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>, ProfilePair<S,C>public interface MutableProfilePair<S extends Sequence<C>,C extends Compound> extends MutableProfile<S,C>, ProfilePair<S,C>
ProfilePair.Profile.StringFormat| Modifier and Type | Method | Description |
|---|---|---|
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. |
setSequencesgetAlignedSequence, getAlignedSequence, getAlignedSequences, getAlignedSequences, getAlignedSequences, getCompoundAt, getCompoundAt, getCompoundCountsAt, getCompoundCountsAt, getCompoundsAt, getCompoundSet, getCompoundWeightsAt, getCompoundWeightsAt, getIndexOf, getIndicesAt, getLastIndexOf, getLength, getOriginalSequences, getSize, getSubProfile, hasGap, isCircular, toString, toString, toStringgetQuery, getTargetvoid setQuery(Profile<S,C> query)
Profile of the pair.query - becomes the first Profile of the pairjava.lang.IllegalArgumentException - if (new) query and (old) target are different lengths