hidden seqs and setOrder bug fixed

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