S
- each element of the alignment Profile
is of type SC
- each element of an AlignedSequence
is a Compound
of type CScorer
MatrixAligner<S,C>
, PairwiseSequenceAligner<S,C>
, PartitionRefiner<S,C>
, ProfileProfileAligner<S,C>
, RescoreRefiner<S,C>
AbstractMatrixAligner
, AbstractPairwiseSequenceAligner
, AbstractProfileProfileAligner
, AnchoredPairwiseSequenceAligner
, GuanUberbacher
, NeedlemanWunsch
, SimpleProfileProfileAligner
, SmithWaterman
, StandardRescoreRefiner
public interface Aligner<S extends Sequence<C>,C extends Compound> extends Scorer
Modifier and Type | Method | Description |
---|---|---|
long |
getComputationTime() |
Returns the computation time needed for an alignment computed in nanoseconds.
|
Profile<S,C> |
getProfile() |
Returns the alignment
Profile produced by this alignment algorithm. |
getDistance, getDistance, getMaxScore, getMinScore, getScore, getSimilarity, getSimilarity