fern.network.sbml

Class SBMLEventHandlerObserver

java.lang.Object

fern.simulation.observer.Observer

fern.simulation.observer.TriggerObserver

fern.network.sbml.SBMLEventHandlerObserver

public class SBMLEventHandlerObserver
extends TriggerObserver

Observer which handles an event of a sbml model.

Author:

Florian Erhard

Constructor Summary

Constructors

Constructor and Description
SBMLEventHandlerObserver(Simulator sim, SBMLNetwork net, SBMLinterpreter interpreter, org.sbml.jsbml.Event event) Creates the observer.

Method Summary

Modifier and Type	Method and Description
void	activateReaction(int mu, double tau, Simulator.FireType fireType, int times) Gets called before a reaction fires.
void	finished() Gets called when a simulation has finished, directly after the termination check.
void	setSimulatorAsync(Simulator sim)
void	started() Gets called when the simulation has started after the initialization and before the termination condition is checked the first time.
void	step() Gets called after each termination check and before Simulator.performStep(fern.simulation.controller.SimulationController) is called.
void	theta(double theta) Gets called by simulators when a certain moment in time is reached.
String	toString()
boolean	trigger() Is executed, whenever a event can trigger (before step and during a theta event).

Methods inherited from class fern.simulation.observer.Observer

getLabelFormat, getNumSimulations, getPrintWriter, getSimulator, getTheta, print, setLabelFormat, setPrintWriter, setTheta

Methods inherited from class java.lang.Object

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

Constructor Detail

SBMLEventHandlerObserver

public SBMLEventHandlerObserver(Simulator sim,
                                SBMLNetwork net,
                                SBMLinterpreter interpreter,
                                org.sbml.jsbml.Event event)
                         throws org.sbml.jsbml.validator.ModelOverdeterminedException

Creates the observer.

Parameters:

sim - the simulator

net - the sbml network

interpreter - the sbmlInterpreter instance to calculate the node values

event - the event object of the sbml model

Throws:

org.sbml.jsbml.validator.ModelOverdeterminedException

Method Detail

activateReaction

public void activateReaction(int mu,
                             double tau,
                             Simulator.FireType fireType,
                             int times)

Description copied from class: Observer

Gets called before a reaction fires.

Specified by:

activateReaction in class Observer

Parameters:

mu - the reaction which is supposed to fire

tau - the time the reaction fires (at this time Simulator.getTime() does not necessarily yield the firing time)

fireType - the type of the firing

times - TODO

finished

public void finished()

Description copied from class: Observer

Gets called when a simulation has finished, directly after the termination check.

Specified by:

finished in class Observer

started

public void started()

Description copied from class: Observer

Gets called when the simulation has started after the initialization and before the termination condition is checked the first time.

Specified by:

started in class Observer

step

public void step()

Description copied from class: Observer

Gets called after each termination check and before Simulator.performStep(fern.simulation.controller.SimulationController) is called.

Specified by:

step in class Observer

trigger

public boolean trigger()

Description copied from class: TriggerObserver

Is executed, whenever a event can trigger (before step and during a theta event).

Specified by:

trigger in class TriggerObserver

Returns:

whether or not the trigger has fired

theta

public void theta(double theta)

Description copied from class: Observer

Gets called by simulators when a certain moment in time is reached. This moment in time has to be registered by Observer.getTheta()

Specified by:

theta in class Observer

Parameters:

theta - moment in time

setSimulatorAsync

public void setSimulatorAsync(Simulator sim)

toString

public String toString()

Overrides:

toString in class Object