FarhadifarTypeModifier< DIM > Class Template Reference

#include <FarhadifarTypeModifier.hpp>

Inheritance diagram for FarhadifarTypeModifier< DIM >:

Collaboration diagram for FarhadifarTypeModifier< DIM >:

Public Member Functions
	FarhadifarTypeModifier ()
virtual	~FarhadifarTypeModifier ()
void	UpdateTargetAreaOfCell (const CellPtr pCell)
void	OutputSimulationModifierParameters (out_stream &rParamsFile)
Public Member Functions inherited from AbstractTargetAreaModifier< DIM >
	AbstractTargetAreaModifier ()
virtual	~AbstractTargetAreaModifier ()
virtual void	UpdateAtEndOfTimeStep (AbstractCellPopulation< DIM, DIM > &rCellPopulation)
virtual void	SetupSolve (AbstractCellPopulation< DIM, DIM > &rCellPopulation, std::string outputDirectory)
double	GetReferenceTargetArea ()
void	SetReferenceTargetArea (double referenceTargetArea)
void	UpdateTargetAreas (AbstractCellPopulation< DIM, DIM > &rCellPopulation)
Public Member Functions inherited from AbstractCellBasedSimulationModifier< DIM, DIM >
	AbstractCellBasedSimulationModifier ()
virtual	~AbstractCellBasedSimulationModifier ()
virtual void	UpdateAtEndOfTimeStep (AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &rCellPopulation)
virtual void	UpdateAtEndOfOutputTimeStep (AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &rCellPopulation)
virtual void	SetupSolve (AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &rCellPopulation, std::string outputDirectory)
virtual void	UpdateAtEndOfSolve (AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &rCellPopulation)
void	OutputSimulationModifierInfo (out_stream &rParamsFile)
Public Member Functions inherited from Identifiable
virtual	~Identifiable ()
std::string	GetIdentifier () const

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

Friends
class	boost::serialization::access

Additional Inherited Members
Protected Attributes inherited from AbstractTargetAreaModifier< DIM >
double	mReferenceTargetArea

Detailed Description

template<unsigned DIM>
class FarhadifarTypeModifier< DIM >

A modifier class in which the target area property of each cell is updated. It is used to implement growth in vertex-based simulations. The precise growth rule is that proposed by:

Farhadifar et al. 2007. The influence of cell mechanics, cell-cell interactions, and proliferation on epithelial packing. Current Biology 17(24):2095-2104. http://dx.doi.org/10.1016/j.cub.2007.11.049

Todo:

Consider renaming as FarhadifarTargetAreaModifier for clarity

Definition at line 58 of file FarhadifarTypeModifier.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

FarhadifarTypeModifier< DIM >::FarhadifarTypeModifier

(

)

Default constructor.

Definition at line 39 of file FarhadifarTypeModifier.cpp.

template<unsigned DIM>

FarhadifarTypeModifier< DIM >::~FarhadifarTypeModifier ( )

virtual

Destructor.

Definition at line 45 of file FarhadifarTypeModifier.cpp.

Member Function Documentation

template<unsigned DIM>

void FarhadifarTypeModifier< DIM >::OutputSimulationModifierParameters ( out_stream &  rParamsFile )

virtual

Overridden OutputSimulationModifierParameters() method. Output any simulation modifier parameters to file.

Parameters

rParamsFile

the file stream to which the parameters are output

Reimplemented from AbstractTargetAreaModifier< DIM >.

Definition at line 100 of file FarhadifarTypeModifier.cpp.

References AbstractTargetAreaModifier< DIM >::OutputSimulationModifierParameters().

template<unsigned DIM>

template<class Archive >

void FarhadifarTypeModifier< DIM >::serialize ( Archive &  archive, const unsigned int  version  )

inlineprivate

Boost Serialization method for archiving/checkpointing. Archives the object and its member variables.

Parameters

archive	The boost archive.
version	The current version of this class.

Definition at line 70 of file FarhadifarTypeModifier.hpp.

template<unsigned DIM>

void FarhadifarTypeModifier< DIM >::UpdateTargetAreaOfCell ( const CellPtr  pCell )

virtual

Helper method to update the target area property of an individual cell.

Parameters

pCell

pointer to a cell

Todo:

: which cells are apoptotic? if they get apoptotic during G2-phase then this line has to be changed

At division, daughter cells inherit the cell data array from the mother cell. Here, we assign the target area that we want daughter cells to have to cells that we know to divide in this time step.

Todo:

This is a little hack that we might want to clean up in the future.

Implements AbstractTargetAreaModifier< DIM >.

Definition at line 50 of file FarhadifarTypeModifier.cpp.

References AbstractCellCycleModel::GetG1Duration(), AbstractCellCycleModel::GetG2Duration(), AbstractCellCycleModel::GetMDuration(), AbstractCellCycleModel::GetSDuration(), SimulationTime::GetTime(), and SimulationTime::Instance().

Friends And Related Function Documentation

template<unsigned DIM>

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 61 of file FarhadifarTypeModifier.hpp.

---

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

• cell_based/src/simulation/modifiers/FarhadifarTypeModifier.hpp
• cell_based/src/simulation/modifiers/FarhadifarTypeModifier.cpp