RNAlib-2.5.1
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
16
64 int pr_size,
65 int i,
66 int max,
67 unsigned int type,
68 void *data);
69
72
76#define VRNA_EXT_LOOP 1U
77
81#define VRNA_HP_LOOP 2U
82
86#define VRNA_INT_LOOP 4U
87
91#define VRNA_MB_LOOP 8U
92
96#define VRNA_ANY_LOOP (VRNA_EXT_LOOP | VRNA_HP_LOOP | VRNA_INT_LOOP | VRNA_MB_LOOP)
97
98
111#define VRNA_PROBS_WINDOW_BPP 4096U
112
125#define VRNA_PROBS_WINDOW_UP 8192U
126
139#define VRNA_PROBS_WINDOW_STACKP 16384U
140
158#define VRNA_PROBS_WINDOW_UP_SPLIT 32768U
159
160
174#define VRNA_PROBS_WINDOW_PF 65536U
175
207int
209 int ulength,
210 unsigned int options,
212 void *data);
213
214/* End basic interface */
243vrna_ep_t *
244vrna_pfl_fold(const char *sequence,
245 int window_size,
246 int max_bp_span,
247 float cutoff);
248
249
272int
273vrna_pfl_fold_cb(const char *sequence,
274 int window_size,
275 int max_bp_span,
277 void *data);
278
279
302double **
303vrna_pfl_fold_up(const char *sequence,
304 int ulength,
305 int window_size,
306 int max_bp_span);
307
308
332int
333vrna_pfl_fold_up_cb(const char *sequence,
334 int ulength,
335 int window_size,
336 int max_bp_span,
338 void *data);
339
340
341/* End simplified interface */
347#endif
Various data structures and pre-processor macros.
The Basic Fold Compound API.
FLT_OR_DBL * pr
A pointer to the base pair probability matrix.
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:148
int max_bp_span
Maximum allowed base pair span.
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.
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)
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.
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:63
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.
double ** vrna_pfl_fold_up(const char *sequence, int ulength, int window_size, int max_bp_span)
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:482
Various utility- and helper-functions for secondary structure parsing, converting,...