// 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;
}
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;
}
static void *thread_start (void *arg)
{
struct thread_info *tinfo = (struct thread_info *) arg;
pthread_barrier_wait (tinfo->barrier);
switch (tinfo->action) {
case ACTION_INSERTION:
insertions (tinfo->map, tinfo->size);
break;
case ACTION_REMOVAL:
removals (tinfo->map, tinfo->size);
break;
case ACTION_RETRIEVAL:
retrievals (tinfo->map, tinfo->size);
break;
}
}
/* 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;
}
// 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;
}