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# /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/cofold.h

Go to the documentation of this file.

    00001 #ifndef __VIENNA_RNA_PACKAGE_COFOLD_H__
    00002 #define __VIENNA_RNA_PACKAGE_COFOLD_H__
    00003
    00004 #include "data_structures.h"
    00005
    00006 #ifdef __GNUC__
    00007 #define DEPRECATED(func) func __attribute__ ((deprecated))
    00008 #else
    00009 #define DEPRECATED(func) func
    00010 #endif
    00011
    00065 float cofold( const char *sequence,
    00066               char *structure);
    00067
    00072 float cofold_par( const char *string,
    00073                   char *structure,
    00074                   paramT *parameters,
    00075                   int is_constrained);
    00076
    00080 void      free_co_arrays(void);
    00081
    00085 void      update_cofold_params(void);
    00086
    00087 void      update_cofold_params_par(paramT *parameters);
    00088
    00089
    00105 void export_cofold_arrays_gq( int **f5_p,
    00106                               int **c_p,
    00107                               int **fML_p,
    00108                               int **fM1_p,
    00109                               int **fc_p,
    00110                               int **ggg_p,
    00111                               int **indx_p,
    00112                               char **ptype_p);
    00113
    00128 void export_cofold_arrays(int **f5_p,
    00129                           int **c_p,
    00130                           int **fML_p,
    00131                           int **fM1_p,
    00132                           int **fc_p,
    00133                           int **indx_p,
    00134                           char **ptype_p);
    00135
    00136
    00153 SOLUTION  *zukersubopt(const char *string);
    00154
    00161 SOLUTION  *zukersubopt_par( const char *string,
    00162                             paramT *parameters);
    00163
    00172 void get_monomere_mfes( float *e1,
    00173                         float *e2);
    00174
    00175
    00180 DEPRECATED(void initialize_cofold(int length));
    00181
    00182 #endif