#include <MarkovChannel.h>

Inheritance diagram for MarkovChannel:

Collaboration diagram for MarkovChannel:

Public Member Functions
vector< double >	getGbars () const

vector< double >	getInitialState () const

double	getLigandConc () const

vector< vector< bool > >	getLigandGated () const

unsigned int	getNumOpenStates () const

unsigned int	getNumStates () const

vector< double >	getState () const

vector< string >	getStateLabels () const

double	getVm () const

void	handleLigandConc (double)

void	handleState (vector< double >)

	MarkovChannel ()

	MarkovChannel (unsigned int, unsigned int)

void	setGbars (vector< double >)

void	setInitialState (vector< double >)

void	setLigandConc (double)

void	setLigandGated (vector< vector< bool > >)

void	setNumOpenStates (unsigned int)

void	setNumStates (unsigned int)

void	setState (vector< double >)

void	setStateLabels (vector< string >)

void	setVm (double)

void	vProcess (const Eref &, const ProcPtr)

void	vReinit (const Eref &, const ProcPtr)

	~MarkovChannel ()

Public Member Functions inherited from ChanCommon
	ChanCommon ()

double	getGbar () const
	Utility function to acces Gbar. More...

double	getModulation () const

double	getVm () const
	Utility function to access Vm. More...

void	sendProcessMsgs (const Eref &e, const ProcPtr info)

void	sendReinitMsgs (const Eref &e, const ProcPtr info)

void	updateIk ()

double	vGetEk (const Eref &e) const

double	vGetGbar (const Eref &e) const

double	vGetGk (const Eref &e) const

double	vGetIk (const Eref &e) const

double	vGetModulation (const Eref &e) const

void	vHandleVm (double Vm)

void	vSetEk (const Eref &e, double Ek)

void	vSetGbar (const Eref &e, double Gbar)

void	vSetGk (const Eref &e, double Gk)

void	vSetIk (const Eref &e, double Ic)

void	vSetModulation (const Eref &e, double modulation)

	~ChanCommon ()

Public Member Functions inherited from ChanBase
	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)

	~ChanBase ()

Static Public Member Functions
static const Cinfo *	initCinfo ()

Static Public Member Functions inherited from ChanCommon
static const Cinfo *	initCinfo ()
	Specify the Class Info static variable for initialization. More...

Static Public Member Functions inherited from ChanBase
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 ()

Private Attributes
double	g_

vector< double >	Gbars_

vector< double >	initialState_

double	ligandConc_

unsigned int	numOpenStates_

unsigned int	numStates_

vector< double >	state_

vector< string >	stateLabels_

Additional Inherited Members
Protected Attributes inherited from ChanCommon
double	Vm_
	Vm_ is input variable from compartment, used for most rates. More...

Detailed Description

Definition at line 15 of file MarkovChannel.h.

Constructor & Destructor Documentation

MarkovChannel::MarkovChannel ( )

Definition at line 130 of file MarkovChannel.cpp.

                              :
     g_(0),
     ligandConc_(0),
     numStates_(0),
     numOpenStates_(0)
 { ; }

MarkovChannel::MarkovChannel	(	unsigned int	numStates,
		unsigned int	numOpenStates
	)

Definition at line 137 of file MarkovChannel.cpp.

References Gbars_, initialState_, state_, and stateLabels_.

                                                                                :
     g_(0), ligandConc_(0), numStates_(numStates), numOpenStates_(numOpenStates)
 {
     stateLabels_.resize( numStates );
     state_.resize( numStates );
     initialState_.resize( numStates );
     Gbars_.resize( numOpenStates ) ;
 }

MarkovChannel::~MarkovChannel ( )

Definition at line 146 of file MarkovChannel.cpp.

 {
     ;
 }

Member Function Documentation

vector< double > MarkovChannel::getGbars ( ) const

Definition at line 217 of file MarkovChannel.cpp.

References Gbars_.

Referenced by initCinfo().

 {
     return Gbars_;
 }

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vector< double > MarkovChannel::getInitialState ( ) const

Definition at line 206 of file MarkovChannel.cpp.

References initialState_.

Referenced by initCinfo().

 {
     return initialState_;
 }

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double MarkovChannel::getLigandConc ( ) const

Definition at line 161 of file MarkovChannel.cpp.

References ligandConc_.

Referenced by initCinfo().

 {
     return ligandConc_;
 }

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vector< vector< bool > > MarkovChannel::getLigandGated ( ) const

unsigned int MarkovChannel::getNumOpenStates ( ) const

Definition at line 181 of file MarkovChannel.cpp.

References numOpenStates_.

Referenced by initCinfo().

 {
     return numOpenStates_;
 }

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unsigned int MarkovChannel::getNumStates ( ) const

Definition at line 171 of file MarkovChannel.cpp.

References numStates_.

Referenced by initCinfo().

 {
     return numStates_;
 }

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vector< double > MarkovChannel::getState ( ) const

Definition at line 201 of file MarkovChannel.cpp.

References state_.

Referenced by initCinfo().

 {
     return state_;
 }

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vector< string > MarkovChannel::getStateLabels ( ) const

Definition at line 191 of file MarkovChannel.cpp.

References stateLabels_.

Referenced by initCinfo().

 {
     return stateLabels_;
 }

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double MarkovChannel::getVm ( ) const

Definition at line 151 of file MarkovChannel.cpp.

References ChanCommon::Vm_.

Referenced by initCinfo().

 {
     return Vm_;
 }

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void MarkovChannel::handleLigandConc ( double ligandConc )

Definition at line 262 of file MarkovChannel.cpp.

References ligandConc_.

Referenced by initCinfo().

 {
     ligandConc_ = ligandConc;
 }

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void MarkovChannel::handleState ( vector< double > state )

Definition at line 267 of file MarkovChannel.cpp.

References state_.

Referenced by initCinfo().

 {
     state_ = state;
 }

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const Cinfo * MarkovChannel::initCinfo ( )

static

Definition at line 22 of file MarkovChannel.cpp.

References getGbars(), getInitialState(), getLigandConc(), getNumOpenStates(), getNumStates(), getState(), getStateLabels(), getVm(), handleLigandConc(), handleState(), ChanBase::initCinfo(), setGbars(), setInitialState(), setLigandConc(), setNumOpenStates(), setNumStates(), setStateLabels(), and setVm().

 {
     //Field information.
     static ValueFinfo< MarkovChannel, double > ligandconc( "ligandConc",
             "Ligand concentration.",
             &MarkovChannel::setLigandConc,
             &MarkovChannel::getLigandConc
             );
 
     static ValueFinfo< MarkovChannel, double > vm( "Vm",
             "Membrane voltage.",
             &MarkovChannel::setVm,
             &MarkovChannel::getVm
             );
 
     static ValueFinfo< MarkovChannel, unsigned int > numstates( "numStates",
             "The number of states that the channel can occupy.",
             &MarkovChannel::setNumStates,
             &MarkovChannel::getNumStates
             );
 
 
     static ValueFinfo< MarkovChannel, unsigned int > numopenstates( "numOpenStates",
             "The number of states which are open/conducting.",
             &MarkovChannel::setNumOpenStates,
             &MarkovChannel::getNumOpenStates
             );
 
     static ValueFinfo< MarkovChannel, vector< string > > labels("labels",
             "Labels for each state.",
             &MarkovChannel::setStateLabels,
             &MarkovChannel::getStateLabels
             );
 
     static ReadOnlyValueFinfo< MarkovChannel, vector< double > > state( "state",
             "This is a row vector that contains the probabilities of finding the channel in each state.",
             &MarkovChannel::getState
             );
 
     static ValueFinfo< MarkovChannel, vector< double > > initialstate( "initialState",
             "This is a row vector that contains the probabilities of finding the channel in each state at t = 0. The state of the channel is reset to this value during a call to reinit()",
             &MarkovChannel::setInitialState,
             &MarkovChannel::getInitialState
             );
 
     static ValueFinfo< MarkovChannel, vector< double > > gbar( "gbar",
             "A row vector containing the conductance associated with each of the open/conducting states.",
             &MarkovChannel::setGbars,
             &MarkovChannel::getGbars
             );
 
     //MsgDest functions
     static DestFinfo handleligandconc( "handleLigandConc",
         "Deals with incoming messages containing information of ligand concentration",
         new OpFunc1< MarkovChannel, double >(&MarkovChannel::handleLigandConc) );
 
     static DestFinfo handlestate("handleState",
         "Deals with incoming message from MarkovSolver object containing state information of the channel.\n",
         new OpFunc1< MarkovChannel, vector< double > >(&MarkovChannel::handleState) );
 
     static Finfo* MarkovChannelFinfos[] =
     {
         &ligandconc,
         &vm,
         &numstates,
         &numopenstates,
         &state,
         &initialstate,
         &labels,
         &gbar,
         &handleligandconc,
         &handlestate,
     };
 
     static string doc[] =
     {
         "Name", "MarkovChannel",
         "Author", "Vishaka Datta S, 2011, NCBS",
         "Description", "MarkovChannel : Multistate ion channel class."
         "It deals with ion channels which can be found in one of multiple states, "
                 "some of which are conducting. This implementation assumes the occurence "
         "of first order kinetics to calculate the probabilities of the channel "
                 "being found in all states. Further, the rates of transition between these "
         "states can be constant, voltage-dependent or ligand dependent (only one "
         "ligand species). The current flow obtained from the channel is calculated "
         "in a deterministic method by solving the system of differential equations "
                 "obtained from the assumptions above."
     };
 
     static Dinfo< MarkovChannel > dinfo;
     static Cinfo MarkovChannelCinfo(
         "MarkovChannel",
         ChanBase::initCinfo(),
         MarkovChannelFinfos,
         sizeof( MarkovChannelFinfos )/ sizeof( Finfo* ),
         &dinfo,
         doc,
         sizeof(doc) / sizeof(string)
     );
 
     return &MarkovChannelCinfo;
 }

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void MarkovChannel::setGbars ( vector< double > Gbars )

Definition at line 222 of file MarkovChannel.cpp.

References Gbars_.

Referenced by initCinfo().

 {
     Gbars_ = Gbars;
 }

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void MarkovChannel::setInitialState ( vector< double > initialState )

Definition at line 211 of file MarkovChannel.cpp.

References initialState_, and state_.

Referenced by initCinfo().

 {
     initialState_ = initialState;
     state_ = initialState;
 }

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void MarkovChannel::setLigandConc ( double ligandConc )

Definition at line 166 of file MarkovChannel.cpp.

References ligandConc_.

Referenced by initCinfo().

 {
     ligandConc_ = ligandConc;
 }

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void MarkovChannel::setLigandGated ( vector< vector< bool > > )

void MarkovChannel::setNumOpenStates ( unsigned int numOpenStates )

Definition at line 186 of file MarkovChannel.cpp.

References numOpenStates_.

Referenced by initCinfo().

 {
     numOpenStates_ = numOpenStates;
 }

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void MarkovChannel::setNumStates ( unsigned int numStates )

Definition at line 176 of file MarkovChannel.cpp.

References numStates_.

Referenced by initCinfo().

 {
     numStates_ = numStates;
 }

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void MarkovChannel::setState ( vector< double > )

void MarkovChannel::setStateLabels ( vector< string > )

Definition at line 196 of file MarkovChannel.cpp.

References stateLabels_.

Referenced by initCinfo().

 {
     stateLabels_ = stateLabels;
 }

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void MarkovChannel::setVm ( double Vm )

Definition at line 156 of file MarkovChannel.cpp.

References ChanCommon::Vm_.

Referenced by initCinfo().

 {
     Vm_ = Vm;
 }

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void MarkovChannel::vProcess	(	const Eref &	e,
		const ProcPtr	p
	)

virtual

Implements ChanBase.

Definition at line 231 of file MarkovChannel.cpp.

References g_, Gbars_, numOpenStates_, ChanCommon::sendProcessMsgs(), ChanBase::setGk(), state_, and ChanCommon::updateIk().

 {
     g_ = 0.0;
 
     //Cannot use the Gbar_ variable of the ChanBase class. The conductance
     //Gk_ calculated here is the "expected conductance" of the channel due to its
     //stochastic nature.
 
     for( unsigned int i = 0; i < numOpenStates_; ++i )
         g_ += Gbars_[i] * state_[i];
 
     setGk( e, g_ );
     updateIk();
 
     sendProcessMsgs( e, p );
 }

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void MarkovChannel::vReinit	(	const Eref &	e,
		const ProcPtr	p
	)

virtual

Implements ChanBase.

Definition at line 248 of file MarkovChannel.cpp.

References g_, initialState_, ChanCommon::sendReinitMsgs(), and state_.

 {
     g_ = 0.0;
 
     if ( initialState_.empty() )
     {
         cerr << "MarkovChannel::reinit : Initial state has not been set.!\n";
         return;
     }
     state_ = initialState_;
 
     sendReinitMsgs( e, p );
 }