RNAlib-2.4.4
Lfold.h
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1 #ifndef VIENNA_RNA_PACKAGE_LFOLD_H
2 #define VIENNA_RNA_PACKAGE_LFOLD_H
3 
10 #ifdef VRNA_WARN_DEPRECATED
11 # if defined(__clang__)
12 # define DEPRECATED(func, msg) func __attribute__ ((deprecated("", msg)))
13 # elif defined(__GNUC__)
14 # define DEPRECATED(func, msg) func __attribute__ ((deprecated(msg)))
15 # else
16 # define DEPRECATED(func, msg) func
17 # endif
18 #else
19 # define DEPRECATED(func, msg) func
20 #endif
21 
22 #include <ViennaRNA/mfe.h>
23 
47 float
48 vrna_Lfold(const char *string,
49  int window_size,
50  FILE *file);
51 
52 
53 float
54 vrna_Lfold_cb(const char *string,
55  int window_size,
57  void *data);
58 
59 
60 #ifdef VRNA_WITH_SVM
61 
88 float
89 vrna_Lfoldz(const char *string,
90  int window_size,
91  double min_z,
92  FILE *file);
93 
94 
95 float
96 vrna_Lfoldz_cb(const char *string,
97  int window_size,
98  double min_z,
99  vrna_mfe_window_zscore_callback *cb,
100  void *data);
101 
102 
103 #endif
104 
105 
113 float vrna_aliLfold(const char **AS,
114  int maxdist,
115  FILE *fp);
116 
117 
118 float vrna_aliLfold_cb(const char **AS,
119  int maxdist,
121  void *data);
122 
123 
124 #ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
125 
136 DEPRECATED(float Lfold(const char *string,
137  char *structure,
138  int maxdist),
139 "Use vrna_Lfold() or vrna_Lfold_cb() instead");
140 
148 DEPRECATED(float Lfoldz(const char *string,
149  char *structure,
150  int maxdist,
151  int zsc,
152  double min_z),
153 "Use vrna_Lfoldz() or vrna_Lfoldz_cb() instead");
154 
165 DEPRECATED(float aliLfold(const char **AS,
166  char *structure,
167  int maxdist),
168 "Use vrna_aliLfold() or vrna_aliLfold_cb() instead");
169 
170 
171 DEPRECATED(float aliLfold_cb(const char **AS,
172  int maxdist,
174  void *data),
175 "Use vrna_aliLfold() or vrna_aliLfold_cb() instead");
176 
177 
178 #endif
179 
180 #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:36
Compute Minimum Free energy (MFE) and backtrace corresponding secondary structures from RNA sequence ...
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().