RNAlib-2.2.0-RC3
alifold.h
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1 #ifndef VIENNA_RNA_PACKAGE_ALIFOLD_H
2 #define VIENNA_RNA_PACKAGE_ALIFOLD_H
3 
5 #include <ViennaRNA/params.h>
6 #include <ViennaRNA/ribo.h>
7 
8 #ifdef __GNUC__
9 #define DEPRECATED(func) func __attribute__ ((deprecated))
10 #else
11 #define DEPRECATED(func) func
12 #endif
13 
53 DEPRECATED(extern double cv_fact);
64 DEPRECATED(extern double nc_fact);
65 
66 /*
67 ##############################################
68 # MFE VARIANTS OF THE ALIFOLD IMPLEMENTATION #
69 ##############################################
70 */
71 
94  char *structure);
95 
116 DEPRECATED(float alifold( const char **strings, char *structure));
117 
131 DEPRECATED(float circalifold( const char **strings, char *structure));
132 
146 DEPRECATED(void free_alifold_arrays(void));
147 
163 DEPRECATED(float energy_of_alistruct(const char **sequences, const char *structure, int n_seq, float *energy));
164 
165 DEPRECATED(float energy_of_ali_gquad_structure(const char **sequences, const char *structure, int n_seq, float *energy));
166 
167 /*
168 #############################################################
169 # PARTITION FUNCTION VARIANTS OF THE ALIFOLD IMPLEMENTATION #
170 #############################################################
171 */
172 
173 
203  char *structure,
204  plist **pl);
205 
220  const char *structure,
221  double threshold);
222 
239 DEPRECATED(float alipf_fold_par( const char **sequences,
240  char *structure,
241  plist **pl,
242  vrna_exp_param_t *parameters,
243  int calculate_bppm,
244  int is_constrained,
245  int is_circular));
246 
265 DEPRECATED(float alipf_fold( const char **sequences, char *structure, plist **pl));
266 
279 DEPRECATED(float alipf_circ_fold(const char **sequences, char *structure, plist **pl));
280 
281 
300 DEPRECATED(FLT_OR_DBL *export_ali_bppm(void));
301 
314 DEPRECATED(void free_alipf_arrays(void));
315 
334 char *vrna_ali_pbacktrack(vrna_fold_compound *vc, double *prob);
335 
346 DEPRECATED(char *alipbacktrack(double *prob));
347 
373 DEPRECATED(int get_alipf_arrays(short ***S_p,
374  short ***S5_p,
375  short ***S3_p,
376  unsigned short ***a2s_p,
377  char ***Ss_p,
378  FLT_OR_DBL **qb_p,
379  FLT_OR_DBL **qm_p,
380  FLT_OR_DBL **q1k_p,
381  FLT_OR_DBL **qln_p,
382  int **pscore));
383 
384 
396 DEPRECATED(void update_alifold_params(void));
397 
398 #endif
float alifold(const char **strings, char *structure)
Compute MFE and according consensus structure of an alignment of sequences.
FLT_OR_DBL * export_ali_bppm(void)
Get a pointer to the base pair probability array.
double cv_fact
This variable controls the weight of the covariance term in the energy function of alignment folding ...
float alipf_fold(const char **sequences, char *structure, plist **pl)
The partition function version of alifold() works in analogy to pf_fold(). Pair probabilities and inf...
char * vrna_ali_pbacktrack(vrna_fold_compound *vc, double *prob)
Sample a consensus secondary structure from the Boltzmann ensemble according its probability ...
float vrna_ali_pf_fold(vrna_fold_compound *vc, char *structure, plist **pl)
Compute partition function and base pair probabilities for a sequence alignment.
void update_alifold_params(void)
Update the energy parameters for alifold function.
double nc_fact
This variable controls the magnitude of the penalty for non-compatible sequences in the covariance te...
float vrna_ali_fold(vrna_fold_compound *vc, char *structure)
Compute MFE and according consensus structure of an alignment of sequences.
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, int **pscore)
Get pointers to (almost) all relavant arrays used in alifold's partition function computation...
void free_alifold_arrays(void)
Free the memory occupied by MFE alifold functions.
The most basic data structure required by many functions throughout the RNAlib.
Definition: data_structures.h:698
float circalifold(const char **strings, char *structure)
Compute MFE and according structure of an alignment of sequences assuming the sequences are circular ...
char * alipbacktrack(double *prob)
Sample a consensus secondary structure from the Boltzmann ensemble according its probability ...
A base pair info structure.
Definition: data_structures.h:171
void free_alipf_arrays(void)
Free the memory occupied by folding matrices allocated by alipf_fold, alipf_circ_fold, etc.
this datastructure is used as input parameter in functions of PS_dot.h and others ...
Definition: data_structures.h:45
float alipf_circ_fold(const char **sequences, char *structure, plist **pl)
float alipf_fold_par(const char **sequences, char *structure, plist **pl, vrna_exp_param_t *parameters, int calculate_bppm, int is_constrained, int is_circular)
pair_info * vrna_ali_get_pair_info(vrna_fold_compound *vc, const char *structure, double threshold)
Retrieve an array of pair_info structures from precomputed pair probabilities.
The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...
Definition: params.h:86
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.
Parse RiboSum Scoring Matrices for Covariance Scoring of Alignments.