X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=b1499118349ab72136665997bc1150c6ef8f2d89;hb=72fb6df14f1ff426bbafa18dcc9a90450da93018;hp=2efa0fb38c702027e3b0b81a237954ee15c4bedd;hpb=bd678dba41df83658dcbd93b3ec57c46f0cd14c9;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 2efa0fb..b149911 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -305,6 +305,15 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
 
     String usrPropsFile = aparser.getValue(ArgsParser.PROPS);
     Cache.loadProperties(usrPropsFile);
+
+    if (aparser.contains(ArgsParser.NODISPLAY)
+            || aparser.contains(ArgsParser.NOGUI)
+            || aparser.contains(ArgsParser.HEADLESS)
+            || "true".equals(System.getProperty("java.awt.headless")))
+    {
+      headless = true;
+    }
+
     if (isJS)
     {
       isJavaAppletTag = aparser.isApplet();
@@ -336,13 +345,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
         showUsage();
         System.exit(0);
       }
-      if (aparser.contains(ArgsParser.NODISPLAY)
-              || aparser.contains(ArgsParser.NOGUI)
-              || aparser.contains(ArgsParser.HEADLESS)
-              || "true".equals(System.getProperty("java.awt.headless")))
-      {
-        headless = true;
-      }
+
 
       // anything else!
 
@@ -398,7 +401,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
 
     try
     {
-      if (Platform.isWin())
+      if (!isJS && Platform.isWin())
        {
         UIManager.setLookAndFeel(
                 headless ? "javax.swing.plaf.metal.MetalLookAndFeel"
@@ -855,12 +858,12 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
                     + "] executed successfully!");
             groovyscript = null;
           }
-          checkOutputFile(aparser, af, format);
           while (aparser.getSize() > 0)
           {
             System.out.println("Unknown arg: " + aparser.nextValue());
           }
         }
+        checkOutputFile(aparser, af, format);
       }
     }
     AlignFrame startUpAlframe = null;