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00001 /* functions from part_func.c */
00002 /* calculate partition function and base pair probabilities */
00003 #ifndef __VIENNA_RNA_PACKAGE_PART_FUNC_CO_H__
00004 #define __VIENNA_RNA_PACKAGE_PART_FUNC_CO_H__
00005 
00006 #include "data_structures.h"
00007 
00008 #ifdef __GNUC__
00009 #define DEPRECATED(func) func __attribute__ ((deprecated))
00010 #else
00011 #define DEPRECATED(func) func
00012 #endif
00013 
00045 extern int    mirnatog;
00046 
00050 extern double F_monomer[2];
00051 
00063 cofoldF co_pf_fold( char *sequence,
00064                     char *structure);
00065 
00075 FLT_OR_DBL *export_co_bppm(void);
00076 
00080 void    free_co_pf_arrays(void);
00081 
00085 void    update_co_pf_params(int length);
00086 
00104 void    compute_probabilities(double FAB,
00105                               double FEA,
00106                               double FEB,
00107                               struct plist  *prAB,
00108                               struct plist  *prA,
00109                               struct plist  *prB,
00110                               int Alength);
00111 
00130 ConcEnt *get_concentrations(double FEAB,
00131                             double FEAA,
00132                             double FEBB,
00133                             double FEA,
00134                             double FEB,
00135                             double *startconc);
00136 
00137 /*
00138 #################################################
00139 # DEPRECATED FUNCTIONS                          #
00140 #################################################
00141 */
00142 
00148 DEPRECATED(plist  *get_plist( struct plist *pl,
00149                               int length,
00150                               double cut_off));
00155 DEPRECATED(void   init_co_pf_fold(int length));
00156 
00157 #endif