RNAlib-2.2.7
|
Files | |
file | string_utils.h |
General utility- and helper-functions for RNA sequence and structure strings used throughout the ViennaRNA Package. | |
Macros | |
#define | XSTR(s) STR(s) |
Stringify a macro after expansion. | |
#define | STR(s) #s |
Stringify a macro argument. | |
#define | FILENAME_MAX_LENGTH 80 |
Maximum length of filenames that are generated by our programs. More... | |
#define | FILENAME_ID_LENGTH 42 |
Maximum length of id taken from fasta header for filename generation. More... | |
Functions | |
char * | vrna_random_string (int l, const char symbols[]) |
Create a random string using characters from a specified symbol set. More... | |
int | vrna_hamming_distance (const char *s1, const char *s2) |
Calculate hamming distance between two sequences. More... | |
int | vrna_hamming_distance_bound (const char *s1, const char *s2, int n) |
Calculate hamming distance between two sequences up to a specified length. More... | |
void | vrna_seq_toRNA (char *sequence) |
Convert an input sequence (possibly containing DNA alphabet characters) to RNA alphabet. More... | |
void | vrna_seq_toupper (char *sequence) |
Convert an input sequence to uppercase. More... | |
char * | vrna_cut_point_insert (const char *string, int cp) |
Add a separating '&' character into a string according to cut-point position. More... | |
char * | vrna_cut_point_remove (const char *string, int *cp) |
Remove a separating '&' character from a string. More... | |
#define FILENAME_MAX_LENGTH 80 |
#include <ViennaRNA/string_utils.h>
Maximum length of filenames that are generated by our programs.
This definition should be used throughout the complete ViennaRNA package wherever a static array holding filenames of output files is declared.
#define FILENAME_ID_LENGTH 42 |
#include <ViennaRNA/string_utils.h>
Maximum length of id taken from fasta header for filename generation.
this has to be smaller than FILENAME_MAX_LENGTH since in most cases, some suffix will be appended to the ID
char* vrna_random_string | ( | int | l, |
const char | symbols[] | ||
) |
#include <ViennaRNA/string_utils.h>
Create a random string using characters from a specified symbol set.
l | The length of the sequence |
symbols | The symbol set |
int vrna_hamming_distance | ( | const char * | s1, |
const char * | s2 | ||
) |
#include <ViennaRNA/string_utils.h>
Calculate hamming distance between two sequences.
s1 | The first sequence |
s2 | The second sequence |
int vrna_hamming_distance_bound | ( | const char * | s1, |
const char * | s2, | ||
int | n | ||
) |
#include <ViennaRNA/string_utils.h>
Calculate hamming distance between two sequences up to a specified length.
This function is similar to vrna_hamming_distance() but instead of comparing both sequences up to their actual length only the first 'n' characters are taken into account
s1 | The first sequence |
s2 | The second sequence |
void vrna_seq_toRNA | ( | char * | sequence | ) |
#include <ViennaRNA/string_utils.h>
Convert an input sequence (possibly containing DNA alphabet characters) to RNA alphabet.
This function substitudes T and t with U and u, respectively
sequence | The sequence to be converted |
void vrna_seq_toupper | ( | char * | sequence | ) |
#include <ViennaRNA/string_utils.h>
Convert an input sequence to uppercase.
sequence | The sequence to be converted |
char* vrna_cut_point_insert | ( | const char * | string, |
int | cp | ||
) |
#include <ViennaRNA/string_utils.h>
Add a separating '&' character into a string according to cut-point position.
If the cut-point position is less or equal to zero, this function just returns a copy of the provided string. Otherwise, the cut-point character is set at the corresponding position
string | The original string |
cp | The cut-point position |
char* vrna_cut_point_remove | ( | const char * | string, |
int * | cp | ||
) |
#include <ViennaRNA/string_utils.h>
Remove a separating '&' character from a string.
This function removes the cut-point indicating '&' character from a string and memorizes its position in a provided integer variable. If not '&' is found in the input, the integer variable is set to -1. The function returns a copy of the input string with the '&' being sliced out.
string | The original string |
cp | The cut-point position |