You don't actually need to run a command from an xterm session, you can run it directly:
String[] arguments = new String[] {"/path/to/executable", "arg0", "arg1", "etc"};
Process proc = new ProcessBuilder(arguments).start();
If the process responds interactively to the input stream, and you want to inject values, then do what you did before:
OutputStream out = proc.getOutputStream();
out.write("command\n");
out.flush();
Don't forget the '\n' at the end though as most apps will use it to identify the end of a single command's input.