RNAlib-2.0.7
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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