X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=159cf7593db0616b3a54f231765fe586d8f90b3e;hb=4fd4608b88401dbb1a86a29f8d607c7481145e27;hp=8fa4ac7dba652ebd041230745aadb187b281a925;hpb=3e8516c59908e9f9f791cf820321c5007bdd58ec;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 8fa4ac7..159cf75 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -532,17 +532,17 @@ public class Jalview
         Jalview.exit(null, 0);
       }
 
-      if (bootstrapArgs.contains(Arg.HEADLESS))
+      // new CLI
+      headlessArg = isHeadless(bootstrapArgs);
+      if (headlessArg)
       {
         System.setProperty("java.awt.headless", "true");
-        // new
-        headlessArg = bootstrapArgs.getBoolean(Arg.HEADLESS);
       }
+      // old CLI
       if (aparser.contains("nodisplay") || aparser.contains("nogui")
               || aparser.contains("headless"))
       {
         System.setProperty("java.awt.headless", "true");
-        // old
         headless = true;
       }
       // anything else!
@@ -1883,4 +1883,26 @@ public class Jalview
     System.out.println("[TESTOUTPUT] arg "
             + (yes ? a.argString() : a.negateArgString()) + " was set");
   }
+
+  private static boolean isHeadless(BootstrapArgs bootstrapArgs)
+  {
+    if (bootstrapArgs == null)
+    {
+      return false;
+    }
+    boolean isHeadless = false;
+    if (bootstrapArgs.contains(Arg.GUI))
+    {
+      isHeadless = !bootstrapArgs.getBoolean(Arg.GUI);
+    }
+    else if (bootstrapArgs.contains(Arg.HEADLESS))
+    {
+      isHeadless = bootstrapArgs.getBoolean(Arg.HEADLESS);
+    }
+    else if (bootstrapArgs.argsHaveOption(Opt.OUTPUTFILE))
+    {
+      isHeadless = true;
+    }
+    return isHeadless;
+  }
 }