Merge remote-tracking branch 'origin/develop' into

[jalview.git] / src / jalview / analysis / scoremodels / SmithWatermanModel.java

diff --git a/src/jalview/analysis/scoremodels/SWScoreModel.java b/src/jalview/analysis/scoremodels/SmithWatermanModel.java
similarity index 65%
rename from src/jalview/analysis/scoremodels/SWScoreModel.java
rename to src/jalview/analysis/scoremodels/SmithWatermanModel.java
index d5d998e..2428b81 100644 (file)
--- a/src/jalview/analysis/scoremodels/SWScoreModel.java
+++ b/src/jalview/analysis/scoremodels/SmithWatermanModel.java
@@ -21,23 +21,40 @@
 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++)
     {
@@ -48,31 +65,22 @@ public class SWScoreModel implements ScoreModelI
         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
@@ -87,8 +95,9 @@ public class SWScoreModel implements ScoreModelI
     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;
   }
 }