#include <Cell.hpp>

Inheritance diagram for Cell:

Collaboration diagram for Cell:

Public Member Functions
	Cell (boost::shared_ptr< AbstractCellProperty > pMutationState, AbstractCellCycleModel pCellCycleModel, AbstractSrnModel pSrnModel=NULL, 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 ()

void	SetSrnModel (AbstractSrnModel *pSrnModel)

AbstractSrnModel *	GetSrnModel () const

void	InitialiseSrnModel ()

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

bool	HasCellVecData () const

boost::shared_ptr< CellVecData >	GetCellVecData () 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

AbstractSrnModel *	mpSrnModel

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 77 of file Cell.hpp.

Constructor & Destructor Documentation

Cell::Cell	(	boost::shared_ptr< AbstractCellProperty >	pMutationState,
		AbstractCellCycleModel *	pCellCycleModel,
		AbstractSrnModel *	pSrnModel = `NULL`,
		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.
pSrnModel	the sub-cellular reaction network model. This MUST be allocated using new, and will be deleted when the cell is destroyed. (Defaults to NULL and is replcaed by a new NullSrnModel in the constructr)
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 61 of file Cell.cpp.

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

Referenced by Divide().

Cell::~Cell ( )

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

Definition at line 148 of file Cell.cpp.

References Kill(), mIsDead, mpCellCycleModel, and mpSrnModel.

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 315 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 475 of file Cell.cpp.

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

double Cell::GetAge ( ) const

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

Definition at line 228 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 433 of file Cell.cpp.

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

double Cell::GetApoptosisTime ( ) const

Returns: mApoptosisTime

Definition at line 366 of file Cell.cpp.

References mApoptosisTime.

double Cell::GetBirthTime ( ) const

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

Definition at line 233 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 198 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 272 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 448 of file Cell.cpp.

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

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

Returns: the cell's proliferative type.

Definition at line 173 of file Cell.cpp.

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

Referenced by SetCellProliferativeType().

boost::shared_ptr< CellVecData > Cell::GetCellVecData ( ) const

Get the CellVecData associated with the cell.

Returns: a pointer to the cell Vec data

Definition at line 290 of file Cell.cpp.

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

Referenced by Divide().

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

Returns: the cell's current mutation state.

Definition at line 257 of file Cell.cpp.

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

Referenced by Divide(), and SetMutationState().

AbstractSrnModel * Cell::GetSrnModel ( ) const

Returns: a pointer to the Cell's SRN model.

Definition at line 218 of file Cell.cpp.

References mpSrnModel.

double Cell::GetStartOfApoptosisTime ( ) const

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

Definition at line 361 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 377 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 356 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 332 of file Cell.hpp.

References CellPropertyCollection::HasProperty(), and mCellPropertyCollection.

bool Cell::HasCellVecData ( ) const

Checks whether there is CellVecData associated with this cell

Returns: whether the current cell stores CellVecData

Definition at line 285 of file Cell.cpp.

References CellPropertyCollection::HasPropertyType(), and mCellPropertyCollection.

Referenced by GetCellVecData().

void Cell::InitialiseCellCycleModel ( )

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

Definition at line 203 of file Cell.cpp.

References AbstractCellCycleModel::Initialise(), and mpCellCycleModel.

void Cell::InitialiseSrnModel ( )

Calls Initialise on the SRN model associated with this cell.

Definition at line 223 of file Cell.cpp.

References AbstractSrnModel::Initialise(), and mpSrnModel.

bool Cell::IsDead ( )

Returns: whether the cell is dead or undergoing apoptosis.

Definition at line 387 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 330 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 400 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 459 of file Cell.cpp.

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

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 305 of file Cell.hpp.

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

CellPropertyCollection & Cell::rGetCellPropertyCollection ( )

Returns: reference to mCellPropertyCollection.

Definition at line 305 of file Cell.cpp.

References mCellPropertyCollection.

const CellPropertyCollection & Cell::rGetCellPropertyCollection ( ) const

Returns: reference to mCellPropertyCollection (used in archiving).

Definition at line 310 of file Cell.cpp.

References mCellPropertyCollection.

template<class Archive >

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

inlineprivate

Archive the member variables.

Parameters

archive	the archive
version	the current version of this class

Definition at line 93 of file Cell.hpp.

References mApoptosisTime, mCanDivide, mDeathTime, mIsDead, mIsLogged, mpCellCycleModel, mpSrnModel, mStartOfApoptosisTime, and mUndergoingApoptosis.

void Cell::SetAncestor ( boost::shared_ptr< AbstractCellProperty > pCellAncestor )

Give the Cell an index which it passes to its children.

Parameters

pCellAncestor the cell's ancestor

Definition at line 412 of file Cell.cpp.

References AddCellProperty(), EXCEPTION, CellPropertyCollection::GetPropertiesType(), CellPropertyCollection::GetSize(), and mCellPropertyCollection.

void Cell::SetApoptosisTime ( double apoptosisTime )

Set mApoptosisTime.

Parameters

apoptosisTime the new value of mApoptosisTime

Definition at line 371 of file Cell.cpp.

References mApoptosisTime.

void Cell::SetBirthTime ( double birthTime )

Set the birth time of the cell - can be negative so that your cells have an age when a simulation begins

Parameters

birthTime The time the cell was born (in hours)

Definition at line 238 of file Cell.cpp.

References mpCellCycleModel, and AbstractCellCycleModel::SetBirthTime().

void Cell::SetCellCycleModel ( AbstractCellCycleModel * pCellCycleModel )

Change the cell-cycle model used. This takes effect immediately.

Parameters

pCellCycleModel pointer to the cell-cycle model to use

Definition at line 188 of file Cell.cpp.

References mpCellCycleModel, and AbstractCellCycleModel::SetCell().

void Cell::SetCellProliferativeType ( boost::shared_ptr< AbstractCellProperty > pProliferativeType )

Set the cell's proliferative type.

Parameters

pProliferativeType the cell's new proliferative type

Definition at line 158 of file Cell.cpp.

References AddCellProperty(), EXCEPTION, GetCellProliferativeType(), mCellPropertyCollection, and CellPropertyCollection::RemoveProperty().

void Cell::SetLogged ( )

Sets a flag to perform special output on this cell only.

Definition at line 325 of file Cell.cpp.

References mIsLogged.

void Cell::SetMutationState ( boost::shared_ptr< AbstractCellProperty > pMutationState )

Set the cell's mutation state.

Parameters

pMutationState the cell's new mutation state

Definition at line 243 of file Cell.cpp.

References AddCellProperty(), EXCEPTION, GetMutationState(), mCellPropertyCollection, and CellPropertyCollection::RemoveProperty().

void Cell::SetSrnModel ( AbstractSrnModel * pSrnModel )

Change the SRN model used. This takes effect immediately.

Parameters

pSrnModel pointer to the SRN model to use

Definition at line 208 of file Cell.cpp.

References mpSrnModel, and AbstractSrnModel::SetCell().

void Cell::StartApoptosis ( bool setDeathTime = true )

Make the cell enter apoptosis and sets mDeathTime using the apoptosis time as defined by mApoptosisTime.

Parameters

setDeathTime whether we tell the cell exactly when to die (defaults to true)

Definition at line 335 of file Cell.cpp.

References AddCellProperty(), EXCEPTION, CellPropertyRegistry::Get(), CellPropertyCollection::GetCellPropertyRegistry(), SimulationTime::GetTime(), SimulationTime::Instance(), IsDead(), mApoptosisTime, mCellPropertyCollection, mDeathTime, mStartOfApoptosisTime, and mUndergoingApoptosis.

Friends And Related Function Documentation

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 85 of file Cell.hpp.

Member Data Documentation

double Cell::mApoptosisTime

protected

The time it takes for a cell to fully undergo apoptosis. Has units of hours.

Definition at line 125 of file Cell.hpp.

Referenced by Divide(), GetApoptosisTime(), IsDead(), serialize(), SetApoptosisTime(), and StartApoptosis().

bool Cell::mCanDivide

private

Caches the result of ReadyToDivide() so Divide() can look at it.

Definition at line 82 of file Cell.hpp.

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

CellPropertyCollection Cell::mCellPropertyCollection

protected

The cell's property collection.

Definition at line 110 of file Cell.hpp.

Referenced by AddCellProperty(), Cell(), Divide(), GetAncestor(), GetCellData(), GetCellId(), GetCellProliferativeType(), GetCellVecData(), GetMutationState(), HasCellProperty(), HasCellVecData(), Kill(), RemoveCellProperty(), rGetCellPropertyCollection(), SetAncestor(), SetCellProliferativeType(), SetMutationState(), and StartApoptosis().

double Cell::mDeathTime

protected

When the cell will/did die.

Definition at line 119 of file Cell.hpp.

Referenced by GetTimeUntilDeath(), IsDead(), serialize(), and StartApoptosis().

bool Cell::mIsDead

protected

Whether the cell is dead or not (they exist in the CellPopulation until they are removed by AbstractCellPopulation::RemoveDeadCells().

Definition at line 134 of file Cell.hpp.

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

bool Cell::mIsLogged

protected

Whether the cell is being tracked specially.

Definition at line 137 of file Cell.hpp.

Referenced by IsLogged(), serialize(), and SetLogged().

AbstractCellCycleModel* Cell::mpCellCycleModel

protected

The cell's cell-cycle model.

Definition at line 113 of file Cell.hpp.

Referenced by Cell(), Divide(), GetAge(), GetBirthTime(), GetCellCycleModel(), InitialiseCellCycleModel(), ReadyToDivide(), serialize(), SetBirthTime(), SetCellCycleModel(), and ~Cell().

AbstractSrnModel* Cell::mpSrnModel

protected

The cell's sub-cellular reaction network (SRN) model.

Definition at line 116 of file Cell.hpp.

Referenced by Cell(), Divide(), GetSrnModel(), InitialiseSrnModel(), ReadyToDivide(), serialize(), SetSrnModel(), and ~Cell().

double Cell::mStartOfApoptosisTime

protected

When the cell was commanded to start apoptosis.

Definition at line 122 of file Cell.hpp.

Referenced by GetStartOfApoptosisTime(), serialize(), and StartApoptosis().

bool Cell::mUndergoingApoptosis

protected

Whether the cell is currently in apoptosis - don't divide.

Definition at line 128 of file Cell.hpp.

Referenced by GetTimeUntilDeath(), HasApoptosisBegun(), IsDead(), ReadyToDivide(), serialize(), and StartApoptosis().

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

cell_based/src/cell/Cell.hpp
cell_based/src/cell/Cell.cpp

Public Member Functions

Protected Attributes

Private Member Functions

Private Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation