SimpleTargetAreaModifier< DIM > Class Template Reference

#include <SimpleTargetAreaModifier.hpp>

Inheritance diagram for SimpleTargetAreaModifier< DIM >:

Collaboration diagram for SimpleTargetAreaModifier< DIM >:

Public Member Functions
	SimpleTargetAreaModifier ()
virtual	~SimpleTargetAreaModifier ()
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

Friends
class	boost::serialization::access

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

Detailed Description

template<unsigned DIM>
class SimpleTargetAreaModifier< DIM >

A target area modifier class in which the target area of a cell grows linearly, up to mReferenceTargetArea, over a prescribed duration.

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 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 up to mReferenceTargetArea 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 SimpleTargetAreaModifier.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

SimpleTargetAreaModifier< DIM >::SimpleTargetAreaModifier

(

)

Default constructor.

Definition at line 41 of file SimpleTargetAreaModifier.cpp.

template<unsigned DIM>

SimpleTargetAreaModifier< DIM >::~SimpleTargetAreaModifier ( )

virtual

Destructor.

Definition at line 48 of file SimpleTargetAreaModifier.cpp.

Member Function Documentation

template<unsigned DIM>

double SimpleTargetAreaModifier< DIM >::GetGrowthDuration

(

)

Returns

mGrowthDuration

Definition at line 124 of file SimpleTargetAreaModifier.cpp.

References SimpleTargetAreaModifier< DIM >::mGrowthDuration.

template<unsigned DIM>

void SimpleTargetAreaModifier< 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 137 of file SimpleTargetAreaModifier.cpp.

References EXPORT_TEMPLATE_CLASS_SAME_DIMS, SimpleTargetAreaModifier< DIM >::mGrowthDuration, and AbstractTargetAreaModifier< DIM >::OutputSimulationModifierParameters().

template<unsigned DIM>

template<class Archive >

void SimpleTargetAreaModifier< 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 SimpleTargetAreaModifier.hpp.

References SimpleTargetAreaModifier< DIM >::mGrowthDuration.

template<unsigned DIM>

void SimpleTargetAreaModifier< DIM >::SetGrowthDuration

(

double

growthDuration

)

Set mGrowthDuration.

Parameters

growthDuration

the new value of mGrowthDuration

Definition at line 130 of file SimpleTargetAreaModifier.cpp.

References SimpleTargetAreaModifier< DIM >::mGrowthDuration.

template<unsigned DIM>

void SimpleTargetAreaModifier< 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 53 of file SimpleTargetAreaModifier.cpp.

References DOUBLE_UNSET, EXCEPTION, AbstractPhaseBasedCellCycleModel::GetG1Duration(), SimulationTime::GetTime(), AbstractPhaseBasedCellCycleModel::GetTransitCellG1Duration(), SimulationTime::Instance(), SimpleTargetAreaModifier< DIM >::mGrowthDuration, and AbstractTargetAreaModifier< DIM >::mReferenceTargetArea.

Friends And Related Function Documentation

template<unsigned DIM>

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 66 of file SimpleTargetAreaModifier.hpp.

Member Data Documentation

template<unsigned DIM>

double SimpleTargetAreaModifier< 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 87 of file SimpleTargetAreaModifier.hpp.

Referenced by SimpleTargetAreaModifier< DIM >::GetGrowthDuration(), SimpleTargetAreaModifier< DIM >::OutputSimulationModifierParameters(), SimpleTargetAreaModifier< DIM >::serialize(), SimpleTargetAreaModifier< DIM >::SetGrowthDuration(), and SimpleTargetAreaModifier< DIM >::UpdateTargetAreaOfCell().

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

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