RNAlib-2.6.0
 
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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
91#if VRNA_WITH_JSON_SUPPORT
92
102void
103vrna_file_json(const char *seq,
104 const char *db,
105 double energy,
106 const char *identifier,
107 FILE *file);
108
109
110#endif
111
121#define VRNA_OPTION_MULTILINE 32U
126#define VRNA_CONSTRAINT_MULTILINE 32U
127
197unsigned int
199 char **sequence,
200 char ***rest,
201 FILE *file,
202 unsigned int options);
203
204
222char *
224 unsigned int length,
225 unsigned int option);
226
227
240int
241vrna_file_SHAPE_read(const char *file_name,
242 int length,
243 double default_value,
244 char *sequence,
245 double *values);
246
247#define VRNA_INPUT_VERBOSE 16384U
248
249
250int
251vrna_file_connect_read_record(FILE *fp,
252 char **id,
253 char **sequence,
254 char **structure,
255 char **remainder,
256 unsigned int options);
257
258int
259vrna_file_RNAstrand_db_read_record(FILE *fp,
260 char **name_p,
261 char **sequence_p,
262 char **structure_p,
263 char **source_p,
264 char **fname_p,
265 char **id_p,
266 unsigned int options);
267
268#ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
269
288DEPRECATED(void vrna_extract_record_rest_constraint(char **cstruc,
289 const char **lines,
290 unsigned int option),
291 "This function is obsolete");
292
297DEPRECATED(char *extract_record_rest_structure(const char **lines,
298 unsigned int length,
299 unsigned int option),
300 "Use vrna_extract_record_rest_structure() instead");
301
308DEPRECATED(unsigned int read_record(char **header,
309 char **sequence,
310 char ***rest,
311 unsigned int options),
312 "Use vrna_file_fasta_read_record() instead");
313
314
315DEPRECATED(unsigned int get_multi_input_line(char **string,
316 unsigned int options),
317 "This function is obsolete");
318
319#endif
320
325#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.