RNAlib-2.5.1
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
64typedef void (vrna_mfe_window_callback)(int start,
65 int end,
66 const char *structure,
67 float en,
68 void *data);
69
70
71#ifdef VRNA_WITH_SVM
72typedef void (vrna_mfe_window_zscore_callback)(int start,
73 int end,
74 const char *structure,
75 float en,
76 float zscore,
77 void *data);
78#endif
79
110float
112 FILE *file);
113
114
115float
116vrna_mfe_window_cb(vrna_fold_compound_t *vc,
118 void *data);
119
120
121#ifdef VRNA_WITH_SVM
147float
149 double min_z,
150 FILE *file);
151
152
153float
154vrna_mfe_window_zscore_cb(vrna_fold_compound_t *vc,
155 double min_z,
156 vrna_mfe_window_zscore_callback *cb,
157 void *data);
158
159
160#endif
161
162/* End basic local MFE interface */
190float
191vrna_Lfold(const char *string,
192 int window_size,
193 FILE *file);
194
195
196float
197vrna_Lfold_cb(const char *string,
198 int window_size,
200 void *data);
201
202
203#ifdef VRNA_WITH_SVM
228float
229vrna_Lfoldz(const char *string,
230 int window_size,
231 double min_z,
232 FILE *file);
233
234
235float
236vrna_Lfoldz_cb(const char *string,
237 int window_size,
238 double min_z,
239 vrna_mfe_window_zscore_callback *cb,
240 void *data);
241
242
243#endif
244
245float vrna_aliLfold(const char **alignment,
246 int maxdist,
247 FILE *fp);
248
249
250float vrna_aliLfold_cb(const char **alignment,
251 int maxdist,
253 void *data);
254
255
256/* End simplified local MFE interface */
259/* End group mfe_fold_window */
263#endif
The Basic Fold Compound API.
The most basic data structure required by many functions throughout the RNAlib.
Definition: fold_compound.h:148
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)
void() vrna_mfe_window_callback(int start, int end, const char *structure, float en, void *data)
The default callback for sliding window MFE structure predictions.
Definition: mfe_window.h:64
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)