set<short*, setcomp> find_equal_energy(encoded &enc, int energy, degen °, bool direct, bool &lm)
{
bool (*old_funct) (short *, int) = deg.opt->f_point;
deg.opt->f_point = equal_energies;
// count how many times called
cnt_move++;
// unused, just for necessity of functions
short *min_pt = allocopy(enc.pt);
// used
deg.current = energy;
// setup
degen_energy = energy;
degen_saddle = false;
degen_done.clear();
degen_undone.clear();
degen_undone.insert(allocopy(enc.pt));
//fprintf(stderr, " ins: %s\n", pt_to_str(enc.pt).c_str() );
while (degen_undone.size()!=0) {
// take first
short *last = enc.pt;
enc.pt = *degen_undone.begin();
degen_undone.erase(degen_undone.begin());
// move it
insertions(enc, energy, min_pt, deg, deg.opt->verbose_lvl>3);
deletions(enc, energy, min_pt, deg, deg.opt->verbose_lvl>3);
// shifts (only if enabled + noLP disabled)
if (deg.opt->shift && !deg.opt->noLP) {
shifts(enc, energy, min_pt, deg, deg.opt->verbose_lvl>3);
}
degen_done.insert(enc.pt);
//fprintf(stderr, "inserting(done): %s\n", pt_to_str(enc.pt).c_str());
enc.pt = last;
}
free(min_pt);
deg.opt->f_point = old_funct;
lm = !degen_saddle;
return degen_done;
}
/* sample usage: */
int main() {
char seq[20] = "ACCCCCCTCTGTAGGGGGA";
char str[20] = ".((.(.........).)).";
/* move to the local minimum and display it */
int energy = move_standard(seq, str, GRADIENT, 0, 0, 0);
fprintf(stdout, "%s %6.2f\n\n", str, energy/100.0);
/* now create an array of every structure in neighbourhood of str structure */
struct_en *list = NULL;
int list_length = 0;
int get_list(struct_en *new_one, struct_en *old_one)
{
/* enlarge the list */
list_length++;
list = (struct_en*) realloc(list, list_length*sizeof(struct_en));
/* copy the structure */
list[list_length-1].energy = new_one->energy;
list[list_length-1].structure = allocopy(new_one->structure);
/* we want to continue -> return 0 */
return 0;
}
// browse neighbours without degeneracy (almost the same as move_set) assume deg.first = true
bool browse_neighs(encoded &enc, int &energy, degen °, int &saddle_en)
{
// count how many times called
cnt_move++;
// unused, just for necessity of functions
short *min_pt = allocopy(enc.pt);
// used
deg.current = energy;
// did we just find escape from basin?
bool escape = false;
//if (deg.opt->verbose_lvl>3) fprintf(stderr, "\n browse neighs:\n %s %d\n\n", pt_to_str(enc.pt).c_str(), energy);
escape = insertions(enc, energy, min_pt, deg, deg.opt->verbose_lvl>3);
//if (deg.opt->verbose_lvl>3) fprintf(stderr, "\n");
// deletions
if (!escape) escape = deletions(enc, energy, min_pt, deg, deg.opt->verbose_lvl>3);
// shifts (only if enabled + noLP disabled)
if (deg.opt->shift && !deg.opt->noLP) {
if (!escape) escape = shifts(enc, energy, min_pt, deg, deg.opt->verbose_lvl>3);
}
if (escape) saddle_en = deg.current;
free(min_pt);
return escape;
}
PUBLIC int
move_adaptive(char *string,
short *ptable,
short *s,
short *s1,
int verbosity_level){
srand(time(NULL));
Encoded enc;
enc.seq = string;
enc.s0 = s;
enc.s1 = s1;
/* moves*/
enc.bp_left=0;
enc.bp_right=0;
enc.bp_left2=0;
enc.bp_right2=0;
/* options*/
enc.noLP=0;
enc.verbose_lvl=verbosity_level;
enc.first=1;
enc.shift=0;
/* degeneracy*/
enc.begin_unpr=0;
enc.begin_pr=0;
enc.end_unpr=0;
enc.end_pr=0;
enc.current_en=0;
// function
enc.funct=NULL;
// allocate memory for moves
enc.moves_from = (int*) space(ptable[0]*ptable[0]*sizeof(int));
enc.moves_to = (int*) space(ptable[0]*ptable[0]*sizeof(int));
int i;
for (i=0; i<MAX_DEGEN; i++) enc.processed[i]=enc.unprocessed[i]=NULL;
struct_en str;
str.structure = allocopy(ptable);
str.energy = energy_of_structure_pt(enc.seq, str.structure, enc.s0, enc.s1, 0);
while (move_rset(&enc, &str)!=0) {
free_degen(&enc);
}
free_degen(&enc);
copy_arr(ptable, str.structure);
free(str.structure);
free(enc.moves_from);
free(enc.moves_to);
return str.energy;
}
PRIVATE int
move_rset(Encoded *Enc, struct_en *str){
/* count better neighbours*/
int cnt = 0;
/* deepest descent*/
struct_en min;
min.structure = allocopy(str->structure);
min.energy = str->energy;
Enc->current_en = str->energy;
if (Enc->verbose_lvl>0) { fprintf(stderr, " start of MR:\n "); print_str(stderr, str->structure); fprintf(stderr, " %d\n\n", str->energy); }
// construct and permute possible moves
construct_moves(Enc, str->structure);
/* find first lower one*/
int i;
for (i=0; i<Enc->num_moves; i++) {
Enc->bp_left = Enc->moves_from[i];
Enc->bp_right = Enc->moves_to[i];
cnt = update_deepest(Enc, str, &min);
if (cnt) break;
}
/* if degeneracy occurs, solve it!*/
if (deal_deg && !cnt && (Enc->end_unpr - Enc->begin_unpr)>0) {
Enc->processed[Enc->end_pr] = str->structure;
Enc->end_pr++;
str->structure = Enc->unprocessed[Enc->begin_unpr];
Enc->unprocessed[Enc->begin_unpr]=NULL;
Enc->begin_unpr++;
cnt += move_rset(Enc, str);
} else {
/* write output to str*/
copy_arr(str->structure, min.structure);
str->energy = min.energy;
}
/* release minimal*/
free(min.structure);
/* resolve degeneracy in local minima*/
if (deal_deg && (Enc->end_pr - Enc->begin_pr)>0) {
Enc->processed[Enc->end_pr]=str->structure;
Enc->end_pr++;
int min = find_min(Enc->processed, Enc->begin_pr, Enc->end_pr);
short *tmp = Enc->processed[min];
Enc->processed[min] = Enc->processed[Enc->begin_pr];
Enc->processed[Enc->begin_pr] = tmp;
str->structure = Enc->processed[Enc->begin_pr];
Enc->begin_pr++;
free_degen(Enc);
}
return cnt;
}
PUBLIC int
move_first( char *string,
short *ptable,
short *s,
short *s1,
int verbosity_level,
int shifts,
int noLP){
cnt_move = 0;
Encoded enc;
enc.seq = string;
enc.s0 = s;
enc.s1 = s1;
/* moves*/
enc.bp_left=0;
enc.bp_right=0;
enc.bp_left2=0;
enc.bp_right2=0;
/* options*/
enc.noLP=noLP;
enc.verbose_lvl=verbosity_level;
enc.first=1;
enc.shift=shifts;
/* degeneracy*/
enc.begin_unpr=0;
enc.begin_pr=0;
enc.end_unpr=0;
enc.end_pr=0;
enc.current_en=0;
/* function */
enc.funct=NULL;
int i;
for (i=0; i<MAX_DEGEN; i++) enc.processed[i]=enc.unprocessed[i]=NULL;
struct_en str;
str.structure = allocopy(ptable);
str.energy = energy_of_structure_pt(enc.seq, str.structure, enc.s0, enc.s1, 0);
while (move_set(&enc, &str)!=0) {
free_degen(&enc);
}
free_degen(&enc);
copy_arr(ptable, str.structure);
free(str.structure);
return str.energy;
}
int DSU::AddLMtoTBD(short *tmp_str, int tmp_en, LMtype type, bool debug)
{
RNAlocmin rna;
rna.energy = tmp_en;
rna.structure = allocopy(tmp_str);
rna.str_ch = pt_to_chars_pk(tmp_str);
//if (pknots) pt_to_str_pk(tmp_str, rna.str_ch);
rna.type = type;
// insert LM and return its number
LM.push_back(rna);
vertex_l[rna]=LM.size()-1;
return LM.size()-1;
}
bool equal_energies(short *str, int energy)
{
if (energy == degen_energy) {
if (degen_done.count(str)==0 && degen_undone.count(str)==0) {
degen_undone.insert(allocopy(str));
//if (DEBUGG) fprintf(stderr, "inserting(undn): %s\n", pt_to_str(str).c_str());
}
}
if (energy < degen_energy) {
degen_saddle = true;
if (!direct) { // collect info about same level structs
unordered_map<short*, struct_info, hash_fncts, hash_eq>::iterator it = struct_map.find(str);
// collect number sets (collect minima information)
if (it!=struct_map.end()) {
if (it->second.LM_nums.size()>0) numbers.insert(it->second.LM_nums);
// collect saddle information
saddles.insert(it->second.saddle_nums.begin(), it->second.saddle_nums.end());
}
}
}
return false;
}
/* move to deepest (or first) neighbour*/
PRIVATE int
move_set(Encoded *Enc, struct_en *str){
/* count how many times called*/
cnt_move++;
/* count better neighbours*/
int cnt = 0;
/* deepest descent*/
struct_en min;
min.structure = allocopy(str->structure);
min.energy = str->energy;
Enc->current_en = str->energy;
if (Enc->verbose_lvl>0) { fprintf(stderr, " start of MS:\n "); print_str(stderr, str->structure); fprintf(stderr, " %d\n\n", str->energy); }
/* if using first dont do all of them*/
bool end = false;
/* insertions*/
if (!end) cnt += insertions(Enc, str, &min);
if (Enc->first && cnt>0) end = true;
if (Enc->verbose_lvl>1) fprintf(stderr, "\n");
/* deletions*/
if (!end) cnt += deletions(Enc, str, &min);
if (Enc->first && cnt>0) end = true;
/* shifts (only if enabled + noLP disabled)*/
if (!end && Enc->shift && !Enc->noLP) {
cnt += shifts(Enc, str, &min);
if (Enc->first && cnt>0) end = true;
}
/* if degeneracy occurs, solve it!*/
if (!end && (Enc->end_unpr - Enc->begin_unpr)>0) {
Enc->processed[Enc->end_pr] = str->structure;
Enc->end_pr++;
str->structure = Enc->unprocessed[Enc->begin_unpr];
Enc->unprocessed[Enc->begin_unpr]=NULL;
Enc->begin_unpr++;
cnt += move_set(Enc, str);
} else {
/* write output to str*/
copy_arr(str->structure, min.structure);
str->energy = min.energy;
}
/* release minimal*/
free(min.structure);
/* resolve degeneracy in local minima*/
if ((Enc->end_pr - Enc->begin_pr)>0) {
Enc->processed[Enc->end_pr]=str->structure;
Enc->end_pr++;
int min = find_min(Enc->processed, Enc->begin_pr, Enc->end_pr);
short *tmp = Enc->processed[min];
Enc->processed[min] = Enc->processed[Enc->begin_pr];
Enc->processed[Enc->begin_pr] = tmp;
str->structure = Enc->processed[Enc->begin_pr];
Enc->begin_pr++;
free_degen(Enc);
}
if (Enc->verbose_lvl>1 && !(Enc->first)) { fprintf(stderr, "\n end of MS:\n "); print_str(stderr, str->structure); fprintf(stderr, " %d\n\n", str->energy); }
return cnt;
}
/* done with all structures along the way to deepest*/
PRIVATE int
update_deepest(Encoded *Enc, struct_en *str, struct_en *min){
/* apply move + get its energy*/
int tmp_en;
tmp_en = str->energy + energy_of_move_pt(str->structure, Enc->s0, Enc->s1, Enc->bp_left, Enc->bp_right);
do_move(str->structure, Enc->bp_left, Enc->bp_right);
if (Enc->bp_left2 != 0) {
tmp_en += energy_of_move_pt(str->structure, Enc->s0, Enc->s1, Enc->bp_left2, Enc->bp_right2);
do_move(str->structure, Enc->bp_left2, Enc->bp_right2);
}
int last_en = str->energy;
str->energy = tmp_en;
/* use f_point if we have it */
if (Enc->funct) {
int end = Enc->funct(str, min);
/* undo moves */
if (Enc->bp_left2!=0) do_move(str->structure, -Enc->bp_left2, -Enc->bp_right2);
do_move(str->structure, -Enc->bp_left, -Enc->bp_right);
str->energy = last_en;
Enc->bp_left=0;
Enc->bp_right=0;
Enc->bp_left2=0;
Enc->bp_right2=0;
return (end?1:0);
}
if (Enc->verbose_lvl>1) { fprintf(stderr, " "); print_str(stderr, str->structure); fprintf(stderr, " %d\n", tmp_en); }
/* better deepest*/
if (tmp_en < min->energy) {
min->energy = tmp_en;
copy_arr(min->structure, str->structure);
/* delete degeneracy*/
free_degen(Enc);
/* undo moves*/
if (Enc->bp_left2!=0) do_move(str->structure, -Enc->bp_left2, -Enc->bp_right2);
do_move(str->structure, -Enc->bp_left, -Enc->bp_right);
str->energy = last_en;
Enc->bp_left=0;
Enc->bp_right=0;
Enc->bp_left2=0;
Enc->bp_right2=0;
return 1;
}
/* degeneracy*/
if ((str->energy == min->energy) && (Enc->current_en == min->energy)) {
int found = 0;
int i;
for (i=Enc->begin_pr; i<Enc->end_pr; i++) {
if (equals(Enc->processed[i], str->structure)) {
found = 1;
break;
}
}
for (i=Enc->begin_unpr; !found && i<Enc->end_unpr; i++) {
if (equals(Enc->unprocessed[i], str->structure)) {
found = 1;
break;
}
}
if (!found) {
/* print_stren(stderr, str); // fprintf(stderr, " %6.2f\n", str->energy); */
Enc->unprocessed[Enc->end_unpr]=allocopy(str->structure);
Enc->end_unpr++;
}
}
/* undo moves*/
if (Enc->bp_left2!=0) do_move(str->structure, -Enc->bp_left2, -Enc->bp_right2);
do_move(str->structure, -Enc->bp_left, -Enc->bp_right);
str->energy = last_en;
Enc->bp_left=0;
Enc->bp_right=0;
Enc->bp_left2=0;
Enc->bp_right2=0;
return 0;
}
// move to deepest (or first) neighbour
int move_set(encoded &enc, int &deepest, degen °)
{
// count how many times called
cnt_move++;
// count better neighbours
int cnt = 0;
// deepest descent
deg.current = deepest;
short *min_pt = allocopy(enc.pt);
if (deg.opt->verbose_lvl>3) fprintf(stderr, "\n start of MS:\n %s %d\n\n", pt_to_str(enc.pt).c_str(), deepest);
// if using first dont do all of them
bool end = false;
// insertions
if (!end) cnt += insertions(enc, deepest, min_pt, deg, deg.opt->verbose_lvl>3);
if (deg.opt->first && cnt>0) end = true;
fprintf(stderr, "\n");
// deletions
if (!end) cnt += deletions(enc, deepest, min_pt, deg, deg.opt->verbose_lvl>3);
if (deg.opt->first && cnt>0) end = true;
fprintf(stderr, "\n");
// shifts (only if enabled + noLP disabled)
if (!end && deg.opt->shift && !deg.opt->noLP) {
cnt += shifts(enc, deepest, min_pt, deg, deg.opt->verbose_lvl>3);
if (deg.opt->first && cnt>0) end = true;
}
if (deg.opt->verbose_lvl>3) fprintf(stderr, "\n %s\n %s\n", enc.seq, pt_to_str(min_pt).c_str());
// if degeneracy occurs, solve it!
if (!end && deg.unprocessed.size()>0) {
deg.processed.insert(allocopy(enc.pt));
// take first
if (enc.pt) free(enc.pt);
enc.pt = (*deg.unprocessed.begin());
deg.unprocessed.erase(deg.unprocessed.begin());
if (deg.opt->minh>0.1001) {
deepest = energy_of_structure_pt(enc.seq, enc.pt, enc.s0, enc.s1, 0);
}
cnt += move_set(enc, deepest, deg);
} else {
copy_arr(enc.pt, min_pt);
}
free(min_pt);
// resolve degeneracy in local minima
if (deg.processed.size()>0) {
deg.processed.insert(enc.pt);
enc.pt = *deg.processed.begin();
deg.processed.erase(deg.processed.begin());
erase_set(deg.processed);
}
return cnt;
}
void DSU::ComputeTBD(TBD &pqueue, int maxkeep, int num_threshold, bool outer, bool noLP, bool shifts, bool debug, vector<RNAsaddle> *output_saddles, int conn_neighs, bool no_new)
{
int cnt = 0;
clock_t time_tbd = clock();
// go through all pairs in queue
while (pqueue.size()>0) {
// check time:
double time_secs = ((clock() - time)/(double)CLOCKS_PER_SEC);
if (stop_after && (time_secs > stop_after)) {
fprintf(stderr, "Time threshold reached (%d secs.), processed %d/%d\n", stop_after, cnt, pqueue.size()+cnt);
break;
}
// just visualisation
if (!output_saddles && cnt%100==0) {
double tim = (clock() - time_tbd)/(double)CLOCKS_PER_SEC;
std::pair<int, int> mem = getValue();
//double one = ((sizeof(char)*strlen(seq) + sizeof(short)*strlen(seq)) + sizeof(RNAsaddle)) / 1024.0;
fprintf(stderr, "Finding path: %7d/%7d; Time: %6.2f; Est.:%6.2f Mem.:%6.1fMB VM %6.1fMB PM\n", cnt, pqueue.size()+cnt, tim, tim/(double)cnt*pqueue.size(), mem.first/1024.0, mem.second/1024.0);
}
// apply threshold
if (cnt>num_threshold) {
fprintf(stderr, "Number threshold reached, processed %d/%d\n", cnt, pqueue.size()+cnt);
break;
} else {
cnt++;
}
// get next
TBDentry tbd = pqueue.get_first();
if (tbd.i==-1) {
fprintf(stderr, "Ending the path-finding -- i = %5d ; j = %5d ; fiber = %c ; type = %s \n", tbd.i, tbd.j, tbd.fiber?'Y':'N', type1_str[tbd.type_clust]);
break;
}
// check no-conn
if (conectivity.size() > 0 && !tbd.fiber && conectivity.joint(tbd.i, tbd.j)) continue;
// get path
if (debug) fprintf(stderr, "path between (%3d, %3d) type=%s fiber=%d:\n", tbd.i, tbd.j, type1_str[tbd.type_clust], tbd.fiber);
//2fprintf(stderr, "depth: %d\n%s\n%s\n%s\n", maxkeep, seq, LM[tbd.i].str_ch, LM[tbd.j].str_ch);
if (pknots) {
path_pk *path = get_path_light_pk(seq, LM[tbd.i].structure, LM[tbd.j].structure, maxkeep);
// variables for outer insertion
double max_energy= -1e8;
path_pk *max_path = path;
// variables for inner loops and insertions
// get the length of path for speed up
int length = 0;
for (path_pk *tmp = path; tmp && tmp->structure; tmp++) {
if (max_path->en < tmp->en) max_path = tmp;
length ++;
}
// create vector of known LM numbers on path (where 0 and length-1 are known)
vector<int> lm_numbers(length, -1);
lm_numbers[0] = tbd.i;
lm_numbers[length-1] = tbd.j;
// debug
if (debug) {
for (int i=0; i<length; i++) {
fprintf(stderr, "path[%3d] %s %6.2f\n", i, pt_to_str_pk(path[i].structure).c_str(), path[i].en/100.0);
}
}
// bisect the path and find new LMs:
unsigned int old_size = LM.size();
FindNumbers(0, length-1, path, lm_numbers, shifts, noLP, debug, no_new);
// if we have found new minima and we want to do more than simple reevaluation of path (--conn-neighs>0)
if (LM.size() - old_size > 0 && conn_neighs > 0 && !no_new) {
for (unsigned int j=old_size; j<LM.size(); j++) {
// sort 'em according to Hamming D. and take first "conn_neighs"
multimap<int, int> distances;
for (unsigned int i=0; i<old_size; i++) {
distances.insert(make_pair(HammingDist(LM[i].structure, LM[j].structure), i));
}
int cnt = 0;
int last_hd = -1;
for (auto it=distances.begin(); it!=distances.end(); it++) {
if (cnt > conn_neighs && last_hd != it->first) {
break;
}
pqueue.insert(it->second, j, EXPERIM, false);
cnt++;
last_hd = it->first;
}
}
}
// debug
if (debug) {
int diff = 1;
int last_num = lm_numbers[0];
for (int i=0; i<length; i++) {
fprintf(stderr, "path[%3d]= %4d (%s %6.2f)\n", i, lm_numbers[i], pt_to_str_pk(path[i].structure).c_str(), path[i].en/100.0);
if (lm_numbers[i]!=last_num && lm_numbers[i]!=-1) {
diff++;
last_num=lm_numbers[i];
}
}
histo[length][diff]++;
histo[length][0]++;
}
// now process the array of found numbers:
int last_num = lm_numbers[0];
for (int i=1; i<length; i++) {
if (lm_numbers[i]!=-1 && lm_numbers[i]!=last_num) {
// get the highest saddle in case we traveled through many "-1" saddles:
int j=i-1;
int highest_num = i;
while (j>0) {
// check if not higher saddle:
if (path[highest_num].en < path[j].en) highest_num = j;
// we found first that is not -1
if (lm_numbers[j]!=-1) break;
j--;
}
// save saddle
SDtype typ = (j==i-1?DIRECT:REDUCED);
RNAsaddle saddle(last_num, lm_numbers[i], typ);
saddle.energy = path[highest_num].en;
saddle.str_ch = NULL;
saddle.structure = allocopy(path[highest_num].structure);
bool inserted = InsertUB(saddle, debug);
// ???
if (output_saddles && inserted) {
output_saddles->push_back(saddle);
}
// try to insert new things into TBD:
if ((lm_numbers[i]!=lm_numbers[length-1] || lm_numbers[i-1]!=lm_numbers[0]) && !no_new) {
// check no-conn
if (conectivity.size() > 0) conectivity.union_set(tbd.i, tbd.j);
pqueue.insert(lm_numbers[i-1], lm_numbers[i], NEW_FOUND, true);
}
last_num = lm_numbers[i];
}
}
// insert saddle between outer structures
if (outer) {
RNAsaddle tmp(tbd.i, tbd.j, NOT_SURE);
tmp.energy = en_fltoi(max_energy);
tmp.str_ch = NULL;
tmp.structure = allocopy(max_path->structure);
bool inserted = InsertUB(tmp, debug);
if (output_saddles && inserted) {
output_saddles->push_back(tmp);
}
}
free_path_pk(path);
} else {
//fprintf(stderr, "%s\n%s\n%s\n", seq, LM[tbd.i].str_ch, LM[tbd.j].str_ch);
path_t *path = get_path(seq, LM[tbd.i].str_ch, LM[tbd.j].str_ch, maxkeep);
// variables for outer insertion
double max_energy= -1e8;
path_t *max_path = path;
// variables for inner loops and insertions
// get the length of path for speed up
int length = 0;
for (path_t *tmp = path; tmp && tmp->s; tmp++) {
if (max_path->en < tmp->en) max_path = tmp;
length ++;
}
// create vector of known LM numbers on path (where 0 and length-1 are known)
vector<int> lm_numbers(length, -1);
lm_numbers[0] = tbd.i;
lm_numbers[length-1] = tbd.j;
// bisect the path and find new LMs:
unsigned int old_size = LM.size();
FindNumbers(0, length-1, path, lm_numbers, shifts, noLP, debug, no_new);
// if we have found new minima and we want to do more than simple reevaluation of path (--conn-neighs>0)
if (LM.size() - old_size > 0 && conn_neighs > 0 && !no_new) {
for (unsigned int j=old_size; j<LM.size(); j++) {
// sort 'em according to Hamming D. and take first "conn_neighs"
multimap<int, int> distances;
for (unsigned int i=0; i<old_size; i++) {
distances.insert(make_pair(HammingDist(LM[i].structure, LM[j].structure), i));
}
int cnt = 0;
int last_hd = -1;
for (auto it=distances.begin(); it!=distances.end(); it++) {
if (cnt > conn_neighs && last_hd != it->first) {
break;
}
pqueue.insert(it->second, j, EXPERIM, false);
cnt++;
last_hd = it->first;
}
}
}
// debug
if (debug) {
int diff = 1;
int last_num = lm_numbers[0];
for (int i=0; i<length; i++) {
fprintf(stderr, "path[%3d]= %4d (%s %6.2f)\n", i, lm_numbers[i], path[i].s, path[i].en);
if (lm_numbers[i]!=last_num && lm_numbers[i]!=-1) {
diff++;
last_num=lm_numbers[i];
}
}
histo[length][diff]++;
histo[length][0]++;
}
// now process the array of found numbers:
int last_num = lm_numbers[0];
for (int i=1; i<length; i++) {
if (lm_numbers[i]!=-1 && lm_numbers[i]!=last_num) {
// get the highest saddle in case we traveled through many "-1" saddles:
int j=i-1;
int highest_num = i;
while (j>0) {
// check if not higher saddle:
if (path[highest_num].en < path[j].en) highest_num = j;
// we found first that is not -1
if (lm_numbers[j]!=-1) break;
j--;
}
// save saddle
SDtype typ = (j==i-1?DIRECT:REDUCED);
RNAsaddle saddle(last_num, lm_numbers[i], typ);
saddle.energy = en_fltoi(path[highest_num].en);
saddle.str_ch = NULL;
saddle.structure = make_pair_table(path[highest_num].s);
bool inserted = InsertUB(saddle, debug);
// ???
if (output_saddles && inserted) {
output_saddles->push_back(saddle);
}
// try to insert new things into TBD:
if ((lm_numbers[i]!=lm_numbers[length-1] || lm_numbers[i-1]!=lm_numbers[0]) && !no_new) {
// check no-conn
if (conectivity.size() > 0) conectivity.union_set(tbd.i, tbd.j);
pqueue.insert(lm_numbers[i-1], lm_numbers[i], NEW_FOUND, true);
}
last_num = lm_numbers[i];
}
}
// insert saddle between outer structures
if (outer) {
RNAsaddle tmp(tbd.i, tbd.j, NOT_SURE);
tmp.energy = en_fltoi(max_energy);
tmp.str_ch = NULL;
tmp.structure = make_pair_table(max_path->s);
bool inserted = InsertUB(tmp, debug);
if (output_saddles && inserted) {
output_saddles->push_back(tmp);
}
}
free_path(path);
}
// free stuff
//if (last_str) free(last_str);
} // all doing while
fprintf(stderr, "The end of finding paths(%d). Size of pqueue = %d\n", cnt, (int)pqueue.size());
}
void DSU::FindNumbers(int begin, int end, path_pk *path, vector<int> &lm_numbers, bool shifts, bool noLP, bool debug, bool no_new)
{
// first resolve small case:
if (end-begin<4) {
bool begins = true;
for (int i=begin+1; i<end; i++) {
// get the minimum
short *tmp_str = allocopy(path[i].structure);
int tmp_en;
if (pknots) {
Structure str(seq, tmp_str, s0, s1);
tmp_en = move_gradient_pk(seq, &str, s0, s1, shifts, 0);
copy_arr(tmp_str, str.str);
} else {
tmp_en = move_gradient(seq, tmp_str, s0, s1, 0, shifts, noLP);
}
// speedup
if (lm_numbers[begin] != -1 && begins && tmp_en == LM[lm_numbers[begin]].energy && str_eq(LM[lm_numbers[begin]].structure, tmp_str)) {
lm_numbers[i] = lm_numbers[begin];
} else {
begins = false;
if (lm_numbers[end] != -1 && tmp_en == LM[lm_numbers[end]].energy && str_eq(LM[lm_numbers[end]].structure, tmp_str)) {
lm_numbers[i] = lm_numbers[end];
}
}
if (lm_numbers[i]==-1) {
lm_numbers[i] = FindNum(tmp_en, tmp_str);
// update UBlist
if (lm_numbers[i]==-1 && !no_new) {
if (gl_maxen < tmp_en) {
//fprintf(stderr, "exceeds en.: %s %6.2f\n", pt_to_str(tmp_str).c_str(), tmp_en/100.0);
lm_numbers[i] = AddLMtoTBD(tmp_str, tmp_en, EE_DSU, debug);
} else {
if (debug) fprintf(stderr, "cannot find: %s %6.2f\n", pt_to_str_pk(tmp_str).c_str(), tmp_en/100.0);
// add to list of minima and count with them later...
lm_numbers[i] = AddLMtoTBD(tmp_str, tmp_en, NORM_CF, debug);
}
}
} else debug_c++;
free(tmp_str);
}
return ;
}
// da middle one
int pivot = (end+begin)/2;
short *tmp_str = allocopy(path[pivot].structure);
//fprintf(stderr, "%s\n", pt_to_str(tmp_str).c_str());
int tmp_en;
if (pknots) {
Structure str(seq, tmp_str, s0, s1);
tmp_en = move_gradient_pk(seq, &str, s0, s1, shifts, 0);
copy_arr(tmp_str, str.str);
} else {
tmp_en = move_gradient(seq, tmp_str, s0, s1, 0, shifts, noLP);
}
//fprintf(stderr, "%s\n", pt_to_str(tmp_str).c_str());
// speed up:
if (lm_numbers[begin] != -1 && tmp_en == LM[lm_numbers[begin]].energy && str_eq(LM[lm_numbers[begin]].structure, tmp_str)) {
lm_numbers[pivot] = lm_numbers[begin];
} else {
if (lm_numbers[end] != -1 && tmp_en == LM[lm_numbers[end]].energy && str_eq(LM[lm_numbers[end]].structure, tmp_str)) {
lm_numbers[pivot] = lm_numbers[end];
}
}
// normal behaviour
if (lm_numbers[pivot]==-1) {
lm_numbers[pivot] = FindNum(tmp_en, tmp_str);
// update UBlist
if (lm_numbers[pivot]==-1 && !no_new) {
if (gl_maxen < tmp_en) {
//fprintf(stderr, "exceeds en.: %s %6.2f\n", pt_to_str(tmp_str).c_str(), tmp_en/100.0);
lm_numbers[pivot] = AddLMtoTBD(tmp_str, tmp_en, EE_DSU, debug);
} else {
if (debug) fprintf(stderr, "cannot find: %s %6.2f\n", pt_to_str_pk(tmp_str).c_str(), tmp_en/100.0);
// add to list of minima and count with them later...
lm_numbers[pivot] = AddLMtoTBD(tmp_str, tmp_en, NORM_CF, debug);
}
}
} else debug_c++;
free(tmp_str);
// continue recursion:
if ((lm_numbers[pivot]!=lm_numbers[begin] || lm_numbers[pivot]==-1) && pivot-begin>1) FindNumbers(begin, pivot, path, lm_numbers, shifts, noLP, debug, no_new);
if ((lm_numbers[pivot]!=lm_numbers[end] || lm_numbers[pivot]==-1) && end-pivot>1) FindNumbers(pivot, end, path, lm_numbers, shifts, noLP, debug, no_new);
// return maximal energy
return ;
}
