H/cofold.h

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#ifndef __VIENNA_RNA_PACKAGE_COFOLD_H__
#define __VIENNA_RNA_PACKAGE_COFOLD_H__

#include "data_structures.h"

#ifdef __GNUC__
#define DEPRECATED(func) func __attribute__ ((deprecated))
#else
#define DEPRECATED(func) func
#endif

float cofold( const char *sequence,
              char *structure);

float cofold_par( const char *string,
                  char *structure,
                  paramT *parameters,
                  int is_constrained);

void      free_co_arrays(void);

void      update_cofold_params(void);

void      update_cofold_params_par(paramT *parameters);

SOLUTION  *zukersubopt(const char *string);

SOLUTION  *zukersubopt_par( const char *string,
                            paramT *parameters);

void get_monomere_mfes( float *e1,
                        float *e2);

void export_cofold_arrays(int **f5_p,
                          int **c_p,
                          int **fML_p,
                          int **fM1_p,
                          int **fc_p,
                          int **indx_p,
                          char **ptype_p);

DEPRECATED(void initialize_cofold(int length));

#endif

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