org.simulator.sedml

Class SEDMLWriter

java.lang.Object

org.simulator.sedml.SEDMLWriter

public class SEDMLWriter
extends Object

Writes a simulation configuration to SED-ML for export and sharing.
Usage:

 SEDMLWriter writer = new SEDMLWriter();
 writer.setComment(comment); // optional note to annotate SED-ML
 writer.saveExperimentToSEDML(start, end,
   stepsize, solver, model,
        modelURI, outputStream);
 

Since:

1.1

Version:

$Rev$

Author:

Richard Adams

Constructor Summary

Constructors

Constructor and Description
SEDMLWriter()

Method Summary

Modifier and Type	Method and Description
void	executeSedML(InputStream SedML)
void	saveExperimentToSEDML(double start, double end, double stepsize, AbstractDESSolver solver, org.sbml.jsbml.Model model, URI modelURI, OutputStream os) Given a configured simulation, will write to SED-ML using the specified OutputStream.
void	setComment(String comment) Set an optional human-readable comment to be added to the SED-ML file.

Methods inherited from class java.lang.Object

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

Constructor Detail

SEDMLWriter

public SEDMLWriter()

Method Detail

setComment

public void setComment(String comment)

Set an optional human-readable comment to be added to the SED-ML file.

Parameters:

comment -

saveExperimentToSEDML

public void saveExperimentToSEDML(double start,
                                  double end,
                                  double stepsize,
                                  AbstractDESSolver solver,
                                  org.sbml.jsbml.Model model,
                                  URI modelURI,
                                  OutputStream os)
                           throws IOException

Given a configured simulation, will write to SED-ML using the specified OutputStream. It is up to the client to manage the OutputStream an ensure it is open and writeable.

Parameters:

start - The start time for the desired output

end - The simulation end time

stepsize - The output step-size

solver - An AbstractDESSolver, not null.

model - A Model, not null

modelURI - A URI pointing to the model location

os - A writeable, open OutputStream

Throws:

IOException

executeSedML

public void executeSedML(InputStream SedML)

Parameters:

SedML -