X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentSorter.java;h=bf18b70e69440be632de857667494430165842a7;hb=d587f1aa61946dc14f6f089cf1dc2a3116cfb773;hp=938aa6aedd1f92e7b1cfc3aec460705e79c6f42d;hpb=9d69f0b2ad93d854ae2f85ec86e59c322d925d09;p=jalview.git

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index 938aa6a..bf18b70 100755
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -113,11 +113,24 @@ public class AlignmentSorter
     {
         // 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));
         }
+
+
+
+
     }
 
     /**