applied copyright 2008

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

diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index 4d0bb93..dd2dbbf 100755 (executable)
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program 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 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program 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 this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -786,21 +786,21 @@ public class NJTree
   }
 
   /**
-   * DOCUMENT ME!
+   * Search for leaf nodes.
    *
-   * @param node DOCUMENT ME!
-   * @param leaves DOCUMENT ME!
+   * @param node root node to search from
+   * @param leaves Vector of leaves to add leaf node objects too.
    *
-   * @return DOCUMENT ME!
+   * @return Vector of leaf nodes on binary tree
    */
   public Vector findLeaves(SequenceNode node, Vector leaves)
-  {
+  { 
     if (node == null)
     {
       return leaves;
     }
 
-    if ( (node.left() == null) && (node.right() == null))
+    if ( (node.left() == null) && (node.right() == null)) // Interior node detection
     {
       leaves.addElement(node);
 
@@ -808,6 +808,10 @@ public class NJTree
     }
     else
     {
+/*  TODO: Identify internal nodes...    if (node.isSequenceLabel())
+      {
+        leaves.addElement(node);
+      }*/
       findLeaves( (SequenceNode) node.left(), leaves);
       findLeaves( (SequenceNode) node.right(), leaves);
     }
@@ -816,12 +820,12 @@ public class NJTree
   }
 
   /**
-   * DOCUMENT ME!
+   * Find the leaf node with a particular ycount 
    *
-   * @param node DOCUMENT ME!
-   * @param count DOCUMENT ME!
+   * @param node initial point on tree to search from
+   * @param count value to search for
    *
-   * @return DOCUMENT ME!
+   * @return null or the node with ycound=count
    */
   public Object findLeaf(SequenceNode node, int count)
   {
@@ -830,13 +834,8 @@ public class NJTree
     return found;
   }
 
-  /**
-   * DOCUMENT ME!
-   *
-   * @param node DOCUMENT ME!
-   * @param count DOCUMENT ME!
+  /*#see findLeaf(SequenceNode node, count)
    *
-   * @return DOCUMENT ME!
    */
   public Object _findLeaf(SequenceNode node, int count)
   {