package jalview.analysis.scoremodels;
import jalview.analysis.AlignSeq;
+import jalview.api.AlignmentViewPanel;
+import jalview.api.analysis.ScoreModelI;
import jalview.api.analysis.SimilarityParamsI;
-import jalview.api.analysis.SimilarityScoreModelI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.SequenceI;
import jalview.math.Matrix;
* A class that computes pairwise similarity scores using the Smith-Waterman
* alignment algorithm
*/
-public class SmithWatermanModel implements SimilarityScoreModelI
+public class SmithWatermanModel extends SimilarityScoreModel
{
private static final String NAME = "Smith Waterman Score";
+ private String description;
+
+ /**
+ * Constructor
+ */
+ public SmithWatermanModel()
+ {
+ }
+
@Override
public MatrixI findSimilarities(AlignmentView seqData,
SimilarityParamsI options)
{
- SequenceI[] sequenceString = seqData.getVisibleAlignment(
- Comparison.GAP_SPACE).getSequencesArray();
+ SequenceI[] sequenceString = seqData
+ .getVisibleAlignment(Comparison.GAP_SPACE).getSequencesArray();
int noseqs = sequenceString.length;
double[][] distances = new double[noseqs][noseqs];
}
@Override
- public String toString()
+ public String getDescription()
+ {
+ return description;
+ }
+
+ @Override
+ public ScoreModelI getInstance(AlignmentViewPanel avp)
{
- return "Score between two sequences aligned with Smith Waterman with default Peptide/Nucleotide matrix";
+ return this;
}
}