Package org.biojava.nbio.core.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, 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
void	setSequences(List<AlignedSequence<S,C>> sequences)	Sets entirely new set of AlignedSequences.

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

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