AbstractTissue< DIM > Class Template Reference

#include <AbstractTissue.hpp>

Inherited by AbstractCellCentreBasedTissue< DIM >.

Collaboration diagram for AbstractTissue< DIM >:

Classes
class	Iterator
Public Member Functions
	AbstractTissue (std::vector< TissueCell > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >())
virtual	~AbstractTissue ()
void	InitialiseCells ()
std::list< TissueCell > &	rGetCells ()
bool	HasMesh ()
virtual unsigned	GetNumNodes ()=0
virtual c_vector< double, DIM >	GetLocationOfCellCentre (TissueCell &rCell)=0
virtual Node< DIM > *	GetNode (unsigned index)=0
virtual unsigned	AddNode (Node< DIM > *pNewNode)=0
virtual void	SetNode (unsigned nodeIndex, ChastePoint< DIM > &rNewLocation)=0
virtual bool	IsCellAssociatedWithADeletedLocation (TissueCell &rCell)=0
virtual void	UpdateNodeLocations (const std::vector< c_vector< double, DIM > > &rNodeForces, double dt)=0
virtual double	GetDampingConstant (unsigned nodeIndex)=0
virtual TissueCell *	AddCell (TissueCell &rNewCell, const c_vector< double, DIM > &rCellDivisionVector, TissueCell *pParentCell=NULL)=0
virtual unsigned	RemoveDeadCells ()=0
virtual void	Update (bool hasHadBirthsOrDeaths=true)=0
std::vector< unsigned >	GetCellMutationStateCount ()
const std::vector< unsigned > &	rGetCellProliferativeTypeCount () const
const std::vector< unsigned > &	rGetCellCyclePhaseCount () const
unsigned	GetNumRealCells ()
void	SetCellAncestorsToLocationIndices ()
void	WriteCellIdDataToFile ()
std::set< unsigned >	GetCellAncestors ()
TissueCell &	rGetCellUsingLocationIndex (unsigned index)
unsigned	GetLocationIndexUsingCell (TissueCell &rCell)
boost::shared_ptr < CellMutationStateRegistry >	GetMutationRegistry ()
void	SetDefaultMutationStateOrdering ()
virtual void	CreateOutputFiles (const std::string &rDirectory, bool cleanOutputDirectory)
virtual void	WriteResultsToFiles ()
void	WriteTimeAndNodeResultsToFiles ()
virtual void	GenerateCellResultsAndWriteToFiles ()=0
virtual void	GenerateCellResults (unsigned locationIndex, std::vector< unsigned > &rCellProliferativeTypeCounter, std::vector< unsigned > &rCellCyclePhaseCounter)
void	WriteCellResultsToFiles (std::vector< unsigned > &rCellProliferativeTypeCounter, std::vector< unsigned > &rCellCyclePhaseCounter)
virtual void	CloseOutputFiles ()
Iterator	Begin ()
Iterator	End ()
Protected Member Functions
virtual void	Validate ()=0
	AbstractTissue ()
Protected Attributes
std::list< TissueCell >	mCells
std::map< unsigned, TissueCell * >	mLocationCellMap
std::map< TissueCell *, unsigned >	mCellLocationMap
std::vector< unsigned >	mCellProliferativeTypeCount
std::vector< unsigned >	mCellCyclePhaseCount
out_stream	mpVizNodesFile
out_stream	mpVizCellProliferativeTypesFile
out_stream	mpCellMutationStatesFile
out_stream	mpCellAncestorsFile
out_stream	mpCellProliferativeTypesFile
out_stream	mpCellCyclePhasesFile
out_stream	mpCellVariablesFile
out_stream	mpCellAgesFile
out_stream	mpCellIdFile
out_stream	mpBoundaryNodesFile
bool	mTissueContainsMesh
boost::shared_ptr < CellMutationStateRegistry >	mpMutationStateRegistry
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 AbstractTissue< DIM >

An abstract facade class encapsulating a tissue.

Contains a group of cells and associated methods.

Definition at line 61 of file AbstractTissue.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

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

Constructor for use by archiving only. Please use the other constructor.

Doesn't take in cells, since these are dealt with by the serialize method.

Definition at line 149 of file AbstractTissue.hpp.

template<unsigned DIM>

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

AbstractTissue Constructor.

Note:: Warning: the passed-in vector of cells will be emptied, even if the constructor throws an exception!

Parameters:

	rCells	a vector of cells. Copies of the cells will be stored in the tissue, and the passed-in vector cleared.
	locationIndices	an optional vector of location indices that correspond to real cells

Todo:: remove explicit use of NUM_CELL_PROLIFERATIVE_TYPES and NUM_CELL_CYCLE_PHASES as these may eventually differ between simulations (see #1285)

Definition at line 33 of file AbstractTissue.cpp.

References AbstractTissue< DIM >::mCellCyclePhaseCount, AbstractTissue< DIM >::mCellLocationMap, AbstractTissue< DIM >::mCellProliferativeTypeCount, AbstractTissue< DIM >::mCells, and AbstractTissue< DIM >::mLocationCellMap.

template<unsigned DIM>

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

Base class with virtual methods needs a virtual destructor.

Definition at line 171 of file AbstractTissue.hpp.

Member Function Documentation

template<unsigned DIM>

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

Add a new cell to the tissue.

As this method is pure virtual, it must be overridden in subclasses.

Parameters:

	rNewCell	the cell to add
	rCellDivisionVector	a vector providing information regarding how the cell division should occur (for cell-centre tissues, this vector is the position of the daughter cell; for vertex tissues it can be used by any subclass of TissueSimulation to as a means of dictating the axis along which the parent cell divides)
	pParentCell	pointer to a parent cell (if required)

Returns:: address of cell as it appears in the cell list (internal of this method uses a copy constructor along the way).

Implemented in AbstractCellCentreBasedTissue< DIM >, MeshBasedTissue< DIM >, MeshBasedTissueWithGhostNodes< DIM >, MeshBasedTissue< 1 >, MeshBasedTissue< 2 >, and MeshBasedTissueWithGhostNodes< 2 >.

template<unsigned DIM>

virtual unsigned AbstractTissue< DIM >::AddNode ( Node< DIM > * pNewNode ) [pure virtual]

Add a new node to the tissue.

As this method is pure virtual, it must be overridden in subclasses.

Parameters:

pNewNode

pointer to the new node

Returns:: global index of new node in tissue.

Implemented in MeshBasedTissue< DIM >, NodeBasedTissue< DIM >, MeshBasedTissue< 1 >, and MeshBasedTissue< 2 >.

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

template<unsigned DIM>

AbstractTissue< DIM >::Iterator AbstractTissue< DIM >::Begin ( ) [inline]

Returns:: iterator pointing to the first cell in the tissue

Definition at line 625 of file AbstractTissue.hpp.

References AbstractTissue< DIM >::mCells.

Referenced by AbstractTissue< DIM >::GetCellAncestors(), CryptStatistics::GetCryptSection(), AbstractTissue< DIM >::GetNumRealCells(), AbstractCryptStatistics::LabelAllCellsAsHealthy(), AbstractCryptStatistics::LabelSPhaseCells(), CryptSimulation2d::SetBottomCellAncestors(), AbstractTissue< DIM >::SetCellAncestorsToLocationIndices(), RandomCellKiller< DIM >::TestAndLabelCellsForApoptosisOrDeath(), SloughingCellKiller< DIM >::TestAndLabelCellsForApoptosisOrDeath(), MeshBasedTissue< DIM >::Update(), AbstractCellCentreBasedTissue< DIM >::UpdateNodeLocations(), NodeBasedTissue< DIM >::Validate(), MeshBasedTissueWithGhostNodes< DIM >::Validate(), MeshBasedTissue< DIM >::Validate(), MeshBasedTissue< DIM >::WriteCellAreaResultsToFile(), AbstractTissue< DIM >::WriteCellIdDataToFile(), MeshBasedTissue< DIM >::WriteTissueAreaResultsToFile(), and MeshBasedTissue< DIM >::WriteVoronoiResultsToFile().

template<unsigned DIM>

void AbstractTissue< DIM >::CloseOutputFiles ( ) [inline, virtual]

Close any output files.

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

Definition at line 268 of file AbstractTissue.cpp.

References TissueConfig::GetOutputCellAges(), TissueConfig::GetOutputCellAncestors(), TissueConfig::GetOutputCellCyclePhases(), TissueConfig::GetOutputCellIdData(), TissueConfig::GetOutputCellMutationStates(), TissueConfig::GetOutputCellProliferativeTypes(), TissueConfig::GetOutputCellVariables(), TissueConfig::Instance(), AbstractTissue< DIM >::mpBoundaryNodesFile, AbstractTissue< DIM >::mpCellAgesFile, AbstractTissue< DIM >::mpCellAncestorsFile, AbstractTissue< DIM >::mpCellCyclePhasesFile, AbstractTissue< DIM >::mpCellIdFile, AbstractTissue< DIM >::mpCellMutationStatesFile, AbstractTissue< DIM >::mpCellProliferativeTypesFile, AbstractTissue< DIM >::mpCellVariablesFile, AbstractTissue< DIM >::mpVizCellProliferativeTypesFile, and AbstractTissue< DIM >::mpVizNodesFile.

template<unsigned DIM>

void AbstractTissue< DIM >::CreateOutputFiles	(	const std::string &	rDirectory,
		bool	cleanOutputDirectory
	)			`[inline, virtual]`

Use an output file handler to create output files for visualizer and post-processing.

Parameters:

	rDirectory	pathname of the output directory, relative to where Chaste output is stored
	cleanOutputDirectory	whether to delete the contents of the output directory prior to output file creation

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

Definition at line 226 of file AbstractTissue.cpp.

References TissueConfig::GetOutputCellAges(), TissueConfig::GetOutputCellAncestors(), TissueConfig::GetOutputCellCyclePhases(), TissueConfig::GetOutputCellIdData(), TissueConfig::GetOutputCellMutationStates(), TissueConfig::GetOutputCellProliferativeTypes(), TissueConfig::GetOutputCellVariables(), TissueConfig::Instance(), AbstractTissue< DIM >::mpBoundaryNodesFile, AbstractTissue< DIM >::mpCellAgesFile, AbstractTissue< DIM >::mpCellAncestorsFile, AbstractTissue< DIM >::mpCellCyclePhasesFile, AbstractTissue< DIM >::mpCellIdFile, AbstractTissue< DIM >::mpCellMutationStatesFile, AbstractTissue< DIM >::mpCellProliferativeTypesFile, AbstractTissue< DIM >::mpCellVariablesFile, AbstractTissue< DIM >::mpVizCellProliferativeTypesFile, AbstractTissue< DIM >::mpVizNodesFile, and OutputFileHandler::OpenOutputFile().

template<unsigned DIM>

AbstractTissue< DIM >::Iterator AbstractTissue< DIM >::End ( ) [inline]

Returns:: iterator pointing to one past the last cell in the tissue

Definition at line 631 of file AbstractTissue.hpp.

References AbstractTissue< DIM >::mCells.

Referenced by AbstractTissue< DIM >::GetCellAncestors(), CryptStatistics::GetCryptSection(), AbstractTissue< DIM >::GetNumRealCells(), AbstractCryptStatistics::LabelAllCellsAsHealthy(), AbstractCryptStatistics::LabelSPhaseCells(), CryptSimulation2d::SetBottomCellAncestors(), AbstractTissue< DIM >::SetCellAncestorsToLocationIndices(), RandomCellKiller< DIM >::TestAndLabelCellsForApoptosisOrDeath(), SloughingCellKiller< DIM >::TestAndLabelCellsForApoptosisOrDeath(), MeshBasedTissue< DIM >::Update(), AbstractCellCentreBasedTissue< DIM >::UpdateNodeLocations(), NodeBasedTissue< DIM >::Validate(), MeshBasedTissueWithGhostNodes< DIM >::Validate(), MeshBasedTissue< DIM >::Validate(), MeshBasedTissue< DIM >::WriteCellAreaResultsToFile(), AbstractTissue< DIM >::WriteCellIdDataToFile(), MeshBasedTissue< DIM >::WriteTissueAreaResultsToFile(), and MeshBasedTissue< DIM >::WriteVoronoiResultsToFile().

template<unsigned DIM>

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

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 in AbstractCellCentreBasedTissue< DIM >.

Definition at line 308 of file AbstractTissue.cpp.

References TissueCell::GetAge(), TissueCell::GetAncestor(), TissueCell::GetCellCycleModel(), TissueCell::GetCellProliferativeType(), AbstractCellCycleModel::GetCurrentCellCyclePhase(), AbstractTissue< DIM >::GetLocationOfCellCentre(), TissueCell::GetMutationState(), TissueConfig::GetOutputCellAges(), TissueConfig::GetOutputCellAncestors(), TissueConfig::GetOutputCellCyclePhases(), TissueConfig::GetOutputCellMutationStates(), TissueConfig::GetOutputCellProliferativeTypes(), TissueConfig::GetOutputCellVariables(), TissueCell::HasApoptosisBegun(), TissueConfig::Instance(), AbstractTissue< DIM >::mLocationCellMap, AbstractTissue< DIM >::mpCellAgesFile, AbstractTissue< DIM >::mpCellAncestorsFile, AbstractTissue< DIM >::mpCellVariablesFile, and AbstractTissue< DIM >::mpVizCellProliferativeTypesFile.

template<unsigned DIM>

virtual void AbstractTissue< DIM >::GenerateCellResultsAndWriteToFiles ( ) [pure virtual]

Calls GenerateCellResults() on each cell then calls WriteCellResultsToFiles().

Implemented in AbstractCellCentreBasedTissue< DIM >.

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

template<unsigned DIM>

std::set< unsigned > AbstractTissue< DIM >::GetCellAncestors ( ) [inline]

Loops over cells and makes a list of the ancestors that are part of the tissue.

Returns:: remaining_ancestors The size of this set tells you how many clonal populations remain.

Definition at line 123 of file AbstractTissue.cpp.

References AbstractTissue< DIM >::Begin(), and AbstractTissue< DIM >::End().

template<unsigned DIM>

std::vector< unsigned > AbstractTissue< DIM >::GetCellMutationStateCount ( ) [inline]

Find out how many cells of each mutation state there are

Returns:: The number of cells of each mutation state (evaluated at each visualizer output) [0] = healthy count [1] = labelled cells [2] = APC one hit [3] = APC two hit [4] = beta catenin one hit

Definition at line 134 of file AbstractTissue.cpp.

References AbstractTissue< DIM >::GetMutationRegistry(), TissueConfig::Instance(), and AbstractTissue< DIM >::SetDefaultMutationStateOrdering().

template<unsigned DIM>

virtual double AbstractTissue< DIM >::GetDampingConstant ( unsigned nodeIndex ) [pure virtual]

Get the damping constant for this node - ie d in drdt = F/d.

As this method is pure virtual, it must be overridden in subclasses.

Parameters:

nodeIndex

the global index of this node

Returns:: the damping constant at the node.

Implemented in AbstractCellCentreBasedTissue< DIM >, MeshBasedTissue< DIM >, MeshBasedTissue< 1 >, and MeshBasedTissue< 2 >.

template<unsigned DIM>

unsigned AbstractTissue< DIM >::GetLocationIndexUsingCell ( TissueCell & rCell ) [inline]

Get the location index corresponding to a given cell.

Currently assumes there is one cell for each location index, and they are ordered identically in their vectors. An assertion fails if not.

Parameters:

rCell

the cell

Returns:: the location index.

Definition at line 193 of file AbstractTissue.cpp.

References AbstractTissue< DIM >::mCellLocationMap.

Referenced by CryptSimulation2d::ApplyTissueBoundaryConditions(), CryptSimulation1d::ApplyTissueBoundaryConditions(), CryptSimulation2d::CalculateCellDivisionVector(), CryptSimulation1d::CalculateCellDivisionVector(), MeshBasedTissue< DIM >::Validate(), and CryptSimulation2d::WriteBetaCatenin().

template<unsigned DIM>

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

Find where a given cell is in space.

Parameters:

rCell

the cell

Returns:: the location of the cell

Implemented in AbstractCellCentreBasedTissue< DIM >.

Referenced by AbstractTissue< DIM >::GenerateCellResults(), SloughingCellKiller< DIM >::TestAndLabelCellsForApoptosisOrDeath(), and AbstractTissue< DIM >::WriteCellIdDataToFile().

template<unsigned DIM>

boost::shared_ptr< CellMutationStateRegistry > AbstractTissue< DIM >::GetMutationRegistry ( ) [inline]

Returns:: registry of mutation states used in this tissue.

Definition at line 199 of file AbstractTissue.cpp.

References AbstractTissue< DIM >::mpMutationStateRegistry.

Referenced by AbstractTissue< DIM >::GetCellMutationStateCount(), AbstractTissue< DIM >::SetDefaultMutationStateOrdering(), and AbstractTissue< DIM >::WriteCellResultsToFiles().

template<unsigned DIM>

virtual Node<DIM>* AbstractTissue< DIM >::GetNode ( unsigned index ) [pure virtual]

As this method is pure virtual, it must be overridden in subclasses.

Parameters:

index

global index of the specified node

Returns:: a pointer to the node with a given index.

Implemented in MeshBasedTissue< DIM >, NodeBasedTissue< DIM >, MeshBasedTissue< 1 >, and MeshBasedTissue< 2 >.

Referenced by GeneralisedLinearSpringForce< DIM >::CalculateForceBetweenNodes(), AbstractCellCentreBasedTissue< DIM >::GenerateCellResultsAndWriteToFiles(), AbstractCellCentreBasedTissue< DIM >::GetNodeCorrespondingToCell(), AbstractCellCentreBasedTissue< DIM >::UpdateNodeLocations(), and AbstractTissue< DIM >::WriteTimeAndNodeResultsToFiles().

template<unsigned DIM>

virtual unsigned AbstractTissue< DIM >::GetNumNodes ( ) [pure virtual]

As this method is pure virtual, it must be overridden in subclasses.

Returns:: the number of nodes in the tissue.

Implemented in MeshBasedTissue< DIM >, NodeBasedTissue< DIM >, MeshBasedTissue< 1 >, and MeshBasedTissue< 2 >.

Referenced by AbstractCellCentreBasedTissue< DIM >::AddCell(), AbstractCellCentreBasedTissue< DIM >::GenerateCellResultsAndWriteToFiles(), and AbstractTissue< DIM >::WriteTimeAndNodeResultsToFiles().

template<unsigned DIM>

unsigned AbstractTissue< DIM >::GetNumRealCells ( ) [inline]

Get the number of real cells.

Definition at line 103 of file AbstractTissue.cpp.

References AbstractTissue< DIM >::Begin(), and AbstractTissue< DIM >::End().

template<unsigned DIM>

bool AbstractTissue< DIM >::HasMesh ( ) [inline]

Todo:: This method returns true if the tissue is a MeshBasedTissue or a VertexBasedTissue, but is actually used to tell force laws whether the tissue is a MeshBasedTissue. See #1303.

Returns:: whether the tissue contains a mesh.

Definition at line 97 of file AbstractTissue.cpp.

References AbstractTissue< DIM >::mTissueContainsMesh.

Referenced by AbstractTwoBodyInteractionForce< DIM >::AddForceContribution(), GeneralisedLinearSpringForce< DIM >::CalculateForceBetweenNodes(), and LinearSpringWithVariableSpringConstantsForce< DIM >::VariableSpringConstantMultiplicationFactor().

template<unsigned DIM>

void AbstractTissue< DIM >::InitialiseCells ( ) [inline]

Initialise each cell's cell cycle model.

Definition at line 82 of file AbstractTissue.cpp.

References AbstractTissue< DIM >::mCells.

template<unsigned DIM>

virtual bool AbstractTissue< DIM >::IsCellAssociatedWithADeletedLocation ( TissueCell & rCell ) [pure virtual]

Helper method for establishing if a cell is real.

As this method is pure virtual, it must be overridden in subclasses.

Parameters:

rCell

the cell

Returns:: whether a given cell is associated with a deleted node (cell-centre models) or element (vertex models).

Implemented in AbstractCellCentreBasedTissue< DIM >.

Referenced by AbstractTissue< DIM >::Iterator::IsRealCell().

template<unsigned DIM>

virtual unsigned AbstractTissue< DIM >::RemoveDeadCells ( ) [pure virtual]

Remove all cells labelled as dead.

As this method is pure virtual, it must be overridden in subclasses.

Returns:: number of cells removed

Implemented in MeshBasedTissue< DIM >, NodeBasedTissue< DIM >, MeshBasedTissue< 1 >, and MeshBasedTissue< 2 >.

template<unsigned DIM>

const std::vector< unsigned > & AbstractTissue< DIM >::rGetCellCyclePhaseCount ( ) const [inline]

Find out how many cells in each cell cycle phase there are

Returns:: The number of cells of each phase (evaluated at each visualizer output) [0] = G_ZERO_PHASE [1] = G_ONE_PHASE [2] = S_PHASE [3] = G_TWO_PHASE [4] = M_PHASE

Definition at line 166 of file AbstractTissue.cpp.

References TissueConfig::Instance(), and AbstractTissue< DIM >::mCellCyclePhaseCount.

template<unsigned DIM>

const std::vector< unsigned > & AbstractTissue< DIM >::rGetCellProliferativeTypeCount ( ) const [inline]

Find out how many cells of each type there are

Returns:: The number of cells of each type (evaluated at each visualizer output) [0] = STEM [1] = TRANSIT [2] = DIFFERENTIATED [3] = APOPTOTIC

Definition at line 156 of file AbstractTissue.cpp.

References TissueConfig::Instance(), and AbstractTissue< DIM >::mCellProliferativeTypeCount.

template<unsigned DIM>

std::list< TissueCell > & AbstractTissue< DIM >::rGetCells ( ) [inline]

Returns:: reference to mCells.

Definition at line 91 of file AbstractTissue.cpp.

References AbstractTissue< DIM >::mCells.

Referenced by AbstractTissue< DIM >::Iterator::IsAtEnd(), and AbstractTissue< DIM >::Iterator::Iterator().

template<unsigned DIM>

TissueCell & AbstractTissue< DIM >::rGetCellUsingLocationIndex ( unsigned index ) [inline]

Get the cell corresponding to a given location index.

Currently assumes there is one cell for each location index, and they are ordered identically in their vectors. An assertion fails if not.

Parameters:

index

the location index

Returns:: the cell.

Definition at line 176 of file AbstractTissue.cpp.

References AbstractTissue< DIM >::mLocationCellMap.

Referenced by GeneralisedLinearSpringForce< DIM >::CalculateForceBetweenNodes(), MeshBasedTissue< DIM >::CheckTissueCellPointers(), AbstractCellCentreBasedTissue< DIM >::GetDampingConstant(), and LinearSpringWithVariableSpringConstantsForce< DIM >::VariableSpringConstantMultiplicationFactor().

template<unsigned DIM>

template<class Archive >

void AbstractTissue< 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 in AbstractCellCentreBasedTissue< DIM >, MeshBasedTissue< DIM >, MeshBasedTissueWithGhostNodes< DIM >, NodeBasedTissue< DIM >, MeshBasedTissue< 1 >, MeshBasedTissue< 2 >, and MeshBasedTissueWithGhostNodes< 2 >.

Definition at line 73 of file AbstractTissue.hpp.

template<unsigned DIM>

void AbstractTissue< DIM >::SetCellAncestorsToLocationIndices ( ) [inline]

Sets the Ancestor index of all the cells at this time to be the same as their location index, can be used to trace clonal populations.

Definition at line 114 of file AbstractTissue.cpp.

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

template<unsigned DIM>

void AbstractTissue< DIM >::SetDefaultMutationStateOrdering ( ) [inline]

Set a default ordering on mutation states, so that existing tests don't need to specify the old ordering explicitly.

Definition at line 205 of file AbstractTissue.cpp.

References AbstractTissue< DIM >::GetMutationRegistry().

Referenced by AbstractTissue< DIM >::GetCellMutationStateCount(), and AbstractTissue< DIM >::WriteCellResultsToFiles().

template<unsigned DIM>

virtual void AbstractTissue< DIM >::SetNode	(	unsigned	nodeIndex,
		ChastePoint< DIM > &	rNewLocation
	)			`[pure virtual]`

Move the node with a given index to a new point in space.

As this method is pure virtual, it must be overridden in subclasses.

Parameters:

	nodeIndex	the index of the node to be moved
	rNewLocation	the new target location of the node

Implemented in MeshBasedTissue< DIM >, NodeBasedTissue< DIM >, MeshBasedTissue< 1 >, and MeshBasedTissue< 2 >.

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

template<unsigned DIM>

virtual void AbstractTissue< DIM >::Update ( bool hasHadBirthsOrDeaths = true ) [pure virtual]

Remove the Nodes (for cell-centre) or VertexElements (for cell-vertex) which have been marked as deleted and update the correspondence with TissueCells.

Parameters:

hasHadBirthsOrDeaths

- a bool saying whether tissue has had Births Or Deaths

Implemented in MeshBasedTissue< DIM >, NodeBasedTissue< DIM >, MeshBasedTissue< 1 >, and MeshBasedTissue< 2 >.

template<unsigned DIM>

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

Update the location of each node in the tissue given a vector of forces on nodes and a time step over which to integrate the equations of motion.

As this method is pure virtual, it must be overridden in subclasses.

Parameters:

	rNodeForces	forces on nodes
	dt	time step

Implemented in AbstractCellCentreBasedTissue< DIM >, MeshBasedTissueWithGhostNodes< DIM >, and MeshBasedTissueWithGhostNodes< 2 >.

template<unsigned DIM>

virtual void AbstractTissue< DIM >::Validate ( ) [protected, pure virtual]

Check consistency of our internal data structures.

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

template<unsigned DIM>

void AbstractTissue< DIM >::WriteCellIdDataToFile ( ) [inline]

Write cell ID data to mpCellIdFile.

Definition at line 587 of file AbstractTissue.cpp.

References AbstractTissue< DIM >::Begin(), AbstractTissue< DIM >::End(), AbstractTissue< DIM >::GetLocationOfCellCentre(), SimulationTime::GetTime(), SimulationTime::Instance(), AbstractTissue< DIM >::mCellLocationMap, and AbstractTissue< DIM >::mpCellIdFile.

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

template<unsigned DIM>

void AbstractTissue< DIM >::WriteCellResultsToFiles	(	std::vector< unsigned > &	rCellProliferativeTypeCounter,
		std::vector< unsigned > &	rCellCyclePhaseCounter
	)			`[inline]`