bool BWSearch1CPU(uint8_t *W, vector *C, vector *C1, comp_matrix *O, comp_matrix *Oi, result *res, results_list *r_list) {
int16_t start, end, half, n;;
SA_TYPE _k, _l;
_k = res->k;
_l = res->l;
start = res->start;
end = res->end;
n = end - start + 1;
half = n / 2;
result r;
init_result(&r, 0);
bound_result(&r, half, end);
change_result(&r, _k, _l, end);
BWExactSearchBackward(W, C, C1, O, &r);
if (r.k <= r.l) {
r.start = start;
r.pos = half-1;
BWSimpleSearch1Backward(W, C, C1, O, &r, r_list);
if (r.k <= r.l) add_result(&r, r_list); //Match
}
half--;
init_result(&r, 1);
bound_result(&r, start, half);
change_result(&r, _k, _l, start);
BWExactSearchForward(W, C, C1, Oi, &r);
if (r.k <= r.l) {
r.pos = half+1;
r.end = end;
BWSimpleSearch1Forward(W, C, C1, Oi, &r, r_list);
}
return false;
}
void BWSearch1CPU(char *W, vector *C, vector *C1, comp_matrix *O, comp_matrix *Oi, result *res, results_list *r_list) {
unsigned int half, n;
int start, end;
unsigned int _k, _l;
_k = res->k;
_l = res->l;
start = res->start;
end = res->end;
n = end - start + 1;
half = n / 2;
result r;
init_result(&r, 0);
bound_result(&r, half, end);
change_result(&r, _k, _l, end);
BWExactSearchBackward(W, C, C1, O, &r);
if (r.k <= r.l) {
r.start = start;
r.pos = half-1;
BWSimpleSearch1Backward(W, C, C1, O, &r, r_list);
if (r.k <= r.l) add_result(&r, r_list); //Match
}
half--;
init_result(&r, 1);
bound_result(&r, start, half);
change_result(&r, _k, _l, start);
BWExactSearchForward(W, C, C1, Oi, &r);
if (r.k <= r.l) {
r.pos = half+1;
r.end = end;
BWSimpleSearch1Forward(W, C, C1, Oi, &r, r_list);
}
}
bool BWSimpleSearch1Forward(uint8_t *W, vector *C, vector *C1, comp_matrix *O, result *res, results_list *r_list) {
SA_TYPE _k, _l, _k_next, _l_next, _k_aux, _l_aux;
SA_TYPE results, results_next;
int16_t start, end, i;
result r;
start = res->pos;
end = res->end;
_k_next = res->k;
_l_next = res->l;
results_next = _l_next - _k_next;
init_result(&r, 1);
bound_result(&r, start, end);
add_mismatch(&r, MATCH, -1, start);
for(i=start; i<=end; i++) {
_k = _k_next;
_l = _l_next;
//printf("%d:\n", i);
if (_k > _l) {
change_result(res, _k, _l, -1);
return false;
}
BWiteration(_k, _l, _k_next, _l_next, W[i], C, C1, O);
results = results_next;
results_next = _l_next - _k_next;
if (results == results_next) continue;
//Deletion
change_result(&r, _k, _l, i+1);
BWExactSearchForward(W, C, C1, O, &r);
if (r.k<=r.l) {
modify_last_mismatch3(&r, DELETION, -1, i);
add_result(&r, r_list);
}
for (uint8_t b=0;b<nA;b++) {
BWiteration(_k, _l, _k_aux, _l_aux, b, C, C1, O);
//printf("W -> %d, %d - %d\n", b, _k_aux, _l_aux);
if (_k_aux > _l_aux) continue;
//Insertion
change_result(&r, _k_aux, _l_aux, i);
BWExactSearchForward(W, C, C1, O, &r);
if (r.k<=r.l) {
modify_last_mismatch3(&r, INSERTION, b, i);
add_result(&r, r_list);
}
//Mismatch
if (b!=(int)W[i]) {
change_result(&r, _k_aux, _l_aux, i+1);
BWExactSearchForward(W, C, C1, O, &r);
if (r.k<=r.l) {
modify_last_mismatch3(&r, MISMATCH, b, i);
add_result(&r, r_list);
}
}
}
}
//Match at exit in res
change_result(res, _k_next, _l_next, -1);
return false;
}
void BWSimpleSearch1Forward(char *W, vector *C, vector *C1, comp_matrix *O, result *res, results_list *r_list) {
BWiterationVariables();
size_t _k, _l, _k_next, _l_next, _k_aux, _l_aux;
size_t results, results_next;
int start, end, i;
result r;
start = res->pos;
end = res->end;
_k_next = res->k;
_l_next = res->l;
results_next = _l_next - _k_next;
init_result(&r, 1);
bound_result(&r, start, end);
add_mismatch(&r, MATCH, XXX, start);
for(i=start; i<=end; i++) {
_k = _k_next;
_l = _l_next;
//printf("%d:\n", i);
if (_k > _l) {
change_result(res, _k, _l, -1);
return;
}
BWiteration(_k, _l, _k_next, _l_next, W[i], C, C1, O);
results = results_next;
results_next = _l_next - _k_next;
if (results == results_next) continue;
//Deletion
change_result(&r, _k, _l, i+1);
modify_last_mismatch_3(&r, DELETION, XXX, i);
BWExactSearchForward(W, C, C1, O, &r);
if (r.k<=r.l) add_result(&r, r_list);
for (unsigned int b=0;b<nA;b++) {
BWiteration(_k, _l, _k_aux, _l_aux, b, C, C1, O);
//printf("W -> %d, %d - %d\n", b, _k_aux, _l_aux);
if (_k_aux > _l_aux) continue;
//Insertion
change_result(&r, _k_aux, _l_aux, i);
modify_last_mismatch_2(&r, INSERTION, b);
BWExactSearchForward(W, C, C1, O, &r);
if (r.k<=r.l) add_result(&r, r_list);
//Mismatch
if (b!=(unsigned int)W[i]) {
change_result(&r, _k_aux, _l_aux, i+1);
modify_last_mismatch_1(&r, MISMATCH);
BWExactSearchForward(W, C, C1, O, &r);
if (r.k<=r.l) add_result(&r, r_list);
}
}
}
//Match at exit in res
change_result(res, _k_next, _l_next, -1);
}
//TODO: Comprobar que funciona igual y borrar el codigo de esta función
void BWSearch1(char *W, int start, int end, size_t *vec_k, size_t *vec_l, size_t *vec_ki, size_t *vec_li, vector *C, vector *C1, comp_matrix *O, comp_matrix *Oi, results_list *r_list) {
BWiterationVariables();
size_t _k, _l, _ki, _li, _k_aux, _l_aux, _ki_aux, _li_aux;
size_t results, results_last;
unsigned int i, j, half, n;
result r;
n = end - start;
half = n / 2;
init_result(&r, 0);
bound_result(&r, start, end);
if (vec_k[0] <= vec_l[0]) {
change_result(&r, vec_k[0], vec_l[0], -1);
add_result(&r, r_list);
}
add_mismatch(&r, MATCH, XXX, start);
results = vec_l[0] - vec_k[0];
results_last = results;
_k = vec_k[1];
_l = vec_l[1];
results = _l - _k;
//printf("B -> %d: %d -> %d, %u, %u\n", 0, results, results_last, _k, _l);
if (results != results_last) {
//printf("*B -> %d: %d -> %d, %u, %u\n", 0, results, results_last, _k, _l);
//printf("%d: %d -> %d\n", 0, results, results_last);
//Deletion
change_result(&r, _k, _l, -1);
modify_last_mismatch_3(&r, DELETION, XXX, start);
add_result(&r, r_list);
for (size_t b=0;b<nA;b++) {
BWiteration(_k, _l, _k_aux, _l_aux, b, C, C1, O);
//printf("W -> %d, %d - %d\n", b, _k_aux, _l_aux);
if (_k_aux > _l_aux) continue;
//printf("*W -> %d, %d - %d\n", b, _k_aux, _l_aux);
size_t b_w = (size_t) W[start];
//Missmatch
if (b!=b_w) {
change_result(&r, _k_aux, _l_aux, -1);
modify_last_mismatch_2(&r, MISMATCH, b);
add_result(&r, r_list);
}
//Insertion
BWiteration(_k_aux, _l_aux, _k_aux, _l_aux, b_w, C, C1, O);
if (_k_aux <= _l_aux) {
change_result(&r, _k_aux, _l_aux, -1);
modify_last_mismatch_3(&r, 3, INSERTION, b);
add_result(&r, r_list);
}
}
}
for (i=start+2, j=2; j<=half; i++, j++) {
results_last = results;
_k = vec_k[j];
_l = vec_l[j];
results = _l - _k;
//printf("B -> %d: %d -> %d, %u, %u\n", j-1, results, results_last, _k, _l);
if (results == results_last) continue;
//printf("*B -> %d: %d -> %d, %u, %u\n", j-1, results, results_last, _k, _l);
//Deletion
change_result(&r, _k, _l, i-2);
modify_last_mismatch_3(&r, DELETION, XXX, i-1);
BWExactSearchBackward(W, C, C1, O, &r);
if (r.k<=r.l) add_result(&r, r_list);
for (size_t b=0;b<nA;b++) {
BWiteration(_k, _l, _k_aux, _l_aux, b, C, C1, O);
if (_k_aux > _l_aux) continue;
//Insertion
change_result(&r, _k_aux, _l_aux, i-1);
modify_last_mismatch_2(&r, INSERTION, b);
BWExactSearchBackward(W, C, C1, O, &r);
if (r.k<=r.l) add_result(&r, r_list);
//Mismatch
if (b!=(size_t)W[i-1]) {
change_result(&r, _k_aux, _l_aux, i-2);
modify_last_mismatch_1(&r, MISMATCH);
BWExactSearchBackward(W, C, C1, O, &r);
if (r.k<=r.l) add_result(&r, r_list);
}
}
}
//printf("\n");
//TODO: Gestionar bien los errores de la busqueda al revés con Si y restas (precalcular Si con |X| - pos)
half--;
results = vec_li[n] - vec_ki[n];
r.dir=1; //Change direction
results_last = results;
_ki = vec_ki[n-1];
_li = vec_li[n-1];
results = _li - _ki;
//printf("F-> %d: %d -> %d, %u, %u\n", n, results, results_last, _ki, _li);
if (results != results_last) {
//printf("*F -> %d: %d -> %d, %u - %u\n", i+1, results, results_last, _ki, _li);
//Deletion
change_result(&r, _ki, _li, -1);
modify_last_mismatch_3(&r, DELETION, XXX, end);
add_result(&r, r_list);
for (size_t b=0;b<nA;b++) {
BWiteration(_ki, _li, _ki_aux, _li_aux, b, C, C1, Oi);
if (_ki_aux > _li_aux) continue;
size_t b_w = (size_t) W[end];
//Mismatch
if (b!=b_w) {
change_result(&r, _ki_aux, _li_aux, -1);
modify_last_mismatch_2(&r, MISMATCH, b);
add_result(&r, r_list);
}
//Insertion
BWiteration(_ki_aux, _li_aux, _ki_aux, _li_aux, b_w, C, C1, Oi);
//printf("\tI -> %d - %d\n", _ki_aux, _li_aux);
if (_ki_aux <= _li_aux){
change_result(&r, _ki_aux, _li_aux, -1);
modify_last_mismatch_2(&r, INSERTION, b);
add_result(&r, r_list);
}
}
}
for(i=end-2,j=n-2; j>=half; i--, j--) {
results_last = results;
_ki = vec_ki[j];
_li = vec_li[j];
results = _li - _ki;
//printf("F -> %d: %d -> %d, %u - %u\n", i+1, results, results_last, _ki, _li);
if (results == results_last) continue;
//printf("*F -> %d: %d -> %d, %u - %u\n", i+1, results, results_last, _ki, _li);
//TODO: Anadir contador para podar cuando se que ya he encontrado las cadenas que permite la variabilidad en este simbolo.
//Deletion
change_result(&r, _ki, _li, i+2);
modify_last_mismatch_3(&r, DELETION, XXX, i+1);
BWExactSearchForward(W, C, C1, Oi, &r);
if (r.k<=r.l) add_result(&r, r_list);
for (size_t b=0;b<nA;b++) {
BWiteration(_ki, _li, _ki_aux, _li_aux, b, C, C1, Oi);
//printf("W -> %d, %d - %d\n", b, _ki_aux, _li_aux);
if (_ki_aux > _li_aux) continue;
//Insertion
change_result(&r, _ki_aux, _li_aux, i+1);
modify_last_mismatch_2(&r, INSERTION, b);
BWExactSearchForward(W, C, C1, Oi, &r);
if (r.k<=r.l) add_result(&r, r_list);
//Mismatch
if (b!= (size_t) W[i+1]) {
change_result(&r, _ki_aux, _li_aux, i+2);
modify_last_mismatch_1(&r, MISMATCH);
BWExactSearchForward(W, C, C1, Oi, &r);
if (r.k<=r.l) add_result(&r, r_list);
}
}
}
//printf("\n");
}
