RNAlib-2.0.6
H/cofold.h
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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 
00033 float cofold( const char *sequence,
00034               char *structure);
00035 
00036 float cofold_par( const char *string,
00037                   char *structure,
00038                   paramT *parameters,
00039                   int is_constrained);
00040 
00044 void      free_co_arrays(void);
00045 
00049 void      update_cofold_params(void);
00050 
00051 void      update_cofold_params_par(paramT *parameters);
00052 
00063 SOLUTION  *zukersubopt(const char *string);
00064 
00065 SOLUTION  *zukersubopt_par( const char *string,
00066                             paramT *parameters);
00067 
00076 void get_monomere_mfes( float *e1,
00077                         float *e2);
00078 
00093 void export_cofold_arrays(int **f5_p,
00094                           int **c_p,
00095                           int **fML_p,
00096                           int **fM1_p,
00097                           int **fc_p,
00098                           int **indx_p,
00099                           char **ptype_p);
00100 
00105 DEPRECATED(void initialize_cofold(int length));
00106 
00107 #endif