RNAlib-2.3.5
LPfold.h
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1 #ifndef VIENNA_RNA_PACKAGE_LPFOLD_H
2 #define VIENNA_RNA_PACKAGE_LPFOLD_H
3 
11 typedef void (vrna_probs_window_callback)(FLT_OR_DBL *pr,
12  int pr_size,
13  int i,
14  int max,
15  unsigned int type,
16  void *data);
17 
19 #include <ViennaRNA/params.h>
20 
21 #ifdef VRNA_WARN_DEPRECATED
22 # ifdef __GNUC__
23 # define DEPRECATED(func) func __attribute__ ((deprecated))
24 # else
25 # define DEPRECATED(func) func
26 # endif
27 #else
28 # define DEPRECATED(func) func
29 #endif
30 
31 
32 #define VRNA_EXT_LOOP 1U
33 #define VRNA_HP_LOOP 2U
34 #define VRNA_INT_LOOP 4U
35 #define VRNA_MB_LOOP 8U
36 #define VRNA_ANY_LOOP (VRNA_EXT_LOOP | VRNA_HP_LOOP | VRNA_INT_LOOP | VRNA_MB_LOOP)
37 
38 
44 #define VRNA_PROBS_WINDOW_BPP 4096U
45 
51 #define VRNA_PROBS_WINDOW_UP 8192U
52 
58 #define VRNA_PROBS_WINDOW_STACKP 16384U
59 
65 #define VRNA_PROBS_WINDOW_UP_SPLIT 32768U
66 
88 vrna_pfl_fold(const char *sequence,
89  int window_size,
90  int max_bp_span,
91  float cutoff);
92 
93 
116 void
117 vrna_pfl_fold_cb(const char *sequence,
118  int window_size,
119  int max_bp_span,
120  vrna_probs_window_callback *cb,
121  void *data);
122 
123 
147 double **
148 vrna_pfl_fold_up(const char *sequence,
149  int ulength,
150  int window_size,
151  int max_bp_span);
152 
153 
178 void
179 vrna_pfl_fold_up_cb(const char *sequence,
180  int ulength,
181  int window_size,
182  int max_bp_span,
183  vrna_probs_window_callback *cb,
184  void *data);
185 
186 
200 void
202  int ulength,
203  vrna_probs_window_callback *cb,
204  void *data,
205  unsigned int options);
206 
207 
208 #ifdef VRNA_BACKWARD_COMPAT
209 
217 DEPRECATED(void update_pf_paramsLP(int length));
218 
219 
226 DEPRECATED(void update_pf_paramsLP_par(int length,
227  vrna_exp_param_t *parameters));
228 
229 
267 DEPRECATED(vrna_plist_t *pfl_fold(char *sequence,
268  int winSize,
269  int pairSize,
270  float cutoffb,
271  double **pU,
272  vrna_plist_t **dpp2,
273  FILE *pUfp,
274  FILE *spup));
275 
276 
283 DEPRECATED(vrna_plist_t *pfl_fold_par(char *sequence,
284  int winSize,
285  int pairSize,
286  float cutoffb,
287  double **pU,
288  vrna_plist_t **dpp2,
289  FILE *pUfp,
290  FILE *spup,
291  vrna_exp_param_t *parameters));
292 
293 
294 DEPRECATED(void putoutpU_prob_par(double **pU,
295  int length,
296  int ulength,
297  FILE *fp,
298  int energies,
299  vrna_exp_param_t *parameters));
300 
301 
316 DEPRECATED(void putoutpU_prob(double **pU,
317  int length,
318  int ulength,
319  FILE *fp,
320  int energies));
321 
322 
323 DEPRECATED(void putoutpU_prob_bin_par(double **pU,
324  int length,
325  int ulength,
326  FILE *fp,
327  int energies,
328  vrna_exp_param_t *parameters));
329 
330 
345 DEPRECATED(void putoutpU_prob_bin(double **pU,
346  int length,
347  int ulength,
348  FILE *fp,
349  int energies));
350 
351 
357 DEPRECATED(void init_pf_foldLP(int length));
358 
359 #endif
360 
361 #endif
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:457
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.
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:99
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.
this datastructure is used as input parameter in functions of PS_dot.h and others ...
Definition: data_structures.h:183
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, vrna_probs_window_callback *cb, void *data, unsigned int options)
Compute various equilibrium probabilities under a sliding window approach.
vrna_plist_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.