org.sStu
Interface ScoreOnlyAligner

All Superinterfaces:
Aligner
All Known Subinterfaces:
AlignmentRangeAligner, SingleAlingmentAligner

public interface ScoreOnlyAligner
extends Aligner

Defines an aligner that returns the score of the best alignment only. This allows to use faster algoritms, increasing the performance up to four times. If the score is above the level of interest, the alignment can be re-computed using other aligners.

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

Method Summary
 int getAlignmentScore()
          Get the score of this alignment
 
Methods inherited from interface org.sStu.Aligner
align, setSequence
 

Method Detail

getAlignmentScore

public int getAlignmentScore()
Get the score of this alignment

Returns:
The score of the alingment.