PUBLIC int
move_standard(char *seq,
char *struc,
enum MOVE_TYPE type,
int verbosity_level,
int shifts,
int noLP){
make_pair_matrix();
short int *s0 = encode_sequence(seq, 0);
short int *s1 = encode_sequence(seq, 1);
short int *str = vrna_ptable(struc);
int energy = 0;
switch (type){
case GRADIENT: energy = move_gradient(seq, str, s0, s1, verbosity_level, shifts, noLP); break;
case FIRST: energy = move_first(seq, str, s0, s1, verbosity_level, shifts, noLP); break;
case ADAPTIVE: energy = move_adaptive(seq, str, s0, s1, verbosity_level); break;
}
int i=1;
for (; i<=str[0]; i++) {
if (str[i]==0) struc[i-1]='.';
else if (str[i]>str[str[i]]) struc[i-1]='(';
else struc[i-1]=')';
}
free(s0);
free(s1);
free(str);
return energy;
}
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 ;
}