fern.network.sbml

Class SBMLNetwork

java.lang.Object

fern.network.AbstractNetworkImpl

fern.network.sbml.SBMLNetwork

All Implemented Interfaces:

Network

public class SBMLNetwork
extends AbstractNetworkImpl

For specifications of the sbml format refer to http:\\www.sbml.org. Not every feature is implemented in FERN (for a list please see the user guide).

When you want to use a sbml model with events included, you have to call registerEvents, since the event handling is treated by SBMLEventHandlerObservers which need to be attached to the Simulator.

Author:

Florian Erhard

Constructor Summary

Constructors

Constructor and Description
SBMLNetwork(File file) Creates a network from a sbmlfile.
SBMLNetwork(File file, boolean ignoreExceptions) Creates a network from a sbml file.

Method Summary

Modifier and Type	Method and Description
long	getInitialAmount(int species) Gets the initial amount of the specified molecule species.
SBMLinterpreter	getSbmlInterpreter()
org.sbml.jsbml.Model	getSBMLModel() Gets the SBML model.
void	registerEvents(Simulator sim) Registers the SBMLEventHandlerObserver for each event in the sbml file to the Simulator.
void	saveToFile(File file) Saves the current SBMLNetwork to a file.
void	saveToFile(File file, int level, int version) Saves the current SBMLNetwork to a sbml file with given level and version.
void	setInitialAmount(int species, long value) Sets the initial amount of the specified molecule species.

Methods inherited from class fern.network.AbstractNetworkImpl

getAmountManager, getAnnotationManager, getName, getNumReactions, getNumSpecies, getProducts, getPropensityCalculator, getReactants, getReactionName, getSpeciesByName, getSpeciesMapping, getSpeciesName

Methods inherited from class java.lang.Object

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

Constructor Detail

SBMLNetwork

public SBMLNetwork(File file)
            throws FeatureNotSupportedException,
                   IOException,
                   XMLStreamException,
                   org.sbml.jsbml.validator.ModelOverdeterminedException

Creates a network from a sbmlfile. If the file contains features not supported by FERN, an exception will be thrown.

Parameters:

file - SBML file

Throws:

FeatureNotSupportedException

IOException

XMLStreamException

org.sbml.jsbml.validator.ModelOverdeterminedException

SBMLNetwork

public SBMLNetwork(File file,
                   boolean ignoreExceptions)
            throws FeatureNotSupportedException,
                   IOException,
                   XMLStreamException,
                   org.sbml.jsbml.validator.ModelOverdeterminedException

Creates a network from a sbml file. If the file contains features not supported by FERN, depending on ignoreExceptions they will be ignored or a exception is thrown.

Parameters:

file - SBML file

ignoreExceptions - wheter or not exceptions should be thrown

Throws:

FeatureNotSupportedException

IOException

XMLStreamException

org.sbml.jsbml.validator.ModelOverdeterminedException

Method Detail

registerEvents

public void registerEvents(Simulator sim)

Registers the SBMLEventHandlerObserver for each event in the sbml file to the Simulator.

Parameters:

sim - the simulator

getInitialAmount

public long getInitialAmount(int species)

Description copied from interface: Network

Gets the initial amount of the specified molecule species.

Parameters:

species - index of the species

Returns:

initial amount of the species

setInitialAmount

public void setInitialAmount(int species,
                             long value)

Description copied from interface: Network

Sets the initial amount of the specified molecule species.

Parameters:

species - index of the species

value - initial amount of the species

getSBMLModel

public org.sbml.jsbml.Model getSBMLModel()

Gets the SBML model.

Returns:

sbml model

saveToFile

public void saveToFile(File file)
                throws IOException,
                       XMLStreamException

Saves the current SBMLNetwork to a file.

Parameters:

file - the file to save the network in

Throws:

IOException - if the file cannot be written

XMLStreamException

saveToFile

public void saveToFile(File file,
                       int level,
                       int version)
                throws IOException,
                       XMLStreamException

Saves the current SBMLNetwork to a sbml file with given level and version.

Parameters:

file - the file to save the network in

level - sbml level

version - sbml version

Throws:

IOException - if the file cannot be written

XMLStreamException

getSbmlInterpreter

public SBMLinterpreter getSbmlInterpreter()