From d06711617796df6df18ec872326a6b6b76d447c8 Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Fri, 3 Aug 2012 17:08:07 +0100
Subject: [PATCH] JAL-1115 reference to List<SequenceI> passed in 'alignment'
 changeSupport message

---
 src/jalview/analysis/NJTree.java |   12 ++++++------
 src/jalview/gui/TreePanel.java   |    4 +++-
 2 files changed, 9 insertions(+), 7 deletions(-)

diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index 67ce460..160d853 100644
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -283,10 +283,10 @@ public class NJTree
    * 
    * used when the alignment associated to a tree has changed.
    * 
-   * @param alignment
-   *          Vector
+   * @param list
+   *          Sequence set to be associated with tree nodes
    */
-  public void UpdatePlaceHolders(Vector alignment)
+  public void UpdatePlaceHolders(List<SequenceI> list)
   {
     Vector leaves = new Vector();
     findLeaves(top, leaves);
@@ -299,7 +299,7 @@ public class NJTree
     {
       SequenceNode leaf = (SequenceNode) leaves.elementAt(i++);
 
-      if (alignment.contains(leaf.element()))
+      if (list.contains(leaf.element()))
       {
         leaf.setPlaceholder(false);
       }
@@ -308,11 +308,11 @@ public class NJTree
         if (seqmatcher == null)
         {
           // Only create this the first time we need it
-          SequenceI[] seqs = new SequenceI[alignment.size()];
+          SequenceI[] seqs = new SequenceI[list.size()];
 
           for (int j = 0; j < seqs.length; j++)
           {
-            seqs[j] = (SequenceI) alignment.elementAt(j);
+            seqs[j] = (SequenceI) list.get(j);
           }
 
           seqmatcher = new SequenceIdMatcher(seqs);
diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 602ded6..14802e7 100755
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -20,6 +20,8 @@ package jalview.gui;
 import java.beans.*;
 import java.io.*;
 import java.util.*;
+import java.util.List;
+
 import javax.imageio.*;
 
 import java.awt.*;
@@ -152,7 +154,7 @@ public class TreePanel extends GTreePanel
                     .println("new alignment sequences vector value is null");
           }
 
-          tree.UpdatePlaceHolders((Vector) evt.getNewValue());
+          tree.UpdatePlaceHolders((List<SequenceI>) evt.getNewValue());
           treeCanvas.nameHash.clear(); // reset the mapping between canvas
           // rectangles and leafnodes
           repaint();
-- 
1.7.10.2