////////////////////////////////////////
// Real time interrupt //
// Higher priority than ATD interrupt //
////////////////////////////////////////
void interrupt 7 RTIhandler()
{
if (isSetup == 0x00) {
setup();
} else {
forwardP();
}
clear_RTI_flag();
}
void scanFile(FILE *fp, Args *args) {
Sequence *seq = NULL;
char *oldChr;
int start, end;
FILE *snp;
oldChr = (char *)emalloc(sizeof(char));
oldChr[0] = '\0';
while (tabGetLine(fp) != NULL) {
/* read chromosome, start, and end of hotspot from line */
if (tabField(0)[0] == '#')
continue;
if (strcmp(oldChr, hotSpotGetChr()) != 0) {
if (seq)
freeSequence(seq);
seq = hotSpotSeq(args);
free(oldChr);
oldChr = estrdup(hotSpotGetChr());
}
start = atoi(tabField(START_FIELD));
end = atoi(tabField(END_FIELD));
if (args->r) {
/* reverse primers are downstream of hotspot */
start = end;
end += args->f;
snp = hotSpotSnp(args, start, end);
if(args->u)
reversePuniv(args, seq, snp, start, end);
else
reverseP(args, seq, snp);
} else {
/* forward primers are upstream of hotspot */
end = start;
start -= args->f;
snp = hotSpotSnp(args, start, end);
if(args->u)
forwardPuniv(args, seq, snp, start, end);
else
forwardP(args, seq, snp);
}
pclose(snp);
}
freeSequence(seq);
free(oldChr);
}
void turnStraight(int speed, int tspeed)
{
while (IR_left < threshold || IR_right < threshold)
{
forwardP(speed);
if(IR_left > threshold && IR_right < threshold)
{
stop();
onlyRight(tspeed);
while (IR_left > threshold && IR_right < threshold)
{}
stop();
}
if (IR_left < threshold && IR_right > threshold)
{
stop();
onlyLeft(speed);
while (IR_left < threshold && IR_right > threshold)
{}
stop();
}
}
stop();
}
