RNAlib-2.4.4
mfe.h
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1 #ifndef VIENNA_RNA_PACKAGE_MFE_H
2 #define VIENNA_RNA_PACKAGE_MFE_H
3 
4 #include <stdio.h>
6 
36 typedef void (vrna_mfe_window_callback)(int start,
37  int end,
38  const char *structure,
39  float en,
40  void *data);
41 
42 
43 #ifdef VRNA_WITH_SVM
44 typedef void (vrna_mfe_window_zscore_callback)(int start,
45  int end,
46  const char *structure,
47  float en,
48  float zscore,
49  void *data);
50 #endif
51 
79 float
81  char *structure);
82 
83 
96  char *structure);
97 
98 
127  FILE *file);
128 
129 
130 float vrna_mfe_window_cb(vrna_fold_compound_t *vc,
132  void *data);
133 
134 
135 #ifdef VRNA_WITH_SVM
136 
164  double min_z,
165  FILE *file);
166 
167 
168 float vrna_mfe_window_zscore_cb(vrna_fold_compound_t *vc,
169  double min_z,
170  vrna_mfe_window_zscore_callback *cb,
171  void *data);
172 
173 
174 #endif
175 
176 void
177 vrna_backtrack_from_intervals(vrna_fold_compound_t *vc,
178  vrna_bp_stack_t *bp_stack,
179  sect bt_stack[],
180  int s);
181 
182 
183 #endif
The most basic data structure required by many functions throughout the RNAlib.
Definition: fold_compound.h:131
Stack of partial structures for backtracking.
Definition: data_structures.h:132
Various data structures and pre-processor macros.
float vrna_mfe_window(vrna_fold_compound_t *vc, FILE *file)
Local MFE prediction using a sliding window approach.
float vrna_mfe_dimer(vrna_fold_compound_t *vc, char *structure)
Compute the minimum free energy of two interacting RNA molecules.
Base pair stack element.
Definition: data_structures.h:141
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.h:36
float vrna_mfe(vrna_fold_compound_t *vc, char *structure)
Compute minimum free energy and an appropriate secondary structure of an RNA sequence, or RNA sequence alignment.
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)