X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAverageDistanceTree.java;h=760962e988682adecbcbbfbbb5a03e9f94cf2723;hb=d0aee5b0b2cbd0805c3dec027c6f2d2ac0148e66;hp=5b0e20aad9a4658213845a5bb43be3d4d238f54e;hpb=a547c517480867ed1bbb2334ee7c51e642588a41;p=jalview.git

diff --git a/src/jalview/analysis/AverageDistanceTree.java b/src/jalview/analysis/AverageDistanceTree.java
index 5b0e20a..760962e 100644
--- a/src/jalview/analysis/AverageDistanceTree.java
+++ b/src/jalview/analysis/AverageDistanceTree.java
@@ -1,10 +1,34 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.analysis;
 
 import jalview.api.analysis.ScoreModelI;
 import jalview.api.analysis.SimilarityParamsI;
-import jalview.datamodel.SequenceNode;
+import jalview.datamodel.BinaryNode;
 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
 {
   /**
@@ -42,8 +66,8 @@ public class AverageDistanceTree extends TreeBuilder
     {
       if ((l != i) && (l != j))
       {
-        newdist[l] = ((distances.getValue(i, l) * noi) + (distances
-                .getValue(j, l) * noj)) / (noi + noj);
+        newdist[l] = ((distances.getValue(i, l) * noi)
+                + (distances.getValue(j, l) * noj)) / (noi + noj);
       }
       else
       {
@@ -59,10 +83,7 @@ public class AverageDistanceTree extends TreeBuilder
   }
 
   /**
-   * 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()
@@ -89,39 +110,32 @@ public class AverageDistanceTree extends TreeBuilder
   }
 
   /**
-   * 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(BinaryNode nodei, BinaryNode nodej,
           double dist)
   {
     double ih = 0;
     double jh = 0;
 
-    SequenceNode sni = tmpi;
-    SequenceNode snj = tmpj;
+    BinaryNode sni = nodei;
+    BinaryNode snj = nodej;
 
     while (sni != null)
     {
       ih = ih + sni.dist;
-      sni = (SequenceNode) sni.left();
+      sni = (BinaryNode) sni.left();
     }
 
     while (snj != null)
     {
       jh = jh + snj.dist;
-      snj = (SequenceNode) snj.left();
+      snj = (BinaryNode) snj.left();
     }
 
-    tmpi.dist = ((dist / 2) - ih);
-    tmpj.dist = ((dist / 2) - jh);
+    nodei.dist = ((dist / 2) - ih);
+    nodej.dist = ((dist / 2) - jh);
   }
 
 }