RNAlib-2.6.3
 
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part_func_window.h
Go to the documentation of this file.
1#ifndef VIENNA_RNA_PACKAGE_PART_FUNC_WINDOW_H
2#define VIENNA_RNA_PACKAGE_PART_FUNC_WINDOW_H
3
4#ifdef VRNA_WARN_DEPRECATED
5# if defined(DEPRECATED)
6# undef DEPRECATED
7# endif
8# if defined(__clang__)
9# define DEPRECATED(func, msg) func __attribute__ ((deprecated("", msg)))
10# elif defined(__GNUC__)
11# define DEPRECATED(func, msg) func __attribute__ ((deprecated(msg)))
12# else
13# define DEPRECATED(func, msg) func
14# endif
15#else
16# define DEPRECATED(func, msg) func
17#endif
18
31
79 int pr_size,
80 int i,
81 int max,
82 unsigned int type,
83 void *data);
84
85DEPRECATED(typedef void (vrna_probs_window_callback)(FLT_OR_DBL *pr,
86 int pr_size,
87 int i,
88 int max,
89 unsigned int type,
90 void *data),
91 "Use vrna_probs_window_f instead!");
92
93
96
100#define VRNA_EXT_LOOP 1U
101
105#define VRNA_HP_LOOP 2U
106
110#define VRNA_INT_LOOP 4U
111
115#define VRNA_MB_LOOP 8U
116
120#define VRNA_ANY_LOOP (VRNA_EXT_LOOP | VRNA_HP_LOOP | VRNA_INT_LOOP | VRNA_MB_LOOP)
121
122
135#define VRNA_PROBS_WINDOW_BPP 4096U
136
149#define VRNA_PROBS_WINDOW_UP 8192U
150
163#define VRNA_PROBS_WINDOW_STACKP 16384U
164
182#define VRNA_PROBS_WINDOW_UP_SPLIT 32768U
183
184
198#define VRNA_PROBS_WINDOW_PF 65536U
199
231int
233 int ulength,
234 unsigned int options,
236 void *data);
237
238/* End basic interface */
266vrna_ep_t *
267vrna_pfl_fold(const char *sequence,
268 int window_size,
269 int max_bp_span,
270 float cutoff);
271
272
295int
296vrna_pfl_fold_cb(const char *sequence,
297 int window_size,
298 int max_bp_span,
300 void *data);
301
302
325double **
326vrna_pfl_fold_up(const char *sequence,
327 int ulength,
328 int window_size,
329 int max_bp_span);
330
331
355int
356vrna_pfl_fold_up_cb(const char *sequence,
357 int ulength,
358 int window_size,
359 int max_bp_span,
361 void *data);
362
363
364/* End simplified interface */
370#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:168
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_up_cb(const char *sequence, int ulength, int window_size, int max_bp_span, vrna_probs_window_f cb, void *data)
Compute probability of contiguous unpaired segments.
int vrna_pfl_fold_cb(const char *sequence, int window_size, int max_bp_span, vrna_probs_window_f cb, void *data)
Compute base pair probabilities using a sliding-window approach (callback version)
void(* vrna_probs_window_f)(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:78
int vrna_probs_window(vrna_fold_compound_t *fc, int ulength, unsigned int options, vrna_probs_window_f cb, void *data)
Compute various equilibrium probabilities under a sliding window approach.
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:486
Various utility- and helper-functions for secondary structure parsing, converting,...