General utility- and helper-functions used throughout the ViennaRNA Package. More...

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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...

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_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...

char *	get_line (FILE *fp)
	Read a line of arbitrary length from a stream. 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...

void	filecopy (FILE from, FILE to)
	Inefficient `cp` More...

char *	time_stamp (void)
	Get a timestamp. More...

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

Detailed Description

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

Function Documentation

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.