RNAlib-2.5.1
boltzmann_sampling.h
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1#ifndef VIENNA_RNA_PACKAGE_BOLTZMANN_SAMPLING_H
2#define VIENNA_RNA_PACKAGE_BOLTZMANN_SAMPLING_H
3
28#define VRNA_PBACKTRACK_DEFAULT 0
29
40#define VRNA_PBACKTRACK_NON_REDUNDANT 1
41
57typedef void (vrna_boltzmann_sampling_callback)(const char *structure,
58 void *data);
59
75typedef struct vrna_pbacktrack_memory_s *vrna_pbacktrack_mem_t;
76
78
108char *
110 unsigned int length);
111
112
157char **
159 unsigned int num_samples,
160 unsigned int length,
161 unsigned int options);
162
163
213unsigned int
215 unsigned int num_samples,
216 unsigned int length,
218 void *data,
219 unsigned int options);
220
221
296char **
298 unsigned int num_samples,
299 unsigned int length,
300 vrna_pbacktrack_mem_t *nr_mem,
301 unsigned int options);
302
303
381unsigned int
383 unsigned int num_samples,
384 unsigned int length,
386 void *data,
387 vrna_pbacktrack_mem_t *nr_mem,
388 unsigned int options);
389
390
418char *
420
421
464char **
466 unsigned int num_samples,
467 unsigned int options);
468
469
517unsigned int
519 unsigned int num_samples,
521 void *data,
522 unsigned int options);
523
524
595char **
597 unsigned int num_samples,
598 vrna_pbacktrack_mem_t *nr_mem,
599 unsigned int options);
600
601
675unsigned int
677 unsigned int num_samples,
679 void *data,
680 vrna_pbacktrack_mem_t *nr_mem,
681 unsigned int options);
682
683
684
685
686
687
688
689
722char *
724 unsigned int start,
725 unsigned int end);
726
727
773char **
775 unsigned int num_samples,
776 unsigned int start,
777 unsigned int end,
778 unsigned int options);
779
780
831unsigned int
833 unsigned int num_samples,
834 unsigned int start,
835 unsigned int end,
837 void *data,
838 unsigned int options);
839
840
916char **
918 unsigned int num_samples,
919 unsigned int start,
920 unsigned int end,
921 vrna_pbacktrack_mem_t *nr_mem,
922 unsigned int options);
923
924
1003unsigned int
1005 unsigned int num_samples,
1006 unsigned int start,
1007 unsigned int end,
1009 void *data,
1010 vrna_pbacktrack_mem_t *nr_mem,
1011 unsigned int options);
1012
1013
1022void
1024
1025
1029#endif
The Basic Fold Compound API.
The most basic data structure required by many functions throughout the RNAlib.
Definition: fold_compound.h:148
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...
unsigned int vrna_pbacktrack5_resume_cb(vrna_fold_compound_t *fc, unsigned int num_samples, unsigned int length, vrna_boltzmann_sampling_callback *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(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.
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_pbacktrack5_cb(vrna_fold_compound_t *fc, unsigned int num_samples, unsigned int length, vrna_boltzmann_sampling_callback *cb, void *data, unsigned int options)
Obtain a set of secondary structure samples for a subsequence from the Boltzmann ensemble according t...
void() vrna_boltzmann_sampling_callback(const char *structure, void *data)
Callback for Boltzmann sampling.
Definition: boltzmann_sampling.h:57
unsigned int vrna_pbacktrack_resume_cb(vrna_fold_compound_t *fc, unsigned int num_samples, vrna_boltzmann_sampling_callback *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(vrna_fold_compound_t *fc, unsigned int length)
Sample a secondary structure of a subsequence from the Boltzmann ensemble according its probability.
unsigned int vrna_pbacktrack_sub_resume_cb(vrna_fold_compound_t *fc, unsigned int num_samples, unsigned int start, unsigned int end, vrna_boltzmann_sampling_callback *bs_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_cb(vrna_fold_compound_t *fc, unsigned int num_samples, vrna_boltzmann_sampling_callback *cb, void *data, unsigned int options)
Obtain a set of secondary structure samples from the Boltzmann ensemble according their probability.
struct vrna_pbacktrack_memory_s * vrna_pbacktrack_mem_t
Boltzmann sampling memory data structure.
Definition: boltzmann_sampling.h:75
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_sub_cb(vrna_fold_compound_t *fc, unsigned int num_samples, unsigned int start, unsigned int end, vrna_boltzmann_sampling_callback *cb, void *data, 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 *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.