RNAlib-2.4.3
Lfold.h
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1 #ifndef VIENNA_RNA_PACKAGE_LFOLD_H
2 #define VIENNA_RNA_PACKAGE_LFOLD_H
3 
10 /* make this interface backward compatible with RNAlib < 2.2.0 */
11 #define VRNA_BACKWARD_COMPAT
12 
13 #ifdef VRNA_WARN_DEPRECATED
14 # ifdef __GNUC__
15 # define DEPRECATED(func) func __attribute__ ((deprecated))
16 # else
17 # define DEPRECATED(func) func
18 # endif
19 #else
20 # define DEPRECATED(func) func
21 #endif
22 
23 #include <ViennaRNA/mfe.h>
24 
48 float
49 vrna_Lfold(const char *string,
50  int window_size,
51  FILE *file);
52 
53 
54 float
55 vrna_Lfold_cb(const char *string,
56  int window_size,
58  void *data);
59 
60 
61 #ifdef VRNA_WITH_SVM
62 
89 float
90 vrna_Lfoldz(const char *string,
91  int window_size,
92  double min_z,
93  FILE *file);
94 
95 
96 float
97 vrna_Lfoldz_cb(const char *string,
98  int window_size,
99  double min_z,
100  vrna_mfe_window_zscore_callback *cb,
101  void *data);
102 
103 
104 #endif
105 
106 
114 float vrna_aliLfold(const char **AS,
115  int maxdist,
116  FILE *fp);
117 
118 
119 float vrna_aliLfold_cb(const char **AS,
120  int maxdist,
122  void *data);
123 
124 
125 #ifdef VRNA_BACKWARD_COMPAT
126 
137 DEPRECATED(float Lfold(const char *string,
138  char *structure,
139  int maxdist));
140 
148 DEPRECATED(float Lfoldz(const char *string,
149  char *structure,
150  int maxdist,
151  int zsc,
152  double min_z));
153 
164 float aliLfold(const char **AS,
165  char *structure,
166  int maxdist);
167 
168 
169 float aliLfold_cb(const char **AS,
170  int maxdist,
172  void *data);
173 
174 
175 #endif
176 
177 #endif
float Lfoldz(const char *string, char *structure, int maxdist, int zsc, double min_z)
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 aliLfold(const char **AS, char *structure, int maxdist)
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
MFE calculations for single RNA sequences.
float vrna_Lfold(const char *string, int window_size, FILE *file)
Local MFE prediction using a sliding window approach (simplified interface)
float Lfold(const char *string, char *structure, int maxdist)
The local analog to fold().