RNAlib-2.6.0b
 
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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
79typedef void (*vrna_mfe_window_f)(int start,
80 int end,
81 const char *structure,
82 float en,
83 void *data);
84
85DEPRECATED(typedef void (vrna_mfe_window_callback)(int start,
86 int end,
87 const char *structure,
88 float en,
89 void *data),
90 "Use vrna_mfe_window_f instead!");
91
92
93
94#ifdef VRNA_WITH_SVM
95typedef void (*vrna_mfe_window_zscore_f)(int start,
96 int end,
97 const char *structure,
98 float en,
99 float zscore,
100 void *data);
101
102DEPRECATED(typedef void (vrna_mfe_window_zscore_callback)(int start,
103 int end,
104 const char *structure,
105 float en,
106 float zscore,
107 void *data),
108 "Use vrna_mfe_window_zscore_f instead!");
109#endif
110
141float
143 FILE *file);
144
145
146float
147vrna_mfe_window_cb(vrna_fold_compound_t *vc,
149 void *data);
150
151
152#ifdef VRNA_WITH_SVM
178float
180 double min_z,
181 FILE *file);
182
183
184float
185vrna_mfe_window_zscore_cb(vrna_fold_compound_t *vc,
186 double min_z,
187 vrna_mfe_window_zscore_f cb,
188 void *data);
189
190
191#endif
192
193/* End basic local MFE interface */
221float
222vrna_Lfold(const char *string,
223 int window_size,
224 FILE *file);
225
226
227float
228vrna_Lfold_cb(const char *string,
229 int window_size,
231 void *data);
232
233
234#ifdef VRNA_WITH_SVM
259float
260vrna_Lfoldz(const char *string,
261 int window_size,
262 double min_z,
263 FILE *file);
264
265
266float
267vrna_Lfoldz_cb(const char *string,
268 int window_size,
269 double min_z,
270 vrna_mfe_window_zscore_f cb,
271 void *data);
272
273
274#endif
275
276float vrna_aliLfold(const char **alignment,
277 int maxdist,
278 FILE *fp);
279
280
281float vrna_aliLfold_cb(const char **alignment,
282 int maxdist,
284 void *data);
285
286
287/* End simplified local MFE interface */
290/* End group mfe_fold_window */
294#endif
The Basic Fold Compound API.
The most basic data structure required by many functions throughout the RNAlib.
Definition: fold_compound.h:156
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(vrna_fold_compound_t *vc, FILE *file)
Local MFE prediction using a sliding window approach.
float vrna_mfe_window_zscore(vrna_fold_compound_t *vc, double min_z, FILE *file)
Local MFE prediction using a sliding window approach (with z-score cut-off)
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:79