fern.simulation.observer

Class ReactionIntervalObserver

java.lang.Object

fern.simulation.observer.Observer

fern.simulation.observer.IntervalObserver

fern.simulation.observer.ReactionIntervalObserver

All Implemented Interfaces:

GnuPlotObserver

public class ReactionIntervalObserver
extends IntervalObserver

Observes number of firings of reactions repeatedly after certain intervals.

This observer does take repeats into account. If you repeat the simulation, you will get an average over the results of each run.

Author:

Florian Erhard

Constructor Summary

Constructors

Constructor and Description
ReactionIntervalObserver(Simulator sim, double interval, int... reactions) Creates the observer for a given simulator, a given interval and given reaction indices.
ReactionIntervalObserver(Simulator sim, double interval, String... speciesNames) Creates the observer for a given simulator, a given interval and given neighbors.

Method Summary

Modifier and Type	Method and Description
void	activateReaction(int mu, double t, Simulator.FireType fireType, int times) Record the firing of mu, if mu is registered.
double	getRecordStart() Gets the moment in time where the recording starts
String[]	getStyles() Gets the styles for the columns.
void	setRecordStart(double recordStart) Sets the moment in time where the recording starts
void	started() Clears the recorded values and registers (if needed) theta

Methods inherited from class fern.simulation.observer.IntervalObserver

finished, getAvgLog, getFinalValue, getRecentData, isPlotQuality, isThetaMethod, setPlotQuality, setThetaMethod, step, theta, toGnuplot, toGnuplot, toGnuplotRecent, toGnuplotRecent, 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

ReactionIntervalObserver

public ReactionIntervalObserver(Simulator sim,
                                double interval,
                                String... speciesNames)

Creates the observer for a given simulator, a given interval and given neighbors.

Parameters:

sim - simulator

interval - interval

speciesNames - the names of the species, each neighboring reaction of any of these is added

ReactionIntervalObserver

public ReactionIntervalObserver(Simulator sim,
                                double interval,
                                int... reactions)

Creates the observer for a given simulator, a given interval and given reaction indices.

Parameters:

sim - simulator

interval - interval

reactions - reaction indices

Method Detail

activateReaction

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

Record the firing of mu, if mu is registered.

Overrides:

activateReaction in class IntervalObserver

Parameters:

mu - the reaction which is supposed to fire

t - 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

started

public void started()

Description copied from class: IntervalObserver

Clears the recorded values and registers (if needed) theta

Overrides:

started in class IntervalObserver

getRecordStart

public double getRecordStart()

Gets the moment in time where the recording starts

Returns:

the recordStart

setRecordStart

public void setRecordStart(double recordStart)

Sets the moment in time where the recording starts

Parameters:

recordStart - the recordStart to set

getStyles

public String[] getStyles()

Description copied from interface: GnuPlotObserver

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

Returns:

styles for the columns