X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAverageDistanceTree.java;h=907109e6d39a6429fc3cb9643efe9297fcc95920;hb=6323f1a33650360f131f25cf2797e5600ceee49f;hp=7e3cfe1864a4d876bd20d803c7f827fe31f73ab7;hpb=be27d7b3cadbfb5c488066034c48b1735799b429;p=jalview.git

diff --git a/src/jalview/analysis/AverageDistanceTree.java b/src/jalview/analysis/AverageDistanceTree.java
index 7e3cfe1..907109e 100644
--- a/src/jalview/analysis/AverageDistanceTree.java
+++ b/src/jalview/analysis/AverageDistanceTree.java
@@ -5,6 +5,10 @@ import jalview.api.analysis.SimilarityParamsI;
 import jalview.datamodel.SequenceNode;
 import jalview.viewmodel.AlignmentViewport;
 
+/**
+ * This class implements distance calculations used in constructing a Average
+ * Distance tree (also known as UPGMA)
+ */
 public class AverageDistanceTree extends TreeBuilder
 {
   /**
@@ -55,17 +59,11 @@ public class AverageDistanceTree extends TreeBuilder
     {
       distances.setValue(i, ii, newdist[ii]);
       distances.setValue(ii, i, newdist[ii]);
-      System.out.println(String.format(
-              "findClusterDistance(%d, %d) newdist to %d is %f", i, j, ii,
-              newdist[ii]));
     }
   }
 
   /**
-   * Returns the minimum distance between two clusters, and also sets the
-   * indices of the clusters in fields mini and minj
-   * 
-   * @return DOCUMENT ME!
+   * {@inheritDoc}
    */
   @Override
   protected double findMinDistance()
@@ -88,30 +86,21 @@ public class AverageDistanceTree extends TreeBuilder
         }
       }
     }
-    System.out.println("findMinDistance found " + min + " at " + mini + ","
-            + minj);
     return min;
   }
 
   /**
-   * DOCUMENT ME!
-   * 
-   * @param tmpi
-   *          DOCUMENT ME!
-   * @param tmpj
-   *          DOCUMENT ME!
-   * @param dist
-   *          DOCUMENT ME!
+   * {@inheritDoc}
    */
   @Override
-  protected void findNewDistances(SequenceNode tmpi, SequenceNode tmpj,
+  protected void findNewDistances(SequenceNode nodei, SequenceNode nodej,
           double dist)
   {
     double ih = 0;
     double jh = 0;
 
-    SequenceNode sni = tmpi;
-    SequenceNode snj = tmpj;
+    SequenceNode sni = nodei;
+    SequenceNode snj = nodej;
 
     while (sni != null)
     {
@@ -125,10 +114,8 @@ public class AverageDistanceTree extends TreeBuilder
       snj = (SequenceNode) snj.left();
     }
 
-    tmpi.dist = ((dist / 2) - ih);
-    tmpj.dist = ((dist / 2) - jh);
-    System.out.println("findNewDistances set tmpi to " + tmpi.dist
-            + ", tmpj to " + tmpj.dist);
+    nodei.dist = ((dist / 2) - ih);
+    nodej.dist = ((dist / 2) - jh);
   }
 
 }