fern.network.modification

Class CatalysedNetwork

java.lang.Object

fern.network.modification.ModifierNetwork

fern.network.modification.CatalysedNetwork

All Implemented Interfaces:

Network

public class CatalysedNetwork
extends ModifierNetwork

Modifies the network by adding reactions X+C → Y+C (where C is each catalyst of the original reaction). If a reaction has n catalysts, there will be n + 1 reactions generated. It is only possible to create a CatalysedNetwork out of a AutocatalyticNetwork (or at least of a ModifierNetwork whose original network is a AutocatalyticNetwork).

The AmountManager automatically monitors the food molecules amounts and whenever it changes, it is reset to the initial value (given by AutocatalyticNetwork.getMonomerAmount().

The PropensityCalculator's constant is AutocatalyticNetwork.getCatalyzedKineticConstant() for each reaction with a catalyst and AutocatalyticNetwork.getUncatalyzedKineticConstant() for the other ones.

The AnnotationManager uses the underlying one but removes the AutocatalyticNetwork.CATALYSTS_FIELD and the field Autocatalytic from not catalyzed reactions.

Author:

Florian Erhard

Constructor Summary

Constructors

Constructor and Description
CatalysedNetwork(Network originalNet) Create a catalyzed network 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
int	getNumReactions() Gets the number of reaction in the original 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.

Methods inherited from class fern.network.modification.ModifierNetwork

getInitialAmount, getName, getNumSpecies, getOriginalNetwork, getParentNetwork, getSpeciesByName, getSpeciesName, setInitialAmount

Methods inherited from class java.lang.Object

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

Constructor Detail

CatalysedNetwork

public CatalysedNetwork(Network originalNet)

Create a catalyzed network from an original network.

Parameters:

originalNet - the original network

Method Detail

getNumReactions

public int getNumReactions()

Description copied from class: ModifierNetwork

Gets the number of reaction in the original network.

Specified by:

getNumReactions in interface Network

Overrides:

getNumReactions in class ModifierNetwork

Returns:

number of reactions in the original network

getReactants

public int[] getReactants(int reaction)

Description copied from class: ModifierNetwork

Gets the reactants of a reaction in the original network.

Specified by:

getReactants in interface Network

Overrides:

getReactants in class ModifierNetwork

Parameters:

reaction - index of the reaction in the original network

Returns:

indices of the reactants in the original network

getProducts

public int[] getProducts(int reaction)

Description copied from class: ModifierNetwork

Gets the products of a reaction in the original network.

Specified by:

getProducts in interface Network

Overrides:

getProducts in class ModifierNetwork

Parameters:

reaction - index of the reaction in the original network

Returns:

indices of the products in the original network

getPropensityCalculator

public PropensityCalculator getPropensityCalculator()

Description copied from class: ModifierNetwork

Gets the PropensityCalculator of the original network.

Specified by:

getPropensityCalculator in interface Network

Overrides:

getPropensityCalculator in class ModifierNetwork

Returns:

PropensityCalculator of the the original network

getAmountManager

public AmountManager getAmountManager()

Description copied from class: ModifierNetwork

Gets the AmountManager of the original network.

Specified by:

getAmountManager in interface Network

Overrides:

getAmountManager in class ModifierNetwork

Returns:

AmountManager of the the original network

getAnnotationManager

public AnnotationManager getAnnotationManager()

Description copied from class: ModifierNetwork

Gets the AnnotationManager of the original network

Specified by:

getAnnotationManager in interface Network

Overrides:

getAnnotationManager in class ModifierNetwork

Returns:

AnnotationManager of the original network

getReactionName

public String getReactionName(int index)

Description copied from class: ModifierNetwork

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

Specified by:

getReactionName in interface Network

Overrides:

getReactionName in class ModifierNetwork

Parameters:

index - index of the reaction in the original network

Returns:

string represenation of the reaction