ucl.physiol.neuroconstruct.mechanisms
Class XMLCellMechanism

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

Direct Known Subclasses:

ChannelMLCellMechanism, NeuroML2Component, SBMLCellMechanism

public abstract class XMLCellMechanism
extends CellMechanism

Base class for all XML 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

protected SimpleXMLDocument

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

XMLCellMechanism()

Method Summary

void	addSimMapping(SimulatorMapping simMapping)
abstract 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	getDescription()
abstract String	getDescriptionXPath()
String	getInstanceName()
abstract String	getMechanismType() Channel or Synaptic mechanism or Ion concentration
abstract String	getNameXPath()
SimulatorMapping	getSimMapping(String simEnv)
ArrayList<SimulatorMapping>	getSimMappings()
String	getValue(String simpleXPathExp)
SimpleXMLDocument	getXMLDoc()
String	getXMLFile()
File	getXMLFile(Project project)
File	initialise(Project project, boolean save) Loads up the xmlDoc with information from the file specified, using the location based on the project directory
void	initPropsFromPropsFile(File propsFile)
boolean	isNeuroML2()
File	reset(Project project, boolean save) Sets the xmlDoc to null and reinitialises
void	saveCurrentState(Project project)
void	setDescription(String description)
void	setInstanceName(String instanceName)
void	setSimMappings(ArrayList<SimulatorMapping> simMappings)
boolean	setValue(String path, String value)
void	setXMLFile(String xmlFile)

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, toString, wait, wait, wait

Field Detail

xmlDoc

protected SimpleXMLDocument xmlDoc

Constructor Detail

XMLCellMechanism

public XMLCellMechanism()

Method Detail

isNeuroML2

public boolean isNeuroML2()

initPropsFromPropsFile

public void initPropsFromPropsFile(File propsFile)
                            throws IOException

Throws:

IOException

getXMLFile

public String getXMLFile()

getXMLFile

public File getXMLFile(Project project)

getXMLDoc

public SimpleXMLDocument getXMLDoc()
                            throws XMLMechanismException

Throws:

XMLMechanismException

setXMLFile

public void setXMLFile(String xmlFile)

getMechanismType

public abstract String getMechanismType()

Description copied from class: CellMechanism

Channel or Synaptic mechanism or Ion concentration

Overrides:

getMechanismType in class CellMechanism

getNameXPath

public abstract String getNameXPath()

getDescriptionXPath

public abstract String getDescriptionXPath()

getDescription

public String getDescription()

Overrides:

getDescription in class CellMechanism

setDescription

public void setDescription(String description)

Overrides:

setDescription in class CellMechanism

getInstanceName

public String getInstanceName()

Overrides:

getInstanceName in class CellMechanism

setInstanceName

public void setInstanceName(String instanceName)

Overrides:

setInstanceName in class CellMechanism

reset

public File reset(Project project,
                  boolean save)
           throws XMLMechanismException

Sets the xmlDoc to null and reinitialises

Throws:

XMLMechanismException

initialise

public File initialise(Project project,
                       boolean save)
                throws XMLMechanismException

Loads up the xmlDoc with information from the file specified, using the location based on the project directory

Returns:

The actual File used

Throws:

XMLMechanismException

saveCurrentState

public void saveCurrentState(Project project)
                      throws XMLMechanismException

Throws:

XMLMechanismException

createImplementationFile

public abstract 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 CellMechanism

addSimMapping

public void addSimMapping(SimulatorMapping simMapping)

getValue

public String getValue(String simpleXPathExp)

setValue

public boolean setValue(String path,
                        String value)

getSimMappings

public ArrayList<SimulatorMapping> getSimMappings()

getSimMapping

public SimulatorMapping getSimMapping(String simEnv)

setSimMappings

public void setSimMappings(ArrayList<SimulatorMapping> simMappings)