PairSint*
sufSubstring (void *space, Suffixarray *arr, Uint *pattern,
Uint len, Uint sublen)
{
Uint i;
PairSint *res, d;
if (len <= sublen)
{
return NULL;
}
res = ALLOCMEMORY(space, NULL, PairSint, len-sublen);
for(i=0; i < len-sublen; i++)
{
d=mmsearch(arr, &pattern[i], sublen, 0, 0, arr->numofsuffixes-1);
res[i].a=d.a;
res[i].b=d.b;
}
return res;
}
int main(int argc, char** argv) {
char* content;
Uint contentlen, i, j, k, l, id, lines=0;
stringset_t *set, *set2, **csv, *que;
CharSequence **s;
Suffixarray *sarray;
MultiCharSeq *mseq;
PairSint d, *matches = NULL;
Uint totallength = 0;
Uint wsize=10;
Uint counter=0;
Uint all=0;
int *space = NULL;
char *pattern= "GGAAGAAAGCGTGGGGTTTG";
char *pattern2= "TGATTAGTGATTAGTGATTA";
char *pattern3= "ACAAACATAT";
char *start;
time_t startsuf, endsuf;
double difsuf;
Uint noofchildren;
List *list;
PairUint **childinterval;
gnuplot_ctrl *h;
double *genome;
//set = readfasta(&space, "HP26695.fasta");
//csv = readcsv(&space, "HP12_GCTC.inserts", "", &lines);
/*s = ALLOCMEMORY(&space, NULL, CharSequence *, set->noofstrings);
for(i=0; i < set->noofstrings/2; i++) {
totallength += set->strings[i].len;
s[i] = ALLOCMEMORY(&space, NULL, CharSequence, 1);
s[i]->sequence = set->strings[i].str;
s[i]->length = set->strings[i].len;
/ printf("%s,", set->strings[i].str);
printf("\n"); /
}*/
s = ALLOCMEMORY(&space, NULL, CharSequence *, 1);
s[0] = ALLOCMEMORY(&space, NULL, CharSequence, 1);
s[0]->sequence = pattern3;
s[0]->length = strlen(pattern3);
genome = ALLOCMEMORY(&space, NULL, double, totallength);
memset(genome, 0, sizeof(double)*totallength);
time (&startsuf);
sarray = constructSufArr(&space, s, 1/*set->noofstrings/2*/, NULL);
constructLcp(space, sarray);
dumplcptab(sarray);
constructchildtab(space, sarray);
time (&endsuf);
difsuf = difftime (endsuf, startsuf);
printf("noofsuffixes: %d\n", sarray->numofsuffixes);
dumpchildtab(sarray);
dumpSufArr(sarray);
list = getChildintervals(space, sarray, 0, 5);
childinterval = (PairUint**) dataList(space, list);
for(i=0; i < list->length; i++) {
printf("[%d,%d]\n", childinterval[i]->a, childinterval[i]->b);
}
constructsuflinks(space, sarray);
for(k=1; k < lines; k+=2) {
// printf("searching %s\n", csv[k]->strings[0].str);
if(csv[k]->strings[0].len > 8) {
if(wsize > csv[k]->strings[0].len) {
d=mmsearch(sarray, csv[k]->strings[0].str, csv[k]->strings[0].len, 0, 0, sarray->numofsuffixes-1);
// printf("suffixes were found at positions (%d, %d)\n",d.a, d.b);
for (j=d.a; j <= d.b; j++) {
genome[sarray->suftab[j]]++;
}
} else {
for(l=0; l < csv[k]->strings[0].len-wsize; l++) {
d=mmsearch(sarray, &csv[k]->strings[0].str[l], wsize, 0, 0, sarray->numofsuffixes-1);
// printf("suffixes were found at positions (%d, %d)\n",d.a, d.b);
for (j=d.a; j <= d.b; j++) {
genome[sarray->suftab[j]]++;
/* start = sarray->suffixptr[sarray->suftab[j]];
printf("pattern was: %s\n", &csv[k]->strings[0].str[l]);
printf("suffix found: ");
for (i=0; i < wsize; i++) {
printf("%c", start[i]);
}
printf("\n");
id = getMultiCharSeqIndex(sarray->seq, sarray->suffixptr[sarray->suftab[j]]);
printf("found in sequence: %d\n", id); */
}
}
}
if (d.a < d.b) counter++;
all++;}
}
destructStringset(&space, set);
writeY("out.xy", genome, totallength);
/*h = gnuplot_init();
gnuplot_setstyle(h, "points");
gnuplot_cmd(h, "set title 'IMBISS - seed statistics' -28,0 font'Helvetica,15'");
gnuplot_cmd(h, "set label 'seed length: %d' at graph 0.05,0.95 font 'Helvetica, 12'", totallength);
gnuplot_set_xlabel(h, "matches");
gnuplot_set_ylabel(h, "position");
gnuplot_plot_x(h, genome, totallength, "position");
*/
printf ("sliding windows of %d sequences (of %d) found\n", counter, all);
printf ("Building the suffixarray has taken %f seconds.\n", difsuf);
printf ("Total length of suffixarray was %d\n", totallength);
while(1);
return EXIT_SUCCESS;
}
