ucl.physiol.neuroconstruct.mechanisms
Class CellMechanism

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

Direct Known Subclasses:

AbstractedCellMechanism, XMLCellMechanism

public abstract class CellMechanism
extends Object

Base class for all Cell Mechanisms (Abstract or ChannelML)

Author:

Padraig Gleeson

Field Summary

static String	ABSTRACTED_CELL_MECHANISM
static String	CHANNEL_MECHANISM Mechanism types
static String	CHANNELML_BASED_CELL_MECHANISM Implementation methods
protected String	description
static String	FILE_BASED_CELL_MECHANISM
static String	GAP_JUNCTION
protected String	instanceName
static String	ION_CONCENTRATION
protected static ClassLogger	logger
protected String	mechanismModel
protected String	mechanismType Channel or Synaptic mechanism or Ion concentration
static String	NEUROML2_ABSTRACT_CELL
static String	NEUROML2_BASED_CELL_MECHANISM
static String	NEUROML2_ION_CHANNEL
static String	POINT_PROCESS
static String	SBML_BASED_CELL_MECHANISM
static String	SBML_MECHANISM
static String	SYNAPTIC_MECHANISM

Constructor Summary

CellMechanism()

Method Summary

abstract boolean	createImplementationFile(String targetEnv, int unitsSystem, File fileToGenerate, Project project, boolean requiresCompilation, boolean includeComments, boolean forceCorrectInit, boolean parallelMode)
String	getDescription()
String	getInstanceName()
String	getMechanismModel()
String	getMechanismType() Channel or Synaptic mechanism or Ion concentration
boolean	isChannelMechanism()
boolean	isGapJunctionMechanism()
boolean	isIonConcMechanism()
boolean	isPointProcess()
boolean	isSynapticMechanism()
void	setDescription(String description)
void	setInstanceName(String instanceName)
void	setMechanismModel(String mechanismModel)
void	setMechanismType(String mechanismType) Channel or Synaptic mechanism or Ion concentration

Methods inherited from class java.lang.Object

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

Field Detail

logger

protected static ClassLogger logger

CHANNEL_MECHANISM

public static final String CHANNEL_MECHANISM

Mechanism types

See Also:

Constant Field Values

SYNAPTIC_MECHANISM

public static final String SYNAPTIC_MECHANISM

See Also:

Constant Field Values

ION_CONCENTRATION

public static final String ION_CONCENTRATION

See Also:

Constant Field Values

POINT_PROCESS

public static final String POINT_PROCESS

See Also:

Constant Field Values

GAP_JUNCTION

public static final String GAP_JUNCTION

See Also:

Constant Field Values

SBML_MECHANISM

public static final String SBML_MECHANISM

See Also:

Constant Field Values

NEUROML2_ION_CHANNEL

public static final String NEUROML2_ION_CHANNEL

See Also:

Constant Field Values

NEUROML2_ABSTRACT_CELL

public static final String NEUROML2_ABSTRACT_CELL

See Also:

Constant Field Values

CHANNELML_BASED_CELL_MECHANISM

public static final String CHANNELML_BASED_CELL_MECHANISM

Implementation methods

See Also:

Constant Field Values

SBML_BASED_CELL_MECHANISM

public static final String SBML_BASED_CELL_MECHANISM

See Also:

Constant Field Values

NEUROML2_BASED_CELL_MECHANISM

public static final String NEUROML2_BASED_CELL_MECHANISM

See Also:

Constant Field Values

ABSTRACTED_CELL_MECHANISM

public static final String ABSTRACTED_CELL_MECHANISM

See Also:

Constant Field Values

FILE_BASED_CELL_MECHANISM

public static final String FILE_BASED_CELL_MECHANISM

See Also:

Constant Field Values

instanceName

protected String instanceName

description

protected String description

mechanismModel

protected String mechanismModel

mechanismType

protected String mechanismType

Channel or Synaptic mechanism or Ion concentration

Constructor Detail

CellMechanism

public CellMechanism()

Method Detail

getDescription

public String getDescription()

setDescription

public void setDescription(String description)

getInstanceName

public String getInstanceName()

setInstanceName

public void setInstanceName(String instanceName)

getMechanismModel

public String getMechanismModel()

getMechanismType

public String getMechanismType()

Channel or Synaptic mechanism or Ion concentration

isChannelMechanism

public boolean isChannelMechanism()

isPointProcess

public boolean isPointProcess()

isGapJunctionMechanism

public boolean isGapJunctionMechanism()

isSynapticMechanism

public boolean isSynapticMechanism()

isIonConcMechanism

public boolean isIonConcMechanism()

setMechanismModel

public void setMechanismModel(String mechanismModel)

setMechanismType

public void setMechanismType(String mechanismType)

Channel or Synaptic mechanism or Ion concentration

createImplementationFile

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