To get rid of the deprecated warning, don't use a deprecated function. Deprecated functions may not meet current standards. They exist only to provide backwards compatibility while the rest of the world catches up. In your case, use another Stream reader instead. I prefer Scanner, but there are plenty more.
Scanner in = new Scanner(System.In);
String[] strings = in.readLine().split(" ");
Java has a built in Arrays.Sort() method that you can use instead of implementing your own, unless you have some special requirements.
Arrays.sort(strings);