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# 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