JAL-2428 Javadoc

[jalview.git] / src / jalview / analysis / AverageDistanceTree.java

diff --git a/src/jalview/analysis/AverageDistanceTree.java b/src/jalview/analysis/AverageDistanceTree.java
index 5b0e20a..907109e 100644 (file)
--- 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
 {
   /**
@@ -59,10 +63,7 @@ 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()
@@ -89,24 +90,17 @@ 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(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)
     {
@@ -120,8 +114,8 @@ public class AverageDistanceTree extends TreeBuilder
       snj = (SequenceNode) snj.left();
     }
 
-    tmpi.dist = ((dist / 2) - ih);
-    tmpj.dist = ((dist / 2) - jh);
+    nodei.dist = ((dist / 2) - ih);
+    nodej.dist = ((dist / 2) - jh);
   }
 
 }