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