S
- each element of the alignment Profile
is of type SC
- each element of an AlignedSequence
is a Compound
of type Cjava.lang.Iterable<S>
, 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>
Profile.StringFormat
Modifier and Type | Method | Description |
---|---|---|
void |
setPair(AlignedSequence<S,C> query,
AlignedSequence<S,C> target) |
Sets both
AlignedSequence s 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. |
setSequences
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
getCompoundInQueryAt, getCompoundInTargetAt, getIndexInQueryAt, getIndexInQueryForTargetAt, getIndexInTargetAt, getIndexInTargetForQueryAt, getNumIdenticals, getNumSimilars, getQuery, getTarget
void setPair(AlignedSequence<S,C> query, AlignedSequence<S,C> target)
AlignedSequence
s of the pair.query
- becomes the first AlignedSequence
of the pairtarget
- becomes the second AlignedSequence
of the pairjava.lang.IllegalArgumentException
- if query and target are different lengthsvoid setQuery(AlignedSequence<S,C> query)
AlignedSequence
of the pair.query
- becomes the first AlignedSequence
of the pairjava.lang.IllegalArgumentException
- if (new) query and (old) target are different lengthsvoid setTarget(AlignedSequence<S,C> target)
AlignedSequence
of the pair.target
- becomes the second AlignedSequence
of the pairjava.lang.IllegalArgumentException
- if (old) query and (new) target are different lengths