing Classes:

SimpleProfilePair

public interface ProfilePair<S extends Sequence<C>,C extends Compound>
extends Profile<S,C>

Defines a data structure for the results of the alignment of a pair of Profiles.

Author:

Mark Chapman, Paolo Pavan

Nested Class Summary

Nested classes/interfaces inherited from interface org.biojava.nbio.core.alignment.template.Profile

Profile.StringFormat

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.core.alignment.template.Profile

getAlignedSequence, getAlignedSequence, getAlignedSequences, getAlignedSequences, getAlignedSequences, getCompoundAt, getCompoundAt, getCompoundCountsAt, getCompoundCountsAt, getCompoundsAt, getCompoundSet, getCompoundWeightsAt, getCompoundWeightsAt, getIndexOf, getIndicesAt, getLastIndexOf, getLength, getOriginalSequences, getSize, getSubProfile, hasGap, isCircular, toString, toString, toString

Methods inherited from interface java.lang.Iterable

forEach, iterator, spliterator

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