X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentOrder.java;h=231009ae807eec9dc3e016d64d3f0e0d61c575af;hb=4eefb40838faa0a3c03be3480ff74ba2ac67a5c1;hp=1fa3b96c90f53ae42f0118709fc1b7bb5fde2cf9;hpb=ab9608a2f5459d16f160bdbb229f47c7d9edbcd9;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentOrder.java b/src/jalview/datamodel/AlignmentOrder.java
index 1fa3b96..231009a 100755
--- a/src/jalview/datamodel/AlignmentOrder.java
+++ b/src/jalview/datamodel/AlignmentOrder.java
@@ -167,7 +167,19 @@ public class AlignmentOrder
     {
         return Order;
     }
-
+    /**
+     * replaces oldref with newref in the alignment order.
+     * @param oldref
+     * @param newref
+     * @return
+     */
+    public boolean updateSequence(SequenceI oldref, SequenceI newref) {
+      int found=Order.indexOf(oldref);
+      if (found>-1) {
+        Order.setElementAt(newref, found);
+      }
+      return found>-1;
+    }
     /**
      * AlignmentOrder
      *