Sequences may be hidden, not in this aligment

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index 938aa6a..e63b6e5 100755 (executable)
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -114,9 +114,11 @@ public class AlignmentSorter
         // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work\r
         Vector algn = align.getSequences();\r
 \r
+        int index = 0;\r
         for (int i = 0; i < seqs.length; i++)\r
         {\r
-            algn.setElementAt(seqs[i], i);\r
+          if(algn.contains(seqs[i]))\r
+            algn.setElementAt(seqs[i], index++);\r
         }\r
     }\r
 \r