org.biojava3.alignment.template
Interface MutableProfilePair<S extends Sequence<C>,C extends Compound>

Type Parameters:
S - each element of the alignment Profile is of type S
C - each element of an AlignedSequence is a Compound of type C
All Superinterfaces:
Iterable<AlignedSequence<S,C>>, MutableProfile<S,C>, Profile<S,C>, ProfilePair<S,C>

public interface MutableProfilePair<S extends Sequence<C>,C extends Compound>
extends MutableProfile<S,C>, ProfilePair<S,C>

Defines a mutable (editable) data structure for a ProfilePair.

Author:
Mark Chapman

Nested Class Summary
 
Nested classes/interfaces inherited from interface org.biojava3.alignment.template.Profile
Profile.StringFormat
 
Method Summary
 void setPair(Profile<S,C> query, Profile<S,C> target)
          Sets both Profiles of the pair.
 void setQuery(Profile<S,C> query)
          Sets the first Profile of the pair.
 void setTarget(Profile<S,C> target)
          Sets the second Profile of the pair.
 
Methods inherited from interface org.biojava3.alignment.template.MutableProfile
setSequences
 
Methods inherited from interface org.biojava3.alignment.template.ProfilePair
getQuery, getTarget
 
Methods inherited from interface org.biojava3.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
iterator
 

Method Detail

setPair

void setPair(Profile<S,C> query,
             Profile<S,C> target)
Sets both Profiles of the pair.

Parameters:
query - becomes the first Profile of the pair
target - becomes the second Profile of the pair
Throws:
IllegalArgumentException - if query and target are different lengths

setQuery

void setQuery(Profile<S,C> query)
Sets the first Profile of the pair.

Parameters:
query - becomes the first Profile of the pair
Throws:
IllegalArgumentException - if (new) query and (old) target are different lengths

setTarget

void setTarget(Profile<S,C> target)
Sets the second Profile of the pair.

Parameters:
target - becomes the second Profile of the pair
Throws:
IllegalArgumentException - if (old) query and (new) target are different lengths