1 #ifndef VIENNA_RNA_PACKAGE_FILE_FORMATS_H
2 #define VIENNA_RNA_PACKAGE_FILE_FORMATS_H
5 #define DEPRECATED(func) func __attribute__ ((deprecated))
7 #define DEPRECATED(func) func
11 #define VRNA_BACKWARD_COMPAT
174 const char *identifier,
188 #if WITH_JSON_SUPPORT
190 void vrna_structure_print_json(
const char *seq,
193 const char *identifier,
266 unsigned int options);
282 char *vrna_extract_record_rest_structure(
const char **lines,
284 unsigned int option);
303 unsigned int option);
319 double default_value,
336 unsigned int options);
338 #ifdef VRNA_BACKWARD_COMPAT
344 DEPRECATED(
char *extract_record_rest_structure(
const char **lines,
346 unsigned int option));
357 unsigned int options));
360 DEPRECATED(
unsigned int get_multi_input_line(
char **
string,
unsigned int options));
void vrna_structure_print_ct(const char *seq, const char *db, float energy, const char *identifier, FILE *file)
Print a secondary structure as connect table.
void vrna_structure_print_hx(const char *seq, const char *db, float energy, FILE *file)
Print a secondary structure as helix list.
unsigned int read_record(char **header, char **sequence, char ***rest, unsigned int options)
Get a data record from stdin.
this datastructure is used as input parameter in functions of PS_dot.h and others ...
Definition: data_structures.h:45
int vrna_read_SHAPE_file(const char *file_name, int length, double default_value, char *sequence, double *values)
Read data from a given SHAPE reactivity input file.
unsigned int vrna_read_fasta_record(char **header, char **sequence, char ***rest, FILE *file, unsigned int options)
Get a (fasta) data set from a file or stdin.
void vrna_structure_print_bpseq(const char *seq, const char *db, FILE *file)
Print a secondary structure in bpseq format.
plist * vrna_read_constraints_file(const char *filename, unsigned int length, unsigned int options)
Read constraints from an input file.
void vrna_extract_record_rest_constraint(char **cstruc, const char **lines, unsigned int option)
Extract a hard constraint encoded as pseudo dot-bracket string.