RNAlib-2.4.14
alifold.h
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1 #ifndef VIENNA_RNA_PACKAGE_ALIFOLD_H
2 #define VIENNA_RNA_PACKAGE_ALIFOLD_H
3 
4 #include <ViennaRNA/datastructures/basic.h>
5 #include <ViennaRNA/params/basic.h>
6 #include <ViennaRNA/ribo.h>
7 #include <ViennaRNA/mfe.h>
8 #include <ViennaRNA/part_func.h>
9 #include <ViennaRNA/utils/alignments.h>
10 #include <ViennaRNA/utils/structures.h>
11 #include <ViennaRNA/boltzmann_sampling.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92  "This function is obsolete");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
cv_fact
double cv_fact
This variable controls the weight of the covariance term in the energy function of alignment folding ...
alignments.h
Various utility- and helper-functions for sequence alignments and comparative structure prediction...
alipf_circ_fold
float alipf_circ_fold(const char **sequences, char *structure, vrna_ep_t **pl)
FLT_OR_DBL
double FLT_OR_DBL
Typename for floating point number in partition function computations.
Definition: basic.h:43
alipf_fold_par
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)
basic.h
Various data structures and pre-processor macros.
circalifold
float circalifold(const char **strings, char *structure)
Compute MFE and according structure of an alignment of sequences assuming the sequences are circular ...
vrna_exp_param_s
The data structure that contains temperature scaled Boltzmann weights of the energy parameters...
Definition: basic.h:103
boltzmann_sampling.h
Boltzmann Sampling of secondary structures from the ensemble.
alipbacktrack
char * alipbacktrack(double *prob)
Sample a consensus secondary structure from the Boltzmann ensemble according its probability.
export_ali_bppm
FLT_OR_DBL * export_ali_bppm(void)
Get a pointer to the base pair probability array.
part_func.h
Partition function implementations.
free_alipf_arrays
void free_alipf_arrays(void)
Free the memory occupied by folding matrices allocated by alipf_fold, alipf_circ_fold, etc.
nc_fact
double nc_fact
This variable controls the magnitude of the penalty for non-compatible sequences in the covariance te...
free_alifold_arrays
void free_alifold_arrays(void)
Free the memory occupied by MFE alifold functions.
basic.h
Functions to deal with sets of energy parameters.
get_alipf_arrays
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...
alifold
float alifold(const char **strings, char *structure)
Compute MFE and according consensus structure of an alignment of sequences.
structures.h
Various utility- and helper-functions for secondary structure parsing, converting, etc.
energy_of_alistruct
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.
mfe.h
Compute Minimum Free energy (MFE) and backtrace corresponding secondary structures from RNA sequence ...
vrna_elem_prob_s
Data structure representing a single entry of an element probability list (e.g. list of pair probabil...
Definition: structures.h:453
update_alifold_params
void update_alifold_params(void)
Update the energy parameters for alifold function.
alipf_fold
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...
ribo.h
Parse RiboSum Scoring Matrices for Covariance Scoring of Alignments.