close menu item true

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index df551b7..5b0ec15 100755 (executable)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -1306,6 +1306,7 @@ public class Jalview2XML
                                        view.getWidth(),
                                        view.getHeight() );
 
+        af.setFileName(file, "Jalview");
 
         //If we just load in the same jar file again, the sequenceSetId
         //will be the same, and we end up with multiple references
@@ -1641,7 +1642,7 @@ public class Jalview2XML
 
       AlignFrame af = LoadFromObject(jm, null, false);
       af.alignPanels.clear();
-      af.closeMenuItem_actionPerformed(null);
+      af.closeMenuItem_actionPerformed(true);
 
       return af.alignPanel;
     }