S
- each element of an alignment Profile
is of type SC
- each element of an AlignedSequence
is a Compound
of type Cjava.lang.Iterable<S>
, Profile<S,C>
, ProfilePair<S,C>
public class SimpleProfilePair<S extends Sequence<C>,C extends Compound> extends SimpleProfile<S,C> implements ProfilePair<S,C>
Profile
s.Profile.StringFormat
matrix
Constructor | Description |
---|---|
SimpleProfilePair(Profile<S,C> query,
Profile<S,C> target,
java.util.List<AlignedSequence.Step> sx,
java.util.List<AlignedSequence.Step> sy) |
Creates a pair profile for the given profiles.
|
Modifier and Type | Method | Description |
---|---|---|
Profile<S,C> |
getQuery() |
Returns the first
Profile of the pair. |
Profile<S,C> |
getTarget() |
Returns the second
Profile of the pair. |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
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
getAlignedSequence, getAlignedSequence, getAlignedSequences, getAlignedSequences, getAlignedSequences, getCompoundAt, getCompoundAt, getCompoundCountsAt, getCompoundCountsAt, getCompoundsAt, getCompoundSet, getCompoundWeightsAt, getCompoundWeightsAt, getIndexOf, getIndicesAt, getLastIndexOf, getLength, getOriginalSequences, getSize, getSubProfile, hasGap, isCircular, iterator, toString, toString, toString
public SimpleProfilePair(Profile<S,C> query, Profile<S,C> target, java.util.List<AlignedSequence.Step> sx, java.util.List<AlignedSequence.Step> sy)
query
- the first profile of the pairtarget
- the second profile of the pairsx
- lists whether the query profile aligns a Compound
or gap at each index of the alignmentsy
- lists whether the target profile aligns a Compound
or gap at each index of the alignmentjava.lang.IllegalArgumentException
- if alignments differ in size or given profiles do not fit in alignmentspublic Profile<S,C> getQuery()
ProfilePair
Profile
of the pair.