JAL-4262 Made deprecation warning properly modal

[jalview.git] / src / jalview / bin / Jalview.java

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index a05c995..d14c919 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -841,8 +841,6 @@ public class Jalview
     cmds.processArgs();
     boolean commandsSuccess = cmds.argsWereParsed();
 
-    cliWarning();
-
     if (commandsSuccess)
     {
       if (headlessArg)
@@ -1252,6 +1250,8 @@ public class Jalview
       }
       desktop.setInBatchMode(false);
     }
+
+    cliWarning();
   }
 
   private static void setLookAndFeel()
@@ -2067,7 +2067,7 @@ public class Jalview
         String cont = MessageManager.getString("label.continue");
 
         Desktop.instance.nonBlockingDialog(32, 2, title, warning, url, cont,
-                JvOptionPane.WARNING_MESSAGE, false, true, false);
+                JvOptionPane.WARNING_MESSAGE, false, true, true);
       }
     }
     if (j.getCommands() != null && j.getCommands().getErrors().size() > 0)