#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)

virtual void	ScaleSrnVariables (const double theta)

Public Member Functions inherited from AbstractSrnModel
	AbstractSrnModel ()

virtual	~AbstractSrnModel ()

virtual void	SetCell (CellPtr pCell)

virtual void	InitialiseDaughterCell ()

CellPtr	GetCell ()

void	SetSimulatedToTime (double simulatedToTime)

double	GetSimulatedToTime () const

virtual AbstractSrnModel *	CreateSrnModel ()=0

void	OutputSrnModelInfo (out_stream &rParamsFile)

void	SetEdgeLocalIndex (unsigned index)

unsigned	GetEdgeLocalIndex ()

bool	HasEdgeModel () const

void	SetEdgeModelIndicator (const bool isEdgeModel)

virtual void	AddSrnQuantities (AbstractSrnModel *pOtherSrn, const double scale=1.0)

virtual void	AddShrunkEdgeSrn (AbstractSrnModel *pShrunkEdgeSrn)

virtual void	AddMergedEdgeSrn (AbstractSrnModel *pMergedEdgeSrn)

virtual void	AddShrunkEdgeToInterior (AbstractSrnModel *pShrunkEdgeSrn)

virtual void	SplitEdgeSrn (const double relativePosition)

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)

virtual void	Initialise ()

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

unsigned	mEdgeLocalIndex = UNSIGNED_UNSET

bool	mIsEdgeBasedModel = false

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, similar in structure to AbstractOdeBasedCellCycleModel.

Definition at line 52 of file AbstractOdeSrnModel.hpp.

Constructor & Destructor Documentation

◆ AbstractOdeSrnModel() [1/2]

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() [2/2]

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::~AbstractOdeSrnModel ( )

virtual

Destructor.

Definition at line 67 of file AbstractOdeSrnModel.cpp.

Member Function Documentation

◆ Initialise() [1/2]

void AbstractSrnModel::Initialise ( )

protectedvirtual

Initialise the SRN model at the start of a simulation.

This method will be called precisely once per cell set up in the initial cell population. It is not called on cell division; use ResetForDivision(), CreateSrnModel() and InitialiseDaughterCell() for that.

By the time this is called, a CellPopulation will have been set up, so the model can know where its cell is located in space. If relevant to the simulation, any singletons will also have been initialised.

Reimplemented from AbstractSrnModel.

Reimplemented in DeltaNotchEdgeSrnModel, DeltaNotchInteriorSrnModel, DeltaNotchSrnModel, and Goldbeter1991SrnModel.

Definition at line 164 of file AbstractSrnModel.cpp.

Referenced by DeltaNotchEdgeSrnModel::Initialise(), DeltaNotchInteriorSrnModel::Initialise(), DeltaNotchSrnModel::Initialise(), and Goldbeter1991SrnModel::Initialise().

◆ Initialise() [2/2]

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().

◆ OutputSrnModelParameters()

void AbstractOdeSrnModel::OutputSrnModelParameters ( out_stream & rParamsFile )

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.

Reimplemented in DeltaNotchEdgeSrnModel, DeltaNotchInteriorSrnModel, DeltaNotchSrnModel, and Goldbeter1991SrnModel.

Definition at line 128 of file AbstractOdeSrnModel.cpp.

References AbstractSrnModel::OutputSrnModelParameters().

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

◆ ResetForDivision()

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.

Reimplemented in DeltaNotchInteriorSrnModel.

Definition at line 115 of file AbstractOdeSrnModel.cpp.

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

◆ ScaleSrnVariables()

void AbstractOdeSrnModel::ScaleSrnVariables ( const double theta )

virtual

Scales all ODE variables by factor theta. Used for example to scale model variables after cell division.

Parameters

theta factor by which to scale all ODE variables.

Reimplemented from AbstractSrnModel.

Definition at line 134 of file AbstractOdeSrnModel.cpp.

References AbstractUntemplatedParameterisedSystem::GetNumberOfStateVariables(), AbstractParameterisedSystem< VECTOR >::GetStateVariable(), CellCycleModelOdeHandler::mpOdeSystem, and AbstractParameterisedSystem< VECTOR >::SetStateVariable().

Referenced by DeltaNotchInteriorSrnModel::ResetForDivision(), and DeltaNotchEdgeSrnModel::SplitEdgeSrn().

◆ serialize()

template<class Archive >

void AbstractOdeSrnModel::serialize	(	Archive &	archive,
		const unsigned int	version
	)

inlineprivate

Archive the SRN model and member variables.

Parameters

archive	the archive
version	the current version of this class

Definition at line 65 of file AbstractOdeSrnModel.hpp.

References mInitialConditions, and mStateSize.

◆ SetInitialConditions()

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

Set mInitialConditions. Used in CreateSrnModel().

Parameters

initialConditions the new value of mInitialConditions

Definition at line 122 of file AbstractOdeSrnModel.cpp.

References mInitialConditions, and mStateSize.

◆ SimulateToCurrentTime()

void AbstractOdeSrnModel::SimulateToCurrentTime ( )

virtual

Here we solve the ODEs associated with the SRN.

Implements AbstractSrnModel.

Reimplemented in DeltaNotchEdgeSrnModel, DeltaNotchInteriorSrnModel, DeltaNotchSrnModel, and Goldbeter1991SrnModel.

Definition at line 71 of file AbstractOdeSrnModel.cpp.

References SimulationTime::GetTime(), SimulationTime::Instance(), CellCycleModelOdeHandler::mFinishedRunningOdes, CellCycleModelOdeHandler::mLastTime, CellCycleModelOdeHandler::mpOdeSystem, AbstractSrnModel::SetSimulatedToTime(), and CellCycleModelOdeHandler::SolveOdeToTime().

Referenced by DeltaNotchEdgeSrnModel::SimulateToCurrentTime(), DeltaNotchInteriorSrnModel::SimulateToCurrentTime(), DeltaNotchSrnModel::SimulateToCurrentTime(), and Goldbeter1991SrnModel::SimulateToCurrentTime().

Friends And Related Symbol Documentation

◆ boost::serialization::access

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 57 of file AbstractOdeSrnModel.hpp.

Member Data Documentation

◆ mInitialConditions

std::vector<double> AbstractOdeSrnModel::mInitialConditions

protected

The initial condition for the ODE state variables.

Definition at line 78 of file AbstractOdeSrnModel.hpp.

Referenced by Initialise(), serialize(), and SetInitialConditions().

◆ mStateSize

unsigned AbstractOdeSrnModel::mStateSize

protected

The number of state variables.

Definition at line 83 of file AbstractOdeSrnModel.hpp.

Referenced by serialize(), and SetInitialConditions().

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

cell_based/src/cell/srn/AbstractOdeSrnModel.hpp
cell_based/src/cell/srn/AbstractOdeSrnModel.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Friends

Detailed Description

Constructor & Destructor Documentation

◆ AbstractOdeSrnModel() [1/2]

◆ AbstractOdeSrnModel() [2/2]

◆ ~AbstractOdeSrnModel()

Member Function Documentation

◆ Initialise() [1/2]

◆ Initialise() [2/2]

◆ OutputSrnModelParameters()

◆ ResetForDivision()

◆ ScaleSrnVariables()

◆ serialize()

◆ SetInitialConditions()

◆ SimulateToCurrentTime()

Friends And Related Symbol Documentation

◆ boost::serialization::access

Member Data Documentation

◆ mInitialConditions

◆ mStateSize