AbstractCellsGenerator< DIM > Class Template Reference

#include <AbstractCellsGenerator.hpp>

Inheritance diagram for AbstractCellsGenerator< DIM >:

Inheritance graph
[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 ()
void GenerateBasic (std::vector< TissueCell > &rCells, const unsigned numCells)
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)

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 43 of file AbstractCellsGenerator.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>
AbstractCellsGenerator< DIM >::AbstractCellsGenerator (  )  [inline]

Default constructor.

Definition at line 50 of file AbstractCellsGenerator.hpp.

template<unsigned DIM>
virtual AbstractCellsGenerator< DIM >::~AbstractCellsGenerator (  )  [inline, virtual]

Destructor.

Definition at line 81 of file AbstractCellsGenerator.hpp.

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 >::GenerateBasic(), and 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 36 of file AbstractCellsGenerator.cpp.

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

template<unsigned DIM>
void AbstractCellsGenerator< DIM >::GenerateBasic ( std::vector< TissueCell > &  rCells,
const unsigned  numCells 
) [inline]

Fills a vector of cells with a specified cell cycle model, to match a given number of cells. Gives them birth times of 0 for node 0, -1 for node 1, -2 for node 2 etc...

Parameters:
rCells An empty vector of cells to fill up.
numCells The number of cells to generate.

Definition at line 158 of file AbstractCellsGenerator.cpp.

References AbstractCellsGenerator< DIM >::CreateCellCycleModel(), and TissueCell::SetBirthTime().

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 42 of file AbstractCellsGenerator.cpp.

References AbstractCellsGenerator< DIM >::CellsCanDifferentiate(), AbstractCellsGenerator< DIM >::CreateCellCycleModel(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNode(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), AbstractCellsGenerator< DIM >::GetTypicalStemCellCycleTime(), AbstractCellsGenerator< DIM >::GetTypicalTransitCellCycleTime(), TissueCell::InitialiseCellCycleModel(), RandomNumberGenerator::Instance(), RandomNumberGenerator::ranf(), and TissueCell::SetBirthTime().

The documentation for this class was generated from the following files:
Generated on Tue Aug 4 16:10:35 2009 for Chaste by  doxygen 1.5.5