#include <DeltaNotchSrnModel.hpp>

Inheritance diagram for DeltaNotchSrnModel:

Collaboration diagram for DeltaNotchSrnModel:

Public Member Functions
	DeltaNotchSrnModel (boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver=boost::shared_ptr< AbstractCellCycleModelOdeSolver >())

AbstractSrnModel *	CreateSrnModel ()

void	Initialise ()

void	SimulateToCurrentTime ()

void	UpdateDeltaNotch ()

double	GetNotch ()

double	GetDelta ()

double	GetMeanNeighbouringDelta ()

void	OutputSrnModelParameters (out_stream &rParamsFile)

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

virtual	~AbstractOdeSrnModel ()

virtual void	ResetForDivision ()

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

Public Member Functions inherited from AbstractSrnModel
	AbstractSrnModel ()

virtual	~AbstractSrnModel ()

void	SetCell (CellPtr pCell)

virtual void	InitialiseDaughterCell ()

CellPtr	GetCell ()

void	SetSimulatedToTime (double simulatedToTime)

double	GetSimulatedToTime () const

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
	DeltaNotchSrnModel (const DeltaNotchSrnModel &rModel)

Protected Member Functions inherited from AbstractOdeSrnModel
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)

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

Friends
class	boost::serialization::access

Additional Inherited Members
Protected Attributes inherited from AbstractOdeSrnModel
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

Detailed Description

A subclass of AbstractOdeSrnModel that includes a Delta-Notch ODE system in the sub-cellular reaction network.

Todo:: #2752 document this class more thoroughly here

Definition at line 50 of file DeltaNotchSrnModel.hpp.

Constructor & Destructor Documentation

DeltaNotchSrnModel::DeltaNotchSrnModel ( const DeltaNotchSrnModel & 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 56 of file DeltaNotchSrnModel.cpp.

References CellCycleModelOdeHandler::GetOdeSystem(), AbstractParameterisedSystem< VECTOR >::rGetStateVariables(), and CellCycleModelOdeHandler::SetOdeSystem().

Referenced by CreateSrnModel(), and serialize().

DeltaNotchSrnModel::DeltaNotchSrnModel ( boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver = boost::shared_ptr<AbstractCellCycleModelOdeSolver>() )

Default constructor calls base class.

Parameters

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 DeltaNotchSrnModel.cpp.

References CellCycleModelOdeSolver< CELL_CYCLE_MODEL, ODE_SOLVER >::Instance(), CellCycleModelOdeHandler::mpOdeSolver, and CellCycleModelOdeHandler::SetDt().

Member Function Documentation

AbstractSrnModel * DeltaNotchSrnModel::CreateSrnModel ( )

virtual

Overridden builder method to create new copies of this SRN model.

Returns: a copy of the current SRN model.

Implements AbstractSrnModel.

Definition at line 78 of file DeltaNotchSrnModel.cpp.

References DeltaNotchSrnModel().

Referenced by serialize().

double DeltaNotchSrnModel::GetDelta ( )

Returns: the current Delta level in this cell.

Definition at line 113 of file DeltaNotchSrnModel.cpp.

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

Referenced by serialize(), and DeltaNotchTrackingModifier< DIM >::UpdateCellData().

double DeltaNotchSrnModel::GetMeanNeighbouringDelta ( )

Returns: the current level of mean Delta in the neighbouring cells.

N.B. This doesn't calculate anything, it just returns the parameter from the DeltaNotchOdeSystem.

Definition at line 120 of file DeltaNotchSrnModel.cpp.

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

Referenced by serialize().

double DeltaNotchSrnModel::GetNotch ( )

Returns: the current Notch level in this cell.

Definition at line 106 of file DeltaNotchSrnModel.cpp.

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

Referenced by serialize(), and DeltaNotchTrackingModifier< DIM >::UpdateCellData().

void DeltaNotchSrnModel::Initialise ( void )

virtual

Initialise the SRN model at the start of a simulation.

This overridden method sets up a new Delta-Notch ODE system.

Reimplemented from AbstractSrnModel.

Definition at line 92 of file DeltaNotchSrnModel.cpp.

References AbstractSrnModel::Initialise().

Referenced by serialize().

void DeltaNotchSrnModel::OutputSrnModelParameters ( out_stream & rParamsFile )

virtual

Output SRN model parameters to file.

Parameters

rParamsFile the file stream to which the parameters are output

Implements AbstractOdeSrnModel.

Definition at line 127 of file DeltaNotchSrnModel.cpp.

References CHASTE_CLASS_EXPORT, and AbstractOdeSrnModel::OutputSrnModelParameters().

Referenced by serialize().

template<class Archive >

void DeltaNotchSrnModel::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 63 of file DeltaNotchSrnModel.hpp.

References CHASTE_CLASS_EXPORT, CreateSrnModel(), DeltaNotchSrnModel(), GetDelta(), GetMeanNeighbouringDelta(), GetNotch(), Initialise(), OutputSrnModelParameters(), SimulateToCurrentTime(), and UpdateDeltaNotch().

void DeltaNotchSrnModel::SimulateToCurrentTime ( )

virtual

Overridden SimulateToTime() method for custom behaviour.

Todo:: #2752 say what it does in this class

Reimplemented from AbstractOdeSrnModel.

Definition at line 83 of file DeltaNotchSrnModel.cpp.

References AbstractOdeSrnModel::SimulateToCurrentTime(), and UpdateDeltaNotch().

Referenced by serialize().

void DeltaNotchSrnModel::UpdateDeltaNotch ( )

Update the current levels of Delta and Notch in the cell.

N.B. Despite the name, this doesn't update the levels of delta or notch, or compute mean levels. It just copies the current mean delta from the CellData (set by DeltaNotchTrackingModifier) to the DeltaNotchOdeSystem.

Todo:: #2752 Improve the name of this method!

Definition at line 97 of file DeltaNotchSrnModel.cpp.

References AbstractSrnModel::mpCell, CellCycleModelOdeHandler::mpOdeSystem, and AbstractParameterisedSystem< VECTOR >::SetParameter().

Referenced by serialize(), and SimulateToCurrentTime().

Friends And Related Function Documentation

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 55 of file DeltaNotchSrnModel.hpp.

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

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

Public Member Functions

Protected Member Functions

Private Member Functions

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation