RNAlib-2.6.0b
 
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boltzmann_sampling.h
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1#ifndef VIENNA_RNA_PACKAGE_BOLTZMANN_SAMPLING_H
2#define VIENNA_RNA_PACKAGE_BOLTZMANN_SAMPLING_H
3
4#ifdef VRNA_WARN_DEPRECATED
5# if defined(DEPRECATED)
6# undef DEPRECATED
7# endif
8# if defined(__clang__)
9# define DEPRECATED(func, msg) func __attribute__ ((deprecated("", msg)))
10# elif defined(__GNUC__)
11# define DEPRECATED(func, msg) func __attribute__ ((deprecated(msg)))
12# else
13# define DEPRECATED(func, msg) func
14# endif
15#else
16# define DEPRECATED(func, msg) func
17#endif
18
43#define VRNA_PBACKTRACK_DEFAULT 0
44
55#define VRNA_PBACKTRACK_NON_REDUNDANT 1
56
72typedef void (*vrna_bs_result_f)(const char *structure,
73 void *data);
74
75DEPRECATED(typedef void (vrna_boltzmann_sampling_callback)(const char *structure,
76 void *data),
77 "Use vrna_bs_result_f instead!");
78
79
95typedef struct vrna_pbacktrack_memory_s *vrna_pbacktrack_mem_t;
96
98
128char *
130 unsigned int length);
131
132
177char **
179 unsigned int num_samples,
180 unsigned int length,
181 unsigned int options);
182
183
233unsigned int
235 unsigned int num_samples,
236 unsigned int length,
238 void *data,
239 unsigned int options);
240
241
316char **
318 unsigned int num_samples,
319 unsigned int length,
320 vrna_pbacktrack_mem_t *nr_mem,
321 unsigned int options);
322
323
401unsigned int
403 unsigned int num_samples,
404 unsigned int length,
406 void *data,
407 vrna_pbacktrack_mem_t *nr_mem,
408 unsigned int options);
409
410
438char *
440
441
484char **
486 unsigned int num_samples,
487 unsigned int options);
488
489
537unsigned int
539 unsigned int num_samples,
541 void *data,
542 unsigned int options);
543
544
615char **
617 unsigned int num_samples,
618 vrna_pbacktrack_mem_t *nr_mem,
619 unsigned int options);
620
621
695unsigned int
697 unsigned int num_samples,
699 void *data,
700 vrna_pbacktrack_mem_t *nr_mem,
701 unsigned int options);
702
703
704
705
706
707
708
709
742char *
744 unsigned int start,
745 unsigned int end);
746
747
793char **
795 unsigned int num_samples,
796 unsigned int start,
797 unsigned int end,
798 unsigned int options);
799
800
851unsigned int
853 unsigned int num_samples,
854 unsigned int start,
855 unsigned int end,
857 void *data,
858 unsigned int options);
859
860
936char **
938 unsigned int num_samples,
939 unsigned int start,
940 unsigned int end,
941 vrna_pbacktrack_mem_t *nr_mem,
942 unsigned int options);
943
944
1023unsigned int
1025 unsigned int num_samples,
1026 unsigned int start,
1027 unsigned int end,
1029 void *data,
1030 vrna_pbacktrack_mem_t *nr_mem,
1031 unsigned int options);
1032
1033
1042void
1044
1045
1049#endif
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.