AbstractCentreBasedCellPopulation< DIM > Class Template Reference

#include <AbstractCentreBasedCellPopulation.hpp>

Inheritance diagram for AbstractCentreBasedCellPopulation< DIM >:

Collaboration diagram for AbstractCentreBasedCellPopulation< DIM >:

List of all members.

Public Member Functions

AbstractCentreBasedCellPopulation (std::vector< CellPtr > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >())

c_vector< double, DIM > GetLocationOfCellCentre (CellPtr pCell)

Node< DIM > * GetNodeCorrespondingToCell (CellPtr pCell)

CellPtr AddCell (CellPtr pNewCell, const c_vector< double, DIM > &rCellDivisionVector, CellPtr pParentCell=CellPtr())

bool IsCellAssociatedWithADeletedLocation (CellPtr pCell)

virtual void UpdateNodeLocations (const std::vector< c_vector< double, DIM > > &rNodeForces, double dt)

virtual double GetDampingConstant (unsigned nodeIndex)

void GenerateCellResults (unsigned locationIndex, std::vector< unsigned > &rCellProliferativeTypeCounter, std::vector< unsigned > &rCellCyclePhaseCounter)

virtual void GenerateCellResultsAndWriteToFiles ()

virtual void WriteTimeAndNodeResultsToFiles ()

virtual bool IsGhostNode (unsigned index)

double GetMeinekeDivisionSeparation ()

void SetMeinekeDivisionSeparation (double divisionSeparation)

virtual void OutputCellPopulationParameters (out_stream &rParamsFile)

Protected Member Functions

AbstractCentreBasedCellPopulation ()

Protected Attributes

double mMeinekeDivisionSeparation

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 AbstractCentreBasedCellPopulation< DIM >

An abstract facade class encapsulating a centre-based cell population, in which each cell corresponds to a Node.

Definition at line 41 of file AbstractCentreBasedCellPopulation.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

AbstractCentreBasedCellPopulation< DIM >::AbstractCentreBasedCellPopulation ( ) [inline, protected]

Constructor for use by archiving only.

Definition at line 41 of file AbstractCentreBasedCellPopulation.cpp.

template<unsigned DIM>

AbstractCentreBasedCellPopulation< DIM >::AbstractCentreBasedCellPopulation	(	std::vector< CellPtr > &	rCells,
		const std::vector< unsigned >	locationIndices = `std::vector<unsigned>()`
	)			`[inline]`

Default constructor.

Parameters:

	rCells	a vector of cells
	locationIndices	an optional vector of location indices that correspond to real cells

Definition at line 32 of file AbstractCentreBasedCellPopulation.cpp.

Member Function Documentation

template<unsigned DIM>

template<class Archive>

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

Serialize the object and its member variables.

Parameters:

	archive	the archive
	version	the current version of this class

Reimplemented from AbstractCellPopulation< DIM >.

Reimplemented in MeshBasedCellPopulation< DIM >, MeshBasedCellPopulationWithGhostNodes< DIM >, NodeBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, MeshBasedCellPopulation< 2 >, and MeshBasedCellPopulationWithGhostNodes< 2 >.

Definition at line 53 of file AbstractCentreBasedCellPopulation.hpp.

References AbstractCentreBasedCellPopulation< DIM >::mMeinekeDivisionSeparation.

template<unsigned DIM>

c_vector< double, DIM > AbstractCentreBasedCellPopulation< DIM >::GetLocationOfCellCentre ( CellPtr pCell ) [inline, virtual]

Overridden GetLocationOfCellCentre() method. Find where a given cell is in space.

Parameters:

pCell

the cell

Returns:: the location of the node corresponding to this cell.

Implements AbstractCellPopulation< DIM >.

Definition at line 49 of file AbstractCentreBasedCellPopulation.cpp.

References AbstractCentreBasedCellPopulation< DIM >::GetNodeCorrespondingToCell().

Referenced by CryptSimulation1d::CalculateCellDivisionVector(), CryptStatistics::GetCryptSection(), and CryptProjectionStatistics::GetCryptSection().

template<unsigned DIM>

Node< DIM > * AbstractCentreBasedCellPopulation< DIM >::GetNodeCorrespondingToCell ( CellPtr pCell ) [inline]

Get a pointer to the node corresponding to a given cell.

Parameters:

pCell

the cell

Returns:: address of the node

Definition at line 56 of file AbstractCentreBasedCellPopulation.cpp.

References AbstractCellPopulation< DIM >::GetNode(), and AbstractCellPopulation< DIM >::mCellLocationMap.

Referenced by CryptSimulation1d::ApplyCellPopulationBoundaryConditions(), AbstractCentreBasedCellPopulation< DIM >::GetLocationOfCellCentre(), AbstractCentreBasedCellPopulation< DIM >::IsCellAssociatedWithADeletedLocation(), NodeBasedCellPopulation< DIM >::RemoveDeadCells(), CellwiseDataGradient< DIM >::SetupGradients(), and MeshBasedCellPopulation< DIM >::Update().

template<unsigned DIM>

CellPtr AbstractCentreBasedCellPopulation< DIM >::AddCell	(	CellPtr	pNewCell,
		const c_vector< double, DIM > &	rCellDivisionVector,
		CellPtr	pParentCell = `CellPtr()`
	)			`[inline, virtual]`

Add a new cell to the cell population.

Parameters:

	pNewCell	the cell to add
	rCellDivisionVector	the position in space at which to put it
	pParentCell	pointer to a parent cell (if required)

Returns:: address of cell as it appears in the cell list

Implements AbstractCellPopulation< DIM >.

Reimplemented in MeshBasedCellPopulation< DIM >, MeshBasedCellPopulationWithGhostNodes< DIM >, MeshBasedCellPopulation< 1 >, MeshBasedCellPopulation< 2 >, and MeshBasedCellPopulationWithGhostNodes< 2 >.

Definition at line 65 of file AbstractCentreBasedCellPopulation.cpp.

References AbstractCellPopulation< DIM >::AddNode(), AbstractCellPopulation< DIM >::GetNumNodes(), AbstractCellPopulation< DIM >::mCellLocationMap, AbstractCellPopulation< DIM >::mCells, and AbstractCellPopulation< DIM >::mLocationCellMap.

Referenced by MeshBasedCellPopulation< DIM >::AddCell().

template<unsigned DIM>

bool AbstractCentreBasedCellPopulation< DIM >::IsCellAssociatedWithADeletedLocation ( CellPtr pCell ) [inline, virtual]

Overridden IsCellAssociatedWithADeletedLocation() method.

Parameters:

pCell

the cell

Returns:: whether a given cell is associated with a deleted node.

Implements AbstractCellPopulation< DIM >.

Definition at line 83 of file AbstractCentreBasedCellPopulation.cpp.

References AbstractCentreBasedCellPopulation< DIM >::GetNodeCorrespondingToCell().

template<unsigned DIM>

void AbstractCentreBasedCellPopulation< DIM >::UpdateNodeLocations	(	const std::vector< c_vector< double, DIM > > &	rNodeForces,
		double	dt
	)			`[inline, virtual]`

Overridden UpdateNodeLocations() method.

Parameters:

	rNodeForces	a vector containing the force on each node in the cell population
	dt	the time step

Implements AbstractCellPopulation< DIM >.

Reimplemented in MeshBasedCellPopulationWithGhostNodes< DIM >, and MeshBasedCellPopulationWithGhostNodes< 2 >.

Definition at line 90 of file AbstractCentreBasedCellPopulation.cpp.

References AbstractCellPopulation< DIM >::Begin(), AbstractCellPopulation< DIM >::End(), AbstractCentreBasedCellPopulation< DIM >::GetDampingConstant(), AbstractCellPopulation< DIM >::GetNode(), AbstractCellPopulation< DIM >::mCellLocationMap, and AbstractCellPopulation< DIM >::SetNode().

Referenced by MeshBasedCellPopulationWithGhostNodes< DIM >::UpdateNodeLocations().

template<unsigned DIM>

double AbstractCentreBasedCellPopulation< DIM >::GetDampingConstant ( unsigned nodeIndex ) [inline, virtual]

Overridden GetDampingConstant() method.

Get the damping constant for the cell associated with this node, i.e. d in drdt = F/d.

If the cell is wild-type, then the normal damping constant is returned. If the cell has a mutation, then the mutant damping constant is returned.

Note that by default, the normal and mutant damping constants are the same. To alter the damping constant for mutant cells, call the method SetDampingConstantMutant() on the CellPopulation.

Parameters:

nodeIndex

the global index of this node

Returns:: the damping constant at the Cell associated with this node

Implements AbstractCellPopulation< DIM >.

Reimplemented in MeshBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, and MeshBasedCellPopulation< 2 >.

Definition at line 116 of file AbstractCentreBasedCellPopulation.cpp.

References AbstractCellPopulation< DIM >::GetCellUsingLocationIndex(), AbstractCellPopulation< DIM >::GetDampingConstantMutant(), and AbstractCellPopulation< DIM >::GetDampingConstantNormal().

Referenced by MeshBasedCellPopulation< DIM >::GetDampingConstant(), and AbstractCentreBasedCellPopulation< DIM >::UpdateNodeLocations().

template<unsigned DIM>

void AbstractCentreBasedCellPopulation< DIM >::GenerateCellResults	(	unsigned	locationIndex,
		std::vector< unsigned > &	rCellProliferativeTypeCounter,
		std::vector< unsigned > &	rCellCyclePhaseCounter
	)			`[inline, virtual]`

Overridden GenerateCellResults() method. Generate results for a given cell in the current cell population state to output files.

Parameters:

	locationIndex	location index of the cell
	rCellProliferativeTypeCounter	cell type counter
	rCellCyclePhaseCounter	cell cycle phase counter

Reimplemented from AbstractCellPopulation< DIM >.

Definition at line 138 of file AbstractCentreBasedCellPopulation.cpp.

References AbstractCellPopulation< DIM >::GenerateCellResults(), AbstractCentreBasedCellPopulation< DIM >::IsGhostNode(), and AbstractCellPopulation< DIM >::mpVizCellProliferativeTypesFile.

Referenced by AbstractCentreBasedCellPopulation< DIM >::GenerateCellResultsAndWriteToFiles().

template<unsigned DIM>

void AbstractCentreBasedCellPopulation< DIM >::GenerateCellResultsAndWriteToFiles ( ) [inline, virtual]

Overridden GenerateCellResultsAndWriteToFiles() method.

Implements AbstractCellPopulation< DIM >.

Definition at line 156 of file AbstractCentreBasedCellPopulation.cpp.

References AbstractCentreBasedCellPopulation< DIM >::GenerateCellResults(), AbstractCellPopulation< DIM >::GetNode(), AbstractCellPopulation< DIM >::GetNumNodes(), AbstractCellPopulation< DIM >::mCellCyclePhaseCount, AbstractCellPopulation< DIM >::mCellProliferativeTypeCount, AbstractCellPopulation< DIM >::mLocationCellMap, and AbstractCellPopulation< DIM >::WriteCellResultsToFiles().

template<unsigned DIM>

void AbstractCentreBasedCellPopulation< DIM >::WriteTimeAndNodeResultsToFiles ( ) [inline, virtual]

Overridden WriteTimeAndNodeResultsToFiles() method.

Reimplemented from AbstractCellPopulation< DIM >.

Definition at line 195 of file AbstractCentreBasedCellPopulation.cpp.

References AbstractCellPopulation< DIM >::GetNode(), AbstractCellPopulation< DIM >::GetNumNodes(), SimulationTime::GetTime(), SimulationTime::Instance(), AbstractCellPopulation< DIM >::mLocationCellMap, AbstractCellPopulation< DIM >::mpVizBoundaryNodesFile, and AbstractCellPopulation< DIM >::mpVizNodesFile.

template<unsigned DIM>

bool AbstractCentreBasedCellPopulation< DIM >::IsGhostNode ( unsigned index ) [inline, virtual]

Find if a given node is a ghost node. The method always returns false but is overridden in MeshBasedCellPopulationWithGhostNodes.

Parameters:

index

the global index of a specified node

Returns:: whether the node is a ghost node

Reimplemented in MeshBasedCellPopulationWithGhostNodes< DIM >, and MeshBasedCellPopulationWithGhostNodes< 2 >.

Definition at line 131 of file AbstractCentreBasedCellPopulation.cpp.

Referenced by AbstractCentreBasedCellPopulation< DIM >::GenerateCellResults(), CellwiseDataGradient< DIM >::SetupGradients(), MeshBasedCellPopulation< DIM >::WriteCellPopulationVolumeResultsToFile(), MeshBasedCellPopulation< DIM >::WriteCellVolumeResultsToFile(), and MeshBasedCellPopulation< DIM >::WriteVtkResultsToFile().

template<unsigned DIM>

double AbstractCentreBasedCellPopulation< DIM >::GetMeinekeDivisionSeparation ( ) [inline]

Returns:: mMeinekeDivisionSeparation

Definition at line 229 of file AbstractCentreBasedCellPopulation.cpp.

References AbstractCentreBasedCellPopulation< DIM >::mMeinekeDivisionSeparation.

Referenced by CryptSimulation2d::CalculateCellDivisionVector(), and CryptSimulation1d::CalculateCellDivisionVector().

template<unsigned DIM>

void AbstractCentreBasedCellPopulation< DIM >::SetMeinekeDivisionSeparation ( double divisionSeparation ) [inline]

Set mMeinekeDivisionSeparation.

Parameters:

divisionSeparation

the new value of mMeinekeDivisionSeparation

Definition at line 235 of file AbstractCentreBasedCellPopulation.cpp.

References AbstractCentreBasedCellPopulation< DIM >::mMeinekeDivisionSeparation.

template<unsigned DIM>

void AbstractCentreBasedCellPopulation< DIM >::OutputCellPopulationParameters ( out_stream & rParamsFile ) [inline, virtual]

Outputs CellPopulation parameters to file

Parameters:

rParamsFile

the file stream to which the parameters are output

Implements AbstractCellPopulation< DIM >.

Reimplemented in MeshBasedCellPopulation< DIM >, MeshBasedCellPopulationWithGhostNodes< DIM >, NodeBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, MeshBasedCellPopulation< 2 >, and MeshBasedCellPopulationWithGhostNodes< 2 >.

Definition at line 243 of file AbstractCentreBasedCellPopulation.cpp.

References AbstractCentreBasedCellPopulation< DIM >::mMeinekeDivisionSeparation, and AbstractCellPopulation< DIM >::OutputCellPopulationParameters().

Referenced by NodeBasedCellPopulation< DIM >::OutputCellPopulationParameters(), and MeshBasedCellPopulation< DIM >::OutputCellPopulationParameters().

Friends And Related Function Documentation

template<unsigned DIM>

friend class boost::serialization::access [friend]

Needed for serialization.

Reimplemented from AbstractCellPopulation< DIM >.

Reimplemented in MeshBasedCellPopulation< DIM >, MeshBasedCellPopulationWithGhostNodes< DIM >, NodeBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, MeshBasedCellPopulation< 2 >, and MeshBasedCellPopulationWithGhostNodes< 2 >.

Definition at line 45 of file AbstractCentreBasedCellPopulation.hpp.

Member Data Documentation

template<unsigned DIM>

double AbstractCentreBasedCellPopulation< DIM >::mMeinekeDivisionSeparation [protected]

Initial separation placement of mother/daughter cells at birth. Has units of cell size at equilibrium rest length

Definition at line 67 of file AbstractCentreBasedCellPopulation.hpp.

Referenced by AbstractCentreBasedCellPopulation< DIM >::GetMeinekeDivisionSeparation(), AbstractCentreBasedCellPopulation< DIM >::OutputCellPopulationParameters(), AbstractCentreBasedCellPopulation< DIM >::serialize(), and AbstractCentreBasedCellPopulation< DIM >::SetMeinekeDivisionSeparation().

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

cell_based/src/population/AbstractCentreBasedCellPopulation.hpp
cell_based/src/population/AbstractCentreBasedCellPopulation.cpp


Public Member Functions
	AbstractCentreBasedCellPopulation (std::vector< CellPtr > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >())
c_vector< double, DIM >	GetLocationOfCellCentre (CellPtr pCell)
Node< DIM > *	GetNodeCorrespondingToCell (CellPtr pCell)
CellPtr	AddCell (CellPtr pNewCell, const c_vector< double, DIM > &rCellDivisionVector, CellPtr pParentCell=CellPtr())
bool	IsCellAssociatedWithADeletedLocation (CellPtr pCell)
virtual void	UpdateNodeLocations (const std::vector< c_vector< double, DIM > > &rNodeForces, double dt)
virtual double	GetDampingConstant (unsigned nodeIndex)
void	GenerateCellResults (unsigned locationIndex, std::vector< unsigned > &rCellProliferativeTypeCounter, std::vector< unsigned > &rCellCyclePhaseCounter)
virtual void	GenerateCellResultsAndWriteToFiles ()
virtual void	WriteTimeAndNodeResultsToFiles ()
virtual bool	IsGhostNode (unsigned index)
double	GetMeinekeDivisionSeparation ()
void	SetMeinekeDivisionSeparation (double divisionSeparation)
virtual void	OutputCellPopulationParameters (out_stream &rParamsFile)
Protected Member Functions
	AbstractCentreBasedCellPopulation ()
Protected Attributes
double	mMeinekeDivisionSeparation
Private Member Functions
template<class Archive>
void	serialize (Archive &archive, const unsigned int version)
Friends
class	boost::serialization::access

AbstractCentreBasedCellPopulation< DIM > Class Template Reference

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Friends

Detailed Description

template<unsigned DIM> class AbstractCentreBasedCellPopulation< DIM >

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation

template<unsigned DIM>
class AbstractCentreBasedCellPopulation< DIM >