fern.example

Class CellGrowthObserver

java.lang.Object

fern.simulation.observer.Observer

fern.example.CellGrowthObserver

public class CellGrowthObserver
extends Observer

Does not observe anything, but it controls the reaction networks cell. At the beginning the volume is set to 1 and then linearly increased to 2 until the generation time is reached. Then a cell division is simulated by dividing each population by 2 and restart the volume at 1.

This class is used for the LacZ examples, so at a cell division the amount of PLac (the promoter) is set to 1.

Author:

Florian Erhard

Constructor Summary

Constructors

Constructor and Description
CellGrowthObserver(Simulator sim, double generationTime, double timeOffset) Creates the observer for given simulator, generation time and a time offset (because the simulator starts at time 0 and for one example it actually starts at time 1000)

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.
long	getNumSteps() Gets the number of steps taken in one simulation
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.

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, toString, wait, wait, wait

Constructor Detail

CellGrowthObserver

public CellGrowthObserver(Simulator sim,
                          double generationTime,
                          double timeOffset)

Creates the observer for given simulator, generation time and a time offset (because the simulator starts at time 0 and for one example it actually starts at time 1000)

Parameters:

sim - the simulator

generationTime - generation time

timeOffset - time offset

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

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

getNumSteps

public long getNumSteps()

Gets the number of steps taken in one simulation

Returns:

number of steps