X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=f59c37f16cae5d38c3848d231c4e168a08e9f57c;hb=a3d82d30b2bc55f250bbf1c94975308407e8aae7;hp=b1499118349ab72136665997bc1150c6ef8f2d89;hpb=c0a37536d35fb247404187b367228e71f85ce373;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index b149911..f59c37f 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -858,12 +858,12 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
                     + "] executed successfully!");
             groovyscript = null;
           }
-          while (aparser.getSize() > 0)
-          {
-            System.out.println("Unknown arg: " + aparser.nextValue());
-          }
         }
         checkOutputFile(aparser, af, format);
+        while (aparser.getSize() > 0)
+        {
+          System.out.println("Unknown arg: " + aparser.nextValue());
+        }
       }
     }
     AlignFrame startUpAlframe = null;
@@ -1052,6 +1052,8 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
       // biojsmsa filename
       String outputFormat = aparser.nextValue();
       String file = aparser.nextValue();
+      System.out.println("format " + outputFormat);
+
       if (outputFormat.equalsIgnoreCase("png"))
       {
         af.createPNG(new File(file));