X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAverageDistanceEngine.java;fp=src%2Fjalview%2Fanalysis%2FAverageDistanceEngine.java;h=286d589c45617c630a334a479edcb7e6b99f008d;hb=eb3e681d6e82ccdd5d312d1981dfb306e7f479f0;hp=d81dd44687d286542f4576034ca76307efdd2e63;hpb=cb31e23d9138e481479623374aed7767bf8934d2;p=jalview.git

diff --git a/src/jalview/analysis/AverageDistanceEngine.java b/src/jalview/analysis/AverageDistanceEngine.java
index d81dd44..286d589 100644
--- a/src/jalview/analysis/AverageDistanceEngine.java
+++ b/src/jalview/analysis/AverageDistanceEngine.java
@@ -55,8 +55,10 @@ public class AverageDistanceEngine extends TreeEngine
   /**
    * compute cosine distance matrix for a given contact matrix and create a
    * UPGMA tree
+   * 
    * @param cm
-   * @param cosineOrDifference false - dot product : true - L1
+   * @param cosineOrDifference
+   *          false - dot product : true - L1
    */
   public AverageDistanceEngine(AlignmentViewport av, AlignmentAnnotation aa,
           ContactMatrixI cm, boolean cosineOrDifference)
@@ -64,12 +66,11 @@ public class AverageDistanceEngine extends TreeEngine
     this.av = av;
     this.aa = aa;
     this.cm = cm;
-    mode = (cosineOrDifference) ? 1 :0; 
+    mode = (cosineOrDifference) ? 1 : 0;
     calculate(cm);
 
   }
 
-
   public void calculate(ContactMatrixI cm)
   {
     this.cm = cm;
@@ -103,7 +104,7 @@ public class AverageDistanceEngine extends TreeEngine
       // compute distance matrix element
       ContactListI ith = cm.getContactList(i);
       distances.setValue(i, i, 0);
-      if (ith==null)
+      if (ith == null)
       {
         continue;
       }