RNAlib-2.2.9

- Main Page
- Related Pages
- Modules
- Data Structures
- Files

- File List
- Globals

file_formats.h
Go to the documentation of this file.
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
30 #include <ViennaRNA/data_structures.h>
31 #include <ViennaRNA/file_formats_msa.h>
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
file_formats_msa.h
Functions dealing with file formats for Multiple Sequence Alignments (MSA)
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_constraints_read
vrna_plist_t * vrna_file_constraints_read(const char *filename, unsigned int length, unsigned int options)
Read constraints from an input file.
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_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.
data_structures.h
read_record
unsigned int read_record(char **header, char **sequence, char ***rest, unsigned int options)
Get a data record from stdin.
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_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_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.
vrna_plist_s
this datastructure is used as input parameter in functions of PS_dot.h and others ...
Definition: data_structures.h:164
vrna_file_bpseq
void vrna_file_bpseq(const char *seq, const char *db, FILE *file)
Print a secondary structure in bpseq format.
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.