AbstractCellCentreBasedTissue< DIM > Class Template Reference

#include <AbstractCellCentreBasedTissue.hpp>

Inherited by MeshBasedTissue< DIM >, MeshBasedTissue< 1 >, MeshBasedTissue< 2 >, and NodeBasedTissue< DIM >.

Collaboration diagram for AbstractCellCentreBasedTissue< DIM >:

Public Member Functions
	AbstractCellCentreBasedTissue (std::vector< TissueCell > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >())
c_vector< double, DIM >	GetLocationOfCellCentre (TissueCell &rCell)
Node< DIM > *	GetNodeCorrespondingToCell (TissueCell &rCell)
TissueCell *	AddCell (TissueCell &rNewCell, const c_vector< double, DIM > &rCellDivisionVector, TissueCell *pParentCell=NULL)
bool	IsCellAssociatedWithADeletedLocation (TissueCell &rCell)
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 bool	IsGhostNode (unsigned index)
Protected Member Functions
	AbstractCellCentreBasedTissue ()
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 AbstractCellCentreBasedTissue< DIM >

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

Definition at line 41 of file AbstractCellCentreBasedTissue.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

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

Constructor for use by archiving - doesn't take in cells, since these are dealt with by the serialize method.

Definition at line 40 of file AbstractCellCentreBasedTissue.cpp.

template<unsigned DIM>

AbstractCellCentreBasedTissue< DIM >::AbstractCellCentreBasedTissue	(	std::vector< TissueCell > &	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 AbstractCellCentreBasedTissue.cpp.

Member Function Documentation

template<unsigned DIM>

TissueCell * AbstractCellCentreBasedTissue< DIM >::AddCell	(	TissueCell &	rNewCell,
		const c_vector< double, DIM > &	rCellDivisionVector,
		TissueCell *	pParentCell = `NULL`
	)			`[inline, virtual]`

Add a new cell to the tissue.

Parameters:

	rNewCell	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 AbstractTissue< DIM >.

Reimplemented in MeshBasedTissue< DIM >, MeshBasedTissueWithGhostNodes< DIM >, MeshBasedTissue< 1 >, MeshBasedTissue< 2 >, and MeshBasedTissueWithGhostNodes< 2 >.

Definition at line 61 of file AbstractCellCentreBasedTissue.cpp.

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

template<unsigned DIM>

void AbstractCellCentreBasedTissue< 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 tissue state to output files.

Parameters:

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

Reimplemented from AbstractTissue< DIM >.

Definition at line 135 of file AbstractCellCentreBasedTissue.cpp.

References AbstractCellCentreBasedTissue< DIM >::IsGhostNode(), and AbstractTissue< DIM >::mpVizCellProliferativeTypesFile.

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

template<unsigned DIM>

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

Overridden GenerateCellResultsAndWriteToFiles() method.

Implements AbstractTissue< DIM >.

Definition at line 153 of file AbstractCellCentreBasedTissue.cpp.

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

template<unsigned DIM>

double AbstractCellCentreBasedTissue< 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 TissueConfig::SetDampingConstantMutant().

Parameters:

nodeIndex

the global index of this node

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

Implements AbstractTissue< DIM >.

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

Definition at line 113 of file AbstractCellCentreBasedTissue.cpp.

References TissueConfig::GetDampingConstantMutant(), TissueConfig::GetDampingConstantNormal(), TissueCell::GetMutationState(), TissueConfig::Instance(), and AbstractTissue< DIM >::rGetCellUsingLocationIndex().

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

template<unsigned DIM>

c_vector< double, DIM > AbstractCellCentreBasedTissue< DIM >::GetLocationOfCellCentre ( TissueCell & rCell ) [inline, virtual]

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

Parameters:

rCell

the cell

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

Implements AbstractTissue< DIM >.

Definition at line 47 of file AbstractCellCentreBasedTissue.cpp.

References AbstractCellCentreBasedTissue< DIM >::GetNodeCorrespondingToCell().

Referenced by CryptSimulation2d::CalculateCellDivisionVector(), CryptSimulation1d::CalculateCellDivisionVector(), CryptStatistics::GetCryptSection(), CryptSimulation2d::SetBottomCellAncestors(), CryptSimulation2d::WriteBetaCatenin(), MeshBasedTissue< DIM >::WriteCellAreaResultsToFile(), and MeshBasedTissue< DIM >::WriteVoronoiResultsToFile().

template<unsigned DIM>

Node< DIM > * AbstractCellCentreBasedTissue< DIM >::GetNodeCorrespondingToCell ( TissueCell & rCell ) [inline]

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

Parameters:

rCell

the cell

Returns:: address of the node

Definition at line 54 of file AbstractCellCentreBasedTissue.cpp.

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

Referenced by CryptSimulation2d::ApplyTissueBoundaryConditions(), CryptSimulation1d::ApplyTissueBoundaryConditions(), AbstractCellCentreBasedTissue< DIM >::GetLocationOfCellCentre(), AbstractCellCentreBasedTissue< DIM >::IsCellAssociatedWithADeletedLocation(), NodeBasedTissue< DIM >::RemoveDeadCells(), and MeshBasedTissue< DIM >::Update().

template<unsigned DIM>

bool AbstractCellCentreBasedTissue< DIM >::IsCellAssociatedWithADeletedLocation ( TissueCell & rCell ) [inline, virtual]

Overridden IsCellAssociatedWithADeletedLocation() method.

Parameters:

rCell

the cell

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

Implements AbstractTissue< DIM >.

Definition at line 80 of file AbstractCellCentreBasedTissue.cpp.

References AbstractCellCentreBasedTissue< DIM >::GetNodeCorrespondingToCell().

template<unsigned DIM>

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

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

Parameters:

index

the global index of a specified node

Returns:: whether the node is a ghost node

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

Definition at line 128 of file AbstractCellCentreBasedTissue.cpp.

Referenced by AbstractCellCentreBasedTissue< DIM >::GenerateCellResults().

template<unsigned DIM>

template<class Archive >

void AbstractCellCentreBasedTissue< 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 AbstractTissue< DIM >.

Reimplemented in MeshBasedTissue< DIM >, MeshBasedTissueWithGhostNodes< DIM >, NodeBasedTissue< DIM >, MeshBasedTissue< 1 >, MeshBasedTissue< 2 >, and MeshBasedTissueWithGhostNodes< 2 >.

Definition at line 53 of file AbstractCellCentreBasedTissue.hpp.

template<unsigned DIM>

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