org.sStu
Interface SingleAlingmentAligner

All Superinterfaces:
Aligner, ScoreOnlyAligner

public interface SingleAlingmentAligner
extends ScoreOnlyAligner

Defines an aligner that returns one (best) alignment and its score. These aligners are used when only the best alignment is the point of interest. They have the intermediate performace between ScoreOnly- and AlinmentRand- aligners.

Author:
Audrius Meskauskas
See Also:
http://www.gnu.org/licenses/gpl.txt

Method Summary
 Alignment getBestAlignment()
          Get the best alignment.
 
Methods inherited from interface org.sStu.ScoreOnlyAligner
getAlignmentScore
 
Methods inherited from interface org.sStu.Aligner
align, setSequence
 

Method Detail

getBestAlignment

public Alignment getBestAlignment()
Get the best alignment.

Returns:
The best alignment