RNAlib-2.4.5
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 # if defined(__clang__)
46 # define DEPRECATED(func, msg) func __attribute__ ((deprecated("", msg)))
47 # elif defined(__GNUC__)
48 # define DEPRECATED(func, msg) func __attribute__ ((deprecated(msg)))
49 # else
50 # define DEPRECATED(func, msg) func
51 # endif
52 #else
53 # define DEPRECATED(func, msg) func
54 #endif
55 
56 
57 #define VRNA_EXT_LOOP 1U
58 #define VRNA_HP_LOOP 2U
59 #define VRNA_INT_LOOP 4U
60 #define VRNA_MB_LOOP 8U
61 #define VRNA_ANY_LOOP (VRNA_EXT_LOOP | VRNA_HP_LOOP | VRNA_INT_LOOP | VRNA_MB_LOOP)
62 
63 
69 #define VRNA_PROBS_WINDOW_BPP 4096U
70 
76 #define VRNA_PROBS_WINDOW_UP 8192U
77 
83 #define VRNA_PROBS_WINDOW_STACKP 16384U
84 
90 #define VRNA_PROBS_WINDOW_UP_SPLIT 32768U
91 
92 
93 #define VRNA_PROBS_WINDOW_PF 65536U
94 
115 vrna_ep_t *
116 vrna_pfl_fold(const char *sequence,
117  int window_size,
118  int max_bp_span,
119  float cutoff);
120 
121 
144 void
145 vrna_pfl_fold_cb(const char *sequence,
146  int window_size,
147  int max_bp_span,
149  void *data);
150 
151 
175 double **
176 vrna_pfl_fold_up(const char *sequence,
177  int ulength,
178  int window_size,
179  int max_bp_span);
180 
181 
206 void
207 vrna_pfl_fold_up_cb(const char *sequence,
208  int ulength,
209  int window_size,
210  int max_bp_span,
212  void *data);
213 
214 
228 void
230  int ulength,
231  unsigned int options,
233  void *data);
234 
235 
236 #ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
237 
245 DEPRECATED(void update_pf_paramsLP(int length),
246 "This function is obsolete");
247 
248 
255 DEPRECATED(void update_pf_paramsLP_par(int length,
256  vrna_exp_param_t *parameters),
257 "Use the new API with vrna_folc_compound_t instead");
258 
259 
297 DEPRECATED(vrna_ep_t *pfl_fold(char *sequence,
298  int winSize,
299  int pairSize,
300  float cutoffb,
301  double **pU,
302  vrna_ep_t **dpp2,
303  FILE *pUfp,
304  FILE *spup),
305 "Use vrna_pfl_fold(), vrna_pfl_fold_cb(), vrna_pfl_fold_up(), or vrna_pfl_fold_up_cb() instead");
306 
307 
314 DEPRECATED(vrna_ep_t *pfl_fold_par(char *sequence,
315  int winSize,
316  int pairSize,
317  float cutoffb,
318  double **pU,
319  vrna_ep_t **dpp2,
320  FILE *pUfp,
321  FILE *spup,
322  vrna_exp_param_t *parameters),
323 "Use the new API and vrna_probs_window() instead");
324 
325 
326 DEPRECATED(void putoutpU_prob_par(double **pU,
327  int length,
328  int ulength,
329  FILE *fp,
330  int energies,
331  vrna_exp_param_t *parameters),
332 "");
333 
334 
349 DEPRECATED(void putoutpU_prob(double **pU,
350  int length,
351  int ulength,
352  FILE *fp,
353  int energies),
354 "");
355 
356 
357 DEPRECATED(void putoutpU_prob_bin_par(double **pU,
358  int length,
359  int ulength,
360  FILE *fp,
361  int energies,
362  vrna_exp_param_t *parameters),
363 "");
364 
365 
380 DEPRECATED(void putoutpU_prob_bin(double **pU,
381  int length,
382  int ulength,
383  FILE *fp,
384  int energies),
385 "");
386 
387 
393 DEPRECATED(void init_pf_foldLP(int length),
394 "This function is obsolete");
395 
396 #endif
397 
398 #endif
void putoutpU_prob_bin(double **pU, int length, int ulength, FILE *fp, int energies)
Writes the unpaired probabilities (pU) or opening energies into a binary file.
vrna_ep_t * pfl_fold(char *sequence, int winSize, int pairSize, float cutoffb, double **pU, vrna_ep_t **dpp2, FILE *pUfp, FILE *spup)
Compute partition functions for locally stable secondary structures.
Data structure representing a single entry of an element probability list (e.g. list of pair probabil...
Definition: structure_utils.h:114
double FLT_OR_DBL
Typename for floating point number in partition function computations.
Definition: data_structures.h:43
The most basic data structure required by many functions throughout the RNAlib.
Definition: fold_compound.h:131
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.
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 init_pf_foldLP(int length)
vrna_ep_t * pfl_fold_par(char *sequence, int winSize, int pairSize, float cutoffb, double **pU, vrna_ep_t **dpp2, FILE *pUfp, FILE *spup, vrna_exp_param_t *parameters)
Compute partition functions for locally stable secondary structures.
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 update_pf_paramsLP(int length)
void putoutpU_prob(double **pU, int length, int ulength, FILE *fp, int energies)
Writes the unpaired probabilities (pU) or opening energies into a file.
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.