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

virtual void	OutputSrnModelParameters (out_stream &rParamsFile)=0

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 () const

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)

std::vector< double >	GetProteinConcentrations () const

void	SetProteinConcentrationsForTestsOnly (double lastTime, std::vector< double > proteinConcentrations)

Protected Member Functions
void	Initialise (AbstractOdeSystem *pOdeSystem)

	AbstractOdeSrnModel (const AbstractOdeSrnModel &rModel)

Protected Member Functions inherited from AbstractSrnModel
	AbstractSrnModel (const AbstractSrnModel &rModel)

Protected Member Functions inherited from CellCycleModelOdeHandler
	CellCycleModelOdeHandler (const CellCycleModelOdeHandler &rHandler)

bool	SolveOdeToTime (double currentTime)

virtual void	AdjustOdeParameters (double currentTime)

Protected Attributes
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

bool	mFinishedRunningOdes

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 56 of file AbstractOdeSrnModel.hpp.

Constructor & Destructor Documentation

AbstractOdeSrnModel::AbstractOdeSrnModel ( const AbstractOdeSrnModel & rModel )

protected

Protected copy-constructor for use by CreateSrnModel(). The only way for external code to create a copy of a SRN model is by calling that method, to ensure that a model of the correct subclass is created. This copy-constructor helps subclasses to ensure that all member variables are correctly copied when this happens.

This method is called by child classes to set member variables for a daughter cell upon cell division. 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().

Parameters

rModel the SRN model to copy.

Definition at line 45 of file AbstractOdeSrnModel.cpp.

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 38 of file AbstractOdeSrnModel.cpp.

AbstractOdeSrnModel::~AbstractOdeSrnModel ( )

virtual

Destructor.

Definition at line 67 of file AbstractOdeSrnModel.cpp.

Member Function Documentation

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 97 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 )

pure virtual

Outputs SRN model parameters to file. Virtual void so needs to be specified in child classes.

Parameters

rParamsFile the file stream to which the parameters are output

Reimplemented from AbstractSrnModel.

Implemented in DeltaNotchSrnModel, and Goldbeter1991SrnModel.

Definition at line 128 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 AbstractSrnModel::ResetForDivision() from inside their version.

Reimplemented from AbstractSrnModel.

Definition at line 115 of file AbstractOdeSrnModel.cpp.

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

template<class Archive >