#include <AbstractOnLatticeCellPopulation.hpp>

Inheritance diagram for AbstractOnLatticeCellPopulation< DIM >:

Collaboration diagram for AbstractOnLatticeCellPopulation< DIM >:

Public Member Functions
	AbstractOnLatticeCellPopulation (AbstractMesh< DIM, DIM > &rMesh, std::vector< CellPtr > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >(), bool deleteMesh=false)

virtual	~AbstractOnLatticeCellPopulation ()

virtual void	UpdateCellLocations (double dt)=0

bool	GetUpdateNodesInRandomOrder ()

void	SetUpdateNodesInRandomOrder (bool updateNodesInRandomOrder)

void	SetIterateRandomlyOverUpdateRuleCollection (bool iterateRandomly)

bool	GetIterateRandomlyOverUpdateRuleCollection ()

void	SetNode (unsigned index, ChastePoint< DIM > &rNewLocation)

std::set< unsigned >	GetNeighbouringNodeIndices (unsigned index)

virtual void	OutputCellPopulationParameters (out_stream &rParamsFile)

virtual double	GetDefaultTimeStep ()

virtual void	AddUpdateRule (boost::shared_ptr< AbstractUpdateRule< DIM > > pUpdateRule)=0

virtual void	RemoveAllUpdateRules ()

virtual const std::vector < boost::shared_ptr < AbstractUpdateRule< DIM > > >	GetUpdateRuleCollection () const

Public Member Functions inherited from AbstractCellPopulation< DIM >
	AbstractCellPopulation (AbstractMesh< ELEMENT_DIM, ELEMENT_DIM > &rMesh, std::vector< CellPtr > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >())

virtual	~AbstractCellPopulation ()

void	InitialiseCells ()

void	SetDataOnAllCells (const std::string &rDataName, double dataValue)

AbstractMesh< ELEMENT_DIM, ELEMENT_DIM > &	rGetMesh ()

virtual TetrahedralMesh < ELEMENT_DIM, ELEMENT_DIM > *	GetTetrahedralMeshForPdeModifier ()=0

virtual bool	IsPdeNodeAssociatedWithNonApoptoticCell (unsigned pdeNodeIndex)

virtual double	GetCellDataItemAtPdeNode (unsigned pdeNodeIndex, std::string &rVariableName, bool dirichletBoundaryConditionApplies=false, double dirichletBoundaryValue=0.0)=0

std::list< CellPtr > &	rGetCells ()

virtual unsigned	GetNumNodes ()=0

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

virtual Node< ELEMENT_DIM > *	GetNode (unsigned index)=0

virtual void	SetNode (unsigned nodeIndex, ChastePoint< ELEMENT_DIM > &rNewLocation)=0

virtual bool	IsCellAssociatedWithADeletedLocation (CellPtr pCell)=0

virtual void	WriteDataToVisualizerSetupFile (out_stream &pVizSetupFile)

virtual CellPtr	AddCell (CellPtr pNewCell, CellPtr pParentCell=CellPtr())=0

virtual unsigned	RemoveDeadCells ()=0

virtual void	Update (bool hasHadBirthsOrDeaths=true)=0

std::vector< unsigned >	GetCellMutationStateCount ()

std::vector< unsigned >	GetCellProliferativeTypeCount ()

std::vector< unsigned >	GetCellCyclePhaseCount ()

unsigned	GetNumRealCells ()

unsigned	GetNumAllCells ()

void	SetCellAncestorsToLocationIndices ()

std::set< unsigned >	GetCellAncestors ()

virtual CellPtr	GetCellUsingLocationIndex (unsigned index)

std::set< CellPtr >	GetCellsUsingLocationIndex (unsigned index)

virtual bool	IsCellAttachedToLocationIndex (unsigned index)

void	SetCellUsingLocationIndex (unsigned index, CellPtr pCell)

virtual void	AddCellUsingLocationIndex (unsigned index, CellPtr pCell)

virtual void	RemoveCellUsingLocationIndex (unsigned index, CellPtr pCell)

void	MoveCellInLocationMap (CellPtr pCell, unsigned old_index, unsigned new_index)

unsigned	GetLocationIndexUsingCell (CellPtr pCell)

boost::shared_ptr < CellPropertyRegistry >	GetCellPropertyRegistry ()

void	SetDefaultCellMutationStateAndProliferativeTypeOrdering ()

virtual double	GetWidth (const unsigned &rDimension)=0

virtual double	GetVolumeOfCell (CellPtr pCell)=0

virtual std::set< unsigned >	GetNeighbouringLocationIndices (CellPtr pCell)=0

c_vector< double, ELEMENT_DIM >	GetCentroidOfCellPopulation ()

virtual void	UpdateCellProcessLocation ()

virtual void	OpenWritersFiles (OutputFileHandler &rOutputFileHandler)

void	CloseWritersFiles ()

virtual void	WriteResultsToFiles (const std::string &rDirectory)

virtual void	AcceptPopulationWriter (boost::shared_ptr< AbstractCellPopulationWriter< ELEMENT_DIM, ELEMENT_DIM > > pPopulationWriter)=0

virtual void	AcceptPopulationCountWriter (boost::shared_ptr< AbstractCellPopulationCountWriter< ELEMENT_DIM, ELEMENT_DIM > > pPopulationCountWriter)=0

virtual void	AcceptCellWriter (boost::shared_ptr< AbstractCellWriter< ELEMENT_DIM, ELEMENT_DIM > > pCellWriter, CellPtr pCell)=0

void	OutputCellPopulationInfo (out_stream &rParamsFile)

virtual void	SimulationSetupHook (AbstractCellBasedSimulation< ELEMENT_DIM, ELEMENT_DIM > *pSimulation)

bool	GetOutputResultsForChasteVisualizer ()

void	AddPopulationWriter ()

void	AddPopulationWriter (boost::shared_ptr< AbstractCellPopulationWriter< ELEMENT_DIM, ELEMENT_DIM > > pPopulationWriter)

void	AddCellWriter ()

void	AddCellWriter (boost::shared_ptr< AbstractCellWriter< ELEMENT_DIM, ELEMENT_DIM > > pCellWriter)

void	AddCellPopulationCountWriter ()

void	AddCellPopulationCountWriter (boost::shared_ptr< AbstractCellPopulationCountWriter< ELEMENT_DIM, ELEMENT_DIM > > pCellPopulationCountWriter)

bool	HasWriter () const

void	SetOutputResultsForChasteVisualizer (bool outputResultsForChasteVisualizer)

c_vector< double, ELEMENT_DIM >	GetSizeOfCellPopulation ()

virtual bool	IsRoomToDivide (CellPtr pCell)

std::pair< unsigned, unsigned >	CreateOrderedPair (unsigned index1, unsigned index2)

Iterator	Begin ()

Iterator	End ()

Public Member Functions inherited from Identifiable
virtual	~Identifiable ()

std::string	GetIdentifier () const

Protected Member Functions
	AbstractOnLatticeCellPopulation (AbstractMesh< DIM, DIM > &rMesh)

Protected Member Functions inherited from AbstractCellPopulation< DIM >
virtual void	Validate ()=0

virtual void	WriteVtkResultsToFile (const std::string &rDirectory)=0

	AbstractCellPopulation (AbstractMesh< ELEMENT_DIM, ELEMENT_DIM > &rMesh)

virtual void	AcceptCellWritersAcrossPopulation ()

Protected Attributes
std::vector< boost::shared_ptr < AbstractUpdateRule< DIM > > >	mUpdateRuleCollection

bool	mDeleteMesh

bool	mUpdateNodesInRandomOrder

bool	mIterateRandomlyOverUpdateRuleCollection

Protected Attributes inherited from AbstractCellPopulation< DIM >
std::map< unsigned, std::set < CellPtr > >	mLocationCellMap

std::map< Cell *, unsigned >	mCellLocationMap

AbstractMesh< ELEMENT_DIM, ELEMENT_DIM > &	mrMesh

std::list< CellPtr >	mCells

c_vector< double, ELEMENT_DIM >	mCentroid

out_stream	mpVtkMetaFile

boost::shared_ptr < CellPropertyRegistry >	mpCellPropertyRegistry

bool	mOutputResultsForChasteVisualizer

std::vector< boost::shared_ptr < AbstractCellWriter < ELEMENT_DIM, ELEMENT_DIM > > >	mCellWriters

std::vector< boost::shared_ptr < AbstractCellPopulationWriter < ELEMENT_DIM, ELEMENT_DIM > > >	mCellPopulationWriters

std::vector< boost::shared_ptr < AbstractCellPopulationCountWriter < ELEMENT_DIM, ELEMENT_DIM > > >	mCellPopulationCountWriters

Private Member Functions
template<class Archive >
void	serialize (Archive &archive, const unsigned int version)

Friends
class	boost::serialization::access

Detailed Description

template<unsigned DIM>
class AbstractOnLatticeCellPopulation< DIM >

An abstract class for on-lattice cell populations.

Definition at line 46 of file AbstractOnLatticeCellPopulation.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

AbstractOnLatticeCellPopulation< DIM >::AbstractOnLatticeCellPopulation ( AbstractMesh< DIM, DIM > & rMesh )

protected

Constructor that just takes in a mesh.

Parameters

rMesh the mesh for the cell population.

Definition at line 57 of file AbstractOnLatticeCellPopulation.cpp.

template<unsigned DIM>

AbstractOnLatticeCellPopulation< DIM >::AbstractOnLatticeCellPopulation	(	AbstractMesh< DIM, DIM > &	rMesh,
		std::vector< CellPtr > &	rCells,
		const std::vector< unsigned >	locationIndices = `std::vector<unsigned>()`,
		bool	deleteMesh = `false`
	)

Default constructor.

Parameters

rMesh	a refernce to the mesh underlying the cell population
rCells	a vector of cells
locationIndices	an optional vector of location indices that correspond to real cells
deleteMesh	set to true if you want the cell population to free the mesh memory on destruction (defaults to false)

Definition at line 39 of file AbstractOnLatticeCellPopulation.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::AddCellUsingLocationIndex(), and AbstractCellPopulation< DIM >::mCells.

template<unsigned DIM>

AbstractOnLatticeCellPopulation< DIM >::~AbstractOnLatticeCellPopulation ( )

virtual

Destructor.

Definition at line 66 of file AbstractOnLatticeCellPopulation.cpp.

Member Function Documentation

template<unsigned DIM>

virtual void AbstractOnLatticeCellPopulation< DIM >::AddUpdateRule ( boost::shared_ptr< AbstractUpdateRule< DIM > > pUpdateRule )

pure virtual

Add an update rule to be used with this population.

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

Parameters

pUpdateRule pointer to an update rule

Implemented in CaBasedCellPopulation< DIM >, and PottsBasedCellPopulation< DIM >.

Referenced by OnLatticeSimulation< DIM >::AddUpdateRule().

template<unsigned DIM>

double AbstractOnLatticeCellPopulation< DIM >::GetDefaultTimeStep ( )

virtual

Overridden GetDefaultTimeStep() method.

Returns: a default value for the time step to use when simulating the cell population.

A hard-coded value of 0.1 is returned. However, note that the time step can be reset by calling SetDt() on the simulation object used to simulate the cell population.

Implements AbstractCellPopulation< DIM >.

Definition at line 119 of file AbstractOnLatticeCellPopulation.cpp.

template<unsigned DIM>

bool AbstractOnLatticeCellPopulation< DIM >::GetIterateRandomlyOverUpdateRuleCollection ( )

Returns: mIterateRandomlyOverUpdateRuleCollection.

Definition at line 89 of file AbstractOnLatticeCellPopulation.cpp.

template<unsigned DIM>

std::set< unsigned > AbstractOnLatticeCellPopulation< DIM >::GetNeighbouringNodeIndices ( unsigned index )

virtual

Overridden GetNeighbouringNodeIndices() method.

This method currently returns an exception as the two types of neighbourhood (Moore and Von Neumann) are defined in the PottsMesh.

Parameters

index the node index

Returns: the set of neighbouring node indices.

Implements AbstractCellPopulation< DIM >.

Definition at line 101 of file AbstractOnLatticeCellPopulation.cpp.

References EXCEPTION.

template<unsigned DIM>

bool AbstractOnLatticeCellPopulation< DIM >::GetUpdateNodesInRandomOrder ( )

Get whether we update nodes in a random order.

Returns: mUpdateNodesInRandomOrder

Definition at line 71 of file AbstractOnLatticeCellPopulation.cpp.

template<unsigned DIM>

const std::vector< boost::shared_ptr< AbstractUpdateRule< DIM > > > AbstractOnLatticeCellPopulation< DIM >::GetUpdateRuleCollection ( ) const

virtual

Get the collection of update rules to be used with this population.

Returns: the update rule collection

Reimplemented in CaBasedCellPopulation< DIM >.

Definition at line 125 of file AbstractOnLatticeCellPopulation.cpp.

Referenced by OnLatticeSimulation< DIM >::OutputAdditionalSimulationSetup().

template<unsigned DIM>

void AbstractOnLatticeCellPopulation< DIM >::OutputCellPopulationParameters ( out_stream & rParamsFile )

virtual

Outputs parameters to file.

Parameters

rParamsFile the file stream to which the parameters are output

Implements AbstractCellPopulation< DIM >.

Reimplemented in CaBasedCellPopulation< DIM >, and PottsBasedCellPopulation< DIM >.

Definition at line 109 of file AbstractOnLatticeCellPopulation.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::OutputCellPopulationParameters().

Referenced by PottsBasedCellPopulation< DIM >::OutputCellPopulationParameters(), and CaBasedCellPopulation< DIM >::OutputCellPopulationParameters().

template<unsigned DIM>

void AbstractOnLatticeCellPopulation< DIM >::RemoveAllUpdateRules ( )

virtual

Remove any update rules previously passed to this population.

Reimplemented in CaBasedCellPopulation< DIM >.

Definition at line 131 of file AbstractOnLatticeCellPopulation.cpp.

Referenced by OnLatticeSimulation< DIM >::RemoveAllUpdateRules(), and CaBasedCellPopulation< DIM >::RemoveAllUpdateRules().

template<unsigned DIM>

template<class Archive >

void AbstractOnLatticeCellPopulation< DIM >::serialize	(	Archive &	archive,
		const unsigned int	version
	)

inlineprivate

Serialize the object and its member variables.

Parameters

archive	the archive
version	the current version of this class

Definition at line 59 of file AbstractOnLatticeCellPopulation.hpp.

References AbstractOnLatticeCellPopulation< DIM >::mIterateRandomlyOverUpdateRuleCollection, AbstractOnLatticeCellPopulation< DIM >::mUpdateNodesInRandomOrder, and AbstractOnLatticeCellPopulation< DIM >::mUpdateRuleCollection.

template<unsigned DIM>

void AbstractOnLatticeCellPopulation< DIM >::SetIterateRandomlyOverUpdateRuleCollection ( bool iterateRandomly )

Set mIterateRandomlyOverUpdateRuleCollection.

Parameters

iterateRandomly whether to iterate randomly over mUpdateRuleCollection

Definition at line 83 of file AbstractOnLatticeCellPopulation.cpp.

template<unsigned DIM>

void AbstractOnLatticeCellPopulation< DIM >::SetNode	(	unsigned	index,
		ChastePoint< DIM > &	rNewLocation
	)

Overridden SetNode() method.

This method throws an exception if called on a subclass of AbstractOnLatticeCellPopulation, since in such classes the lattice is assumed to be fixed.

Parameters

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

Definition at line 95 of file AbstractOnLatticeCellPopulation.cpp.

References EXCEPTION.

template<unsigned DIM>

void AbstractOnLatticeCellPopulation< DIM >::SetUpdateNodesInRandomOrder ( bool updateNodesInRandomOrder )

Get whether we update nodes in a random order.

Parameters

updateNodesInRandomOrder Whether to update nodes in a random order.

Definition at line 77 of file AbstractOnLatticeCellPopulation.cpp.

template<unsigned DIM>

virtual void AbstractOnLatticeCellPopulation< DIM >::UpdateCellLocations ( double dt )

pure virtual

Update cell locations over the course of a time step of specified length.

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

Parameters

dt time step

Implemented in CaBasedCellPopulation< DIM >, and PottsBasedCellPopulation< DIM >.

Referenced by OnLatticeSimulation< DIM >::UpdateCellLocationsAndTopology().

Friends And Related Function Documentation

template<unsigned DIM>

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 51 of file AbstractOnLatticeCellPopulation.hpp.

Member Data Documentation

template<unsigned DIM>

bool AbstractOnLatticeCellPopulation< DIM >::mDeleteMesh

protected

Whether to delete the mesh when we are destroyed. Needed if this cell population has been de-serialized.

Definition at line 79 of file AbstractOnLatticeCellPopulation.hpp.

template<unsigned DIM>

bool AbstractOnLatticeCellPopulation< DIM >::mIterateRandomlyOverUpdateRuleCollection

protected

Whether to iterate randomly over mUpdateRuleCollection when updating cell locations. Initialized to false in the constructor.

Definition at line 91 of file AbstractOnLatticeCellPopulation.hpp.

Referenced by AbstractOnLatticeCellPopulation< DIM >::serialize().

template<unsigned DIM>

bool AbstractOnLatticeCellPopulation< DIM >::mUpdateNodesInRandomOrder

protected

Whether to update nodes in random order. Initialized to true in the constructor.

Definition at line 85 of file AbstractOnLatticeCellPopulation.hpp.

Referenced by AbstractOnLatticeCellPopulation< DIM >::serialize().

template<unsigned DIM>

std::vector<boost::shared_ptr<AbstractUpdateRule<DIM> > > AbstractOnLatticeCellPopulation< DIM >::mUpdateRuleCollection

protected

The update rules used to determine the new location of the cells. These rules specify how individual cells move into free spaces.

Definition at line 73 of file AbstractOnLatticeCellPopulation.hpp.

Referenced by AbstractOnLatticeCellPopulation< DIM >::serialize().

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

cell_based/src/population/AbstractOnLatticeCellPopulation.hpp
cell_based/src/population/AbstractOnLatticeCellPopulation.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Friends

Detailed Description

template<unsigned DIM> class AbstractOnLatticeCellPopulation< DIM >

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation

template<unsigned DIM>
class AbstractOnLatticeCellPopulation< DIM >