CryptSimulation2d Class Reference

#include <CryptSimulation2d.hpp>

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	PostSolve ()
void	AfterSolve ()
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 46 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 35 of file CryptSimulation2d.cpp.

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

CryptSimulation2d::~CryptSimulation2d ( ) [virtual]

Destructor.

This frees the CryptSimulationBoundaryCondition.

Definition at line 78 of file CryptSimulation2d.cpp.

Member Function Documentation

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

Overridden AfterSolve() method.

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

Reimplemented from OffLatticeSimulation< 2 >.

Definition at line 237 of file CryptSimulation2d.cpp.

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

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 82 of file CryptSimulation2d.cpp.

References RandomNumberGenerator::Instance(), AbstractCellBasedSimulation< 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 284 of file CryptSimulation2d.cpp.

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

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

Overridden PostSolve() method.

Write current beta catenin results to file if required.

Reimplemented from AbstractCellBasedSimulation< DIM >.

Definition at line 214 of file CryptSimulation2d.cpp.

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

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 63 of file CryptSimulation2d.hpp.

References 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 259 of file CryptSimulation2d.cpp.

References AbstractCellBasedSimulation< 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 195 of file CryptSimulation2d.cpp.

References SimulationTime::GetTime(), SimulationTime::Instance(), AbstractCellBasedSimulation< 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 162 of file CryptSimulation2d.cpp.

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

Referenced by SetupSolve().

void CryptSimulation2d::UseJiggledBottomCells ( )

Set method for mUseJiggledBottomCells.

Definition at line 253 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 169 of file CryptSimulation2d.cpp.

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

Referenced by PostSolve(), and SetupSolve().

Friends And Related Function Documentation

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

Needed for serialization.

Reimplemented from OffLatticeSimulation< 2 >.

Definition at line 55 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 88 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 82 of file CryptSimulation2d.hpp.

Referenced by AfterSolve(), SetupWriteBetaCatenin(), 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 79 of file CryptSimulation2d.hpp.

Referenced by AfterSolve(), CryptSimulation2d(), PostSolve(), serialize(), SetupSolve(), and WriteBetaCatenin().

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