X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2Fscoremodels%2FPIDModel.java;h=ddfe5e47832613cdace055a45e34bd79c8eda58f;hb=ed9e188d91dd661fb6d59cd8fd783cd4f9f47564;hp=985918bdfb3e3dd4af56b82bd5f5b81f1583ea46;hpb=e5c87d2dd1d3ebceea890ef92c8a6374c62d3c83;p=jalview.git

diff --git a/src/jalview/analysis/scoremodels/PIDModel.java b/src/jalview/analysis/scoremodels/PIDModel.java
index 985918b..ddfe5e4 100644
--- a/src/jalview/analysis/scoremodels/PIDModel.java
+++ b/src/jalview/analysis/scoremodels/PIDModel.java
@@ -1,6 +1,28 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.analysis.scoremodels;
 
+import jalview.api.AlignmentViewPanel;
 import jalview.api.analysis.PairwiseScoreModelI;
+import jalview.api.analysis.ScoreModelI;
 import jalview.api.analysis.SimilarityParamsI;
 import jalview.datamodel.AlignmentView;
 import jalview.math.Matrix;
@@ -9,10 +31,11 @@ import jalview.util.Comparison;
 
 /**
  * A class to provide sequence pairwise similarity based on residue identity.
- * Instances of this class are immutable and thread-safe.
+ * Instances of this class are immutable and thread-safe, so the same object is
+ * returned from calls to getInstance().
  */
-public class PIDModel extends SimilarityScoreModel implements
-        PairwiseScoreModelI
+public class PIDModel extends SimilarityScoreModel
+        implements PairwiseScoreModelI
 {
   private static final String NAME = "PID";
 
@@ -129,15 +152,17 @@ public class PIDModel extends SimilarityScoreModel implements
   protected MatrixI findSimilarities(String[] seqs,
           SimilarityParamsI options)
   {
-    // TODO reuse code in ScoreMatrix instead somehow
-    double[][] values = new double[seqs.length][];
+    /*
+     * calculation is symmetric so just compute lower diagonal
+     */
+    double[][] values = new double[seqs.length][seqs.length];
     for (int row = 0; row < seqs.length; row++)
     {
-      values[row] = new double[seqs.length];
-      for (int col = 0; col < seqs.length; col++)
+      for (int col = row; col < seqs.length; col++)
       {
         double total = computePID(seqs[row], seqs[col], options);
         values[row][col] = total;
+        values[col][row] = total;
       }
     }
     return new Matrix(values);
@@ -231,4 +256,10 @@ public class PIDModel extends SimilarityScoreModel implements
 
     return divideBy == 0 ? 0D : 100D * total / divideBy;
   }
+
+  @Override
+  public ScoreModelI getInstance(AlignmentViewPanel avp)
+  {
+    return this;
+  }
 }