RNAlib-2.0.1
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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 00025 extern int st_back; 00026 00027 /* 00028 ################################################# 00029 # PARTITION FUNCTION COMPUTATION # 00030 ################################################# 00031 */ 00032 00059 float pf_fold(const char *sequence, 00060 char *structure); 00061 00071 float pf_circ_fold( const char *sequence, 00072 char *structure); 00073 00080 char *pbacktrack(char *sequence); 00081 00089 char *pbacktrack_circ(char *sequence); 00090 00094 void free_pf_arrays(void); 00095 00102 void update_pf_params(int length); 00103 00113 FLT_OR_DBL *export_bppm(void); 00114 00115 /* 00116 ################################################# 00117 # OTHER PARTITION FUNCTION RELATED DECLARATIONS # 00118 ################################################# 00119 */ 00120 00138 void assign_plist_from_pr( plist **pl, 00139 FLT_OR_DBL *probs, 00140 int length, 00141 double cutoff); 00142 00155 int get_pf_arrays(short **S_p, 00156 short **S1_p, 00157 char **ptype_p, 00158 FLT_OR_DBL **qb_p, 00159 FLT_OR_DBL **qm_p, 00160 FLT_OR_DBL **q1k_p, 00161 FLT_OR_DBL **qln_p); 00162 00178 char *get_centroid_struct_pl(int length, 00179 double *dist, 00180 plist *pl); 00181 00197 char *get_centroid_struct_pr(int length, 00198 double *dist, 00199 FLT_OR_DBL *pr); 00200 00209 double mean_bp_distance(int length); 00210 00226 double mean_bp_distance_pr(int length, 00227 FLT_OR_DBL *pr); 00228 00232 void bppm_to_structure(char *structure, 00233 FLT_OR_DBL *pr, 00234 unsigned int length); 00235 00236 plist *stackProb(double cutoff); 00237 00241 char bppm_symbol(const float *x); 00242 00243 00244 /* 00245 ################################################# 00246 # DEPRECATED FUNCTIONS # 00247 ################################################# 00248 */ 00249 00255 DEPRECATED(void init_pf_fold(int length)); 00256 00261 DEPRECATED(char *centroid(int length, 00262 double *dist)); /* mean pair distance of ensemble */ 00263 00269 DEPRECATED(double mean_bp_dist(int length)); 00270 00274 DEPRECATED(double expLoopEnergy(int u1, 00275 int u2, 00276 int type, 00277 int type2, 00278 short si1, 00279 short sj1, 00280 short sp1, 00281 short sq1)); 00282 00286 DEPRECATED(double expHairpinEnergy( int u, 00287 int type, 00288 short si1, 00289 short sj1, 00290 const char *string)); 00291 00292 #endif