fern.network.fernml

Class FernMLNetwork

java.lang.Object

fern.network.AbstractNetworkImpl

fern.network.fernml.FernMLNetwork

All Implemented Interfaces:

Network

public class FernMLNetwork
extends AbstractNetworkImpl

A FernMLNetwork is usually loaded from a file. For specifications see the included FernMLSchema.xsd or the examples. Additionally, a FernMLNetwork can be created out of an arbitrary Network. By using the saveToFile method, every Network can be saved as a fernml-File.

Author:

Florian Erhard

Constructor Summary

Constructors

Constructor and Description
FernMLNetwork(File file) Creates a FernMLNetwork from a file.
FernMLNetwork(Network net) Create a FernMLNetwork from an existing Network.
FernMLNetwork(Network net, double[] kineticConstants) Creates a FernMLNetwork out of an existing network (e.g., to save it to a fernml file) using explicitly given kineticConstants (when net} doesn't use KineticConstantPropensityCalculator If kineticConstants is null or to short, a default value of 1 is taken.

Method Summary

Modifier and Type	Method and Description
long	getInitialAmount(int species) Gets the initial amount of the specified molecule species.
int	getNumReactions() Gets the number of reaction within the network.
int	getNumSpecies() Gets the number of species within the network.
ArrayKineticConstantPropensityCalculator	getPropensityCalculator() Gets the PropensityCalculator for this network.
void	saveToFile(File file) Saves the actual FernMLNetwork to a file.
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, getProducts, getReactants, getReactionName, getSpeciesByName, getSpeciesMapping, getSpeciesName

Methods inherited from class java.lang.Object

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

Constructor Detail

FernMLNetwork

public FernMLNetwork(File file)
              throws IOException,
                     org.jdom.JDOMException

Creates a FernMLNetwork from a file.

Parameters:

file - file containing the network

Throws:

IOException - if the file cannot be read

org.jdom.JDOMException - if the file is malformed

FernMLNetwork

public FernMLNetwork(Network net)

Create a FernMLNetwork from an existing Network. If the network's PropensityCalculator is not an AbstractKineticConstantPropensityCalculator, the constant for the rate reaction is obtained by the propensity calculator by setting each reactant species' amount to 1. If the stoichiometry of some reactant is greater than 1 the value is set accordingly.

Parameters:

net - the network to create a FernMLNetwork from

FernMLNetwork

public FernMLNetwork(Network net,
                     double[] kineticConstants)

Creates a FernMLNetwork out of an existing network (e.g., to save it to a fernml file) using explicitly given kineticConstants (when net} doesn't use KineticConstantPropensityCalculator If kineticConstants is null or to short, a default value of 1 is taken.

Parameters:

net - An existing network

kineticConstants - kinetic constants for each reaction in net

Method Detail

getPropensityCalculator

public ArrayKineticConstantPropensityCalculator getPropensityCalculator()

Description copied from interface: Network

Gets the PropensityCalculator for this network.

Specified by:

getPropensityCalculator in interface Network

Overrides:

getPropensityCalculator in class AbstractNetworkImpl

Returns:

the PropensityCalculator

getNumReactions

public int getNumReactions()

Description copied from interface: Network

Gets the number of reaction within the network.

Specified by:

getNumReactions in interface Network

Overrides:

getNumReactions in class AbstractNetworkImpl

Returns:

number of reactions

getNumSpecies

public int getNumSpecies()

Description copied from interface: Network

Gets the number of species within the network.

Specified by:

getNumSpecies in interface Network

Overrides:

getNumSpecies in class AbstractNetworkImpl

Returns:

number of 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

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

saveToFile

public void saveToFile(File file)
                throws IOException

Saves the actual FernMLNetwork to a file.

Parameters:

file - the file to save the network in

Throws:

IOException - if the file cannot be written