moose::Compartment Class Reference

#include <Compartment.h>

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List of all members.

Public Member Functions
	Compartment ()
virtual	~Compartment ()
virtual void	vSetVm (const Eref &e, double Vm)
virtual double	vGetVm (const Eref &e) const
virtual void	vSetEm (const Eref &e, double Em)
virtual double	vGetEm (const Eref &e) const
virtual void	vSetCm (const Eref &e, double Cm)
virtual double	vGetCm (const Eref &e) const
virtual void	vSetRm (const Eref &e, double Rm)
virtual double	vGetRm (const Eref &e) const
virtual void	vSetRa (const Eref &e, double Ra)
virtual double	vGetRa (const Eref &e) const
virtual double	vGetIm (const Eref &e) const
virtual void	vSetInject (const Eref &e, double Inject)
virtual double	vGetInject (const Eref &e) const
virtual void	vSetInitVm (const Eref &e, double initVm)
virtual double	vGetInitVm (const Eref &e) const
void	vProcess (const Eref &e, ProcPtr p)
void	vReinit (const Eref &e, ProcPtr p)
void	vInitProc (const Eref &e, ProcPtr p)
void	vInitReinit (const Eref &e, ProcPtr p)
void	vHandleChannel (const Eref &e, double Gk, double Ek)
void	vHandleRaxial (double Ra, double Vm)
void	vHandleAxial (double Vm)
void	vInjectMsg (const Eref &e, double current)
void	vRandInject (const Eref &e, double prob, double current)
void	cable ()
Static Public Member Functions
static const Cinfo *	initCinfo ()
Protected Attributes
double	Vm_
double	initVm_
double	Em_
double	Cm_
double	Rm_
double	Ra_
double	Im_
double	lastIm_
double	inject_
double	A_
double	B_
double	sumInject_

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Constructor & Destructor Documentation

Compartment::Compartment

(

)

References A_, B_, Cm_, Em_, Im_, initVm_, inject_, lastIm_, Ra_, Rm_, sumInject_, and Vm_.

Compartment::~Compartment

(

)

[virtual]

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Member Function Documentation

void moose::Compartment::cable

(

)

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

Reimplemented from moose::CompartmentBase.

const Cinfo * Compartment::initCinfo

(

)

[static]

Initializes the class info.

The initCinfo() function sets up the Compartment 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 from moose::CompartmentBase.

Reimplemented in SymCompartment.

References moose::CompartmentBase::initCinfo().

Referenced by SymCompartment::initCinfo().

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double Compartment::vGetCm

(

const Eref &

e

)

const [virtual]

Implements moose::CompartmentBase.

References Cm_.

double Compartment::vGetEm

(

const Eref &

e

)

const [virtual]

Implements moose::CompartmentBase.

References Em_.

double Compartment::vGetIm

(

const Eref &

e

)

const [virtual]

Implements moose::CompartmentBase.

References lastIm_.

double Compartment::vGetInitVm

(

const Eref &

e

)

const [virtual]

Implements moose::CompartmentBase.

References initVm_.

double Compartment::vGetInject

(

const Eref &

e

)

const [virtual]

Implements moose::CompartmentBase.

References inject_.

double Compartment::vGetRa

(

const Eref &

e

)

const [virtual]

Implements moose::CompartmentBase.

References Ra_.

double Compartment::vGetRm

(

const Eref &

e

)

const [virtual]

Implements moose::CompartmentBase.

References Rm_.

double Compartment::vGetVm

(

const Eref &

e

)

const [virtual]

Implements moose::CompartmentBase.

References Vm_.

void Compartment::vHandleAxial

(

double

Vm

)

[virtual]

handleAxial handles incoming axial message data.

Implements moose::CompartmentBase.

References A_, B_, Im_, Ra_, and Vm_.

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

handleChannel handles information coming from the channel to the compartment

Implements moose::CompartmentBase.

References A_, and B_.

void Compartment::vHandleRaxial	(	double	Ra,
		double	Vm
	)			[virtual]

handleRaxial handles incoming raxial message data.

Implements moose::CompartmentBase.

References A_, B_, Im_, and Vm_.

void Compartment::vInitProc	(	const Eref &	e,
		ProcPtr	p
	)			[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.

Implements moose::CompartmentBase.

Reimplemented in SymCompartment.

References Ra_, SrcFinfo2< T1, T2 >::send(), SrcFinfo1< T >::send(), and Vm_.

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void Compartment::vInitReinit	(	const Eref &	e,
		ProcPtr	p
	)			[virtual]

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

Implements moose::CompartmentBase.

Reimplemented in SymCompartment.

void Compartment::vInjectMsg	(	const Eref &	e,
		double	current
	)			[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.

Implements moose::CompartmentBase.

References Im_, and sumInject_.

void Compartment::vProcess	(	const Eref &	e,
		ProcPtr	p
	)			[virtual]

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

Implements moose::CompartmentBase.

References A_, B_, Cm_, ProcInfo::dt, Em_, Im_, inject_, lastIm_, sumInject_, Vm_, and moose::CompartmentBase::VmOut().

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void Compartment::vRandInject	(	const Eref &	e,
		double	prob,
		double	current
	)			[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.

Implements moose::CompartmentBase.

References Im_, mtrand(), and sumInject_.

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void Compartment::vReinit	(	const Eref &	e,
		ProcPtr	p
	)			[virtual]

The reinit function reinitializes all fields.

Implements moose::CompartmentBase.

Reimplemented in SymCompartment.

References A_, B_, ProcInfo::dt, Im_, initVm_, lastIm_, sumInject_, Vm_, and moose::CompartmentBase::VmOut().

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void Compartment::vSetCm	(	const Eref &	e,
		double	Cm
	)			[virtual]

Implements moose::CompartmentBase.

References Cm_, and moose::CompartmentBase::rangeWarning().

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void Compartment::vSetEm	(	const Eref &	e,
		double	Em
	)			[virtual]

Implements moose::CompartmentBase.

References Em_.

void Compartment::vSetInitVm	(	const Eref &	e,
		double	initVm
	)			[virtual]

Implements moose::CompartmentBase.

References initVm_.

void Compartment::vSetInject	(	const Eref &	e,
		double	Inject
	)			[virtual]

Implements moose::CompartmentBase.

References inject_.

void Compartment::vSetRa	(	const Eref &	e,
		double	Ra
	)			[virtual]

Implements moose::CompartmentBase.

References Ra_, and moose::CompartmentBase::rangeWarning().

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void Compartment::vSetRm	(	const Eref &	e,
		double	Rm
	)			[virtual]

Implements moose::CompartmentBase.

References moose::CompartmentBase::rangeWarning(), and Rm_.

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void Compartment::vSetVm	(	const Eref &	e,
		double	Vm
	)			[virtual]

Implements moose::CompartmentBase.

References Vm_.

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Member Data Documentation

double moose::Compartment::A_ [protected]

Referenced by Compartment(), SymCompartment::raxialCylinder(), SymCompartment::raxialSphere(), SymCompartment::raxialSym(), vHandleAxial(), vHandleChannel(), vHandleRaxial(), vProcess(), and vReinit().

double moose::Compartment::B_ [protected]

Referenced by Compartment(), SymCompartment::raxialCylinder(), SymCompartment::raxialSphere(), SymCompartment::raxialSym(), vHandleAxial(), vHandleChannel(), vHandleRaxial(), vProcess(), and vReinit().

double moose::Compartment::Cm_ [protected]

Referenced by Compartment(), vGetCm(), vProcess(), and vSetCm().

double moose::Compartment::Em_ [protected]

Referenced by Compartment(), vGetEm(), vProcess(), and vSetEm().

double moose::Compartment::Im_ [protected]

Referenced by Compartment(), SymCompartment::raxialCylinder(), SymCompartment::raxialSphere(), SymCompartment::raxialSym(), vHandleAxial(), vHandleRaxial(), vInjectMsg(), vProcess(), vRandInject(), and vReinit().

double moose::Compartment::initVm_ [protected]

Referenced by Compartment(), vGetInitVm(), vReinit(), and vSetInitVm().

double moose::Compartment::inject_ [protected]

Referenced by Compartment(), vGetInject(), vProcess(), and vSetInject().

double moose::Compartment::lastIm_ [protected]

Referenced by Compartment(), vGetIm(), vProcess(), and vReinit().

double moose::Compartment::Ra_ [protected]

Referenced by Compartment(), SymCompartment::raxialSphere(), SymCompartment::sumRaxial(), vGetRa(), vHandleAxial(), SymCompartment::vInitProc(), vInitProc(), SymCompartment::vReinit(), and vSetRa().

double moose::Compartment::Rm_ [protected]

Referenced by Compartment(), vGetRm(), and vSetRm().

double moose::Compartment::sumInject_ [protected]

Referenced by Compartment(), vInjectMsg(), vProcess(), vRandInject(), and vReinit().

double moose::Compartment::Vm_ [protected]

Referenced by Compartment(), SymCompartment::raxialCylinder(), SymCompartment::raxialSphere(), SymCompartment::raxialSym(), vGetVm(), vHandleAxial(), vHandleRaxial(), SymCompartment::vInitProc(), vInitProc(), vProcess(), vReinit(), and vSetVm().

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

• biophysics/Compartment.h
• biophysics/Compartment.cpp