neobio.textui
Class RandomFactorSequenceGenerator

java.lang.Object
  |
  +--neobio.textui.RandomFactorSequenceGenerator

public class RandomFactorSequenceGenerator

extends java.lang.Object

This class is a simple command line based utility for generating random sequences with optimal LZ78 factorisation.

The main method takes three parameters from the command line to generate a sequence: type, size and file, where:

• type is either DNA for DNA sequences or PROT for protein sequences.
• size is the number os characters.
• file (optional) is the name of a file (if ommited, sequence is written to standard output).

Author:

Sergio A. de Carvalho Jr.

Field Summary

private static char[]	DNA_CHARS Character set for DNA sequences.
private static char[]	PROT_CHARS Character set for protein sequences.

Constructor Summary

RandomFactorSequenceGenerator()

Method Summary

static void	main(java.lang.String[] args) The main method takes three parameters from the command line to generate a sequence.
private static void	usage() Prints command line usage.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

DNA_CHARS

private static final char[] DNA_CHARS

Character set for DNA sequences.

PROT_CHARS

private static final char[] PROT_CHARS

Character set for protein sequences.

Constructor Detail

RandomFactorSequenceGenerator

public RandomFactorSequenceGenerator()

Method Detail

main

public static void main(java.lang.String[] args)

The main method takes three parameters from the command line to generate a sequence. See the class description for details.

Parameters:

args - command line arguments

usage

private static void usage()

Prints command line usage.