void checksuflinks(Suffixarray *s, Uint i, Uint j){
Uint k, childlcp, suflcp, *space = NULL;
PairUint* child, childsuf;
Container *children;
// ignore singletons as initial input
if (i == j){
return;
}
children = getChildintervals(space, s, i, j, 0);
for (k = 0; k < bl_containerSize(children); k++){
child = (PairUint *) bl_containerGet(children, k);
// exclude singletons
if (child->a == child->b){
return;
}
// check suflink of child
childlcp = getlcpval(s, child->a, child->b);
childsuf = getSuflink(s, child->a, child->b);
suflcp = getlcpval(s, childsuf.a, childsuf.b);
if (childlcp != suflcp + 1){
DBG("suf[%u, %u, %u]=[%u, %u, %u]\n", child->a, child->b, childlcp,
childsuf.a, childsuf.b, suflcp);
}
// recursively check all children of child
checksuflinks(s, child->a, child->b);
}
bl_containerDestruct(children, NULL);
free(children);
}
PairUint
getCharInterval(void *space,
Suffixarray *s,
Uint i,
Uint j,
Uint pos,
char ch)
{
List *list;
Uint lcp=0;
PairUint lr;
lr.a = 1;
lr.b = 0;
if(i==j) return lr;
list = getChildintervals(space, s, i, j);
lcp = getlcpval(s, i, j);
for(i=0; i < list->length; i++) {
if(s->suffixptr[s->suftab[((PairUint*)list->nodes[i].data)->a]][lcp] == ch) {
lr.a = ((PairUint*)list->nodes[i].data)->a;
lr.b = ((PairUint*)list->nodes[i].data)->b;
break;
}
}
wrapList(space, list, destructinterval);
return lr;
}
void
constructsuflinks(void *space, Suffixarray *s) {
Uint i,
j,
a,
b,
k,
nooflists,
lcp,
pos;
Stack istack;
Stack jstack;
List *children,
**lists;
PairUint **data,
slinkinterval;
nooflists = maxlcp(s) +1;
lists = ALLOCMEMORY(space, NULL, List*, nooflists);
memset(lists, 0, sizeof(List*)*nooflists);
initStack(space, &istack, 1000);
initStack(space, &jstack, 1000);
stackpush(space, &istack, 0);
stackpush(space, &jstack, s->numofsuffixes-1);
while(!stackisempty(&istack)) {
i = stackpop(&istack);
j = stackpop(&jstack);
lcp = getlcpval(s, i, j);
/*printf("adding list %d\n", lcp);*/
if (lists[lcp] == NULL) {
lists[lcp] = initList(space, 10);
}
addinterval(space, lists[lcp], i, j);
/*printf("lcp: %d-[%d,%d]\n", lcp, i, j);*/
children = getChildintervals(space, s, i, j);
data = (PairUint**) dataList(space, children);
for(k=children->length; k > 0; k--) {
a = data[k-1]->a;
b = data[k-1]->b;
FREEMEMORY(space, data[k-1]);
if(a != b) {
stackpush(space, &istack, a);
stackpush(space, &jstack, b);
}
}
FREEMEMORY(space, data);
wrapList(space, children, NULL);
}
destructStack(space, &istack);
destructStack(space, &jstack);
s->suflink_l = ALLOCMEMORY(space, NULL, Uint, s->numofsuffixes);
s->suflink_r = ALLOCMEMORY(space, NULL, Uint, s->numofsuffixes);
memset(s->suflink_l, 0, sizeof(Uint)*s->numofsuffixes);
memset(s->suflink_r, 0, sizeof(Uint)*s->numofsuffixes);
for(i=1; i < nooflists; i++) {
if(lists[i] != NULL && lists[i-1] !=NULL) {
for(j=0; j < lists[i]->length; j++) {
/*printf("looking at interval [%d,%d], list %d\n", ((PairUint*)lists[i]->nodes[j].data)->a, ((PairUint*)lists[i]->nodes[j].data)->b, i);*/
slinkinterval = findslinkinterval(space, s, lists, i, j);
pos = getfirstlindex(s, ((PairUint*)lists[i]->nodes[j].data)->a, ((PairUint*)lists[i]->nodes[j].data)->b);
/*printf("store at %d: [%d,%d]\n", pos, slinkinterval.a, slinkinterval.b);*/
s->suflink_l[pos]=slinkinterval.a;
s->suflink_r[pos]=slinkinterval.b;
}
}
wrapList(space, lists[i-1], destructinterval);
}
FREEMEMORY(space, lists);
return;
}
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;
}
