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!");
130 unsigned int length);
179 unsigned int num_samples,
181 unsigned int options);
235 unsigned int num_samples,
239 unsigned int options);
318 unsigned int num_samples,
321 unsigned int options);
403 unsigned int num_samples,
408 unsigned int options);
486 unsigned int num_samples,
487 unsigned int options);
539 unsigned int num_samples,
542 unsigned int options);
617 unsigned int num_samples,
619 unsigned int options);
697 unsigned int num_samples,
701 unsigned int options);
795 unsigned int num_samples,
798 unsigned int options);
853 unsigned int num_samples,
858 unsigned int options);
938 unsigned int num_samples,
942 unsigned int options);
1025 unsigned int num_samples,
1031 unsigned int options);
The Basic Fold Compound API.
The most basic data structure required by many functions throughout the RNAlib.
Definition: fold_compound.h:156
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_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.
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.
char ** vrna_pbacktrack5_resume(vrna_fold_compound_t *vc, 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...
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_sub_resume(vrna_fold_compound_t *vc, 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_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.