X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FTreeBuilder.java;fp=src%2Fjalview%2Fanalysis%2FTreeBuilder.java;h=5381880e05d8b31c1894a1cbb1fe23084457a1b0;hb=21d7606604dab27e62ed700a39425b983901cef1;hp=5347ba23cb8a9723b8f2d31ab49d05561c92bc85;hpb=933794f42ed55d57850424e3459a54cd2d92c933;p=jalview.git

diff --git a/src/jalview/analysis/TreeBuilder.java b/src/jalview/analysis/TreeBuilder.java
index 5347ba2..5381880 100644
--- a/src/jalview/analysis/TreeBuilder.java
+++ b/src/jalview/analysis/TreeBuilder.java
@@ -253,6 +253,12 @@ public abstract class TreeBuilder
     findMaxDist(top);
   }
 
+  /**
+   * Returns the minimum distance between two clusters, and also sets the
+   * indices of the clusters in fields mini and minj
+   * 
+   * @return
+   */
   protected abstract double findMinDistance();
 
   /**
@@ -295,10 +301,10 @@ public abstract class TreeBuilder
   }
 
   /**
-   * DOCUMENT ME!
+   * Finds the node, at or below the given node, with the maximum distance, and
+   * saves the node and the distance value
    * 
    * @param nd
-   *          DOCUMENT ME!
    */
   void findMaxDist(SequenceNode nd)
   {
@@ -325,14 +331,12 @@ public abstract class TreeBuilder
   }
 
   /**
-   * DOCUMENT ME!
+   * Calculates and returns r, whatever that is
    * 
    * @param i
-   *          DOCUMENT ME!
    * @param j
-   *          DOCUMENT ME!
    * 
-   * @return DOCUMENT ME!
+   * @return
    */
   protected double findr(int i, int j)
   {
@@ -428,8 +432,12 @@ public abstract class TreeBuilder
     done.set(j);
   }
 
-  protected abstract void findNewDistances(SequenceNode tmpi, SequenceNode tmpj,
-          double dist);
+  /*
+   * Computes and stores new distances for nodei and nodej, given the previous
+   * distance between them
+   */
+  protected abstract void findNewDistances(SequenceNode nodei,
+          SequenceNode nodej, double previousDistance);
 
   /**
    * Calculates and saves the distance between the combination of cluster(i) and