#include <DifferentialAdhesionPottsUpdateRule.hpp>

Inheritance diagram for DifferentialAdhesionPottsUpdateRule< DIM >:

Collaboration diagram for DifferentialAdhesionPottsUpdateRule< DIM >:

Public Member Functions
	DifferentialAdhesionPottsUpdateRule ()

virtual	~DifferentialAdhesionPottsUpdateRule ()

virtual double	GetCellCellAdhesionEnergy (CellPtr pCellA, CellPtr pCellB)

virtual double	GetCellBoundaryAdhesionEnergy (CellPtr pCell)

double	GetLabelledCellLabelledCellAdhesionEnergyParameter ()

double	GetLabelledCellCellAdhesionEnergyParameter ()

double	GetLabelledCellBoundaryAdhesionEnergyParameter ()

void	SetLabelledCellLabelledCellAdhesionEnergyParameter (double labelledCellLabelledCellAdhesionEnergyParameter)

void	SetLabelledCellCellAdhesionEnergyParameter (double labelledCellCellAdhesionEnergyParameter)

void	SetLabelledCellBoundaryAdhesionEnergyParameter (double labelledCellBoundaryAdhesionEnergyParameter)

void	OutputUpdateRuleParameters (out_stream &rParamsFile)

Public Member Functions inherited from AdhesionPottsUpdateRule< DIM >
	AdhesionPottsUpdateRule ()

virtual	~AdhesionPottsUpdateRule ()

double	EvaluateHamiltonianContribution (unsigned currentNodeIndex, unsigned targetNodeIndex, PottsBasedCellPopulation< DIM > &rCellPopulation)

double	GetCellCellAdhesionEnergyParameter ()

double	GetCellBoundaryAdhesionEnergyParameter ()

void	SetCellCellAdhesionEnergyParameter (double cellCellAdhesionEnergyEnergyParameter)

void	SetCellBoundaryAdhesionEnergyParameter (double cellBoundaryAdhesionEnergyParameter)

Public Member Functions inherited from AbstractPottsUpdateRule< DIM >
	AbstractPottsUpdateRule ()

virtual	~AbstractPottsUpdateRule ()

Public Member Functions inherited from AbstractUpdateRule< DIM >
	AbstractUpdateRule ()

virtual	~AbstractUpdateRule ()

void	OutputUpdateRuleInfo (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	mLabelledCellLabelledCellAdhesionEnergyParameter

double	mLabelledCellCellAdhesionEnergyParameter

double	mLabelledCellBoundaryAdhesionEnergyParameter

Friends
class	TestPottsUpdateRules

class	boost::serialization::access

Detailed Description

template<unsigned DIM>
class DifferentialAdhesionPottsUpdateRule< DIM >

An adhesion update rule for use in cell-based simulations using the cellular Potts model. This rule implements differential adhesion between unlabelled and labelled cells

Definition at line 50 of file DifferentialAdhesionPottsUpdateRule.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

DifferentialAdhesionPottsUpdateRule< DIM >::DifferentialAdhesionPottsUpdateRule ( )

Constructor.

Definition at line 41 of file DifferentialAdhesionPottsUpdateRule.cpp.

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

template<unsigned DIM>

DifferentialAdhesionPottsUpdateRule< DIM >::~DifferentialAdhesionPottsUpdateRule ( )

virtual

Destructor.

Definition at line 50 of file DifferentialAdhesionPottsUpdateRule.cpp.

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

Member Function Documentation

template<unsigned DIM>

double DifferentialAdhesionPottsUpdateRule< DIM >::GetCellBoundaryAdhesionEnergy ( CellPtr pCell )

virtual

Overridden GetCellBoundaryAdhesionEnergy method to implement differential adhesion.

Parameters

pCell pointer to the cell

Returns: Cell boundary interaction adhesion energy for the cell

Reimplemented from AdhesionPottsUpdateRule< DIM >.

Definition at line 72 of file DifferentialAdhesionPottsUpdateRule.cpp.

References AdhesionPottsUpdateRule< DIM >::GetCellBoundaryAdhesionEnergyParameter(), and DifferentialAdhesionPottsUpdateRule< DIM >::GetLabelledCellBoundaryAdhesionEnergyParameter().

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

template<unsigned DIM>

double DifferentialAdhesionPottsUpdateRule< DIM >::GetCellCellAdhesionEnergy	(	CellPtr	pCellA,
		CellPtr	pCellB
	)

virtual

Overridden GetCellCellAdhesionEnergy method to implement differential adhesion.

Parameters

pCellA	pointer to the 1st cell
pCellB	pointer to the 2nd cell

Returns: The cell cell interaction adhesion energy between the two cells

Reimplemented from AdhesionPottsUpdateRule< DIM >.

Definition at line 55 of file DifferentialAdhesionPottsUpdateRule.cpp.

References AdhesionPottsUpdateRule< DIM >::GetCellCellAdhesionEnergyParameter(), DifferentialAdhesionPottsUpdateRule< DIM >::GetLabelledCellCellAdhesionEnergyParameter(), and DifferentialAdhesionPottsUpdateRule< DIM >::GetLabelledCellLabelledCellAdhesionEnergyParameter().

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

template<unsigned DIM>

double DifferentialAdhesionPottsUpdateRule< DIM >::GetLabelledCellBoundaryAdhesionEnergyParameter ( )

Returns: mLabelledCellBoundaryAdhesionEnergyParameter

Definition at line 97 of file DifferentialAdhesionPottsUpdateRule.cpp.

References DifferentialAdhesionPottsUpdateRule< DIM >::mLabelledCellBoundaryAdhesionEnergyParameter.

Referenced by DifferentialAdhesionPottsUpdateRule< DIM >::GetCellBoundaryAdhesionEnergy(), and DifferentialAdhesionPottsUpdateRule< DIM >::serialize().

template<unsigned DIM>

double DifferentialAdhesionPottsUpdateRule< DIM >::GetLabelledCellCellAdhesionEnergyParameter ( )

Returns: mLabelledCellCellAdhesionEnergyParameter

Definition at line 91 of file DifferentialAdhesionPottsUpdateRule.cpp.

References DifferentialAdhesionPottsUpdateRule< DIM >::mLabelledCellCellAdhesionEnergyParameter.

Referenced by DifferentialAdhesionPottsUpdateRule< DIM >::GetCellCellAdhesionEnergy(), and DifferentialAdhesionPottsUpdateRule< DIM >::serialize().

template<unsigned DIM>

double DifferentialAdhesionPottsUpdateRule< DIM >::GetLabelledCellLabelledCellAdhesionEnergyParameter ( )

Returns: mLabelledCellLabelledCellAdhesionEnergyParameter

Definition at line 85 of file DifferentialAdhesionPottsUpdateRule.cpp.

References DifferentialAdhesionPottsUpdateRule< DIM >::mLabelledCellLabelledCellAdhesionEnergyParameter.

Referenced by DifferentialAdhesionPottsUpdateRule< DIM >::GetCellCellAdhesionEnergy(), and DifferentialAdhesionPottsUpdateRule< DIM >::serialize().

template<unsigned DIM>

void DifferentialAdhesionPottsUpdateRule< DIM >::OutputUpdateRuleParameters ( out_stream & rParamsFile )

virtual

Overridden OutputUpdateRuleParameters() method.

Parameters

rParamsFile the file stream to which the parameters are output

Reimplemented from AdhesionPottsUpdateRule< DIM >.

Definition at line 121 of file DifferentialAdhesionPottsUpdateRule.cpp.

References EXPORT_TEMPLATE_CLASS_SAME_DIMS, DifferentialAdhesionPottsUpdateRule< DIM >::mLabelledCellBoundaryAdhesionEnergyParameter, DifferentialAdhesionPottsUpdateRule< DIM >::mLabelledCellCellAdhesionEnergyParameter, DifferentialAdhesionPottsUpdateRule< DIM >::mLabelledCellLabelledCellAdhesionEnergyParameter, and AdhesionPottsUpdateRule< DIM >::OutputUpdateRuleParameters().

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

template<unsigned DIM>

template<class Archive >

void DifferentialAdhesionPottsUpdateRule< 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 86 of file DifferentialAdhesionPottsUpdateRule.hpp.

template<unsigned DIM>

void DifferentialAdhesionPottsUpdateRule< DIM >::SetLabelledCellBoundaryAdhesionEnergyParameter ( double labelledCellBoundaryAdhesionEnergyParameter )

Set mLabelledCellBoundaryAdhesionEnergyParameter.

Parameters

labelledCellBoundaryAdhesionEnergyParameter the new value of mLabelledCellBoundaryAdhesionEnergyParameter

Definition at line 115 of file DifferentialAdhesionPottsUpdateRule.cpp.

References DifferentialAdhesionPottsUpdateRule< DIM >::mLabelledCellBoundaryAdhesionEnergyParameter.

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

template<unsigned DIM>

void DifferentialAdhesionPottsUpdateRule< DIM >::SetLabelledCellCellAdhesionEnergyParameter ( double labelledCellCellAdhesionEnergyParameter )

Set mLabelledCellCellAdhesionEnergyParameter.

Parameters

labelledCellCellAdhesionEnergyParameter the new value of mLabelledCelldCellAdhesionEnergyParameter

Definition at line 109 of file DifferentialAdhesionPottsUpdateRule.cpp.

References DifferentialAdhesionPottsUpdateRule< DIM >::mLabelledCellCellAdhesionEnergyParameter.

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

template<unsigned DIM>

void DifferentialAdhesionPottsUpdateRule< DIM >::SetLabelledCellLabelledCellAdhesionEnergyParameter ( double labelledCellLabelledCellAdhesionEnergyParameter )

Set mLabelledCellLabelledCellAdhesionEnergyParameter.

Parameters

labelledCellLabelledCellAdhesionEnergyParameter the new value of mLabelledCellLabelledCellAdhesionEnergyParameter

Definition at line 103 of file DifferentialAdhesionPottsUpdateRule.cpp.

References DifferentialAdhesionPottsUpdateRule< DIM >::mLabelledCellLabelledCellAdhesionEnergyParameter.

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

Member Data Documentation

template<unsigned DIM>

double DifferentialAdhesionPottsUpdateRule< DIM >::mLabelledCellBoundaryAdhesionEnergyParameter

private

LabelledCell-boundary adhesion energy parameter. Set to the default value 0.2 in the constructor.

Todo:: provide units

Definition at line 75 of file DifferentialAdhesionPottsUpdateRule.hpp.

Referenced by DifferentialAdhesionPottsUpdateRule< DIM >::GetLabelledCellBoundaryAdhesionEnergyParameter(), DifferentialAdhesionPottsUpdateRule< DIM >::OutputUpdateRuleParameters(), DifferentialAdhesionPottsUpdateRule< DIM >::serialize(), and DifferentialAdhesionPottsUpdateRule< DIM >::SetLabelledCellBoundaryAdhesionEnergyParameter().

template<unsigned DIM>

double DifferentialAdhesionPottsUpdateRule< DIM >::mLabelledCellCellAdhesionEnergyParameter

private

LablledCell-cell adhesion energy parameter. Set to the default value 0.1 in the constructor.

Todo:: provide units

Definition at line 68 of file DifferentialAdhesionPottsUpdateRule.hpp.

Referenced by DifferentialAdhesionPottsUpdateRule< DIM >::GetLabelledCellCellAdhesionEnergyParameter(), DifferentialAdhesionPottsUpdateRule< DIM >::OutputUpdateRuleParameters(), DifferentialAdhesionPottsUpdateRule< DIM >::serialize(), and DifferentialAdhesionPottsUpdateRule< DIM >::SetLabelledCellCellAdhesionEnergyParameter().

template<unsigned DIM>

double DifferentialAdhesionPottsUpdateRule< DIM >::mLabelledCellLabelledCellAdhesionEnergyParameter

private

LabelledCell-LabelledCell adhesion energy parameter. Set to the default value 0.1 in the constructor.

Todo:: provide units

Definition at line 61 of file DifferentialAdhesionPottsUpdateRule.hpp.

Referenced by DifferentialAdhesionPottsUpdateRule< DIM >::GetLabelledCellLabelledCellAdhesionEnergyParameter(), DifferentialAdhesionPottsUpdateRule< DIM >::OutputUpdateRuleParameters(), DifferentialAdhesionPottsUpdateRule< DIM >::serialize(), and DifferentialAdhesionPottsUpdateRule< DIM >::SetLabelledCellLabelledCellAdhesionEnergyParameter().

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

cell_based/src/population/update_rules/DifferentialAdhesionPottsUpdateRule.hpp
cell_based/src/population/update_rules/DifferentialAdhesionPottsUpdateRule.cpp

Public Member Functions

Private Member Functions

Private Attributes

Friends

Detailed Description

template<unsigned DIM> class DifferentialAdhesionPottsUpdateRule< DIM >

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

template<unsigned DIM>
class DifferentialAdhesionPottsUpdateRule< DIM >