X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentSorter.java;h=bf18b70e69440be632de857667494430165842a7;hb=d587f1aa61946dc14f6f089cf1dc2a3116cfb773;hp=bfe8f1eeb49ba9cc0b515260e733276869a1e47c;hpb=174230b4233d9ce80f94527768d2cd2f76da11ab;p=jalview.git

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index bfe8f1e..bf18b70 100755
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -109,15 +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));
         }
+
+
+
+
     }
 
     /**