From: jprocter <Jim Procter>
Date: Sun, 17 Jun 2007 12:41:36 +0000 (+0000)
Subject: javadoc
X-Git-Tag: Release_2_4~381
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=cc190cfe952a4d8ef8c38247ee35b1a4675da572;p=jalview.git

javadoc
---

diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index 4d0bb93..88bb51c 100755
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -786,12 +786,12 @@ 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)
   {
@@ -816,12 +816,12 @@ 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 +830,8 @@ 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)
   {
diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 64a21dd..731b646 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -182,10 +182,11 @@ public interface SequenceI
   public int[] gapMap();
 
   /**
-   * DOCUMENT ME!
+   * Delete a range of aligned sequence columns, creating a new dataset sequence if necessary
+   * and adjusting start and end positions accordingly.
    *
-   * @param i DOCUMENT ME!
-   * @param j DOCUMENT ME!
+   * @param i first column in range to delete
+   * @param j last column in range to delete
    */
   public void deleteChars(int i, int j);