RNAlib-2.2.0
alifold.h
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1 #ifndef VIENNA_RNA_PACKAGE_ALIFOLD_H
2 #define VIENNA_RNA_PACKAGE_ALIFOLD_H
3 
4 /* make this interface backward compatible with RNAlib < 2.2.0 */
5 #define VRNA_BACKWARD_COMPAT
6 
8 #include <ViennaRNA/params.h>
9 #include <ViennaRNA/ribo.h>
10 #include <ViennaRNA/mfe.h>
11 #include <ViennaRNA/part_func.h>
13 
14 #ifdef DEPRECATION_WARNINGS
15 # ifdef __GNUC__
16 # define DEPRECATED(func) func __attribute__ ((deprecated))
17 # else
18 # define DEPRECATED(func) func
19 # endif
20 #else
21 # define DEPRECATED(func) func
22 #endif
23 
53 /*
54 ##############################################
55 # MFE VARIANTS OF THE ALIFOLD IMPLEMENTATION #
56 ##############################################
57 */
58 
82 float
83 vrna_alifold( const char **ssequences,
84  char *structure);
85 
112 float
113 vrna_circalifold( const char **ssequences,
114  char *structure);
115 
116 /*
117 #############################################################
118 # PARTITION FUNCTION VARIANTS OF THE ALIFOLD IMPLEMENTATION #
119 #############################################################
120 */
121 
122 
154 float vrna_pf_alifold(const char **strings, char *structure, vrna_plist_t **pl);
155 
182 float vrna_pf_circalifold(const char **sequences, char *structure, vrna_plist_t **pl);
183 
184 #ifdef VRNA_BACKWARD_COMPAT
185 
186 /*
187 #################################################
188 # DEPRECATED FUNCTIONS #
189 #################################################
190 */
191 
192 
213 DEPRECATED(float alifold( const char **strings, char *structure));
214 
228 DEPRECATED(float circalifold( const char **strings, char *structure));
229 
243 DEPRECATED(void free_alifold_arrays(void));
244 
260 DEPRECATED(float energy_of_alistruct(const char **sequences, const char *structure, int n_seq, float *energy));
261 
262 DEPRECATED(float energy_of_ali_gquad_structure(const char **sequences, const char *structure, int n_seq, float *energy));
263 
274 DEPRECATED(extern double cv_fact);
285 DEPRECATED(extern double nc_fact);
286 
303 DEPRECATED(float alipf_fold_par( const char **sequences,
304  char *structure,
305  vrna_plist_t **pl,
306  vrna_exp_param_t *parameters,
307  int calculate_bppm,
308  int is_constrained,
309  int is_circular));
310 
329 DEPRECATED(float alipf_fold( const char **sequences, char *structure, vrna_plist_t **pl));
330 
343 DEPRECATED(float alipf_circ_fold(const char **sequences, char *structure, vrna_plist_t **pl));
344 
345 
364 DEPRECATED(FLT_OR_DBL *export_ali_bppm(void));
365 
378 DEPRECATED(void free_alipf_arrays(void));
379 
390 DEPRECATED(char *alipbacktrack(double *prob));
391 
417 DEPRECATED(int get_alipf_arrays(short ***S_p,
418  short ***S5_p,
419  short ***S3_p,
420  unsigned short ***a2s_p,
421  char ***Ss_p,
422  FLT_OR_DBL **qb_p,
423  FLT_OR_DBL **qm_p,
424  FLT_OR_DBL **q1k_p,
425  FLT_OR_DBL **qln_p,
426  int **pscore));
427 
428 
440 DEPRECATED(void update_alifold_params(void));
441 
442 #endif
443 
444 
445 #endif
float vrna_pf_circalifold(const char **sequences, char *structure, vrna_plist_t **pl)
Compute Partition function (and base pair probabilities) for an alignment of circular RNA sequences ...
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 ...
double FLT_OR_DBL
Typename for floating point number in partition function computations.
Definition: data_structures.h:39
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_circalifold(const char **ssequences, char *structure)
Compute Minimum Free Energy (MFE), and a corresponding consensus secondary structure for a sequence a...
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&#39;s partition function computation...
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 ...
char * alipbacktrack(double *prob)
Sample a consensus secondary structure from the Boltzmann ensemble according its probability.
void free_alipf_arrays(void)
Free the memory occupied by folding matrices allocated by alipf_fold, alipf_circ_fold, etc.
The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...
Definition: params.h:94
float alipf_fold_par(const char **sequences, char *structure, vrna_plist_t **pl, vrna_exp_param_t *parameters, int calculate_bppm, int is_constrained, int is_circular)
Boltzmann Sampling of secondary structures from the ensemble.
float alipf_fold(const char **sequences, char *structure, vrna_plist_t **pl)
The partition function version of alifold() works in analogy to pf_fold(). Pair probabilities and inf...
float vrna_pf_alifold(const char **strings, char *structure, vrna_plist_t **pl)
Compute Partition function (and base pair probabilities) for an RNA sequence alignment using a compa...
this datastructure is used as input parameter in functions of PS_dot.h and others ...
Definition: data_structures.h:163
Partition function of single RNA sequences.
float alipf_circ_fold(const char **sequences, char *structure, vrna_plist_t **pl)
MFE calculations for single RNA 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.
float vrna_alifold(const char **ssequences, char *structure)
Compute Minimum Free Energy (MFE), and a corresponding consensus secondary structure for an RNA seque...
Parse RiboSum Scoring Matrices for Covariance Scoring of Alignments.