RNAlib-2.2.8
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 
31 
40 void vrna_file_helixlist( const char *seq,
41  const char *db,
42  float energy,
43  FILE *file);
44 
68 void vrna_file_connect( const char *seq,
69  const char *db,
70  float energy,
71  const char *identifier,
72  FILE *file);
73 
81 void vrna_file_bpseq( const char *seq,
82  const char *db,
83  FILE *file);
84 
85 #if WITH_JSON_SUPPORT
86 
96 void vrna_file_json(const char *seq,
97  const char *db,
98  double energy,
99  const char *identifier,
100  FILE *file);
101 
102 #endif
103 
113 #define VRNA_OPTION_MULTILINE 32U
114 
118 #define VRNA_CONSTRAINT_MULTILINE 32U
119 
184 unsigned int vrna_file_fasta_read_record(char **header,
185  char **sequence,
186  char ***rest,
187  FILE *file,
188  unsigned int options);
189 
206 char *vrna_extract_record_rest_structure( const char **lines,
207  unsigned int length,
208  unsigned int option);
209 
222 int vrna_file_SHAPE_read( const char *file_name,
223  int length,
224  double default_value,
225  char *sequence,
226  double *values);
227 
239 vrna_plist_t *vrna_file_constraints_read( const char *filename,
240  unsigned int length,
241  unsigned int options);
242 
243 #ifdef VRNA_BACKWARD_COMPAT
244 
261 DEPRECATED(void vrna_extract_record_rest_constraint( char **cstruc, const char **lines, unsigned int option));
262 
267 DEPRECATED(char *extract_record_rest_structure( const char **lines,
268  unsigned int length,
269  unsigned int option));
270 
277 DEPRECATED(unsigned int read_record(char **header,
278  char **sequence,
279  char ***rest,
280  unsigned int options));
281 
282 
283 DEPRECATED(unsigned int get_multi_input_line(char **string, unsigned int options));
284 
285 #endif
286 
291 #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.
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.