JAL-1370 mark Jpred query sequence as reference sequence

diff --git a/src/jalview/ws/jws1/JPredThread.java b/src/jalview/ws/jws1/JPredThread.java
index 62566cf..a8a49d0 100644 (file)
--- a/src/jalview/ws/jws1/JPredThread.java
+++ b/src/jalview/ws/jws1/JPredThread.java
@@ -586,6 +586,8 @@ class JPredThread extends JWS1Thread implements WSClientI
         if (newWindow)
         {
           AlignFrame af;
+          ((AlignmentI) res[0]).setSeqrep(((AlignmentI) res[0])
+                  .getSequenceAt(0));
           if (input == null)
           {
             if (res[1] != null)