1#ifndef VIENNA_RNA_PACKAGE_ALIFOLD_H
2#define VIENNA_RNA_PACKAGE_ALIFOLD_H
13#ifdef VRNA_WARN_DEPRECATED
14# if defined(__clang__)
15# define DEPRECATED(func, msg) func __attribute__ ((deprecated("", msg)))
16# elif defined(__GNUC__)
17# define DEPRECATED(func, msg) func __attribute__ ((deprecated(msg)))
19# define DEPRECATED(func, msg) func
22# define DEPRECATED(func, msg) func
32#ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
63DEPRECATED(
float alifold(
const char **strings,
char *structure),
64 "Use vrna_alifold() or vrna_mfe() instead");
77DEPRECATED(
float circalifold(
const char **strings,
char *structure),
78 "Use vrna_alicircfold() or vrna_mfe() instead");
92 "This function is obsolete");
112DEPRECATED(
float energy_of_alistruct(
const char **sequences,
const char *structure,
int n_seq,
float *energy),
113 "Use vrna_eval_structure() and vrna_eval_covar_structure() instead");
115DEPRECATED(
float energy_of_ali_gquad_structure(
const char **sequences,
const char *structure,
int n_seq,
float *energy),
116 "Use vrna_eval_structure() and vrna_eval_covar_structure() instead");
128DEPRECATED(
extern double cv_fact,
129 "Use the cv_fact attribute of the vrna_md_t datastructure instead");
140DEPRECATED(
extern double nc_fact,
141 "Use the nc_fact attribute of the vrna_md_t datastructure instead");
169 "Use vrna_pf_alifold() or vrna_pf() instead");
188 "Use vrna_pf_alifold() or vrna_pf() instead");
201 "Use vrna_pf_circalifold() or vrna_pf() instead");
221 "Use the new API with vrna_fold_compound_t datastructure instead");
234 "This function is obsolete");
245 "Use the new API and vrna_pbacktrack() instead");
274 unsigned short ***a2s_p,
281 "Use the new API with vrna_fold_compound_t datastructure instead");
299 "Use the new API with vrna_fold_compound_t datastructure instead");
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.
double nc_fact
This variable controls the magnitude of the penalty for non-compatible sequences in the covariance te...
void update_alifold_params(void)
Update the energy parameters for alifold function.
double cv_fact
This variable controls the weight of the covariance term in the energy function of alignment folding ...
Boltzmann Sampling of secondary structures from the ensemble.
Various data structures and pre-processor macros.
double FLT_OR_DBL
Typename for floating point number in partition function computations.
Definition: basic.h:43
The data structure that contains temperature scaled Boltzmann weights of the energy parameters.
Definition: basic.h:103
float alifold(const char **strings, char *structure)
Compute MFE and according consensus structure of an alignment of sequences.
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 ...
void free_alipf_arrays(void)
Free the memory occupied by folding matrices allocated by alipf_fold, alipf_circ_fold,...
float alipf_fold(const char **sequences, char *structure, vrna_ep_t **pl)
The partition function version of alifold() works in analogy to pf_fold(). Pair probabilities and inf...
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, short **pscore)
Get pointers to (almost) all relavant arrays used in alifold's partition function computation.
float alipf_circ_fold(const char **sequences, char *structure, vrna_ep_t **pl)
char * alipbacktrack(double *prob)
Sample a consensus secondary structure from the Boltzmann ensemble according its probability.
float alipf_fold_par(const char **sequences, char *structure, vrna_ep_t **pl, vrna_exp_param_t *parameters, int calculate_bppm, int is_constrained, int is_circular)
FLT_OR_DBL * export_ali_bppm(void)
Get a pointer to the base pair probability array.
Data structure representing a single entry of an element probability list (e.g. list of pair probabil...
Definition: structures.h:482
Compute Minimum Free energy (MFE) and backtrace corresponding secondary structures from RNA sequence ...
Functions to deal with sets of energy parameters.
Partition function implementations.
Parse RiboSum Scoring Matrices for Covariance Scoring of Alignments.
Various utility- and helper-functions for sequence alignments and comparative structure prediction.
Various utility- and helper-functions for secondary structure parsing, converting,...