fern.network.modification

Class ReversibleNetwork

java.lang.Object

fern.network.modification.ModifierNetwork

fern.network.modification.ReversibleNetwork

All Implemented Interfaces:

Network

public class ReversibleNetwork
extends ModifierNetwork

Doubles each reaction in a way that each original unidirectional reaction becomes reversible.As proposed by ModifierNetwork, the reactions are not copied but the indices are redirected.

Note: The reverse reactions do not have any annotation, unless in the original network the reactions have annotation with fields ending with REVERSIBLE_SUFFIX. If such annotations are present in the original network, the corresponding reactions in the reversible network will not have these annotations but the corresponding reversible reactions will have these annotations without this suffix (e.g., if you create an AutocatalyticNetwork, the reactions have annotations Catalyst and CatalystReversible, if you create a ReversibleNetwork out of this, each reaction will have only the annotation Catalyst).

For the new reactions you have to specify a new PropensityCalculator whose index space is equal to the original network's index space. If you have, for instance, in your original network two reactions, A + A → B, B → C, the PropensityCalculatory has to calculate the propensity for A + A ← B when index 0 is given, the propensity for B ← C, when index 1 is given.

Author:

Florian Erhard

Field Summary

Fields

Modifier and Type	Field and Description
static String	REVERSIBLE_SUFFIX Suffix which marks annotations for virtually created reverse reactions.

Constructor Summary

Constructors

Constructor and Description
ReversibleNetwork(Network originalNet, PropensityCalculator reversiblePropensityCalculator) Creates a new network from an original network and virtually creates for each reaction a new inverse reaction.

Method Summary

Modifier and Type	Method and Description
AmountManager	getAmountManager() Gets the AmountManager for the modified network.
AnnotationManager	getAnnotationManager() Gets the AnnotationManager for the modified network.
int	getNumReactions() Gets the number of reactions in the modified network (which is 2*number of reaction in the original network).
int[]	getProducts(int reaction) Gets the products of a reaction
PropensityCalculator	getPropensityCalculator() Gets the PropensityCalculator for the modified network.
int[]	getReactants(int reaction) Gets the reactants of a reaction
String	getReactionName(int index) Gets a string representation of the reaction in the modified 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

Field Detail

REVERSIBLE_SUFFIX

public static final String REVERSIBLE_SUFFIX

Suffix which marks annotations for virtually created reverse reactions. If there are no annotations with this suffix in the original network, the reverse reactions will have no annotations.

See Also:

Constant Field Values

Constructor Detail

ReversibleNetwork

public ReversibleNetwork(Network originalNet,
                         PropensityCalculator reversiblePropensityCalculator)

Creates a new network from an original network and virtually creates for each reaction a new inverse reaction. For the reverse reactions a PropensityCalculator has to be given.

Parameters:

originalNet - the original network

reversiblePropensityCalculator - the PropensityCalculator for the reverse reactions

Method Detail

getAmountManager

public AmountManager getAmountManager()

Gets the AmountManager for the modified network.

Specified by:

getAmountManager in interface Network

Overrides:

getAmountManager in class ModifierNetwork

Returns:

AmountManager for the modified network

getNumReactions

public int getNumReactions()

Gets the number of reactions in the modified network (which is 2*number of reaction in the original network).

Specified by:

getNumReactions in interface Network

Overrides:

getNumReactions in class ModifierNetwork

Returns:

number of reactions in the modified network

getProducts

public int[] getProducts(int reaction)

Gets the products of a reaction

Specified by:

getProducts in interface Network

Overrides:

getProducts in class ModifierNetwork

Parameters:

reaction - index of the reaction

Returns:

indices of the products

getReactants

public int[] getReactants(int reaction)

Gets the reactants of a reaction

Specified by:

getReactants in interface Network

Overrides:

getReactants in class ModifierNetwork

Parameters:

reaction - index of the reaction

Returns:

indices of the reactants

getPropensityCalculator

public PropensityCalculator getPropensityCalculator()

Gets the PropensityCalculator for the modified network. If the original PropensityCalculator and the one for the reverse reactions is a AbstractKineticConstantPropensityCalculator, an AbstractKineticConstantPropensityCalculator is returned.

Specified by:

getPropensityCalculator in interface Network

Overrides:

getPropensityCalculator in class ModifierNetwork

Returns:

the PropensityCalculator for the modified network

getAnnotationManager

public AnnotationManager getAnnotationManager()

Gets the AnnotationManager for the modified network.

Specified by:

getAnnotationManager in interface Network

Overrides:

getAnnotationManager in class ModifierNetwork

Returns:

AnnotationManager for the modified network.

getReactionName

public String getReactionName(int index)

Gets a string representation of the reaction in the modified network.

Specified by:

getReactionName in interface Network

Overrides:

getReactionName in class ModifierNetwork

Parameters:

index - index of the reaction

Returns:

string representation of the reaction