part_func_co.h

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#ifndef VIENNA_RNA_PACKAGE_PART_FUNC_CO_H
#define VIENNA_RNA_PACKAGE_PART_FUNC_CO_H

#include <ViennaRNA/data_structures.h>
#include <ViennaRNA/params.h>

#ifdef __GNUC__
#define DEPRECATED(func) func __attribute__ ((deprecated))
#else
#define DEPRECATED(func) func
#endif

extern int    mirnatog;

extern double F_monomer[2];

cofoldF vrna_co_pf_fold(vrna_fold_compound *vc,
                        char *structure);

void  vrna_co_pf_dimer_probs( double FAB,
                              double FA,
                              double FB,
                              struct plist *prAB,
                              const plist *prA,
                              const plist *prB,
                              int Alength,
                              const vrna_exp_param_t *exp_params);

ConcEnt *vrna_co_pf_get_concentrations( double FcAB,
                                        double FcAA,
                                        double FcBB,
                                        double FEA,
                                        double FEB,
                                        const double *startconc,
                                        const vrna_exp_param_t *exp_params);

/*
#################################################
# DEPRECATED FUNCTIONS                          #
#################################################
*/

DEPRECATED(cofoldF co_pf_fold( char *sequence, char *structure));

DEPRECATED(cofoldF co_pf_fold_par(char *sequence, char *structure, vrna_exp_param_t *parameters, int calculate_bppm, int is_constrained));

DEPRECATED(plist  *get_plist( struct plist *pl,
                              int length,
                              double cut_off));

DEPRECATED(void compute_probabilities(double FAB, double FEA, double FEB, struct plist  *prAB, struct plist  *prA, struct plist  *prB, int Alength));

DEPRECATED(ConcEnt *get_concentrations(double FEAB, double FEAA, double FEBB, double FEA, double FEB, double *startconc));

DEPRECATED(void   init_co_pf_fold(int length));

DEPRECATED(FLT_OR_DBL *export_co_bppm(void));

DEPRECATED(void free_co_pf_arrays(void));

DEPRECATED(void update_co_pf_params(int length));

DEPRECATED(void update_co_pf_params_par(int length, vrna_exp_param_t *parameters));

#endif