X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentSorter.java;h=bf18b70e69440be632de857667494430165842a7;hb=bb105fcca41253815982584f4c8f6fae1f8e10a3;hp=c2814b894a65b2a9f3a6c92274e3b932b94ee724;hpb=df9b85c1cf39894039018499fe802406cc37f209;p=jalview.git

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index c2814b8..bf18b70 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).getSequence(),
+                                       s.getSequence());
             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));
         }
+
+
+
+
     }
 
     /**