fold_compound.h

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#ifndef VIENNA_RNA_PACKAGE_FOLD_COMPOUND_H
#define VIENNA_RNA_PACKAGE_FOLD_COMPOUND_H

typedef struct vrna_fc_s vrna_fold_compound_t;

typedef void (vrna_callback_free_auxdata)(void *data);

typedef void (vrna_callback_recursion_status)(unsigned char status,
                                              void          *data);

#define VRNA_STATUS_MFE_PRE     (unsigned char)1

#define VRNA_STATUS_MFE_POST    (unsigned char)2

#define VRNA_STATUS_PF_PRE      (unsigned char)3

#define VRNA_STATUS_PF_POST     (unsigned char)4


#include <ViennaRNA/model.h>
#include <ViennaRNA/params/basic.h>
#include <ViennaRNA/sequence.h>
#include <ViennaRNA/dp_matrices.h>
#include <ViennaRNA/constraints/hard.h>
#include <ViennaRNA/constraints/soft.h>
#include <ViennaRNA/grammar.h>
#include "ViennaRNA/structured_domains.h"
#include "ViennaRNA/unstructured_domains.h"

typedef enum {
  VRNA_FC_TYPE_SINGLE,      
  VRNA_FC_TYPE_COMPARATIVE  
} vrna_fc_type_e;


struct vrna_fc_s {
  const vrna_fc_type_e type;        
  unsigned int      length;         
  int               cutpoint;       
  unsigned int      *strand_number; 
  unsigned int      *strand_order;  
  unsigned int      *strand_start;  
  unsigned int      *strand_end;    
  unsigned int      strands;
  vrna_seq_t        *nucleotides;
  vrna_msa_t        *alignment;

  vrna_hc_t         *hc;            
  vrna_mx_mfe_t     *matrices;      
  vrna_mx_pf_t      *exp_matrices;  
  vrna_param_t      *params;        
  vrna_exp_param_t  *exp_params;    
  int               *iindx;         
  int               *jindx;         
  vrna_callback_recursion_status  *stat_cb;       
  void                            *auxdata;       
  vrna_callback_free_auxdata      *free_auxdata;  
  /* data structure to adjust additional structural domains, such as G-quadruplexes */
  vrna_sd_t     *domains_struc;             
  /* data structure to adjust additional contributions to unpaired stretches, e.g. due to protein binding */
  vrna_ud_t     *domains_up;                
  /* auxiliary (user-defined) extension to the folding grammar */
  vrna_gr_aux_t *aux_grammar;

#ifndef VRNA_DISABLE_C11_FEATURES
  /* C11 support for unnamed unions/structs */
  union {
    struct {
#endif

      char *sequence;                   
      short *sequence_encoding;         
  short *sequence_encoding2;
      char *ptype;                      
      char *ptype_pf_compat;            
      vrna_sc_t *sc;                    
#ifndef VRNA_DISABLE_C11_FEATURES
  /* C11 support for unnamed unions/structs */
};
struct {
#endif

      char          **sequences;        
      unsigned int  n_seq;              
      char          *cons_seq;          
      short         *S_cons;            
      short         **S;                
      short         **S5;               
      short         **S3;               
  char          **Ss;
  unsigned int  **a2s;
      int           *pscore;              
      int           **pscore_local;       
      short         *pscore_pf_compat;    
      vrna_sc_t     **scs;                
  int           oldAliEn;

#ifndef VRNA_DISABLE_C11_FEATURES
};
};
#endif

  unsigned int  maxD1;            
  unsigned int  maxD2;            
  short         *reference_pt1;   
  short         *reference_pt2;   
  unsigned int  *referenceBPs1;   
  unsigned int  *referenceBPs2;   
  unsigned int  *bpdist;          
  unsigned int  *mm1;             
  unsigned int  *mm2;             
  int   window_size;              
  char  **ptype_local;            
};


/* the definitions below should be used for functions that return/receive/destroy fold compound data structures */

#define VRNA_OPTION_DEFAULT         0U

#define VRNA_OPTION_MFE             1U

#define VRNA_OPTION_PF              2U

#define VRNA_OPTION_HYBRID          4U

#define VRNA_OPTION_EVAL_ONLY       8U

#define VRNA_OPTION_WINDOW          16U

vrna_fold_compound_t *
vrna_fold_compound(const char   *sequence,
                   vrna_md_t    *md_p,
                   unsigned int options);


vrna_fold_compound_t *
vrna_fold_compound_comparative(const char   **sequences,
                               vrna_md_t    *md_p,
                               unsigned int options);


vrna_fold_compound_t *
vrna_fold_compound_comparative2(const char                **sequences,
                                const char                **names,
                                const unsigned char       *orientation,
                                const unsigned long long  *start,
                                const unsigned long long  *genome_size,
                                vrna_md_t                 *md_p,
                                unsigned int              options);


vrna_fold_compound_t *
vrna_fold_compound_TwoD(const char    *sequence,
                        const char    *s1,
                        const char    *s2,
                        vrna_md_t     *md_p,
                        unsigned int  options);


int
vrna_fold_compound_prepare(vrna_fold_compound_t *fc,
                           unsigned int         options);


void
vrna_fold_compound_free(vrna_fold_compound_t *fc);


void
vrna_fold_compound_add_auxdata(vrna_fold_compound_t       *fc,
                               void                       *data,
                               vrna_callback_free_auxdata *f);


void
vrna_fold_compound_add_callback(vrna_fold_compound_t            *fc,
                                vrna_callback_recursion_status  *f);


#endif