RNAlib-2.6.3
 
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mfe_window.h
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1#ifndef VIENNA_RNA_PACKAGE_MFE_WINDOW_H
2#define VIENNA_RNA_PACKAGE_MFE_WINDOW_H
3
4#include <stdio.h>
6
7#ifdef VRNA_WITH_SVM
8#include <ViennaRNA/zscore.h>
9#endif
10
11#ifdef VRNA_WARN_DEPRECATED
12# if defined(DEPRECATED)
13# undef DEPRECATED
14# endif
15# if defined(__clang__)
16# define DEPRECATED(func, msg) func __attribute__ ((deprecated("", msg)))
17# elif defined(__GNUC__)
18# define DEPRECATED(func, msg) func __attribute__ ((deprecated(msg)))
19# else
20# define DEPRECATED(func, msg) func
21# endif
22#else
23# define DEPRECATED(func, msg) func
24#endif
25
80typedef void (*vrna_mfe_window_f)(int start,
81 int end,
82 const char *structure,
83 float en,
84 void *data);
85
86DEPRECATED(typedef void (vrna_mfe_window_callback)(int start,
87 int end,
88 const char *structure,
89 float en,
90 void *data),
91 "Use vrna_mfe_window_f instead!");
92
93
94
95#ifdef VRNA_WITH_SVM
96typedef void (*vrna_mfe_window_zscore_f)(int start,
97 int end,
98 const char *structure,
99 float en,
100 float zscore,
101 void *data);
102
103DEPRECATED(typedef void (vrna_mfe_window_zscore_callback)(int start,
104 int end,
105 const char *structure,
106 float en,
107 float zscore,
108 void *data),
109 "Use vrna_mfe_window_zscore_f instead!");
110#endif
111
142float
144 FILE *file);
145
146
147float
148vrna_mfe_window_cb(vrna_fold_compound_t *fc,
150 void *data);
151
152
153#ifdef VRNA_WITH_SVM
179float
181 double min_z,
182 FILE *file);
183
184
185float
186vrna_mfe_window_zscore_cb(vrna_fold_compound_t *fc,
187 double min_z,
188 vrna_mfe_window_zscore_f cb,
189 void *data);
190
191
192#endif
193
194/* End basic local MFE interface */
222float
223vrna_Lfold(const char *string,
224 int window_size,
225 FILE *file);
226
227
228float
229vrna_Lfold_cb(const char *string,
230 int window_size,
232 void *data);
233
234
235#ifdef VRNA_WITH_SVM
260float
261vrna_Lfoldz(const char *string,
262 int window_size,
263 double min_z,
264 FILE *file);
265
266
267float
268vrna_Lfoldz_cb(const char *string,
269 int window_size,
270 double min_z,
271 vrna_mfe_window_zscore_f cb,
272 void *data);
273
274
275#endif
276
277float vrna_aliLfold(const char **alignment,
278 int maxdist,
279 FILE *fp);
280
281
282float vrna_aliLfold_cb(const char **alignment,
283 int maxdist,
285 void *data);
286
287
288/* End simplified local MFE interface */
291/* End group mfe_fold_window */
295#endif
The Basic Fold Compound API.
The most basic data structure required by many functions throughout the RNAlib.
Definition fold_compound.h:168
float vrna_Lfoldz(const char *string, int window_size, double min_z, FILE *file)
Local MFE prediction using a sliding window approach with z-score cut-off (simplified interface)
float vrna_Lfold(const char *string, int window_size, FILE *file)
Local MFE prediction using a sliding window approach (simplified interface)
float vrna_mfe_window_zscore(vrna_fold_compound_t *fc, double min_z, FILE *file)
Local MFE prediction using a sliding window approach (with z-score cut-off)
float vrna_mfe_window(vrna_fold_compound_t *fc, FILE *file)
Local MFE prediction using a sliding window approach.
void(* vrna_mfe_window_f)(int start, int end, const char *structure, float en, void *data)
The default callback for sliding window MFE structure predictions.
Definition mfe_window.h:80