You presumably want to work in binary, so try:
Scanner keysIn = new Scanner(System.in);
System.out.print("Please enter your number: ");
long originalNum = keysIn.nextLong(2); // specify radix of 2
System.out.println(Long.toBinaryString(~originalNum)); // print binary string
keysIn.close();
Please enter your number: 0111011 1111111111111111111111111111111111111111111111111111111111000100
As you can see, all bits are flipped. Bear in mind that there are leading 0s in front of the binary number you entered.