jp.sbi.celldesigner.plugin.simulation

Class PluginSimulation

java.lang.Object

jp.sbi.celldesigner.plugin.simulation.PluginSimulation

public class PluginSimulation
extends java.lang.Object

Plugin class for executing simulation with given PluginModel. For example, you can run a simulation with following lines of code.

 
 PluginModel pm = plugin.getSelectedModel();
 PluginSimulation psim = new PluginSimulation(pm);
 psim.setEndTime(20);
 psim.setNumOfSteps(1000);
 psim.runSimulation();
 
 

Simulation results will be stored in "plugin_simulation_result.txt". While there is no output file specified in the above example code, CellDesigner will use default output filename "plugin_simulation_result.txt". You can specify the output file and run a simulation with following code.

 
 PluginModel pm = plugin.getSelectedModel();
 PluginSimulation psim = new PluginSimulation(pm);
 psim.setOutputFile("result.txt");
 psim.setEndTime(20);
 psim.setNumOfSteps(1000);
 psim.runSimulation();
 
 

Author:

Akira Funahashi Akira Funahashi

Constructor Summary

Constructors

Constructor and Description
PluginSimulation(PluginModel pluginModel) Class constructor specifying pluginModel
PluginSimulation(PluginModel pluginModel, double endtime, long numstep) Class constructor specifying pluginModel, endtime and numstep

Method Summary

Modifier and Type	Method and Description
double	getEndTime() Returns endTime.
long	getNumOfSteps() Returns numOfSteps.
java.lang.String	getOutputFile() Returns outputFilename
void	runSimulation() Run a simulation with given pluginModel, endtime and numsteps.
void	setEndTime(double endTime) Sets endTime.
void	setNumOfSteps(long numstep) Sets numOfSteps
void	setOutputFile(java.lang.String outputFile) Sets outpuFilename

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

PluginSimulation

public PluginSimulation(PluginModel pluginModel)

Class constructor specifying pluginModel

Parameters:

pluginModel - the model which is an object for simulation.

PluginSimulation

public PluginSimulation(PluginModel pluginModel,
                        double endtime,
                        long numstep)

Class constructor specifying pluginModel, endtime and numstep

Parameters:

pluginModel - the model which is an object for simulation.

endtime - simulation time.

numstep - num of steps for numerical integration.

Method Detail

runSimulation

public void runSimulation()

Run a simulation with given pluginModel, endtime and numsteps. SOSlib is used for numerical integration. Simulation result will be written in "plugin_simulation_result.txt" if outputFilename is not set. If you want to specify the result filename, please use setOutputFile(String filename) before calling this method.

getEndTime

public double getEndTime()

Returns endTime.

Returns:

endTime if already set, otherwise default value (10) is returned.

setEndTime

public void setEndTime(double endTime)

Sets endTime.

Parameters:

endTime - double

getNumOfSteps

public long getNumOfSteps()

Returns numOfSteps.

Returns:

numOfSteps if already set, otherwise default value (100) is returned.

setNumOfSteps

public void setNumOfSteps(long numstep)

Sets numOfSteps

Parameters:

numstep - long

getOutputFile

public java.lang.String getOutputFile()

Returns outputFilename

Returns:

outputFilename if already set, otherwise default vallue ("plugin_simulation_result.txt") is returned.

setOutputFile

public void setOutputFile(java.lang.String outputFile)

Sets outpuFilename

Parameters:

outputFile - String