Cell Class Reference

#include <Cell.hpp>

Inherits boost::noncopyable, and boost::enable_shared_from_this< Cell >.

Collaboration diagram for Cell:

Public Member Functions
	Cell (boost::shared_ptr< AbstractCellProperty > pMutationState, AbstractCellCycleModel *pCellCycleModel, bool archiving=false, CellPropertyCollection cellPropertyCollection=CellPropertyCollection())
	~Cell ()
boost::shared_ptr < AbstractCellProliferativeType >	GetCellProliferativeType () const
void	SetCellProliferativeType (boost::shared_ptr< AbstractCellProperty > pProliferativeType)
void	SetBirthTime (double birthTime)
void	SetCellCycleModel (AbstractCellCycleModel *pCellCycleModel)
AbstractCellCycleModel *	GetCellCycleModel () const
void	InitialiseCellCycleModel ()
double	GetAge () const
double	GetBirthTime () const
double	GetStartOfApoptosisTime () const
double	GetApoptosisTime () const
void	SetApoptosisTime (double apoptosisTime)
boost::shared_ptr < AbstractCellMutationState >	GetMutationState () const
boost::shared_ptr< CellData >	GetCellData () const
void	SetMutationState (boost::shared_ptr< AbstractCellProperty > pMutationState)
CellPropertyCollection &	rGetCellPropertyCollection ()
const CellPropertyCollection &	rGetCellPropertyCollection () const
void	AddCellProperty (const boost::shared_ptr< AbstractCellProperty > &rProperty)
template<typename CLASS >
void	RemoveCellProperty ()
template<typename CLASS >
bool	HasCellProperty () const
bool	ReadyToDivide ()
CellPtr	Divide ()
void	StartApoptosis (bool setDeathTime=true)
void	Kill ()
bool	HasApoptosisBegun () const
double	GetTimeUntilDeath () const
bool	IsDead ()
void	SetLogged ()
bool	IsLogged ()
void	SetAncestor (boost::shared_ptr< AbstractCellProperty > pCellAncestor)
unsigned	GetAncestor () const
unsigned	GetCellId () const
Protected Attributes
CellPropertyCollection	mCellPropertyCollection
AbstractCellCycleModel *	mpCellCycleModel
double	mDeathTime
double	mStartOfApoptosisTime
double	mApoptosisTime
bool	mUndergoingApoptosis
bool	mIsDead
bool	mIsLogged
Private Member Functions
template<class Archive >
void	serialize (Archive &archive, const unsigned int version)
Private Attributes
bool	mCanDivide
Friends
class	boost::serialization::access

Detailed Description

Cell is the basic container for all the biological information about a cell. It contains the cell-cycle model and all other biological properties such as mutation state, cell type, whether it is undergoing apoptosis or not.

This class should not store any spatial information - cells are linked to space by the AbstractCellPopulation subclasses.

Definition at line 75 of file Cell.hpp.

Constructor & Destructor Documentation

Cell::Cell	(	boost::shared_ptr< AbstractCellProperty >	pMutationState,
		AbstractCellCycleModel *	pCellCycleModel,
		bool	archiving = `false`,
		CellPropertyCollection	cellPropertyCollection = `CellPropertyCollection()`
	)

Create a new cell.

Parameters:

	pMutationState	the mutation state of the cell
	pCellCycleModel	the cell-cycle model to use to decide when the cell divides. This MUST be allocated using new, and will be deleted when the cell is destroyed.
	archiving	whether this constructor is being called by the archiver - do things slightly differently! (defaults to false)
	cellPropertyCollection	the cell property collection (defaults to NULL)

Definition at line 58 of file Cell.cpp.

References CellPropertyCollection::AddProperty(), CellPropertyCollection::Begin(), CellPropertyCollection::End(), EXCEPTION, CellPropertyCollection::HasProperty(), CellPropertyCollection::HasPropertyType(), CellPropertyRegistry::Instance(), SimulationTime::Instance(), MAKE_PTR, mCellPropertyCollection, mpCellCycleModel, and AbstractCellCycleModel::SetCell().

Referenced by Divide().

Cell::~Cell ( )

Destructor, which frees the memory allocated for our cell-cycle model.

Definition at line 134 of file Cell.cpp.

References Kill(), mIsDead, and mpCellCycleModel.

Member Function Documentation

void Cell::AddCellProperty ( const boost::shared_ptr< AbstractCellProperty > & rProperty )

Add a cell property to the cell. Use this method instead of calling rGetCellPropertyCollection().AddProperty() directly, to ensure that the cell property keeps correct track of the number of cells with it (if this is done).

Parameters:

rProperty

the property to add

Definition at line 260 of file Cell.cpp.

References CellPropertyCollection::AddProperty(), CellPropertyCollection::HasProperty(), and mCellPropertyCollection.

Referenced by SetAncestor(), SetCellProliferativeType(), SetMutationState(), and StartApoptosis().

CellPtr Cell::Divide ( )

Divide this cell to produce a daughter cell. ReadyToDivide MUST have been called at the current time, and returned true.

Returns:: the new daughter cell

Definition at line 417 of file Cell.cpp.

References CellPropertyCollection::AddProperty(), Cell(), AbstractCellCycleModel::CreateCellCycleModel(), GetCellData(), GetMutationState(), CellPropertyCollection::HasPropertyType(), IsDead(), MAKE_PTR_ARGS, mApoptosisTime, mCanDivide, mCellPropertyCollection, mpCellCycleModel, CellPropertyCollection::RemoveProperty(), and AbstractCellCycleModel::ResetForDivision().

double Cell::GetAge ( ) const

Returns:: the cell's age from its cell-cycle model.

Definition at line 193 of file Cell.cpp.

References AbstractCellCycleModel::GetAge(), and mpCellCycleModel.

unsigned Cell::GetAncestor ( ) const

Returns:: The ancestor object, inherited from parents or set using the method above, used for monoclonality experiments.

Definition at line 378 of file Cell.cpp.

References CellPropertyCollection::GetPropertiesType(), CellPropertyCollection::GetProperty(), CellPropertyCollection::GetSize(), mCellPropertyCollection, and UNSIGNED_UNSET.

double Cell::GetApoptosisTime ( ) const

Returns:: mApoptosisTime

Definition at line 311 of file Cell.cpp.

References mApoptosisTime.

double Cell::GetBirthTime ( ) const

Returns:: the cell's birth time from its cell-cycle model.

Definition at line 198 of file Cell.cpp.

References AbstractCellCycleModel::GetBirthTime(), and mpCellCycleModel.

AbstractCellCycleModel * Cell::GetCellCycleModel ( ) const

Returns:: a pointer to the Cell's cell-cycle model.

Definition at line 183 of file Cell.cpp.

References mpCellCycleModel.

boost::shared_ptr< CellData > Cell::GetCellData ( ) const

Get the CellData associated with the cell.

Returns:: a pointer to the cell data

Definition at line 237 of file Cell.cpp.

References CellPropertyCollection::GetPropertiesType(), CellPropertyCollection::GetProperty(), CellPropertyCollection::GetSize(), and mCellPropertyCollection.

Referenced by Divide().

unsigned Cell::GetCellId ( ) const

Returns:: The cell identifier.

Definition at line 393 of file Cell.cpp.

References CellPropertyCollection::GetPropertiesType(), CellPropertyCollection::GetProperty(), CellPropertyCollection::GetSize(), and mCellPropertyCollection.

boost::shared_ptr< AbstractCellProliferativeType > Cell::GetCellProliferativeType ( ) const

Returns:: the cell's proliferative type.

Definition at line 158 of file Cell.cpp.

References CellPropertyCollection::GetPropertiesType(), CellPropertyCollection::GetProperty(), CellPropertyCollection::GetSize(), and mCellPropertyCollection.

Referenced by SetCellProliferativeType().

boost::shared_ptr< AbstractCellMutationState > Cell::GetMutationState ( ) const

Returns:: the cell's current mutation state.

Definition at line 222 of file Cell.cpp.

References CellPropertyCollection::GetPropertiesType(), CellPropertyCollection::GetProperty(), CellPropertyCollection::GetSize(), and mCellPropertyCollection.

Referenced by Divide(), and SetMutationState().

double Cell::GetStartOfApoptosisTime ( ) const

Returns:: the time at which apoptosis was commanded to start.

Definition at line 306 of file Cell.cpp.

References mStartOfApoptosisTime.

double Cell::GetTimeUntilDeath ( ) const

Returns:: How long until the cell dies (if it is in apoptosis, throws an exception if not)

Definition at line 322 of file Cell.cpp.

References EXCEPTION, SimulationTime::GetTime(), SimulationTime::Instance(), mDeathTime, and mUndergoingApoptosis.

bool Cell::HasApoptosisBegun ( ) const

Returns:: whether the cell is undergoing apoptosis or not.

Definition at line 301 of file Cell.cpp.

References mUndergoingApoptosis.

template<typename CLASS >

bool Cell::HasCellProperty ( ) const [inline]

Returns:: whether the cell property collection contains a property that has the exact type CLASS. Just calls mCellPropertyCollection.HasProperty().

Definition at line 291 of file Cell.hpp.

References CellPropertyCollection::HasProperty(), and mCellPropertyCollection.

void Cell::InitialiseCellCycleModel ( )

Calls Initialise on the cell-cycle model associated with this cell.

Definition at line 188 of file Cell.cpp.

References AbstractCellCycleModel::Initialise(), and mpCellCycleModel.

bool Cell::IsDead ( )

Returns:: whether the cell is dead or undergoing apoptosis.

Definition at line 332 of file Cell.cpp.

References SimulationTime::Instance(), Kill(), mApoptosisTime, mDeathTime, mIsDead, and mUndergoingApoptosis.

Referenced by Divide(), ReadyToDivide(), and StartApoptosis().

bool Cell::IsLogged ( )

Returns:: Whether the cell is being tracked.

Definition at line 275 of file Cell.cpp.

References mIsLogged.

void Cell::Kill ( )

This labels the cell as dead, it does not delete the cell, it remains in the CellPopulation until AbstractCellPopulation::RemoveDeadCells() is called.

Definition at line 345 of file Cell.cpp.

References CellPropertyCollection::Begin(), CellPropertyCollection::End(), mCellPropertyCollection, and mIsDead.

Referenced by IsDead(), and ~Cell().

bool Cell::ReadyToDivide ( )

Returns:: whether this cell is ready to divide at the present simulation time. MUST be called before calling Divide().

Definition at line 404 of file Cell.cpp.

References IsDead(), mCanDivide, mpCellCycleModel, mUndergoingApoptosis, and AbstractCellCycleModel::ReadyToDivide().

template<typename CLASS >

void Cell::RemoveCellProperty ( ) [inline]

Remove a cell property of the given type. Use this method instead of calling rGetCellPropertyCollection().AddProperty() directly, to ensure that the cell property keeps correct track of the number of cells with it (if this is done).

Definition at line 264 of file Cell.hpp.

References CellPropertyCollection::Begin(), CellPropertyCollection::End(), mCellPropertyCollection, and CellPropertyCollection::RemoveProperty().

const CellPropertyCollection & Cell::rGetCellPropertyCollection ( ) const