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# H/part_func.h

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    00001 #ifndef __VIENNA_RNA_PACKAGE_PART_FUNC_H__
    00002 #define __VIENNA_RNA_PACKAGE_PART_FUNC_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
    00012
    00031 extern  int st_back;
    00032
    00033 /*
    00034 #################################################
    00035 # PARTITION FUNCTION COMPUTATION                #
    00036 #################################################
    00037 */
    00038
    00070 float   pf_fold_par(  const char *sequence,
    00071                       char *structure,
    00072                       pf_paramT *parameters,
    00073                       int calculate_bppm,
    00074                       int is_constrained,
    00075                       int is_circular);
    00076
    00104 float   pf_fold(const char *sequence,
    00105                 char *structure);
    00106
    00116 float   pf_circ_fold( const char *sequence,
    00117                       char *structure);
    00118
    00131 char    *pbacktrack(char *sequence);
    00132
    00145 char    *pbacktrack_circ(char *sequence);
    00146
    00159 void  free_pf_arrays(void);
    00160
    00167 void  update_pf_params(int length);
    00168
    00169 void update_pf_params_par(int length, pf_paramT *parameters);
    00170
    00183 FLT_OR_DBL  *export_bppm(void);
    00184
    00185 /*
    00186 #################################################
    00187 # OTHER PARTITION FUNCTION RELATED DECLARATIONS #
    00188 #################################################
    00189 */
    00190
    00208 void  assign_plist_from_pr( plist **pl,
    00209                             FLT_OR_DBL *probs,
    00210                             int length,
    00211                             double cutoff);
    00212
    00229 int get_pf_arrays(short **S_p,
    00230                   short **S1_p,
    00231                   char **ptype_p,
    00232                   FLT_OR_DBL **qb_p,
    00233                   FLT_OR_DBL **qm_p,
    00234                   FLT_OR_DBL **q1k_p,
    00235                   FLT_OR_DBL **qln_p);
    00236
    00240 double get_subseq_F(int i, int j);
    00241
    00257 char  *get_centroid_struct_pl(int length,
    00258                               double *dist,
    00259                               plist *pl);
    00260
    00276 char  *get_centroid_struct_pr(int length,
    00277                               double *dist,
    00278                               FLT_OR_DBL *pr);
    00279
    00290 double  mean_bp_distance(int length);
    00291
    00307 double  mean_bp_distance_pr(int length,
    00308                             FLT_OR_DBL *pr);
    00309
    00313 void  bppm_to_structure(char *structure,
    00314                         FLT_OR_DBL *pr,
    00315                         unsigned int length);
    00316
    00317 plist *stackProb(double cutoff);
    00318
    00322 char    bppm_symbol(const float *x);
    00323
    00324
    00325 /*
    00326 #################################################
    00327 # DEPRECATED FUNCTIONS                          #
    00328 #################################################
    00329 */
    00330
    00336 DEPRECATED(void init_pf_fold(int length));
    00337
    00342 DEPRECATED(char *centroid(int length,
    00343                           double *dist));     /* mean pair distance of ensemble */
    00344
    00350 DEPRECATED(double mean_bp_dist(int length));
    00351
    00355 DEPRECATED(double expLoopEnergy(int u1,
    00356                                 int u2,
    00357                                 int type,
    00358                                 int type2,
    00359                                 short si1,
    00360                                 short sj1,
    00361                                 short sp1,
    00362                                 short sq1));
    00363
    00367 DEPRECATED(double expHairpinEnergy( int u,
    00368                                     int type,
    00369                                     short si1,
    00370                                     short sj1,
    00371                                     const char *string));
    00372
    00373 #endif