broadwick.stochastic

Interface AmountManager

public interface AmountManager

An amount manager is responsible for keeping track of the populations within the simulation. Each StochasticProcess calls the performEvent method when it fires an event. The amount manager then

Method Summary

Modifier and Type	Method and Description
void	performEvent(SimulationEvent reaction, int times) Reflects a (multiple) firing of a reaction by adjusting the populations of the states.
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.
String	toVerboseString() Get a detailed description of the states and their sizes (potentially for debugging).

Method Detail

performEvent

void performEvent(SimulationEvent reaction,
                  int times)

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

Parameters:

reaction - the index of the reaction fired

times - the number of firings

toVerboseString

String toVerboseString()

Get a detailed description of the states and their sizes (potentially for debugging).

Returns:

a detailed description of the states in the manager.

resetAmount

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.

save

void save()

Makes a copy of the amount array.

rollback

void rollback()

Restore the amount array from the recently saved one.