1 #ifndef __VIENNA_RNA_PACKAGE_ALIFOLD_H__
2 #define __VIENNA_RNA_PACKAGE_ALIFOLD_H__
5 #include <ViennaRNA/ribo.h>
8 #define DEPRECATED(func) func __attribute__ ((deprecated))
10 #define DEPRECATED(func) func
52 DEPRECATED(
extern double cv_fact);
63 DEPRECATED(
extern double nc_fact);
115 DEPRECATED(
float alifold(
const char **strings,
char *structure));
130 DEPRECATED(
float circalifold(
const char **strings,
char *structure));
161 const char *structure,
165 float energy_of_ali_gquad_structure(
const char **sequences,
166 const char *structure,
223 const char *structure,
268 DEPRECATED(
float alipf_fold(
const char **sequences,
char *structure,
plist **pl));
379 unsigned short ***a2s_p,
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.