applications

Class FlexfluxKO

java.lang.Object

applications.FlexfluxKO

public class FlexfluxKO
extends java.lang.Object

Computes an KO analysis given a metabolic network, an objective function and constraints.

A KO analysis consists in setting network entities values to 0, and observe the effect on the objective function.

There are 3 ways to perform this KO analysis :

• Mode 0: the KO analysis is performed on reactions.
• Mode 1: the KO analysis is performed on genes.
• If a list of biological entities is specified (with argument -e) the KO analysis is performed on it.

Author:

lmarmiesse 6 mars 2013

Field Summary

Fields

Modifier and Type	Field and Description
java.lang.String	condFile
java.lang.String	entities
java.lang.String	example
boolean	extended
boolean	h
java.lang.String	intFile
double	liberty
java.lang.String	message
int	mode
boolean	nointInSolver
int	nThreads
java.lang.String	outName
boolean	plot
int	precision
java.lang.String	sbmlFile
java.lang.String	solver

Constructor Summary

Constructors

Constructor and Description
FlexfluxKO()

Method Summary

Methods

Modifier and Type	Method and Description
static void	main(java.lang.String[] args)

Methods inherited from class java.lang.Object

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

Field Detail

message

public java.lang.String message

example

public java.lang.String example

sbmlFile

public java.lang.String sbmlFile

condFile

public java.lang.String condFile

intFile

public java.lang.String intFile

solver

public java.lang.String solver

nointInSolver

public boolean nointInSolver

plot

public boolean plot

entities

public java.lang.String entities

mode

public int mode

outName

public java.lang.String outName

nThreads

public int nThreads

liberty

public double liberty

precision

public int precision

extended

public boolean extended

h

public boolean h

Constructor Detail

FlexfluxKO

public FlexfluxKO()

Method Detail

main

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