RNAlib-2.4.3
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 
7 
25 typedef void (vrna_mfe_window_callback)(int start,
26  int end,
27  const char *structure,
28  float en,
29  void *data);
30 
31 
32 #ifdef VRNA_WITH_SVM
33 typedef void (vrna_mfe_window_zscore_callback)(int start,
34  int end,
35  const char *structure,
36  float en,
37  float zscore,
38  void *data);
39 #endif
40 
68 float
70  char *structure);
71 
72 
85  char *structure);
86 
87 
116  FILE *file);
117 
118 
119 float vrna_mfe_window_cb(vrna_fold_compound_t *vc,
121  void *data);
122 
123 
124 #ifdef VRNA_WITH_SVM
125 
153  double min_z,
154  FILE *file);
155 
156 
157 float vrna_mfe_window_zscore_cb(vrna_fold_compound_t *vc,
158  double min_z,
159  vrna_mfe_window_zscore_callback *cb,
160  void *data);
161 
162 
163 #endif
164 
165 void
166 vrna_backtrack_from_intervals(vrna_fold_compound_t *vc,
167  vrna_bp_stack_t *bp_stack,
168  sect bt_stack[],
169  int s);
170 
171 
172 #endif
The most basic data structure required by many functions throughout the RNAlib.
Definition: fold_compound.h:130
Stack of partial structures for backtracking.
Definition: data_structures.h:135
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:144
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:25
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)