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;
}
