...

import java.io.*;

...

public class Reader {

	...

	public static void main(String[] args) ... {

		...
		
		// system standard input reader
		BufferedReader sysIn = new BufferedReader( new InputStreamReader( System.in ) );
		
		// file reader
		BufferedReader fileIn = null;
		try {
			fileIn = new BufferedReader( new FileReader( "/sciezka/do/pliku" ) );
		} catch (FileNotFoundException e) {
			...
		}

		// read stream line by line
		try {
			String sysLine = sysIn.readLine();
			while (sysLine != null) { // you can end input stream e.g. by ctrl+d in Unix
				...
				sysLine = sysIn.readLine();
			}				
			sysIn.close();
			
			String fileLine = fileIn.readLine();
			while (fileLine != null) {
				...
				fileLine = fileIn.readLine();
			}				
			fileIn.close();
		} catch (IOException e) { // thrown by readLine() or close()
			...
		}
	}

	...

}