1.1 compatible

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 8c320f7..588134a 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -811,7 +811,7 @@ public class Alignment implements AlignmentI
   {
     SeqCigar alseqs[] = new SeqCigar[sequences.size()];
     for (int i=0; i<sequences.size(); i++) {
-      alseqs[i] = new SeqCigar((SequenceI) sequences.get(i));
+      alseqs[i] = new SeqCigar((SequenceI) sequences.elementAt(i));
     }
     return new CigarArray(alseqs);
   }