From 256f99fa9de8ee5a2f206163a6a55be69b35e00c Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 7 Nov 2006 11:51:49 +0000
Subject: [PATCH] hidden seqs and setOrder bug fixed

---
 src/jalview/analysis/AlignmentSorter.java |   15 +++++++++++++--
 1 file changed, 13 insertions(+), 2 deletions(-)

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index e63b6e5..c80c326 100755
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -113,13 +113,24 @@ public class AlignmentSorter
     {
         // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work
         Vector algn = align.getSequences();
+        Vector tmp = new Vector();
 
-        int index = 0;
         for (int i = 0; i < seqs.length; i++)
         {
           if(algn.contains(seqs[i]))
-            algn.setElementAt(seqs[i], index++);
+            tmp.addElement(seqs[i]);
+        }
+
+        algn.clear();
+        //User may have hidden seqs, then clicked undo or redo
+        for (int i = 0; i < tmp.size(); i++)
+        {
+          algn.addElement(tmp.elementAt(i));
         }
+
+
+
+
     }
 
     /**
-- 
1.7.10.2