X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAverageDistanceEngine.java;h=d81dd44687d286542f4576034ca76307efdd2e63;hb=032527014a1eafae4110666a53aad60992a29576;hp=f4d69d5cb4b3e592df21768a2ada643d983ce886;hpb=cd5f5840fc9dbf8edc58b010ab1caae9a695c5fe;p=jalview.git

diff --git a/src/jalview/analysis/AverageDistanceEngine.java b/src/jalview/analysis/AverageDistanceEngine.java
index f4d69d5..d81dd44 100644
--- a/src/jalview/analysis/AverageDistanceEngine.java
+++ b/src/jalview/analysis/AverageDistanceEngine.java
@@ -44,29 +44,31 @@ 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)
   {