RNAlib-2.4.14
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 
30 #include <ViennaRNA/datastructures/basic.h>
31 
40 void
41 vrna_file_helixlist(const char *seq,
42  const char *db,
43  float energy,
44  FILE *file);
45 
46 
70 void
71 vrna_file_connect(const char *seq,
72  const char *db,
73  float energy,
74  const char *identifier,
75  FILE *file);
76 
77 
85 void
86 vrna_file_bpseq(const char *seq,
87  const char *db,
88  FILE *file);
89 
90 
91 #if VRNA_WITH_JSON_SUPPORT
92 
102 void
103 vrna_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
122 
126 #define VRNA_CONSTRAINT_MULTILINE 32U
127 
193 unsigned int
194 vrna_file_fasta_read_record(char **header,
195  char **sequence,
196  char ***rest,
197  FILE *file,
198  unsigned int options);
199 
200 
217 char *
218 vrna_extract_record_rest_structure(const char **lines,
219  unsigned int length,
220  unsigned int option);
221 
222 
235 int
236 vrna_file_SHAPE_read(const char *file_name,
237  int length,
238  double default_value,
239  char *sequence,
240  double *values);
241 
242 
243 #ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
244 
261 DEPRECATED(void vrna_extract_record_rest_constraint(char **cstruc,
262  const char **lines,
263  unsigned int option),
264  "This function is obsolete");
265 
270 DEPRECATED(char *extract_record_rest_structure(const char **lines,
271  unsigned int length,
272  unsigned int option),
273  "Use vrna_extract_record_rest_structure() instead");
274 
281 DEPRECATED(unsigned int read_record(char **header,
282  char **sequence,
283  char ***rest,
284  unsigned int options),
285  "Use vrna_file_fasta_read_record() instead");
286 
287 
288 DEPRECATED(unsigned int get_multi_input_line(char **string,
289  unsigned int options),
290  "This function is obsolete");
291 
292 #endif
293 
298 #endif
vrna_file_helixlist
void vrna_file_helixlist(const char *seq, const char *db, float energy, FILE *file)
Print a secondary structure as helix list.
vrna_file_SHAPE_read
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.
basic.h
Various data structures and pre-processor macros.
read_record
unsigned int read_record(char **header, char **sequence, char ***rest, unsigned int options)
Get a data record from stdin.
vrna_file_json
void vrna_file_json(const char *seq, const char *db, double energy, const char *identifier, FILE *file)
Print a secondary structure in jsonformat.
vrna_file_bpseq
void vrna_file_bpseq(const char *seq, const char *db, FILE *file)
Print a secondary structure in bpseq format.
vrna_file_fasta_read_record
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.
vrna_file_connect
void vrna_file_connect(const char *seq, const char *db, float energy, const char *identifier, FILE *file)
Print a secondary structure as connect table.
vrna_extract_record_rest_structure
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.
vrna_extract_record_rest_constraint
void vrna_extract_record_rest_constraint(char **cstruc, const char **lines, unsigned int option)
Extract a hard constraint encoded as pseudo dot-bracket string.