RNAlib-2.2.0-RC2
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Files | |
file | utils.h |
General utility- and helper-functions used throughout the ViennaRNA Package. | |
Macros | |
#define | VRNA_INPUT_ERROR 1U |
Output flag of get_input_line(): "An ERROR has occured, maybe EOF". | |
#define | VRNA_INPUT_QUIT 2U |
Output flag of get_input_line(): "the user requested quitting the program". | |
#define | VRNA_INPUT_MISC 4U |
Output flag of get_input_line(): "something was read". | |
#define | VRNA_INPUT_FASTA_HEADER 8U |
Input/Output flag of get_input_line(): if used as input option this tells get_input_line() that the data to be read should comply with the FASTA format. More... | |
#define | VRNA_INPUT_CONSTRAINT 32U |
Input flag for get_input_line(): Tell get_input_line() that we assume to read a structure constraint. More... | |
#define | VRNA_INPUT_NO_TRUNCATION 256U |
Input switch for get_input_line(): "do not trunkate the line by eliminating white spaces at end of line". | |
#define | VRNA_INPUT_NO_REST 512U |
Input switch for vrna_read_fasta_record(): "do fill rest array". | |
#define | VRNA_INPUT_NO_SPAN 1024U |
Input switch for vrna_read_fasta_record(): "never allow data to span more than one line". | |
#define | VRNA_INPUT_NOSKIP_BLANK_LINES 2048U |
Input switch for vrna_read_fasta_record(): "do not skip empty lines". | |
#define | VRNA_INPUT_BLANK_LINE 4096U |
Output flag for vrna_read_fasta_record(): "read an empty line". | |
#define | VRNA_INPUT_NOSKIP_COMMENTS 128U |
#define | VRNA_INPUT_COMMENT 8192U |
Output flag for vrna_read_fasta_record(): "read a comment". | |
#define | VRNA_OPTION_MULTILINE 32U |
Tell a function that an input is assumed to span several lines. More... | |
#define | MIN2(A, B) ((A) < (B) ? (A) : (B)) |
Get the minimum of two comparable values. | |
#define | MAX2(A, B) ((A) > (B) ? (A) : (B)) |
Get the maximum of two comparable values. | |
#define | MIN3(A, B, C) (MIN2( (MIN2((A),(B))) ,(C))) |
Get the minimum of three comparable values. | |
#define | MAX3(A, B, C) (MAX2( (MAX2((A),(B))) ,(C))) |
Get the maximum of three comparable values. | |
#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 | |
void * | vrna_alloc (unsigned size) |
Allocate space safely. More... | |
void * | vrna_realloc (void *p, unsigned size) |
Reallocate space safely. More... | |
void | vrna_message_error (const char message[]) |
Die with an error message. More... | |
void | vrna_message_warning (const char message[]) |
Print a warning message. More... | |
void | vrna_init_rand (void) |
Initialize seed for random number generator. | |
double | vrna_urn (void) |
get a random number from [0..1] More... | |
int | vrna_int_urn (int from, int to) |
Generates a pseudo random integer in a specified range. More... | |
void | vrna_file_copy (FILE *from, FILE *to) |
Inefficient `cp'. | |
char * | vrna_time_stamp (void) |
Get a timestamp. More... | |
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... | |
char * | get_line (FILE *fp) |
Read a line of arbitrary length from a stream. More... | |
unsigned int | get_input_line (char **string, unsigned int options) |
void | vrna_message_input_seq_simple (void) |
Print a line to stdout that asks for an input sequence. More... | |
void | vrna_message_input_seq (const char *s) |
Print a line with a user defined string and a ruler to stdout. 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... | |
int * | vrna_get_iindx (unsigned int length) |
Get an index mapper array (iindx) for accessing the energy matrices, e.g. in partition function related functions. More... | |
int * | vrna_get_indx (unsigned int length) |
Get an index mapper array (indx) for accessing the energy matrices, e.g. in MFE related functions. More... | |
short * | vrna_seq_encode (const char *sequence, vrna_md_t *md) |
Get a numerical representation of the nucleotide sequence. | |
short * | vrna_seq_encode_simple (const char *sequence, vrna_md_t *md) |
Get a numerical representation of the nucleotide sequence (simple version) | |
int | vrna_nucleotide_encode (char c, vrna_md_t *md) |
Encode a nucleotide character to numerical value. More... | |
char | vrna_nucleotide_decode (int enc, vrna_md_t *md) |
Decode a numerical representation of a nucleotide back into nucleotide alphabet. More... | |
char * | vrna_get_ptypes (const short *S, vrna_md_t *md) |
Get an array of the numerical encoding for each possible base pair (i,j) More... | |
void | str_uppercase (char *sequence) |
Convert an input sequence to uppercase. More... | |
void | str_DNA2RNA (char *sequence) |
Convert a DNA input sequence to RNA alphabet. More... | |
void | print_tty_input_seq (void) |
Print a line to stdout that asks for an input sequence. More... | |
void | print_tty_input_seq_str (const char *s) |
Print a line with a user defined string and a ruler to stdout. More... | |
void | warn_user (const char message[]) |
Print a warning message. More... | |
void | nrerror (const char message[]) |
Die with an error message. More... | |
void * | space (unsigned size) |
Allocate space safely. More... | |
void * | xrealloc (void *p, unsigned size) |
Reallocate space safely. More... | |
void | init_rand (void) |
Make random number seeds. More... | |
double | urn (void) |
get a random number from [0..1] More... | |
int | int_urn (int from, int to) |
Generates a pseudo random integer in a specified range. More... | |
char * | random_string (int l, const char symbols[]) |
Create a random string using characters from a specified symbol set. More... | |
void | filecopy (FILE *from, FILE *to) |
Inefficient cp More... | |
char * | time_stamp (void) |
Get a timestamp. More... | |
int | hamming (const char *s1, const char *s2) |
Calculate hamming distance between two sequences. More... | |
int | hamming_bound (const char *s1, const char *s2, int n) |
Calculate hamming distance between two sequences up to a specified length. More... | |
Variables | |
unsigned short | xsubi [3] |
Current 48 bit random number. More... | |
#define VRNA_INPUT_FASTA_HEADER 8U |
Input/Output flag of get_input_line():
if used as input option this tells get_input_line() that the data to be read should comply with the FASTA format.
the function will return this flag if a fasta header was read
#define VRNA_INPUT_CONSTRAINT 32U |
Input flag for get_input_line():
Tell get_input_line() that we assume to read a structure constraint.
#define VRNA_INPUT_NOSKIP_COMMENTS 128U |
switch for get_input_line(): "do not skip comment lines"
#define VRNA_OPTION_MULTILINE 32U |
Tell a function that an input is assumed to span several lines.
If used as input-option a function might also be returning this state telling that it has read data from multiple lines.
#define FILENAME_MAX_LENGTH 80 |
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 |
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
void* vrna_alloc | ( | unsigned | size | ) |
Allocate space safely.
size | The size of the memory to be allocated in bytes |
void* vrna_realloc | ( | void * | p, |
unsigned | size | ||
) |
Reallocate space safely.
p | A pointer to the memory region to be reallocated |
size | The size of the memory to be allocated in bytes |
void vrna_message_error | ( | const char | message[] | ) |
Die with an error message.
message | The error message to be printed before exiting with 'FAILURE' |
void vrna_message_warning | ( | const char | message[] | ) |
Print a warning message.
Print a warning message to stderr
message | The warning message |
double vrna_urn | ( | void | ) |
get a random number from [0..1]
int vrna_int_urn | ( | int | from, |
int | to | ||
) |
Generates a pseudo random integer in a specified range.
from | The first number in range |
to | The last number in range |
char* vrna_time_stamp | ( | void | ) |
Get a timestamp.
Returns a string containing the current date in the format
Fri Mar 19 21:10:57 1993
char* vrna_random_string | ( | int | l, |
const char | symbols[] | ||
) |
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 | ||
) |
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 | ||
) |
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 |
char* get_line | ( | FILE * | fp | ) |
Read a line of arbitrary length from a stream.
Returns a pointer to the resulting string. The necessary memory is allocated and should be released using free() when the string is no longer needed.
fp | A file pointer to the stream where the function should read from |
unsigned int get_input_line | ( | char ** | string, |
unsigned int | options | ||
) |
Retrieve a line from 'stdin' savely while skipping comment characters and other features This function returns the type of input it has read if recognized. An option argument allows to switch between different reading modes.
Currently available options are:
#VRNA_INPUT_NOPRINT_COMMENTS, VRNA_INPUT_NOSKIP_COMMENTS, #VRNA_INPUT_NOELIM_WS_SUFFIX
pass a collection of options as one value like this:
get_input_line(string, option_1 | option_2 | option_n)
If the function recognizes the type of input, it will report it in the return value. It also reports if a user defined 'quit' command (@-sign on 'stdin') was given. Possible return values are:
VRNA_INPUT_FASTA_HEADER, VRNA_INPUT_ERROR, VRNA_INPUT_MISC, VRNA_INPUT_QUIT
string | A pointer to the character array that contains the line read |
options | A collection of options for switching the functions behavior |
void vrna_message_input_seq_simple | ( | void | ) |
Print a line to stdout that asks for an input sequence.
There will also be a ruler (scale line) printed that helps orientation of the sequence positions
void vrna_message_input_seq | ( | const char * | s | ) |
Print a line with a user defined string and a ruler to stdout.
(usually this is used to ask for user input) There will also be a ruler (scale line) printed that helps orientation of the sequence positions
s | A user defined string that will be printed to stdout |
void vrna_seq_toRNA | ( | char * | sequence | ) |
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 | ) |
Convert an input sequence to uppercase.
sequence | The sequence to be converted |
int* vrna_get_iindx | ( | unsigned int | length | ) |
Get an index mapper array (iindx) for accessing the energy matrices, e.g. in partition function related functions.
Access of a position "(i,j)" is then accomplished by using
(i,j) ~ iindx[i]-j
This function is necessary as most of the two-dimensional energy matrices are actually one-dimensional arrays throughout the ViennaRNA Package
Consult the implemented code to find out about the mapping formula ;)
length | The length of the RNA sequence |
int* vrna_get_indx | ( | unsigned int | length | ) |
Get an index mapper array (indx) for accessing the energy matrices, e.g. in MFE related functions.
Access of a position "(i,j)" is then accomplished by using
(i,j) ~ indx[j]+i
This function is necessary as most of the two-dimensional energy matrices are actually one-dimensional arrays throughout the ViennaRNAPackage
Consult the implemented code to find out about the mapping formula ;)
length | The length of the RNA sequence |
int vrna_nucleotide_encode | ( | char | c, |
vrna_md_t * | md | ||
) |
Encode a nucleotide character to numerical value.
This function encodes a nucleotide character to its numerical representation as required by many functions in RNAlib.
c | The nucleotide character to encode |
md | The model details that determine the kind of encoding |
char vrna_nucleotide_decode | ( | int | enc, |
vrna_md_t * | md | ||
) |
Decode a numerical representation of a nucleotide back into nucleotide alphabet.
This function decodes a numerical representation of a nucleotide character back into nucleotide alphabet
enc | The encoded nucleotide |
md | The model details that determine the kind of decoding |
char* vrna_get_ptypes | ( | const short * | S, |
vrna_md_t * | md | ||
) |
Get an array of the numerical encoding for each possible base pair (i,j)
void str_uppercase | ( | char * | sequence | ) |
Convert an input sequence to uppercase.
void str_DNA2RNA | ( | char * | sequence | ) |
Convert a DNA input sequence to RNA alphabet.
void print_tty_input_seq | ( | void | ) |
Print a line to stdout that asks for an input sequence.
There will also be a ruler (scale line) printed that helps orientation of the sequence positions
void print_tty_input_seq_str | ( | const char * | s | ) |
Print a line with a user defined string and a ruler to stdout.
(usually this is used to ask for user input) There will also be a ruler (scale line) printed that helps orientation of the sequence positions
void warn_user | ( | const char | message[] | ) |
Print a warning message.
Print a warning message to stderr
void nrerror | ( | const char | message[] | ) |
Die with an error message.
void* space | ( | unsigned | size | ) |
Allocate space safely.
void* xrealloc | ( | void * | p, |
unsigned | size | ||
) |
Reallocate space safely.
void init_rand | ( | void | ) |
Make random number seeds.
double urn | ( | void | ) |
get a random number from [0..1]
int int_urn | ( | int | from, |
int | to | ||
) |
Generates a pseudo random integer in a specified range.
char* random_string | ( | int | l, |
const char | symbols[] | ||
) |
Create a random string using characters from a specified symbol set.
void filecopy | ( | FILE * | from, |
FILE * | to | ||
) |
Inefficient cp
char* time_stamp | ( | void | ) |
Get a timestamp.
int hamming | ( | const char * | s1, |
const char * | s2 | ||
) |
Calculate hamming distance between two sequences.
int hamming_bound | ( | const char * | s1, |
const char * | s2, | ||
int | n | ||
) |
Calculate hamming distance between two sequences up to a specified length.
unsigned short xsubi[3] |
Current 48 bit random number.
This variable is used by vrna_urn(). These should be set to some random number seeds before the first call to vrna_urn().