DeltaNotchTrackingModifier< DIM > Class Template Reference

#include <DeltaNotchTrackingModifier.hpp>

Inherits AbstractCellBasedSimulationModifier< DIM, 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)
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 ( ) [inline]

Default constructor.

Definition at line 40 of file DeltaNotchTrackingModifier.cpp.

template<unsigned DIM>

DeltaNotchTrackingModifier< DIM >::~DeltaNotchTrackingModifier ( ) [inline, virtual]

Destructor.

Definition at line 46 of file DeltaNotchTrackingModifier.cpp.

Member Function Documentation

template<unsigned DIM>

void DeltaNotchTrackingModifier< DIM >::OutputSimulationModifierParameters ( out_stream & rParamsFile ) [inline, 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.

template<unsigned DIM>

template<class Archive >

void DeltaNotchTrackingModifier< DIM >::serialize	(	Archive &	archive,
		const unsigned int	version
	)			`[inline, private]`

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.

Reimplemented from AbstractCellBasedSimulationModifier< DIM, DIM >.

Definition at line 62 of file DeltaNotchTrackingModifier.hpp.

template<unsigned DIM>

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

template<unsigned DIM>

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

template<unsigned DIM>

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

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(), DeltaNotchCellCycleModel::GetDelta(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNeighbouringLocationIndices(), DeltaNotchCellCycleModel::GetNotch(), and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Update().

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