ucl.physiol.neuroconstruct.mechanisms
Class ChannelMLCellMechanism

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

public class ChannelMLCellMechanism
extends XMLCellMechanism

Base class for all ChannelML 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 SimulatorMapping 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

ChannelMLCellMechanism()

Method Summary

static ChannelMLCellMechanism	createFromTemplate(File templateDir, Project project) To support the templates of common channels included in the neuroConstruct distribution
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()
String	getUnitsUsedInFile()
protected void	initPropsFromTemplate(File templateDir, Project project)
boolean	isPassiveNonSpecificCond() Needed as GENESIS treats the first passive, non specific conductance on a compartment differently (adjusts the memb resistance)
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

ChannelMLCellMechanism

public ChannelMLCellMechanism()

Method Detail

createFromTemplate

public static ChannelMLCellMechanism createFromTemplate(File templateDir,
                                                        Project project)
                                                 throws ChannelMLException

To support the templates of common channels included in the neuroConstruct distribution

Throws:

ChannelMLException

initPropsFromTemplate

protected void initPropsFromTemplate(File templateDir,
                                     Project project)
                              throws ChannelMLException

Throws:

ChannelMLException

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

getUnitsUsedInFile

public String getUnitsUsedInFile()

isPassiveNonSpecificCond

public boolean isPassiveNonSpecificCond()
                                 throws CMLMechNotInitException

Needed as GENESIS treats the first passive, non specific conductance on a compartment differently (adjusts the memb resistance)

Throws:

CMLMechNotInitException

main

public static void main(String[] args)