org.simulator.comp

Class CompSimulator

java.lang.Object

org.simulator.comp.CompSimulator

public class CompSimulator
extends Object

Class for simulating models encoded in the SBML comp package.

This class allows to simulate models encoded in the SBML hierarchical model composition package comp (http://sbml.org/Documents/Specifications/SBML_Level_3/Packages/comp). The models are simulated by applying model flattening, i.e., reducing the hierarchical models to standard (flat) SBML models.

This class currently is limited to SBML core models (ODE). TODO: support additional simulations (FBA, stochastic)

Since:

1.5

Version:

$Rev$

Author:

Shalin Shah, Matthias König

Constructor Summary

Constructors

Constructor and Description
CompSimulator(File file) Constructor for the CompSimulator class.

Method Summary

Modifier and Type	Method and Description
org.sbml.jsbml.SBMLDocument	getDoc()
org.sbml.jsbml.SBMLDocument	getFlattenedDoc()
MultiTable	solve(double timeEnd, double stepSize) This method initializes the RosenbrockSolver and passes it to solve the flattened model.
MultiTable	solve(double timeEnd, double stepSize, DESSolver solver) This method computes the numerical solution of the flattened SBML Model simulated using the RosenbrockSolver and then maps the solutions from the flattened model back to the original model.

Methods inherited from class java.lang.Object

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

Constructor Detail

CompSimulator

public CompSimulator(File file)
              throws IOException,
                     XMLStreamException

Constructor for the CompSimulator class. It reads the SBMLDocument and flattens the hierarchical SBML Model (consisting of multiple sub-models) into the non-hierarchical version by using the CompFlatteningConverter class of JSBML.

Parameters:

file - the input SBML file with comp extension that is to be simulated

Throws:

IOException

XMLStreamException

Method Detail

getDoc

public org.sbml.jsbml.SBMLDocument getDoc()

getFlattenedDoc

public org.sbml.jsbml.SBMLDocument getFlattenedDoc()

solve

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

This method initializes the RosenbrockSolver and passes it to solve the flattened model.

Parameters:

timeEnd -

stepSize -

Returns:

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

This method computes the numerical solution of the flattened SBML Model simulated using the RosenbrockSolver and then maps the solutions from the flattened model back to the original model.

Parameters:

timeEnd -

stepSize -

solver -

Returns:

Throws:

org.apache.commons.math.ode.DerivativeException

org.sbml.jsbml.validator.ModelOverdeterminedException