X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentSorter.java;h=778142c24fed58fc045634860caf4029f5be35ee;hb=3d9d1f6c1c1da3b2657f9ebb95430d0bc8dde873;hp=20101dc908c91448b86c396dc648548c6024b45c;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index 20101dc..778142c 100755
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -1,6 +1,6 @@
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
@@ -52,7 +52,8 @@ public class AlignmentSorter
 
         for (int i = 0; i < nSeq; i++)
         {
-            scores[i] = Comparison.PID(align.getSequenceAt(i), s);
+            scores[i] = Comparison.PID(align.getSequenceAt(i).getSequenceAsString(),
+                                       s.getSequenceAsString());
             seqs[i] = align.getSequenceAt(i);
         }
 
@@ -108,15 +109,28 @@ public class AlignmentSorter
      * @param align DOCUMENT ME!
      * @param seqs sequences as an array
      */
-    private static void setOrder(AlignmentI align, SequenceI[] seqs)
+    public static void setOrder(AlignmentI align, SequenceI[] seqs)
     {
         // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work
         Vector algn = align.getSequences();
+        Vector tmp = new Vector();
 
         for (int i = 0; i < seqs.length; i++)
         {
-            algn.setElementAt(seqs[i], i);
+          if(algn.contains(seqs[i]))
+            tmp.addElement(seqs[i]);
+        }
+
+        algn.removeAllElements();
+        //User may have hidden seqs, then clicked undo or redo
+        for (int i = 0; i < tmp.size(); i++)
+        {
+          algn.addElement(tmp.elementAt(i));
         }
+
+
+
+
     }
 
     /**