FileParse object can be re-used to read different files concatenated together

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

diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index 4d0bb93..3569be1 100755 (executable)
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -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!
+  /*#see findLeaf(SequenceNode node, count)
    *
-   * @param node DOCUMENT ME!
-   * @param count DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
    */
   public Object _findLeaf(SequenceNode node, int count)
   {