#include <DeltaNotchTrackingModifier.hpp>

Inheritance diagram for DeltaNotchTrackingModifier< DIM >:

Collaboration diagram for DeltaNotchTrackingModifier< DIM >:

Public Member Functions
	DeltaNotchTrackingModifier ()

virtual	~DeltaNotchTrackingModifier ()

virtual void	UpdateAtEndOfTimeStep (AbstractCellPopulation< DIM, DIM > &rCellPopulation)

virtual void	SetupSolve (AbstractCellPopulation< DIM, DIM > &rCellPopulation, std::string outputDirectory)

void	UpdateCellData (AbstractCellPopulation< DIM, DIM > &rCellPopulation)

void	OutputSimulationModifierParameters (out_stream &rParamsFile)

Public Member Functions inherited from AbstractCellBasedSimulationModifier< DIM, DIM >
	AbstractCellBasedSimulationModifier ()

virtual	~AbstractCellBasedSimulationModifier ()

virtual void	UpdateAtEndOfTimeStep (AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &rCellPopulation)=0

virtual void	UpdateAtEndOfOutputTimeStep (AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &rCellPopulation)

virtual void	SetupSolve (AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &rCellPopulation, std::string outputDirectory)=0

virtual void	UpdateAtEndOfSolve (AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &rCellPopulation)

void	OutputSimulationModifierInfo (out_stream &rParamsFile)

Public Member Functions inherited from Identifiable
virtual	~Identifiable ()

std::string	GetIdentifier () const

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

Friends
class	boost::serialization::access

Detailed Description

template<unsigned DIM>
class DeltaNotchTrackingModifier< DIM >

A modifier class in which the mean levels of Delta in neighbouring cells are computed and stored in CellData. To be used in conjunction with Delta Notch cell cycle models.

Definition at line 50 of file DeltaNotchTrackingModifier.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

DeltaNotchTrackingModifier< DIM >::DeltaNotchTrackingModifier ( )

Default constructor.

Definition at line 40 of file DeltaNotchTrackingModifier.cpp.

Referenced by DeltaNotchTrackingModifier< DIM >::serialize().

template<unsigned DIM>

DeltaNotchTrackingModifier< DIM >::~DeltaNotchTrackingModifier ( )

virtual

Destructor.

Definition at line 46 of file DeltaNotchTrackingModifier.cpp.

Referenced by DeltaNotchTrackingModifier< DIM >::serialize().

Member Function Documentation

template<unsigned DIM>

void DeltaNotchTrackingModifier< DIM >::OutputSimulationModifierParameters ( out_stream & rParamsFile )

virtual

Overridden OutputSimulationModifierParameters() method. Output any simulation modifier parameters to file.

Parameters

rParamsFile the file stream to which the parameters are output

Implements AbstractCellBasedSimulationModifier< DIM, DIM >.

Definition at line 117 of file DeltaNotchTrackingModifier.cpp.

References EXPORT_TEMPLATE_CLASS_SAME_DIMS, and AbstractCellBasedSimulationModifier< ELEMENT_DIM, SPACE_DIM >::OutputSimulationModifierParameters().

Referenced by DeltaNotchTrackingModifier< DIM >::serialize().

template<unsigned DIM>

template<class Archive >

void DeltaNotchTrackingModifier< DIM >::serialize	(	Archive &	archive,
		const unsigned int	version
	)

inlineprivate

Boost Serialization method for archiving/checkpointing. Archives the object and its member variables.

Parameters

archive	The boost archive.
version	The current version of this class.

Definition at line 62 of file DeltaNotchTrackingModifier.hpp.

References DeltaNotchTrackingModifier< DIM >::DeltaNotchTrackingModifier(), EXPORT_TEMPLATE_CLASS_SAME_DIMS, DeltaNotchTrackingModifier< DIM >::OutputSimulationModifierParameters(), DeltaNotchTrackingModifier< DIM >::SetupSolve(), DeltaNotchTrackingModifier< DIM >::UpdateAtEndOfTimeStep(), DeltaNotchTrackingModifier< DIM >::UpdateCellData(), and DeltaNotchTrackingModifier< DIM >::~DeltaNotchTrackingModifier().

template<unsigned DIM>

void DeltaNotchTrackingModifier< DIM >::SetupSolve	(	AbstractCellPopulation< DIM, DIM > &	rCellPopulation,
		std::string	outputDirectory
	)

virtual

Overridden SetupSolve() method.

Specifies what to do in the simulation before the start of the time loop.

Parameters

rCellPopulation	reference to the cell population
outputDirectory	the output directory, relative to where Chaste output is stored

Definition at line 57 of file DeltaNotchTrackingModifier.cpp.

References DeltaNotchTrackingModifier< DIM >::UpdateCellData().

Referenced by DeltaNotchTrackingModifier< DIM >::serialize().

template<unsigned DIM>

void DeltaNotchTrackingModifier< DIM >::UpdateAtEndOfTimeStep ( AbstractCellPopulation< DIM, DIM > & rCellPopulation )

virtual

Overridden UpdateAtEndOfTimeStep() method.

Specifies what to do in the simulation at the end of each time step.

Parameters

rCellPopulation reference to the cell population

Definition at line 51 of file DeltaNotchTrackingModifier.cpp.

References DeltaNotchTrackingModifier< DIM >::UpdateCellData().

Referenced by DeltaNotchTrackingModifier< DIM >::serialize().

template<unsigned DIM>

void DeltaNotchTrackingModifier< DIM >::UpdateCellData ( AbstractCellPopulation< DIM, DIM > & rCellPopulation )

Helper method to compute the mean level of Delta in each cell's neighbours and store these in the CellData.

Note: If using a CaBasedCellPopulation, we assume a Moore neighbourhood and unit carrying capacity. If a cell has no neighbours (such as an isolated cell in a CaBasedCellPopulation), we store the value -1 in the CellData.

Parameters

rCellPopulation reference to the cell population

Definition at line 67 of file DeltaNotchTrackingModifier.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Begin(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::End(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCellUsingLocationIndex(), DeltaNotchSrnModel::GetDelta(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNeighbouringLocationIndices(), DeltaNotchSrnModel::GetNotch(), and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Update().

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