RNAlib-2.0.2
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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 00071 float pf_fold(const char *sequence, 00072 char *structure); 00073 00089 float pf_circ_fold( const char *sequence, 00090 char *structure); 00091 00092 float pf_fold_par( const char *sequence, 00093 char *structure, 00094 pf_paramT *parameters, 00095 int calculate_bppm, 00096 int is_circular); 00097 00110 char *pbacktrack(char *sequence); 00111 00124 char *pbacktrack_circ(char *sequence); 00125 00138 void free_pf_arrays(void); 00139 00146 void update_pf_params(int length); 00147 00148 void update_pf_params_par(int length, pf_paramT *parameters); 00149 00162 FLT_OR_DBL *export_bppm(void); 00163 00164 /* 00165 ################################################# 00166 # OTHER PARTITION FUNCTION RELATED DECLARATIONS # 00167 ################################################# 00168 */ 00169 00187 void assign_plist_from_pr( plist **pl, 00188 FLT_OR_DBL *probs, 00189 int length, 00190 double cutoff); 00191 00208 int get_pf_arrays(short **S_p, 00209 short **S1_p, 00210 char **ptype_p, 00211 FLT_OR_DBL **qb_p, 00212 FLT_OR_DBL **qm_p, 00213 FLT_OR_DBL **q1k_p, 00214 FLT_OR_DBL **qln_p); 00215 00231 char *get_centroid_struct_pl(int length, 00232 double *dist, 00233 plist *pl); 00234 00250 char *get_centroid_struct_pr(int length, 00251 double *dist, 00252 FLT_OR_DBL *pr); 00253 00264 double mean_bp_distance(int length); 00265 00281 double mean_bp_distance_pr(int length, 00282 FLT_OR_DBL *pr); 00283 00287 void bppm_to_structure(char *structure, 00288 FLT_OR_DBL *pr, 00289 unsigned int length); 00290 00291 plist *stackProb(double cutoff); 00292 00296 char bppm_symbol(const float *x); 00297 00298 00299 /* 00300 ################################################# 00301 # DEPRECATED FUNCTIONS # 00302 ################################################# 00303 */ 00304 00310 DEPRECATED(void init_pf_fold(int length)); 00311 00316 DEPRECATED(char *centroid(int length, 00317 double *dist)); /* mean pair distance of ensemble */ 00318 00324 DEPRECATED(double mean_bp_dist(int length)); 00325 00329 DEPRECATED(double expLoopEnergy(int u1, 00330 int u2, 00331 int type, 00332 int type2, 00333 short si1, 00334 short sj1, 00335 short sp1, 00336 short sq1)); 00337 00341 DEPRECATED(double expHairpinEnergy( int u, 00342 int type, 00343 short si1, 00344 short sj1, 00345 const char *string)); 00346 00347 #endif