file_formats.h
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#ifndef VIENNA_RNA_PACKAGE_FILE_FORMATS_H
#define VIENNA_RNA_PACKAGE_FILE_FORMATS_H
#ifdef DEPRECATION_WARNINGS
# ifdef __GNUC__
# define DEPRECATED(func) func __attribute__ ((deprecated))
# else
# define DEPRECATED(func) func
# endif
#else
# define DEPRECATED(func) func
#endif
/* make this interface backward compatible with RNAlib < 2.2.0 */
#define VRNA_BACKWARD_COMPAT
#include <stdio.h>
#include <ViennaRNA/data_structures.h>
void vrna_file_helixlist( const char *seq,
const char *db,
float energy,
FILE *file);
void vrna_file_connect( const char *seq,
const char *db,
float energy,
const char *identifier,
FILE *file);
void vrna_file_bpseq( const char *seq,
const char *db,
FILE *file);
#if WITH_JSON_SUPPORT
void vrna_file_json(const char *seq,
const char *db,
double energy,
const char *identifier,
FILE *file);
#endif
#define VRNA_OPTION_MULTILINE 32U
#define VRNA_CONSTRAINT_MULTILINE 32U
unsigned int vrna_file_fasta_read_record(char **header,
char **sequence,
char ***rest,
FILE *file,
unsigned int options);
char *vrna_extract_record_rest_structure( const char **lines,
unsigned int length,
unsigned int option);
int vrna_file_SHAPE_read( const char *file_name,
int length,
double default_value,
char *sequence,
double *values);
vrna_plist_t *vrna_file_constraints_read( const char *filename,
unsigned int length,
unsigned int options);
#ifdef VRNA_BACKWARD_COMPAT
DEPRECATED(void vrna_extract_record_rest_constraint( char **cstruc, const char **lines, unsigned int option));
DEPRECATED(char *extract_record_rest_structure( const char **lines,
unsigned int length,
unsigned int option));
DEPRECATED(unsigned int read_record(char **header,
char **sequence,
char ***rest,
unsigned int options));
DEPRECATED(unsigned int get_multi_input_line(char **string, unsigned int options));
#endif
#endif
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.