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exact.c
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#include <assert.h>
#include "rld.h"
#include "kstring.h"
#include "fermi.h"
#include "kvec.h"
uint64_t fm_backward_search(const rld_t *e, int len, const uint8_t *str, uint64_t *sa_beg, uint64_t *sa_end)
{
uint64_t k, l, ok, ol;
int i, c;
c = str[len - 1];
k = e->cnt[c]; l = e->cnt[c + 1] - 1;
for (i = len - 2; i >= 0; --i) {
c = str[i];
rld_rank21(e, k - 1, l, c, &ok, &ol);
k = e->cnt[c] + ok;
l = e->cnt[c] + ol - 1;
if (k > l) break;
}
if (k > l) return 0;
*sa_beg = k; *sa_end = l;
return l - k + 1;
}
uint64_t fm_multi_backward_search(int n, rld_t *const*e, int len, const uint8_t *str, uint64_t *sa_beg, uint64_t *sa_end)
{
uint64_t *k, *l, ok, ol;
int i, j, c, finished = 0;
int8_t *done;
c = str[len - 1];
k = alloca(n * 8);
l = alloca(n * 8);
done = alloca(n);
for (j = 0; j < n; ++j) {
k[j] = e[j]->cnt[c];
l[j] = e[j]->cnt[c + 1];
done[j] = 0;
}
for (i = len - 2; i >= 0; --i) {
c = str[i];
for (j = 0; j < n; ++j) {
// printf("%d,%d,[%lld,%lld]%c\n", i, j, k[j], l[j], done[j]? '*' : '.');
if (!done[j]) {
rld_rank21(e[j], k[j] - 1, l[j] - 1, c, &ok, &ol);
k[j] = e[j]->cnt[c] + ok;
l[j] = e[j]->cnt[c] + ol;
if (k[j] == l[j]) done[j] = 1, ++finished;
} else k[j] = l[j] = e[j]->cnt[c] + rld_rank11(e[j], k[j] - 1, c);
}
if (finished == n) break;
}
if (finished == n) return 0;
for (j = 0, *sa_beg = *sa_end = 0; j < n; ++j)
*sa_beg += k[j], *sa_end += l[j];
--*sa_end;
return *sa_end - *sa_beg + 1;
}
int64_t fm_retrieve(const rld_t *e, uint64_t x, kstring_t *s)
{
uint64_t k = x, *ok;
ok = alloca(8 * e->asize);
s->l = 0;
while (1) {
int c = rld_rank1a(e, k, ok);
k = e->cnt[c] + ok[c] - 1;
if (c == 0) return k;
kputc(c, s);
}
}
int fm6_extend(const rld_t *e, const fmintv_t *ik, fmintv_t ok[6], int is_back)
{ // FIXME: this can be accelerated a little by using rld_rank1a() when ik.x[2]==1
uint64_t tk[6], tl[6];
int i;
rld_rank2a(e, ik->x[!is_back] - 1, ik->x[!is_back] - 1 + ik->x[2], tk, tl);
for (i = 0; i < 6; ++i) {
ok[i].x[!is_back] = e->cnt[i] + tk[i];
ok[i].x[2] = (tl[i] -= tk[i]);
}
ok[0].x[is_back] = ik->x[is_back];
ok[4].x[is_back] = ok[0].x[is_back] + tl[0];
ok[3].x[is_back] = ok[4].x[is_back] + tl[4];
ok[2].x[is_back] = ok[3].x[is_back] + tl[3];
ok[1].x[is_back] = ok[2].x[is_back] + tl[2];
ok[5].x[is_back] = ok[1].x[is_back] + tl[1];
return 0;
}
int fm6_extend0(const rld_t *e, const fmintv_t *ik, fmintv_t *ok0, int is_back)
{ // FIXME: this can be accelerated a little by using rld_rank1a() when ik.x[2]==1
uint64_t tk[6], tl[6];
rld_rank2a(e, ik->x[!is_back] - 1, ik->x[!is_back] - 1 + ik->x[2], tk, tl);
ok0->x[!is_back] = tk[0];
ok0->x[is_back] = ik->x[is_back];
ok0->x[2] = tl[0] - tk[0];
return 0;
}
uint64_t fm6_retrieve(const rld_t *e, uint64_t x, kstring_t *s, fmintv_t *k2, int *contained)
{
uint64_t k = x, ok[6];
fmintv_t ok2[6];
s->l = 0; *contained = 0;
while (1) {
int c = rld_rank1a(e, k, ok);
k = e->cnt[c] + ok[c] - 1;
if (c == 0) break;
if (s->l > 0) {
if (k2->x[2] == 1) k2->x[0] = k;
else {
fm6_extend(e, k2, ok2, 1);
*k2 = ok2[c];
}
} else fm6_set_intv(e, c, *k2);
kputc(c, s);
}
if (k2->x[2] != 1) {
fm6_extend(e, k2, ok2, 1);
if (ok2[0].x[2] != k2->x[2]) *contained |= 1; // left contained
*k2 = ok2[0];
} else k2->x[0] = k;
fm6_extend(e, k2, ok2, 0);
if (ok2[0].x[2] != k2->x[2]) *contained |= 2; // right contained
*k2 = ok2[0];
return k;
}
void fm_reverse_fmivec(fmintv_v *p)
{
if (p->n > 1) {
int j;
for (j = 0; j < p->n>>1; ++j) {
fmintv_t tmp = p->a[p->n - 1 - j];
p->a[p->n - 1 - j] = p->a[j];
p->a[j] = tmp;
}
}
}
fmintv_t *fm6_traverse(const rld_t *e, int depth)
{
fmintv_t *rst, ok[6], ik;
fmintv_v stack;
rst = calloc(1<<depth*2, sizeof(fmintv_t));
ik.x[0] = ik.x[1] = 0; ik.x[2] = e->mcnt[0]; ik.info = 0;
kv_init(stack);
kv_push(fmintv_t, stack, ik);
while (stack.n) {
int c, d;
ik = kv_pop(stack);
d = ik.info&0xffffffff; // depth of the node
if (d != depth) {
if (ik.x[2] == e->mcnt[0]) {
for (c = 1; c < 5; ++c)
fm6_set_intv(e, c, ok[c]);
} else fm6_extend(e, &ik, ok, 1);
for (c = 1; c < 5; ++c) {
if (ok[c].x[2]) {
ok[c].info = ik.info + 1;
ok[c].info |= (uint64_t)(c - 1) << (32 + d * 2);
kv_push(fmintv_t, stack, ok[c]);
}
}
} else rst[ik.info>>32] = ik;
}
free(stack.a);
return rst;
}