1 #ifndef VIENNA_RNA_PACKAGE_FILE_FORMATS_H
2 #define VIENNA_RNA_PACKAGE_FILE_FORMATS_H
4 #ifdef DEPRECATION_WARNINGS
6 # define DEPRECATED(func) func __attribute__ ((deprecated))
8 # define DEPRECATED(func) func
11 # define DEPRECATED(func) func
15 #define VRNA_BACKWARD_COMPAT
70 const char *identifier,
98 const char *identifier,
112 #define VRNA_OPTION_MULTILINE 32U
117 #define VRNA_CONSTRAINT_MULTILINE 32U
187 unsigned int options);
207 unsigned int option);
223 double default_value,
240 unsigned int options);
242 #ifdef VRNA_BACKWARD_COMPAT
266 DEPRECATED(
char *extract_record_rest_structure(
const char **lines,
268 unsigned int option));
279 unsigned int options));
282 DEPRECATED(
unsigned int get_multi_input_line(
char **
string,
unsigned int options));
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.