JAL-629 Added Arg.Types and additional --help-type args to be --help with a type...

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

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 3d20d3c..fb31189 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -49,6 +49,7 @@ import java.util.Vector;
 import java.util.logging.ConsoleHandler;
 import java.util.logging.Level;
 import java.util.logging.Logger;
+import java.util.stream.Collectors;
 
 import javax.swing.JDialog;
 import javax.swing.JFrame;
@@ -345,6 +346,7 @@ public class Jalview
       final File appdir = new File(appdirString);
       new Thread()
       {
+
         @Override
         public void run()
         {
@@ -492,10 +494,12 @@ public class Jalview
      * @j2sIgnore
      */
     {
-      if (bootstrapArgs.containsType(Type.HELP))
+      if (bootstrapArgs.contains(Arg.HELP))
       {
-        List<Arg> helpArgs = bootstrapArgs.getArgsOfType(Type.HELP);
-        System.out.println(Arg.usage(helpArgs));
+        List<Map.Entry<Type, String>> helpArgs = bootstrapArgs
+                .getList(Arg.HELP);
+        System.out.println(Arg.usage(helpArgs.stream().map(e -> e.getKey())
+                .collect(Collectors.toList())));
         Jalview.exit(null, 0);
       }
       if (aparser.contains("help") || aparser.contains("h"))
@@ -1698,14 +1702,40 @@ public class Jalview
 
   public static void exit(String message, int exitcode)
   {
-    Console.debug("Using Jalview.exit");
-    if (message != null)
-      if (exitcode == 0)
-        Console.info(message);
-      else
-        Console.error(message);
+    if (Console.log == null)
+    {
+      // Don't start the logger just to exit!
+      if (message != null)
+      {
+        if (exitcode == 0)
+        {
+          System.out.println(message);
+        }
+        else
+        {
+          System.err.println(message);
+        }
+      }
+    }
+    else
+    {
+      Console.debug("Using Jalview.exit");
+      if (message != null)
+      {
+        if (exitcode == 0)
+        {
+          Console.info(message);
+        }
+        else
+        {
+          Console.error(message);
+        }
+      }
+    }
     if (exitcode > -1)
+    {
       System.exit(exitcode);
+    }
   }
 
   /*