From f1c14e59249205e7dea2379a61633bf17536ea00 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Tue, 24 May 2005 17:17:08 +0000
Subject: [PATCH] extended the UpdatePlaceholders to check for any new
 associations.

---
 src/jalview/analysis/NJTree.java |   19 +++++++++++++++++--
 1 file changed, 17 insertions(+), 2 deletions(-)

diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index cf15d78..f44f990 100755
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -96,13 +96,28 @@ public class NJTree {
     Vector leaves = new Vector();
     findLeaves(top, leaves);
     int sz = leaves.size();
+    SequenceIdMatcher seqmatcher=null;
     int i=0;
     while (i<sz) {
       SequenceNode leaf = (SequenceNode) leaves.elementAt(i++);
       if (alignment.contains(leaf.element()))
         leaf.setPlaceholder(false);
-      else
-        leaf.setPlaceholder(true);
+      else {
+        if (seqmatcher==null) {
+          // Only create this the first time we need it
+          SequenceI[] seqs = new SequenceI[alignment.size()];
+          for (int j=0; j<seqs.length; j++)
+            seqs[j] = (SequenceI) alignment.elementAt(j);
+          seqmatcher = new SequenceIdMatcher(seqs);
+        }
+        SequenceI nam = seqmatcher.findIdMatch(leaf.getName());
+        if (nam!=null) {
+          leaf.setPlaceholder(false);
+          leaf.setElement(nam);
+        } else {
+          leaf.setPlaceholder(true);
+        }
+      }
     }
   }
 
-- 
1.7.10.2