RNAlib-2.4.8
alifold.h
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1 #ifndef VIENNA_RNA_PACKAGE_ALIFOLD_H
2 #define VIENNA_RNA_PACKAGE_ALIFOLD_H
3 
6 #include <ViennaRNA/ribo.h>
7 #include <ViennaRNA/mfe.h>
8 #include <ViennaRNA/part_func.h>
11 
12 #ifdef VRNA_WARN_DEPRECATED
13 # if defined(__clang__)
14 # define DEPRECATED(func, msg) func __attribute__ ((deprecated("", msg)))
15 # elif defined(__GNUC__)
16 # define DEPRECATED(func, msg) func __attribute__ ((deprecated(msg)))
17 # else
18 # define DEPRECATED(func, msg) func
19 # endif
20 #else
21 # define DEPRECATED(func, msg) func
22 #endif
23 
31 #ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
32 
33 /*
34 #################################################
35 # DEPRECATED FUNCTIONS #
36 #################################################
37 */
38 
62 DEPRECATED(float alifold( const char **strings, char *structure),
63  "Use vrna_alifold() or vrna_mfe() instead");
64 
76 DEPRECATED(float circalifold( const char **strings, char *structure),
77  "Use vrna_alicircfold() or vrna_mfe() instead");
78 
90 DEPRECATED(void free_alifold_arrays(void),
91  "This function is obsolete");
92 
93 /* End group mfe_global_deprecated */
111 DEPRECATED(float energy_of_alistruct(const char **sequences, const char *structure, int n_seq, float *energy),
112  "Use vrna_eval_structure() and vrna_eval_covar_structure() instead");
113 
114 DEPRECATED(float energy_of_ali_gquad_structure(const char **sequences, const char *structure, int n_seq, float *energy),
115  "Use vrna_eval_structure() and vrna_eval_covar_structure() instead");
116 
127 DEPRECATED(extern double cv_fact,
128  "Use the cv_fact attribute of the vrna_md_t datastructure instead");
139 DEPRECATED(extern double nc_fact,
140  "Use the nc_fact attribute of the vrna_md_t datastructure instead");
141 
161 DEPRECATED(float alipf_fold_par( const char **sequences,
162  char *structure,
163  vrna_ep_t **pl,
164  vrna_exp_param_t *parameters,
165  int calculate_bppm,
166  int is_constrained,
167  int is_circular),
168  "Use vrna_pf_alifold() or vrna_pf() instead");
169 
186 DEPRECATED(float alipf_fold( const char **sequences, char *structure, vrna_ep_t **pl),
187  "Use vrna_pf_alifold() or vrna_pf() instead");
188 
199 DEPRECATED(float alipf_circ_fold(const char **sequences, char *structure, vrna_ep_t **pl),
200  "Use vrna_pf_circalifold() or vrna_pf() instead");
201 
202 
219 DEPRECATED(FLT_OR_DBL *export_ali_bppm(void),
220  "Use the new API with vrna_fold_compound_t datastructure instead");
221 
232 DEPRECATED(void free_alipf_arrays(void),
233  "This function is obsolete");
234 
243 DEPRECATED(char *alipbacktrack(double *prob),
244  "Use the new API and vrna_pbacktrack() instead");
245 
270 DEPRECATED(int get_alipf_arrays(short ***S_p,
271  short ***S5_p,
272  short ***S3_p,
273  unsigned short ***a2s_p,
274  char ***Ss_p,
275  FLT_OR_DBL **qb_p,
276  FLT_OR_DBL **qm_p,
277  FLT_OR_DBL **q1k_p,
278  FLT_OR_DBL **qln_p,
279  short **pscore),
280  "Use the new API with vrna_fold_compound_t datastructure instead");
281 
282 
283 /* End group part_func_global_deprecated */
297 DEPRECATED(void update_alifold_params(void),
298  "Use the new API with vrna_fold_compound_t datastructure instead");
299 
300 #endif
301 
302 
303 #endif
double cv_fact
This variable controls the weight of the covariance term in the energy function of alignment folding ...
Various utility- and helper-functions for sequence alignments and comparative structure prediction...
float alipf_circ_fold(const char **sequences, char *structure, vrna_ep_t **pl)
double FLT_OR_DBL
Typename for floating point number in partition function computations.
Definition: basic.h:43
float alipf_fold_par(const char **sequences, char *structure, vrna_ep_t **pl, vrna_exp_param_t *parameters, int calculate_bppm, int is_constrained, int is_circular)
Various data structures and pre-processor macros.
float circalifold(const char **strings, char *structure)
Compute MFE and according structure of an alignment of sequences assuming the sequences are circular ...
The data structure that contains temperature scaled Boltzmann weights of the energy parameters...
Definition: basic.h:101
Boltzmann Sampling of secondary structures from the ensemble.
char * alipbacktrack(double *prob)
Sample a consensus secondary structure from the Boltzmann ensemble according its probability.
FLT_OR_DBL * export_ali_bppm(void)
Get a pointer to the base pair probability array.
Partition function implementations.
void free_alipf_arrays(void)
Free the memory occupied by folding matrices allocated by alipf_fold, alipf_circ_fold, etc.
double nc_fact
This variable controls the magnitude of the penalty for non-compatible sequences in the covariance te...
void free_alifold_arrays(void)
Free the memory occupied by MFE alifold functions.
Functions to deal with sets of energy parameters.
int get_alipf_arrays(short ***S_p, short ***S5_p, short ***S3_p, unsigned short ***a2s_p, char ***Ss_p, FLT_OR_DBL **qb_p, FLT_OR_DBL **qm_p, FLT_OR_DBL **q1k_p, FLT_OR_DBL **qln_p, short **pscore)
Get pointers to (almost) all relavant arrays used in alifold&#39;s partition function computation...
float alifold(const char **strings, char *structure)
Compute MFE and according consensus structure of an alignment of sequences.
float energy_of_alistruct(const char **sequences, const char *structure, int n_seq, float *energy)
Calculate the free energy of a consensus structure given a set of aligned sequences.
Compute Minimum Free energy (MFE) and backtrace corresponding secondary structures from RNA sequence ...
Data structure representing a single entry of an element probability list (e.g. list of pair probabil...
Definition: structures.h:358
void update_alifold_params(void)
Update the energy parameters for alifold function.
float alipf_fold(const char **sequences, char *structure, vrna_ep_t **pl)
The partition function version of alifold() works in analogy to pf_fold(). Pair probabilities and inf...
Parse RiboSum Scoring Matrices for Covariance Scoring of Alignments.