static void printFuncCall(FILE* file, struct func_call_t* funcCall)
{
fprintf(file, "<");
if (funcCall->funcPtr)
printUStr(file, funcCall->ident);
if (funcCall->fieldOfView)
printChain(file, funcCall->fieldOfView);
if (funcCall->subCall)
{
fprintf(file, "[");
printChain(file, funcCall->subCall);
fprintf(file, "]");
}
fprintf(file, ">");
}
int main(){
int i, j;
assert(signal(SIGINT, caught_signal) != SIG_ERR);
mpz_init(total);
for(i=0; i<X;i++){
for(j=0; j<X; j++){
prepcode[i][j]=Unknown;
tcode[i][j]=0;
}
tate[i]=0;
yoko[i]=0;
}
chaincont=0;
chain_main();
dputs("Long overdue. This program will follow below steps.");
printChain();
dputs("\nThe structure is this.");
/*TODO: Can't use pfCode because the argument type is different.*/
/*Note that the argument type of pfCode was originaly enum trident.*/
for(i=0; i<X; i++){
for(j=0; j<X; j++){
if(!prepcode[j][i])
will_and_die("There still be Unknown in prepcode.", \
EXIT_FAILURE);
printf("%c", prepcode[j][i]==1?'f':'a');
}
putchar('\n');
}
printf("Chaincount:%d\n", chaincont);
for(i=0; i<Ceilings; i++)
dned[i]=False;
for(i=0; i<X; i++)
sum_tate[i]=sum_yoko[i]=0;
for(i=0; i<2; i++)
sum_name[i]=0;
follow(0);
fputs("Total: ", stdout);
mpz_out_str(stdout, BASE, total);
putchar('\n');
mpz_clear(total);
return 0;
}
/* Recursively prints out the optimal chain in order. Counts hits and bps. */
unsigned int printChain(const Querymatch* matches, const int bestmatch, Info* info) {
if(bestmatch == -1) {
return 0;
} else {
info->hits = printChain(matches, matches[bestmatch].prec, info);
info->hits++;
Querymatch m = matches[bestmatch];
/* Count covered bps in ref and query */
info->query_bps_optimal = info->query_bps_optimal + m.querylen;
/* print details */
printf("%lu\t%lu\t%lu\t%lu\n", m.queryseqnum, m.querystart_fwdstrand,
m.queryend, m.score);
return info->hits;
}
}
static void printChain(FILE* file, struct lterm_t* chain)
{
if (chain->tag != L_TERM_CHAIN_TAG)
PRINT_AND_EXIT(DEBUG_PRINT_BAD_CHAIN);
struct lterm_t* currTerm = chain->next;
while (currTerm != chain)
{
switch (currTerm->tag)
{
case L_TERM_FRAGMENT_TAG :
{
printFragmentTogether(file, currTerm->fragment);
break;
}
case L_TERM_CHAIN_KEEPER_TAG:
{
fprintf(file, "(");
printChain(file, currTerm->chain);
fprintf(file, ")");
break;
}
case L_TERM_FUNC_CALL:
{
printFuncCall(file, currTerm->funcCall);
break;
}
default:
PRINT_AND_EXIT(BAD_TAG_AT_ASSEMBLY);
}
currTerm = currTerm->next;
}
}
void printFieldOfView(FILE* file, struct lterm_t* fov)
{
printChain(file, fov);
fprintf(file, "\n");
}
int main(int argc, char* argv[]) {
unsigned int queryseqlen;
Info* info;
FILE* fp;
char* filename;
Querymatch* matches;
unsigned int* match_num;
if(argc != 3) {
fprintf(stderr, "False number of arguments.\nUsage: " \
"[queryseqlength] [matches]\n");
return EXIT_FAILURE;
}
if (sscanf(argv[1], "%u", &queryseqlen) != 1) {
fprintf(stderr, "error - sequence length argument is not an integer!");
return EXIT_FAILURE;
}
/* Get matches file */
filename = argv[2];
fp = fopen(filename, "r");
if(fp == NULL) {
fprintf(stderr, "Could not load file (it's your fault): %s\n", filename);
return EXIT_FAILURE;
}
info = malloc(sizeof(struct Info));
/* Initialize some important variables (use default struct setup?) */
info->query_bps_optimal = 0;
info->query_bps_total = queryseqlen;
/* space for match data in RAM -- extended by realloc later */
matches = malloc(sizeof(struct Querymatches_s));
match_num = malloc(sizeof(unsigned int));
matches = readQuerymatches(fp, matches, match_num);
fclose(fp);
/* sort matches by x-coordinate of end-point */
qsort(matches, *match_num, sizeof(Querymatch), compare);
/* DEBUG PRINT */
int debug = 0;
if(debug) {
int i;
for(i = 0; i < *match_num; i++) {
Querymatch m = matches[i];
printf("%lu\t%lu\t%lu\t%lu\n", m.queryseqnum, m.querystart_fwdstrand,
m.queryend, m.score);
}
return EXIT_SUCCESS;
}
unsigned int bestmatch = findOptimalScore(matches, match_num, info);
info->hits = printChain(matches, bestmatch, info);
printInfo(info);
/* don't forget to free the enslaved RAM */
free(matches);
free(match_num);
free(info);
return EXIT_SUCCESS;
}
