RNAlib-2.1.9
cofold.h
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1 #ifndef __VIENNA_RNA_PACKAGE_COFOLD_H__
2 #define __VIENNA_RNA_PACKAGE_COFOLD_H__
3 
4 #include "data_structures.h"
5 
6 #ifdef __GNUC__
7 #define DEPRECATED(func) func __attribute__ ((deprecated))
8 #else
9 #define DEPRECATED(func) func
10 #endif
11 
65 float cofold( const char *sequence,
66  char *structure);
67 
72 float cofold_par( const char *string,
73  char *structure,
74  paramT *parameters,
75  int is_constrained);
76 
80 void free_co_arrays(void);
81 
85 void update_cofold_params(void);
86 
87 void update_cofold_params_par(paramT *parameters);
88 
89 
105 void export_cofold_arrays_gq( int **f5_p,
106  int **c_p,
107  int **fML_p,
108  int **fM1_p,
109  int **fc_p,
110  int **ggg_p,
111  int **indx_p,
112  char **ptype_p);
113 
128 void export_cofold_arrays(int **f5_p,
129  int **c_p,
130  int **fML_p,
131  int **fM1_p,
132  int **fc_p,
133  int **indx_p,
134  char **ptype_p);
135 
136 
153 SOLUTION *zukersubopt(const char *string);
154 
161 SOLUTION *zukersubopt_par( const char *string,
162  paramT *parameters);
163 
172 void get_monomere_mfes( float *e1,
173  float *e2);
174 
175 
180 DEPRECATED(void initialize_cofold(int length));
181 
182 #endif