JAL-629 correct a timeout. Correct passing html flag.

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

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index dbc1d88..7518fce 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -642,14 +642,12 @@ public class Jalview
     try
     {
       Console.initLogger();
-    } catch (
-
-    NoClassDefFoundError error)
+    } catch (NoClassDefFoundError error)
     {
       error.printStackTrace();
       String message = "\nEssential logging libraries not found."
               + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview";
-      Jalview.exit(message, ExitCode.OK);
+      Jalview.exit(message, ExitCode.NO_LOGGING);
     }
     desktop = null;
 
@@ -841,8 +839,6 @@ public class Jalview
     cmds.processArgs();
     boolean commandsSuccess = cmds.argsWereParsed();
 
-    cliWarning();
-
     if (commandsSuccess)
     {
       if (headlessArg)
@@ -1252,6 +1248,8 @@ public class Jalview
       }
       desktop.setInBatchMode(false);
     }
+
+    cliWarning();
   }
 
   private static void setLookAndFeel()
@@ -1632,9 +1630,8 @@ public class Jalview
      */
     PromptUserConfig prompter = new PromptUserConfig(Desktop.desktop,
             "USAGESTATS",
-            MessageManager.getString("prompt.plausible_analytics_title"),
-            MessageManager.getString("prompt.plausible_analytics"),
-            new Runnable()
+            MessageManager.getString("prompt.analytics_title"),
+            MessageManager.getString("prompt.analytics"), new Runnable()
             {
               @Override
               public void run()
@@ -1862,7 +1859,7 @@ public class Jalview
     // only add new ones to the end of the list (to preserve ordinal values)
     OK, FILE_NOT_FOUND, FILE_NOT_READABLE, NO_FILES, INVALID_FORMAT,
     INVALID_ARGUMENT, INVALID_VALUE, MIXED_CLI_ARGUMENTS,
-    ERROR_RUNNING_COMMANDS;
+    ERROR_RUNNING_COMMANDS, NO_LOGGING;
   }
 
   /******************************
@@ -2041,8 +2038,8 @@ public class Jalview
               j.getArgParser().getMixedExamples());
       String quit = MessageManager.getString("action.quit");
 
-      Desktop.instance.nonBlockingDialog(title, warning, quit,
-              JvOptionPane.WARNING_MESSAGE, false, true);
+      Desktop.instance.nonBlockingDialog(title, warning, null, quit,
+              JvOptionPane.WARNING_MESSAGE, false, false, true, 30000);
 
       Jalview.exit(
               "Exiting due to mixed old and new command line arguments.",
@@ -2060,14 +2057,14 @@ public class Jalview
     if (oldStyle)
     {
       String warning = MessageManager
-              .getString("warning.using_old_command_line_arguments")
-              + "https://www.jalview.org/help/html/features/commandline.html";
+              .getString("warning.using_old_command_line_arguments");
+      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, cont,
-                JvOptionPane.WARNING_MESSAGE, false, false);
+        Desktop.instance.nonBlockingDialog(title, warning, url, cont,
+                JvOptionPane.WARNING_MESSAGE, false, true, true, 30000);
       }
     }
     if (j.getCommands() != null && j.getCommands().getErrors().size() > 0)
@@ -2077,9 +2074,17 @@ public class Jalview
         String message = MessageManager
                 .getString("warning.the_following_errors");
         String ok = MessageManager.getString("action.ok");
-        Desktop.instance.nonBlockingDialog(60, 16, title,
-                message + "\n" + j.getCommands().errorsToString(), ok,
-                JvOptionPane.WARNING_MESSAGE, true, true);
+        int shortest = 60;
+        List<String> errors = j.getCommands().getErrors();
+        for (int i = 0; i < errors.size(); i++)
+        {
+          shortest = Math.min(shortest, errors.get(i).length());
+        }
+        Desktop.instance.nonBlockingDialog(
+                Math.max(message.length(), Math.min(60, shortest)),
+                Math.min(errors.size(), 20), title, message,
+                j.getCommands().errorsToString(), ok,
+                JvOptionPane.WARNING_MESSAGE, true, false, true, -1);
       }
     }
   }