fern.simulation.observer

Class LeapObserver

java.lang.Object

fern.simulation.observer.Observer

fern.simulation.observer.LeapObserver

All Implemented Interfaces:

GnuPlotObserver

public class LeapObserver
extends Observer
implements GnuPlotObserver

Observes the amount of given molecule species at each step. It particularly makes sense for the approximative leaping algorithms whose steps are precisely the leaps and you want to know about amount differences after each leap.

This observer does not take repeats into account. If you repeat the simulation, you will just get the results of the recent run.

Author:

Florian Erhard

Constructor Summary

Constructors

Constructor and Description
LeapObserver(Simulator sim, String... speciesNames) Creates the observer with a given simulator and given species

Method Summary

Modifier and Type	Method and Description
void	activateReaction(int mu, double tau, Simulator.FireType fireType, int times) Do nothing.
void	finished() Do nothing.
int	getNumLeaps() Gets the number of the performed leaps
String[]	getStyles() Gets the styles for the columns.
void	started() Clears the recorded data.
void	step() Record the time and amounts of the species.
void	theta(double theta) Do nothing.
GnuPlot	toGnuplot() Creates a new GnuPlot object and passes the actual observer data to it.
GnuPlot	toGnuplot(GnuPlot gnuplot) Passes the actual observer data to a GnuPlot object.
String	toString()

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

LeapObserver

public LeapObserver(Simulator sim,
                    String... speciesNames)

Creates the observer with a given simulator and given species

Parameters:

sim - simulator

speciesNames - names of the species

Method Detail

activateReaction

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

Do nothing.

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()

Do nothing.

Specified by:

finished in class Observer

started

public void started()

Clears the recorded data.

Specified by:

started in class Observer

step

public void step()

Record the time and amounts of the species.

Specified by:

step in class Observer

theta

public void theta(double theta)

Do nothing.

Specified by:

theta in class Observer

Parameters:

theta - moment in time

toGnuplot

public GnuPlot toGnuplot()
                  throws IOException

Description copied from interface: GnuPlotObserver

Creates a new GnuPlot object and passes the actual observer data to it.

Specified by:

toGnuplot in interface GnuPlotObserver

Returns:

the created GnuPlot object

Throws:

IOException - if gnuplot could not be accessed

toGnuplot

public GnuPlot toGnuplot(GnuPlot gnuplot)
                  throws IOException

Description copied from interface: GnuPlotObserver

Passes the actual observer data to a GnuPlot object.

Specified by:

toGnuplot in interface GnuPlotObserver

Parameters:

gnuplot - the GnuPlot object to pass the data to

Returns:

the GnuPlot object

Throws:

IOException - if gnuplot could not be accessed

getNumLeaps

public int getNumLeaps()

Gets the number of the performed leaps

Returns:

number of leaps.

getStyles

public String[] getStyles()

Description copied from interface: GnuPlotObserver

Gets the styles for the columns. If you don't want styles, just return null!

Specified by:

getStyles in interface GnuPlotObserver

Returns:

styles for the columns

toString

public String toString()

Overrides:

toString in class Object