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
