AbstractTissue< DIM > Class Template Reference

#include <AbstractTissue.hpp>

Inheritance diagram for AbstractTissue< DIM >:

Collaboration diagram for AbstractTissue< DIM >:

List of all members.

Public Member Functions

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

AbstractTissue ()

virtual ~AbstractTissue ()

void InitialiseCells ()

std::list< TissueCell > & rGetCells ()

bool HasMesh ()

virtual unsigned GetNumNodes ()=0

virtual c_vector< double, DIM > GetLocationOfCellCentre (TissueCell *pCell)=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 IsCellAssociatedWithADeletedNode (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, c_vector< double, DIM > newLocation, TissueCell *pParentCell=NULL)=0

virtual unsigned RemoveDeadCells ()=0

virtual void Update (bool hasHadBirthsOrDeaths=true)=0

c_vector< unsigned,
NUM_CELL_MUTATION_STATES > GetCellMutationStateCount ()

c_vector< unsigned,
NUM_CELL_TYPES > GetCellTypeCount ()

c_vector< unsigned, 5 > GetCellCyclePhaseCount ()

virtual bool IsGhostNode (unsigned index)

unsigned GetNumRealCells ()

void SetCellAncestorsToNodeIndices ()

void WriteCellIdDataToFile ()

std::set< unsigned > GetCellAncestors ()

TissueCell & rGetCellUsingLocationIndex (unsigned index)

unsigned GetLocationIndexUsingCell (TissueCell *pCell)

virtual void CreateOutputFiles (const std::string &rDirectory, bool cleanOutputDirectory)

virtual void WriteResultsToFiles ()

void WriteTimeAndNodeResultsToFiles (std::vector< unsigned > &rCellTypeCounter, std::vector< unsigned > &rCellMutationStateCounter, std::vector< unsigned > &rCellCyclePhaseCounter)

virtual void GenerateCellResultsAndWriteToFiles (std::vector< unsigned > &rCellTypeCounter, std::vector< unsigned > &rCellMutationStateCounter, std::vector< unsigned > &rCellCyclePhaseCounter)

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

void WriteCellResultsToFiles (std::vector< unsigned > &rCellTypeCounter, std::vector< unsigned > &rCellMutationStateCounter, std::vector< unsigned > &rCellCyclePhaseCounter)

virtual void CloseOutputFiles ()

Iterator Begin ()

Iterator End ()

Protected Member Functions

virtual void Validate ()=0

Protected Attributes

std::list< TissueCell > mCells

std::map< unsigned, TissueCell * > mLocationCellMap

std::map< TissueCell *, unsigned > mCellLocationMap

c_vector< unsigned,
NUM_CELL_MUTATION_STATES > mCellMutationStateCount

c_vector< unsigned,
NUM_CELL_TYPES > mCellTypeCount

c_vector< unsigned, 5 > mCellCyclePhaseCount

out_stream mpVizNodesFile

out_stream mpVizCellTypesFile

out_stream mpCellMutationStatesFile

out_stream mpCellAncestorsFile

out_stream mpCellTypesFile

out_stream mpCellCyclePhasesFile

out_stream mpCellVariablesFile

out_stream mpCellAgesFile

out_stream mpCellIdFile

bool mTissueContainsMesh

Private Member Functions

template<class Archive>

void serialize (Archive &archive, const unsigned int version)

Friends

class boost::serialization::access

Classes

class Iterator

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 50 of file AbstractTissue.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

AbstractTissue< DIM >::AbstractTissue	(	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 34 of file AbstractTissue.cpp.

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

template<unsigned DIM>

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

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

Definition at line 140 of file AbstractTissue.hpp.

template<unsigned DIM>

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

Base class with virtual methods needs a virtual destructor.

Definition at line 146 of file AbstractTissue.hpp.

Member Function Documentation

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< 2 >, and MeshBasedTissueWithGhostNodes< 2 >.

Definition at line 62 of file AbstractTissue.hpp.

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< 2 >, and MeshBasedTissueWithGhostNodes< 2 >.

template<unsigned DIM>

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

Initialise each cell's cell cycle model.

Definition at line 83 of file AbstractTissue.cpp.

References AbstractTissue< DIM >::mCells.

template<unsigned DIM>

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

Returns:: reference to mCells.

Definition at line 94 of file AbstractTissue.cpp.

References AbstractTissue< DIM >::mCells.

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

template<unsigned DIM>

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

Returns:: whether the tissue contains a mesh.

Definition at line 100 of file AbstractTissue.cpp.

References AbstractTissue< DIM >::mTissueContainsMesh.

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

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 >, and MeshBasedTissue< 2 >.

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

template<unsigned DIM>

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

Find where a given cell is in space.

Parameters:

pCell

pointer to 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>

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 >, and MeshBasedTissue< 2 >.

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

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 >, and MeshBasedTissue< 2 >.

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

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 >, and MeshBasedTissue< 2 >.

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

template<unsigned DIM>

virtual bool AbstractTissue< DIM >::IsCellAssociatedWithADeletedNode ( 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.

Implemented in AbstractCellCentreBasedTissue< DIM >.

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

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 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 >, and MeshBasedTissue< 2 >.

template<unsigned DIM>

virtual TissueCell* AbstractTissue< DIM >::AddCell	(	TissueCell &	rNewCell,
		c_vector< double, DIM >	newLocation,
		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
	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 (internal of this method uses a copy constructor along the way).

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

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 >, and MeshBasedTissue< 2 >.

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 >, and MeshBasedTissue< 2 >.

template<unsigned DIM>

c_vector< unsigned, NUM_CELL_MUTATION_STATES > 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 137 of file AbstractTissue.cpp.

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

template<unsigned DIM>

c_vector< unsigned, NUM_CELL_TYPES > AbstractTissue< DIM >::GetCellTypeCount ( ) [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 147 of file AbstractTissue.cpp.

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

template<unsigned DIM>

c_vector< unsigned, 5 > AbstractTissue< DIM >::GetCellCyclePhaseCount ( ) [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 157 of file AbstractTissue.cpp.

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

template<unsigned DIM>

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

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

Parameters:

index

the global index of a specified node

Returns:: whether the node is a ghost node

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

Definition at line 167 of file AbstractTissue.cpp.

Referenced by GeneralisedLinearSpringForce< DIM >::CalculateForceBetweenNodes(), and AbstractTissue< DIM >::GenerateCellResults().

template<unsigned DIM>

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

Get the number of real cells.

Definition at line 106 of file AbstractTissue.cpp.

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

template<unsigned DIM>

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

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

Definition at line 117 of file AbstractTissue.cpp.

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

template<unsigned DIM>

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

Write cell ID data to mpCellIdFile.

Definition at line 613 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>

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 126 of file AbstractTissue.cpp.

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

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 173 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>

unsigned AbstractTissue< DIM >::GetLocationIndexUsingCell ( TissueCell * pCell ) [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:

pCell

the cell

Returns:: the location index.

Definition at line 186 of file AbstractTissue.cpp.

References AbstractTissue< DIM >::mCellLocationMap.

Referenced by CryptSimulation2d::ApplyTissueBoundaryConditions(), CryptSimulation2d::CalculateDividingCellCentreLocations(), AbstractTissue< DIM >::GenerateCellResultsAndWriteToFiles(), MeshBasedTissue< DIM >::Validate(), and CryptSimulation2d::WriteBetaCatenin().

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 >, and MeshBasedTissue< 2 >.

Definition at line 198 of file AbstractTissue.cpp.

References TissueConfig::Instance(), AbstractTissue< DIM >::mpCellAgesFile, AbstractTissue< DIM >::mpCellAncestorsFile, AbstractTissue< DIM >::mpCellCyclePhasesFile, AbstractTissue< DIM >::mpCellIdFile, AbstractTissue< DIM >::mpCellMutationStatesFile, AbstractTissue< DIM >::mpCellTypesFile, AbstractTissue< DIM >::mpCellVariablesFile, AbstractTissue< DIM >::mpVizCellTypesFile, AbstractTissue< DIM >::mpVizNodesFile, and OutputFileHandler::OpenOutputFile().

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

template<unsigned DIM>

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

Write results from the current tissue state to output files.

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

Definition at line 593 of file AbstractTissue.cpp.

References AbstractTissue< DIM >::GenerateCellResultsAndWriteToFiles(), TissueConfig::Instance(), AbstractTissue< DIM >::WriteCellIdDataToFile(), and AbstractTissue< DIM >::WriteTimeAndNodeResultsToFiles().

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

template<unsigned DIM>

void AbstractTissue< DIM >::WriteTimeAndNodeResultsToFiles	(	std::vector< unsigned > &	rCellTypeCounter,
		std::vector< unsigned > &	rCellMutationStateCounter,
		std::vector< unsigned > &	rCellCyclePhaseCounter
	)			`[inline]`

Write the current time and node results to output files.

Parameters:

	rCellTypeCounter	cell type counter
	rCellMutationStateCounter	cell mutation state counter
	rCellCyclePhaseCounter	cell cycle phase counter

Todo:: Vertex meshes output nans here if the node does not exist.

Definition at line 510 of file AbstractTissue.cpp.

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

template<unsigned DIM>

void AbstractTissue< DIM >::GenerateCellResultsAndWriteToFiles	(	std::vector< unsigned > &	rCellTypeCounter,
		std::vector< unsigned > &	rCellMutationStateCounter,
		std::vector< unsigned > &	rCellCyclePhaseCounter
	)			`[inline, virtual]`

Call GenerateCellResults() on each cell then call WriteCellResultsToFiles().

Parameters:

	rCellTypeCounter	cell type counter
	rCellMutationStateCounter	cell mutation state counter
	rCellCyclePhaseCounter	cell cycle phase counter

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

Definition at line 433 of file AbstractTissue.cpp.

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

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

template<unsigned DIM>

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

Generate results for a given cell in the current tissue state to output files.

Parameters:

	locationIndex	location index of the cell
	rCellTypeCounter	cell type counter
	rCellMutationStateCounter	cell mutation state counter
	rCellCyclePhaseCounter	cell cycle phase counter

Definition at line 272 of file AbstractTissue.cpp.

References TissueCell::GetAge(), TissueCell::GetAncestor(), TissueCell::GetCellCycleModel(), TissueCell::GetCellType(), AbstractCellCycleModel::GetCurrentCellCyclePhase(), AbstractTissue< DIM >::GetLocationOfCellCentre(), TissueCell::GetMutationState(), TissueConfig::GetOutputCellAges(), TissueConfig::GetOutputCellAncestors(), TissueConfig::GetOutputCellMutationStates(), TissueConfig::GetOutputCellTypes(), TissueConfig::GetOutputCellVariables(), TissueCell::HasApoptosisBegun(), TissueConfig::Instance(), AbstractTissue< DIM >::IsGhostNode(), AbstractTissue< DIM >::mLocationCellMap, AbstractTissue< DIM >::mpCellAgesFile, AbstractTissue< DIM >::mpCellAncestorsFile, AbstractTissue< DIM >::mpCellVariablesFile, and AbstractTissue< DIM >::mpVizCellTypesFile.

Referenced by MeshBasedTissueWithGhostNodes< DIM >::GenerateCellResultsAndWriteToFiles(), and AbstractTissue< DIM >::GenerateCellResultsAndWriteToFiles().

template<unsigned DIM>

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

Write the current state of each cell to output files.

Parameters:

	rCellTypeCounter	cell type counter
	rCellMutationStateCounter	cell mutation state counter
	rCellCyclePhaseCounter	cell cycle phase counter

Definition at line 453 of file AbstractTissue.cpp.

References TissueConfig::Instance(), AbstractTissue< DIM >::mCellCyclePhaseCount, AbstractTissue< DIM >::mCellMutationStateCount, AbstractTissue< DIM >::mCellTypeCount, AbstractTissue< DIM >::mpCellAgesFile, AbstractTissue< DIM >::mpCellAncestorsFile, AbstractTissue< DIM >::mpCellCyclePhasesFile, AbstractTissue< DIM >::mpCellMutationStatesFile, AbstractTissue< DIM >::mpCellTypesFile, AbstractTissue< DIM >::mpCellVariablesFile, and AbstractTissue< DIM >::mpVizCellTypesFile.

Referenced by MeshBasedTissueWithGhostNodes< DIM >::GenerateCellResultsAndWriteToFiles(), and AbstractTissue< DIM >::GenerateCellResultsAndWriteToFiles().

template<unsigned DIM>

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

Close any output files.

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

Definition at line 236 of file AbstractTissue.cpp.

References TissueConfig::Instance(), AbstractTissue< DIM >::mpCellAgesFile, AbstractTissue< DIM >::mpCellAncestorsFile, AbstractTissue< DIM >::mpCellCyclePhasesFile, AbstractTissue< DIM >::mpCellIdFile, AbstractTissue< DIM >::mpCellMutationStatesFile, AbstractTissue< DIM >::mpCellTypesFile, AbstractTissue< DIM >::mpCellVariablesFile, AbstractTissue< DIM >::mpVizCellTypesFile, and AbstractTissue< DIM >::mpVizNodesFile.

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

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 >::GenerateCellResultsAndWriteToFiles(), AbstractTissue< DIM >::GetCellAncestors(), CryptStatistics::GetCryptSection(), AbstractTissue< DIM >::GetNumRealCells(), AbstractCryptStatistics::LabelAllCellsAsHealthy(), AbstractCryptStatistics::LabelSPhaseCells(), MeshBasedTissue< DIM >::SetBottomCellAncestors(), AbstractTissue< DIM >::SetCellAncestorsToNodeIndices(), SloughingCellKiller< DIM >::TestAndLabelCellsForApoptosisOrDeath(), RandomCellKiller< DIM >::TestAndLabelCellsForApoptosisOrDeath(), 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>

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 >::GenerateCellResultsAndWriteToFiles(), AbstractTissue< DIM >::GetCellAncestors(), CryptStatistics::GetCryptSection(), AbstractTissue< DIM >::GetNumRealCells(), AbstractCryptStatistics::LabelAllCellsAsHealthy(), AbstractCryptStatistics::LabelSPhaseCells(), MeshBasedTissue< DIM >::SetBottomCellAncestors(), AbstractTissue< DIM >::SetCellAncestorsToNodeIndices(), SloughingCellKiller< DIM >::TestAndLabelCellsForApoptosisOrDeath(), RandomCellKiller< DIM >::TestAndLabelCellsForApoptosisOrDeath(), 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().

Friends And Related Function Documentation

template<unsigned DIM>

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

Needed for serialization.

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

Definition at line 54 of file AbstractTissue.hpp.

Member Data Documentation

template<unsigned DIM>

std::list<TissueCell> AbstractTissue< DIM >::mCells [protected]

List of cells

Definition at line 73 of file AbstractTissue.hpp.

Referenced by AbstractTissue< DIM >::AbstractTissue(), AbstractCellCentreBasedTissue< DIM >::AddCell(), AbstractTissue< DIM >::Begin(), MeshBasedTissue< DIM >::CheckTissueCellPointers(), AbstractTissue< DIM >::End(), AbstractTissue< DIM >::InitialiseCells(), MeshBasedTissue< DIM >::MeshBasedTissue(), NodeBasedTissue< DIM >::RemoveDeadCells(), MeshBasedTissue< DIM >::RemoveDeadCells(), AbstractTissue< DIM >::rGetCells(), AbstractTissue< SPACE_DIM >::serialize(), and MeshBasedTissue< DIM >::Update().

template<unsigned DIM>

std::map<unsigned, TissueCell*> AbstractTissue< DIM >::mLocationCellMap [protected]

Map location (node or VertexElement) indices back to cells

Definition at line 76 of file AbstractTissue.hpp.

Referenced by AbstractTissue< DIM >::AbstractTissue(), AbstractCellCentreBasedTissue< DIM >::AddCell(), AbstractTissue< DIM >::GenerateCellResults(), MeshBasedTissue< DIM >::RemoveDeadCells(), AbstractTissue< DIM >::rGetCellUsingLocationIndex(), AbstractTissue< SPACE_DIM >::serialize(), NodeBasedTissue< DIM >::Update(), and MeshBasedTissue< DIM >::Update().

template<unsigned DIM>

std::map<TissueCell*, unsigned> AbstractTissue< DIM >::mCellLocationMap [protected]

Map cells to location (node or VertexElement) indices

Definition at line 79 of file AbstractTissue.hpp.

template<unsigned DIM>

c_vector<unsigned, NUM_CELL_MUTATION_STATES> AbstractTissue< DIM >::mCellMutationStateCount [protected]

Current cell mutation state counts

Definition at line 82 of file AbstractTissue.hpp.

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

template<unsigned DIM>

c_vector<unsigned, NUM_CELL_TYPES> AbstractTissue< DIM >::mCellTypeCount [protected]

Current cell type counts

Definition at line 85 of file AbstractTissue.hpp.

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

template<unsigned DIM>

c_vector<unsigned, 5> AbstractTissue< DIM >::mCellCyclePhaseCount [protected]

Current cell cycle phase counts

Definition at line 88 of file AbstractTissue.hpp.

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

template<unsigned DIM>

out_stream AbstractTissue< DIM >::mpVizNodesFile [protected]

Results file for node visualization

Definition at line 91 of file AbstractTissue.hpp.

Referenced by AbstractTissue< DIM >::CloseOutputFiles(), AbstractTissue< DIM >::CreateOutputFiles(), and AbstractTissue< DIM >::WriteTimeAndNodeResultsToFiles().

template<unsigned DIM>

out_stream AbstractTissue< DIM >::mpVizCellTypesFile [protected]

Results file for cell visualization

Definition at line 94 of file AbstractTissue.hpp.

Referenced by AbstractTissue< DIM >::CloseOutputFiles(), AbstractTissue< DIM >::CreateOutputFiles(), AbstractTissue< DIM >::GenerateCellResults(), AbstractTissue< DIM >::WriteCellResultsToFiles(), and AbstractTissue< DIM >::WriteTimeAndNodeResultsToFiles().

template<unsigned DIM>

out_stream AbstractTissue< DIM >::mpCellMutationStatesFile [protected]

Results file for cell mutation states

Definition at line 97 of file AbstractTissue.hpp.

Referenced by AbstractTissue< DIM >::CloseOutputFiles(), AbstractTissue< DIM >::CreateOutputFiles(), AbstractTissue< DIM >::WriteCellResultsToFiles(), and AbstractTissue< DIM >::WriteTimeAndNodeResultsToFiles().

template<unsigned DIM>

out_stream AbstractTissue< DIM >::mpCellAncestorsFile [protected]

Results file for cell ancestors

Definition at line 100 of file AbstractTissue.hpp.

Referenced by AbstractTissue< DIM >::CloseOutputFiles(), AbstractTissue< DIM >::CreateOutputFiles(), AbstractTissue< DIM >::GenerateCellResults(), AbstractTissue< DIM >::WriteCellResultsToFiles(), and AbstractTissue< DIM >::WriteTimeAndNodeResultsToFiles().

template<unsigned DIM>

out_stream AbstractTissue< DIM >::mpCellTypesFile [protected]

Results file for cell types

Definition at line 103 of file AbstractTissue.hpp.

Referenced by AbstractTissue< DIM >::CloseOutputFiles(), AbstractTissue< DIM >::CreateOutputFiles(), AbstractTissue< DIM >::WriteCellResultsToFiles(), and AbstractTissue< DIM >::WriteTimeAndNodeResultsToFiles().

template<unsigned DIM>

out_stream AbstractTissue< DIM >::mpCellCyclePhasesFile [protected]

Results file for cell cycle phases

Definition at line 106 of file AbstractTissue.hpp.

Referenced by AbstractTissue< DIM >::CloseOutputFiles(), AbstractTissue< DIM >::CreateOutputFiles(), AbstractTissue< DIM >::WriteCellResultsToFiles(), and AbstractTissue< DIM >::WriteTimeAndNodeResultsToFiles().

template<unsigned DIM>

out_stream AbstractTissue< DIM >::mpCellVariablesFile [protected]

Results file for cell variables

Definition at line 109 of file AbstractTissue.hpp.

Referenced by AbstractTissue< DIM >::CloseOutputFiles(), AbstractTissue< DIM >::CreateOutputFiles(), AbstractTissue< DIM >::GenerateCellResults(), AbstractTissue< DIM >::WriteCellResultsToFiles(), and AbstractTissue< DIM >::WriteTimeAndNodeResultsToFiles().

template<unsigned DIM>

out_stream AbstractTissue< DIM >::mpCellAgesFile [protected]

Results file for cell ages

Definition at line 112 of file AbstractTissue.hpp.

Referenced by AbstractTissue< DIM >::CloseOutputFiles(), AbstractTissue< DIM >::CreateOutputFiles(), AbstractTissue< DIM >::GenerateCellResults(), AbstractTissue< DIM >::WriteCellResultsToFiles(), and AbstractTissue< DIM >::WriteTimeAndNodeResultsToFiles().

template<unsigned DIM>

out_stream AbstractTissue< DIM >::mpCellIdFile [protected]

Results file for logged cell data.

Definition at line 115 of file AbstractTissue.hpp.

Referenced by AbstractTissue< DIM >::CloseOutputFiles(), AbstractTissue< DIM >::CreateOutputFiles(), and AbstractTissue< DIM >::WriteCellIdDataToFile().

template<unsigned DIM>

bool AbstractTissue< DIM >::mTissueContainsMesh [protected]

Whether the tissue contains a mesh

Definition at line 118 of file AbstractTissue.hpp.

Referenced by AbstractTissue< DIM >::HasMesh(), MeshBasedTissue< DIM >::MeshBasedTissue(), and AbstractTissue< SPACE_DIM >::serialize().

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

/tmp/release_1.1/cancer/src/tissue/AbstractTissue.hpp
/tmp/release_1.1/cancer/src/tissue/AbstractTissue.cpp


Public Member Functions
	AbstractTissue (const std::vector< TissueCell > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >())
	AbstractTissue ()
virtual	~AbstractTissue ()
void	InitialiseCells ()
std::list< TissueCell > &	rGetCells ()
bool	HasMesh ()
virtual unsigned	GetNumNodes ()=0
virtual c_vector< double, DIM >	GetLocationOfCellCentre (TissueCell *pCell)=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	IsCellAssociatedWithADeletedNode (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, c_vector< double, DIM > newLocation, TissueCell *pParentCell=NULL)=0
virtual unsigned	RemoveDeadCells ()=0
virtual void	Update (bool hasHadBirthsOrDeaths=true)=0
c_vector< unsigned, NUM_CELL_MUTATION_STATES >	GetCellMutationStateCount ()
c_vector< unsigned, NUM_CELL_TYPES >	GetCellTypeCount ()
c_vector< unsigned, 5 >	GetCellCyclePhaseCount ()
virtual bool	IsGhostNode (unsigned index)
unsigned	GetNumRealCells ()
void	SetCellAncestorsToNodeIndices ()
void	WriteCellIdDataToFile ()
std::set< unsigned >	GetCellAncestors ()
TissueCell &	rGetCellUsingLocationIndex (unsigned index)
unsigned	GetLocationIndexUsingCell (TissueCell *pCell)
virtual void	CreateOutputFiles (const std::string &rDirectory, bool cleanOutputDirectory)
virtual void	WriteResultsToFiles ()
void	WriteTimeAndNodeResultsToFiles (std::vector< unsigned > &rCellTypeCounter, std::vector< unsigned > &rCellMutationStateCounter, std::vector< unsigned > &rCellCyclePhaseCounter)
virtual void	GenerateCellResultsAndWriteToFiles (std::vector< unsigned > &rCellTypeCounter, std::vector< unsigned > &rCellMutationStateCounter, std::vector< unsigned > &rCellCyclePhaseCounter)
void	GenerateCellResults (unsigned locationIndex, std::vector< unsigned > &rCellTypeCounter, std::vector< unsigned > &rCellMutationStateCounter, std::vector< unsigned > &rCellCyclePhaseCounter)
void	WriteCellResultsToFiles (std::vector< unsigned > &rCellTypeCounter, std::vector< unsigned > &rCellMutationStateCounter, std::vector< unsigned > &rCellCyclePhaseCounter)
virtual void	CloseOutputFiles ()
Iterator	Begin ()
Iterator	End ()
Protected Member Functions
virtual void	Validate ()=0
Protected Attributes
std::list< TissueCell >	mCells
std::map< unsigned, TissueCell * >	mLocationCellMap
std::map< TissueCell *, unsigned >	mCellLocationMap
c_vector< unsigned, NUM_CELL_MUTATION_STATES >	mCellMutationStateCount
c_vector< unsigned, NUM_CELL_TYPES >	mCellTypeCount
c_vector< unsigned, 5 >	mCellCyclePhaseCount
out_stream	mpVizNodesFile
out_stream	mpVizCellTypesFile
out_stream	mpCellMutationStatesFile
out_stream	mpCellAncestorsFile
out_stream	mpCellTypesFile
out_stream	mpCellCyclePhasesFile
out_stream	mpCellVariablesFile
out_stream	mpCellAgesFile
out_stream	mpCellIdFile
bool	mTissueContainsMesh
Private Member Functions
template<class Archive>
void	serialize (Archive &archive, const unsigned int version)
Friends
class	boost::serialization::access
Classes
class	Iterator

AbstractTissue< DIM > Class Template Reference

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Friends

Classes

Detailed Description

template<unsigned DIM> class AbstractTissue< DIM >

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation

template<unsigned DIM>
class AbstractTissue< DIM >