1 #ifndef VIENNA_RNA_PACKAGE_ALIFOLD_H
2 #define VIENNA_RNA_PACKAGE_ALIFOLD_H
9 #define DEPRECATED(func) func __attribute__ ((deprecated))
11 #define DEPRECATED(func) func
53 DEPRECATED(
extern double cv_fact);
64 DEPRECATED(
extern double nc_fact);
116 DEPRECATED(
float alifold(
const char **strings,
char *structure));
131 DEPRECATED(
float circalifold(
const char **strings,
char *structure));
163 DEPRECATED(
float energy_of_alistruct(
const char **sequences,
const char *structure,
int n_seq,
float *energy));
165 DEPRECATED(
float energy_of_ali_gquad_structure(
const char **sequences,
const char *structure,
int n_seq,
float *energy));
220 const char *structure,
265 DEPRECATED(
float alipf_fold(
const char **sequences,
char *structure,
plist **pl));
376 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.
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:689
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.