RNAlib-2.6.3
 
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io.h
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1#ifndef VIENNA_RNA_PACKAGE_PARAMS_IO_H
2#define VIENNA_RNA_PACKAGE_PARAMS_IO_H
3
4#ifdef VRNA_WARN_DEPRECATED
5# if defined(__clang__)
6# define DEPRECATED(func, msg) func __attribute__ ((deprecated("", msg)))
7# elif defined(__GNUC__)
8# define DEPRECATED(func, msg) func __attribute__ ((deprecated(msg)))
9# else
10# define DEPRECATED(func, msg) func
11# endif
12#else
13# define DEPRECATED(func, msg) func
14#endif
15
36#define VRNA_PARAMETER_FORMAT_DEFAULT 0
37
38
52int
53vrna_params_load(const char fname[],
54 unsigned int options);
55
56
66int
67vrna_params_save(const char fname[],
68 unsigned int options);
69
70
89int
91 const char *name,
92 unsigned int options);
93
94
109int
111
112
129int
131
132
150int
152
153
170int
172
173
190int
192
193
211int
213
214
232int
234
235
253int
255
256
257#ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
258
263enum parset {
264 UNKNOWN= -1, QUIT,
265 S, S_H, HP, HP_H, B, B_H, IL, IL_H, MMH, MMH_H, MMI, MMI_H,
266 MMI1N, MMI1N_H, MMI23, MMI23_H, MMM, MMM_H, MME, MME_H, D5, D5_H, D3, D3_H,
267 INT11, INT11_H, INT21, INT21_H, INT22, INT22_H, ML, TL,
268 TRI, HEX, NIN, MISC
269};
270
271
277const char *
279
280
287DEPRECATED(void
288 read_parameter_file(const char fname[]),
289 "Use vrna_params_load() instead!");
290
291
298DEPRECATED(void
299 write_parameter_file(const char fname[]),
300 "Use vrna_params_save() instead!");
301
302
307enum parset
308gettype(const char *ident);
309
310
315char *
316settype(enum parset s);
317
318
323#endif
324
325#endif
int vrna_params_load_RNA_misc_special_hairpins(void)
Load Misc Special Hairpin RNA energy parameter set.
int vrna_params_save(const char fname[], unsigned int options)
Save energy parameters to a file.
void read_parameter_file(const char fname[])
Read energy parameters from a file.
int vrna_params_load_RNA_Langdon2018(void)
Load Langdon 2018 RNA energy parameter set.
int vrna_params_load_defaults(void)
Load default RNA energy parameter set.
int vrna_params_load_DNA_Mathews1999(void)
Load Mathews 1999 DNA energy parameter set.
int vrna_params_load_RNA_Andronescu2007(void)
Load Andronsecu 2007 RNA energy parameter set.
int vrna_params_load_RNA_Turner2004(void)
Load Turner 2004 RNA energy parameter set.
int vrna_params_load_RNA_Turner1999(void)
Load Turner 1999 RNA energy parameter set.
void write_parameter_file(const char fname[])
Write energy parameters to a file.
const char * last_parameter_file(void)
Get the file name of the parameter file that was most recently loaded.
int vrna_params_load(const char fname[], unsigned int options)
Load energy parameters from a file.
int vrna_params_load_from_string(const char *string, const char *name, unsigned int options)
Load energy paramters from string.
int vrna_params_load_DNA_Mathews2004(void)
Load Mathews 2004 DNA energy parameter set.