#include <CryptSimulation2d.hpp>

Inheritance diagram for CryptSimulation2d:

Collaboration diagram for CryptSimulation2d:

Public Member Functions
	CryptSimulation2d (AbstractCellPopulation< 2 > &rCellPopulation, bool deleteCellPopulationInDestructor=false, bool initialiseCells=true)

virtual	~CryptSimulation2d ()

void	UseJiggledBottomCells ()

void	SetBottomCellAncestors ()

void	OutputSimulationParameters (out_stream &rParamsFile)

Public Member Functions inherited from OffLatticeSimulation< 2 >
	OffLatticeSimulation (AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM > &rCellPopulation, bool deleteCellPopulationInDestructor=false, bool initialiseCells=true)

void	AddForce (boost::shared_ptr< AbstractForce< ELEMENT_DIM, ELEMENT_DIM > > pForce)

void	RemoveAllForces ()

void	AddCellPopulationBoundaryCondition (boost::shared_ptr< AbstractCellPopulationBoundaryCondition< ELEMENT_DIM, ELEMENT_DIM > > pBoundaryCondition)

void	RemoveAllCellPopulationBoundaryConditions ()

void	OutputAdditionalSimulationSetup (out_stream &rParamsFile)

Public Member Functions inherited from AbstractCellBasedSimulation< ELEMENT_DIM, ELEMENT_DIM >
	AbstractCellBasedSimulation (AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &rCellPopulation, bool deleteCellPopulationInDestructor=false, bool initialiseCells=true)

virtual	~AbstractCellBasedSimulation ()

void	SetCellBasedPdeHandler (CellBasedPdeHandler< SPACE_DIM > *pCellBasedPdeHandler)

CellBasedPdeHandler< SPACE_DIM > *	GetCellBasedPdeHandler ()

std::vector< double >	GetNodeLocation (const unsigned &rNodeIndex)

double	GetDt ()

unsigned	GetNumBirths ()

unsigned	GetNumDeaths ()

std::string	GetOutputDirectory ()

void	SetDt (double dt)

void	SetEndTime (double endTime)

void	SetOutputDirectory (std::string outputDirectory)

void	SetSamplingTimestepMultiple (unsigned samplingTimestepMultiple)

void	SetNoBirth (bool noBirth)

void	SetUpdateCellPopulationRule (bool updateCellPopulation)

bool	GetUpdateCellPopulationRule ()

void	AddCellKiller (boost::shared_ptr< AbstractCellKiller< SPACE_DIM > > pCellKiller)

void	RemoveAllCellKillers ()

void	AddSimulationModifier (boost::shared_ptr< AbstractCellBasedSimulationModifier< ELEMENT_DIM, SPACE_DIM > > pSimulationModifier)

std::vector< boost::shared_ptr < AbstractCellBasedSimulationModifier < ELEMENT_DIM, SPACE_DIM > > > *	GetSimulationModifiers ()

void	Solve ()

AbstractCellPopulation < ELEMENT_DIM, SPACE_DIM > &	rGetCellPopulation ()

const AbstractCellPopulation < ELEMENT_DIM, SPACE_DIM > &	rGetCellPopulation () const

bool	GetOutputDivisionLocations ()

void	SetOutputDivisionLocations (bool outputDivisionLocations)

bool	GetOutputCellVelocities ()

void	SetOutputCellVelocities (bool outputCellVelocities)

Public Member Functions inherited from Identifiable
virtual	~Identifiable ()

std::string	GetIdentifier () const

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

c_vector< double, 2 >	CalculateCellDivisionVector (CellPtr pParentCell)

void	SetupSolve ()

Protected Member Functions inherited from OffLatticeSimulation< 2 >
virtual void	UpdateCellLocationsAndTopology ()

virtual void	UpdateNodePositions ()

virtual void	WriteVisualizerSetupFile ()

Protected Member Functions inherited from AbstractCellBasedSimulation< ELEMENT_DIM, ELEMENT_DIM >
virtual unsigned	DoCellBirth ()

unsigned	DoCellRemoval ()

virtual bool	StoppingEventHasOccurred ()

virtual void	UpdateCellPopulation ()

void	OutputSimulationSetup ()

Protected Attributes
bool	mUsingMeshBasedCellPopulation

Protected Attributes inherited from OffLatticeSimulation< 2 >
std::vector< boost::shared_ptr < AbstractForce< ELEMENT_DIM, ELEMENT_DIM > > >	mForceCollection

std::vector< boost::shared_ptr < AbstractCellPopulationBoundaryCondition < ELEMENT_DIM, ELEMENT_DIM > > >	mBoundaryConditions

Protected Attributes inherited from AbstractCellBasedSimulation< ELEMENT_DIM, ELEMENT_DIM >
double	mDt

double	mEndTime

AbstractCellPopulation < ELEMENT_DIM, SPACE_DIM > &	mrCellPopulation

bool	mDeleteCellPopulationInDestructor

bool	mInitialiseCells

bool	mNoBirth

bool	mUpdateCellPopulation

std::string	mOutputDirectory

std::string	mSimulationOutputDirectory

out_stream	mpVizSetupFile

unsigned	mNumBirths

unsigned	mNumDeaths

bool	mOutputDivisionLocations

out_stream	mpDivisionLocationFile

bool	mOutputCellVelocities

out_stream	mpCellVelocitiesFile

std::vector< boost::shared_ptr < AbstractCellKiller < SPACE_DIM > > >	mCellKillers

std::vector< boost::shared_ptr < AbstractCellBasedSimulationModifier < ELEMENT_DIM, SPACE_DIM > > >	mSimulationModifiers

unsigned	mSamplingTimestepMultiple

CellBasedPdeHandler< SPACE_DIM > *	mpCellBasedPdeHandler

Friends
class	TestCryptSimulation2dWithMeshBasedCellPopulation

class	TestCryptSimulation2dWithVertexBasedCellPopulation

class	boost::serialization::access

Detailed Description

A 2D crypt simulation object. For more details on the crypt geometry, see the papers by van Leeuwen et al (2009) [doi:10.1111/j.1365-2184.2009.00627.x] and Osborne et al (2010) [doi:10.1098/rsta.2010.0173].

Definition at line 52 of file CryptSimulation2d.hpp.

Constructor & Destructor Documentation

CryptSimulation2d::CryptSimulation2d	(	AbstractCellPopulation< 2 > &	rCellPopulation,
		bool	deleteCellPopulationInDestructor = `false`,
		bool	initialiseCells = `true`
	)

Constructor.

Parameters

rCellPopulation	A cell population object
deleteCellPopulationInDestructor	Whether to delete the cell population on destruction to free up memory (defaults to false)
initialiseCells	whether to initialise cells (defaults to true, set to false when loading from an archive)

Definition at line 44 of file CryptSimulation2d.cpp.

References OffLatticeSimulation< 2 >::AddCellPopulationBoundaryCondition(), EXCEPTION, MAKE_PTR_ARGS, AbstractCellBasedSimulation< ELEMENT_DIM, ELEMENT_DIM >::mDeleteCellPopulationInDestructor, AbstractCellBasedSimulation< ELEMENT_DIM, ELEMENT_DIM >::mrCellPopulation, and mUsingMeshBasedCellPopulation.

CryptSimulation2d::~CryptSimulation2d ( )

virtual

Destructor.

This frees the CryptSimulationBoundaryCondition.

Definition at line 75 of file CryptSimulation2d.cpp.

Member Function Documentation

c_vector< double, 2 > CryptSimulation2d::CalculateCellDivisionVector ( CellPtr pParentCell )

protectedvirtual

In the case of a MeshBasedCellPopulationWithGhostNodes, this method calculates the new locations of a dividing cell's cell centres. The node correspond to the dividing cell is moved a bit and the co-ordinates of the new node are returned. This is done by drawing a random direction (0->2PI) and placing the parent and daughter nodes in opposing directions along this axis.

In the case of a VertexBasedCellPopulation, by default this method calls the AbstractVertexBasedDivisionRule. If the parent cell is a stem cell, then this method returns the vector (0,1). This is then used by the VertexBasedCellPopulation method AddCell() as the axis along which the cell divides.

Parameters

pParentCell the parent cell

Returns: daughter_coords the coordinates for the daughter cell.

Reimplemented from OffLatticeSimulation< 2 >.

Definition at line 79 of file CryptSimulation2d.cpp.

References WntConcentration< DIM >::Destroy(), WntConcentration< DIM >::Instance(), RandomNumberGenerator::Instance(), WntConcentration< DIM >::IsWntSetUp(), AbstractCellBasedSimulation< ELEMENT_DIM, ELEMENT_DIM >::mrCellPopulation, mUsingMeshBasedCellPopulation, and RandomNumberGenerator::ranf().

void CryptSimulation2d::OutputSimulationParameters ( out_stream & rParamsFile )

virtual

Outputs simulation 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

Reimplemented from OffLatticeSimulation< 2 >.

Definition at line 218 of file CryptSimulation2d.cpp.

References OffLatticeSimulation< 2 >::mBoundaryConditions, AbstractCellBasedSimulation< ELEMENT_DIM, ELEMENT_DIM >::mrCellPopulation, and OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::OutputSimulationParameters().

template<class Archive >

void CryptSimulation2d::serialize	(	Archive &	archive,
		const unsigned int	version
	)

inlineprotected

Archive the simulation and member variable.

Parameters

archive	the archive
version	the current version of this class

Definition at line 69 of file CryptSimulation2d.hpp.

References SerializableSingleton< SINGLETON_CLASS >::GetSerializationWrapper(), and WntConcentration< DIM >::Instance().

void CryptSimulation2d::SetBottomCellAncestors ( )

Sets the Ancestor index of all the cells at the bottom in order, can be used to trace clonal populations.

Definition at line 192 of file CryptSimulation2d.cpp.

References MAKE_PTR_ARGS, AbstractCellBasedSimulation< ELEMENT_DIM, ELEMENT_DIM >::mrCellPopulation, and mUsingMeshBasedCellPopulation.

void CryptSimulation2d::SetupSolve ( )

protectedvirtual

Overridden SetupSolve() method.

Write initial beta catenin results to file if required.

Reimplemented from OffLatticeSimulation< 2 >.

Definition at line 164 of file CryptSimulation2d.cpp.

References AbstractCellBasedSimulation< ELEMENT_DIM, ELEMENT_DIM >::mpVizSetupFile, AbstractCellBasedSimulation< ELEMENT_DIM, ELEMENT_DIM >::mrCellPopulation, and OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::SetupSolve().

void CryptSimulation2d::UseJiggledBottomCells ( )

Set method for mUseJiggledBottomCells.

Definition at line 186 of file CryptSimulation2d.cpp.

References OffLatticeSimulation< 2 >::mBoundaryConditions.

Friends And Related Function Documentation

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 61 of file CryptSimulation2d.hpp.

Member Data Documentation

bool CryptSimulation2d::mUsingMeshBasedCellPopulation

protected

Helper member that stores whether we are using a MeshBasedCellPopulationWithGhostNodes (if not, then we are assumed to be using a VertexBasedCellPopulation).

Definition at line 81 of file CryptSimulation2d.hpp.

Referenced by CalculateCellDivisionVector(), CryptSimulation2d(), and SetBottomCellAncestors().

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

crypt/src/simulation/CryptSimulation2d.hpp
crypt/src/simulation/CryptSimulation2d.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation