org.simulator.fba

Class FluxBalanceAnalysis

java.lang.Object

org.simulator.fba.FluxBalanceAnalysis

public class FluxBalanceAnalysis
extends Object

Support for Flux Balance Analysis (FBA).

This class provides implementation of fba using the information from the SBML fbc packages. This solver implementation supports SBML models with FBC package versions 1 or 2.

Since:

1.5

Author:

Andreas Dräger, Ali Ebrahim, Shalin Shah, Matthias König

Constructor Summary

Constructors

Constructor and Description
FluxBalanceAnalysis(org.sbml.jsbml.SBMLDocument doc) Initializes the linear program and all data structures based on the definitions in the given SBMLDocument.

Method Summary

Modifier and Type	Method and Description
String	getActiveObjective() Gets the id of the active objective function
double	getEpsilon() Gets the value of the EPSILON
double	getObjectiveValue() Returns the objective value of the current solution.
Map<String,Double>	getSolution() Returns solution values as a HashMap with key as reaction Id and value as the flux.
double	getValue(String reactionId) Returns the solution value for the Reaction variable with the given identifier.
double[]	getValues() Returns solution values for an array of Reaction variables.
void	setEpsilon(double eps) Set the value of the EPSILON specific to a particular FBC instance
boolean	solve() Solves the linear program that is defined in the SBMLDocument with which this solver was initialized.

Methods inherited from class java.lang.Object

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

Constructor Detail

FluxBalanceAnalysis

public FluxBalanceAnalysis(org.sbml.jsbml.SBMLDocument doc)
                    throws org.sbml.jsbml.SBMLException,
                           org.sbml.jsbml.validator.ModelOverdeterminedException

Initializes the linear program and all data structures based on the definitions in the given SBMLDocument. This implementation should work for diverse levels and versions of SBML Models given that the model contains an fbc package in version 1 or 2.

Parameters:

doc - the SBML container from which the Model is taken. This implementation only understands SBML core (diverse levels and versions) in combination with fbc versions 1 and 2.

Throws:

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 boolean solve()
              throws NullPointerException

Solves the linear program that is defined in the SBMLDocument with which this solver was initialized.

Returns:

A Boolean value reporting whether a feasible solution has been found. This solution is not necessarily optimal. If false is returned, a feasible solution may still be present, but IloCplex has not been able to prove its feasibility.

Throws:

NullPointerException - If the method fails, an exception of type NullPointerException, or one of its derived classes, is thrown.

getObjectiveValue

public double getObjectiveValue()
                         throws NullPointerException

Returns the objective value of the current solution.

Returns:

the objective value of the current solution.

Throws:

NullPointerException - If the method fails, an exception of type IloException, or one of its derived classes, is thrown.

getValue

public double getValue(String reactionId)
                throws NullPointerException,
                       ArrayIndexOutOfBoundsException

Returns the solution value for the Reaction variable with the given identifier.

Parameters:

reactionId - the identifier of the Reaction of interest.

Returns:

The value the Reaction takes for the current solution.

Throws:

NullPointerException - If the Reaction identifier is not in the active model.

ArrayIndexOutOfBoundsException - If the method fails, an exception of type ArrayIndexOutOfBoundsException, or one of its derived classes, is thrown.

getValues

public double[] getValues()
                   throws NullPointerException

Returns solution values for an array of Reaction variables.

Returns:

The solution values for the variables in the list of reactions.

Throws:

NullPointerException - If the method fails, an exception of type NullPointerException, or one of its derived classes, is thrown.

getSolution

public Map<String,Double> getSolution()

Returns solution values as a HashMap with key as reaction Id and value as the flux.

Returns:

The flux values for the each of the reactions

getEpsilon

public double getEpsilon()

Gets the value of the EPSILON

Returns:

the epsilon value

setEpsilon

public void setEpsilon(double eps)

Set the value of the EPSILON specific to a particular FBC instance

Parameters:

eps -

getActiveObjective

public String getActiveObjective()

Gets the id of the active objective function

Returns: