Package org.simulator.examples

Class COBRAsolverExample

java.lang.Object

org.simulator.examples.COBRAsolverExample

public class COBRAsolverExample
extends Object

A simple test class to demonstrate the capabilities of the FBA implementation in Simulation Core Library. This is based on an installation of CPLEX. In order to run this example, it is necessary to launch the JVM with the argument -Djava.library.path=/path/to/the/binaries/of/CPLEX/. Note that this project does not redistribute CPLEX.

Version:

1.5

Author:

Andreas Dräger, Shalin Shah

Constructor Summary

Constructors

Constructor	Description
COBRAsolverExample(File file)

Method Summary

Modifier and Type	Method	Description
static void	main(String[] args)	Simple test function that reads and solves an SBML file in a flux balance constraints framework.
void	solve(File file)

Methods inherited from class java.lang.Object

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

Constructor Detail

COBRAsolverExample

public COBRAsolverExample(File file)
                   throws org.sbml.jsbml.SBMLException,
                          org.sbml.jsbml.validator.ModelOverdeterminedException,
                          XMLStreamException,
                          IOException

Parameters:

file - can be a file or a directory.

Throws:

org.sbml.jsbml.SBMLException - if the model is invalid or inappropriate for flux balance analysis.

XMLStreamException - if the file cannot be parsed into an SBMLDocument.

IOException - if the given path is invalid or cannot be read

org.sbml.jsbml.validator.ModelOverdeterminedException - if the model is over determined through AlgebraicRules.

org.sbml.jsbml.SBMLException - if the model is invalid or inappropriate for flux balance analysis.

Method Detail

solve

public void solve(File file)
           throws org.sbml.jsbml.SBMLException,
                  org.sbml.jsbml.validator.ModelOverdeterminedException,
                  XMLStreamException,
                  IOException

Parameters:

file - can be a file or a directory. In the latter case, the directory will be recursively queried.

Throws:

org.sbml.jsbml.SBMLException - if the model is invalid or inappropriate for flux balance analysis.

XMLStreamException - if the file cannot be parsed into an SBMLDocument.

IOException - if the given path is invalid or cannot be read

org.sbml.jsbml.validator.ModelOverdeterminedException - if the model is over determined through AlgebraicRules.

org.sbml.jsbml.SBMLException - if the model is invalid or inappropriate for flux balance analysis.

main

public static void main(String[] args)
                 throws FileNotFoundException

Simple test function that reads and solves an SBML file in a flux balance constraints framework.

Parameters:

args - the path to a valid SBML file with fbc version 2.

Throws:

FileNotFoundException