AbstractCellsGenerator< DIM > Class Template Reference

#include <AbstractCellsGenerator.hpp>

Inheritance diagram for AbstractCellsGenerator< DIM >:

[legend]

List of all members.

Public Member Functions
	AbstractCellsGenerator ()
virtual AbstractCellCycleModel *	CreateCellCycleModel ()=0
virtual double	GetTypicalTransitCellCycleTime ()=0
virtual double	GetTypicalStemCellCycleTime ()=0
virtual bool	CellsCanDifferentiate ()
virtual	~AbstractCellsGenerator ()
virtual void	GenerateForCrypt (std::vector< TissueCell > &rCells, TetrahedralMesh< 2, 2 > &rMesh, const std::vector< unsigned > locationIndices, bool randomBirthTimes, double y0=0.3, double y1=2.0, double y2=3.0, double y3=4.0, bool initialiseCells=false)

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Detailed Description

template<unsigned DIM>
class AbstractCellsGenerator< DIM >

A helper class for generating a vector of cells for a given mesh.

It is subclassed for different types of cell model.

Definition at line 42 of file AbstractCellsGenerator.hpp.

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Constructor & Destructor Documentation

template<unsigned DIM>

AbstractCellsGenerator< DIM >::AbstractCellsGenerator

(

)

[inline]

Default constructor.

Definition at line 49 of file AbstractCellsGenerator.hpp.

template<unsigned DIM>

virtual AbstractCellsGenerator< DIM >::~AbstractCellsGenerator

(

)

[inline, virtual]

Destructor.

Definition at line 80 of file AbstractCellsGenerator.hpp.

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Member Function Documentation

template<unsigned DIM>

virtual AbstractCellCycleModel* AbstractCellsGenerator< DIM >::CreateCellCycleModel

(

)

[pure virtual]

Returns:

a pointer to a new cell cycle model (should be implemented in subclasses)

Implemented in FixedDurationGenerationBasedCellCycleModelCellsGenerator< DIM >, IngeWntSwatCellCycleModelCellsGenerator< DIM >, SimpleWntCellCycleModelCellsGenerator< DIM >, StochasticDurationGenerationBasedCellCycleModelCellsGenerator< DIM >, StochasticWntCellCycleModelCellsGenerator< DIM >, TysonNovakCellCycleModelCellsGenerator< DIM >, and WntCellCycleModelCellsGenerator< DIM >.

Referenced by AbstractCellsGenerator< DIM >::GenerateForCrypt().

template<unsigned DIM>

virtual double AbstractCellsGenerator< DIM >::GetTypicalTransitCellCycleTime

(

)

[pure virtual]

Return the typical cell cycle duration for a transit cell, in hours. Used when giving cells random ages - the ages will follow a uniform distribution with this value as the upper limit.

Implemented in FixedDurationGenerationBasedCellCycleModelCellsGenerator< DIM >, IngeWntSwatCellCycleModelCellsGenerator< DIM >, SimpleWntCellCycleModelCellsGenerator< DIM >, StochasticDurationGenerationBasedCellCycleModelCellsGenerator< DIM >, StochasticWntCellCycleModelCellsGenerator< DIM >, TysonNovakCellCycleModelCellsGenerator< DIM >, and WntCellCycleModelCellsGenerator< DIM >.

Referenced by AbstractCellsGenerator< DIM >::GenerateForCrypt().

template<unsigned DIM>

virtual double AbstractCellsGenerator< DIM >::GetTypicalStemCellCycleTime

(

)

[pure virtual]

Return the typical cell cycle duration for a stem cell, in hours. Used when giving cells random ages - the ages will follow a uniform distribution with this value as the upper limit.

Implemented in FixedDurationGenerationBasedCellCycleModelCellsGenerator< DIM >, IngeWntSwatCellCycleModelCellsGenerator< DIM >, SimpleWntCellCycleModelCellsGenerator< DIM >, StochasticDurationGenerationBasedCellCycleModelCellsGenerator< DIM >, StochasticWntCellCycleModelCellsGenerator< DIM >, TysonNovakCellCycleModelCellsGenerator< DIM >, and WntCellCycleModelCellsGenerator< DIM >.

Referenced by AbstractCellsGenerator< DIM >::GenerateForCrypt().

template<unsigned DIM>

bool AbstractCellsGenerator< DIM >::CellsCanDifferentiate

(

)

[inline, virtual]

Whether cells are able to fully differentiate. Defaults to false unless overridden.

Reimplemented in FixedDurationGenerationBasedCellCycleModelCellsGenerator< DIM >, and StochasticDurationGenerationBasedCellCycleModelCellsGenerator< DIM >.

Definition at line 114 of file AbstractCellsGenerator.hpp.

Referenced by AbstractCellsGenerator< DIM >::GenerateForCrypt().

template<unsigned DIM>

void AbstractCellsGenerator< DIM >::GenerateForCrypt	(	std::vector< TissueCell > &	rCells,
		TetrahedralMesh< 2, 2 > &	rMesh,
		const std::vector< unsigned >	locationIndices,
		bool	randomBirthTimes,
		double	y0 = 0.3,
		double	y1 = 2.0,
		double	y2 = 3.0,
		double	y3 = 4.0,
		bool	initialiseCells = false
	)			[inline, virtual]

Generates cells of a specified cell cycle type under the correct crypt conditions and gives random ages if required, or gives them an age of 0.0 - creates least work for solver startup.

Parameters:

	rCells	An empty cells vector for this function to fill up
	rMesh	The crypt mesh (can be cylindrical)
	locationIndices	the node indices corresponding to real cells
	randomBirthTimes	Whether to assign the cells random birth times (this can be expensive computationally with ODE models)
	y0	below this line cells are generation 0 (defaults to 0.3)
	y1	below this line cells are generation 1 (defaults to 2.0)
	y2	below this line cells are generation 2 (defaults to 3.0)
	y3	below this line cells are generation 3 (defaults to 4.0)
	initialiseCells	whether to initialise the cell cycle models as each cell is created

Definition at line 120 of file AbstractCellsGenerator.hpp.

References AbstractCellsGenerator< DIM >::CellsCanDifferentiate(), AbstractCellsGenerator< DIM >::CreateCellCycleModel(), AbstractCellsGenerator< DIM >::GetTypicalStemCellCycleTime(), AbstractCellsGenerator< DIM >::GetTypicalTransitCellCycleTime(), TissueCell::InitialiseCellCycleModel(), and TissueCell::SetBirthTime().

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

• /tmp/release_1/cancer/src/tissue/cell/AbstractCellsGenerator.hpp