RNAlib-2.2.0RC0
alifold.h
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1 #ifndef __VIENNA_RNA_PACKAGE_ALIFOLD_H__
2 #define __VIENNA_RNA_PACKAGE_ALIFOLD_H__
3 
5 #include <ViennaRNA/ribo.h>
6 
7 #ifdef __GNUC__
8 #define DEPRECATED(func) func __attribute__ ((deprecated))
9 #else
10 #define DEPRECATED(func) func
11 #endif
12 
52 DEPRECATED(extern double cv_fact);
63 DEPRECATED(extern double nc_fact);
64 
65 /*
66 ##############################################
67 # MFE VARIANTS OF THE ALIFOLD IMPLEMENTATION #
68 ##############################################
69 */
70 
93  char *structure);
94 
115 DEPRECATED(float alifold( const char **strings, char *structure));
116 
130 DEPRECATED(float circalifold( const char **strings, char *structure));
131 
145 DEPRECATED(void free_alifold_arrays(void));
146 
160 float energy_of_alistruct(const char **sequences,
161  const char *structure,
162  int n_seq,
163  float *energy);
164 
165 float energy_of_ali_gquad_structure(const char **sequences,
166  const char *structure,
167  int n_seq,
168  float *energy);
169 
170 /*
171 #############################################################
172 # PARTITION FUNCTION VARIANTS OF THE ALIFOLD IMPLEMENTATION #
173 #############################################################
174 */
175 
176 
206  char *structure,
207  plist **pl);
208 
223  const char *structure,
224  double threshold);
225 
242 DEPRECATED(float alipf_fold_par( const char **sequences,
243  char *structure,
244  plist **pl,
245  pf_paramT *parameters,
246  int calculate_bppm,
247  int is_constrained,
248  int is_circular));
249 
268 DEPRECATED(float alipf_fold( const char **sequences, char *structure, plist **pl));
269 
282 DEPRECATED(float alipf_circ_fold(const char **sequences, char *structure, plist **pl));
283 
284 
303 DEPRECATED(FLT_OR_DBL *export_ali_bppm(void));
304 
317 DEPRECATED(void free_alipf_arrays(void));
318 
337 char *vrna_ali_pbacktrack(vrna_fold_compound *vc, double *prob);
338 
349 DEPRECATED(char *alipbacktrack(double *prob));
350 
376 DEPRECATED(int get_alipf_arrays(short ***S_p,
377  short ***S5_p,
378  short ***S3_p,
379  unsigned short ***a2s_p,
380  char ***Ss_p,
381  FLT_OR_DBL **qb_p,
382  FLT_OR_DBL **qm_p,
383  FLT_OR_DBL **q1k_p,
384  FLT_OR_DBL **qln_p,
385  int **pscore));
386 
387 
399 DEPRECATED(void update_alifold_params(void));
400 
401 #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.
float alipf_fold_par(const char **sequences, char *structure, plist **pl, pf_paramT *parameters, int calculate_bppm, int is_constrained, int is_circular)
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.
The datastructure that contains temperature scaled Boltzmann weights of the energy parameters...
Definition: data_structures.h:225
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.
Definition: data_structures.h:359
float circalifold(const char **strings, char *structure)
Compute MFE and according structure of an alignment of sequences assuming the sequences are circular ...
All datastructures and typedefs shared among the Vienna RNA Package can be found here.
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:499
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:94
float alipf_circ_fold(const char **sequences, char *structure, plist **pl)
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.
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.