X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAverageDistanceEngine.java;h=286d589c45617c630a334a479edcb7e6b99f008d;hb=a73dbb370e06bfaae2caf3487fde655d9b177045;hp=20b3e83678cd53c1f82a05a806279037556d5aa6;hpb=80b889f0cca49103e1b20ed806755a0719789906;p=jalview.git

diff --git a/src/jalview/analysis/AverageDistanceEngine.java b/src/jalview/analysis/AverageDistanceEngine.java
index 20b3e83..286d589 100644
--- a/src/jalview/analysis/AverageDistanceEngine.java
+++ b/src/jalview/analysis/AverageDistanceEngine.java
@@ -44,30 +44,33 @@ public class AverageDistanceEngine extends TreeEngine
 
   AlignmentAnnotation aa;
 
+  // 0 - normalised dot product
+  // 1 - L1 - ie (abs(v_1-v_2)/dim(v))
+  // L1 is more rational - since can reason about value of difference,
+  // normalised dot product might give cleaner clusters, but more difficult to
+  // understand.
+
+  int mode = 1;
+
   /**
    * compute cosine distance matrix for a given contact matrix and create a
    * UPGMA tree
    * 
    * @param cm
+   * @param cosineOrDifference
+   *          false - dot product : true - L1
    */
   public AverageDistanceEngine(AlignmentViewport av, AlignmentAnnotation aa,
-          ContactMatrixI cm)
+          ContactMatrixI cm, boolean cosineOrDifference)
   {
     this.av = av;
     this.aa = aa;
     this.cm = cm;
+    mode = (cosineOrDifference) ? 1 : 0;
     calculate(cm);
 
   }
 
-  // 0 - normalised dot product
-  // 1 - L1 - ie (abs(v_1-v_2)/dim(v))
-  // L1 is more rational - since can reason about value of difference,
-  // normalised dot product might give cleaner clusters, but more difficult to
-  // understand.
-
-  int mode = 1;
-
   public void calculate(ContactMatrixI cm)
   {
     this.cm = cm;
@@ -100,10 +103,13 @@ public class AverageDistanceEngine extends TreeEngine
 
       // compute distance matrix element
       ContactListI ith = cm.getContactList(i);
-
+      distances.setValue(i, i, 0);
+      if (ith == null)
+      {
+        continue;
+      }
       for (int j = 0; j < i; j++)
       {
-        distances.setValue(i, i, 0);
         ContactListI jth = cm.getContactList(j);
         if (jth == null)
         {