fern.cytoscape
Class CytoscapeColorChangeObserver

java.lang.Object
  fern.simulation.observer.Observer
      fern.cytoscape.CytoscapeColorChangeObserver

public class CytoscapeColorChangeObserver
extends Observer

Constructor Summary

CytoscapeColorChangeObserver(boolean visualize, boolean showTrendSteps, Simulator sim, CytoscapeNetworkWrapper net, FernVisualStyle style, String[] trendSpecies, double time)

Method Summary

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	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

CytoscapeColorChangeObserver

public CytoscapeColorChangeObserver(boolean visualize,
                                    boolean showTrendSteps,
                                    Simulator sim,
                                    CytoscapeNetworkWrapper net,
                                    FernVisualStyle style,
                                    String[] trendSpecies,
                                    double time)

Method Detail

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

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

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