fold.h

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#ifndef VIENNA_RNA_PACKAGE_FOLD_H
#define VIENNA_RNA_PACKAGE_FOLD_H

#ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY

#include <ViennaRNA/datastructures/basic.h>
#include <ViennaRNA/params/basic.h>
#include <ViennaRNA/mfe.h>
#include <ViennaRNA/eval.h>

#ifdef VRNA_WARN_DEPRECATED
# if defined(__clang__)
#  define DEPRECATED(func, msg) func __attribute__ ((deprecated("", msg)))
# elif defined(__GNUC__)
#  define DEPRECATED(func, msg) func __attribute__ ((deprecated(msg)))
# else
#  define DEPRECATED(func, msg) func
# endif
#else
# define DEPRECATED(func, msg) func
#endif

DEPRECATED(float
fold_par( const char *sequence,
          char *structure,
          vrna_param_t *parameters,
          int is_constrained,
          int is_circular),
"Use the new API and vrna_mfe() instead");

DEPRECATED(float fold( const char *sequence, char *structure),
"Use vrna_fold() or vrna_mfe() instead");

DEPRECATED(float circfold( const char *sequence, char *structure),
"Use vrna_circfold() or vrna_mfe() instead");


DEPRECATED(void free_arrays(void),
"This function is obsolete");



DEPRECATED(void update_fold_params(void),
"This function is obsolete");

DEPRECATED(void update_fold_params_par(vrna_param_t *parameters),
"Use the new API with vrna_fold_compound_t datastructure instead");

DEPRECATED(void
export_fold_arrays( int **f5_p,
                    int **c_p,
                    int **fML_p,
                    int **fM1_p,
                    int **indx_p,
                    char **ptype_p),
"Use the new API with vrna_fold_compound_t datastructure instead");

DEPRECATED(void
export_fold_arrays_par( int **f5_p,
                        int **c_p,
                        int **fML_p,
                        int **fM1_p,
                        int **indx_p,
                        char **ptype_p,
                        vrna_param_t **P_p),
"Use the new API with vrna_fold_compound_t datastructure instead");

DEPRECATED(void
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),
"Use the new API with vrna_fold_compound_t datastructure instead");

DEPRECATED(void
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),
"Use the new API with vrna_fold_compound_t datastructure instead");



/* finally moved the loop energy function declarations to this header...  */
/* BUT: The functions only exist for backward compatibility reasons!      */
/* You better include "loop_energies.h" and call the functions:           */
/* E_Hairpin() and E_IntLoop() which are (almost) threadsafe as they get  */
/* a pointer to the energy parameter data structure as additional argument */

DEPRECATED(int LoopEnergy(int n1,
                          int n2,
                          int type,
                          int type_2,
                          int si1,
                          int sj1,
                          int sp1,
                          int sq1),
"This function is obsolete");

DEPRECATED(int HairpinE(int size,
                        int type,
                        int si1,
                        int sj1,
                        const char *string),
"Use E_Hairpin() instead");

DEPRECATED(void initialize_fold(int length),
"This function is obsolete");

DEPRECATED(char *backtrack_fold_from_pair(char *sequence,
                                          int i,
                                          int j),
"This function is obsolete. Consider using vrna_backtrack_from_intervals() instead");


#endif

#endif