#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)
Protected Member Functions
template<class Archive >
void	serialize (Archive &archive, const unsigned int version)
c_vector< double, 2 >	CalculateCellDivisionVector (CellPtr pParentCell)
void	SetupWriteBetaCatenin ()
virtual void	WriteBetaCatenin (double time)
void	SetupSolve ()
void	UpdateAtEndOfTimeStep ()
void	UpdateAtEndOfSolve ()
Protected Attributes
bool	mWriteBetaCatenin
out_stream	mVizBetaCateninResultsFile
bool	mUsingMeshBasedCellPopulation
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 53 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 42 of file CryptSimulation2d.cpp.

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

CryptSimulation2d::~CryptSimulation2d ( ) [virtual]

Destructor.

This frees the CryptSimulationBoundaryCondition.

Definition at line 85 of file CryptSimulation2d.cpp.

Member Function Documentation

c_vector< double, 2 > CryptSimulation2d::CalculateCellDivisionVector ( CellPtr pParentCell ) [protected, virtual]

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 returns the zero vector. 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 89 of file CryptSimulation2d.cpp.

References 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 289 of file CryptSimulation2d.cpp.

References OffLatticeSimulation< 2 >::mBoundaryConditions, and AbstractCellBasedSimulation< ELEMENT_DIM, ELEMENT_DIM >::mrCellPopulation.

template<class Archive >

void CryptSimulation2d::serialize	(	Archive &	archive,
		const unsigned int	version
	)		`[inline, protected]`

Archive the simulation and member variable.

Parameters:

archive	the archive
version	the current version of this class

Reimplemented from OffLatticeSimulation< 2 >.

Definition at line 70 of file CryptSimulation2d.hpp.

References SerializableSingleton< SINGLETON_CLASS >::GetSerializationWrapper(), and mWriteBetaCatenin.

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 263 of file CryptSimulation2d.cpp.

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

void CryptSimulation2d::SetupSolve ( ) [protected, virtual]

Overridden SetupSolve() method.

Write initial beta catenin results to file if required.

Reimplemented from OffLatticeSimulation< 2 >.

Definition at line 202 of file CryptSimulation2d.cpp.

References SimulationTime::GetTime(), SimulationTime::Instance(), AbstractCellBasedSimulation< ELEMENT_DIM, ELEMENT_DIM >::mrCellPopulation, mWriteBetaCatenin, SetupWriteBetaCatenin(), and WriteBetaCatenin().

void CryptSimulation2d::SetupWriteBetaCatenin ( ) [protected]

Use an output file handler to create a beta catenin results file.

Definition at line 169 of file CryptSimulation2d.cpp.

References AbstractCellBasedSimulation< ELEMENT_DIM, ELEMENT_DIM >::mpVizSetupFile, AbstractCellBasedSimulation< ELEMENT_DIM, ELEMENT_DIM >::mSimulationOutputDirectory, mVizBetaCateninResultsFile, and OutputFileHandler::OpenOutputFile().

Referenced by SetupSolve().

void CryptSimulation2d::UpdateAtEndOfSolve ( ) [protected, virtual]

Overridden UpdateAtEndOfSolve() method.

Closes beta catenin results file if required, then calls the base class method.

Reimplemented from OffLatticeSimulation< 2 >.

Definition at line 241 of file CryptSimulation2d.cpp.

References AbstractCellBasedSimulation< ELEMENT_DIM, ELEMENT_DIM >::mrCellPopulation, mVizBetaCateninResultsFile, and mWriteBetaCatenin.

void CryptSimulation2d::UpdateAtEndOfTimeStep ( ) [protected, virtual]

Overridden UpdateAtEndOfTimeStep() method.

Write current beta catenin results to file if required.

Reimplemented from AbstractCellBasedSimulation< ELEMENT_DIM, ELEMENT_DIM >.

Definition at line 221 of file CryptSimulation2d.cpp.

References SimulationTime::GetTime(), SimulationTime::GetTimeStep(), SimulationTime::GetTimeStepsElapsed(), SimulationTime::Instance(), AbstractCellBasedSimulation< ELEMENT_DIM, ELEMENT_DIM >::mrCellPopulation, AbstractCellBasedSimulation< ELEMENT_DIM, ELEMENT_DIM >::mSamplingTimestepMultiple, mWriteBetaCatenin, and WriteBetaCatenin().

void CryptSimulation2d::UseJiggledBottomCells ( )

Set method for mUseJiggledBottomCells.

Definition at line 257 of file CryptSimulation2d.cpp.

References OffLatticeSimulation< 2 >::mBoundaryConditions.

void CryptSimulation2d::WriteBetaCatenin ( double time ) [protected, virtual]

Write beta catenin results to file.

Parameters:

time	the current time

Definition at line 176 of file CryptSimulation2d.cpp.

References AbstractVanLeeuwen2009WntSwatCellCycleModel::GetCytoplasmicBetaCateninLevel(), AbstractVanLeeuwen2009WntSwatCellCycleModel::GetMembraneBoundBetaCateninLevel(), AbstractVanLeeuwen2009WntSwatCellCycleModel::GetNuclearBetaCateninLevel(), AbstractCellBasedSimulation< ELEMENT_DIM, ELEMENT_DIM >::mrCellPopulation, mVizBetaCateninResultsFile, and mWriteBetaCatenin.

Referenced by SetupSolve(), and UpdateAtEndOfTimeStep().

Friends And Related Function Documentation

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

Needed for serialization.

Reimplemented from OffLatticeSimulation< 2 >.

Definition at line 62 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 95 of file CryptSimulation2d.hpp.

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

out_stream CryptSimulation2d::mVizBetaCateninResultsFile [protected]

The file that the values of beta catenin is written out to.

Definition at line 89 of file CryptSimulation2d.hpp.

Referenced by SetupWriteBetaCatenin(), UpdateAtEndOfSolve(), and WriteBetaCatenin().

bool CryptSimulation2d::mWriteBetaCatenin [protected]

Whether the simulation includes the cell-cycle models VanLeeuwen2009WntSwatCellCycleModelHypothesisOne or VanLeeuwen2009WntSwatCellCycleModelHypothesisOne, and hence whether beta catenin results are written to file.

Definition at line 86 of file CryptSimulation2d.hpp.

Referenced by CryptSimulation2d(), serialize(), SetupSolve(), UpdateAtEndOfSolve(), UpdateAtEndOfTimeStep(), and WriteBetaCatenin().

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