Global alipf_fold_par (const char **sequences, char *structure, vrna_plist_t **pl, vrna_exp_param_t *parameters, int calculate_bppm, int is_constrained, int is_circular)
Usage of this function is discouraged! The new vrna_fold_compound_t allows direct access to the folding matrices, including the pair probabilities! The pair probability array returned here reflects the one of the latest call to vrna_pf(), or any of the old API calls for consensus structure partition function folding.
Global export_circfold_arrays (int *Fc_p, int *FcH_p, int *FcI_p, int *FcM_p, int **fM2_p, int **f5_p, int **c_p, int **fML_p, int **fM1_p, int **indx_p, char **ptype_p)
Global export_circfold_arrays_par (int *Fc_p, int *FcH_p, int *FcI_p, int *FcM_p, int **fM2_p, int **f5_p, int **c_p, int **fML_p, int **fM1_p, int **indx_p, char **ptype_p, vrna_param_t **P_p)
This function is deprecated and will be removed soon! The base pair probability array is available through the vrna_fold_compound_t data structure, and its associated vrna_mx_pf_t member.
Global export_cofold_arrays (int **f5_p, int **c_p, int **fML_p, int **fM1_p, int **fc_p, int **indx_p, char **ptype_p)
folding matrices now reside within the vrna_fold_compound_t. Thus, this function will only work in conjunction with a prior call to the deprecated functions cofold() or cofold_par()
Global export_cofold_arrays_gq (int **f5_p, int **c_p, int **fML_p, int **fM1_p, int **fc_p, int **ggg_p, int **indx_p, char **ptype_p)
folding matrices now reside within the fold compound. Thus, this function will only work in conjunction with a prior call to cofold() or cofold_par()
Global export_fold_arrays (int **f5_p, int **c_p, int **fML_p, int **fM1_p, int **indx_p, char **ptype_p)
Usage of this function is discouraged! It only affects memory being free'd that was allocated by an old API function before. Release of memory occupied by the newly introduced vrna_fold_compound_t is handled by vrna_vrna_fold_compound_free()
Usage of this function is discouraged! This function only free's memory allocated by old API function calls. Memory allocated by any of the new API calls (starting with vrna_) will be not affected!
See vrna_fold_compound_t and its related functions for how to free memory occupied by the dynamic programming matrices
Global get_alipf_arrays (short ***S_p, short ***S5_p, short ***S3_p, unsigned short ***a2s_p, char ***Ss_p, FLT_OR_DBL **qb_p, FLT_OR_DBL **qm_p, FLT_OR_DBL **q1k_p, FLT_OR_DBL **qln_p, int **pscore)
It is discouraged to use this function! The new vrna_fold_compound_t allows direct access to all necessary consensus structure prediction related variables!
Usage of this function is discouraged! The new API uses vrna_fold_compound_t to lump all folding related necessities together, including the energy parameters. Use vrna_update_fold_params() to update the energy parameters within a vrna_fold_compound_t.