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.);
}
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 vrna_fold_compound_t *
vrna_fold_compound_comparative( const char **sequences,
vrna_md_t *md_p,
unsigned int options){
int s, n_seq, length;
vrna_fold_compound_t *vc;
vrna_md_t md;
unsigned int aux_options;
aux_options = 0L;
if(sequences == NULL) return NULL;
for(s=0;sequences[s];s++); /* count the sequences */
n_seq = s;
length = strlen(sequences[0]);
/* sanity check */
if(length == 0)
vrna_message_error("vrna_fold_compound_comparative: sequence length must be greater 0");
for(s = 0; s < n_seq; s++)
if(strlen(sequences[s]) != length)
vrna_message_error("vrna_fold_compound_comparative: uneqal sequence lengths in alignment");
vc = vrna_alloc(sizeof(vrna_fold_compound_t));
vc->type = VRNA_VC_TYPE_ALIGNMENT;
vc->n_seq = n_seq;
vc->length = length;
vc->sequences = vrna_alloc(sizeof(char *) * (vc->n_seq + 1));
for(s = 0; sequences[s]; s++)
vc->sequences[s] = strdup(sequences[s]);
/* get a copy of the model details */
if(md_p)
md = *md_p;
else /* this fallback relies on global parameters and thus is not threadsafe */
vrna_md_set_default(&md);
aux_options |= WITH_PTYPE;
if(options & VRNA_OPTION_PF)
aux_options |= WITH_PTYPE_COMPAT;
set_fold_compound(vc, &md, options, aux_options);
make_pscores(vc);
if(!(options & VRNA_OPTION_EVAL_ONLY)){
/* add default hard constraints */
vrna_hc_init(vc);
/* add DP matrices (if required) */
vrna_mx_add(vc, VRNA_MX_DEFAULT, options);
}
return vc;
}