soft.h

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#ifndef VIENNA_RNA_PACKAGE_CONSTRAINTS_SOFT_H
#define VIENNA_RNA_PACKAGE_CONSTRAINTS_SOFT_H

#include <ViennaRNA/datastructures/basic.h>
#include <ViennaRNA/fold_compound.h>
#include <ViennaRNA/constraints/basic.h>

typedef struct  vrna_sc_s vrna_sc_t;

typedef int (vrna_callback_sc_energy)(int           i,
                                      int           j,
                                      int           k,
                                      int           l,
                                      unsigned char d,
                                      void          *data);

typedef FLT_OR_DBL (vrna_callback_sc_exp_energy)(int            i,
                                                 int            j,
                                                 int            k,
                                                 int            l,
                                                 unsigned char  d,
                                                 void           *data);

typedef vrna_basepair_t *(vrna_callback_sc_backtrack)(int           i,
                                                      int           j,
                                                      int           k,
                                                      int           l,
                                                      unsigned char d,
                                                      void          *data);


typedef enum {
  VRNA_SC_DEFAULT,  
  VRNA_SC_WINDOW    
} vrna_sc_type_e;


typedef struct {
  unsigned int interval_start;
  unsigned int interval_end;
  int          e;
} vrna_sc_bp_storage_t;


struct vrna_sc_s {
  vrna_sc_type_e        type;
  unsigned int          n;

  unsigned char         state;

  int                   **energy_up;      
  FLT_OR_DBL            **exp_energy_up;  
  int                   *up_storage;      
  vrna_sc_bp_storage_t  **bp_storage;     
#ifndef VRNA_DISABLE_C11_FEATURES
  /* C11 support for unnamed unions/structs */
  union {
    struct {
#endif
      int *energy_bp;                           
      FLT_OR_DBL *exp_energy_bp;                
#ifndef VRNA_DISABLE_C11_FEATURES
  /* C11 support for unnamed unions/structs */
    };
    struct {
#endif
      int         **energy_bp_local;                    
      FLT_OR_DBL  **exp_energy_bp_local;                
#ifndef VRNA_DISABLE_C11_FEATURES
  /* C11 support for unnamed unions/structs */
    };
  };
#endif

  int                         *energy_stack;      
  FLT_OR_DBL                  *exp_energy_stack;  
  /* generic soft contraints below */
  vrna_callback_sc_energy     *f;     
  vrna_callback_sc_backtrack  *bt;    
  vrna_callback_sc_exp_energy *exp_f; 
  void                        *data;  
  vrna_callback_free_auxdata  *free_data;
};

void vrna_sc_init(vrna_fold_compound_t *vc);


void
vrna_sc_prepare(vrna_fold_compound_t  *vc,
                unsigned int          options);


void
vrna_sc_update(vrna_fold_compound_t *vc,
               unsigned int         i,
               unsigned int         options);


void vrna_sc_set_bp(vrna_fold_compound_t  *vc,
                    const FLT_OR_DBL      **constraints,
                    unsigned int          options);


void vrna_sc_add_bp(vrna_fold_compound_t  *vc,
                    int                   i,
                    int                   j,
                    FLT_OR_DBL            energy,
                    unsigned int          options);


void vrna_sc_set_up(vrna_fold_compound_t  *vc,
                    const FLT_OR_DBL      *constraints,
                    unsigned int          options);


void vrna_sc_add_up(vrna_fold_compound_t  *vc,
                    int                   i,
                    FLT_OR_DBL            energy,
                    unsigned int          options);


void vrna_sc_set_stack(vrna_fold_compound_t *vc,
                       const FLT_OR_DBL     *constraints,
                       unsigned int         options);


void vrna_sc_add_stack(vrna_fold_compound_t *vc,
                       int                  i,
                       FLT_OR_DBL           energy,
                       unsigned int         options);


void vrna_sc_remove(vrna_fold_compound_t *vc);


void vrna_sc_free(vrna_sc_t *sc);


void vrna_sc_add_data(vrna_fold_compound_t        *vc,
                      void                        *data,
                      vrna_callback_free_auxdata  *free_data);


void vrna_sc_add_f(vrna_fold_compound_t     *vc,
                   vrna_callback_sc_energy  *f);


void vrna_sc_add_bt(vrna_fold_compound_t        *vc,
                    vrna_callback_sc_backtrack  *f);


void vrna_sc_add_exp_f(vrna_fold_compound_t         *vc,
                       vrna_callback_sc_exp_energy  *exp_f);


#endif