1 #ifndef VIENNA_RNA_PACKAGE_FILE_FORMATS_H 2 #define VIENNA_RNA_PACKAGE_FILE_FORMATS_H 4 #ifdef VRNA_WARN_DEPRECATED 5 # if defined(__clang__) 6 # define DEPRECATED(func, msg) func __attribute__ ((deprecated("", msg))) 7 # elif defined(__GNUC__) 8 # define DEPRECATED(func, msg) func __attribute__ ((deprecated(msg))) 10 # define DEPRECATED(func, msg) func 13 # define DEPRECATED(func, msg) func 71 const char *identifier,
85 #if VRNA_WITH_JSON_SUPPORT 99 const char *identifier,
113 #define VRNA_OPTION_MULTILINE 32U 118 #define VRNA_CONSTRAINT_MULTILINE 32U 188 unsigned int options);
208 unsigned int option);
224 double default_value,
229 #ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY 248 "This function is obsolete");
254 DEPRECATED(
char *extract_record_rest_structure(
const char **lines,
256 unsigned int option),
257 "Use vrna_extract_record_rest_structure() instead");
268 unsigned int options),
269 "Use vrna_file_fasta_read_record() instead");
272 DEPRECATED(
unsigned int get_multi_input_line(
char **
string,
unsigned int options),
273 "This function is obsolete");
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.
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.
Various data structures and pre-processor macros.
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.
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.