Reader rdr = new InputStreamReader(System.in);
BufferedReader br = new BufferedReader(rdr);
String s;
s = br.readLine();
br.close();
Scanner sc = new Scanner(System.
Looks like you need:
http://commons.apache.org/io/apidocs/org/apache/commons/io/input/CloseShieldInputStream.html
Wrap that around System.in before making your reader, and then all will be well, since you won't do that when you are using a FileInputStream.
If you just want to get input from keyboard by System.in, please use static BufferedReader wrapping InputStreamReader (also wrapping System.in). Like this:
Public BufferedReader is = new BufferedReader(new InputStreamReader(System.in));
And is.close(); would be needed right before your application terminated.