RNAlib-2.4.14
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>
5 #include <ViennaRNA/fold_compound.h>
6 
60 typedef void (vrna_mfe_window_callback)(int start,
61  int end,
62  const char *structure,
63  float en,
64  void *data);
65 
66 
67 #ifdef VRNA_WITH_SVM
68 typedef void (vrna_mfe_window_zscore_callback)(int start,
69  int end,
70  const char *structure,
71  float en,
72  float zscore,
73  void *data);
74 #endif
75 
106 float
107 vrna_mfe_window(vrna_fold_compound_t *vc,
108  FILE *file);
109 
110 
111 float
112 vrna_mfe_window_cb(vrna_fold_compound_t *vc,
113  vrna_mfe_window_callback *cb,
114  void *data);
115 
116 
117 #ifdef VRNA_WITH_SVM
118 
143 float
144 vrna_mfe_window_zscore(vrna_fold_compound_t *vc,
145  double min_z,
146  FILE *file);
147 
148 
149 float
150 vrna_mfe_window_zscore_cb(vrna_fold_compound_t *vc,
151  double min_z,
152  vrna_mfe_window_zscore_callback *cb,
153  void *data);
154 
155 
156 #endif
157 
158 /* End basic local MFE interface */
186 float
187 vrna_Lfold(const char *string,
188  int window_size,
189  FILE *file);
190 
191 
192 float
193 vrna_Lfold_cb(const char *string,
194  int window_size,
195  vrna_mfe_window_callback *cb,
196  void *data);
197 
198 
199 #ifdef VRNA_WITH_SVM
200 
224 float
225 vrna_Lfoldz(const char *string,
226  int window_size,
227  double min_z,
228  FILE *file);
229 
230 
231 float
232 vrna_Lfoldz_cb(const char *string,
233  int window_size,
234  double min_z,
235  vrna_mfe_window_zscore_callback *cb,
236  void *data);
237 
238 
239 #endif
240 
241 float vrna_aliLfold(const char **alignment,
242  int maxdist,
243  FILE *fp);
244 
245 
246 float vrna_aliLfold_cb(const char **alignment,
247  int maxdist,
248  vrna_mfe_window_callback *cb,
249  void *data);
250 
251 
252 /* End simplified local MFE interface */
255 /* End group mfe_fold_window */
259 #endif
vrna_mfe_window
float vrna_mfe_window(vrna_fold_compound_t *vc, FILE *file)
Local MFE prediction using a sliding window approach.
vrna_fc_s
The most basic data structure required by many functions throughout the RNAlib.
Definition: fold_compound.h:132
vrna_Lfoldz
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) ...
vrna_Lfold
float vrna_Lfold(const char *string, int window_size, FILE *file)
Local MFE prediction using a sliding window approach (simplified interface)
vrna_mfe_window_callback
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:60
vrna_mfe_window_zscore
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)
fold_compound.h
The Basic Fold Compound API.