X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2Fscoremodels%2FSmithWatermanModel.java;h=ca6d27983c9dd221b222a2564392245b776e58d4;hb=3d0101179759ef157b088ea135423cd909512d9f;hp=eec08ed595eaf66651c5d8a258caf77ea5746c50;hpb=43dc9a8834f510a1cfe20d1a1346635e4c0b47b2;p=jalview.git

diff --git a/src/jalview/analysis/scoremodels/SmithWatermanModel.java b/src/jalview/analysis/scoremodels/SmithWatermanModel.java
index eec08ed..ca6d279 100644
--- a/src/jalview/analysis/scoremodels/SmithWatermanModel.java
+++ b/src/jalview/analysis/scoremodels/SmithWatermanModel.java
@@ -21,8 +21,9 @@
 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;
@@ -33,16 +34,25 @@ import jalview.util.Comparison;
  * 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];
 
@@ -88,8 +98,14 @@ public class SmithWatermanModel implements SimilarityScoreModelI
   }
 
   @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;
   }
 }