Use the Apache Commons CLI library commandline.getArgs() to get arg1, arg2, arg3, and arg4. Here is some code:

    import org.apache.commons.cli.CommandLine;
    import org.apache.commons.cli.Option;
    import org.apache.commons.cli.Options;
    import org.apache.commons.cli.Option.Builder;
    import org.apache.commons.cli.CommandLineParser;
    import org.apache.commons.cli.DefaultParser;
    import org.apache.commons.cli.ParseException;

    public static void main(String[] parameters)
    {
        CommandLine commandLine;
        Option option_A = Option.builder("A")
            .required(true)
            .desc("The A option")
            .longOpt("opt3")
            .build();
        Option option_r = Option.builder("r")
            .required(true)
            .desc("The r option")
            .longOpt("opt1")
            .build();
        Option option_S = Option.builder("S")
            .required(true)
            .desc("The S option")
            .longOpt("opt2")
            .build();
        Option option_test = Option.builder()
            .required(true)
            .desc("The test option")
            .longOpt("test")
            .build();
        Options options = new Options();
        CommandLineParser parser = new DefaultParser();

        String[] testArgs =
        { "-r", "opt1", "-S", "opt2", "arg1", "arg2",
          "arg3", "arg4", "--test", "-A", "opt3", };

        options.addOption(option_A);
        options.addOption(option_r);
        options.addOption(option_S);
        options.addOption(option_test);

        try
        {
            commandLine = parser.parse(options, testArgs);

            if (commandLine.hasOption("A"))
            {
                System.out.print("Option A is present.  The value is: ");
                System.out.println(commandLine.getOptionValue("A"));
            }

            if (commandLine.hasOption("r"))
            {
                System.out.print("Option r is present.  The value is: ");
                System.out.println(commandLine.getOptionValue("r"));
            }

            if (commandLine.hasOption("S"))
            {
                System.out.print("Option S is present.  The value is: ");
                System.out.println(commandLine.getOptionValue("S"));
            }

            if (commandLine.hasOption("test"))
            {
                System.out.println("Option test is present.  This is a flag option.");
            }

            {
                String[] remainder = commandLine.getArgs();
                System.out.print("Remaining arguments: ");
                for (String argument : remainder)
                {
                    System.out.print(argument);
                    System.out.print(" ");
                }

                System.out.println();
            }

        }
        catch (ParseException exception)
        {
            System.out.print("Parse error: ");
            System.out.println(exception.getMessage());
        }
    }