CaConcBase Class Reference

#include <CaConcBase.h>

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List of all members.

Public Member Functions
	CaConcBase ()
void	reinit (const Eref &, ProcPtr info)
void	process (const Eref &, ProcPtr info)
void	current (const Eref &e, double I)
void	currentFraction (const Eref &e, double I, double fraction)
void	increase (const Eref &e, double I)
void	decrease (const Eref &e, double I)
virtual void	vReinit (const Eref &, ProcPtr info)=0
virtual void	vProcess (const Eref &, ProcPtr info)=0
virtual void	vCurrent (const Eref &e, double I)=0
virtual void	vCurrentFraction (const Eref &e, double I, double fraction)=0
virtual void	vIncrease (const Eref &e, double I)=0
virtual void	vDecrease (const Eref &e, double I)=0
void	setCa (const Eref &e, double val)
double	getCa (const Eref &e) const
void	setCaBasal (const Eref &e, double val)
double	getCaBasal (const Eref &e) const
void	setTau (const Eref &e, double val)
double	getTau (const Eref &e) const
void	setB (const Eref &e, double val)
double	getB (const Eref &e) const
void	setCeiling (const Eref &e, double val)
double	getCeiling (const Eref &e) const
void	setFloor (const Eref &e, double val)
double	getFloor (const Eref &e) const
void	setThickness (const Eref &e, double val)
double	getThickness (const Eref &e) const
void	setLength (const Eref &e, double val)
double	getLength (const Eref &e) const
void	setDiameter (const Eref &e, double val)
double	getDiameter (const Eref &e) const
virtual void	vSetCa (const Eref &e, double val)=0
virtual double	vGetCa (const Eref &e) const =0
virtual void	vSetCaBasal (const Eref &e, double val)=0
virtual double	vGetCaBasal (const Eref &e) const =0
virtual void	vSetTau (const Eref &e, double val)=0
virtual double	vGetTau (const Eref &e) const =0
virtual void	vSetB (const Eref &e, double val)=0
virtual double	vGetB (const Eref &e) const =0
virtual void	vSetCeiling (const Eref &e, double val)=0
virtual double	vGetCeiling (const Eref &e) const =0
virtual void	vSetFloor (const Eref &e, double val)=0
virtual double	vGetFloor (const Eref &e) const =0
void	updateDimensions (const Eref &e)
virtual void	vSetSolver (const Eref &e, Id hsolve)
	Used to set up the solver. Dummy for regular classes.
Static Public Member Functions
static void	zombify (Element *orig, const Cinfo *zClass, Id hsolve)
static SrcFinfo1< double > *	concOut ()
static const Cinfo *	initCinfo ()

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Detailed Description

This is the base class for CaConc. It handles calcium current influx, conversion to calcium concentration, buffering, and pumps. It obeys the equation:

dC/dt = B*Ik - C/tau where Ca = Ca_base + C.

From the GENESIS notes: In SI units, where concentration is moles/m^3 (milli-moles/liter) and current is in amperes, theory gives B = 5.2e-6/(shell volume). In practice, B is a parameter to be fitted or estimated from experiment, as buffering, non-uniform distribution of Ca, etc., will modify this value. If thick = 0, the readcell routine calculates B by dividing the "density" parameter in the cell parameter file by the volume of the compartment. Otherwise, it scales as a true shell, with the volume of a shell having thickness thick. A negative value of the "density" parameter may be used to indicate that it should be taken as an absolute value of B, without scaling.

This is a base class to provide the interface functions.

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Constructor & Destructor Documentation

CaConcBase::CaConcBase

(

)

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Member Function Documentation

SrcFinfo1< double > * CaConcBase::concOut

(

)

[static]

Referenced by initCinfo(), CaConc::vProcess(), and CaConc::vReinit().

void CaConcBase::current	(	const Eref &	e,
		double	I
	)

References vCurrent().

Referenced by initCinfo().

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void CaConcBase::currentFraction	(	const Eref &	e,
		double	I,
		double	fraction
	)

References vCurrentFraction().

Referenced by initCinfo().

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void CaConcBase::decrease	(	const Eref &	e,
		double	I
	)

References vDecrease().

Referenced by initCinfo().

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double CaConcBase::getB

(

const Eref &

e

)

const

References vGetB().

Referenced by initCinfo(), and zombify().

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double CaConcBase::getCa

(

const Eref &

e

)

const

References vGetCa().

Referenced by initCinfo(), and zombify().

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double CaConcBase::getCaBasal

(

const Eref &

e

)

const

References vGetCaBasal().

Referenced by initCinfo(), and zombify().

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double CaConcBase::getCeiling

(

const Eref &

e

)

const

References vGetCeiling().

Referenced by initCinfo(), and zombify().

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double CaConcBase::getDiameter

(

const Eref &

e

)

const

Referenced by initCinfo(), and zombify().

double CaConcBase::getFloor

(

const Eref &

e

)

const

References vGetFloor().

Referenced by initCinfo(), and zombify().

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double CaConcBase::getLength

(

const Eref &

e

)

const

Referenced by initCinfo(), and zombify().

double CaConcBase::getTau

(

const Eref &

e

)

const

References vGetTau().

Referenced by initCinfo(), and zombify().

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double CaConcBase::getThickness

(

const Eref &

e

)

const

Referenced by initCinfo(), and zombify().

void CaConcBase::increase	(	const Eref &	e,
		double	I
	)

References vIncrease().

Referenced by initCinfo().

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const Cinfo * CaConcBase::initCinfo

(

)

[static]

Reimplemented in CaConc, and ZombieCaConc.

References concOut(), current(), currentFraction(), decrease(), getB(), getCa(), getCaBasal(), getCeiling(), getDiameter(), getFloor(), getLength(), getTau(), getThickness(), increase(), Neutral::initCinfo(), process(), reinit(), setB(), setCa(), setCaBasal(), setCeiling(), setDiameter(), setFloor(), setLength(), setTau(), and setThickness().

Referenced by ZombieCaConc::initCinfo(), and CaConc::initCinfo().

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void CaConcBase::process	(	const Eref &	e,
		ProcPtr	info
	)

References vProcess().

Referenced by initCinfo().

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void CaConcBase::reinit	(	const Eref &	e,
		ProcPtr	info
	)

References vReinit().

Referenced by initCinfo().

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void CaConcBase::setB	(	const Eref &	e,
		double	val
	)

References vSetB().

Referenced by initCinfo(), and zombify().

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void CaConcBase::setCa	(	const Eref &	e,
		double	val
	)

References vSetCa().

Referenced by initCinfo(), and zombify().

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void CaConcBase::setCaBasal	(	const Eref &	e,
		double	val
	)

References vSetCaBasal().

Referenced by initCinfo(), and zombify().

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void CaConcBase::setCeiling	(	const Eref &	e,
		double	val
	)

References vSetCeiling().

Referenced by initCinfo(), and zombify().

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void CaConcBase::setDiameter	(	const Eref &	e,
		double	val
	)

References updateDimensions().

Referenced by initCinfo(), and zombify().

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void CaConcBase::setFloor	(	const Eref &	e,
		double	val
	)

References vSetFloor().

Referenced by initCinfo(), and zombify().

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void CaConcBase::setLength	(	const Eref &	e,
		double	val
	)

References updateDimensions().

Referenced by initCinfo(), and zombify().

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void CaConcBase::setTau	(	const Eref &	e,
		double	val
	)

References vSetTau().

Referenced by initCinfo(), and zombify().

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void CaConcBase::setThickness	(	const Eref &	e,
		double	val
	)

References updateDimensions().

Referenced by initCinfo(), and zombify().

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void CaConcBase::updateDimensions

(

const Eref &

e

)

References FaradayConst, PI, and vSetB().

Referenced by setDiameter(), setLength(), and setThickness().

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virtual void CaConcBase::vCurrent	(	const Eref &	e,
		double	I
	)			[pure virtual]

Implemented in CaConc, and ZombieCaConc.

Referenced by current().

virtual void CaConcBase::vCurrentFraction	(	const Eref &	e,
		double	I,
		double	fraction
	)			[pure virtual]

Implemented in CaConc, and ZombieCaConc.

Referenced by currentFraction().

virtual void CaConcBase::vDecrease	(	const Eref &	e,
		double	I
	)			[pure virtual]

Implemented in CaConc, and ZombieCaConc.

Referenced by decrease().

virtual double CaConcBase::vGetB

(

const Eref &

e

)

const [pure virtual]

Implemented in CaConc, and ZombieCaConc.

Referenced by getB().

virtual double CaConcBase::vGetCa

(

const Eref &

e

)

const [pure virtual]

Implemented in CaConc, and ZombieCaConc.

Referenced by getCa().

virtual double CaConcBase::vGetCaBasal

(

const Eref &

e

)

const [pure virtual]

Implemented in CaConc, and ZombieCaConc.

Referenced by getCaBasal().

virtual double CaConcBase::vGetCeiling

(

const Eref &

e

)

const [pure virtual]

Implemented in CaConc, and ZombieCaConc.

Referenced by getCeiling().

virtual double CaConcBase::vGetFloor

(

const Eref &

e

)

const [pure virtual]

Implemented in CaConc, and ZombieCaConc.

Referenced by getFloor().

virtual double CaConcBase::vGetTau

(

const Eref &

e

)

const [pure virtual]

Implemented in CaConc, and ZombieCaConc.

Referenced by getTau().

virtual void CaConcBase::vIncrease	(	const Eref &	e,
		double	I
	)			[pure virtual]

Implemented in CaConc, and ZombieCaConc.

Referenced by increase().

virtual void CaConcBase::vProcess	(	const Eref &	,
		ProcPtr	info
	)			[pure virtual]

Implemented in CaConc, and ZombieCaConc.

Referenced by process().

virtual void CaConcBase::vReinit	(	const Eref &	,
		ProcPtr	info
	)			[pure virtual]

Implemented in CaConc, and ZombieCaConc.

Referenced by reinit().

virtual void CaConcBase::vSetB	(	const Eref &	e,
		double	val
	)			[pure virtual]

Implemented in CaConc, and ZombieCaConc.

Referenced by setB(), and updateDimensions().

virtual void CaConcBase::vSetCa	(	const Eref &	e,
		double	val
	)			[pure virtual]

Implemented in CaConc, and ZombieCaConc.

Referenced by setCa().

virtual void CaConcBase::vSetCaBasal	(	const Eref &	e,
		double	val
	)			[pure virtual]

Implemented in CaConc, and ZombieCaConc.

Referenced by setCaBasal().

virtual void CaConcBase::vSetCeiling	(	const Eref &	e,
		double	val
	)			[pure virtual]

Implemented in CaConc, and ZombieCaConc.

Referenced by setCeiling().

virtual void CaConcBase::vSetFloor	(	const Eref &	e,
		double	val
	)			[pure virtual]

Implemented in CaConc, and ZombieCaConc.

Referenced by setFloor().

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

Used to set up the solver. Dummy for regular classes.

Reimplemented in ZombieCaConc.

Referenced by zombify().

virtual void CaConcBase::vSetTau	(	const Eref &	e,
		double	val
	)			[pure virtual]

Implemented in CaConc, and ZombieCaConc.

Referenced by setTau().

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

Swaps Cinfos in order to make Zombies.

References Element::cinfo(), Eref::data(), getB(), getCa(), getCaBasal(), getCeiling(), getDiameter(), getFloor(), getLength(), getTau(), getThickness(), Element::localDataStart(), Element::numLocalData(), setB(), setCa(), setCaBasal(), setCeiling(), setDiameter(), setFloor(), setLength(), setTau(), setThickness(), vSetSolver(), and Element::zombieSwap().

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

• biophysics/CaConcBase.h
• biophysics/CaConcBase.cpp