RNAlib-2.2.7
Utilities
+ Collaboration diagram for Utilities:

Modules

 Parsing, Converting, and Comparing - Functions to Manipulate Sequence and Structure Strings
 
 Parsing, Converting, and Comparing - Functions to Manipulate Secondary Structures
 
 Various utilities for Sequence Alignments, and Comparative Structure Prediction
 
 Functions to Read/Write several File Formats for RNA Sequences, Structures, and Alignments
 
 Functions for Creating RNA Secondary Structures Plots, Dot-Plots, and More
 

Files

file  alphabet.h
 Functions to process, convert, and generally handle different nucleotide and/or base pair alphabets.
 
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_file_fasta_read_record(): "do fill rest array".
 
#define VRNA_INPUT_NO_SPAN   1024U
 Input switch for vrna_file_fasta_read_record(): "never allow data to span more than one line".
 
#define VRNA_INPUT_NOSKIP_BLANK_LINES   2048U
 Input switch for vrna_file_fasta_read_record(): "do not skip empty lines".
 
#define VRNA_INPUT_BLANK_LINE   4096U
 Output flag for vrna_file_fasta_read_record(): "read an empty line".
 
#define VRNA_INPUT_NOSKIP_COMMENTS   128U
 Input switch for get_input_line(): "do not skip comment lines".
 
#define VRNA_INPUT_COMMENT   8192U
 Output flag for vrna_file_fasta_read_record(): "read a comment".
 
#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.
 

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 * 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...
 
int * vrna_idx_row_wise (unsigned int length)
 Get an index mapper array (iindx) for accessing the energy matrices, e.g. in partition function related functions. More...
 
int * vrna_idx_col_wise (unsigned int length)
 Get an index mapper array (indx) for accessing the energy matrices, e.g. in MFE related functions. More...
 

Variables

unsigned short xsubi [3]
 Current 48 bit random number. More...
 

Detailed Description

Macro Definition Documentation

#define VRNA_INPUT_FASTA_HEADER   8U

#include <ViennaRNA/utils.h>

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

#include <ViennaRNA/utils.h>

Input flag for get_input_line():
Tell get_input_line() that we assume to read a structure constraint.

Function Documentation

void* vrna_alloc ( unsigned  size)

#include <ViennaRNA/utils.h>

Allocate space safely.

Parameters
sizeThe size of the memory to be allocated in bytes
Returns
A pointer to the allocated memory
void* vrna_realloc ( void *  p,
unsigned  size 
)

#include <ViennaRNA/utils.h>

Reallocate space safely.

Parameters
pA pointer to the memory region to be reallocated
sizeThe size of the memory to be allocated in bytes
Returns
A pointer to the newly allocated memory
void vrna_message_error ( const char  message[])

#include <ViennaRNA/utils.h>

Die with an error message.

See also
vrna_message_warning()
Parameters
messageThe error message to be printed before exiting with 'FAILURE'
void vrna_message_warning ( const char  message[])

#include <ViennaRNA/utils.h>

Print a warning message.

Print a warning message to stderr

Parameters
messageThe warning message
double vrna_urn ( void  )

#include <ViennaRNA/utils.h>

get a random number from [0..1]

See also
vrna_int_urn(), vrna_init_rand()
Note
Usually implemented by calling erand48().
Returns
A random number in range [0..1]
int vrna_int_urn ( int  from,
int  to 
)

#include <ViennaRNA/utils.h>

Generates a pseudo random integer in a specified range.

See also
vrna_urn(), vrna_init_rand()
Parameters
fromThe first number in range
toThe last number in range
Returns
A pseudo random number in range [from, to]
char* vrna_time_stamp ( void  )

#include <ViennaRNA/utils.h>

Get a timestamp.

Returns a string containing the current date in the format

Fri Mar 19 21:10:57 1993 
Returns
A string containing the timestamp
char* get_line ( FILE *  fp)

#include <ViennaRNA/utils.h>

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.

Parameters
fpA file pointer to the stream where the function should read from
Returns
A pointer to the resulting string
unsigned int get_input_line ( char **  string,
unsigned int  options 
)

#include <ViennaRNA/utils.h>

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

Parameters
stringA pointer to the character array that contains the line read
optionsA collection of options for switching the functions behavior
Returns
A flag with information about what has been read
void vrna_message_input_seq_simple ( void  )

#include <ViennaRNA/utils.h>

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)

#include <ViennaRNA/utils.h>

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

Parameters
sA user defined string that will be printed to stdout
int* vrna_idx_row_wise ( unsigned int  length)

#include <ViennaRNA/utils.h>

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 ;)

See also
vrna_idx_col_wise()
Parameters
lengthThe length of the RNA sequence
Returns
The mapper array
int* vrna_idx_col_wise ( unsigned int  length)

#include <ViennaRNA/utils.h>

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 ;)

See also
vrna_idx_row_wise()
Parameters
lengthThe length of the RNA sequence
Returns
The mapper array

Variable Documentation

unsigned short xsubi[3]

#include <ViennaRNA/utils.h>

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().

See also
vrna_urn()