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# /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/part_func_co.h

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    00001 #ifndef __VIENNA_RNA_PACKAGE_PART_FUNC_CO_H__
    00002 #define __VIENNA_RNA_PACKAGE_PART_FUNC_CO_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
    00055 extern int    mirnatog;
    00056
    00060 extern double F_monomer[2];
    00061
    00080 cofoldF co_pf_fold( char *sequence,
    00081                     char *structure);
    00082
    00100 cofoldF co_pf_fold_par( char *sequence,
    00101                         char *structure,
    00102                         pf_paramT *parameters,
    00103                         int calculate_bppm,
    00104                         int is_constrained);
    00105
    00115 FLT_OR_DBL *export_co_bppm(void);
    00116
    00120 void    free_co_pf_arrays(void);
    00121
    00136 void    update_co_pf_params(int length);
    00137
    00157 void    update_co_pf_params_par(int length,
    00158                                 pf_paramT *parameters);
    00159
    00177 void    compute_probabilities(double FAB,
    00178                               double FEA,
    00179                               double FEB,
    00180                               struct plist  *prAB,
    00181                               struct plist  *prA,
    00182                               struct plist  *prB,
    00183                               int Alength);
    00184
    00203 ConcEnt *get_concentrations(double FEAB,
    00204                             double FEAA,
    00205                             double FEBB,
    00206                             double FEA,
    00207                             double FEB,
    00208                             double *startconc);
    00209
    00210
    00215 /*
    00216 #################################################
    00217 # DEPRECATED FUNCTIONS                          #
    00218 #################################################
    00219 */
    00220
    00226 DEPRECATED(plist  *get_plist( struct plist *pl,
    00227                               int length,
    00228                               double cut_off));
    00233 DEPRECATED(void   init_co_pf_fold(int length));
    00234
    00235 #endif