RNAlib-2.2.5
string_utils.h
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1 #ifndef VIENNA_RNA_PACKAGE_STRING_UTILS_H
2 #define VIENNA_RNA_PACKAGE_STRING_UTILS_H
3 
4 /* make this interface backward compatible with RNAlib < 2.2.0 */
5 #define VRNA_BACKWARD_COMPAT
6 
7 #ifdef DEPRECATION_WARNINGS
8 # ifdef __GNUC__
9 # define DEPRECATED(func) func __attribute__ ((deprecated))
10 # else
11 # define DEPRECATED(func) func
12 # endif
13 #else
14 # define DEPRECATED(func) func
15 #endif
16 
29 
33 #define XSTR(s) STR(s)
34 
38 #define STR(s) #s
39 
40 #ifndef FILENAME_MAX_LENGTH
41 
48 #define FILENAME_MAX_LENGTH 80
49 
56 #define FILENAME_ID_LENGTH 42
57 
58 #endif
59 
60 #ifdef HAVE_CONFIG_H
61 #include <config.h>
62 #ifndef HAVE_STRDUP
63 char *strdup(const char *s);
64 #endif
65 #endif
66 
74 char *vrna_random_string(int l, const char symbols[]);
75 
83 int vrna_hamming_distance(const char *s1, const char *s2);
84 
94 int vrna_hamming_distance_bound(const char *s1, const char *s2, int n);
95 
103 void vrna_seq_toRNA(char *sequence);
104 
110 void vrna_seq_toupper(char *sequence);
111 
123 char *vrna_cut_point_insert(const char *string,
124  int cp);
125 
138 char *vrna_cut_point_remove(const char *string,
139  int *cp);
140 
145 #ifdef VRNA_BACKWARD_COMPAT
146 
151 DEPRECATED(void str_uppercase(char *sequence));
152 
158 DEPRECATED(void str_DNA2RNA(char *sequence));
159 
165 DEPRECATED(char *random_string(int l, const char symbols[]));
166 
172 DEPRECATED(int hamming(const char *s1, const char *s2));
173 
179 DEPRECATED(int hamming_bound(const char *s1, const char *s2, int n));
180 
181 #endif
182 
183 #endif
void str_uppercase(char *sequence)
Convert an input sequence to uppercase.
int vrna_hamming_distance(const char *s1, const char *s2)
Calculate hamming distance between two sequences.
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.
Various data structures and pre-processor macros.
void vrna_seq_toRNA(char *sequence)
Convert an input sequence (possibly containing DNA alphabet characters) to RNA alphabet.
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.
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.