1 #ifndef VIENNA_RNA_PACKAGE_STRING_UTILS_H
2 #define VIENNA_RNA_PACKAGE_STRING_UTILS_H
5 #define VRNA_BACKWARD_COMPAT
7 #ifdef DEPRECATION_WARNINGS
9 # define DEPRECATED(func) func __attribute__ ((deprecated))
11 # define DEPRECATED(func) func
14 # define DEPRECATED(func) func
30 #define XSTR(s) STR(s)
37 #ifndef FILENAME_MAX_LENGTH
45 #define FILENAME_MAX_LENGTH 80
53 #define FILENAME_ID_LENGTH 42
60 char *strdup(
const char *s);
151 void vrna_aln_encode(
const char *sequence,
156 unsigned short **as_p,
192 #ifdef VRNA_BACKWARD_COMPAT
212 DEPRECATED(
char *
random_string(
int l,
const char symbols[]));
219 DEPRECATED(
int hamming(
const char *s1,
const char *s2));
226 DEPRECATED(
int hamming_bound(
const char *s1,
const char *s2,
int n));
void str_uppercase(char *sequence)
Convert an input sequence to uppercase.
short * vrna_seq_encode_simple(const char *sequence, vrna_md_t *md)
Get a numerical representation of the nucleotide sequence (simple version)
int vrna_hamming_distance(const char *s1, const char *s2)
Calculate hamming distance between two sequences.
char vrna_nucleotide_decode(int enc, vrna_md_t *md)
Decode a numerical representation of a nucleotide back into nucleotide alphabet.
int vrna_hamming_distance_bound(const char *s1, const char *s2, int n)
Calculate hamming distance between two sequences up to a specified length.
char * vrna_random_string(int l, const char symbols[])
Create a random string using characters from a specified symbol set.
void vrna_seq_toRNA(char *sequence)
Convert an input sequence (possibly containing DNA alphabet characters) to RNA alphabet.
The data structure that contains the complete model details used throughout the calculations.
Definition: model.h:187
char * vrna_cut_point_insert(const char *string, int cp)
Add a separating '&' character into a string according to cut-point position.
void str_DNA2RNA(char *sequence)
Convert a DNA input sequence to RNA alphabet.
char * vrna_cut_point_remove(const char *string, int *cp)
Remove a separating '&' character from a string.
int hamming(const char *s1, const char *s2)
Calculate hamming distance between two sequences.
char * random_string(int l, const char symbols[])
Create a random string using characters from a specified symbol set.
int vrna_nucleotide_encode(char c, vrna_md_t *md)
Encode a nucleotide character to numerical value.
short * vrna_seq_encode(const char *sequence, vrna_md_t *md)
Get a numerical representation of the nucleotide sequence.
void vrna_seq_toupper(char *sequence)
Convert an input sequence to uppercase.
int hamming_bound(const char *s1, const char *s2, int n)
Calculate hamming distance between two sequences up to a specified length.