AbstractCellPopulation< DIM > Class Template Reference

#include <AbstractCellPopulation.hpp>

Inheritance diagram for AbstractCellPopulation< DIM >:

Collaboration diagram for AbstractCellPopulation< DIM >:

List of all members.

Public Member Functions

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

virtual ~AbstractCellPopulation ()

void InitialiseCells ()

std::list< CellPtr > & rGetCells ()

bool IsMeshBasedCellPopulation ()

virtual unsigned GetNumNodes ()=0

virtual c_vector< double, DIM > GetLocationOfCellCentre (CellPtr 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 IsCellAssociatedWithADeletedLocation (CellPtr pCell)=0

virtual void UpdateNodeLocations (const std::vector< c_vector< double, DIM > > &rNodeForces, double dt)=0

virtual double GetDampingConstant (unsigned nodeIndex)=0

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

CellPtr GetCellUsingLocationIndex (unsigned index)

unsigned GetLocationIndexUsingCell (CellPtr pCell)

boost::shared_ptr
< CellPropertyRegistry > GetCellPropertyRegistry ()

void SetDefaultMutationStateOrdering ()

virtual double GetWidth (const unsigned &rDimension)=0

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

virtual void WriteResultsToFiles ()

virtual 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 ()

void OutputCellPopulationInfo (out_stream &rParamsFile)

virtual void OutputCellPopulationParameters (out_stream &rParamsFile)=0

double GetDampingConstantNormal ()

double GetDampingConstantMutant ()

bool GetOutputCellIdData ()

bool GetOutputCellMutationStates ()

bool GetOutputCellAncestors ()

bool GetOutputCellProliferativeTypes ()

bool GetOutputCellVariables ()

bool GetOutputCellCyclePhases ()

bool GetOutputCellAges ()

bool GetOutputCellVolumes ()

void SetDampingConstantNormal (double dampingConstantNormal)

void SetDampingConstantMutant (double dampingConstantMutant)

void SetOutputCellIdData (bool outputCellIdData)

void SetOutputCellMutationStates (bool outputCellMutationStates)

void SetOutputCellAncestors (bool outputCellAncestors)

void SetOutputCellProliferativeTypes (bool outputCellProliferativeTypes)

void SetOutputCellVariables (bool outputCellVariables)

void SetOutputCellCyclePhases (bool outputCellCyclePhases)

void SetOutputCellAges (bool outputCellAges)

virtual void SetOutputCellVolumes (bool outputCellVolumes)

Iterator Begin ()

Iterator End ()

Protected Member Functions

virtual void Validate ()=0

virtual void WriteVtkResultsToFile ()=0

AbstractCellPopulation ()

Protected Attributes

std::list< CellPtr > mCells

std::map< unsigned, CellPtr > mLocationCellMap

std::map< Cell *, unsigned > mCellLocationMap

std::vector< unsigned > mCellProliferativeTypeCount

std::vector< unsigned > mCellCyclePhaseCount

out_stream mpVizNodesFile

out_stream mpVizCellProliferativeTypesFile

out_stream mpCellMutationStatesFile

out_stream mpVizCellAncestorsFile

out_stream mpCellProliferativeTypesFile

out_stream mpCellCyclePhasesFile

out_stream mpCellVariablesFile

out_stream mpCellAgesFile

out_stream mpCellIdFile

out_stream mpVizBoundaryNodesFile

std::string mDirPath

out_stream mpVtkMetaFile

bool mCellPopulationContainsMesh

boost::shared_ptr
< CellPropertyRegistry > mpCellPropertyRegistry

double mDampingConstantNormal

double mDampingConstantMutant

bool mOutputCellIdData

bool mOutputCellMutationStates

bool mOutputCellAncestors

bool mOutputCellProliferativeTypes

bool mOutputCellVariables

bool mOutputCellCyclePhases

bool mOutputCellAges

bool mOutputCellVolumes

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 AbstractCellPopulation< DIM >

An abstract facade class encapsulating a cell population.

Contains a group of cells and associated methods.

Definition at line 65 of file AbstractCellPopulation.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

AbstractCellPopulation< DIM >::AbstractCellPopulation ( ) [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 215 of file AbstractCellPopulation.hpp.

template<unsigned DIM>

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

AbstractCellPopulation 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 cell population, and the passed-in vector cleared.
	locationIndices	an optional vector of location indices that correspond to real cells

Definition at line 34 of file AbstractCellPopulation.cpp.

References EXCEPTION, AbstractCellPopulation< DIM >::mCellCyclePhaseCount, AbstractCellPopulation< DIM >::mCellLocationMap, AbstractCellPopulation< DIM >::mCellProliferativeTypeCount, AbstractCellPopulation< DIM >::mCells, AbstractCellPopulation< DIM >::mLocationCellMap, and AbstractCellPopulation< DIM >::mpCellPropertyRegistry.

template<unsigned DIM>

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

Base class with virtual methods needs a virtual destructor.

Definition at line 101 of file AbstractCellPopulation.cpp.

Member Function Documentation

template<unsigned DIM>

template<class Archive>

void AbstractCellPopulation< 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 AbstractCentreBasedCellPopulation< DIM >, MeshBasedCellPopulation< DIM >, MeshBasedCellPopulationWithGhostNodes< DIM >, NodeBasedCellPopulation< DIM >, VertexBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, MeshBasedCellPopulation< 2 >, and MeshBasedCellPopulationWithGhostNodes< 2 >.

Definition at line 77 of file AbstractCellPopulation.hpp.

template<unsigned DIM>

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

Check consistency of our internal data structures.

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

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

template<unsigned DIM>

virtual void AbstractCellPopulation< DIM >::WriteVtkResultsToFile ( ) [protected, pure virtual]

Write the current results to mpVtkMetaFile.

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

Implemented in AbstractCentreBasedCellPopulation< DIM >, MeshBasedCellPopulation< DIM >, MeshBasedCellPopulationWithGhostNodes< DIM >, NodeBasedCellPopulation< DIM >, VertexBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, MeshBasedCellPopulation< 2 >, and MeshBasedCellPopulationWithGhostNodes< 2 >.

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

template<unsigned DIM>

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

Initialise each cell's cell-cycle model.

Definition at line 106 of file AbstractCellPopulation.cpp.

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

template<unsigned DIM>

std::list< CellPtr > & AbstractCellPopulation< DIM >::rGetCells ( ) [inline]

Returns:: reference to mCells.

Definition at line 115 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mCells.

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

template<unsigned DIM>

bool AbstractCellPopulation< DIM >::IsMeshBasedCellPopulation ( ) [inline]

Returns:: whether the cell population is a MeshBasedCellPopulation.

Definition at line 121 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mCellPopulationContainsMesh.

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

template<unsigned DIM>

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

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

Returns:: the number of nodes in the cell population.

Implemented in MeshBasedCellPopulation< DIM >, NodeBasedCellPopulation< DIM >, VertexBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, and MeshBasedCellPopulation< 2 >.

Referenced by AbstractCentreBasedCellPopulation< DIM >::AddCell(), AbstractCentreBasedCellPopulation< DIM >::GenerateCellResultsAndWriteToFiles(), AbstractCentreBasedCellPopulation< DIM >::WriteTimeAndNodeResultsToFiles(), and AbstractCellPopulation< DIM >::WriteTimeAndNodeResultsToFiles().

template<unsigned DIM>

virtual c_vector<double, DIM> AbstractCellPopulation< DIM >::GetLocationOfCellCentre ( CellPtr pCell ) [pure virtual]

Find where a given cell is in space.

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

Parameters:

pCell

the cell

Returns:: the location of the cell

Implemented in AbstractCentreBasedCellPopulation< DIM >, and VertexBasedCellPopulation< DIM >.

Referenced by AbstractCellPopulation< DIM >::GenerateCellResults(), SloughingCellKiller< DIM >::TestAndLabelCellsForApoptosisOrDeath(), RadialSloughingCellKiller::TestAndLabelCellsForApoptosisOrDeath(), PlaneBasedCellKiller< DIM >::TestAndLabelCellsForApoptosisOrDeath(), CryptProjectionForce::UpdateNode3dLocationMap(), and AbstractCellPopulation< DIM >::WriteCellIdDataToFile().

template<unsigned DIM>

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

Get a pointer to the node with a given index.

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 MeshBasedCellPopulation< DIM >, NodeBasedCellPopulation< DIM >, VertexBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, and MeshBasedCellPopulation< 2 >.

Referenced by CryptProjectionForce::CalculateForceBetweenNodes(), GeneralisedLinearSpringForce< DIM >::CalculateForceBetweenNodes(), AbstractCentreBasedCellPopulation< DIM >::GenerateCellResultsAndWriteToFiles(), AbstractCentreBasedCellPopulation< DIM >::GetNodeCorrespondingToCell(), AbstractCentreBasedCellPopulation< DIM >::UpdateNodeLocations(), AbstractCentreBasedCellPopulation< DIM >::WriteTimeAndNodeResultsToFiles(), and AbstractCellPopulation< DIM >::WriteTimeAndNodeResultsToFiles().

template<unsigned DIM>

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

Add a new node to the cell population.

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 cell population.

Implemented in MeshBasedCellPopulation< DIM >, NodeBasedCellPopulation< DIM >, VertexBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, and MeshBasedCellPopulation< 2 >.

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

template<unsigned DIM>

virtual void AbstractCellPopulation< 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 MeshBasedCellPopulation< DIM >, NodeBasedCellPopulation< DIM >, VertexBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, and MeshBasedCellPopulation< 2 >.

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

template<unsigned DIM>

virtual bool AbstractCellPopulation< DIM >::IsCellAssociatedWithADeletedLocation ( CellPtr pCell ) [pure virtual]

Helper method for establishing if a cell is real.

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

Parameters:

pCell

the cell

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

Implemented in AbstractCentreBasedCellPopulation< DIM >, and VertexBasedCellPopulation< DIM >.

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

template<unsigned DIM>

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

Update the location of each node in the cell population 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 AbstractCentreBasedCellPopulation< DIM >, MeshBasedCellPopulationWithGhostNodes< DIM >, VertexBasedCellPopulation< DIM >, and MeshBasedCellPopulationWithGhostNodes< 2 >.

template<unsigned DIM>

virtual double AbstractCellPopulation< 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 AbstractCentreBasedCellPopulation< DIM >, MeshBasedCellPopulation< DIM >, VertexBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, and MeshBasedCellPopulation< 2 >.

template<unsigned DIM>

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

Add a new cell to the cell population.

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

Parameters:

	pNewCell	the cell to add
	rCellDivisionVector	a vector providing information regarding how the cell division should occur (for cell-centre cell populations, this vector is the position of the daughter cell; for vertex cell populations it can be used by any subclass of CellBasedSimulation 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 AbstractCentreBasedCellPopulation< DIM >, MeshBasedCellPopulation< DIM >, MeshBasedCellPopulationWithGhostNodes< DIM >, VertexBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, MeshBasedCellPopulation< 2 >, and MeshBasedCellPopulationWithGhostNodes< 2 >.

template<unsigned DIM>

virtual unsigned AbstractCellPopulation< 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 MeshBasedCellPopulation< DIM >, NodeBasedCellPopulation< DIM >, VertexBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, and MeshBasedCellPopulation< 2 >.

template<unsigned DIM>

virtual void AbstractCellPopulation< 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 Cells.

Parameters:

hasHadBirthsOrDeaths

- a bool saying whether cell population has had Births Or Deaths

Implemented in MeshBasedCellPopulation< DIM >, NodeBasedCellPopulation< DIM >, VertexBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, and MeshBasedCellPopulation< 2 >.

template<unsigned DIM>

std::vector< unsigned > AbstractCellPopulation< 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] = APC one hit [2] = APC two hit [3] = beta catenin one hit

Definition at line 158 of file AbstractCellPopulation.cpp.

References EXCEPTION, AbstractCellPopulation< DIM >::mOutputCellMutationStates, AbstractCellPopulation< DIM >::mpCellPropertyRegistry, and AbstractCellPopulation< DIM >::SetDefaultMutationStateOrdering().

Referenced by AbstractCellPopulation< DIM >::WriteCellResultsToFiles().

template<unsigned DIM>

const std::vector< unsigned > & AbstractCellPopulation< 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

Definition at line 184 of file AbstractCellPopulation.cpp.

References EXCEPTION, AbstractCellPopulation< DIM >::mCellProliferativeTypeCount, and AbstractCellPopulation< DIM >::mOutputCellProliferativeTypes.

template<unsigned DIM>

const std::vector< unsigned > & AbstractCellPopulation< 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 194 of file AbstractCellPopulation.cpp.

References EXCEPTION, AbstractCellPopulation< DIM >::mCellCyclePhaseCount, and AbstractCellPopulation< DIM >::mOutputCellCyclePhases.

template<unsigned DIM>

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

Get the number of real cells.

Definition at line 127 of file AbstractCellPopulation.cpp.

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

Referenced by TargetedCellKiller< DIM >::TestAndLabelCellsForApoptosisOrDeath().

template<unsigned DIM>

void AbstractCellPopulation< 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 138 of file AbstractCellPopulation.cpp.

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

template<unsigned DIM>

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

Write cell ID data to mpCellIdFile.

Definition at line 618 of file AbstractCellPopulation.cpp.

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

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

template<unsigned DIM>

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

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

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

Definition at line 147 of file AbstractCellPopulation.cpp.

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

template<unsigned DIM>

CellPtr AbstractCellPopulation< DIM >::GetCellUsingLocationIndex ( 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 204 of file AbstractCellPopulation.cpp.

References EXCEPTION, and AbstractCellPopulation< DIM >::mLocationCellMap.

Referenced by NagaiHondaForce< DIM >::AddForceContribution(), CryptProjectionForce::CalculateForceBetweenNodes(), GeneralisedLinearSpringForce< DIM >::CalculateForceBetweenNodes(), MeshBasedCellPopulation< DIM >::CheckCellPointers(), VertexBasedCellPopulation< DIM >::GetDampingConstant(), AbstractCentreBasedCellPopulation< DIM >::GetDampingConstant(), CellwiseDataGradient< DIM >::SetupGradients(), TargetedCellKiller< DIM >::TestAndLabelCellsForApoptosisOrDeath(), and LinearSpringWithVariableSpringConstantsForce< DIM >::VariableSpringConstantMultiplicationFactor().

template<unsigned DIM>

unsigned AbstractCellPopulation< DIM >::GetLocationIndexUsingCell ( CellPtr 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 221 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mCellLocationMap.

Referenced by CryptProjectionForce::AddForceContribution(), ChemotacticForce< DIM >::AddForceContribution(), CryptSimulation1d::ApplyCellPopulationBoundaryConditions(), CryptSimulation1d::CalculateCellDivisionVector(), VertexBasedCellPopulation< DIM >::GenerateCellResultsAndWriteToFiles(), CellwiseDataGradient< DIM >::SetupGradients(), CryptProjectionForce::UpdateNode3dLocationMap(), VertexBasedCellPopulation< DIM >::Validate(), MeshBasedCellPopulation< DIM >::Validate(), VertexBasedCellPopulation< DIM >::WriteCellVolumeResultsToFile(), VertexBasedCellPopulation< DIM >::WriteResultsToFiles(), NodeBasedCellPopulation< DIM >::WriteVtkResultsToFile(), and MeshBasedCellPopulation< DIM >::WriteVtkResultsToFile().

template<unsigned DIM>

boost::shared_ptr< CellPropertyRegistry > AbstractCellPopulation< DIM >::GetCellPropertyRegistry ( ) [inline]

Returns:: registry of cell properties used in this cell population.

Definition at line 227 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mpCellPropertyRegistry.

Referenced by AbstractCellPopulation< DIM >::SetDefaultMutationStateOrdering().

template<unsigned DIM>

void AbstractCellPopulation< 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 233 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::GetCellPropertyRegistry().

Referenced by AbstractCellPopulation< DIM >::CreateOutputFiles(), and AbstractCellPopulation< DIM >::GetCellMutationStateCount().

template<unsigned DIM>

virtual double AbstractCellPopulation< DIM >::GetWidth ( const unsigned & rDimension ) [pure virtual]

Calculate the 'width' of any dimension of the cell population.

This method is overridden in some daughter classes.

Parameters:

rDimension

a dimension (0,1 or 2)

Returns:: The maximum distance between any nodes in this dimension.

Implemented in MeshBasedCellPopulation< DIM >, NodeBasedCellPopulation< DIM >, VertexBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, and MeshBasedCellPopulation< 2 >.

template<unsigned DIM>

void AbstractCellPopulation< 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 MeshBasedCellPopulation< DIM >, VertexBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, and MeshBasedCellPopulation< 2 >.

Definition at line 253 of file AbstractCellPopulation.cpp.

Referenced by VertexBasedCellPopulation< DIM >::CreateOutputFiles(), and MeshBasedCellPopulation< DIM >::CreateOutputFiles().

template<unsigned DIM>

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

Write results from the current cell population state to output files.

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

Definition at line 573 of file AbstractCellPopulation.cpp.

Referenced by VertexBasedCellPopulation< DIM >::WriteResultsToFiles(), and MeshBasedCellPopulation< DIM >::WriteResultsToFiles().

template<unsigned DIM>

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

Write the current time and node results to output files.

Reimplemented in AbstractCentreBasedCellPopulation< DIM >.

Definition at line 547 of file AbstractCellPopulation.cpp.

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

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

template<unsigned DIM>

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

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

Implemented in AbstractCentreBasedCellPopulation< DIM >, and VertexBasedCellPopulation< DIM >.

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

template<unsigned DIM>

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

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 in AbstractCentreBasedCellPopulation< DIM >.

Definition at line 359 of file AbstractCellPopulation.cpp.

Referenced by AbstractCentreBasedCellPopulation< DIM >::GenerateCellResults(), and VertexBasedCellPopulation< DIM >::GenerateCellResultsAndWriteToFiles().

template<unsigned DIM>

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

Write the current state of each cell to output files.

Parameters:

	rCellProliferativeTypeCounter	cell type counter
	rCellCyclePhaseCounter	cell cycle phase counter

Definition at line 490 of file AbstractCellPopulation.cpp.

Referenced by VertexBasedCellPopulation< DIM >::GenerateCellResultsAndWriteToFiles(), and AbstractCentreBasedCellPopulation< DIM >::GenerateCellResultsAndWriteToFiles().

template<unsigned DIM>

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

Close any output files.

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

Definition at line 317 of file AbstractCellPopulation.cpp.

Referenced by VertexBasedCellPopulation< DIM >::CloseOutputFiles(), and MeshBasedCellPopulation< DIM >::CloseOutputFiles().

template<unsigned DIM>

void AbstractCellPopulation< DIM >::OutputCellPopulationInfo ( out_stream & rParamsFile ) [inline]

Outputs CellPopulation used in the simulation to file and then calls OutputCellPopulationParameters to output all relevant parameters.

Parameters:

rParamsFile

the file stream to which the parameters are output

Definition at line 641 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::Begin(), AbstractCellPopulation< DIM >::End(), Identifiable::GetIdentifier(), and AbstractCellPopulation< DIM >::OutputCellPopulationParameters().

template<unsigned DIM>

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

Outputs CellPopulation parameters to file

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

Parameters:

rParamsFile

the file stream to which the parameters are output

Implemented in AbstractCentreBasedCellPopulation< DIM >, MeshBasedCellPopulation< DIM >, MeshBasedCellPopulationWithGhostNodes< DIM >, NodeBasedCellPopulation< DIM >, VertexBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, MeshBasedCellPopulation< 2 >, and MeshBasedCellPopulationWithGhostNodes< 2 >.

Definition at line 682 of file AbstractCellPopulation.cpp.

Referenced by AbstractCellPopulation< DIM >::OutputCellPopulationInfo(), VertexBasedCellPopulation< DIM >::OutputCellPopulationParameters(), and AbstractCentreBasedCellPopulation< DIM >::OutputCellPopulationParameters().

template<unsigned DIM>

double AbstractCellPopulation< DIM >::GetDampingConstantNormal ( ) [inline]

Returns:: mDampingConstantNormal

Definition at line 701 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mDampingConstantNormal.

Referenced by VertexBasedCellPopulation< DIM >::GetDampingConstant(), AbstractCentreBasedCellPopulation< DIM >::GetDampingConstant(), and MeshBasedCellPopulationWithGhostNodes< DIM >::UpdateGhostPositions().

template<unsigned DIM>

double AbstractCellPopulation< DIM >::GetDampingConstantMutant ( ) [inline]

Returns:: mDampingConstantMutant

Definition at line 707 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mDampingConstantMutant.

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

template<unsigned DIM>

bool AbstractCellPopulation< DIM >::GetOutputCellIdData ( ) [inline]

Returns:: mOutputCellIdData

Definition at line 713 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mOutputCellIdData.

template<unsigned DIM>

bool AbstractCellPopulation< DIM >::GetOutputCellMutationStates ( ) [inline]

Returns:: mOutputCellMutationStates

Definition at line 719 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mOutputCellMutationStates.

template<unsigned DIM>

bool AbstractCellPopulation< DIM >::GetOutputCellAncestors ( ) [inline]

Returns:: mOutputCellAncestors

Definition at line 725 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mOutputCellAncestors.

template<unsigned DIM>

bool AbstractCellPopulation< DIM >::GetOutputCellProliferativeTypes ( ) [inline]

Returns:: mOutputCellProliferativeTypes

Definition at line 731 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mOutputCellProliferativeTypes.

template<unsigned DIM>

bool AbstractCellPopulation< DIM >::GetOutputCellVariables ( ) [inline]

Returns:: mOutputCellVariables

Definition at line 737 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mOutputCellVariables.

template<unsigned DIM>

bool AbstractCellPopulation< DIM >::GetOutputCellCyclePhases ( ) [inline]

Returns:: mOutputCellCyclePhases

Definition at line 743 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mOutputCellCyclePhases.

template<unsigned DIM>

bool AbstractCellPopulation< DIM >::GetOutputCellAges ( ) [inline]

Returns:: mOutputCellAges

Definition at line 749 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mOutputCellAges.

template<unsigned DIM>

bool AbstractCellPopulation< DIM >::GetOutputCellVolumes ( ) [inline]

Returns:: mOutputCellVolumes

Definition at line 755 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mOutputCellVolumes.

template<unsigned DIM>

void AbstractCellPopulation< DIM >::SetDampingConstantNormal ( double dampingConstantNormal ) [inline]

Set mDampingConstantNormal.

Parameters:

dampingConstantNormal

the new value of mDampingConstantNormal

Definition at line 765 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mDampingConstantNormal.

template<unsigned DIM>

void AbstractCellPopulation< DIM >::SetDampingConstantMutant ( double dampingConstantMutant ) [inline]

Set mDampingConstantMutant.

Parameters:

dampingConstantMutant

the new value of mDampingConstantMutant

Definition at line 772 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mDampingConstantMutant.

template<unsigned DIM>

void AbstractCellPopulation< DIM >::SetOutputCellIdData ( bool outputCellIdData ) [inline]

Set mOutputCellIdData.

Parameters:

outputCellIdData

the new value of mOutputCellIdData

Definition at line 779 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mOutputCellIdData.

template<unsigned DIM>

void AbstractCellPopulation< DIM >::SetOutputCellMutationStates ( bool outputCellMutationStates ) [inline]

Set mOutputCellMutationStates.

Parameters:

outputCellMutationStates

the new value of mOutputCellMutationStates

Definition at line 785 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mOutputCellMutationStates.

template<unsigned DIM>

void AbstractCellPopulation< DIM >::SetOutputCellAncestors ( bool outputCellAncestors ) [inline]

Set mOutputCellAncestors.

Parameters:

outputCellAncestors

the new value of mOutputCellAncestors

Definition at line 791 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mOutputCellAncestors.

template<unsigned DIM>

void AbstractCellPopulation< DIM >::SetOutputCellProliferativeTypes ( bool outputCellProliferativeTypes ) [inline]

Set mOutputCellProliferativeTypes.

Parameters:

outputCellProliferativeTypes

the new value of mOutputCellProliferativeTypes

Definition at line 797 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mOutputCellProliferativeTypes.

template<unsigned DIM>

void AbstractCellPopulation< DIM >::SetOutputCellVariables ( bool outputCellVariables ) [inline]

Set mOutputCellVariables.

Parameters:

outputCellVariables

the new value of mOutputCellVariables

Definition at line 803 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mOutputCellVariables.

template<unsigned DIM>

void AbstractCellPopulation< DIM >::SetOutputCellCyclePhases ( bool outputCellCyclePhases ) [inline]

Set mOutputCellCyclePhases.

Parameters:

outputCellCyclePhases

the new value of mOutputCellCyclePhases

Definition at line 809 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mOutputCellCyclePhases.

template<unsigned DIM>

void AbstractCellPopulation< DIM >::SetOutputCellAges ( bool outputCellAges ) [inline]

Set mOutputCellAges.

Parameters:

outputCellAges

the new value of mOutputCellAges

Definition at line 815 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mOutputCellAges.

template<unsigned DIM>

void AbstractCellPopulation< DIM >::SetOutputCellVolumes ( bool outputCellVolumes ) [inline, virtual]

Set mOutputCellVolumes.

Parameters:

outputCellVolumes

the new value of mOutputCellVolumes

Reimplemented in NodeBasedCellPopulation< DIM >.

Definition at line 821 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mOutputCellVolumes.

template<unsigned DIM>

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

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

Definition at line 830 of file AbstractCellPopulation.hpp.

References AbstractCellPopulation< DIM >::mCells.

template<unsigned DIM>

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

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

Definition at line 836 of file AbstractCellPopulation.hpp.

References AbstractCellPopulation< DIM >::mCells.

Friends And Related Function Documentation

template<unsigned DIM>

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

Needed for serialization.

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

Definition at line 69 of file AbstractCellPopulation.hpp.

Member Data Documentation

template<unsigned DIM>

std::list<CellPtr> AbstractCellPopulation< DIM >::mCells [protected]

List of cells

Definition at line 101 of file AbstractCellPopulation.hpp.

template<unsigned DIM>

std::map<unsigned, CellPtr> AbstractCellPopulation< DIM >::mLocationCellMap [protected]

Map location (node or VertexElement) indices back to cells

Definition at line 104 of file AbstractCellPopulation.hpp.

template<unsigned DIM>

std::map<Cell*, unsigned> AbstractCellPopulation< DIM >::mCellLocationMap [protected]

Map cells to location (node or VertexElement) indices

Definition at line 107 of file AbstractCellPopulation.hpp.

template<unsigned DIM>

std::vector<unsigned> AbstractCellPopulation< DIM >::mCellProliferativeTypeCount [protected]

Current cell type counts

Definition at line 110 of file AbstractCellPopulation.hpp.

Referenced by AbstractCellPopulation< DIM >::AbstractCellPopulation(), VertexBasedCellPopulation< DIM >::GenerateCellResultsAndWriteToFiles(), AbstractCentreBasedCellPopulation< DIM >::GenerateCellResultsAndWriteToFiles(), AbstractCellPopulation< DIM >::rGetCellProliferativeTypeCount(), AbstractCellPopulation< SPACE_DIM >::serialize(), and AbstractCellPopulation< DIM >::WriteCellResultsToFiles().

template<unsigned DIM>

std::vector<unsigned> AbstractCellPopulation< DIM >::mCellCyclePhaseCount [protected]

Current cell cycle phase counts

Definition at line 113 of file AbstractCellPopulation.hpp.

Referenced by AbstractCellPopulation< DIM >::AbstractCellPopulation(), VertexBasedCellPopulation< DIM >::GenerateCellResultsAndWriteToFiles(), AbstractCentreBasedCellPopulation< DIM >::GenerateCellResultsAndWriteToFiles(), AbstractCellPopulation< DIM >::rGetCellCyclePhaseCount(), AbstractCellPopulation< SPACE_DIM >::serialize(), and AbstractCellPopulation< DIM >::WriteCellResultsToFiles().

template<unsigned DIM>

out_stream AbstractCellPopulation< DIM >::mpVizNodesFile [protected]

Results file for node visualization

Definition at line 116 of file AbstractCellPopulation.hpp.

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

template<unsigned DIM>

out_stream AbstractCellPopulation< DIM >::mpVizCellProliferativeTypesFile [protected]

Results file for cell visualization

Definition at line 119 of file AbstractCellPopulation.hpp.

Referenced by AbstractCellPopulation< DIM >::CloseOutputFiles(), AbstractCellPopulation< DIM >::CreateOutputFiles(), AbstractCentreBasedCellPopulation< DIM >::GenerateCellResults(), AbstractCellPopulation< DIM >::GenerateCellResults(), AbstractCellPopulation< DIM >::WriteCellResultsToFiles(), and AbstractCellPopulation< DIM >::WriteResultsToFiles().

template<unsigned DIM>

out_stream AbstractCellPopulation< DIM >::mpCellMutationStatesFile [protected]

Results file for cell mutation states

Definition at line 122 of file AbstractCellPopulation.hpp.

Referenced by AbstractCellPopulation< DIM >::CloseOutputFiles(), AbstractCellPopulation< DIM >::CreateOutputFiles(), AbstractCellPopulation< DIM >::WriteCellResultsToFiles(), and AbstractCellPopulation< DIM >::WriteResultsToFiles().

template<unsigned DIM>

out_stream AbstractCellPopulation< DIM >::mpVizCellAncestorsFile [protected]

Results file for cell ancestors

Definition at line 125 of file AbstractCellPopulation.hpp.

Referenced by AbstractCellPopulation< DIM >::CloseOutputFiles(), AbstractCellPopulation< DIM >::CreateOutputFiles(), AbstractCellPopulation< DIM >::GenerateCellResults(), AbstractCellPopulation< DIM >::WriteCellResultsToFiles(), and AbstractCellPopulation< DIM >::WriteResultsToFiles().

template<unsigned DIM>

out_stream AbstractCellPopulation< DIM >::mpCellProliferativeTypesFile [protected]

Results file for cell types

Definition at line 128 of file AbstractCellPopulation.hpp.

Referenced by AbstractCellPopulation< DIM >::CloseOutputFiles(), AbstractCellPopulation< DIM >::CreateOutputFiles(), AbstractCellPopulation< DIM >::WriteCellResultsToFiles(), and AbstractCellPopulation< DIM >::WriteResultsToFiles().

template<unsigned DIM>

out_stream AbstractCellPopulation< DIM >::mpCellCyclePhasesFile [protected]

Results file for cell cycle phases

Definition at line 131 of file AbstractCellPopulation.hpp.

Referenced by AbstractCellPopulation< DIM >::CloseOutputFiles(), AbstractCellPopulation< DIM >::CreateOutputFiles(), AbstractCellPopulation< DIM >::WriteCellResultsToFiles(), and AbstractCellPopulation< DIM >::WriteResultsToFiles().

template<unsigned DIM>

out_stream AbstractCellPopulation< DIM >::mpCellVariablesFile [protected]

Results file for cell variables

Definition at line 134 of file AbstractCellPopulation.hpp.

Referenced by AbstractCellPopulation< DIM >::CloseOutputFiles(), AbstractCellPopulation< DIM >::CreateOutputFiles(), AbstractCellPopulation< DIM >::GenerateCellResults(), AbstractCellPopulation< DIM >::WriteCellResultsToFiles(), and AbstractCellPopulation< DIM >::WriteResultsToFiles().

template<unsigned DIM>

out_stream AbstractCellPopulation< DIM >::mpCellAgesFile [protected]

Results file for cell ages

Definition at line 137 of file AbstractCellPopulation.hpp.

Referenced by AbstractCellPopulation< DIM >::CloseOutputFiles(), AbstractCellPopulation< DIM >::CreateOutputFiles(), AbstractCellPopulation< DIM >::GenerateCellResults(), AbstractCellPopulation< DIM >::WriteCellResultsToFiles(), and AbstractCellPopulation< DIM >::WriteResultsToFiles().

template<unsigned DIM>

out_stream AbstractCellPopulation< DIM >::mpCellIdFile [protected]

Results file for logged cell data.

Definition at line 140 of file AbstractCellPopulation.hpp.

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

template<unsigned DIM>

out_stream AbstractCellPopulation< DIM >::mpVizBoundaryNodesFile [protected]

Results file for boundary nodes.

Definition at line 143 of file AbstractCellPopulation.hpp.

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

template<unsigned DIM>

std::string AbstractCellPopulation< DIM >::mDirPath [protected]

A cache of where the results are going (used for VTK writer).

Definition at line 146 of file AbstractCellPopulation.hpp.

Referenced by AbstractCellPopulation< DIM >::CreateOutputFiles(), VertexBasedCellPopulation< DIM >::WriteVtkResultsToFile(), NodeBasedCellPopulation< DIM >::WriteVtkResultsToFile(), MeshBasedCellPopulationWithGhostNodes< DIM >::WriteVtkResultsToFile(), and MeshBasedCellPopulation< DIM >::WriteVtkResultsToFile().

template<unsigned DIM>

out_stream AbstractCellPopulation< DIM >::mpVtkMetaFile [protected]

Meta results file for VTK.

Definition at line 149 of file AbstractCellPopulation.hpp.

Referenced by AbstractCellPopulation< DIM >::CloseOutputFiles(), AbstractCellPopulation< DIM >::CreateOutputFiles(), VertexBasedCellPopulation< DIM >::WriteVtkResultsToFile(), NodeBasedCellPopulation< DIM >::WriteVtkResultsToFile(), MeshBasedCellPopulationWithGhostNodes< DIM >::WriteVtkResultsToFile(), and MeshBasedCellPopulation< DIM >::WriteVtkResultsToFile().

template<unsigned DIM>

bool AbstractCellPopulation< DIM >::mCellPopulationContainsMesh [protected]

Whether the cell population contains a mesh.

Definition at line 152 of file AbstractCellPopulation.hpp.

Referenced by AbstractCellPopulation< DIM >::IsMeshBasedCellPopulation(), MeshBasedCellPopulation< DIM >::MeshBasedCellPopulation(), and AbstractCellPopulation< SPACE_DIM >::serialize().

template<unsigned DIM>

boost::shared_ptr<CellPropertyRegistry> AbstractCellPopulation< DIM >::mpCellPropertyRegistry [protected]

Cell property registry.

Definition at line 155 of file AbstractCellPopulation.hpp.

Referenced by AbstractCellPopulation< DIM >::AbstractCellPopulation(), AbstractCellPopulation< DIM >::CreateOutputFiles(), AbstractCellPopulation< DIM >::GetCellMutationStateCount(), AbstractCellPopulation< DIM >::GetCellPropertyRegistry(), and AbstractCellPopulation< SPACE_DIM >::serialize().

template<unsigned DIM>

double AbstractCellPopulation< DIM >::mDampingConstantNormal [protected]

Damping constant for normal cells has units of kg s^-1 Represented by the parameter eta in the model by Meineke et al (2001) in their off-lattice model of the intestinal crypt (doi:10.1046/j.0960-7722.2001.00216.x).

Definition at line 163 of file AbstractCellPopulation.hpp.

Referenced by AbstractCellPopulation< DIM >::GetDampingConstantNormal(), AbstractCellPopulation< DIM >::OutputCellPopulationParameters(), AbstractCellPopulation< SPACE_DIM >::serialize(), and AbstractCellPopulation< DIM >::SetDampingConstantNormal().

template<unsigned DIM>

double AbstractCellPopulation< DIM >::mDampingConstantMutant [protected]

Damping constant for mutant cells has units of kg s^-1

Definition at line 168 of file AbstractCellPopulation.hpp.

Referenced by AbstractCellPopulation< DIM >::GetDampingConstantMutant(), AbstractCellPopulation< DIM >::OutputCellPopulationParameters(), AbstractCellPopulation< SPACE_DIM >::serialize(), and AbstractCellPopulation< DIM >::SetDampingConstantMutant().

template<unsigned DIM>

bool AbstractCellPopulation< DIM >::mOutputCellIdData [protected]

Whether to write cell ID data to file.

Definition at line 171 of file AbstractCellPopulation.hpp.

Referenced by AbstractCellPopulation< DIM >::CloseOutputFiles(), AbstractCellPopulation< DIM >::CreateOutputFiles(), AbstractCellPopulation< DIM >::GetOutputCellIdData(), AbstractCellPopulation< DIM >::OutputCellPopulationParameters(), AbstractCellPopulation< SPACE_DIM >::serialize(), AbstractCellPopulation< DIM >::SetOutputCellIdData(), and AbstractCellPopulation< DIM >::WriteResultsToFiles().

template<unsigned DIM>

bool AbstractCellPopulation< DIM >::mOutputCellMutationStates [protected]

Whether to count the number of each cell mutation state and output to file.

Definition at line 174 of file AbstractCellPopulation.hpp.

template<unsigned DIM>

bool AbstractCellPopulation< DIM >::mOutputCellAncestors [protected]

Whether to output the ancestor of each cell to a visualizer file.

Definition at line 177 of file AbstractCellPopulation.hpp.

template<unsigned DIM>

bool AbstractCellPopulation< DIM >::mOutputCellProliferativeTypes [protected]

Whether to count the number of each cell type and output to file.

Definition at line 180 of file AbstractCellPopulation.hpp.

template<unsigned DIM>

bool AbstractCellPopulation< DIM >::mOutputCellVariables [protected]

Whether to write the cell variables to a file.

Definition at line 183 of file AbstractCellPopulation.hpp.

Referenced by AbstractCellPopulation< DIM >::CloseOutputFiles(), AbstractCellPopulation< DIM >::CreateOutputFiles(), AbstractCellPopulation< DIM >::GenerateCellResults(), AbstractCellPopulation< DIM >::GetOutputCellVariables(), AbstractCellPopulation< DIM >::OutputCellPopulationParameters(), AbstractCellPopulation< SPACE_DIM >::serialize(), AbstractCellPopulation< DIM >::SetOutputCellVariables(), AbstractCellPopulation< DIM >::WriteCellResultsToFiles(), and AbstractCellPopulation< DIM >::WriteResultsToFiles().

template<unsigned DIM>

bool AbstractCellPopulation< DIM >::mOutputCellCyclePhases [protected]

Whether to write the cell cycle phases to a file.

Definition at line 186 of file AbstractCellPopulation.hpp.

template<unsigned DIM>

bool AbstractCellPopulation< DIM >::mOutputCellAges [protected]

Whether to write the cell ages to a file.

Definition at line 189 of file AbstractCellPopulation.hpp.

template<unsigned DIM>

bool AbstractCellPopulation< DIM >::mOutputCellVolumes [protected]

Whether to write the cell volumes (in 3D) or areas (in 2D) to a file.

Definition at line 192 of file AbstractCellPopulation.hpp.

Referenced by VertexBasedCellPopulation< DIM >::CloseOutputFiles(), MeshBasedCellPopulation< DIM >::CloseOutputFiles(), VertexBasedCellPopulation< DIM >::CreateOutputFiles(), MeshBasedCellPopulation< DIM >::CreateOutputFiles(), AbstractCellPopulation< DIM >::GetOutputCellVolumes(), AbstractCellPopulation< DIM >::OutputCellPopulationParameters(), AbstractCellPopulation< SPACE_DIM >::serialize(), AbstractCellPopulation< DIM >::SetOutputCellVolumes(), MeshBasedCellPopulation< DIM >::Update(), VertexBasedCellPopulation< DIM >::WriteResultsToFiles(), MeshBasedCellPopulation< DIM >::WriteResultsToFiles(), VertexBasedCellPopulation< DIM >::WriteVtkResultsToFile(), MeshBasedCellPopulationWithGhostNodes< DIM >::WriteVtkResultsToFile(), and MeshBasedCellPopulation< DIM >::WriteVtkResultsToFile().

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

cell_based/src/population/AbstractCellPopulation.hpp
cell_based/src/population/AbstractCellPopulation.cpp


Public Member Functions
	AbstractCellPopulation (std::vector< CellPtr > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >())
virtual	~AbstractCellPopulation ()
void	InitialiseCells ()
std::list< CellPtr > &	rGetCells ()
bool	IsMeshBasedCellPopulation ()
virtual unsigned	GetNumNodes ()=0
virtual c_vector< double, DIM >	GetLocationOfCellCentre (CellPtr 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	IsCellAssociatedWithADeletedLocation (CellPtr pCell)=0
virtual void	UpdateNodeLocations (const std::vector< c_vector< double, DIM > > &rNodeForces, double dt)=0
virtual double	GetDampingConstant (unsigned nodeIndex)=0
virtual CellPtr	AddCell (CellPtr pNewCell, const c_vector< double, DIM > &rCellDivisionVector, CellPtr pParentCell=CellPtr())=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 ()
CellPtr	GetCellUsingLocationIndex (unsigned index)
unsigned	GetLocationIndexUsingCell (CellPtr pCell)
boost::shared_ptr < CellPropertyRegistry >	GetCellPropertyRegistry ()
void	SetDefaultMutationStateOrdering ()
virtual double	GetWidth (const unsigned &rDimension)=0
virtual void	CreateOutputFiles (const std::string &rDirectory, bool cleanOutputDirectory)
virtual void	WriteResultsToFiles ()
virtual 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 ()
void	OutputCellPopulationInfo (out_stream &rParamsFile)
virtual void	OutputCellPopulationParameters (out_stream &rParamsFile)=0
double	GetDampingConstantNormal ()
double	GetDampingConstantMutant ()
bool	GetOutputCellIdData ()
bool	GetOutputCellMutationStates ()
bool	GetOutputCellAncestors ()
bool	GetOutputCellProliferativeTypes ()
bool	GetOutputCellVariables ()
bool	GetOutputCellCyclePhases ()
bool	GetOutputCellAges ()
bool	GetOutputCellVolumes ()
void	SetDampingConstantNormal (double dampingConstantNormal)
void	SetDampingConstantMutant (double dampingConstantMutant)
void	SetOutputCellIdData (bool outputCellIdData)
void	SetOutputCellMutationStates (bool outputCellMutationStates)
void	SetOutputCellAncestors (bool outputCellAncestors)
void	SetOutputCellProliferativeTypes (bool outputCellProliferativeTypes)
void	SetOutputCellVariables (bool outputCellVariables)
void	SetOutputCellCyclePhases (bool outputCellCyclePhases)
void	SetOutputCellAges (bool outputCellAges)
virtual void	SetOutputCellVolumes (bool outputCellVolumes)
Iterator	Begin ()
Iterator	End ()
Protected Member Functions
virtual void	Validate ()=0
virtual void	WriteVtkResultsToFile ()=0
	AbstractCellPopulation ()
Protected Attributes
std::list< CellPtr >	mCells
std::map< unsigned, CellPtr >	mLocationCellMap
std::map< Cell *, unsigned >	mCellLocationMap
std::vector< unsigned >	mCellProliferativeTypeCount
std::vector< unsigned >	mCellCyclePhaseCount
out_stream	mpVizNodesFile
out_stream	mpVizCellProliferativeTypesFile
out_stream	mpCellMutationStatesFile
out_stream	mpVizCellAncestorsFile
out_stream	mpCellProliferativeTypesFile
out_stream	mpCellCyclePhasesFile
out_stream	mpCellVariablesFile
out_stream	mpCellAgesFile
out_stream	mpCellIdFile
out_stream	mpVizBoundaryNodesFile
std::string	mDirPath
out_stream	mpVtkMetaFile
bool	mCellPopulationContainsMesh
boost::shared_ptr < CellPropertyRegistry >	mpCellPropertyRegistry
double	mDampingConstantNormal
double	mDampingConstantMutant
bool	mOutputCellIdData
bool	mOutputCellMutationStates
bool	mOutputCellAncestors
bool	mOutputCellProliferativeTypes
bool	mOutputCellVariables
bool	mOutputCellCyclePhases
bool	mOutputCellAges
bool	mOutputCellVolumes
Private Member Functions
template<class Archive>
void	serialize (Archive &archive, const unsigned int version)
Friends
class	boost::serialization::access
Classes
class	Iterator

AbstractCellPopulation< DIM > Class Template Reference

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Friends

Classes

Detailed Description

template<unsigned DIM> class AbstractCellPopulation< DIM >

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation

template<unsigned DIM>
class AbstractCellPopulation< DIM >