jigcell.xpp
Class XPPSimulator

java.lang.Object
  jigcell.simulation.Simulator
      jigcell.xpp.XPPSimulator

All Implemented Interfaces:

jigcell.simulation.ISimulator

Direct Known Subclasses:

Oscill8Simulator

public class XPPSimulator
extends jigcell.simulation.Simulator

Makes the XPP simulator available to the simulator API. This code is licensed under the DARPA BioCOMP Open Source License. See LICENSE for more details.

Author:

Nicholas Allen

Nested Class Summary

Nested classes/interfaces inherited from interface jigcell.simulation.ISimulator

jigcell.simulation.ISimulator.Category

Field Summary

protected SBMLToXPPTranslator

translator XPP simulator

Constructor Summary

	XPPSimulator() Creates a new simulator.
protected	XPPSimulator(jigcell.simulation.Capabilities capabilities) Creates a new simulator.

Method Summary

protected void	applySimulatorCapabilities(double timeStart, double timeEnd, double stepSize, int numberOfPoints) Combines the existing simulator capability settings and simulation parameters to determine the capabilities that will be used for this simulation.
private static jigcell.simulation.Capabilities	createDefaultCapabilities() Default capabilities for this simulator.
protected java.util.List	getSelectableNamesInternal()
protected double	getValueInternal(java.lang.String name)
protected java.util.List	getValueNamesInternal()
protected void	loadSBMLInternal(jigcell.sbml2.Model model)
protected void	loadSBMLInternal(jigcell.sbml2.Model model, boolean displayConcentration, int volumeColumn)
protected double	setValueInternal(java.lang.String name, double value)
protected jigcell.compare.IDataElement	simulateInternal(double timeStart, double timeEnd, double stepSize, int numberOfPoints)

Methods inherited from class jigcell.simulation.Simulator

getCapabilities, getCategory, getClassForSimulator, getLastError, getModel, getRegisteredSimulators, getSelectableNames, getSelectedNames, getValue, getValueNames, getValues, loadSBML, loadSBML, registerSimulator, reset, resetValues, setCapabilities, setNumberOfPoints, setSelectedNames, setStepSize, setTimeRange, setValue, setValues, simulate

Methods inherited from class java.lang.Object

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

Field Detail

translator

protected SBMLToXPPTranslator translator

XPP simulator

Constructor Detail

XPPSimulator

public XPPSimulator()

Creates a new simulator.

XPPSimulator

protected XPPSimulator(jigcell.simulation.Capabilities capabilities)

Creates a new simulator.

Parameters:

capabilities - Default capabilities

Method Detail

createDefaultCapabilities

private static jigcell.simulation.Capabilities createDefaultCapabilities()

Default capabilities for this simulator.

applySimulatorCapabilities

protected void applySimulatorCapabilities(double timeStart,
                                          double timeEnd,
                                          double stepSize,
                                          int numberOfPoints)

Combines the existing simulator capability settings and simulation parameters to determine the capabilities that will be used for this simulation.

Parameters:

timeStart - Start time, or NaN if not provided

timeEnd - End time, or NaN if not provided

stepSize - Distance between each reported step, or NaN if not provided

numberOfPoints - Number of steps to return, or 0 if not provided

getSelectableNamesInternal

protected java.util.List getSelectableNamesInternal()

Overrides:

getSelectableNamesInternal in class jigcell.simulation.Simulator

getValueInternal

protected double getValueInternal(java.lang.String name)

Overrides:

getValueInternal in class jigcell.simulation.Simulator

getValueNamesInternal

protected java.util.List getValueNamesInternal()

Overrides:

getValueNamesInternal in class jigcell.simulation.Simulator

loadSBMLInternal

protected void loadSBMLInternal(jigcell.sbml2.Model model,
                                boolean displayConcentration,
                                int volumeColumn)

Specified by:

loadSBMLInternal in class jigcell.simulation.Simulator

loadSBMLInternal

protected void loadSBMLInternal(jigcell.sbml2.Model model)

Specified by:

loadSBMLInternal in class jigcell.simulation.Simulator

setValueInternal

protected double setValueInternal(java.lang.String name,
                                  double value)

Overrides:

setValueInternal in class jigcell.simulation.Simulator

simulateInternal

protected jigcell.compare.IDataElement simulateInternal(double timeStart,
                                                        double timeEnd,
                                                        double stepSize,
                                                        int numberOfPoints)

Specified by:

simulateInternal in class jigcell.simulation.Simulator