Ion channel. More...

#include <IonChannel.h>

Inheritance diagram for IntegrateFireSim::IonChannel:

Collaboration diagram for IntegrateFireSim::IonChannel:

Public Member Functions
	IonChannel ()
	Default constructor. More...

virtual	~IonChannel ()
	Destructor. More...

virtual float	CalculateCurrent (float fltStep, float fltVm)
	Calculates the current. More...

virtual void	Enabled (bool bVal)
	Enables the ion channel. More...

virtual bool	Enabled ()
	Gets whether this channel is enabled. More...

void	EquilibriumPotential (float fltVal)
	Sets the equilibrium potential. More...

float	EquilibriumPotential ()
	Gets the equilibrium potential. More...

virtual float *	GetDataPointer (const std::string &strDataType)
	Returns a float pointer to a data item of interest in this object. More...

void	Ginit (float fltVal)
	Sets initial conductance. More...

float	Ginit ()
	Sets initial conductance. More...

void	Gmax (float fltVal)
	Sets maximum conductance. More...

float	Gmax ()
	Gets maximum conductance. More...

AnimatSim::Gains::Gain *	Hinf ()
	Gets the Hinf. More...

void	Hinf (AnimatSim::Gains::Gain *lpGain)
	Sets the Hinf equation. More...

void	Hinf (std::string strXml)
	Sets the Hinf gain using an xml packet. More...

void	Hinit (float fltVal)
	Sets Hinit. More...

float	Hinit ()
	Gets Hinit. More...

void	HPower (float fltVal)
	Sets HPower. More...

float	HPower ()
	Gets HPower. More...

virtual void	Load (CStdXml &oXml)

AnimatSim::Gains::Gain *	Minf ()
	Gets the minf. More...

void	Minf (AnimatSim::Gains::Gain *lpGain)
	Sets the Minf equation. More...

void	Minf (std::string strXml)
	Sets the Minf gain using an xml packet. More...

void	Minit (float fltVal)
	Sets Minit. More...

float	Minit ()
	Gets Minit. More...

void	MPower (float fltVal)
	Sets MPower. More...

float	MPower ()
	Gets MPower. More...

void	Nh (float fltVal)
	Sets Nh. More...

float	Nh ()
	Gets Nh. More...

void	Nm (float fltVal)
	Sets Nm. More...

float	Nm ()
	Gets Nm. More...

virtual void	QueryProperties (CStdPtrArray< TypeProperty > &aryProperties)

virtual void	ResetSimulation ()
	Resets the simulation back to time 0. More...

virtual bool	SetData (const std::string &strDataType, const std::string &strValue, bool bThrowError=true)
	Set a variable based on a string data type name. More...

AnimatSim::Gains::Gain *	Th ()
	Gets the Th. More...

void	Th (AnimatSim::Gains::Gain *lpGain)
	Sets the Hinf equation. More...

void	Th (std::string strXml)
	Sets the Th gain using an xml packet. More...

AnimatSim::Gains::Gain *	Tm ()
	Gets the Tm. More...

void	Tm (AnimatSim::Gains::Gain *lpGain)
	Sets the Tm equation. More...

void	Tm (std::string strXml)
	Sets the Tm gain using an xml packet. More...

Public Member Functions inherited from AnimatSim::AnimatBase
	AnimatBase ()
	Constructs an AnimatBase object. More...

virtual	~AnimatBase ()
	Destroys the AnimatBase object.. More...

virtual bool	AddItem (const std::string &strItemType, const std::string &strXml, bool bThrowError=true, bool bDoNotInit=false)
	Adds a new object to this parent. More...

virtual void	AfterResetSimulation ()
	Called after a simulation reset for some objects. More...

virtual long	CalculateSnapshotByteSize ()
	Calculates the snapshot byte size. More...

virtual void	Copy (CStdSerialize *lpSource)

virtual NeuralModule *	GetNeuralModule ()
	Gets the neural module. More...

virtual Node *	GetNode ()
	Gets the node. More...

virtual Simulator *	GetSimulator ()
	Gets the simulator pointer. More...

virtual Structure *	GetStructure ()
	Gets the structure for this node. More...

virtual bool	HasProperty (const std::string &strName)
	Queries this object if it has a property with the given name. More...

virtual std::string	ID ()
	Gets the unique GUID ID of this object. More...

virtual void	ID (std::string strValue)
	Sets the unique GUID ID of the object. More...

virtual void	Initialize ()
	Initializes this object. More...

virtual void	Kill (bool bState=true)
	Kills. More...

virtual void	Load (StdUtils::CStdXml &oXml)
	Loads the item using an XML data packet. More...

virtual void	LoadKeyFrameSnapshot (byte *aryBytes, long &lIndex)
	Loads a key frame snapshot. More...

virtual std::string	Name ()
	Gets the name of this object. More...

virtual void	Name (std::string strValue)
	Sets the name of the object. Blank is acceptable. More...

virtual AnimatPropertyType	PropertyType (const std::string &strName)

virtual void	QueryProperties (CStdPtrArray< TypeProperty > &aryProperties)
	Queries this object for a list of properties that can be changed using SetData. More...

virtual void	ReInitialize ()
	Re-initialize this object. More...

virtual bool	RemoveItem (const std::string &strItemType, const std::string &strID, bool bThrowError=true)
	Removes a child item from this parent. More...

virtual void	Reset ()
	Resets this object. More...

virtual void	RigidBodyAdded (std::string strID)

virtual void	RigidBodyRemoved (std::string strID)

virtual void	SaveKeyFrameSnapshot (byte *aryBytes, long &lIndex)
	Saves a key frame snapshot. More...

virtual bool	Selected ()
	Tells if this items is selected or not. More...

virtual void	Selected (bool bValue, bool bSelectMultiple)
	Selects this object. More...

virtual bool	SetData (const std::string &strDataType, const float fltValue, bool bThrowError=true)
	Set a variable based on a string data type name. More...

virtual bool	SetData (const std::string &strDataType, const long lValue, bool bThrowError=true)
	Set a variable based on a string data type name. More...

virtual void	SetSystemPointers (Simulator lpSim, Structure lpStructure, NeuralModule lpModule, Node lpNode, bool bVerify)
	Sets the system pointers. More...

virtual void	SimPausing ()
	Called just before the simulation pauses. More...

virtual void	SimStarting ()
	Called just before the simulation starts. More...

virtual void	SimStopping ()
	Called just before the simulation stops. More...

virtual void	StepSimulation ()
	Step the simulation for this object. More...

virtual void	TimeStepModified ()
	Notification method that the time step modified has been modified. Objects should recalculate any slice times as needed. More...

virtual std::string	Type ()
	returns the string type name of this object. More...

virtual void	Type (std::string strValue)
	Sets the class type for this object. More...

virtual void	VerifySystemPointers ()
	Verify that system pointers have been set correctly. More...

virtual void	VisualSelectionModeChanged (int iNewMode)
	Visual selection mode changed. More...

Protected Attributes
float	m_fltEquilibriumPotential
	The equilibrium potential.

float	m_fltG
	The active conductance.

float	m_fltGInit
	The initial conductance.

float	m_fltGmax
	The maximum conductance.

float	m_fltH
	The current inactivation level.

float	m_fltHinf
	The Hinf value.

float	m_fltHInit
	The initial inactivation.

float	m_fltHPower
	The inactivation exponent in the equation.

float	m_fltI
	The current.

float	m_fltM
	The current activation level.

float	m_fltMinf
	The Minf value.

float	m_fltMInit
	The initial activation.

float	m_fltMPower
	The activation exponent in the equation.

float	m_fltNh
	The Nh.

float	m_fltNm
	The Nm.

float	m_fltTh
	The Th value.

float	m_fltTm
	The Tm value.

float	m_fltTotalAct
	The total activation level.

AnimatSim::Gains::Gain *	m_lpHinf
	The Hinf gain function.

AnimatSim::Gains::Gain *	m_lpMinf
	The Minf gain function.

AnimatSim::Gains::Gain *	m_lpTh
	The Th gain function.

AnimatSim::Gains::Gain *	m_lpTm
	The Tm gain function.

Protected Attributes inherited from AnimatSim::AnimatBase
bool	m_bEnabled
	Tells if this item is enabled or not. If it is not enabled then it is not run.

bool	m_bSelected
	Tells whether the object is selected or not.

AnimatSim::Behavior::NeuralModule *	m_lpModule
	The pointer to this items parentNeuralModule. If this is not relevant for this object then this is NULL.

Node *	m_lpNode
	The pointer to this items parent Node. If this is not relevant for this object then this is NULL.

Simulator *	m_lpSim
	The pointer to a Simulation.

AnimatSim::Environment::Structure *	m_lpStructure
	The pointer to this items parent Structure. If this is not relevant for this object then this is NULL.

std::string	m_strID
	The unique Id for this object.

std::string	m_strName
	The name for this object.

std::string	m_strType
	The type for this object. Examples are Box, Plane, Neuron, etc..

Detailed Description

Ion channel.

This implemements a basic Hodgkin-Huxely ion channel that can be added to the Neuron.

Author: dcofer

Date: 3/31/2011

Definition at line 14 of file IonChannel.h.

Constructor & Destructor Documentation

IntegrateFireSim::IonChannel::IonChannel ( )

Default constructor.

Author: dcofer

Date: 3/31/2011

Definition at line 29 of file IonChannel.cpp.

References AnimatSim::AnimatBase::m_bEnabled, m_fltEquilibriumPotential, m_fltG, m_fltGInit, m_fltGmax, m_fltH, m_fltHinf, m_fltHInit, m_fltHPower, m_fltI, m_fltM, m_fltMinf, m_fltMInit, m_fltMPower, m_fltNh, m_fltNm, m_fltTh, m_fltTm, m_fltTotalAct, m_lpHinf, m_lpMinf, m_lpTh, and m_lpTm.

IntegrateFireSim::IonChannel::~IonChannel ( )

virtual

Destructor.

Author: dcofer

Date: 3/31/2011

Definition at line 66 of file IonChannel.cpp.

References m_lpHinf, m_lpMinf, m_lpTh, m_lpTm, and StdUtils::Std_TraceMsg().

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Member Function Documentation

float IntegrateFireSim::IonChannel::CalculateCurrent	(	float	fltStep,
		float	fltVm
	)

virtual

Calculates the current.

Author: dcofer

Date: 3/31/2011

Parameters

fltStep	The time step.
fltVm	The membrane votlage.

Returns: The calculated current.

Definition at line 500 of file IonChannel.cpp.

References AnimatSim::Gains::Gain::CalculateGain(), AnimatSim::AnimatBase::m_bEnabled, m_fltEquilibriumPotential, m_fltG, m_fltGmax, m_fltH, m_fltHinf, m_fltHPower, m_fltI, m_fltM, m_fltMinf, m_fltMPower, m_fltNh, m_fltNm, m_fltTh, m_fltTm, m_fltTotalAct, m_lpHinf, m_lpMinf, m_lpTh, and m_lpTm.

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void IntegrateFireSim::IonChannel::Enabled ( bool bVal )

virtual

Enables the ion channel.

Author: dcofer

Date: 3/31/2011

Parameters

bVal	true to enable.

Reimplemented from AnimatSim::AnimatBase.

Definition at line 91 of file IonChannel.cpp.

References AnimatSim::AnimatBase::m_bEnabled.

bool IntegrateFireSim::IonChannel::Enabled ( )

virtual

Gets whether this channel is enabled.

Author: dcofer

Date: 3/31/2011

Returns: true if enabled, false else.

Reimplemented from AnimatSim::AnimatBase.

Definition at line 101 of file IonChannel.cpp.

References AnimatSim::AnimatBase::m_bEnabled.

Referenced by SetData().

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void IntegrateFireSim::IonChannel::EquilibriumPotential ( float fltVal )

Sets the equilibrium potential.

Author: dcofer

Date: 3/31/2011

Parameters

fltVal The new value.

Definition at line 252 of file IonChannel.cpp.

References m_fltEquilibriumPotential.

float IntegrateFireSim::IonChannel::EquilibriumPotential ( )

Gets the equilibrium potential.

Author: dcofer

Date: 3/31/2011

Returns: equilibrium potential.

Definition at line 262 of file IonChannel.cpp.

References m_fltEquilibriumPotential.

Referenced by SetData().

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float * IntegrateFireSim::IonChannel::GetDataPointer ( const std::string & strDataType )

virtual

Returns a float pointer to a data item of interest in this object.

This is a generic method used to get a pointer to data variable of interest. It is used by a variety of systems in the simulation. The most prominent are the data charting and stimulus classes. Within this method we associate a variable with a string name. By passing in the name of the data type we are interested in we can recieve back a float pointer to that data type. We can use that to read or set the data item in other classes. For example, the data charting system gets the pointer and then each time it needs to log a data point it reads the value into an array.

Author: dcofer

Date: 2/22/2011

Parameters

strDataType name of the data item for which we are looking.

Returns: float pointer of the data item. If not found then it throws an exception.

Exceptions

If	DataType is not found.

Reimplemented from AnimatSim::AnimatBase.

Definition at line 544 of file IonChannel.cpp.

References m_fltG, m_fltH, m_fltHinf, m_fltI, m_fltM, m_fltMinf, m_fltTh, m_fltTm, m_fltTotalAct, and StdUtils::Std_CheckString().

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void IntegrateFireSim::IonChannel::Ginit ( float fltVal )

Sets initial conductance.

Author: dcofer

Date: 3/31/2011

Parameters

fltVal The new value.

Definition at line 131 of file IonChannel.cpp.

References m_fltG, and m_fltGInit.

float IntegrateFireSim::IonChannel::Ginit ( )

Sets initial conductance.

Author: dcofer

Date: 3/31/2011

Returns: conductance.

Definition at line 148 of file IonChannel.cpp.

References m_fltGInit.

Referenced by SetData().

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void IntegrateFireSim::IonChannel::Gmax ( float fltVal )

Sets maximum conductance.

Author: dcofer

Date: 3/31/2011

Parameters

fltVal The new value.

Definition at line 111 of file IonChannel.cpp.

References m_fltGmax.

float IntegrateFireSim::IonChannel::Gmax ( )

Gets maximum conductance.

Author: dcofer

Date: 3/31/2011

Returns: maximum conductance.

Definition at line 121 of file IonChannel.cpp.

References m_fltGmax.

Referenced by SetData().

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AnimatSim::Gains::Gain * IntegrateFireSim::IonChannel::Hinf ( )

Gets the Hinf.

Author: dcofer

Date: 9/28/2011

Returns: null if it fails, else.

Definition at line 404 of file IonChannel.cpp.

References m_lpHinf.

Referenced by Hinf(), and SetData().

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void IntegrateFireSim::IonChannel::Hinf ( AnimatSim::Gains::Gain * lpGain )

Sets the Hinf equation.

Author: dcofer

Date: 3/29/2011

Parameters

[in,out] lpGain Pointer to a gain.

Definition at line 414 of file IonChannel.cpp.

References m_lpHinf.

void IntegrateFireSim::IonChannel::Hinf ( std::string strXml )

Sets the Hinf gain using an xml packet.

Author: dcofer

Date: 3/29/2011

Parameters

strXml The xml packet defining the gain.

Definition at line 432 of file IonChannel.cpp.

References Hinf(), AnimatSim::Gains::LoadGain(), and AnimatSim::AnimatBase::m_lpSim.

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void IntegrateFireSim::IonChannel::Hinit ( float fltVal )

Sets Hinit.

Author: dcofer

Date: 3/31/2011

Parameters

fltVal The new value.

Definition at line 158 of file IonChannel.cpp.

References m_fltH, and m_fltHInit.

float IntegrateFireSim::IonChannel::Hinit ( )

Gets Hinit.

Author: dcofer

Date: 3/31/2011

Returns: Hinit.

Definition at line 175 of file IonChannel.cpp.

References m_fltHInit.

Referenced by SetData().

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void IntegrateFireSim::IonChannel::HPower ( float fltVal )

Sets HPower.

Author: dcofer

Date: 3/31/2011

Parameters

fltVal The new value.

Definition at line 232 of file IonChannel.cpp.

References m_fltHPower.

float IntegrateFireSim::IonChannel::HPower ( )

Gets HPower.

Author: dcofer

Date: 3/31/2011

Returns: HPower.

Definition at line 242 of file IonChannel.cpp.

References m_fltHPower.

Referenced by SetData().

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AnimatSim::Gains::Gain * IntegrateFireSim::IonChannel::Minf ( )

Gets the minf.

Author: dcofer

Date: 9/28/2011

Returns: null if it fails, else.

Definition at line 312 of file IonChannel.cpp.

References m_lpMinf.

Referenced by Minf(), and SetData().

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void IntegrateFireSim::IonChannel::Minf ( AnimatSim::Gains::Gain * lpGain )

Sets the Minf equation.

Author: dcofer

Date: 3/29/2011

Parameters

[in,out] lpGain Pointer to a gain.

Definition at line 322 of file IonChannel.cpp.

References m_lpMinf.

void IntegrateFireSim::IonChannel::Minf ( std::string strXml )

Sets the Minf gain using an xml packet.

Author: dcofer

Date: 3/29/2011

Parameters

strXml The xml packet defining the gain.

Definition at line 340 of file IonChannel.cpp.

References AnimatSim::Gains::LoadGain(), AnimatSim::AnimatBase::m_lpSim, and Minf().

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void IntegrateFireSim::IonChannel::Minit ( float fltVal )

Sets Minit.

Author: dcofer

Date: 3/31/2011

Parameters

fltVal The new value.

Definition at line 185 of file IonChannel.cpp.

References m_fltM, and m_fltMInit.

float IntegrateFireSim::IonChannel::Minit ( )

Gets Minit.

Author: dcofer

Date: 3/31/2011

Returns: Minit.

Definition at line 202 of file IonChannel.cpp.

References m_fltMInit.

Referenced by SetData().

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void IntegrateFireSim::IonChannel::MPower ( float fltVal )

Sets MPower.

Author: dcofer

Date: 3/31/2011

Parameters

fltVal The new value.

Definition at line 212 of file IonChannel.cpp.

References m_fltMPower.

float IntegrateFireSim::IonChannel::MPower ( )

Gets MPower.

Author: dcofer

Date: 3/31/2011

Returns: MPower.

Definition at line 222 of file IonChannel.cpp.

References m_fltMPower.

Referenced by SetData().

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void IntegrateFireSim::IonChannel::Nh ( float fltVal )

Sets Nh.

Author: dcofer

Date: 3/31/2011

Parameters

fltVal The new value.

Definition at line 292 of file IonChannel.cpp.

References m_fltNh.

float IntegrateFireSim::IonChannel::Nh ( )

Gets Nh.

Author: dcofer

Date: 3/31/2011

Returns: Nh.

Definition at line 302 of file IonChannel.cpp.

References m_fltNh.

Referenced by SetData().

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void IntegrateFireSim::IonChannel::Nm ( float fltVal )

Sets Nm.

Author: dcofer

Date: 3/31/2011

Parameters

fltVal The new value.

Definition at line 272 of file IonChannel.cpp.

References m_fltNm.

float IntegrateFireSim::IonChannel::Nm ( )

Gets Nm.

Author: dcofer

Date: 3/31/2011

Returns: Nm.

Definition at line 282 of file IonChannel.cpp.

References m_fltNm.

Referenced by SetData().

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void IntegrateFireSim::IonChannel::ResetSimulation ( )

virtual

Resets the simulation back to time 0.

This method calls the ResetSimulation method on all subitems in order to reset the simulation back to the beginning.

Author: dcofer

Date: 3/1/2011

Reimplemented from AnimatSim::AnimatBase.

Definition at line 529 of file IonChannel.cpp.

References m_fltG, m_fltH, m_fltHinf, m_fltHInit, m_fltI, m_fltM, m_fltMinf, m_fltMInit, m_fltTh, m_fltTm, and m_fltTotalAct.

bool IntegrateFireSim::IonChannel::SetData	(	const std::string &	strDataType,
		const std::string &	strValue,
		bool	bThrowError = `true`
	)

virtual

Set a variable based on a string data type name.

This is a generic method that can be used to set any variable in an AnimatBase object by specifying the name of the variable and a string representation of that data. The GUI uses this method to set data into variables in the simulation when the user changes them in the UI. The value string can be as simple as a float or int, or as complex as an xml packet. It is the developers responsibilty to know what type of data is needed and to process it accordingly.

Author: dcofer

Date: 2/22/2011

Parameters

strDataType	string name of the data type to set.
strValue	The string value of the data. It is up to the developer to determine what this should be. For example, in most cases it is simply a float and you just have to convert it to a float and make the appropriate mutator method call. However, it can be any type of string, including an entire xml packet. It is the developers responsibility to know how to set and process the data as required.
bThrowError	true to throw error if there is a problem. If false then it will not return an error, just return false.

Returns: true if it succeeds, false if it fails.

Reimplemented from AnimatSim::AnimatBase.

Definition at line 581 of file IonChannel.cpp.

References Enabled(), EquilibriumPotential(), Ginit(), Gmax(), Hinf(), Hinit(), HPower(), Minf(), Minit(), MPower(), Nh(), Nm(), StdUtils::Std_CheckString(), StdUtils::Std_ToBool(), Th(), and Tm().

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AnimatSim::Gains::Gain * IntegrateFireSim::IonChannel::Th ( )

Gets the Th.

Author: dcofer

Date: 9/28/2011

Returns: null if it fails, else.

Definition at line 450 of file IonChannel.cpp.

References m_lpTh.

Referenced by SetData(), and Th().

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void IntegrateFireSim::IonChannel::Th ( AnimatSim::Gains::Gain * lpGain )

Sets the Hinf equation.

Author: dcofer

Date: 3/29/2011

Parameters

[in,out] lpGain Pointer to a gain.

Definition at line 460 of file IonChannel.cpp.

References m_lpTh.

void IntegrateFireSim::IonChannel::Th ( std::string strXml )

Sets the Th gain using an xml packet.

Author: dcofer

Date: 3/29/2011

Parameters

strXml The xml packet defining the gain.

Definition at line 478 of file IonChannel.cpp.

References AnimatSim::Gains::LoadGain(), AnimatSim::AnimatBase::m_lpSim, and Th().

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AnimatSim::Gains::Gain * IntegrateFireSim::IonChannel::Tm ( )

Gets the Tm.

Author: dcofer

Date: 9/28/2011

Returns: null if it fails, else.

Definition at line 358 of file IonChannel.cpp.

References m_lpTm.

Referenced by SetData(), and Tm().

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void IntegrateFireSim::IonChannel::Tm ( AnimatSim::Gains::Gain * lpGain )

Sets the Tm equation.

Author: dcofer

Date: 3/29/2011

Parameters

[in,out] lpGain Pointer to a gain.

Definition at line 368 of file IonChannel.cpp.

References m_lpTm.

void IntegrateFireSim::IonChannel::Tm ( std::string strXml )

Sets the Tm gain using an xml packet.

Author: dcofer

Date: 3/29/2011

Parameters

strXml The xml packet defining the gain.

Definition at line 386 of file IonChannel.cpp.

References AnimatSim::Gains::LoadGain(), AnimatSim::AnimatBase::m_lpSim, and Tm().

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

Public Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation