moose::CompartmentBase Class Reference

#include <CompartmentBase.h>

Inheritance diagram for moose::CompartmentBase:

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List of all members.

Public Member Functions
	CompartmentBase ()
virtual	~CompartmentBase ()
void	setVm (const Eref &e, double Vm)
double	getVm (const Eref &e) const
void	setEm (const Eref &e, double Em)
double	getEm (const Eref &e) const
void	setCm (const Eref &e, double Cm)
double	getCm (const Eref &e) const
void	setRm (const Eref &e, double Rm)
double	getRm (const Eref &e) const
void	setRa (const Eref &e, double Ra)
double	getRa (const Eref &e) const
double	getIm (const Eref &e) const
void	setInject (const Eref &e, double Inject)
double	getInject (const Eref &e) const
void	setInitVm (const Eref &e, double initVm)
double	getInitVm (const Eref &e) const
void	setDiameter (double diameter)
double	getDiameter () const
void	setLength (double length)
double	getLength () const
void	setX0 (double value)
double	getX0 () const
void	setY0 (double value)
double	getY0 () const
void	setZ0 (double value)
double	getZ0 () const
void	setX (double value)
double	getX () const
void	setY (double value)
double	getY () const
void	setZ (double value)
double	getZ () const
void	process (const Eref &e, ProcPtr p)
void	reinit (const Eref &e, ProcPtr p)
void	initProc (const Eref &e, ProcPtr p)
void	initReinit (const Eref &e, ProcPtr p)
void	handleChannel (const Eref &e, double Gk, double Ek)
void	handleRaxial (double Ra, double Vm)
void	handleAxial (double Vm)
void	injectMsg (const Eref &e, double current)
void	randInject (const Eref &e, double prob, double current)
void	cable ()
void	displace (double dx, double dy, double dz)
	Displaces compartment by specified distance vector.
void	setGeomAndElec (const Eref &e, double length, double dia)
	Scales electrical values along with setting length, dia.
virtual void	vSetVm (const Eref &e, double Vm)=0
virtual double	vGetVm (const Eref &e) const =0
virtual void	vSetEm (const Eref &e, double Em)=0
virtual double	vGetEm (const Eref &e) const =0
virtual void	vSetCm (const Eref &e, double Cm)=0
virtual double	vGetCm (const Eref &e) const =0
virtual void	vSetRm (const Eref &e, double Rm)=0
virtual double	vGetRm (const Eref &e) const =0
virtual void	vSetRa (const Eref &e, double Ra)=0
virtual double	vGetRa (const Eref &e) const =0
virtual double	vGetIm (const Eref &e) const =0
virtual void	vSetInject (const Eref &e, double Inject)=0
virtual double	vGetInject (const Eref &e) const =0
virtual void	vSetInitVm (const Eref &e, double initVm)=0
virtual double	vGetInitVm (const Eref &e) const =0
virtual void	vProcess (const Eref &e, ProcPtr p)=0
virtual void	vReinit (const Eref &e, ProcPtr p)=0
virtual void	vInitProc (const Eref &e, ProcPtr p)=0
virtual void	vInitReinit (const Eref &e, ProcPtr p)=0
virtual void	vHandleChannel (const Eref &e, double Gk, double Ek)=0
virtual void	vHandleRaxial (double Ra, double Vm)=0
virtual void	vHandleAxial (double Vm)=0
virtual void	vInjectMsg (const Eref &e, double current)=0
virtual void	vRandInject (const Eref &e, double prob, double current)=0
virtual void	vSetSolver (const Eref &e, Id hsolve)
bool	rangeWarning (const string &field, double value)
void	updateLength ()
Static Public Member Functions
static const Cinfo *	initCinfo ()
static SrcFinfo1< double > *	VmOut ()
static void	zombify (Element *orig, const Cinfo *zClass, Id hsolve)

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Constructor & Destructor Documentation

CompartmentBase::CompartmentBase

(

)

CompartmentBase::~CompartmentBase

(

)

[virtual]

---

Member Function Documentation

void CompartmentBase::cable

(

)

Dummy function to act as recipient of 'cable' message, which is just for grouping compartments.

Reimplemented in moose::Compartment.

Referenced by initCinfo().

void CompartmentBase::displace	(	double	dx,
		double	dy,
		double	dz
	)

Displaces compartment by specified distance vector.

Referenced by initCinfo().

double CompartmentBase::getCm

(

const Eref &

e

)

const

References vGetCm().

Referenced by initCinfo(), and moose::CompartmentDataHolder::readData().

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double CompartmentBase::getDiameter

(

)

const

Referenced by initCinfo(), and moose::CompartmentDataHolder::readData().

double CompartmentBase::getEm

(

const Eref &

e

)

const

References vGetEm().

Referenced by initCinfo(), and moose::CompartmentDataHolder::readData().

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double CompartmentBase::getIm

(

const Eref &

e

)

const

References vGetIm().

Referenced by initCinfo().

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double CompartmentBase::getInitVm

(

const Eref &

e

)

const

References vGetInitVm().

Referenced by initCinfo(), and moose::CompartmentDataHolder::readData().

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double CompartmentBase::getInject

(

const Eref &

e

)

const

References vGetInject().

Referenced by initCinfo(), and moose::CompartmentDataHolder::readData().

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double CompartmentBase::getLength

(

)

const

Referenced by initCinfo(), and moose::CompartmentDataHolder::readData().

double CompartmentBase::getRa

(

const Eref &

e

)

const

References vGetRa().

Referenced by initCinfo(), and moose::CompartmentDataHolder::readData().

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double CompartmentBase::getRm

(

const Eref &

e

)

const

References vGetRm().

Referenced by initCinfo(), and moose::CompartmentDataHolder::readData().

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double CompartmentBase::getVm

(

const Eref &

e

)

const

References vGetVm().

Referenced by initCinfo().

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double CompartmentBase::getX

(

)

const

Referenced by initCinfo(), and moose::CompartmentDataHolder::readData().

double CompartmentBase::getX0

(

)

const

Referenced by initCinfo(), and moose::CompartmentDataHolder::readData().

double CompartmentBase::getY

(

)

const

Referenced by initCinfo(), and moose::CompartmentDataHolder::readData().

double CompartmentBase::getY0

(

)

const

Referenced by initCinfo(), and moose::CompartmentDataHolder::readData().

double CompartmentBase::getZ

(

)

const

Referenced by initCinfo(), and moose::CompartmentDataHolder::readData().

double CompartmentBase::getZ0

(

)

const

Referenced by initCinfo(), and moose::CompartmentDataHolder::readData().

void CompartmentBase::handleAxial

(

double

Vm

)

handleAxial handles incoming axial message data.

References vHandleAxial().

Referenced by initCinfo().

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void CompartmentBase::handleChannel	(	const Eref &	e,
		double	Gk,
		double	Ek
	)

handleChannel handles information coming from the channel to the compartment

References vHandleChannel().

Referenced by initCinfo().

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void CompartmentBase::handleRaxial	(	double	Ra,
		double	Vm
	)

handleRaxial handles incoming raxial message data.

References vHandleRaxial().

Referenced by initCinfo().

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const Cinfo * CompartmentBase::initCinfo

(

)

[static]

Initializes the class info.

The initCinfo() function sets up the CompartmentBase class. This function uses the common trick of having an internal static value which is created the first time the function is called. There are several static arrays set up here. The ones which use SharedFinfos are for shared messages where multiple kinds of information go along the same connection.

Reimplemented in moose::Compartment, SymCompartment, and ZombieCompartment.

References axialOut, cable(), displace(), getCm(), getDiameter(), getEm(), getIm(), getInitVm(), getInject(), getLength(), getRa(), getRm(), getVm(), getX(), getX0(), getY(), getY0(), getZ(), getZ0(), handleAxial(), handleChannel(), handleRaxial(), init(), Neutral::initCinfo(), initProc(), initReinit(), injectMsg(), process(), randInject(), raxialOut, reinit(), setCm(), setDiameter(), setEm(), setGeomAndElec(), setInitVm(), setInject(), setLength(), setRa(), setRm(), setVm(), setX(), setX0(), setY(), setY0(), setZ(), setZ0(), VmOut(), and y.

Referenced by moose::Compartment::initCinfo().

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void CompartmentBase::initProc	(	const Eref &	e,
		ProcPtr	p
	)

The initProc function is for a second phase of 'process' operations. It sends the axial and raxial messages to other compartments. It has to be executed out of phase with the main process so that all compartments are equivalent and there is no calling order dependence in the results.

References vInitProc().

Referenced by initCinfo().

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void CompartmentBase::initReinit	(	const Eref &	e,
		ProcPtr	p
	)

Empty function to do another reinit step out of phase with the main one. Nothing needs doing there.

References vInitReinit().

Referenced by initCinfo().

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void CompartmentBase::injectMsg	(	const Eref &	e,
		double	current
	)

Injects a constantly updated current into the compartment. Unlike the 'inject' field, this injected current is applicable only for a single timestep. So this is meant to be used as the destination of a message rather than as a one-time assignment.

References vInjectMsg().

Referenced by initCinfo().

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void CompartmentBase::process	(	const Eref &	e,
		ProcPtr	p
	)

The process function does the object updating and sends out messages to channels, nernsts, and so on.

References vProcess().

Referenced by initCinfo().

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void CompartmentBase::randInject	(	const Eref &	e,
		double	prob,
		double	current
	)

Injects a constantly updated current into the compartment, with a probability prob. Note that it isn't the current amplitude that is random, it is the presence or absence of the current that is probabilistic.

References vRandInject().

Referenced by initCinfo().

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bool moose::CompartmentBase::rangeWarning	(	const string &	field,
		double	value
	)

A utility function to check for assignment to fields that must be > 0

Referenced by setCm(), setRa(), setRm(), ZombieCompartment::vSetCm(), moose::Compartment::vSetCm(), ZombieCompartment::vSetRa(), moose::Compartment::vSetRa(), ZombieCompartment::vSetRm(), and moose::Compartment::vSetRm().

void CompartmentBase::reinit	(	const Eref &	e,
		ProcPtr	p
	)

The reinit function reinitializes all fields.

References vReinit().

Referenced by initCinfo().

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void CompartmentBase::setCm	(	const Eref &	e,
		double	Cm
	)

References rangeWarning(), and vSetCm().

Referenced by initCinfo(), and moose::CompartmentDataHolder::writeData().

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void CompartmentBase::setDiameter

(

double

diameter

)

Referenced by initCinfo(), setGeomAndElec(), and moose::CompartmentDataHolder::writeData().

void CompartmentBase::setEm	(	const Eref &	e,
		double	Em
	)

References vSetEm().

Referenced by initCinfo(), and moose::CompartmentDataHolder::writeData().

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void CompartmentBase::setGeomAndElec	(	const Eref &	e,
		double	length,
		double	dia
	)

Scales electrical values along with setting length, dia.

References allChildren(), ALLDATA, doubleEq(), Eref::objId(), setDiameter(), setLength(), vGetCm(), vGetRa(), vGetRm(), vSetCm(), vSetRa(), and vSetRm().

Referenced by initCinfo().

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void CompartmentBase::setInitVm	(	const Eref &	e,
		double	initVm
	)

References vSetInitVm().

Referenced by initCinfo(), and moose::CompartmentDataHolder::writeData().

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void CompartmentBase::setInject	(	const Eref &	e,
		double	Inject
	)

References vSetInject().

Referenced by initCinfo(), and moose::CompartmentDataHolder::writeData().

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void CompartmentBase::setLength

(

double

length

)

References doubleEq().

Referenced by initCinfo(), setGeomAndElec(), and moose::CompartmentDataHolder::writeData().

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void CompartmentBase::setRa	(	const Eref &	e,
		double	Ra
	)

References rangeWarning(), and vSetRa().

Referenced by initCinfo(), and moose::CompartmentDataHolder::writeData().

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void CompartmentBase::setRm	(	const Eref &	e,
		double	Rm
	)

References rangeWarning(), and vSetRm().

Referenced by initCinfo(), and moose::CompartmentDataHolder::writeData().

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void CompartmentBase::setVm	(	const Eref &	e,
		double	Vm
	)

References vSetVm().

Referenced by initCinfo().

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void CompartmentBase::setX

(

double

value

)

References updateLength().

Referenced by initCinfo(), and moose::CompartmentDataHolder::writeData().

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void CompartmentBase::setX0

(

double

value

)

References updateLength().

Referenced by initCinfo(), and moose::CompartmentDataHolder::writeData().

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void CompartmentBase::setY

(

double

value

)

References updateLength().

Referenced by initCinfo(), and moose::CompartmentDataHolder::writeData().

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void CompartmentBase::setY0

(

double

value

)

References updateLength().

Referenced by initCinfo(), and moose::CompartmentDataHolder::writeData().

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void CompartmentBase::setZ

(

double

value

)

References updateLength().

Referenced by initCinfo(), and moose::CompartmentDataHolder::writeData().

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void CompartmentBase::setZ0

(

double

value

)

References updateLength().

Referenced by initCinfo(), and moose::CompartmentDataHolder::writeData().

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void CompartmentBase::updateLength

(

)

A utility function update length if any of the coords change

Referenced by setX(), setX0(), setY(), setY0(), setZ(), and setZ0().

virtual double moose::CompartmentBase::vGetCm

(

const Eref &

e

)

const [pure virtual]

Implemented in moose::Compartment, and ZombieCompartment.

Referenced by getCm(), and setGeomAndElec().

virtual double moose::CompartmentBase::vGetEm

(

const Eref &

e

)

const [pure virtual]

Implemented in moose::Compartment, and ZombieCompartment.

Referenced by getEm().

virtual double moose::CompartmentBase::vGetIm

(

const Eref &

e

)

const [pure virtual]

Implemented in moose::Compartment, and ZombieCompartment.

Referenced by getIm().

virtual double moose::CompartmentBase::vGetInitVm

(

const Eref &

e

)

const [pure virtual]

Implemented in moose::Compartment, and ZombieCompartment.

Referenced by getInitVm().

virtual double moose::CompartmentBase::vGetInject

(

const Eref &

e

)

const [pure virtual]

Implemented in moose::Compartment, and ZombieCompartment.

Referenced by getInject().

virtual double moose::CompartmentBase::vGetRa

(

const Eref &

e

)

const [pure virtual]

Implemented in moose::Compartment, and ZombieCompartment.

Referenced by getRa(), and setGeomAndElec().

virtual double moose::CompartmentBase::vGetRm

(

const Eref &

e

)

const [pure virtual]

Implemented in moose::Compartment, and ZombieCompartment.

Referenced by getRm(), and setGeomAndElec().

virtual double moose::CompartmentBase::vGetVm

(

const Eref &

e

)

const [pure virtual]

Implemented in moose::Compartment, and ZombieCompartment.

Referenced by getVm().

virtual void moose::CompartmentBase::vHandleAxial

(

double

Vm

)

[pure virtual]

handleAxial handles incoming axial message data.

Implemented in moose::Compartment, and ZombieCompartment.

Referenced by handleAxial().

virtual void moose::CompartmentBase::vHandleChannel	(	const Eref &	e,
		double	Gk,
		double	Ek
	)			[pure virtual]

handleChannel handles information coming from the channel to the compartment

Implemented in moose::Compartment, and ZombieCompartment.

Referenced by handleChannel().

virtual void moose::CompartmentBase::vHandleRaxial	(	double	Ra,
		double	Vm
	)			[pure virtual]

handleRaxial handles incoming raxial message data.

Implemented in moose::Compartment, and ZombieCompartment.

Referenced by handleRaxial().

virtual void moose::CompartmentBase::vInitProc	(	const Eref &	e,
		ProcPtr	p
	)			[pure virtual]

The initProc function is for a second phase of 'process' operations. It sends the axial and raxial messages to other compartments. It has to be executed out of phase with the main process so that all compartments are equivalent and there is no calling order dependence in the results.

Implemented in moose::Compartment, SymCompartment, and ZombieCompartment.

Referenced by initProc().

virtual void moose::CompartmentBase::vInitReinit	(	const Eref &	e,
		ProcPtr	p
	)			[pure virtual]

Empty function to do another reinit step out of phase with the main one. Nothing needs doing there.

Implemented in moose::Compartment, SymCompartment, and ZombieCompartment.

Referenced by initReinit().

virtual void moose::CompartmentBase::vInjectMsg	(	const Eref &	e,
		double	current
	)			[pure virtual]

Injects a constantly updated current into the compartment. Unlike the 'inject' field, this injected current is applicable only for a single timestep. So this is meant to be used as the destination of a message rather than as a one-time assignment.

Implemented in moose::Compartment, and ZombieCompartment.

Referenced by injectMsg().

SrcFinfo1< double > * CompartmentBase::VmOut

(

)

[static]

This Finfo is used to send out Vm to channels, spikegens, etc

It is exposed here so that HSolve can also use it to send out the Vm to the recipients.

Referenced by initCinfo(), moose::Compartment::vProcess(), and moose::Compartment::vReinit().

virtual void moose::CompartmentBase::vProcess	(	const Eref &	e,
		ProcPtr	p
	)			[pure virtual]

The process function does the object updating and sends out messages to channels, nernsts, and so on.

Implemented in moose::Compartment, and ZombieCompartment.

Referenced by process().

virtual void moose::CompartmentBase::vRandInject	(	const Eref &	e,
		double	prob,
		double	current
	)			[pure virtual]

Injects a constantly updated current into the compartment, with a probability prob. Note that it isn't the current amplitude that is random, it is the presence or absence of the current that is probabilistic.

Implemented in moose::Compartment, and ZombieCompartment.

Referenced by randInject().

virtual void moose::CompartmentBase::vReinit	(	const Eref &	e,
		ProcPtr	p
	)			[pure virtual]

The reinit function reinitializes all fields.

Implemented in moose::Compartment, SymCompartment, and ZombieCompartment.

Referenced by reinit().

virtual void moose::CompartmentBase::vSetCm	(	const Eref &	e,
		double	Cm
	)			[pure virtual]

Implemented in moose::Compartment, and ZombieCompartment.

Referenced by setCm(), and setGeomAndElec().

virtual void moose::CompartmentBase::vSetEm	(	const Eref &	e,
		double	Em
	)			[pure virtual]

Implemented in moose::Compartment, and ZombieCompartment.

Referenced by setEm().

virtual void moose::CompartmentBase::vSetInitVm	(	const Eref &	e,
		double	initVm
	)			[pure virtual]

Implemented in moose::Compartment, and ZombieCompartment.

Referenced by setInitVm().

virtual void moose::CompartmentBase::vSetInject	(	const Eref &	e,
		double	Inject
	)			[pure virtual]

Implemented in moose::Compartment, and ZombieCompartment.

Referenced by setInject().

virtual void moose::CompartmentBase::vSetRa	(	const Eref &	e,
		double	Ra
	)			[pure virtual]

Implemented in moose::Compartment, and ZombieCompartment.

Referenced by setGeomAndElec(), and setRa().

virtual void moose::CompartmentBase::vSetRm	(	const Eref &	e,
		double	Rm
	)			[pure virtual]

Implemented in moose::Compartment, and ZombieCompartment.

Referenced by setGeomAndElec(), and setRm().

void CompartmentBase::vSetSolver	(	const Eref &	e,
		Id	hsolve
	)			[virtual]

Reimplemented in ZombieCompartment.

Referenced by zombify().

virtual void moose::CompartmentBase::vSetVm	(	const Eref &	e,
		double	Vm
	)			[pure virtual]

Implemented in moose::Compartment, and ZombieCompartment.

Referenced by setVm().

void CompartmentBase::zombify	(	Element *	orig,
		const Cinfo *	zClass,
		Id	hsolve
	)			[static]

This function is used to swap Cinfos of any CompartmentBase derived class. Used for making ZombieCompartments.

References Element::cinfo(), Eref::data(), Element::localDataStart(), Element::numLocalData(), vSetSolver(), and Element::zombieSwap().

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The documentation for this class was generated from the following files:

• biophysics/CompartmentBase.h
• biophysics/CompartmentBase.cpp