Package org.biojava.nbio.alignment.template

Interface Aligner<S extends Sequence<C>,C extends Compound>

Type Parameters:

S - each element of the alignment Profile is of type S

C - each element of a sequence is a Compound of type C

All Superinterfaces:

Scorer

All Known Subinterfaces:

MatrixAligner<S,C>, PairwiseSequenceAligner<S,C>, PartitionRefiner<S,C>, ProfileProfileAligner<S,C>, RescoreRefiner<S,C>

All Known Implementing Classes:

AbstractMatrixAligner, AbstractPairwiseSequenceAligner, AbstractProfileProfileAligner, AnchoredPairwiseSequenceAligner, GuanUberbacher, NeedlemanWunsch, SimpleProfileProfileAligner, SmithWaterman, StandardRescoreRefiner

public interface Aligner<S extends Sequence<C>,C extends Compound>
extends Scorer

Defines an algorithm which computes an alignment Profile from a list of Sequences.

Author:

Mark Chapman

Method Summary

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.

Methods inherited from interface org.biojava.nbio.alignment.template.Scorer

getDistance, getDistance, getMaxScore, getMinScore, getScore, getSimilarity, getSimilarity

Method Details

getComputationTime

long getComputationTime()

Returns the computation time needed for an alignment computed in nanoseconds.

Returns:

the computation time in nanoseconds

getProfile

Profile<S,C> getProfile()

Returns the alignment Profile produced by this alignment algorithm.

Returns:

the alignment profile