int tr_filter_task(int argc, char *argv[])
{
int c, is_collapse = 0;
int is_nucl = 0;
int cut_off = 15;
FILE *fp;
int is_mask = 1;
int is_mask_segments = 1;
MultiAlign *ma;
while ((c = getopt(argc, argv, "F:ngMN")) >= 0) {
switch (c) {
case 'n': is_nucl = 1; break;
case 'g': is_collapse = 1; break;
case 'N': is_mask_segments = 0; break;
case 'M': is_mask = 0; break;
case 'F': cut_off = atoi(optarg); break;
}
}
if (optind == argc) return tr_filter_usage();
fp = tr_get_fp(argv[optind]);
ma = ma_read_alignment(fp, is_nucl);
if (is_mask) ma_apply_mask(ma);
ma_filter(ma, is_collapse, cut_off, is_mask_segments);
tr_align_output(stdout, ma);
ma_free(ma);
if (fp != stdin) fclose(fp);
return 0;
}
int main() {
printf("Begin\n");
/* @param system_init initialize GPIO and ADC structs for pins and ADC variables using system_init()
* @param SysTick_Config set ticks by dividing systemCoreClock with systick frequency (168MHz/50Hz)
* @param read_temperature() used to convert digital signal to temperature reading
* @param filtered defined as moving average to reduce noise
* @param motor_rotate_to for the servo motor measurements (with filtered angle measurements)
* @param alarm_temperature defined to raise the alarm if the temperature goes above threshold
*/
system_init();
SysTick_Config(SystemCoreClock / SYSTICK_FREQUENCY);
//running while loop to control the frequency measurement readings of the temperature
//waits for interrupt to read the temperature readings
while (1) {
while (!system_ticks);
read_temperature();
float filtered = ma_filter(temperature_reading);
motor_rotate_to(temperature_to_angle(filtered));
alarm_temperature(filtered);
system_ticks = 0;
}
return 0;
}
