ChanBase Class Reference

#include <ChanBase.h>

Inheritance diagram for ChanBase:

Collaboration diagram for ChanBase:

Public Member Functions
	ChanBase ()
double	getEk (const Eref &e) const
double	getGbar (const Eref &e) const
double	getGk (const Eref &e) const
double	getIk (const Eref &e) const
double	getModulation (const Eref &e) const
void	handleVm (double Vm)
void	process (const Eref &e, const ProcPtr info)
void	reinit (const Eref &e, const ProcPtr info)
void	setEk (const Eref &e, double Ek)
void	setGbar (const Eref &e, double Gbar)
void	setGk (const Eref &e, double Gk)
void	setIk (const Eref &e, double Ic)
void	setModulation (const Eref &e, double modulation)
virtual double	vGetEk (const Eref &e) const =0
virtual double	vGetGbar (const Eref &e) const =0
virtual double	vGetGk (const Eref &e) const =0
virtual double	vGetIk (const Eref &e) const =0
virtual double	vGetModulation (const Eref &e) const =0
virtual void	vHandleVm (double Vm)=0
virtual void	vProcess (const Eref &e, const ProcPtr info)=0
virtual void	vReinit (const Eref &e, const ProcPtr info)=0
virtual void	vSetEk (const Eref &e, double Ek)=0
virtual void	vSetGbar (const Eref &e, double Gbar)=0
virtual void	vSetGk (const Eref &e, double Gk)=0
virtual void	vSetIk (const Eref &e, double Ik)=0
virtual void	vSetModulation (const Eref &e, double modulation)=0
	~ChanBase ()

Static Public Member Functions
static SrcFinfo2< double, double > *	channelOut ()
static SrcFinfo1< double > *	IkOut ()
static const Cinfo *	initCinfo ()
	Specify the Class Info static variable for initialization. More...
static SrcFinfo1< double > *	permeability ()

Detailed Description

The ChanBase is the base class for all ion channel classes in MOOSE. It knows how to communicate with the parent compartment, not much else.

Definition at line 19 of file ChanBase.h.

Constructor & Destructor Documentation

ChanBase::ChanBase

(

)

Definition at line 175 of file ChanBase.cpp.

{ ; }

ChanBase::~ChanBase

(

)

Definition at line 178 of file ChanBase.cpp.

{;}

Member Function Documentation

SrcFinfo2< double, double > * ChanBase::channelOut ( )

static

Definition at line 21 of file ChanBase.cpp.

Referenced by initCinfo(), ChanCommon::sendProcessMsgs(), and ChanCommon::sendReinitMsgs().

{
    static SrcFinfo2< double, double > channelOut( "channelOut",
        "Sends channel variables Gk and Ek to compartment" );
    return &channelOut;
}

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double ChanBase::getEk

(

const Eref &

e

)

const

Definition at line 211 of file ChanBase.cpp.

References vGetEk().

Referenced by initCinfo().

{
    return vGetEk( e );
}

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double ChanBase::getGbar

(

const Eref &

e

)

const

Definition at line 191 of file ChanBase.cpp.

References vGetGbar().

Referenced by NMDAChan::initCinfo(), initCinfo(), HHChannel2D::vProcess(), and HHChannel2D::vReinit().

{
    return vGetGbar( e );
}

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double ChanBase::getGk

(

const Eref &

e

)

const

Definition at line 220 of file ChanBase.cpp.

References vGetGk().

Referenced by initCinfo().

{
    return vGetGk( e );
}

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double ChanBase::getIk

(

const Eref &

e

)

const

Definition at line 229 of file ChanBase.cpp.

References vGetIk().

Referenced by initCinfo().

{
    return vGetIk( e );
}

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double ChanBase::getModulation

(

const Eref &

e

)

const

Definition at line 202 of file ChanBase.cpp.

References vGetModulation().

Referenced by initCinfo().

{
    return vGetModulation( e );
}

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void ChanBase::handleVm

(

double

Vm

)

Assign the local Vm_ to the incoming Vm from the compartment

Definition at line 238 of file ChanBase.cpp.

References vHandleVm().

Referenced by initCinfo().

{
    vHandleVm( Vm );
}

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SrcFinfo1< double > * ChanBase::IkOut ( )

static

Definition at line 28 of file ChanBase.cpp.

Referenced by initCinfo(), ChanCommon::sendProcessMsgs(), ChanCommon::sendReinitMsgs(), and HSolveActive::sendValues().

{
    static SrcFinfo1< double > IkOut( "IkOut",
        "Channel current. This message typically goes to concen"
        "objects that keep track of ion concentration." );
    return &IkOut;
}

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const Cinfo * ChanBase::initCinfo ( )

static

Specify the Class Info static variable for initialization.

ChannelOut SrcFinfo defined above.

Permability SrcFinfo defined above.

Definition at line 36 of file ChanBase.cpp.

References channelOut(), getEk(), getGbar(), getGk(), getIk(), getModulation(), handleVm(), IkOut(), Neutral::initCinfo(), permeability(), process(), reinit(), setEk(), setGbar(), setGk(), and setModulation().

Referenced by MarkovChannel::initCinfo(), Leakage::initCinfo(), MgBlock::initCinfo(), SynChan::initCinfo(), HHChannel2D::initCinfo(), and HHChannelBase::initCinfo().

{
    // Shared messages
    static DestFinfo process( "process",
        "Handles process call",
        new ProcOpFunc< ChanBase >( &ChanBase::process ) );
    static DestFinfo reinit( "reinit",
        "Handles reinit call",
        new ProcOpFunc< ChanBase >( &ChanBase::reinit ) );

    static Finfo* processShared[] =
    {
        &process, &reinit
    };

    static SharedFinfo proc( "proc",
        "Shared message to receive Process message from scheduler",
        processShared, sizeof( processShared ) / sizeof( Finfo* ) );

    static DestFinfo Vm( "Vm",
        "Handles Vm message coming in from compartment",
        new OpFunc1< ChanBase, double >( &ChanBase::handleVm ) );

    static Finfo* channelShared[] =
    {
        channelOut(), &Vm
    };
    static SharedFinfo channel( "channel",
        "This is a shared message to couple channel to compartment. "
        "The first entry is a MsgSrc to send Gk and Ek to the compartment "
        "The second entry is a MsgDest for Vm from the compartment.",
        channelShared, sizeof( channelShared ) / sizeof( Finfo* )
    );

    // Here we reuse the Vm DestFinfo declared above.

    static Finfo* ghkShared[] =
    {
        &Vm, permeability()
    };
    static SharedFinfo ghk( "ghk",
        "Message to Goldman-Hodgkin-Katz object",
        ghkShared, sizeof( ghkShared ) / sizeof( Finfo* ) );

// Field definitions

        static ElementValueFinfo< ChanBase, double > Gbar( "Gbar",
            "Maximal channel conductance",
            &ChanBase::setGbar,
            &ChanBase::getGbar
        );
        static ElementValueFinfo< ChanBase, double > modulation( "modulation",
            "Modulation, i.e, scale factor for channel conductance."
            "Note that this is a regular parameter, it is not "
            "recomputed each timestep. Thus one can use a slow update, "
            "say, from a molecule pool, to send a message to set "
            "the modulation, and it will stay at the set value even if "
            "the channel runs many timesteps before the next assignment. "
            "This differs from the GENESIS semantics of a similar message,"
            "which required update each timestep. ",
            &ChanBase::setModulation,
            &ChanBase::getModulation
        );
        static ElementValueFinfo< ChanBase, double > Ek( "Ek",
            "Reversal potential of channel",
            &ChanBase::setEk,
            &ChanBase::getEk
        );
        static ElementValueFinfo< ChanBase, double > Gk( "Gk",
            "Channel conductance variable",
            &ChanBase::setGk,
            &ChanBase::getGk
        );
        static ReadOnlyElementValueFinfo< ChanBase, double > Ik( "Ik",
            "Channel current variable",
            &ChanBase::getIk
        );

// MsgSrc definitions
    // IkOut SrcFinfo defined above.

// MsgDest definitions

    static Finfo* ChanBaseFinfos[] =
    {
        &channel,           // Shared
        &ghk,               // Shared
        &Gbar,              // Value
        &modulation,        // Value
        &Ek,                // Value
        &Gk,                // Value
        &Ik,                // ReadOnlyValue
        IkOut(),            // Src
        &proc,              // Shared
    };

    static string doc[] =
    {
        "Name", "ChanBase",
        "Author", "Upinder S. Bhalla, 2007-2014, NCBS",
        "Description", "ChanBase: Base class for assorted ion channels."
        "Presents a common interface for all of them. ",
    };

        static  ZeroSizeDinfo< int > dinfo;

    static Cinfo ChanBaseCinfo(
        "ChanBase",
        Neutral::initCinfo(),
        ChanBaseFinfos,
        sizeof( ChanBaseFinfos )/sizeof(Finfo *),
                &dinfo,
                doc,
                sizeof(doc)/sizeof(string)
    );

    return &ChanBaseCinfo;
}

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SrcFinfo1< double > * ChanBase::permeability ( )

static

Definition at line 14 of file ChanBase.cpp.

Referenced by NMDAChan::initCinfo(), initCinfo(), ChanCommon::sendProcessMsgs(), and ChanCommon::sendReinitMsgs().

{
    static SrcFinfo1< double > permeability( "permeabilityOut",
        "Conductance term going out to GHK object" );
    return &permeability;
}

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

Takes over the Process and reinit functions of all derived classes.

Definition at line 248 of file ChanBase.cpp.

References vProcess().

Referenced by initCinfo().

{
    vProcess( e, info );
}

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

Definition at line 254 of file ChanBase.cpp.

References vReinit().

Referenced by initCinfo().

{
    vReinit( e, info );
}

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void ChanBase::setEk	(	const Eref &	e,
		double	Ek
	)

Definition at line 207 of file ChanBase.cpp.

References vSetEk().

Referenced by initCinfo(), and MgBlock::origChannel().

{
    vSetEk( e, Ek );
}

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void ChanBase::setGbar	(	const Eref &	e,
		double	Gbar
	)

Definition at line 185 of file ChanBase.cpp.

References vSetGbar().

Referenced by NMDAChan::initCinfo(), and initCinfo().

{
    // Call virtual functions of derived classes for this operation.
    vSetGbar( e, Gbar );
}

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void ChanBase::setGk	(	const Eref &	e,
		double	Gk
	)

Definition at line 216 of file ChanBase.cpp.

References vSetGk().

Referenced by initCinfo(), MgBlock::vProcess(), SynChan::vProcess(), NMDAChan::vProcess(), MarkovChannel::vProcess(), HHChannel2D::vProcess(), SynChan::vReinit(), and HHChannel2D::vReinit().

{
    vSetGk( e, Gk );
}

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void ChanBase::setIk	(	const Eref &	e,
		double	Ic
	)

Definition at line 225 of file ChanBase.cpp.

References vSetIk().

Referenced by SynChan::vReinit().

{
    vSetIk( e, Ik );
}

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void ChanBase::setModulation	(	const Eref &	e,
		double	modulation
	)

Definition at line 196 of file ChanBase.cpp.

References vSetModulation().

Referenced by initCinfo().

{
    // Call virtual functions of derived classes for this operation.
    vSetModulation( e, modulation );
}

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virtual double ChanBase::vGetEk ( const Eref &  e ) const

pure virtual

Implemented in ZombieHHChannel, and ChanCommon.

Referenced by getEk(), and HHChannelBase::zombify().

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virtual double ChanBase::vGetGbar ( const Eref &  e ) const

pure virtual

Implemented in ZombieHHChannel, and ChanCommon.

Referenced by getGbar(), and HHChannelBase::zombify().

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virtual double ChanBase::vGetGk ( const Eref &  e ) const

pure virtual

Implemented in ZombieHHChannel, and ChanCommon.

Referenced by getGk().

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virtual double ChanBase::vGetIk ( const Eref &  e ) const

pure virtual

Implemented in ZombieHHChannel, and ChanCommon.

Referenced by getIk().

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virtual double ChanBase::vGetModulation ( const Eref &  e ) const

pure virtual

Implemented in HHChannel, HHChannelBase, and ChanCommon.

Referenced by getModulation().

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virtual void ChanBase::vHandleVm ( double  Vm )

pure virtual

Implemented in ZombieHHChannel, and ChanCommon.

Referenced by handleVm().

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virtual void ChanBase::vProcess ( const Eref &  e, const ProcPtr  info  )

pure virtual

Implemented in HHChannel, HHChannel2D, ZombieHHChannel, MarkovChannel, NMDAChan, Leakage, SynChan, and MgBlock.

Referenced by process().

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virtual void ChanBase::vReinit ( const Eref &  e, const ProcPtr  info  )

pure virtual

Implemented in HHChannel, HHChannel2D, ZombieHHChannel, MarkovChannel, NMDAChan, Leakage, MgBlock, and SynChan.

Referenced by reinit().

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virtual void ChanBase::vSetEk ( const Eref &  e, double  Ek  )

pure virtual

Implemented in ZombieHHChannel, and ChanCommon.

Referenced by setEk(), and HHChannelBase::zombify().

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virtual void ChanBase::vSetGbar ( const Eref &  e, double  Gbar  )

pure virtual

Implemented in Leakage, ZombieHHChannel, SynChan, and ChanCommon.

Referenced by setGbar(), and HHChannelBase::zombify().

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virtual void ChanBase::vSetGk ( const Eref &  e, double  Gk  )

pure virtual

Implemented in ZombieHHChannel, and ChanCommon.

Referenced by setGk().

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virtual void ChanBase::vSetIk ( const Eref &  e, double  Ik  )

pure virtual

Implemented in ZombieHHChannel, and ChanCommon.

Referenced by setIk().

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virtual void ChanBase::vSetModulation ( const Eref &  e, double  modulation  )

pure virtual

Implemented in ZombieHHChannel, HHChannel, and ChanCommon.

Referenced by setModulation().

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

• moose-core/biophysics/ChanBase.h
• moose-core/biophysics/ChanBase.cpp