Package org.simulator.comp

Class CompSimulator

java.lang.Object

org.simulator.comp.CompSimulator

public class CompSimulator
extends Object

Class for simulating comp models. TODO: support different simulation types (FBA, stochastic), currently limited to ode

Since:

1.5

Version:

$Rev$

Author:

Shalin Shah, atthias König

Constructor Summary

Constructors

Constructor	Description
CompSimulator(File file)

Method Summary

Modifier and Type	Method	Description
org.sbml.jsbml.SBMLDocument	getDoc()
org.sbml.jsbml.SBMLDocument	getDocFlat()
MultiTable	solve(double timeEnd, double stepSize)
MultiTable	solve(double timeEnd, double stepSize, DESSolver solver)

Methods inherited from class java.lang.Object

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

Constructor Detail

CompSimulator

public CompSimulator(File file)
              throws IOException,
                     XMLStreamException

Throws:

IOException

XMLStreamException

Method Detail

getDoc

public org.sbml.jsbml.SBMLDocument getDoc()

getDocFlat

public org.sbml.jsbml.SBMLDocument getDocFlat()

solve

public MultiTable solve(double timeEnd,
                        double stepSize)
                 throws org.apache.commons.math.ode.DerivativeException,
                        org.sbml.jsbml.validator.ModelOverdeterminedException

Throws:

org.apache.commons.math.ode.DerivativeException

org.sbml.jsbml.validator.ModelOverdeterminedException

solve

public MultiTable solve(double timeEnd,
                        double stepSize,
                        DESSolver solver)
                 throws org.apache.commons.math.ode.DerivativeException,
                        org.sbml.jsbml.validator.ModelOverdeterminedException

Throws:

org.apache.commons.math.ode.DerivativeException

org.sbml.jsbml.validator.ModelOverdeterminedException