RNAlib-2.3.1
Utilities
+ Collaboration diagram for Utilities:

Modules

 Parsing, converting, and comparing sequences
 
 Parsing, converting, comparing secondary structures
 
 Utilities for sequence alignments
 
 Functions to Read/Write several File Formats for RNA Sequences, Structures, and Alignments
 Functions dealing with file formats for RNA sequences, structures, and alignments.
 
 Functions for Creating RNA Secondary Structures Plots, Dot-Plots, and More
 
 Functions to convert between various units
 

Files

file  aln_util.h
 Various utility- and helper-functions for sequence alignments and comparative structure prediction.
 
file  alphabet.h
 Functions to process, convert, and generally handle different nucleotide and/or base pair alphabets.
 
file  combinatorics.h
 Various implementations that deal with combinatorial aspects of RNA/DNA folding.
 
file  string_utils.h
 General utility- and helper-functions for RNA sequence and structure strings used throughout the ViennaRNA Package.
 
file  structure_utils.h
 Various utility- and helper-functions for secondary structure parsing, converting, etc.
 
file  utils.h
 General utility- and helper-functions used throughout the ViennaRNA Package.
 
char * vrna_ptypes (const short *S, vrna_md_t *md)
 Get an array of the numerical encoding for each possible base pair (i,j) 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...
 
unsigned int ** vrna_enumerate_necklaces (const unsigned int *type_counts)
 Enumerate all necklaces with fixed content. More...
 
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 *format,...)
 Print an error message and die. More...
 
void vrna_message_verror (const char *format, va_list args)
 Print an error message and die. More...
 
void vrna_message_warning (const char *format,...)
 Print a warning message. More...
 
void vrna_message_vwarning (const char *format, va_list args)
 Print a warning message. More...
 
void vrna_message_info (FILE *fp, const char *format,...)
 Print an info message. More...
 
void vrna_message_vinfo (FILE *fp, const char *format, va_list args)
 Print an info 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...
 
char * vrna_time_stamp (void)
 Get a timestamp. 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...
 
#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.
 
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

unsigned int ** vrna_enumerate_necklaces ( const unsigned int *  type_counts)

#include <ViennaRNA/combinatorics.h>

Enumerate all necklaces with fixed content.

This function implements A fast algorithm to generate necklaces with fixed content as published by Joe Sawada in 2003 [16].

The function receives a list of counts (the elements on the necklace) for each type of object within a necklace. The list starts at index 0 and ends with an entry that has a count of 0. The algorithm then enumerates all non-cyclic permutations of the content, returned as a list of necklaces. This list, again, is zero-terminated, i.e. the last entry of the list is a NULL pointer.

Parameters
type_countsA 0-terminated list of entity counts
Returns
A list of all non-cyclic permutations of the entities
SWIG Wrapper Notes:
This function is available as global function enumerate_necklaces() which accepts lists input, an produces list of lists output.
char* vrna_ptypes ( const short *  S,
vrna_md_t md 
)

#include <ViennaRNA/alphabet.h>

Get an array of the numerical encoding for each possible base pair (i,j)

Note
This array is always indexed in column-wise order, in contrast to previously different indexing between mfe and pf variants!
See also
vrna_idx_col_wise(), vrna_fold_compound_t
int vrna_nucleotide_encode ( char  c,
vrna_md_t md 
)

#include <ViennaRNA/alphabet.h>

Encode a nucleotide character to numerical value.

This function encodes a nucleotide character to its numerical representation as required by many functions in RNAlib.

See also
vrna_nucleotide_decode(), vrna_seq_encode()
Parameters
cThe nucleotide character to encode
mdThe model details that determine the kind of encoding
Returns
The encoded nucleotide
char vrna_nucleotide_decode ( int  enc,
vrna_md_t md 
)

#include <ViennaRNA/alphabet.h>

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

See also
vrna_nucleotide_encode(), vrna_seq_encode()
Parameters
encThe encoded nucleotide
mdThe model details that determine the kind of decoding
Returns
The decoded nucleotide character
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 *  format,
  ... 
)

#include <ViennaRNA/utils.h>

Print an error message and die.

This function is a wrapper to fprintf(stderr, ...) that puts a capital ERROR: in front of the message and then exits the calling program.

See also
vrna_message_verror(), vrna_message_warning(), vrna_message_info()
Parameters
formatThe error message to be printed
...Optional arguments for the formatted message string
void vrna_message_verror ( const char *  format,
va_list  args 
)

#include <ViennaRNA/utils.h>

Print an error message and die.

This function is a wrapper to vfprintf(stderr, ...) that puts a capital ERROR: in front of the message and then exits the calling program.

See also
vrna_message_error(), vrna_message_warning(), vrna_message_info()
Parameters
formatThe error message to be printed
argsThe argument list for the formatted message string
void vrna_message_warning ( const char *  format,
  ... 
)

#include <ViennaRNA/utils.h>

Print a warning message.

This function is a wrapper to fprintf(stderr, ...) that puts a capital WARNING: in front of the message.

See also
vrna_message_vwarning(), vrna_message_error(), vrna_message_info()
Parameters
formatThe warning message to be printed
...Optional arguments for the formatted message string
void vrna_message_vwarning ( const char *  format,
va_list  args 
)

#include <ViennaRNA/utils.h>

Print a warning message.

This function is a wrapper to fprintf(stderr, ...) that puts a capital WARNING: in front of the message.

See also
vrna_message_vwarning(), vrna_message_error(), vrna_message_info()
Parameters
formatThe warning message to be printed
argsThe argument list for the formatted message string
void vrna_message_info ( FILE *  fp,
const char *  format,
  ... 
)

#include <ViennaRNA/utils.h>

Print an info message.

This function is a wrapper to fprintf(...).

See also
vrna_message_vinfo(), vrna_message_error(), vrna_message_warning()
Parameters
fpThe file pointer where the message is printed to
formatThe warning message to be printed
...Optional arguments for the formatted message string
void vrna_message_vinfo ( FILE *  fp,
const char *  format,
va_list  args 
)

#include <ViennaRNA/utils.h>

Print an info message.

This function is a wrapper to fprintf(...).

See also
vrna_message_vinfo(), vrna_message_error(), vrna_message_warning()
Parameters
fpThe file pointer where the message is printed to
formatThe info message to be printed
argsThe argument list for the formatted message string
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
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 one 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()