RNAlib-2.4.10
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 
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 
107  FILE *file);
108 
109 
110 float vrna_mfe_window_cb(vrna_fold_compound_t *vc,
112  void *data);
113 
114 #ifdef VRNA_WITH_SVM
115 
141  double min_z,
142  FILE *file);
143 
144 
145 float vrna_mfe_window_zscore_cb(vrna_fold_compound_t *vc,
146  double min_z,
147  vrna_mfe_window_zscore_callback *cb,
148  void *data);
149 
150 #endif
151 
152 /* End basic local MFE interface */
180 float
181 vrna_Lfold(const char *string,
182  int window_size,
183  FILE *file);
184 
185 
186 float
187 vrna_Lfold_cb(const char *string,
188  int window_size,
190  void *data);
191 
192 
193 #ifdef VRNA_WITH_SVM
194 
218 float
219 vrna_Lfoldz(const char *string,
220  int window_size,
221  double min_z,
222  FILE *file);
223 
224 
225 float
226 vrna_Lfoldz_cb(const char *string,
227  int window_size,
228  double min_z,
229  vrna_mfe_window_zscore_callback *cb,
230  void *data);
231 
232 
233 #endif
234 
235 float vrna_aliLfold(const char **alignment,
236  int maxdist,
237  FILE *fp);
238 
239 
240 float vrna_aliLfold_cb(const char **alignment,
241  int maxdist,
243  void *data);
244 
245 /* End simplified local MFE interface */
248 /* End group mfe_fold_window */
252 #endif
float vrna_mfe_window(vrna_fold_compound_t *vc, FILE *file)
Local MFE prediction using a sliding window approach.
The most basic data structure required by many functions throughout the RNAlib.
Definition: fold_compound.h:132
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) ...
Various data structures and pre-processor macros.
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:60
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)