org.biojava.nbio.core.alignment.template

Interface MutableSequencePair<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>, SequencePair<S,C>

public interface MutableSequencePair<S extends Sequence<C>,C extends Compound>
extends MutableProfile<S,C>, SequencePair<S,C>

Defines a mutable (editable) data structure for the results of pairwise sequence alignment.

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
void	setPair(AlignedSequence<S,C> query, AlignedSequence<S,C> target) Sets both AlignedSequences of the pair.
void	setQuery(AlignedSequence<S,C> query) Sets the first AlignedSequence of the pair.
void	setTarget(AlignedSequence<S,C> target) Sets the second AlignedSequence of the pair.

Methods inherited from interface org.biojava.nbio.core.alignment.template.MutableProfile

setSequences

Methods inherited from interface org.biojava.nbio.core.alignment.template.SequencePair

getCompoundInQueryAt, getCompoundInTargetAt, getIndexInQueryAt, getIndexInQueryForTargetAt, getIndexInTargetAt, getIndexInTargetForQueryAt, getNumIdenticals, getNumSimilars, getPercentageOfIdentity, getQuery, getTarget

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

setPair

void setPair(AlignedSequence<S,C> query,
             AlignedSequence<S,C> target)

Sets both AlignedSequences of the pair.

Parameters:

query - becomes the first AlignedSequence of the pair

target - becomes the second AlignedSequence of the pair

Throws:

IllegalArgumentException - if query and target are different lengths

setQuery

void setQuery(AlignedSequence<S,C> query)

Sets the first AlignedSequence of the pair.

Parameters:

query - becomes the first AlignedSequence of the pair

Throws:

IllegalArgumentException - if (new) query and (old) target are different lengths

setTarget

void setTarget(AlignedSequence<S,C> target)

Sets the second AlignedSequence of the pair.

Parameters:

target - becomes the second AlignedSequence of the pair

Throws:

IllegalArgumentException - if (old) query and (new) target are different lengths