neobio.textui
Class NeoBio

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

public class NeoBio

extends java.lang.Object

This class is a simple command line based utility for computing pairwise sequence alignments using one of the the algorithms provided in the neobio.alignment package.

The main method takes the follwing parameters from the command line:

NeoBio <alg> <S1> <S2> [M <matrix> | S <match> <mismatch> <gap>]

• <alg> is either NW for Needleman & Wunsch (global alignment), SW for Smith & Waterman (local alignment), CLZG for Crochemore, Landau & Ziv-Ukelson global alignment or CLZL for Crochemore, Landau & Ziv-Ukelson local alignment;
• <S1> is the first sequence file;
• <S2> is the second sequence file;
• M <matrix> is for using a scoring matrix file;
• S <match> <mismatch> <gap> is for using a simple scoring scheme, where <match> is the match reward value, <mismatch> is the mismatch penalty value and <gap> is the cost of a gap (linear gap cost function).

Author:

Sergio A. de Carvalho Jr.

Constructor Summary

NeoBio()

Method Summary

static void	main(java.lang.String[] args) The main method takes parameters from the command line to compute a pairwise sequence alignment.
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

Constructor Detail

NeoBio

public NeoBio()

Method Detail

main

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

The main method takes parameters from the command line to compute a pairwise sequence alignment. See the class description for details.

Parameters:

args - command line arguments

usage

public static void usage()

Prints command line usage.