X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fbin%2FJalview.java;h=6a59093047939cc74d559162723d223133918ca2;hb=c13784724ba3826e6cc3faeb85571cf30776592d;hp=fc6d23e52363bb33943c4bd4b73b000b4e14585d;hpb=ee684c859bd7cddaa517a81cf11e168d4596ddbe;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index fc6d23e..6a59093 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -179,6 +179,7 @@ public class Jalview
     if (!headless)
     {
       desktop = new Desktop();
+      desktop.setInBatchMode(true); // indicate we are starting up
       desktop.setVisible(true);
       desktop.startServiceDiscovery();
       if (!aparser.contains("nousagestats"))
@@ -411,7 +412,7 @@ public class Jalview
           ex.printStackTrace(System.err);
         }
       }
-      // todo - load PDB structure to alignment
+      // TODO - load PDB structure(s) to alignment JAL-629
       // (associate with identical sequence in alignment, or a specified
       // sequence)
 
@@ -536,7 +537,7 @@ public class Jalview
         startFeatureFetching(getFeatures);
       }
     }
-    // execute a groovy script.
+    // Once all other stuff is done, execute any groovy scripts (in order)
     if (groovyscript != null)
     {
       if (jalview.bin.Cache.groovyJarsPresent())
@@ -551,8 +552,11 @@ public class Jalview
                         + groovyscript);
       }
     }
-
-    // Once all other stuff is done, execute any groovy scripts (in order)
+    // and finally, turn off batch mode indicator - if the desktop still exists
+    if (desktop!=null)
+    {
+      desktop.setInBatchMode(false);
+    }
   }
 
   private static void startUsageStats(final Desktop desktop)