RNAlib-2.4.14
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 
57 typedef void (vrna_boltzmann_sampling_callback)(const char *stucture,
58  void *data);
59 
75 typedef struct vrna_pbacktrack_memory_s *vrna_pbacktrack_mem_t;
76 
77 #include <ViennaRNA/fold_compound.h>
78 
108 char *
109 vrna_pbacktrack5(vrna_fold_compound_t *fc,
110  unsigned int length);
111 
112 
157 char **
158 vrna_pbacktrack5_num(vrna_fold_compound_t *fc,
159  unsigned int num_samples,
160  unsigned int length,
161  unsigned int options);
162 
163 
213 unsigned int
214 vrna_pbacktrack5_cb(vrna_fold_compound_t *fc,
215  unsigned int num_samples,
216  unsigned int length,
217  vrna_boltzmann_sampling_callback *cb,
218  void *data,
219  unsigned int options);
220 
221 
296 char **
297 vrna_pbacktrack5_resume(vrna_fold_compound_t *vc,
298  unsigned int num_samples,
299  unsigned int length,
300  vrna_pbacktrack_mem_t *nr_mem,
301  unsigned int options);
302 
303 
381 unsigned int
382 vrna_pbacktrack5_resume_cb(vrna_fold_compound_t *fc,
383  unsigned int num_samples,
384  unsigned int length,
385  vrna_boltzmann_sampling_callback *cb,
386  void *data,
387  vrna_pbacktrack_mem_t *nr_mem,
388  unsigned int options);
389 
390 
418 char *
419 vrna_pbacktrack(vrna_fold_compound_t *fc);
420 
421 
464 char **
465 vrna_pbacktrack_num(vrna_fold_compound_t *fc,
466  unsigned int num_samples,
467  unsigned int options);
468 
469 
517 unsigned int
518 vrna_pbacktrack_cb(vrna_fold_compound_t *fc,
519  unsigned int num_samples,
520  vrna_boltzmann_sampling_callback *cb,
521  void *data,
522  unsigned int options);
523 
524 
595 char **
596 vrna_pbacktrack_resume(vrna_fold_compound_t *fc,
597  unsigned int num_samples,
598  vrna_pbacktrack_mem_t *nr_mem,
599  unsigned int options);
600 
601 
675 unsigned int
676 vrna_pbacktrack_resume_cb(vrna_fold_compound_t *fc,
677  unsigned int num_samples,
678  vrna_boltzmann_sampling_callback *cb,
679  void *data,
680  vrna_pbacktrack_mem_t *nr_mem,
681  unsigned int options);
682 
683 
692 void
693 vrna_pbacktrack_mem_free(vrna_pbacktrack_mem_t s);
694 
695 
699 #endif
vrna_pbacktrack5_resume
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...
vrna_pbacktrack5_num
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...
vrna_fc_s
The most basic data structure required by many functions throughout the RNAlib.
Definition: fold_compound.h:132
vrna_pbacktrack_mem_free
void vrna_pbacktrack_mem_free(vrna_pbacktrack_mem_t s)
Release memory occupied by a Boltzmann sampling memory data structure.
vrna_pbacktrack5
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...
vrna_pbacktrack_resume_cb
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...
vrna_pbacktrack5_resume_cb
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...
vrna_pbacktrack
char * vrna_pbacktrack(vrna_fold_compound_t *fc)
Sample a secondary structure from the Boltzmann ensemble according its probability.
vrna_pbacktrack_num
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...
vrna_boltzmann_sampling_callback
void( vrna_boltzmann_sampling_callback)(const char *stucture, void *data)
Callback for Boltzmann sampling.
Definition: boltzmann_sampling.h:57
vrna_pbacktrack5_cb
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...
vrna_pbacktrack_resume
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...
fold_compound.h
The Basic Fold Compound API.
vrna_pbacktrack_mem_t
struct vrna_pbacktrack_memory_s * vrna_pbacktrack_mem_t
Boltzmann sampling memory data structure.
Definition: boltzmann_sampling.h:75
vrna_pbacktrack_cb
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...