RNAlib-2.4.18
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 
64 typedef 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
72 typedef 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 
110 float
112  FILE *file);
113 
114 
115 float
116 vrna_mfe_window_cb(vrna_fold_compound_t *vc,
118  void *data);
119 
120 
121 #ifdef VRNA_WITH_SVM
147 float
149  double min_z,
150  FILE *file);
151 
152 
153 float
154 vrna_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 */
190 float
191 vrna_Lfold(const char *string,
192  int window_size,
193  FILE *file);
194 
195 
196 float
197 vrna_Lfold_cb(const char *string,
198  int window_size,
200  void *data);
201 
202 
203 #ifdef VRNA_WITH_SVM
228 float
229 vrna_Lfoldz(const char *string,
230  int window_size,
231  double min_z,
232  FILE *file);
233 
234 
235 float
236 vrna_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 
245 float vrna_aliLfold(const char **alignment,
246  int maxdist,
247  FILE *fp);
248 
249 
250 float 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:137
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)