RNAlib-2.4.18
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>
12 
13 #ifdef VRNA_WARN_DEPRECATED
14 # if defined(__clang__)
15 # define DEPRECATED(func, msg) func __attribute__ ((deprecated("", msg)))
16 # elif defined(__GNUC__)
17 # define DEPRECATED(func, msg) func __attribute__ ((deprecated(msg)))
18 # else
19 # define DEPRECATED(func, msg) func
20 # endif
21 #else
22 # define DEPRECATED(func, msg) func
23 #endif
24 
32 #ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
33 
34 /*
35 #################################################
36 # DEPRECATED FUNCTIONS #
37 #################################################
38 */
39 
63 DEPRECATED(float alifold( const char **strings, char *structure),
64  "Use vrna_alifold() or vrna_mfe() instead");
65 
77 DEPRECATED(float circalifold( const char **strings, char *structure),
78  "Use vrna_alicircfold() or vrna_mfe() instead");
79 
91 DEPRECATED(void free_alifold_arrays(void),
92  "This function is obsolete");
93 
94 /* End group mfe_global_deprecated */
112 DEPRECATED(float energy_of_alistruct(const char **sequences, const char *structure, int n_seq, float *energy),
113  "Use vrna_eval_structure() and vrna_eval_covar_structure() instead");
114 
115 DEPRECATED(float energy_of_ali_gquad_structure(const char **sequences, const char *structure, int n_seq, float *energy),
116  "Use vrna_eval_structure() and vrna_eval_covar_structure() instead");
117 
128 DEPRECATED(extern double cv_fact,
129  "Use the cv_fact attribute of the vrna_md_t datastructure instead");
140 DEPRECATED(extern double nc_fact,
141  "Use the nc_fact attribute of the vrna_md_t datastructure instead");
142 
162 DEPRECATED(float alipf_fold_par( const char **sequences,
163  char *structure,
164  vrna_ep_t **pl,
165  vrna_exp_param_t *parameters,
166  int calculate_bppm,
167  int is_constrained,
168  int is_circular),
169  "Use vrna_pf_alifold() or vrna_pf() instead");
170 
187 DEPRECATED(float alipf_fold( const char **sequences, char *structure, vrna_ep_t **pl),
188  "Use vrna_pf_alifold() or vrna_pf() instead");
189 
200 DEPRECATED(float alipf_circ_fold(const char **sequences, char *structure, vrna_ep_t **pl),
201  "Use vrna_pf_circalifold() or vrna_pf() instead");
202 
203 
220 DEPRECATED(FLT_OR_DBL *export_ali_bppm(void),
221  "Use the new API with vrna_fold_compound_t datastructure instead");
222 
233 DEPRECATED(void free_alipf_arrays(void),
234  "This function is obsolete");
235 
244 DEPRECATED(char *alipbacktrack(double *prob),
245  "Use the new API and vrna_pbacktrack() instead");
246 
271 DEPRECATED(int get_alipf_arrays(short ***S_p,
272  short ***S5_p,
273  short ***S3_p,
274  unsigned short ***a2s_p,
275  char ***Ss_p,
276  FLT_OR_DBL **qb_p,
277  FLT_OR_DBL **qm_p,
278  FLT_OR_DBL **q1k_p,
279  FLT_OR_DBL **qln_p,
280  short **pscore),
281  "Use the new API with vrna_fold_compound_t datastructure instead");
282 
283 
284 /* End group part_func_global_deprecated */
298 DEPRECATED(void update_alifold_params(void),
299  "Use the new API with vrna_fold_compound_t datastructure instead");
300 
301 #endif
302 
303 
304 #endif
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.
double nc_fact
This variable controls the magnitude of the penalty for non-compatible sequences in the covariance te...
void update_alifold_params(void)
Update the energy parameters for alifold function.
double cv_fact
This variable controls the weight of the covariance term in the energy function of alignment folding ...
Boltzmann Sampling of secondary structures from the ensemble.
Various data structures and pre-processor macros.
double FLT_OR_DBL
Typename for floating point number in partition function computations.
Definition: basic.h:43
The data structure that contains temperature scaled Boltzmann weights of the energy parameters.
Definition: basic.h:103
float alifold(const char **strings, char *structure)
Compute MFE and according consensus structure of an alignment of sequences.
void free_alifold_arrays(void)
Free the memory occupied by MFE alifold functions.
float circalifold(const char **strings, char *structure)
Compute MFE and according structure of an alignment of sequences assuming the sequences are circular ...
void free_alipf_arrays(void)
Free the memory occupied by folding matrices allocated by alipf_fold, alipf_circ_fold,...
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.
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...
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's partition function computation.
float alipf_circ_fold(const char **sequences, char *structure, vrna_ep_t **pl)
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)
Data structure representing a single entry of an element probability list (e.g. list of pair probabil...
Definition: structures.h:459
Compute Minimum Free energy (MFE) and backtrace corresponding secondary structures from RNA sequence ...
Functions to deal with sets of energy parameters.
Partition function implementations.
Parse RiboSum Scoring Matrices for Covariance Scoring of Alignments.
Various utility- and helper-functions for sequence alignments and comparative structure prediction.
Various utility- and helper-functions for secondary structure parsing, converting,...