basic.h

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#ifndef VIENNA_RNA_PACKAGE_DATA_STRUCTURES_H
#define VIENNA_RNA_PACKAGE_DATA_STRUCTURES_H

/* below are several convenience typedef's we use throughout the ViennaRNA library */

typedef struct vrna_basepair_s vrna_basepair_t;

typedef struct vrna_elem_prob_s vrna_plist_t;

typedef struct vrna_bp_stack_s vrna_bp_stack_t;

typedef struct vrna_cpair_s vrna_cpair_t;

typedef struct vrna_sect_s vrna_sect_t;

typedef struct vrna_data_linear_s vrna_data_lin_t;

typedef struct vrna_color_s vrna_color_t;

#ifdef  USE_FLOAT_PF
typedef float FLT_OR_DBL;
#else
typedef double FLT_OR_DBL;
#endif


#ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY

/* the following typedefs are for backward compatibility only */

typedef struct vrna_basepair_s PAIR;

typedef struct vrna_elem_prob_s plist;
typedef struct vrna_cpair_s cpair;

typedef struct vrna_sect_s sect;

typedef struct vrna_bp_stack_s bondT;

#endif

#include <ViennaRNA/params/constants.h>
#include <ViennaRNA/fold_compound.h>
#include <ViennaRNA/model.h>
#include <ViennaRNA/params/basic.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"
#include "ViennaRNA/utils/structures.h"

/*
 * ############################################################
 * Here are the type definitions of various datastructures
 * shared among the Vienna RNA Package
 * ############################################################
 */

struct vrna_basepair_s {
  int i;
  int j;
};

struct vrna_cpair_s {
  int   i, j, mfe;
  float p, hue, sat;
  int   type;
};

struct vrna_color_s {
  float hue;
  float sat;
  float bri;
};

struct vrna_data_linear_s {
  unsigned int  position;
  float         value;
  vrna_color_t  color;
};


struct vrna_sect_s {
  int i;
  int j;
  int ml;
};

struct vrna_bp_stack_s {
  unsigned int  i;
  unsigned int  j;
};


/*
 * ############################################################
 * RNAup data structures
 * ############################################################
 */

typedef struct pu_contrib {
  double  **H;    
  double  **I;    
  double  **M;    
  double  **E;    
  int     length; 
  int     w;      
} pu_contrib;

typedef struct interact {
  double  *Pi;      
  double  *Gi;      
  double  Gikjl;    
  double  Gikjl_wo; 
  int     i;        
  int     k;        
  int     j;        
  int     l;        
  int     length;   
} interact;

typedef struct pu_out {
  int     len;        
  int     u_vals;     
  int     contribs;   
  char    **header;   
  double  **u_values; 
} pu_out;

typedef struct constrain {
  int   *indx;
  char  *ptype;
} constrain;

/*
 * ############################################################
 * RNAduplex data structures
 * ############################################################
 */

typedef struct {
  int     i;
  int     j;
  int     end;
  char    *structure;
  double  energy;
  double  energy_backtrack;
  double  opening_backtrack_x;
  double  opening_backtrack_y;
  int     offset;
  double  dG1;
  double  dG2;
  double  ddG;
  int     tb;
  int     te;
  int     qb;
  int     qe;
} duplexT;

/*
 * ############################################################
 * RNAsnoop data structures
 * ############################################################
 */

typedef struct node {
  int         k;
  int         energy;
  struct node *next;
} folden;

typedef struct {
  int   i;
  int   j;
  int   u;
  char  *structure;
  float energy;
  float Duplex_El;
  float Duplex_Er;
  float Loop_E;
  float Loop_D;
  float pscd;
  float psct;
  float pscg;
  float Duplex_Ol;
  float Duplex_Or;
  float Duplex_Ot;
  float fullStemEnergy;
} snoopT;


/*
 * ############################################################
 * PKplex data structures
 * ############################################################
 */

typedef struct dupVar {
  int     i;
  int     j;
  int     end;
  char    *pk_helix;
  char    *structure;
  double  energy;
  int     offset;
  double  dG1;
  double  dG2;
  double  ddG;
  int     tb;
  int     te;
  int     qb;
  int     qe;
  int     inactive;
  int     processed;
} dupVar;

#ifndef VRNA_DISABLE_C11_FEATURES
void vrna_C11_features(void);


#endif

#endif