I would just use
int a = Integer.parseInt(thirdLine.substring(0, indexOf(" ")));
tempString = thirdLine.subString(indexOf(" "), thirdLine.length());
int b = Integer.parseInt(tempString.subString(0, indexOf(" ")));
and so on...


String inLine = "0 5 0 3 0 0"; int[] nums = new int[6]; for (int i = 0; i < 6; i++) nums[i] = Integer.valueOf("" + inLine.charAt(i * 2));
for (int i = 0; i < 6; i++) set[i] = Integer.valueOf("" + lines.charAt(i * 2));
for (int i = 0; i < 6; i++) set[i] = Integer.valueOf("" + lines.charAt(i )); //<-- use i instead of i*2