JAL-3205 faster calculation with symmetric score matrix

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

diff --git a/src/jalview/analysis/scoremodels/PIDModel.java b/src/jalview/analysis/scoremodels/PIDModel.java
index c1e8b42..ddfe5e4 100644 (file)
--- a/src/jalview/analysis/scoremodels/PIDModel.java
+++ b/src/jalview/analysis/scoremodels/PIDModel.java
@@ -152,15 +152,17 @@ public class PIDModel extends SimilarityScoreModel
   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);