Rather than use the parallel port, have you considered using a serial device? Since you have a TTL signal, you'll possibly need a level converter to convert TTL to RS232 +/- 12V levels. Once you're using a serial device, you can use the standard serial ioctl() calls to detect a change in control signal status.
Specifically, you could use the TIOCMIWAIT ioctl on the connected serial device to wait for a change on say the DCD line, which you would connect to your clock source.
Your user space application would be blocked waiting in the TIOCMIWAIT ioctl system call until there is a change of status on your clock line, at which point your app would become runnable and return from the ioctl. You might have to take care to ensure that you handle the case where you get a change of status interrupt on both rising and falling edges of your serial control signals. On some UART hardware (eg TL16C554A UART) it's possible that you'll only get an interrupt for a signal transitioning in a single direction. For the TL16C554A for example, the TIOCMIWAIT would only fall through on the rising edge of any Ring Indicate signal change.
Using the serial ioctls in this manner also has the advantage that you could use a USB-Serial dongle that supports TIOCMIWAIT if required (eg PL2303), and still retain user level software compatibility, albeit at the expense of increased latency due to USB.
If you require lower latency than can be achieved through user space, you'd be best to write a kernel driver module which can handle the timing and sampling, but I wouldn't suggest this route unless absolutely needed. It's easier to develop user space code.
Here's some incomplete sample C code snippets for using the TIOCMIWAIT ioctl.
int serial_fd = open(cmdline.device_name, O_RDWR | O_NONBLOCK | O_NOCTTY);
static const unsigned int ri_flag = TIOCM_RNG;
/* Set up serial port here using tcsetattr. Set CRTSCTS | CLOCAL to ensure status interrupts
* are generated.
*/
while (1) {
/* Wait for positive RI transition. TIOCMIWAIT takes a mask
* as argument, only returning when the appropriate signal has changed.
*/
if (ioctl(serial_fd, TIOCMIWAIT, ri_flag)) {
fprintf(stderr, "ioctl() failed waiting for RI edge [%s]\n", strerror(errno));
break;
}
/* Do sensor sampling here. You could use TIOCMGET to first verify that
* the clock line is in the expected state, eg high, before continuing.
*/
}
