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RNAlib-2.2.10
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Collaboration diagram for Parsing, Converting, and Comparing - Functions to Manipulate Sequence and Structure Strings: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 |
| n | The length of the subsequences to consider (starting from the 5' end) |
| 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 |