fern.simulation.observer

Class AmountAtMomentObserver

java.lang.Object

fern.simulation.observer.Observer

fern.simulation.observer.AmountAtMomentObserver

All Implemented Interfaces:

SimulationController, GnuPlotObserver

public class AmountAtMomentObserver
extends Observer
implements SimulationController, GnuPlotObserver

Observes the amount of some molecule species at a certain moment. In order to accomplish that, this class also implements a SimulationController and registers a theta at the simulator. The data produced after are histograms for each species representing the distribution of amounts at theta.

Author:

Florian Erhard

See Also:

Observer.getTheta()

Constructor Summary

Constructors

Constructor and Description
AmountAtMomentObserver(Simulator sim, double moment, int... speciesIndices) Creates the observer for the given simulator, the given theta and the given species
AmountAtMomentObserver(Simulator sim, double moment, String... speciesName) Creates the observer for the given simulator, the given theta and the 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.
Map<Integer,Integer>	getHistogram(int species) Gets the histogram of the distribution for a species
String[]	getStyles() Gets the styles for the columns.
boolean	goOn(Simulator sim) Causes the simulator to stop when theta has been passed and the amounts have been recorded.
void	started() Register theta at the simulator.
void	step() Do nothing.
void	theta(double theta) Records the amounts of the species and puts it into the histogram.
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

AmountAtMomentObserver

public AmountAtMomentObserver(Simulator sim,
                              double moment,
                              String... speciesName)

Creates the observer for the given simulator, the given theta and the given species

Parameters:

sim - simulator

moment - theta

speciesName - names of the species to observe

AmountAtMomentObserver

public AmountAtMomentObserver(Simulator sim,
                              double moment,
                              int... speciesIndices)

Creates the observer for the given simulator, the given theta and the given species

Parameters:

sim - simulator

moment - theta

speciesIndices - indices of the species to observe

Method Detail

goOn

public boolean goOn(Simulator sim)

Causes the simulator to stop when theta has been passed and the amounts have been recorded.

Specified by:

goOn in interface SimulationController

Parameters:

sim - simulation

Returns:

whether or not to go on

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

theta

public void theta(double theta)

Records the amounts of the species and puts it into the histogram.

Specified by:

theta in class Observer

Parameters:

theta - moment in time

finished

public void finished()

Do nothing.

Specified by:

finished in class Observer

started

public void started()

Register theta at the simulator.

Specified by:

started in class Observer

step

public void step()

Do nothing.

Specified by:

step in class Observer

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

getHistogram

public Map<Integer,Integer> getHistogram(int species)

Gets the histogram of the distribution for a species

Parameters:

species - species index (but not in network index space - i means the ith passed species)

Returns:

histogram as map

toString

public String toString()

Overrides:

toString in class Object

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