fern.network.modification

Class ModifierNetwork

java.lang.Object

fern.network.modification.ModifierNetwork

All Implemented Interfaces:

Network

Direct Known Subclasses:

CatalysedNetwork, ExtractSubNetwork, ReversibleNetwork

public abstract class ModifierNetwork
extends Object
implements Network

Base class for modified networks, which implements the full Network interface. Extending classes should override each method which is different in the modified network (e.g. in the ReversibleNetwork only reactions are virtually doubled, so each method concerning the species do not change).

Note: An extending class should definitely not copy the whole network but should rather redirect indices to the original network when possible in order to minimize the necessary memory.

Author:

Florian Erhard

Constructor Summary

Constructors

Constructor and Description
ModifierNetwork(Network originalNet) Creates a ModifierNetwork from an original network.

Method Summary

Modifier and Type	Method and Description
AmountManager	getAmountManager() Gets the AmountManager of the original network.
AnnotationManager	getAnnotationManager() Gets the AnnotationManager of the original network
long	getInitialAmount(int species) Gets the initial amount of the specified molecule species.
String	getName() Gets the name of the original network
int	getNumReactions() Gets the number of reaction in the original network.
int	getNumSpecies() Gets the number of species in the original network.
Network	getOriginalNetwork() Gets the original network.
Network	getParentNetwork() Gets the parent network.
int[]	getProducts(int reaction) Gets the products of a reaction in the original network.
PropensityCalculator	getPropensityCalculator() Gets the PropensityCalculator of the original network.
int[]	getReactants(int reaction) Gets the reactants of a reaction in the original network.
String	getReactionName(int index) Gets a string representation of the reactio in the original network.
int	getSpeciesByName(String name) Gets the index of the species by its name in the original network.
String	getSpeciesName(int index) Gets the name of the species by index in the original network.
void	setInitialAmount(int species, long value) Sets the initial amount of the specified molecule species.

Methods inherited from class java.lang.Object

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

Constructor Detail

ModifierNetwork

public ModifierNetwork(Network originalNet)

Creates a ModifierNetwork from an original network.

Parameters:

originalNet - the network to modify

Method Detail

getName

public String getName()

Gets the name of the original network

Specified by:

getName in interface Network

Returns:

name of the original network.

getAnnotationManager

public AnnotationManager getAnnotationManager()

Gets the AnnotationManager of the original network

Specified by:

getAnnotationManager in interface Network

Returns:

AnnotationManager of the original network

getNumReactions

public int getNumReactions()

Gets the number of reaction in the original network.

Specified by:

getNumReactions in interface Network

Returns:

number of reactions in the original network

getNumSpecies

public int getNumSpecies()

Gets the number of species in the original network.

Specified by:

getNumSpecies in interface Network

Returns:

number of species in the original network

getProducts

public int[] getProducts(int reaction)

Gets the products of a reaction in the original network.

Specified by:

getProducts in interface Network

Parameters:

reaction - index of the reaction in the original network

Returns:

indices of the products in the original network

getReactants

public int[] getReactants(int reaction)

Gets the reactants of a reaction in the original network.

Specified by:

getReactants in interface Network

Parameters:

reaction - index of the reaction in the original network

Returns:

indices of the reactants in the original network

getSpeciesName

public String getSpeciesName(int index)

Gets the name of the species by index in the original network.

Specified by:

getSpeciesName in interface Network

Parameters:

index - index of the species the original network

Returns:

name of the species

getSpeciesByName

public int getSpeciesByName(String name)

Gets the index of the species by its name in the original network.

Specified by:

getSpeciesByName in interface Network

Parameters:

name - name of the species

Returns:

index of the species in the original network

getAmountManager

public AmountManager getAmountManager()

Gets the AmountManager of the original network.

Specified by:

getAmountManager in interface Network

Returns:

AmountManager of the the original network

getPropensityCalculator

public PropensityCalculator getPropensityCalculator()

Gets the PropensityCalculator of the original network.

Specified by:

getPropensityCalculator in interface Network

Returns:

PropensityCalculator of the the original network

getReactionName

public String getReactionName(int index)

Gets a string representation of the reactio in the original network.

Specified by:

getReactionName in interface Network

Parameters:

index - index of the reaction in the original network

Returns:

string represenation of the reaction

getInitialAmount

public long getInitialAmount(int species)

Description copied from interface: Network

Gets the initial amount of the specified molecule species.

Specified by:

getInitialAmount in interface Network

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.

Specified by:

setInitialAmount in interface Network

Parameters:

species - index of the species

value - initial amount of the species

getOriginalNetwork

public Network getOriginalNetwork()

Gets the original network. If there is a higher hierarchy of modified networks (e.g. a ExtractSubNetwork of a ReversibleNetwork of a AutocatalyticNetworkExample), the highest network (here the AutocatalyticNetworkExample is returned.

Returns:

the original network

getParentNetwork

public Network getParentNetwork()

Gets the parent network. If there is a higher hierarchy of modified networks (e.g. a ExtractSubNetwork of a ReversibleNetwork of a AutocatalyticNetworkExample), the parental network (here the ReversibleNetwork is returned.

Returns:

the parent network