#include <AbstractOdeSrnModel.hpp>

Inheritance diagram for AbstractOdeSrnModel:

Collaboration diagram for AbstractOdeSrnModel:

Public Member Functions
	AbstractOdeSrnModel (unsigned stateSize, boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver=boost::shared_ptr< AbstractCellCycleModelOdeSolver >())

virtual	~AbstractOdeSrnModel ()

virtual void	SimulateToCurrentTime ()

virtual void	ResetForDivision ()

void	SetFinishedRunningOdes (bool finishedRunningOdes)

void	SetInitialConditions (std::vector< double > initialConditions)

const std::vector< double > &	GetStateVariables ()

virtual void	OutputSrnModelParameters (out_stream &rParamsFile)

Public Member Functions inherited from AbstractSrnModel
	AbstractSrnModel ()

virtual	~AbstractSrnModel ()

void	SetCell (CellPtr pCell)

virtual void	Initialise ()

virtual void	InitialiseDaughterCell ()

CellPtr	GetCell ()

void	SetSimulatedToTime (double simulatedToTime)

double	GetSimulatedToTime ()

virtual AbstractSrnModel *	CreateSrnModel ()=0

void	OutputSrnModelInfo (out_stream &rParamsFile)

Public Member Functions inherited from Identifiable
virtual	~Identifiable ()

std::string	GetIdentifier () const

Public Member Functions inherited from CellCycleModelOdeHandler
	CellCycleModelOdeHandler (double lastTime=SimulationTime::Instance() ->GetTime(), boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver=boost::shared_ptr< AbstractCellCycleModelOdeSolver >())

virtual	~CellCycleModelOdeHandler ()

AbstractOdeSystem *	GetOdeSystem () const

void	SetOdeSystem (AbstractOdeSystem *pOdeSystem)

const boost::shared_ptr < AbstractCellCycleModelOdeSolver >	GetOdeSolver () const

void	SetLastTime (double lastTime)

double	GetDt ()

void	SetDt (double timeStep)

void	SetStateVariables (const std::vector< double > &rStateVariables)

Protected Member Functions
void	Initialise (AbstractOdeSystem *pOdeSystem)

AbstractSrnModel *	CreateSrnModel (AbstractOdeSrnModel *pModel)

Protected Member Functions inherited from CellCycleModelOdeHandler
bool	SolveOdeToTime (double currentTime)

virtual void	AdjustOdeParameters (double currentTime)

Protected Attributes
bool	mFinishedRunningOdes

std::vector< double >	mInitialConditions

unsigned	mStateSize

Protected Attributes inherited from AbstractSrnModel
CellPtr	mpCell

double	mSimulatedToTime

Protected Attributes inherited from CellCycleModelOdeHandler
double	mDt

AbstractOdeSystem *	mpOdeSystem

boost::shared_ptr < AbstractCellCycleModelOdeSolver >	mpOdeSolver

double	mLastTime

Private Member Functions
template<class Archive >
void	serialize (Archive &archive, const unsigned int version)

Friends
class	boost::serialization::access

Detailed Description

This class contains the abstract code for an ODE sub-cellular reaction network (SRN) model

based on AbstractOdeBasedCellCycleModel

Todo:: #2752 Thoroughly document this class

Definition at line 55 of file AbstractOdeSrnModel.hpp.

Constructor & Destructor Documentation

AbstractOdeSrnModel::AbstractOdeSrnModel	(	unsigned	stateSize,
		boost::shared_ptr< AbstractCellCycleModelOdeSolver >	pOdeSolver = `boost::shared_ptr<AbstractCellCycleModelOdeSolver>()`
	)

Create an AbstractOdeSrnModel.

Parameters

stateSize	The number of state variables in the ODE system.
pOdeSolver	An optional pointer to a cell-cycle model ODE solver object (allows the use of different ODE solvers).

Definition at line 41 of file AbstractOdeSrnModel.cpp.

AbstractOdeSrnModel::~AbstractOdeSrnModel ( )

virtual

Destructor.

Definition at line 49 of file AbstractOdeSrnModel.cpp.

Member Function Documentation

AbstractSrnModel * AbstractOdeSrnModel::CreateSrnModel ( AbstractOdeSrnModel * pModel )

protected

Overridden CreateSrnModel() method.

Builder method to create new instances of the SRN model. Each concrete subclass must implement this method to create an instance of that subclass.

This method is called by Cell::Divide() to create a SRN model for the daughter cell. Note that the parent SRN model will have had ResetForDivision() called just before CreateSrnModel() is called, so performing an exact copy of the parent is suitable behaviour. Any daughter-cell-specific initialisation can be done in InitialiseDaughterCell().

Note bring virtual functions from AbstractSrnModel into derived namespace so overloading virtual works.

Parameters

pModel pointer to an ODE SRN model

Returns: new SRN model

Definition at line 103 of file AbstractOdeSrnModel.cpp.

References mFinishedRunningOdes, mInitialConditions, CellCycleModelOdeHandler::mpOdeSystem, AbstractSrnModel::mSimulatedToTime, mStateSize, AbstractParameterisedSystem< VECTOR >::rGetStateVariables(), SetFinishedRunningOdes(), SetInitialConditions(), CellCycleModelOdeHandler::SetLastTime(), AbstractSrnModel::SetSimulatedToTime(), and CellCycleModelOdeHandler::SetStateVariables().

const std::vector< double > & AbstractOdeSrnModel::GetStateVariables ( )

Returns: reference to the ODE system state values.

Definition at line 150 of file AbstractOdeSrnModel.cpp.

References CellCycleModelOdeHandler::mpOdeSystem, mStateSize, and AbstractParameterisedSystem< VECTOR >::rGetStateVariables().

void AbstractOdeSrnModel::Initialise ( AbstractOdeSystem * pOdeSystem )

protected

Overridden Initialise() method, which here sets up the ODE system.

Note we bring virtual functions from AbstractSrnModel into derived namespace so overloading virtual works.

Parameters

pOdeSystem pointer to an ODE system

Definition at line 85 of file AbstractOdeSrnModel.cpp.

References AbstractParameterisedSystem< VECTOR >::GetInitialConditions(), mInitialConditions, AbstractSrnModel::mpCell, CellCycleModelOdeHandler::mpOdeSystem, AbstractSrnModel::mSimulatedToTime, CellCycleModelOdeHandler::SetLastTime(), and AbstractParameterisedSystem< VECTOR >::SetStateVariables().

void AbstractOdeSrnModel::OutputSrnModelParameters ( out_stream & rParamsFile )

virtual

Outputs cell cycle model parameters to file.

Parameters

rParamsFile the file stream to which the parameters are output

Reimplemented from AbstractSrnModel.

Reimplemented in DeltaNotchSrnModel, and Goldbeter1991SrnModel.

Definition at line 157 of file AbstractOdeSrnModel.cpp.

References AbstractSrnModel::OutputSrnModelParameters().

Referenced by Goldbeter1991SrnModel::OutputSrnModelParameters(), and DeltaNotchSrnModel::OutputSrnModelParameters().

void AbstractOdeSrnModel::ResetForDivision ( )

virtual

For a naturally cycling model this does not need to be overridden in the subclasses. But most models should override this function and then call AbstractOdeBasedCellCycleModel::ResetForDivision() from inside their version.

Reimplemented from AbstractSrnModel.

Definition at line 132 of file AbstractOdeSrnModel.cpp.

References mFinishedRunningOdes, CellCycleModelOdeHandler::mLastTime, AbstractSrnModel::mSimulatedToTime, and AbstractSrnModel::ResetForDivision().

template<class Archive >