RNAlib-2.4.0
LPfold.h
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1 #ifndef VIENNA_RNA_PACKAGE_LPFOLD_H
2 #define VIENNA_RNA_PACKAGE_LPFOLD_H
3 
35  int pr_size,
36  int i,
37  int max,
38  unsigned int type,
39  void *data);
40 
42 #include <ViennaRNA/params.h>
43 
44 #ifdef VRNA_WARN_DEPRECATED
45 # ifdef __GNUC__
46 # define DEPRECATED(func) func __attribute__ ((deprecated))
47 # else
48 # define DEPRECATED(func) func
49 # endif
50 #else
51 # define DEPRECATED(func) func
52 #endif
53 
54 
55 #define VRNA_EXT_LOOP 1U
56 #define VRNA_HP_LOOP 2U
57 #define VRNA_INT_LOOP 4U
58 #define VRNA_MB_LOOP 8U
59 #define VRNA_ANY_LOOP (VRNA_EXT_LOOP | VRNA_HP_LOOP | VRNA_INT_LOOP | VRNA_MB_LOOP)
60 
61 
67 #define VRNA_PROBS_WINDOW_BPP 4096U
68 
74 #define VRNA_PROBS_WINDOW_UP 8192U
75 
81 #define VRNA_PROBS_WINDOW_STACKP 16384U
82 
88 #define VRNA_PROBS_WINDOW_UP_SPLIT 32768U
89 
90 
91 #define VRNA_PROBS_WINDOW_PF 65536U
92 
113 vrna_ep_t *
114 vrna_pfl_fold(const char *sequence,
115  int window_size,
116  int max_bp_span,
117  float cutoff);
118 
119 
142 void
143 vrna_pfl_fold_cb(const char *sequence,
144  int window_size,
145  int max_bp_span,
147  void *data);
148 
149 
173 double **
174 vrna_pfl_fold_up(const char *sequence,
175  int ulength,
176  int window_size,
177  int max_bp_span);
178 
179 
204 void
205 vrna_pfl_fold_up_cb(const char *sequence,
206  int ulength,
207  int window_size,
208  int max_bp_span,
210  void *data);
211 
212 
226 void
228  int ulength,
229  unsigned int options,
231  void *data);
232 
233 
234 #ifdef VRNA_BACKWARD_COMPAT
235 
243 DEPRECATED(void update_pf_paramsLP(int length));
244 
245 
252 DEPRECATED(void update_pf_paramsLP_par(int length,
253  vrna_exp_param_t *parameters));
254 
255 
293 DEPRECATED(vrna_ep_t *pfl_fold(char *sequence,
294  int winSize,
295  int pairSize,
296  float cutoffb,
297  double **pU,
298  vrna_ep_t **dpp2,
299  FILE *pUfp,
300  FILE *spup));
301 
302 
309 DEPRECATED(vrna_ep_t *pfl_fold_par(char *sequence,
310  int winSize,
311  int pairSize,
312  float cutoffb,
313  double **pU,
314  vrna_ep_t **dpp2,
315  FILE *pUfp,
316  FILE *spup,
317  vrna_exp_param_t *parameters));
318 
319 
320 DEPRECATED(void putoutpU_prob_par(double **pU,
321  int length,
322  int ulength,
323  FILE *fp,
324  int energies,
325  vrna_exp_param_t *parameters));
326 
327 
342 DEPRECATED(void putoutpU_prob(double **pU,
343  int length,
344  int ulength,
345  FILE *fp,
346  int energies));
347 
348 
349 DEPRECATED(void putoutpU_prob_bin_par(double **pU,
350  int length,
351  int ulength,
352  FILE *fp,
353  int energies,
354  vrna_exp_param_t *parameters));
355 
356 
371 DEPRECATED(void putoutpU_prob_bin(double **pU,
372  int length,
373  int ulength,
374  FILE *fp,
375  int energies));
376 
377 
383 DEPRECATED(void init_pf_foldLP(int length));
384 
385 #endif
386 
387 #endif
Data structure representing a single entry of an element probability list (e.g. list of pair probabil...
Definition: structure_utils.h:69
double FLT_OR_DBL
Typename for floating point number in partition function computations.
Definition: data_structures.h:48
The most basic data structure required by many functions throughout the RNAlib.
Definition: data_structures.h:463
void vrna_pfl_fold_up_cb(const char *sequence, int ulength, int window_size, int max_bp_span, vrna_probs_window_callback *cb, void *data)
Compute probability of contiguous unpaired segments.
vrna_ep_t * vrna_pfl_fold(const char *sequence, int window_size, int max_bp_span, float cutoff)
Compute base pair probabilities using a sliding-window approach.
Various data structures and pre-processor macros.
Functions to deal with sets of energy parameters.
The data structure that contains temperature scaled Boltzmann weights of the energy parameters...
Definition: params.h:101
void( vrna_probs_window_callback)(FLT_OR_DBL *pr, int pr_size, int i, int max, unsigned int type, void *data)
Sliding window probability computation callback.
Definition: LPfold.h:34
void vrna_pfl_fold_cb(const char *sequence, int window_size, int max_bp_span, vrna_probs_window_callback *cb, void *data)
Compute base pair probabilities using a sliding-window approach (callback version) ...
double ** vrna_pfl_fold_up(const char *sequence, int ulength, int window_size, int max_bp_span)
Compute probability of contiguous unpaired segments.
FLT_OR_DBL * pr
A pointer to the base pair probability matrix.
int max_bp_span
Maximum allowed base pair span.
void vrna_probs_window(vrna_fold_compound_t *fc, int ulength, unsigned int options, vrna_probs_window_callback *cb, void *data)
Compute various equilibrium probabilities under a sliding window approach.