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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