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# /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/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
    00041 extern  int st_back;
    00042
    00043 /*
    00044 #################################################
    00045 # PARTITION FUNCTION COMPUTATION                #
    00046 #################################################
    00047 */
    00048
    00087 float   pf_fold_par(  const char *sequence,
    00088                       char *structure,
    00089                       pf_paramT *parameters,
    00090                       int calculate_bppm,
    00091                       int is_constrained,
    00092                       int is_circular);
    00093
    00133 float   pf_fold(const char *sequence,
    00134                 char *structure);
    00135
    00161 float   pf_circ_fold( const char *sequence,
    00162                       char *structure);
    00163
    00173 char    *pbacktrack(char *sequence);
    00174
    00186 char    *pbacktrack_circ(char *sequence);
    00187
    00203 void  free_pf_arrays(void);
    00204
    00214 void  update_pf_params(int length);
    00215
    00222 void update_pf_params_par(int length, pf_paramT *parameters);
    00223
    00240 FLT_OR_DBL  *export_bppm(void);
    00241
    00242 /*
    00243 #################################################
    00244 # OTHER PARTITION FUNCTION RELATED DECLARATIONS #
    00245 #################################################
    00246 */
    00247
    00265 void  assign_plist_from_pr( plist **pl,
    00266                             FLT_OR_DBL *probs,
    00267                             int length,
    00268                             double cutoff);
    00269
    00270 /* this doesn't work if free_pf_arrays() is called before */
    00271 void assign_plist_gquad_from_pr(plist **pl,
    00272                                 int length,
    00273                                 double cut_off);
    00274
    00275 char *get_centroid_struct_gquad_pr(int length,
    00276                                   double *dist);
    00277
    00293 int get_pf_arrays(short **S_p,
    00294                   short **S1_p,
    00295                   char **ptype_p,
    00296                   FLT_OR_DBL **qb_p,
    00297                   FLT_OR_DBL **qm_p,
    00298                   FLT_OR_DBL **q1k_p,
    00299                   FLT_OR_DBL **qln_p);
    00300
    00304 double get_subseq_F(int i, int j);
    00305
    00322 char  *get_centroid_struct_pl(int length,
    00323                               double *dist,
    00324                               plist *pl);
    00325
    00342 char  *get_centroid_struct_pr(int length,
    00343                               double *dist,
    00344                               FLT_OR_DBL *pr);
    00345
    00358 double  mean_bp_distance(int length);
    00359
    00377 double  mean_bp_distance_pr(int length,
    00378                             FLT_OR_DBL *pr);
    00379
    00383 void  bppm_to_structure(char *structure,
    00384                         FLT_OR_DBL *pr,
    00385                         unsigned int length);
    00386
    00387 plist *stackProb(double cutoff);
    00388
    00392 char    bppm_symbol(const float *x);
    00393
    00394
    00395 /*
    00396 #################################################
    00397 # DEPRECATED FUNCTIONS                          #
    00398 #################################################
    00399 */
    00400
    00406 DEPRECATED(void init_pf_fold(int length));
    00407
    00412 DEPRECATED(char *centroid(int length,
    00413                           double *dist));     /* mean pair distance of ensemble */
    00414
    00420 DEPRECATED(double mean_bp_dist(int length));
    00421
    00425 DEPRECATED(double expLoopEnergy(int u1,
    00426                                 int u2,
    00427                                 int type,
    00428                                 int type2,
    00429                                 short si1,
    00430                                 short sj1,
    00431                                 short sp1,
    00432                                 short sq1));
    00433
    00437 DEPRECATED(double expHairpinEnergy( int u,
    00438                                     int type,
    00439                                     short si1,
    00440                                     short sj1,
    00441                                     const char *string));
    00442
    00443 #endif