Aligner (biojava-alignment 5.2.0 API)

Type Parameters:

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

C - each element of an AlignedSequence 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 org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.Compound>
extends Scorer
```
Defines an algorithm which computes an alignment Profile from a list of Sequences.

Author:

Mark Chapman

Method Summary

All Methods Instance Methods Abstract Methods
Modifier and Type	Method	Description
`long`	`getComputationTime()`	Returns the computation time needed for an alignment computed in nanoseconds.
`org.biojava.nbio.core.alignment.template.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 Detail
  - getComputationTime
```
long getComputationTime()
```
    Returns the computation time needed for an alignment computed in nanoseconds.
    
    Returns:
    
    the computation time in nanoseconds
  - getProfile
```
org.biojava.nbio.core.alignment.template.Profile<S,C> getProfile()
```
    Returns the alignment Profile produced by this alignment algorithm.
    
    Returns:
    
    the alignment profile