RNAlib-2.6.3
 
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file_formats.h
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1#ifndef VIENNA_RNA_PACKAGE_FILE_FORMATS_H
2#define VIENNA_RNA_PACKAGE_FILE_FORMATS_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
28#include <stdio.h>
29
31
40void
41vrna_file_helixlist(const char *seq,
42 const char *db,
43 float energy,
44 FILE *file);
45
46
70void
71vrna_file_connect(const char *seq,
72 const char *db,
73 float energy,
74 const char *identifier,
75 FILE *file);
76
77
85void
86vrna_file_bpseq(const char *seq,
87 const char *db,
88 FILE *file);
89
90
100void
101vrna_file_json(const char *seq,
102 const char *db,
103 double energy,
104 const char *identifier,
105 FILE *file);
106
116#define VRNA_OPTION_MULTILINE 32U
121#define VRNA_CONSTRAINT_MULTILINE 32U
122
192unsigned int
194 char **sequence,
195 char ***rest,
196 FILE *file,
197 unsigned int options);
198
199
217char *
219 unsigned int length,
220 unsigned int option);
221
222
235int
236vrna_file_SHAPE_read(const char *file_name,
237 int length,
238 double default_value,
239 char *sequence,
240 double *values);
241
242#define VRNA_INPUT_VERBOSE 16384U
243
244
245int
246vrna_file_connect_read_record(FILE *fp,
247 char **id,
248 char **sequence,
249 char **structure,
250 char **remainder,
251 unsigned int options);
252
253int
254vrna_file_RNAstrand_db_read_record(FILE *fp,
255 char **name_p,
256 char **sequence_p,
257 char **structure_p,
258 char **source_p,
259 char **fname_p,
260 char **id_p,
261 unsigned int options);
262
263#ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
264
283DEPRECATED(void vrna_extract_record_rest_constraint(char **cstruc,
284 const char **lines,
285 unsigned int option),
286 "This function is obsolete");
287
292DEPRECATED(char *extract_record_rest_structure(const char **lines,
293 unsigned int length,
294 unsigned int option),
295 "Use vrna_extract_record_rest_structure() instead");
296
303DEPRECATED(unsigned int read_record(char **header,
304 char **sequence,
305 char ***rest,
306 unsigned int options),
307 "Use vrna_file_fasta_read_record() instead");
308
309
310DEPRECATED(unsigned int get_multi_input_line(char **string,
311 unsigned int options),
312 "This function is obsolete");
313
314#endif
315
320#endif
Various data structures and pre-processor macros.
void vrna_file_json(const char *seq, const char *db, double energy, const char *identifier, FILE *file)
Print a secondary structure in jsonformat.
void vrna_extract_record_rest_constraint(char **cstruc, const char **lines, unsigned int option)
Extract a hard constraint encoded as pseudo dot-bracket string.
int vrna_file_SHAPE_read(const char *file_name, int length, double default_value, char *sequence, double *values)
Read data from a given SHAPE reactivity input file.
unsigned int vrna_file_fasta_read_record(char **header, char **sequence, char ***rest, FILE *file, unsigned int options)
Get a (fasta) data set from a file or stdin.
void vrna_file_bpseq(const char *seq, const char *db, FILE *file)
Print a secondary structure in bpseq format.
void vrna_file_helixlist(const char *seq, const char *db, float energy, FILE *file)
Print a secondary structure as helix list.
void vrna_file_connect(const char *seq, const char *db, float energy, const char *identifier, FILE *file)
Print a secondary structure as connect table.
char * vrna_extract_record_rest_structure(const char **lines, unsigned int length, unsigned int option)
Extract a dot-bracket structure string from (multiline)character array.
unsigned int read_record(char **header, char **sequence, char ***rest, unsigned int options)
Get a data record from stdin.