RNAlib-2.5.1
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
35#define VRNA_PARAMETER_FORMAT_DEFAULT 0
36
37
51int
52vrna_params_load(const char fname[],
53 unsigned int options);
54
55
65int
66vrna_params_save(const char fname[],
67 unsigned int options);
68
69
89int
91 const char *name,
92 unsigned int options);
93
94
110int
112
113
126int
128
129
142int
144
145
158int
160
161
174int
176
177
190int
192
193
206int
208
209
222int
224
225
226#ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
227
232enum parset {
233 UNKNOWN= -1, QUIT,
234 S, S_H, HP, HP_H, B, B_H, IL, IL_H, MMH, MMH_H, MMI, MMI_H,
235 MMI1N, MMI1N_H, MMI23, MMI23_H, MMM, MMM_H, MME, MME_H, D5, D5_H, D3, D3_H,
236 INT11, INT11_H, INT21, INT21_H, INT22, INT22_H, ML, TL,
237 TRI, HEX, NIN, MISC
238};
239
240
246const char *
248
249
256DEPRECATED(void
257 read_parameter_file(const char fname[]),
258 "Use vrna_params_load() instead!");
259
260
267DEPRECATED(void
268 write_parameter_file(const char fname[]),
269 "Use vrna_params_save() instead!");
270
271
276enum parset
277gettype(const char *ident);
278
279
284char *
285settype(enum parset s);
286
287
292#endif
293
294#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.