1#ifndef VIENNA_RNA_PACKAGE_BOLTZMANN_SAMPLING_H
2#define VIENNA_RNA_PACKAGE_BOLTZMANN_SAMPLING_H
4#ifdef VRNA_WARN_DEPRECATED
5# if defined(DEPRECATED)
9# define DEPRECATED(func, msg) func __attribute__ ((deprecated("", msg)))
10# elif defined(__GNUC__)
11# define DEPRECATED(func, msg) func __attribute__ ((deprecated(msg)))
13# define DEPRECATED(func, msg) func
16# define DEPRECATED(func, msg) func
43#define VRNA_PBACKTRACK_DEFAULT 0
55#define VRNA_PBACKTRACK_NON_REDUNDANT 1
75DEPRECATED(
typedef void (vrna_boltzmann_sampling_callback)(
const char *structure,
77 "Use vrna_bs_result_f instead!");
132 unsigned int length);
183 unsigned int num_samples,
185 unsigned int options);
241 unsigned int num_samples,
245 unsigned int options);
326 unsigned int num_samples,
329 unsigned int options);
413 unsigned int num_samples,
418 unsigned int options);
500 unsigned int num_samples,
501 unsigned int options);
555 unsigned int num_samples,
558 unsigned int options);
635 unsigned int num_samples,
637 unsigned int options);
717 unsigned int num_samples,
721 unsigned int options);
819 unsigned int num_samples,
822 unsigned int options);
879 unsigned int num_samples,
884 unsigned int options);
966 unsigned int num_samples,
970 unsigned int options);
1055 unsigned int num_samples,
1061 unsigned int options);
The Basic Fold Compound API.
The most basic data structure required by many functions throughout the RNAlib.
Definition fold_compound.h:168
unsigned int vrna_pbacktrack5_cb(vrna_fold_compound_t *fc, unsigned int num_samples, unsigned int length, vrna_bs_result_f cb, void *data, unsigned int options)
Obtain a set of secondary structure samples for a subsequence from the Boltzmann ensemble according t...
unsigned int vrna_pbacktrack5_resume_cb(vrna_fold_compound_t *fc, unsigned int num_samples, unsigned int length, vrna_bs_result_f cb, void *data, vrna_pbacktrack_mem_t *nr_mem, unsigned int options)
Obtain a set of secondary structure samples for a subsequence from the Boltzmann ensemble according t...
char ** vrna_pbacktrack_sub_num(vrna_fold_compound_t *fc, unsigned int num_samples, unsigned int start, unsigned int end, unsigned int options)
Obtain a set of secondary structure samples for a subsequence from the Boltzmann ensemble according t...
char ** vrna_pbacktrack_sub_resume(vrna_fold_compound_t *fc, unsigned int num_samples, unsigned int start, unsigned int end, vrna_pbacktrack_mem_t *nr_mem, unsigned int options)
Obtain a set of secondary structure samples for a subsequence from the Boltzmann ensemble according t...
char ** vrna_pbacktrack5_num(vrna_fold_compound_t *fc, unsigned int num_samples, unsigned int length, unsigned int options)
Obtain a set of secondary structure samples for a subsequence from the Boltzmann ensemble according t...
char * vrna_pbacktrack_sub(vrna_fold_compound_t *fc, unsigned int start, unsigned int end)
Sample a secondary structure of a subsequence from the Boltzmann ensemble according its probability.
void(* vrna_bs_result_f)(const char *structure, void *data)
Callback for Boltzmann sampling.
Definition boltzmann_sampling.h:72
char * vrna_pbacktrack(vrna_fold_compound_t *fc)
Sample a secondary structure from the Boltzmann ensemble according its probability.
char ** vrna_pbacktrack_num(vrna_fold_compound_t *fc, unsigned int num_samples, unsigned int options)
Obtain a set of secondary structure samples from the Boltzmann ensemble according their probability.
unsigned int vrna_pbacktrack_sub_cb(vrna_fold_compound_t *fc, unsigned int num_samples, unsigned int start, unsigned int end, vrna_bs_result_f cb, void *data, unsigned int options)
Obtain a set of secondary structure samples for a subsequence from the Boltzmann ensemble according t...
char * vrna_pbacktrack5(vrna_fold_compound_t *fc, unsigned int length)
Sample a secondary structure of a subsequence from the Boltzmann ensemble according its probability.
char ** vrna_pbacktrack5_resume(vrna_fold_compound_t *fc, unsigned int num_samples, unsigned int length, vrna_pbacktrack_mem_t *nr_mem, unsigned int options)
Obtain a set of secondary structure samples for a subsequence from the Boltzmann ensemble according t...
struct vrna_pbacktrack_memory_s * vrna_pbacktrack_mem_t
Boltzmann sampling memory data structure.
Definition boltzmann_sampling.h:95
unsigned int vrna_pbacktrack_sub_resume_cb(vrna_fold_compound_t *fc, unsigned int num_samples, unsigned int start, unsigned int end, vrna_bs_result_f cb, void *data, vrna_pbacktrack_mem_t *nr_mem, unsigned int options)
Obtain a set of secondary structure samples for a subsequence from the Boltzmann ensemble according t...
unsigned int vrna_pbacktrack_resume_cb(vrna_fold_compound_t *fc, unsigned int num_samples, vrna_bs_result_f cb, void *data, vrna_pbacktrack_mem_t *nr_mem, unsigned int options)
Obtain a set of secondary structure samples from the Boltzmann ensemble according their probability.
unsigned int vrna_pbacktrack_cb(vrna_fold_compound_t *fc, unsigned int num_samples, vrna_bs_result_f cb, void *data, unsigned int options)
Obtain a set of secondary structure samples from the Boltzmann ensemble according their probability.
char ** vrna_pbacktrack_resume(vrna_fold_compound_t *fc, unsigned int num_samples, vrna_pbacktrack_mem_t *nr_mem, unsigned int options)
Obtain a set of secondary structure samples from the Boltzmann ensemble according their probability.
void vrna_pbacktrack_mem_free(vrna_pbacktrack_mem_t s)
Release memory occupied by a Boltzmann sampling memory data structure.