RNAlib-2.6.3
 
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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
130char *
132 unsigned int length);
133
134
181char **
183 unsigned int num_samples,
184 unsigned int length,
185 unsigned int options);
186
187
239unsigned int
241 unsigned int num_samples,
242 unsigned int length,
244 void *data,
245 unsigned int options);
246
247
324char **
326 unsigned int num_samples,
327 unsigned int length,
328 vrna_pbacktrack_mem_t *nr_mem,
329 unsigned int options);
330
331
411unsigned int
413 unsigned int num_samples,
414 unsigned int length,
416 void *data,
417 vrna_pbacktrack_mem_t *nr_mem,
418 unsigned int options);
419
420
450char *
452
453
498char **
500 unsigned int num_samples,
501 unsigned int options);
502
503
553unsigned int
555 unsigned int num_samples,
557 void *data,
558 unsigned int options);
559
560
633char **
635 unsigned int num_samples,
636 vrna_pbacktrack_mem_t *nr_mem,
637 unsigned int options);
638
639
715unsigned int
717 unsigned int num_samples,
719 void *data,
720 vrna_pbacktrack_mem_t *nr_mem,
721 unsigned int options);
722
723
724
725
726
727
728
729
764char *
766 unsigned int start,
767 unsigned int end);
768
769
817char **
819 unsigned int num_samples,
820 unsigned int start,
821 unsigned int end,
822 unsigned int options);
823
824
877unsigned int
879 unsigned int num_samples,
880 unsigned int start,
881 unsigned int end,
883 void *data,
884 unsigned int options);
885
886
964char **
966 unsigned int num_samples,
967 unsigned int start,
968 unsigned int end,
969 vrna_pbacktrack_mem_t *nr_mem,
970 unsigned int options);
971
972
1053unsigned int
1055 unsigned int num_samples,
1056 unsigned int start,
1057 unsigned int end,
1059 void *data,
1060 vrna_pbacktrack_mem_t *nr_mem,
1061 unsigned int options);
1062
1063
1072void
1074
1075
1079#endif
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.