ProfilePair

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

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 java.lang.Iterable
forEach, iterator, spliterator

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

Method Details
- 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