public class MyApp {

    private static MyApp instance = null;

    private static boolean started = false;

    public MyApp() {
        if (instance != null) {
            throw new IllegalStateException("MyApp already initialized");
        }
        instance = this;
    }

    public static MyApp getInstance() {
        return instance;
    }

    public void startup() {
        synchronized (LOCK) {
            if (started == true) {
                throw new IllegalStateException("MyApp is already running");
            }
        }
       // do things to start the GUI, etc...
       //  ... ... ...
       started = true;
    }

}

public class Launcher {

    public static void main(String[] args) {
        new Launcher().start();
    }

    private void start() {
        // create custom classloader ...
        // ... ... ...
        Class<?> myAppClass = myLoader.loadClass("com.something.MyApp");
        // calls the MyApp constructor and sets the "instance" static var to "this"
        Object instance = myAppClass.newInstance();

        Method startupMethod = myAppClass.getMethod("startup");
        // this seems to call the MyApp constructor again!, exception thrown...
        startupMethod.invoke(instance);
    }

}