fern.network

Class DefaultAmountManager

java.lang.Object

fern.network.DefaultAmountManager

All Implemented Interfaces:

AmountManager

public class DefaultAmountManager
extends Object
implements AmountManager

Default implementation of an amount manager, that stores the amounts in arrays.

Author:

erhard

Constructor Summary

Constructors

Constructor and Description
DefaultAmountManager(Network net) Creates an AmountManager for a given network

Method Summary

Modifier and Type	Method and Description
long	getAmount(int species) Gets the current amount of a species.
void	performReaction(int reaction, int times) Reflects a (multiple) firing of a reaction by adjusting the populations of the reactants and the products.
void	resetAmount() Resets the amount of each species to the initial amount retrieved by the networks AnnotationManager.
void	rollback() Restore the amount array from the recently saved one.
void	save() Makes a copy of the amount array.
void	setAmount(int species, long amount) Sets the current amount of a species.

Methods inherited from class java.lang.Object

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

Constructor Detail

DefaultAmountManager

public DefaultAmountManager(Network net)

Creates an AmountManager for a given network

Parameters:

net - the network

Method Detail

performReaction

public void performReaction(int reaction,
                            int times)

Reflects a (multiple) firing of a reaction by adjusting the populations of the reactants and the products. If a population becomes negative, a RuntimeException is thrown.

Specified by:

performReaction in interface AmountManager

Parameters:

reaction - the index of the reaction fired

times - the number of firings

getAmount

public long getAmount(int species)

Gets the current amount of a species.

Specified by:

getAmount in interface AmountManager

Parameters:

species - index of the species

Returns:

actual amount of the species

setAmount

public void setAmount(int species,
                      long amount)

Sets the current amount of a species.

Specified by:

setAmount in interface AmountManager

Parameters:

species - index of the species

resetAmount

public void resetAmount()

Resets the amount of each species to the initial amount retrieved by the networks AnnotationManager. This is called whenever a Simulator is started.

Specified by:

resetAmount in interface AmountManager

save

public void save()

Makes a copy of the amount array.

Specified by:

save in interface AmountManager

rollback

public void rollback()

Restore the amount array from the recently saved one.

Specified by:

rollback in interface AmountManager