X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2Fscoremodels%2FScoreMatrix.java;h=b206339805cf4d1f026c15eb34f3987a21a543b9;hb=a2032664d7eb6954072d43b424e11d219f28df62;hp=efaeb430d86bc58ace6f251d11c9e9b852c33601;hpb=333d483bec66b894088e71902095a78e902a462f;p=jalview.git

diff --git a/src/jalview/analysis/scoremodels/ScoreMatrix.java b/src/jalview/analysis/scoremodels/ScoreMatrix.java
index efaeb43..b206339 100644
--- a/src/jalview/analysis/scoremodels/ScoreMatrix.java
+++ b/src/jalview/analysis/scoremodels/ScoreMatrix.java
@@ -36,8 +36,8 @@ import java.util.Arrays;
  * symbols. Instances of this class are immutable and thread-safe, so the same
  * object is returned from calls to getInstance().
  */
-public class ScoreMatrix extends SimilarityScoreModel implements
-        PairwiseScoreModelI
+public class ScoreMatrix extends SimilarityScoreModel
+        implements PairwiseScoreModelI
 {
   private static final char GAP_CHARACTER = Comparison.GAP_DASH;
 
@@ -98,7 +98,9 @@ public class ScoreMatrix extends SimilarityScoreModel implements
   private float minValue;
 
   private float maxValue;
-  
+
+  private boolean symmetric;
+
   /**
    * Constructor given a name, symbol alphabet, and matrix of scores for pairs
    * of symbols. The matrix should be square and of the same size as the
@@ -130,8 +132,8 @@ public class ScoreMatrix extends SimilarityScoreModel implements
    * @param values
    *          Pairwise scores indexed according to the symbol alphabet
    */
-  public ScoreMatrix(String theName, String theDescription,
-          char[] alphabet, float[][] values)
+  public ScoreMatrix(String theName, String theDescription, char[] alphabet,
+          float[][] values)
   {
     if (alphabet.length != values.length)
     {
@@ -156,6 +158,8 @@ public class ScoreMatrix extends SimilarityScoreModel implements
 
     findMinMax();
 
+    symmetric = checkSymmetry();
+
     /*
      * crude heuristic for now...
      */
@@ -163,6 +167,27 @@ public class ScoreMatrix extends SimilarityScoreModel implements
   }
 
   /**
+   * Answers true if the matrix is symmetric, else false. Usually, substitution
+   * matrices are symmetric, which allows calculations to be short cut.
+   * 
+   * @return
+   */
+  private boolean checkSymmetry()
+  {
+    for (int i = 0; i < matrix.length; i++)
+    {
+      for (int j = i; j < matrix.length; j++)
+      {
+        if (matrix[i][j] != matrix[j][i])
+        {
+          return false;
+        }
+      }
+    }
+    return true;
+  }
+
+  /**
    * Record the minimum and maximum score values
    */
   protected void findMinMax()
@@ -454,16 +479,20 @@ public class ScoreMatrix extends SimilarityScoreModel implements
    * @param params
    * @return
    */
-  protected MatrixI findSimilarities(String[] seqs, SimilarityParamsI params)
+  protected MatrixI findSimilarities(String[] seqs,
+          SimilarityParamsI params)
   {
-    double[][] values = new double[seqs.length][];
+    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 = symmetric ? row : 0; col < seqs.length; col++)
       {
         double total = computeSimilarity(seqs[row], seqs[col], params);
         values[row][col] = total;
+        if (symmetric)
+        {
+          values[col][row] = total;
+        }
       }
     }
     return new Matrix(values);
@@ -591,4 +620,9 @@ public class ScoreMatrix extends SimilarityScoreModel implements
   {
     return this;
   }
+
+  public boolean isSymmetric()
+  {
+    return symmetric;
+  }
 }