JAL-2403 JAL-1483 changes to ScoreModelI hierarchy and signatures to

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

diff --git a/src/jalview/analysis/scoremodels/PIDDistanceModel.java b/src/jalview/analysis/scoremodels/PIDDistanceModel.java
index f72b0fc..154ff02 100644 (file)
--- a/src/jalview/analysis/scoremodels/PIDDistanceModel.java
+++ b/src/jalview/analysis/scoremodels/PIDDistanceModel.java
@@ -20,20 +20,22 @@
  */
 package jalview.analysis.scoremodels;
 
-import jalview.api.analysis.DistanceModelI;
+import jalview.api.analysis.DistanceScoreModelI;
 import jalview.datamodel.AlignmentView;
+import jalview.math.Matrix;
+import jalview.math.MatrixI;
 import jalview.util.Comparison;
 
-public class PIDDistanceModel implements DistanceModelI
+public class PIDDistanceModel implements DistanceScoreModelI
 {
 
   @Override
-  public float[][] findDistances(AlignmentView seqData)
+  public MatrixI findDistances(AlignmentView seqData)
   {
     String[] sequenceString = seqData
             .getSequenceStrings(Comparison.GAP_SPACE);
     int noseqs = sequenceString.length;
-    float[][] distance = new float[noseqs][noseqs];
+    double[][] distance = new double[noseqs][noseqs];
     for (int i = 0; i < (noseqs - 1); i++)
     {
       for (int j = i; j < noseqs; j++)
@@ -51,7 +53,7 @@ public class PIDDistanceModel implements DistanceModelI
         }
       }
     }
-    return distance;
+    return new Matrix(distance);
   }
 
   @Override