multiple web service jobs from visible blocks of an alignment.

[jalview.git] / src / jalview / datamodel / AlignmentOrder.java

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