X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=ce421742f1be8c9910fd1a08bdfd4462fc3a808a;hb=dfa04e77181fccfa6229ffef1591fc9c622d9b39;hp=c7fa0908d76fe121c2c8e6c508089a4a13f09e94;hpb=918c7b4a347bec48eb12646947a0086acb62a084;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index c7fa090..ce42174 100644
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -3737,6 +3737,20 @@ public class Jalview2XML
         if (sq != dsq)
         { // make this dataset sequence sq's dataset sequence
           sq.setDatasetSequence(dsq);
+          // and update the current dataset alignment
+          if (ds==null) {
+            if (dseqs!=null) {
+              if (!dseqs.contains(dsq))
+              {
+                dseqs.add(dsq);
+              }
+            } else {
+              if (ds.findIndex(dsq)<0)
+              {
+                ds.addSequence(dsq);
+              }
+            }
+          }
         }
       }
     }