X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=f12d106d166b1394c8bc77a32e53e2621ca36231;hb=74d1897e700018c3a1eb01b6d6ed94f26b171824;hp=1633a5da21056634cf9472215259846dbd3f8b4e;hpb=ef0288b7a00ee17ffa92e80bbd808508d567e7e2;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 1633a5d..f12d106 100644
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -2276,12 +2276,20 @@ public class Jalview2XML
           if (true) // !skipViewport(object))
           {
             _af = loadFromObject(object, file, true, jprovider);
-            if (object.getJalviewModelSequence().getViewportCount() > 0)
+            if (_af != null
+                    && object.getJalviewModelSequence().getViewportCount() > 0)
             {
-              af = _af;
-              if (af.viewport.isGatherViewsHere())
+              if (af == null)
               {
-                gatherToThisFrame.put(af.viewport.getSequenceSetId(), af);
+                // store a reference to the first view
+                af = _af;
+              }
+              if (_af.viewport.isGatherViewsHere())
+              {
+                // if this is a gathered view, keep its reference since
+                // after gathering views, only this frame will remain
+                af = _af;
+                gatherToThisFrame.put(_af.viewport.getSequenceSetId(), _af);
               }
             }
           }