jigcell.xpp
Class Oscill8Simulator

java.lang.Object
  jigcell.simulation.Simulator
      jigcell.xpp.XPPSimulator
          jigcell.xpp.Oscill8Simulator

All Implemented Interfaces:

jigcell.simulation.ISimulator

public class Oscill8Simulator
extends XPPSimulator

Makes the Oscill8 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

Fields inherited from class jigcell.xpp.XPPSimulator

translator

Constructor Summary

Oscill8Simulator()
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 void	loadSBMLInternal(jigcell.sbml2.Model model)

Methods inherited from class jigcell.xpp.XPPSimulator

getSelectableNamesInternal, getValueInternal, getValueNamesInternal, loadSBMLInternal, setValueInternal, simulateInternal

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

Constructor Detail

Oscill8Simulator

public Oscill8Simulator()

Creates a new simulator.

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.

Overrides:

applySimulatorCapabilities in class XPPSimulator

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

loadSBMLInternal

protected void loadSBMLInternal(jigcell.sbml2.Model model)

Overrides:

loadSBMLInternal in class XPPSimulator