hard.h

Go to the documentation of this file.

#ifndef VIENNA_RNA_PACKAGE_CONSTRAINTS_HARD_H
#define VIENNA_RNA_PACKAGE_CONSTRAINTS_HARD_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


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

typedef struct  vrna_hc_s vrna_hc_t;

typedef struct vrna_hc_up_s vrna_hc_up_t;

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

#define VRNA_CONSTRAINT_NO_HEADER         0

#define VRNA_CONSTRAINT_DB                16384U

#define VRNA_CONSTRAINT_DB_ENFORCE_BP           32768U

#define VRNA_CONSTRAINT_DB_PIPE              65536U

#define VRNA_CONSTRAINT_DB_DOT               131072U

#define VRNA_CONSTRAINT_DB_X                 262144U

#define VRNA_CONSTRAINT_DB_ANG_BRACK         524288U

#define VRNA_CONSTRAINT_DB_RND_BRACK         1048576U

#define VRNA_CONSTRAINT_DB_INTRAMOL    2097152U

#define VRNA_CONSTRAINT_DB_INTERMOL    4194304U

#define VRNA_CONSTRAINT_DB_GQUAD                8388608U

#define VRNA_CONSTRAINT_DB_CANONICAL_BP         16777216U

#define VRNA_CONSTRAINT_DB_WUSS                 33554432U


#define VRNA_CONSTRAINT_DB_DEFAULT \
  (VRNA_CONSTRAINT_DB \
   | VRNA_CONSTRAINT_DB_PIPE \
   | VRNA_CONSTRAINT_DB_DOT \
   | VRNA_CONSTRAINT_DB_X \
   | VRNA_CONSTRAINT_DB_ANG_BRACK \
   | VRNA_CONSTRAINT_DB_RND_BRACK \
   | VRNA_CONSTRAINT_DB_INTRAMOL \
   | VRNA_CONSTRAINT_DB_INTERMOL \
   | VRNA_CONSTRAINT_DB_GQUAD \
  )

#define VRNA_CONSTRAINT_CONTEXT_EXT_LOOP      (unsigned char)0x01

#define VRNA_CONSTRAINT_CONTEXT_HP_LOOP       (unsigned char)0x02

#define VRNA_CONSTRAINT_CONTEXT_INT_LOOP      (unsigned char)0x04

#define VRNA_CONSTRAINT_CONTEXT_INT_LOOP_ENC  (unsigned char)0x08

#define VRNA_CONSTRAINT_CONTEXT_MB_LOOP       (unsigned char)0x10

#define VRNA_CONSTRAINT_CONTEXT_MB_LOOP_ENC   (unsigned char)0x20

#define VRNA_CONSTRAINT_CONTEXT_ENFORCE       (unsigned char)0x40

#define VRNA_CONSTRAINT_CONTEXT_NO_REMOVE     (unsigned char)0x80


#define VRNA_CONSTRAINT_CONTEXT_NONE          (unsigned char)0

#define VRNA_CONSTRAINT_CONTEXT_CLOSING_LOOPS (unsigned char)(VRNA_CONSTRAINT_CONTEXT_EXT_LOOP | \
                                                              VRNA_CONSTRAINT_CONTEXT_HP_LOOP | \
                                                              VRNA_CONSTRAINT_CONTEXT_INT_LOOP | \
                                                              VRNA_CONSTRAINT_CONTEXT_MB_LOOP)

#define VRNA_CONSTRAINT_CONTEXT_ENCLOSED_LOOPS  (unsigned char)(VRNA_CONSTRAINT_CONTEXT_INT_LOOP_ENC | \
                                                                VRNA_CONSTRAINT_CONTEXT_MB_LOOP_ENC)

#define VRNA_CONSTRAINT_CONTEXT_ALL_LOOPS     (unsigned char)(VRNA_CONSTRAINT_CONTEXT_CLOSING_LOOPS | \
                                                              VRNA_CONSTRAINT_CONTEXT_ENCLOSED_LOOPS)


typedef enum {
  VRNA_HC_DEFAULT,  
  VRNA_HC_WINDOW    
} vrna_hc_type_e;


typedef struct {
  int           interval_start;
  int           interval_end;
  unsigned char loop_type;
  unsigned char replace : 1;
} vrna_hc_bp_storage_t;

struct vrna_hc_s {
  vrna_hc_type_e  type;
  unsigned int    n;

#ifndef VRNA_DISABLE_C11_FEATURES
  /* C11 support for unnamed unions/structs */
  union {
    struct {
#endif
      unsigned char *matrix;     
      unsigned char *mx;
#ifndef VRNA_DISABLE_C11_FEATURES
    };
    struct {
#endif
      unsigned char         **matrix_local;
      unsigned char         *up_storage;
      vrna_hc_bp_storage_t  **bp_storage;
#ifndef VRNA_DISABLE_C11_FEATURES
    };
  };
#endif

  int                         *up_ext;    
  int                         *up_hp;     
  int                         *up_int;    
  int                         *up_ml;     
  vrna_callback_hc_evaluate   *f;         
  void                        *data;      
  vrna_callback_free_auxdata  *free_data; 
};

struct vrna_hc_up_s {
  int position;           
  unsigned char options;  
};

void vrna_message_constraint_options(unsigned int option);


void vrna_message_constraint_options_all(void);


void vrna_hc_init(vrna_fold_compound_t *vc);


void vrna_hc_init_window(vrna_fold_compound_t *vc);


void
vrna_hc_update(vrna_fold_compound_t *fc,
               unsigned int         i);


void vrna_hc_add_up(vrna_fold_compound_t  *vc,
                    int                   i,
                    unsigned char         option);


int
vrna_hc_add_up_batch(vrna_fold_compound_t *vc,
                     vrna_hc_up_t         *constraints);


void vrna_hc_add_bp(vrna_fold_compound_t  *vc,
                    int                   i,
                    int                   j,
                    unsigned char         option);


void vrna_hc_add_bp_nonspecific(vrna_fold_compound_t  *vc,
                                int                   i,
                                int                   d,
                                unsigned char         option);


void vrna_hc_free(vrna_hc_t *hc);


void vrna_hc_add_f(vrna_fold_compound_t       *vc,
                   vrna_callback_hc_evaluate  *f);


void vrna_hc_add_data(vrna_fold_compound_t        *vc,
                      void                        *data,
                      vrna_callback_free_auxdata  *f);


int
vrna_hc_add_from_db(vrna_fold_compound_t  *vc,
                    const char            *constraint,
                    unsigned int          options);


#ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY

DEPRECATED(void print_tty_constraint(unsigned int option),
          "Use vrna_message_constraint_options() instead");

DEPRECATED(void print_tty_constraint_full(void),
          "Use vrna_message_constraint_options_all() instead");

DEPRECATED(void constrain_ptypes(const char   *constraint,
                                 unsigned int length,
                                 char         *ptype,
                                 int          *BP,
                                 int          min_loop_size,
                                 unsigned int idx_type),
          "Use the new API and the hard constraint framework instead");

#endif

#endif