PRIVATE float
wrap_pf_fold( const char *sequence,
char *structure,
vrna_exp_param_t *parameters,
int calculate_bppm,
int is_constrained,
int is_circular){
vrna_fold_compound_t *vc;
vrna_md_t md;
vc = NULL;
/* we need vrna_exp_param_t datastructure to correctly init default hard constraints */
if(parameters)
md = parameters->model_details;
else{
set_model_details(&md); /* get global default parameters */
}
md.circ = is_circular;
md.compute_bpp = calculate_bppm;
vc = vrna_fold_compound(sequence, &md, VRNA_OPTION_DEFAULT);
/* prepare exp_params and set global pf_scale */
vc->exp_params = vrna_exp_params(&md);
vc->exp_params->pf_scale = pf_scale;
if(is_constrained && structure){
unsigned int constraint_options = 0;
constraint_options |= VRNA_CONSTRAINT_DB
| VRNA_CONSTRAINT_DB_PIPE
| VRNA_CONSTRAINT_DB_DOT
| VRNA_CONSTRAINT_DB_X
| VRNA_CONSTRAINT_DB_ANG_BRACK
| VRNA_CONSTRAINT_DB_RND_BRACK;
vrna_constraints_add(vc, (const char *)structure, constraint_options);
}
if(backward_compat_compound && backward_compat)
vrna_fold_compound_free(backward_compat_compound);
backward_compat_compound = vc;
backward_compat = 1;
iindx = backward_compat_compound->iindx;
return vrna_pf(vc, structure);
}
PRIVATE void
add_params( vrna_fold_compound_t *vc,
vrna_md_t *md_p,
unsigned int options){
/* ALWAYS add regular energy parameters */
vc->params = vrna_params(md_p);
if(options & VRNA_OPTION_PF){
vc->exp_params = (vc->type == VRNA_VC_TYPE_SINGLE) ? \
vrna_exp_params(md_p) : \
vrna_exp_params_comparative(vc->n_seq, md_p);
}
}
PUBLIC int
vrna_fold_compound_prepare( vrna_fold_compound_t *vc,
unsigned int options){
int ret = 1; /* success */
if(options & VRNA_OPTION_MFE){ /* prepare for MFE computation */
switch(vc->type){
case VRNA_VC_TYPE_SINGLE: if(!vc->ptype)
vc->ptype = vrna_ptypes(vc->sequence_encoding2,
&(vc->params->model_details));
break;
case VRNA_VC_TYPE_ALIGNMENT: break;
default: break;
}
if(options & VRNA_OPTION_WINDOW){ /* Windowing approach, a.k.a. locally optimal */
/* check whether we have the correct DP matrices attached, and if there is
enough memory allocated
*/
if(!vc->matrices || (vc->matrices->type != VRNA_MX_WINDOW) || (vc->matrices->length < vc->length)){
/* here we simply pass '0' as options, since we call mx_mfe_add() explicitely */
vrna_mx_mfe_add(vc, VRNA_MX_WINDOW, options);
}
} else { /* default is regular MFE */
/* check whether we have the correct DP matrices attached, and if there is
enough memory allocated
*/
if(!vc->matrices || (vc->matrices->type != VRNA_MX_DEFAULT) || (vc->matrices->length < vc->length)){
vrna_mx_mfe_add(vc, VRNA_MX_DEFAULT, options);
}
}
}
if(options & VRNA_OPTION_PF){ /* prepare for partition function computation */
switch(vc->type){
case VRNA_VC_TYPE_SINGLE: /* get pre-computed Boltzmann factors if not present*/
if(!vc->exp_params)
vc->exp_params = vrna_exp_params(&(vc->params->model_details));
if(!vc->ptype)
vc->ptype = vrna_ptypes(vc->sequence_encoding2, &(vc->exp_params->model_details));
#ifdef VRNA_BACKWARD_COMPAT
/* backward compatibility ptypes */
if(!vc->ptype_pf_compat)
vc->ptype_pf_compat = get_ptypes(vc->sequence_encoding2, &(vc->exp_params->model_details), 1);
#endif
/* get precomputed Boltzmann factors for soft-constraints (if any) */
if(vc->sc){
if(!vc->sc->exp_energy_up)
vrna_sc_add_up(vc, NULL, VRNA_OPTION_PF);
if(!vc->sc->exp_energy_bp)
vrna_sc_add_bp(vc, NULL, VRNA_OPTION_PF);
if(!vc->sc->exp_energy_stack)
vrna_sc_add_SHAPE_deigan(vc, NULL, 0, 0, VRNA_OPTION_PF);
}
break;
case VRNA_VC_TYPE_ALIGNMENT: /* get pre-computed Boltzmann factors if not present*/
if(!vc->exp_params)
vc->exp_params = vrna_exp_params_comparative(vc->n_seq, &(vc->params->model_details));
break;
default: break;
}
/* Add DP matrices, if not they are not present */
if(!vc->exp_matrices || (vc->exp_matrices->type != VRNA_MX_DEFAULT) || (vc->exp_matrices->length < vc->length)){
vrna_mx_pf_add(vc, VRNA_MX_DEFAULT, options);
}
}
return ret;
}
int main(int argc, char *argv[]){
struct ct2db_args_info args_info;
char *line = NULL;
int pkfree = 0;
int verbose = 0;
char *seq = NULL;
char *structure = NULL;
plist *pairs = NULL;
int num_pairs = 0;
unsigned int seq_pos = 0;
unsigned int length = 0;
/*
#############################################
# check the command line prameters
#############################################
*/
if(ct2db_cmdline_parser (argc, argv, &args_info) != 0) exit(1);
/* remove Pseudknots? */
if(args_info.removePK_given)
pkfree = 1;
/* be verbose ? */
if(args_info.verbose_given)
verbose = 1;
/* free allocated memory of command line data structure */
ct2db_cmdline_parser_free (&args_info);
do{
if ((line = get_line(stdin))==NULL) break;
/* skip comment lines */
while ((*line=='*')||(*line=='\0')||(*line=='>')||(*line=='#')) {
free(line);
if ((line = get_line(stdin))==NULL) break;
}
if ((line ==NULL) || (strcmp(line, "@") == 0)) break;
if(length != 0){
if(!seq){
/*
printf("sequence length: %u\n", length);
*/
seq = (char *)vrna_alloc(sizeof(char) * (length + 1));
pairs = (plist *)vrna_alloc(sizeof(plist) * (2*length));
}
}
char *ptr, c;
int row = 0;
long int curr_int = -1;
long int last_int = -1;
int i = -1;
int j = -1;
ptr = strtok(line, " \t");
while(ptr != NULL){
/*
printf("%d. %s\n", row, ptr);
*/
char* end;
curr_int = strtol(ptr, &end, 10);
if(*end) curr_int = -1; /* not read an int */
switch(row){
case 0: if( curr_int != -1)
i = (int) curr_int;
break;
case 4: if( curr_int != -1 )
if((i != -1) && (curr_int > i)){
j = curr_int;
pairs[num_pairs].i = i;
pairs[num_pairs].j = j;
pairs[num_pairs].p = 1.;
pairs[num_pairs++].type = 0;
}
break;
case 1: if(sscanf(ptr, "%c", &c)){
switch(c){
case 'E': if(!strcmp("ENERGY", ptr)){
if(last_int != -1)
length = (unsigned int)last_int;
}
break;
case 'A':
case 'U':
case 'T':
case 'C':
case 'G': if(seq_pos < length){
seq[seq_pos++] = c;
}
break;
default: break;
}
}
break;
default: break;
}
ptr = strtok(NULL, " \t");
if(curr_int != -1)
last_int = curr_int;
row++;
}
free(line);
} while(1);
if(seq){
pairs = vrna_realloc(pairs, sizeof(plist) * (num_pairs+1));
pairs[num_pairs].i = 0;
pairs[num_pairs].j = 0;
pairs[num_pairs].p = 0.;
pairs[num_pairs].type = 0;
/*
plist *p = pairs;
for(p = pairs; (*p).i; p++)
printf("pair (%d,%d)\n", (*p).i, (*p).j);
*/
if(pkfree){
float mea, MEAgamma;
MEAgamma = 2.0;
vrna_exp_param_t *params = vrna_exp_params(NULL);
structure = (char *)vrna_alloc(sizeof(char) * (length + 1));
strcpy(structure, seq);
mea = MEA_seq(pairs, seq, structure, MEAgamma, params);
char *structure_tmp = vrna_db_from_plist(pairs, length);
int d = vrna_bp_distance((const char *)structure, (const char *)structure_tmp);
if(verbose && (d > 0))
fprintf(stderr, "removed %d pairs from pseudoknotted structure\n", d);
free(structure_tmp);
free(params);
} else {
structure = vrna_db_from_plist(pairs, length);
}
printf("%s\n%s\n", seq, structure);
free(pairs);
free(seq);
}
return(EXIT_SUCCESS);
}
