package jalview.analysis.scoremodels;
import jalview.analysis.AlignSeq;
-import jalview.api.analysis.ScoreModelI;
+import jalview.api.analysis.SimilarityParamsI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.SequenceI;
+import jalview.math.Matrix;
+import jalview.math.MatrixI;
import jalview.util.Comparison;
-public class SWScoreModel implements ScoreModelI
+/**
+ * A class that computes pairwise similarity scores using the Smith-Waterman
+ * alignment algorithm
+ */
+public class SmithWatermanModel extends SimilarityScoreModel
{
+ private static final String NAME = "Smith Waterman Score";
+
+ private String description;
+
+ /**
+ * Constructor
+ */
+ public SmithWatermanModel()
+ {
+ }
@Override
- public float[][] findDistances(AlignmentView seqData)
+ public MatrixI findSimilarities(AlignmentView seqData,
+ SimilarityParamsI options)
{
SequenceI[] sequenceString = seqData.getVisibleAlignment(
- Comparison.GapChars.charAt(0)).getSequencesArray();
+ Comparison.GAP_SPACE).getSequencesArray();
int noseqs = sequenceString.length;
- float[][] distance = new float[noseqs][noseqs];
+ double[][] distances = new double[noseqs][noseqs];
- float max = -1;
+ double max = -1;
for (int i = 0; i < (noseqs - 1); i++)
{
as.calcScoreMatrix();
as.traceAlignment();
as.printAlignment(System.out);
- distance[i][j] = (float) as.maxscore;
+ distances[i][j] = as.maxscore;
- if (max < distance[i][j])
+ if (max < distances[i][j])
{
- max = distance[i][j];
+ max = distances[i][j];
}
}
}
- for (int i = 0; i < (noseqs - 1); i++)
- {
- for (int j = i; j < noseqs; j++)
- {
- distance[i][j] = max - distance[i][j];
- distance[j][i] = distance[i][j];
- }
- }
-
- return distance;
+ return new Matrix(distances);
}
@Override
public String getName()
{
- return "Smith Waterman Score";
+ return NAME;
}
@Override
return true;
}
- public String toString()
+ @Override
+ public String getDescription()
{
- return "Score between two sequences aligned with Smith Waterman with default Peptide/Nucleotide matrix";
+ return description;
}
}