org.biojava3.alignment.template
Interface MutableProfile<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>>, Profile<S,C>
All Known Subinterfaces:
MutableProfilePair<S,C>, MutableSequencePair<S,C>

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

Defines a mutable (editable) data structure for a Profile. Returned Lists are modifiable.

Author:
Mark Chapman

Nested Class Summary
 
Nested classes/interfaces inherited from interface org.biojava3.alignment.template.Profile
Profile.StringFormat
 
Method Summary
 void setSequences(List<AlignedSequence<S,C>> sequences)
          Sets entirely new set of AlignedSequences.
 
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

setSequences

void setSequences(List<AlignedSequence<S,C>> sequences)
Sets entirely new set of AlignedSequences.

Parameters:
sequences - new set of sequences
Throws:
IllegalArgumentException - if sequences have different lengths