model.h

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#ifndef VIENNA_RNA_PACKAGE_MODEL_H
#define VIENNA_RNA_PACKAGE_MODEL_H

#ifndef NBASES
#define NBASES 8
#endif

typedef struct vrna_md_s vrna_md_t;

#define VRNA_MODEL_DEFAULT_TEMPERATURE    37.0

#define VRNA_MODEL_DEFAULT_PF_SCALE       -1

#define VRNA_MODEL_DEFAULT_BETA_SCALE     1.

#define VRNA_MODEL_DEFAULT_DANGLES        2

#define VRNA_MODEL_DEFAULT_SPECIAL_HP     1

#define VRNA_MODEL_DEFAULT_NO_LP          0

#define VRNA_MODEL_DEFAULT_NO_GU          0

#define VRNA_MODEL_DEFAULT_NO_GU_CLOSURE  0

#define VRNA_MODEL_DEFAULT_CIRC           0

#define VRNA_MODEL_DEFAULT_GQUAD          0

#define VRNA_MODEL_DEFAULT_UNIQ_ML        0

#define VRNA_MODEL_DEFAULT_ENERGY_SET     0

#define VRNA_MODEL_DEFAULT_BACKTRACK      1

#define VRNA_MODEL_DEFAULT_BACKTRACK_TYPE 'F'

#define VRNA_MODEL_DEFAULT_COMPUTE_BPP    1

#define VRNA_MODEL_DEFAULT_MAX_BP_SPAN    -1

#define VRNA_MODEL_DEFAULT_WINDOW_SIZE    -1

#define VRNA_MODEL_DEFAULT_LOG_ML         0

#define VRNA_MODEL_DEFAULT_ALI_OLD_EN     0

#define VRNA_MODEL_DEFAULT_ALI_RIBO       0

#define VRNA_MODEL_DEFAULT_ALI_CV_FACT    1.

#define VRNA_MODEL_DEFAULT_ALI_NC_FACT    1.


#define VRNA_MODEL_DEFAULT_PF_SMOOTH      1


#ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY

#ifndef MAXALPHA

#define MAXALPHA              20
#endif

#endif

struct vrna_md_s {
  double  temperature;                      
  double  betaScale;                        
  int     pf_smooth;                        
  int     dangles;                          
  int     special_hp;                       
  int     noLP;                             
  int     noGU;                             
  int     noGUclosure;                      
  int     logML;                            
  int     circ;                             
  int     gquad;                            
  int     uniq_ML;                          
  int     energy_set;                       
  int     backtrack;                        
  char    backtrack_type;                   
  int     compute_bpp;                      
  char    nonstandards[64];                 
  int     max_bp_span;                      
  int     min_loop_size;                    
  int     window_size;                      
  int     oldAliEn;                         
  int     ribo;                             
  double  cv_fact;                          
  double  nc_fact;                          
  double  sfact;                            
  int     rtype[8];                         
  short   alias[MAXALPHA + 1];              
  int     pair[MAXALPHA + 1][MAXALPHA + 1]; 
};


void
vrna_md_set_default(vrna_md_t *md);


void
vrna_md_update(vrna_md_t *md);


vrna_md_t *
vrna_md_copy(vrna_md_t        *md_to,
             const vrna_md_t  *md_from);


char *
vrna_md_option_string(vrna_md_t *md);


void
vrna_md_set_nonstandards(vrna_md_t  *md,
                         const char *ns_bases);


void
vrna_md_defaults_reset(vrna_md_t *md_p);


void
vrna_md_defaults_temperature(double T);


double
vrna_md_defaults_temperature_get(void);


void
vrna_md_defaults_betaScale(double b);


double
vrna_md_defaults_betaScale_get(void);


void
vrna_md_defaults_pf_smooth(int s);


int
vrna_md_defaults_pf_smooth_get(void);


void
vrna_md_defaults_dangles(int d);


int
vrna_md_defaults_dangles_get(void);


void
vrna_md_defaults_special_hp(int flag);


int
vrna_md_defaults_special_hp_get(void);


void
vrna_md_defaults_noLP(int flag);


int
vrna_md_defaults_noLP_get(void);


void
vrna_md_defaults_noGU(int flag);


int
vrna_md_defaults_noGU_get(void);


void
vrna_md_defaults_noGUclosure(int flag);


int
vrna_md_defaults_noGUclosure_get(void);


void
vrna_md_defaults_logML(int flag);


int
vrna_md_defaults_logML_get(void);


void
vrna_md_defaults_circ(int flag);


int
vrna_md_defaults_circ_get(void);


void
vrna_md_defaults_gquad(int flag);


int
vrna_md_defaults_gquad_get(void);


void
vrna_md_defaults_uniq_ML(int flag);


int
vrna_md_defaults_uniq_ML_get(void);


void
vrna_md_defaults_energy_set(int e);


int
vrna_md_defaults_energy_set_get(void);


void
vrna_md_defaults_backtrack(int flag);


int
vrna_md_defaults_backtrack_get(void);


void
vrna_md_defaults_backtrack_type(char t);


char
vrna_md_defaults_backtrack_type_get(void);


void
vrna_md_defaults_compute_bpp(int flag);


int
vrna_md_defaults_compute_bpp_get(void);


void
vrna_md_defaults_max_bp_span(int span);


int
vrna_md_defaults_max_bp_span_get(void);


void
vrna_md_defaults_min_loop_size(int size);


int
vrna_md_defaults_min_loop_size_get(void);


void
vrna_md_defaults_window_size(int size);


int
vrna_md_defaults_window_size_get(void);


void
vrna_md_defaults_oldAliEn(int flag);


int
vrna_md_defaults_oldAliEn_get(void);


void
vrna_md_defaults_ribo(int flag);


int
vrna_md_defaults_ribo_get(void);


void
vrna_md_defaults_cv_fact(double factor);


double
vrna_md_defaults_cv_fact_get(void);


void
vrna_md_defaults_nc_fact(double factor);


double
vrna_md_defaults_nc_fact_get(void);


void
vrna_md_defaults_sfact(double factor);


double
vrna_md_defaults_sfact_get(void);


#ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY

#define model_detailsT        vrna_md_t               /* restore compatibility of struct rename */

/* BEGIN deprecated global variables: */

extern double temperature;

extern double pf_scale;

extern int dangles;

extern int tetra_loop;

extern int  noLonelyPairs;

extern int  noGU;

extern int  no_closingGU;

extern int  circ;

extern int  gquad;

extern int  uniq_ML;

extern int energy_set;

extern int do_backtrack;

extern char backtrack_type;

extern char *nonstandards;

extern int    max_bp_span;

extern int    oldAliEn;

extern int    ribo;

extern double cv_fact;

extern double nc_fact;

extern int    logML;

/* END deprecated global variables: */

void
set_model_details(vrna_md_t *md);


char *
option_string(void);


#endif

#endif