AbstractCellCentreBasedTissue< DIM > Class Template Reference

#include <AbstractCellCentreBasedTissue.hpp>

Inheritance diagram for AbstractCellCentreBasedTissue< DIM >:

Collaboration diagram for AbstractCellCentreBasedTissue< DIM >:

List of all members.

Public Member Functions

AbstractCellCentreBasedTissue (const std::vector< TissueCell > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >())

AbstractCellCentreBasedTissue ()

c_vector< double, DIM > GetLocationOfCellCentre (TissueCell *pCell)

Node< DIM > * GetNodeCorrespondingToCell (TissueCell *pCell)

TissueCell * AddCell (TissueCell &rNewCell, c_vector< double, DIM > newLocation, TissueCell *pParentCell=NULL)

bool IsCellAssociatedWithADeletedNode (TissueCell &rCell)

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

virtual double GetDampingConstant (unsigned nodeIndex)

virtual void WriteResultsToFiles (bool outputCellMutationStates, bool outputCellTypes, bool outputCellVariables, bool outputCellCyclePhases, bool outputCellAncestors)

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 38 of file AbstractCellCentreBasedTissue.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

AbstractCellCentreBasedTissue< DIM >::AbstractCellCentreBasedTissue	(	const 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 33 of file AbstractCellCentreBasedTissue.cpp.

template<unsigned DIM>

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

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

Definition at line 41 of file AbstractCellCentreBasedTissue.cpp.

Member Function Documentation

template<unsigned DIM>

template<class Archive>

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

Serialize the facade.

Parameters:

	archive
	version

Reimplemented from AbstractTissue< DIM >.

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

Definition at line 51 of file AbstractCellCentreBasedTissue.hpp.

template<unsigned DIM>

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

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

Parameters:

pCell

pointer to the cell

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

Implements AbstractTissue< DIM >.

Definition at line 48 of file AbstractCellCentreBasedTissue.cpp.

References AbstractCellCentreBasedTissue< DIM >::GetNodeCorrespondingToCell().

Referenced by CryptSimulation2d::CalculateDividingCellCentreLocations(), CryptStatistics::GetCryptSection(), CryptSimulation2d::WriteBetaCatenin(), and MeshBasedTissue< DIM >::WriteVoronoiResultsToFile().

template<unsigned DIM>

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

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

Parameters:

pCell

pointer to the cell

Returns:: address of the node

Definition at line 55 of file AbstractCellCentreBasedTissue.cpp.

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

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

template<unsigned DIM>

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

Add a new cell to the tissue.

Parameters:

	rNewCell	the cell to add
	newLocation	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< 2 >, and MeshBasedTissueWithGhostNodes< 2 >.

Definition at line 62 of file AbstractCellCentreBasedTissue.cpp.

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

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

template<unsigned DIM>

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

Overridden IsCellAssociatedWithADeletedNode() method.

Parameters:

rCell

the cell

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

Implements AbstractTissue< DIM >.

Definition at line 81 of file AbstractCellCentreBasedTissue.cpp.

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

template<unsigned DIM>

void AbstractCellCentreBasedTissue< 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 tissue
	dt	the time step

Implements AbstractTissue< DIM >.

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

Definition at line 88 of file AbstractCellCentreBasedTissue.cpp.

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

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

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. This depends on whether using area-based viscosity has been switched on, and on whether the cell is a mutant or not.

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 >, and MeshBasedTissue< 2 >.

Definition at line 114 of file AbstractCellCentreBasedTissue.cpp.

References CancerParameters::GetDampingConstantMutant(), CancerParameters::GetDampingConstantNormal(), CancerParameters::Instance(), and AbstractTissue< DIM >::rGetCellUsingLocationIndex().

Referenced by MeshBasedTissue< DIM >::GetDampingConstant(), and AbstractCellCentreBasedTissue< DIM >::UpdateNodeLocations().

template<unsigned DIM>

void AbstractCellCentreBasedTissue< DIM >::WriteResultsToFiles	(	bool	outputCellMutationStates,
		bool	outputCellTypes,
		bool	outputCellVariables,
		bool	outputCellCyclePhases,
		bool	outputCellAncestors
	)			`[inline, virtual]`

Write results from the current tissue state to output files.

Parameters:

	outputCellMutationStates	whether to output cell mutation state results
	outputCellTypes	whether to output cell type results
	outputCellVariables	whether to output cell-cycle variable results
	outputCellCyclePhases	whether to output cell-cycle phase results
	outputCellAncestors	whether to output cell ancestor results

Implements AbstractTissue< DIM >.

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

Definition at line 131 of file AbstractCellCentreBasedTissue.cpp.

References AbstractTissue< DIM >::GenerateCellResults(), AbstractTissue< DIM >::GetNode(), AbstractTissue< DIM >::GetNumNodes(), AbstractTissue< DIM >::WriteCellResultsToFiles(), and AbstractTissue< DIM >::WriteTimeAndNodeResultsToFiles().

Referenced by MeshBasedTissue< DIM >::WriteResultsToFiles().

Friends And Related Function Documentation

template<unsigned DIM>

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

Needed for serialization.

Reimplemented from AbstractTissue< DIM >.

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

Definition at line 43 of file AbstractCellCentreBasedTissue.hpp.

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

/tmp/release_1/cancer/src/tissue/AbstractCellCentreBasedTissue.hpp
/tmp/release_1/cancer/src/tissue/AbstractCellCentreBasedTissue.cpp


Public Member Functions
	AbstractCellCentreBasedTissue (const std::vector< TissueCell > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >())
	AbstractCellCentreBasedTissue ()
c_vector< double, DIM >	GetLocationOfCellCentre (TissueCell *pCell)
Node< DIM > *	GetNodeCorrespondingToCell (TissueCell *pCell)
TissueCell *	AddCell (TissueCell &rNewCell, c_vector< double, DIM > newLocation, TissueCell *pParentCell=NULL)
bool	IsCellAssociatedWithADeletedNode (TissueCell &rCell)
virtual void	UpdateNodeLocations (const std::vector< c_vector< double, DIM > > &rNodeForces, double dt)
virtual double	GetDampingConstant (unsigned nodeIndex)
virtual void	WriteResultsToFiles (bool outputCellMutationStates, bool outputCellTypes, bool outputCellVariables, bool outputCellCyclePhases, bool outputCellAncestors)
Private Member Functions
template<class Archive>
void	serialize (Archive &archive, const unsigned int version)
Friends
class	boost::serialization::access

AbstractCellCentreBasedTissue< DIM > Class Template Reference

Public Member Functions

Private Member Functions

Friends

Detailed Description

template<unsigned DIM> class AbstractCellCentreBasedTissue< DIM >

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

template<unsigned DIM>
class AbstractCellCentreBasedTissue< DIM >