Detailed Description

Collaboration diagram for Utilities:

Modules
	Utilities to deal with Nucleotide Alphabets
	Functions to cope with various aspects related to the nucleotide sequence alphabet.

	(Nucleic Acid Sequence) String Utilitites
	Functions to parse, convert, manipulate, create, and compare (nucleic acid sequence) strings.

	Secondary Structure Utilities
	Functions to create, parse, convert, manipulate, and compare secondary structure representations.

	Multiple Sequence Alignment Utilities
	Functions to extract features from and to manipulate multiple sequence alignments.

	Files and I/O
	Functions to parse, write, and convert various file formats and to deal with file system related issues.

	Plotting
	Functions for Creating Secondary Structure Plots, Dot-Plots, and More.

	Search Algorithms
	Implementations of various search algorithms to detect strings of objects within other strings of objects.

	Combinatorics Algorithms
	Implementations to solve various combinatorial aspects for strings of objects.

	(Abstract) Data Structures
	All datastructures and typedefs shared among the ViennaRNA Package can be found here.

	Messages
	Functions to print various kind of messages.

	Unit Conversion
	Functions to convert between various physical units.

Files
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 objects.

file	commands.h
	Parse and apply different commands that alter the behavior of secondary structure prediction and evaluation.

file	sequence.h
	Functions and data structures related to sequence representations ,.

file	units.h
	Physical Units and Functions to convert them into each other.

file	file_formats_msa.h
	Functions dealing with file formats for Multiple Sequence Alignments (MSA)

file	utils.h
	Several utilities for file handling.

file	utils.h
	Various utilities to assist in plotting secondary structures and consensus structures.

file	alignments.h
	Various utility- and helper-functions for sequence alignments and comparative structure prediction.

file	basic.h
	General utility- and helper-functions used throughout the ViennaRNA Package.

file	strings.h
	General utility- and helper-functions for RNA sequence and structure strings used throughout the ViennaRNA Package.

file	BoyerMoore.h
	Variants of the Boyer-Moore string search algorithm.

file	char_stream.h
	Implementation of a dynamic, buffered character stream.

file	stream_output.h
	An implementation of a buffered, ordered stream output data structure.

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_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)

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...

Macro Definition Documentation

#define VRNA_INPUT_FASTA_HEADER 8U

#include <ViennaRNA/utils/basic.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/basic.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/basic.h>

Allocate space safely.

Parameters

size	The 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/basic.h>

Reallocate space safely.

Parameters

p	A pointer to the memory region to be reallocated
size	The size of the memory to be allocated in bytes

Returns: A pointer to the newly allocated memory

double vrna_urn ( void )

#include <ViennaRNA/utils/basic.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/basic.h>

Generates a pseudo random integer in a specified range.

See also: vrna_urn(), vrna_init_rand()

Parameters

from	The first number in range
to	The last number in range

Returns: A pseudo random number in range [from, to]

char* vrna_time_stamp ( void )

#include <ViennaRNA/utils/basic.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/basic.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