RNAlib-2.2.5
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 DEPRECATION_WARNINGS
5 # ifdef __GNUC__
6 # define DEPRECATED(func) func __attribute__ ((deprecated))
7 # else
8 # define DEPRECATED(func) func
9 # endif
10 #else
11 # define DEPRECATED(func) func
12 #endif
13 
14 /* make this interface backward compatible with RNAlib < 2.2.0 */
15 #define VRNA_BACKWARD_COMPAT
16 
33 #include <stdio.h>
34 
36 
44 void vrna_file_helixlist( const char *seq,
45  const char *db,
46  float energy,
47  FILE *file);
48 
72 void vrna_file_connect( const char *seq,
73  const char *db,
74  float energy,
75  const char *identifier,
76  FILE *file);
77 
85 void vrna_file_bpseq( const char *seq,
86  const char *db,
87  FILE *file);
88 
89 #if WITH_JSON_SUPPORT
90 
100 void vrna_file_json(const char *seq,
101  const char *db,
102  double energy,
103  const char *identifier,
104  FILE *file);
105 
106 #endif
107 
117 #define VRNA_OPTION_MULTILINE 32U
118 
122 #define VRNA_CONSTRAINT_MULTILINE 32U
123 
188 unsigned int vrna_file_fasta_read_record(char **header,
189  char **sequence,
190  char ***rest,
191  FILE *file,
192  unsigned int options);
193 
210 char *vrna_extract_record_rest_structure( const char **lines,
211  unsigned int length,
212  unsigned int option);
213 
226 int vrna_file_SHAPE_read( const char *file_name,
227  int length,
228  double default_value,
229  char *sequence,
230  double *values);
231 
243 vrna_plist_t *vrna_file_constraints_read( const char *filename,
244  unsigned int length,
245  unsigned int options);
246 
247 #ifdef VRNA_BACKWARD_COMPAT
248 
265 DEPRECATED(void vrna_extract_record_rest_constraint( char **cstruc, const char **lines, unsigned int option));
266 
271 DEPRECATED(char *extract_record_rest_structure( const char **lines,
272  unsigned int length,
273  unsigned int option));
274 
281 DEPRECATED(unsigned int read_record(char **header,
282  char **sequence,
283  char ***rest,
284  unsigned int options));
285 
286 
287 DEPRECATED(unsigned int get_multi_input_line(char **string, unsigned int options));
288 
289 #endif
290 
295 #endif
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_plist_t * vrna_file_constraints_read(const char *filename, unsigned int length, unsigned int options)
Read constraints from an input file.
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_file_connect(const char *seq, const char *db, float energy, const char *identifier, FILE *file)
Print a secondary structure as connect table.
Various data structures and pre-processor macros.
unsigned int read_record(char **header, char **sequence, char ***rest, unsigned int options)
Get a data record from stdin.
void vrna_file_helixlist(const char *seq, const char *db, float energy, FILE *file)
Print a secondary structure as helix list.
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.
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.
this datastructure is used as input parameter in functions of PS_dot.h and others ...
Definition: data_structures.h:171
void vrna_file_bpseq(const char *seq, const char *db, FILE *file)
Print a secondary structure in bpseq format.
void vrna_extract_record_rest_constraint(char **cstruc, const char **lines, unsigned int option)
Extract a hard constraint encoded as pseudo dot-bracket string.