#include <NormallyDistributedTargetAreaModifier.hpp>

Inheritance diagram for NormallyDistributedTargetAreaModifier< DIM >:

Collaboration diagram for NormallyDistributedTargetAreaModifier< DIM >:

Public Member Functions
	NormallyDistributedTargetAreaModifier ()

virtual	~NormallyDistributedTargetAreaModifier ()

virtual void	UpdateTargetAreaOfCell (const CellPtr pCell)

double	GetGrowthDuration ()

void	SetGrowthDuration (double growthDuration)

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)=0

virtual void	UpdateAtEndOfOutputTimeStep (AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &rCellPopulation)

virtual void	SetupSolve (AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &rCellPopulation, std::string outputDirectory)=0

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)

Private Attributes
double	mGrowthDuration

std::vector< double >	mNormalRandomNumbers

Friends
class	boost::serialization::access

class	TestNormallyDistributedTargetAreaModifier

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

Detailed Description

template<unsigned DIM>
class NormallyDistributedTargetAreaModifier< DIM >

A target area modifier class in which the target area of a cell grows linearly, up to mReferenceTargetArea * n, over a prescribed duration, where n is picked from a normal distribution.

If used with a phase-based cell-cycle model (such as FixedG1GenerationalCellCycleModel), the target area of a cell increases linearly from the value 0.5*mReferenceTargetArea*n up to mReferenceTargetArea over the course of the cell's G1 phase.

If used with a non-phase-based cell-cycle model, the target area of a cell increases linearly from the value 0.5*mReferenceTargetArea*n up to mReferenceTargetArea*n while the cell's age is less than mGrowthDuration.

Here mReferenceTargetArea and mGrowthDuration are settable member variables. The default value of mReferenceTargetArea is 1.0 and the default value of mGrowthDuration is DOUBLE_UNSET.

Note that if mGrowthDuration is set by the user, then this value is are used to prescribe target area growth as described earlier, regardless of whether a phase-based cell-cycle model is present.

Definition at line 63 of file NormallyDistributedTargetAreaModifier.hpp.

Constructor & Destructor Documentation

◆ NormallyDistributedTargetAreaModifier()

template<unsigned DIM>

NormallyDistributedTargetAreaModifier< DIM >::NormallyDistributedTargetAreaModifier ( )

Default constructor.

Definition at line 44 of file NormallyDistributedTargetAreaModifier.cpp.

◆ ~NormallyDistributedTargetAreaModifier()

template<unsigned DIM>

NormallyDistributedTargetAreaModifier< DIM >::~NormallyDistributedTargetAreaModifier ( )

virtual

Destructor.

Definition at line 51 of file NormallyDistributedTargetAreaModifier.cpp.

Member Function Documentation

◆ GetGrowthDuration()

template<unsigned DIM>

double NormallyDistributedTargetAreaModifier< DIM >::GetGrowthDuration ( )

Returns: mGrowthDuration

Definition at line 140 of file NormallyDistributedTargetAreaModifier.cpp.

◆ OutputSimulationModifierParameters()

template<unsigned DIM>

void NormallyDistributedTargetAreaModifier< 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 153 of file NormallyDistributedTargetAreaModifier.cpp.

References AbstractTargetAreaModifier< DIM >::OutputSimulationModifierParameters().

◆ serialize()

template<unsigned DIM>

template<class Archive >

void NormallyDistributedTargetAreaModifier< 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 75 of file NormallyDistributedTargetAreaModifier.hpp.

References NormallyDistributedTargetAreaModifier< DIM >::mGrowthDuration.

◆ SetGrowthDuration()

template<unsigned DIM>

void NormallyDistributedTargetAreaModifier< DIM >::SetGrowthDuration ( double growthDuration )

Set mGrowthDuration.

Parameters

growthDuration the new value of mGrowthDuration

Definition at line 146 of file NormallyDistributedTargetAreaModifier.cpp.

◆ UpdateTargetAreaOfCell()

template<unsigned DIM>

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

virtual

Overridden UpdateTargetAreaOfCell() method.

Parameters

pCell pointer to the cell

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 56 of file NormallyDistributedTargetAreaModifier.cpp.

References DOUBLE_UNSET, EXCEPTION, AbstractPhaseBasedCellCycleModel::GetG1Duration(), SimulationTime::GetTime(), AbstractPhaseBasedCellCycleModel::GetTransitCellG1Duration(), SimulationTime::Instance(), RandomNumberGenerator::Instance(), and RandomNumberGenerator::NormalRandomDeviate().

Friends And Related Symbol Documentation

◆ boost::serialization::access

template<unsigned DIM>

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 66 of file NormallyDistributedTargetAreaModifier.hpp.

◆ TestNormallyDistributedTargetAreaModifier

template<unsigned DIM>

friend class TestNormallyDistributedTargetAreaModifier

friend

Definition at line 81 of file NormallyDistributedTargetAreaModifier.hpp.

Member Data Documentation

◆ mGrowthDuration

template<unsigned DIM>

double NormallyDistributedTargetAreaModifier< DIM >::mGrowthDuration

private

The duration that a cell's target area to increase from 0.5*mReferenceTargetArea to mReferenceTargetArea at the start of its cell cycle. Defaults to DOUBLE_UNSET. If this variable is set using SetGrowthDuration(), then it is used regardless of whether a phase-based cell-cycle model is used.

Definition at line 89 of file NormallyDistributedTargetAreaModifier.hpp.

Referenced by NormallyDistributedTargetAreaModifier< DIM >::serialize().