X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=d14c919247e058d39339ca7f20a616f7a9bf4722;hb=refs%2Fheads%2Ffeature%2FJAL-4274_configurable_bitmap_export_preferences;hp=2c07296dff3db9e74f9048f293b8472fecd1d3c8;hpb=fd86db8856109e69c21a5f4102bc8dd94664ae1f;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 2c07296..d14c919 100755
--- 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()
@@ -2061,13 +2061,13 @@ public class Jalview
     {
       String warning = MessageManager
               .getString("warning.using_old_command_line_arguments");
-      String url = "https://www.jalview.org/help/html/features/commandline.html";
+      String url = "<a href=\"https://www.jalview.org/help/html/features/commandline.html\">https://www.jalview.org/help/html/features/commandline.html</a>";
       if (Desktop.instance != null)
       {
         String cont = MessageManager.getString("label.continue");
 
         Desktop.instance.nonBlockingDialog(32, 2, title, warning, url, cont,
-                JvOptionPane.WARNING_MESSAGE, false, false);
+                JvOptionPane.WARNING_MESSAGE, false, true, true);
       }
     }
     if (j.getCommands() != null && j.getCommands().getErrors().size() > 0)
@@ -2087,7 +2087,7 @@ public class Jalview
                 Math.max(message.length(), Math.min(60, shortest)),
                 Math.min(errors.size(), 20), title, message,
                 j.getCommands().errorsToString(), ok,
-                JvOptionPane.WARNING_MESSAGE, true, true);
+                JvOptionPane.WARNING_MESSAGE, true, false, true);
       }
     }
   }