PUBLIC float alifold(const char **strings, char *structure){
int length, energy, s, n_seq;
circular = 0;
length = (int) strlen(strings[0]);
#ifdef _OPENMP
/* always init everything since all global static variables are uninitialized when entering a thread */
init_alifold(length);
#else
if (length>init_length) init_alifold(length);
#endif
if (fabs(P->temperature - temperature)>1e-6) update_alifold_params();
for (s=0; strings[s]!=NULL; s++);
n_seq = s;
alloc_sequence_arrays(strings, &S, &S5, &S3, &a2s, &Ss, circular);
make_pscores((const short **) S, strings, n_seq, structure);
energy = fill_arrays((const char **)strings);
backtrack((const char **)strings, 0);
#ifdef PAREN
parenthesis_structure(structure, base_pair2, length);
#else
letter_structure(structure, base_pair2, length);
#endif
/*
* Backward compatibility:
* This block may be removed if deprecated functions
* relying on the global variable "base_pair" vanishs from within the package!
*/
base_pair = base_pair2;
/*
{
if(base_pair) free(base_pair);
base_pair = (bondT *)space(sizeof(bondT) * (1+length/2));
memcpy(base_pair, base_pair2, sizeof(bondT) * (1+length/2));
}
*/
free_sequence_arrays(n_seq, &S, &S5, &S3, &a2s, &Ss);
if (backtrack_type=='C')
return (float) c[indx[length]+1]/(n_seq*100.);
else if (backtrack_type=='M')
return (float) fML[indx[length]+1]/(n_seq*100.);
else
return (float) f5[length]/(n_seq*100.);
}
PUBLIC float alifold(const char **strings, char *structure){
int length, energy, s, n_seq;
circ = 0;
length = (int) strlen(strings[0]);
if (length>init_length) init_alifold(length);
if ((P==NULL)||(fabs(P->temperature - temperature)>1e-6)) {
update_fold_params(); P = scale_parameters();
}
for (s=0; strings[s]!=NULL; s++);
n_seq = s;
alloc_sequence_arrays(strings, &S, &S5, &S3, &a2s, &Ss, circ);
make_pscores((const short **) S, strings, n_seq, structure);
energy = fill_arrays((const char **)strings);
backtrack((const char **)strings, 0);
parenthesis_structure(structure, length);
free_sequence_arrays(n_seq, &S, &S5, &S3, &a2s, &Ss);
if (backtrack_type=='C')
return (float) c[indx[length]+1]/(n_seq*100.);
else if (backtrack_type=='M')
return (float) fML[indx[length]+1]/(n_seq*100.);
else
return (float) f5[length]/(n_seq*100.);
}