RNAlib-2.2.10
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 
28 #include <stdio.h>
29 
32 
41 void vrna_file_helixlist( const char *seq,
42  const char *db,
43  float energy,
44  FILE *file);
45 
69 void vrna_file_connect( const char *seq,
70  const char *db,
71  float energy,
72  const char *identifier,
73  FILE *file);
74 
82 void vrna_file_bpseq( const char *seq,
83  const char *db,
84  FILE *file);
85 
86 #if WITH_JSON_SUPPORT
87 
97 void vrna_file_json(const char *seq,
98  const char *db,
99  double energy,
100  const char *identifier,
101  FILE *file);
102 
103 #endif
104 
114 #define VRNA_OPTION_MULTILINE 32U
115 
119 #define VRNA_CONSTRAINT_MULTILINE 32U
120 
185 unsigned int vrna_file_fasta_read_record(char **header,
186  char **sequence,
187  char ***rest,
188  FILE *file,
189  unsigned int options);
190 
207 char *vrna_extract_record_rest_structure( const char **lines,
208  unsigned int length,
209  unsigned int option);
210 
223 int vrna_file_SHAPE_read( const char *file_name,
224  int length,
225  double default_value,
226  char *sequence,
227  double *values);
228 
240 vrna_plist_t *vrna_file_constraints_read( const char *filename,
241  unsigned int length,
242  unsigned int options);
243 
244 
245 #ifdef VRNA_BACKWARD_COMPAT
246 
263 DEPRECATED(void vrna_extract_record_rest_constraint( char **cstruc, const char **lines, unsigned int option));
264 
269 DEPRECATED(char *extract_record_rest_structure( const char **lines,
270  unsigned int length,
271  unsigned int option));
272 
279 DEPRECATED(unsigned int read_record(char **header,
280  char **sequence,
281  char ***rest,
282  unsigned int options));
283 
284 
285 DEPRECATED(unsigned int get_multi_input_line(char **string, unsigned int options));
286 
287 #endif
288 
293 #endif
Functions dealing with file formats for Multiple Sequence Alignments (MSA)
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.
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:164
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.