ucl.physiol.neuroconstruct.mechanisms
Class SBMLCellMechanism

java.lang.Object
  ucl.physiol.neuroconstruct.mechanisms.CellMechanism
      ucl.physiol.neuroconstruct.mechanisms.XMLCellMechanism
          ucl.physiol.neuroconstruct.mechanisms.SBMLCellMechanism

public class SBMLCellMechanism
extends XMLCellMechanism

Base class for all SBML based Cell Mechanism. Contains (in addition to info in CellMechanism class) a string with the name of the file and a SimpleXMLDocument containing the contents of the xml (once initialised) and a number of mappings to NEURON, etc.

Author:

Padraig Gleeson

Field Summary

Fields inherited from class ucl.physiol.neuroconstruct.mechanisms.XMLCellMechanism

xmlDoc

Fields inherited from class ucl.physiol.neuroconstruct.mechanisms.CellMechanism

ABSTRACTED_CELL_MECHANISM, CHANNEL_MECHANISM, CHANNELML_BASED_CELL_MECHANISM, description, FILE_BASED_CELL_MECHANISM, GAP_JUNCTION, instanceName, ION_CONCENTRATION, logger, mechanismModel, mechanismType, NEUROML2_ABSTRACT_CELL, NEUROML2_BASED_CELL_MECHANISM, NEUROML2_ION_CHANNEL, POINT_PROCESS, SBML_BASED_CELL_MECHANISM, SBML_MECHANISM, SYNAPTIC_MECHANISM

Constructor Summary

SBMLCellMechanism()

Method Summary

boolean	createImplementationFile(String targetEnv, int unitsSystem, File fileToGenerate, Project project, boolean requiresCompilation, boolean includeComments, boolean forceCorrectInit, boolean parallelMode) Create a script file for the specified simulation environment
String	getDescriptionXPath()
String	getMechanismType() Channel or Synaptic mechanism or Ion concentration
String	getNameXPath()
static void	main(String[] args)
String	toString()

Methods inherited from class ucl.physiol.neuroconstruct.mechanisms.XMLCellMechanism

addSimMapping, getDescription, getInstanceName, getSimMapping, getSimMappings, getValue, getXMLDoc, getXMLFile, getXMLFile, initialise, initPropsFromPropsFile, isNeuroML2, reset, saveCurrentState, setDescription, setInstanceName, setSimMappings, setValue, setXMLFile

Methods inherited from class ucl.physiol.neuroconstruct.mechanisms.CellMechanism

getMechanismModel, isChannelMechanism, isGapJunctionMechanism, isIonConcMechanism, isPointProcess, isSynapticMechanism, setMechanismModel, setMechanismType

Methods inherited from class java.lang.Object

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

Constructor Detail

SBMLCellMechanism

public SBMLCellMechanism()

Method Detail

toString

public String toString()

Overrides:

toString in class Object

getNameXPath

public String getNameXPath()

Specified by:

getNameXPath in class XMLCellMechanism

getDescriptionXPath

public String getDescriptionXPath()

Specified by:

getDescriptionXPath in class XMLCellMechanism

getMechanismType

public String getMechanismType()

Description copied from class: CellMechanism

Channel or Synaptic mechanism or Ion concentration

Specified by:

getMechanismType in class XMLCellMechanism

createImplementationFile

public boolean createImplementationFile(String targetEnv,
                                        int unitsSystem,
                                        File fileToGenerate,
                                        Project project,
                                        boolean requiresCompilation,
                                        boolean includeComments,
                                        boolean forceCorrectInit,
                                        boolean parallelMode)

Create a script file for the specified simulation environment

Specified by:

createImplementationFile in class XMLCellMechanism

main

public static void main(String[] args)