RNAlib-2.4.10
part_func_window.h
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1 #ifndef VIENNA_RNA_PACKAGE_PART_FUNC_WINDOW_H
2 #define VIENNA_RNA_PACKAGE_PART_FUNC_WINDOW_H
3 
62  int pr_size,
63  int i,
64  int max,
65  unsigned int type,
66  void *data);
67 
69 #include <ViennaRNA/params/basic.h>
70 
74 #define VRNA_EXT_LOOP 1U
75 
79 #define VRNA_HP_LOOP 2U
80 
84 #define VRNA_INT_LOOP 4U
85 
89 #define VRNA_MB_LOOP 8U
90 
94 #define VRNA_ANY_LOOP (VRNA_EXT_LOOP | VRNA_HP_LOOP | VRNA_INT_LOOP | VRNA_MB_LOOP)
95 
96 
109 #define VRNA_PROBS_WINDOW_BPP 4096U
110 
123 #define VRNA_PROBS_WINDOW_UP 8192U
124 
137 #define VRNA_PROBS_WINDOW_STACKP 16384U
138 
156 #define VRNA_PROBS_WINDOW_UP_SPLIT 32768U
157 
158 
172 #define VRNA_PROBS_WINDOW_PF 65536U
173 
205 int
207  int ulength,
208  unsigned int options,
210  void *data);
211 
212 /* End basic interface */
241 vrna_ep_t *
242 vrna_pfl_fold(const char *sequence,
243  int window_size,
244  int max_bp_span,
245  float cutoff);
246 
247 
270 int
271 vrna_pfl_fold_cb(const char *sequence,
272  int window_size,
273  int max_bp_span,
275  void *data);
276 
277 
300 double **
301 vrna_pfl_fold_up(const char *sequence,
302  int ulength,
303  int window_size,
304  int max_bp_span);
305 
306 
330 int
331 vrna_pfl_fold_up_cb(const char *sequence,
332  int ulength,
333  int window_size,
334  int max_bp_span,
336  void *data);
337 
338 
339 /* End simplified interface */
345 #endif
int 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 FLT_OR_DBL
Typename for floating point number in partition function computations.
Definition: basic.h:43
The most basic data structure required by many functions throughout the RNAlib.
Definition: fold_compound.h:132
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: part_func_window.h:61
Various data structures and pre-processor macros.
int 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.
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.
FLT_OR_DBL * pr
A pointer to the base pair probability matrix.
Functions to deal with sets of energy parameters.
int max_bp_span
Maximum allowed base pair span.
int 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.
Data structure representing a single entry of an element probability list (e.g. list of pair probabil...
Definition: structures.h:358
double ** vrna_pfl_fold_up(const char *sequence, int ulength, int window_size, int max_bp_span)
Compute probability of contiguous unpaired segments.