X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=6238c7db80e5e87c2f65c01cb23b83c2b8739835;hb=09eebd8c6997a33049084e307078717cc1a693a6;hp=1f011258d30e3521ba3c45cd78610f4e46051e77;hpb=97708f316b561ec5f9f03d402945b522085b0d5b;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 1f01125..6238c7d 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -565,7 +565,10 @@ public class Jalview
 
     if (argparser.isSet(Arg.HEADLESS))
       headless = argparser.getBool(Arg.HEADLESS);
-    Commands.processArgs(argparser, headless);
+    if (Commands.processArgs(argparser, headless))
+    {
+      System.exit(1);
+    }
 
     String file = null, data = null;
     FileFormatI format = null;