utils.h File Reference
Utilities

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_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...
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

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

Deprecated:
  Use vrna_message_input_seq_simple() instead!

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

Deprecated:
  Use vrna_message_input_seq() instead!

void warn_user | ( | const char | message[] | ) |

Print a warning message.

Print a warning message to stderr

Deprecated:
  Use vrna_message_warning() instead!

void nrerror | ( | const char | message[] | ) |

Die with an error message.

Deprecated:
  Use vrna_message_error() instead!

void* space | ( | unsigned | size | ) |

Allocate space safely.

Deprecated:
  Use vrna_alloc() instead!

void* xrealloc | ( | void * | p,
|  | unsigned | size
| ) |  |

Reallocate space safely.

Deprecated:
  Use vrna_realloc() instead!

void init_rand | ( | void |  | ) |

Make random number seeds.

Deprecated:
  Use vrna_init_rand() instead!

double urn | ( | void |  | ) |

get a random number from [0..1]

Deprecated:
  Use vrna_urn() instead!

int int_urn | ( | int | from,
|  | int | to
| ) |  |

Generates a pseudo random integer in a specified range.

Deprecated:
  Use vrna_int_urn() instead!

void filecopy | ( | FILE * | from,
|  | FILE * | to
| ) |  |

Inefficient `cp`

Deprecated:
  Use vrna_file_copy() instead!

char* time_stamp | ( | void |  | ) |

Get a timestamp.

Deprecated:
  Use vrna_time_stamp() instead!