WntConcentration< DIM > Class Template Reference

#include <WntConcentration.hpp>

Inheritance diagram for WntConcentration< DIM >:

Collaboration diagram for WntConcentration< DIM >:

Public Member Functions
virtual	~WntConcentration ()
double	GetWntLevel (double height)
double	GetWntLevel (CellPtr pCell)
c_vector< double, DIM >	GetWntGradient (c_vector< double, DIM > &rLocation)
c_vector< double, DIM >	GetWntGradient (CellPtr pCell)
void	SetCellPopulation (AbstractCellPopulation< DIM > &rCellPopulation)
AbstractCellPopulation< DIM > &	rGetCellPopulation ()
double	GetCryptLength ()
void	SetCryptLength (double cryptLength)
WntConcentrationType	GetType ()
void	SetType (WntConcentrationType type)
void	SetConstantWntValueForTesting (double value)
bool	IsWntSetUp ()
double	GetWntConcentrationParameter ()
void	SetWntConcentrationParameter (double wntConcentrationParameter)
double	GetCryptProjectionParameterA ()
double	GetCryptProjectionParameterB ()
void	SetCryptProjectionParameterA (double cryptProjectionParameterA)
void	SetCryptProjectionParameterB (double cryptProjectionParameterB)
Public Member Functions inherited from SerializableSingleton< WntConcentration< DIM > >
SerializableSingleton< WntConcentration< DIM > > *	GetSerializationWrapper () const

Static Public Member Functions
static WntConcentration *	Instance ()
static void	Destroy ()

Protected Member Functions
	WntConcentration ()

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

Private Attributes
double	mCryptLength
bool	mLengthSet
WntConcentrationType	mWntType
AbstractCellPopulation< DIM > *	mpCellPopulation
bool	mTypeSet
double	mConstantWntValueForTesting
bool	mUseConstantWntValueForTesting
double	mWntConcentrationParameter
double	mCryptProjectionParameterA
double	mCryptProjectionParameterB

Static Private Attributes
static WntConcentration *	mpInstance = nullptr

Friends
class	boost::serialization::access

Detailed Description

template<unsigned DIM>
class WntConcentration< DIM >

Singleton Wnt concentration object.

Definition at line 66 of file WntConcentration.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

WntConcentration< DIM >::WntConcentration ( )

protected

Protected constuctor. Not to be called, use Instance() instead.

Definition at line 52 of file WntConcentration.cpp.

References WntConcentration< DIM >::mpInstance.

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

template<unsigned DIM>

WntConcentration< DIM >::~WntConcentration ( )

virtual

Destructor - frees up the singleton instance.

Definition at line 69 of file WntConcentration.cpp.

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

Member Function Documentation

template<unsigned DIM>

void WntConcentration< DIM >::Destroy ( )

static

Destroy the current WntConcentration instance. Should be called at the end of a simulation.

Definition at line 74 of file WntConcentration.cpp.

References WntConcentration< DIM >::mpInstance.

Referenced by CryptVertexBasedDivisionRule< SPACE_DIM >::CalculateCellDivisionVector(), CryptSimulationBoundaryCondition< DIM >::ImposeBoundaryCondition(), and WntConcentration< DIM >::serialize().

template<unsigned DIM>

double WntConcentration< DIM >::GetCryptLength

(

)

Returns

mCryptLength

Definition at line 140 of file WntConcentration.cpp.

References WntConcentration< DIM >::mCryptLength.

Referenced by WntConcentration< DIM >::GetWntGradient(), WntConcentration< DIM >::GetWntLevel(), and WntConcentration< DIM >::serialize().

template<unsigned DIM>

double WntConcentration< DIM >::GetCryptProjectionParameterA

(

)

Returns

mCryptProjectionParameterA

Definition at line 299 of file WntConcentration.cpp.

References WntConcentration< DIM >::mCryptProjectionParameterA.

Referenced by CryptProjectionForce::CryptProjectionForce(), WntConcentration< DIM >::GetWntGradient(), WntConcentration< DIM >::GetWntLevel(), and WntConcentration< DIM >::serialize().

template<unsigned DIM>

double WntConcentration< DIM >::GetCryptProjectionParameterB

(

)

Returns

mCryptProjectionParameterB

Definition at line 305 of file WntConcentration.cpp.

References WntConcentration< DIM >::mCryptProjectionParameterB.

Referenced by CryptProjectionForce::CryptProjectionForce(), WntConcentration< DIM >::GetWntGradient(), WntConcentration< DIM >::GetWntLevel(), and WntConcentration< DIM >::serialize().

template<unsigned DIM>

WntConcentrationType WntConcentration< DIM >::GetType

(

)

Returns

the type of Wnt concentration.

Definition at line 159 of file WntConcentration.cpp.

References WntConcentration< DIM >::mWntType.

Referenced by SimpleWntCellCycleModel::GetWntType(), and WntConcentration< DIM >::serialize().

template<unsigned DIM>

double WntConcentration< DIM >::GetWntConcentrationParameter

(

)

Returns

mWntConcentrationParameter

Definition at line 286 of file WntConcentration.cpp.

References WntConcentration< DIM >::mWntConcentrationParameter.

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

template<unsigned DIM>

c_vector< double, DIM > WntConcentration< DIM >::GetWntGradient

(

c_vector< double, DIM > &

rLocation

)

Returns

the Wnt gradient at a given location in the crypt.

Parameters

rLocation

the location at which we want the Wnt gradient

Definition at line 219 of file WntConcentration.cpp.

References EXCEPTION, WntConcentration< DIM >::GetCryptLength(), WntConcentration< DIM >::GetCryptProjectionParameterA(), WntConcentration< DIM >::GetCryptProjectionParameterB(), WntConcentration< DIM >::mWntConcentrationParameter, and WntConcentration< DIM >::mWntType.

Referenced by CryptProjectionForce::AddForceContribution(), WntConcentration< DIM >::GetWntGradient(), and WntConcentration< DIM >::serialize().

template<unsigned DIM>

c_vector< double, DIM > WntConcentration< DIM >::GetWntGradient

(

CellPtr

pCell

)

Returns

the Wnt gradient at a given cell in the crypt.

Parameters

pCell

the cell at which we want the Wnt gradient

Definition at line 112 of file WntConcentration.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetLocationOfCellCentre(), WntConcentration< DIM >::GetWntGradient(), WntConcentration< DIM >::mLengthSet, WntConcentration< DIM >::mpCellPopulation, WntConcentration< DIM >::mTypeSet, and WntConcentration< DIM >::mUseConstantWntValueForTesting.

template<unsigned DIM>

double WntConcentration< DIM >::GetWntLevel

(

double

height

)

Get the Wnt level at a given height in the crypt.

Parameters

height

the height of the cell at which we want the Wnt concentration

Returns

the Wnt concentration at this height in the crypt (dimensionless)

Definition at line 176 of file WntConcentration.cpp.

References WntConcentration< DIM >::GetCryptLength(), WntConcentration< DIM >::mLengthSet, WntConcentration< DIM >::mWntConcentrationParameter, and WntConcentration< DIM >::mWntType.

Referenced by AbstractWntOdeBasedCellCycleModel::GetWntLevel(), SimpleWntCellCycleModel::GetWntLevel(), WntConcentration< DIM >::GetWntLevel(), and WntConcentration< DIM >::serialize().

template<unsigned DIM>

double WntConcentration< DIM >::GetWntLevel

(

CellPtr

pCell

)

Get the Wnt level at a given cell in the crypt. The crypt must be set for this.

Parameters

pCell

the cell at which we want the Wnt concentration

Returns

the Wnt concentration at this cell

Definition at line 84 of file WntConcentration.cpp.

References WntConcentration< DIM >::GetCryptProjectionParameterA(), WntConcentration< DIM >::GetCryptProjectionParameterB(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetLocationOfCellCentre(), WntConcentration< DIM >::GetWntLevel(), WntConcentration< DIM >::mConstantWntValueForTesting, WntConcentration< DIM >::mLengthSet, WntConcentration< DIM >::mpCellPopulation, WntConcentration< DIM >::mTypeSet, WntConcentration< DIM >::mUseConstantWntValueForTesting, and WntConcentration< DIM >::mWntType.

template<unsigned DIM>

WntConcentration< DIM > * WntConcentration< DIM >::Instance ( )

static

Return a pointer to the WntConcentration object. The first time this is called, the object is created.

Returns

A pointer to the singleton WntConcentration object.

Definition at line 42 of file WntConcentration.cpp.

Referenced by CryptProjectionForce::AddForceContribution(), CryptVertexBasedDivisionRule< SPACE_DIM >::CalculateCellDivisionVector(), CryptProjectionForce::CryptProjectionForce(), AbstractWntOdeBasedCellCycleModel::GetWntLevel(), SimpleWntCellCycleModel::GetWntLevel(), SimpleWntCellCycleModel::GetWntType(), CryptSimulationBoundaryCondition< DIM >::ImposeBoundaryCondition(), CryptSimulation2d::serialize(), CryptSimulation1d::serialize(), and WntConcentration< DIM >::serialize().

template<unsigned DIM>

bool WntConcentration< DIM >::IsWntSetUp

(

)

Whether a Wnt concentration has been set up.

For archiving, and to let a CellBasedSimulation find out whether whether a WntConcentration has been set up or not, i.e. whether stem cells should be motile.

Returns

whether the Wnt concentration is set up

Definition at line 260 of file WntConcentration.cpp.

References WntConcentration< DIM >::mLengthSet, WntConcentration< DIM >::mpCellPopulation, WntConcentration< DIM >::mTypeSet, and WntConcentration< DIM >::mWntType.

Referenced by CryptVertexBasedDivisionRule< SPACE_DIM >::CalculateCellDivisionVector(), CryptSimulationBoundaryCondition< DIM >::ImposeBoundaryCondition(), and WntConcentration< DIM >::serialize().

template<unsigned DIM>

AbstractCellPopulation< DIM > & WntConcentration< DIM >::rGetCellPopulation

(

)

Returns

reference to the CellPopulation.

Definition at line 134 of file WntConcentration.cpp.

References WntConcentration< DIM >::mpCellPopulation.

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

template<unsigned DIM>

template<class Archive >

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

inlineprivate

Archive the object and its member variables.

Parameters

archive	the archive
version	the current version of this class

Definition at line 146 of file WntConcentration.hpp.

References WntConcentration< DIM >::Destroy(), WntConcentration< DIM >::GetCryptLength(), WntConcentration< DIM >::GetCryptProjectionParameterA(), WntConcentration< DIM >::GetCryptProjectionParameterB(), WntConcentration< DIM >::GetType(), WntConcentration< DIM >::GetWntConcentrationParameter(), WntConcentration< DIM >::GetWntGradient(), WntConcentration< DIM >::GetWntLevel(), WntConcentration< DIM >::Instance(), WntConcentration< DIM >::IsWntSetUp(), WntConcentration< DIM >::mConstantWntValueForTesting, WntConcentration< DIM >::mCryptLength, WntConcentration< DIM >::mCryptProjectionParameterA, WntConcentration< DIM >::mCryptProjectionParameterB, WntConcentration< DIM >::mLengthSet, WntConcentration< DIM >::mpCellPopulation, WntConcentration< DIM >::mTypeSet, WntConcentration< DIM >::mUseConstantWntValueForTesting, WntConcentration< DIM >::mWntConcentrationParameter, WntConcentration< DIM >::mWntType, WntConcentration< DIM >::rGetCellPopulation(), WntConcentration< DIM >::SetCellPopulation(), WntConcentration< DIM >::SetConstantWntValueForTesting(), WntConcentration< DIM >::SetCryptLength(), WntConcentration< DIM >::SetCryptProjectionParameterA(), WntConcentration< DIM >::SetCryptProjectionParameterB(), WntConcentration< DIM >::SetType(), WntConcentration< DIM >::SetWntConcentrationParameter(), WntConcentration< DIM >::WntConcentration(), and WntConcentration< DIM >::~WntConcentration().

template<unsigned DIM>

void WntConcentration< DIM >::SetCellPopulation

(

AbstractCellPopulation< DIM > &

rCellPopulation

)

Set the crypt. Must be called before GetWntLevel().

Parameters

rCellPopulation

reference to the cell population

Definition at line 128 of file WntConcentration.cpp.

References WntConcentration< DIM >::mpCellPopulation.

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

template<unsigned DIM>

void WntConcentration< DIM >::SetConstantWntValueForTesting

(

double

value

)

Force the Wnt concentration to return a given value for all cells. Only for testing.

Parameters

value

the constant value to set the Wnt concentration to be

Definition at line 271 of file WntConcentration.cpp.

References EXCEPTION, WntConcentration< DIM >::mConstantWntValueForTesting, WntConcentration< DIM >::mTypeSet, WntConcentration< DIM >::mUseConstantWntValueForTesting, and WntConcentration< DIM >::mWntType.

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

template<unsigned DIM>

void WntConcentration< DIM >::SetCryptLength

(

double

cryptLength

)

Set mCryptLength. Must be called before GetWntLevel().

Parameters

cryptLength

the new value of mCryptLength

Definition at line 146 of file WntConcentration.cpp.

References EXCEPTION, WntConcentration< DIM >::mCryptLength, and WntConcentration< DIM >::mLengthSet.

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

template<unsigned DIM>

void WntConcentration< DIM >::SetCryptProjectionParameterA

(

double

cryptProjectionParameterA

)

Set mCryptProjectionParameterA.

Parameters

cryptProjectionParameterA

the new value of mCryptProjectionParameterA

Definition at line 311 of file WntConcentration.cpp.

References WntConcentration< DIM >::mCryptProjectionParameterA.

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

template<unsigned DIM>

void WntConcentration< DIM >::SetCryptProjectionParameterB

(

double

cryptProjectionParameterB

)

Set mCryptProjectionParameterB.

Parameters

cryptProjectionParameterB

the new value of mCryptProjectionParameterB

Definition at line 318 of file WntConcentration.cpp.

References WntConcentration< DIM >::mCryptProjectionParameterB.

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

template<unsigned DIM>

void WntConcentration< DIM >::SetType

(

WntConcentrationType

type

)

Set the type of Wnt concentration. Must be called before GetWntLevel().

Parameters

type	the type of Wnt concentration

Definition at line 165 of file WntConcentration.cpp.

References EXCEPTION, WntConcentration< DIM >::mTypeSet, and WntConcentration< DIM >::mWntType.

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

template<unsigned DIM>

void WntConcentration< DIM >::SetWntConcentrationParameter

(

double

wntConcentrationParameter

)

Set mWntConcentrationParameter.

Parameters

wntConcentrationParameter

the new value of mWntConcentrationParameter

Definition at line 292 of file WntConcentration.cpp.

References WntConcentration< DIM >::mWntConcentrationParameter.

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

Friends And Related Function Documentation

template<unsigned DIM>

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 138 of file WntConcentration.hpp.

Member Data Documentation

template<unsigned DIM>

double WntConcentration< DIM >::mConstantWntValueForTesting

private

A value to return for testing purposes.

Definition at line 104 of file WntConcentration.hpp.

Referenced by WntConcentration< DIM >::GetWntLevel(), WntConcentration< DIM >::serialize(), and WntConcentration< DIM >::SetConstantWntValueForTesting().

template<unsigned DIM>

double WntConcentration< DIM >::mCryptLength

private

The length of the crypt.

Definition at line 76 of file WntConcentration.hpp.

Referenced by WntConcentration< DIM >::GetCryptLength(), WntConcentration< DIM >::serialize(), and WntConcentration< DIM >::SetCryptLength().

template<unsigned DIM>

double WntConcentration< DIM >::mCryptProjectionParameterA

private

Parameter a, for use in crypt projection simulations, in which the crypt surface is given in cylindrical polar coordinates by z = a*r^b. mCryptProjectionParameterA has no units

Definition at line 128 of file WntConcentration.hpp.

Referenced by WntConcentration< DIM >::GetCryptProjectionParameterA(), WntConcentration< DIM >::serialize(), and WntConcentration< DIM >::SetCryptProjectionParameterA().

template<unsigned DIM>

double WntConcentration< DIM >::mCryptProjectionParameterB

private

Parameter b, for use in crypt projection simulations, in which the crypt surface is given in cylindrical polar coordinates by z = a*r^b. mCryptProjectionParameterB has no units

Definition at line 135 of file WntConcentration.hpp.

Referenced by WntConcentration< DIM >::GetCryptProjectionParameterB(), WntConcentration< DIM >::serialize(), and WntConcentration< DIM >::SetCryptProjectionParameterB().

template<unsigned DIM>

bool WntConcentration< DIM >::mLengthSet

private

Whether this WntConcentration object has had its crypt length set.

Definition at line 81 of file WntConcentration.hpp.

Referenced by WntConcentration< DIM >::GetWntGradient(), WntConcentration< DIM >::GetWntLevel(), WntConcentration< DIM >::IsWntSetUp(), WntConcentration< DIM >::serialize(), and WntConcentration< DIM >::SetCryptLength().

template<unsigned DIM>

AbstractCellPopulation<DIM>* WntConcentration< DIM >::mpCellPopulation

private

The cell population in which the WntConcentration occurs.

Definition at line 94 of file WntConcentration.hpp.

Referenced by WntConcentration< DIM >::GetWntGradient(), WntConcentration< DIM >::GetWntLevel(), WntConcentration< DIM >::IsWntSetUp(), WntConcentration< DIM >::rGetCellPopulation(), WntConcentration< DIM >::serialize(), and WntConcentration< DIM >::SetCellPopulation().

template<unsigned DIM>

WntConcentration< DIM > * WntConcentration< DIM >::mpInstance = nullptr

staticprivate

Pointer to the singleton instance of WntConcentration

Pointer to the single instance

Definition at line 71 of file WntConcentration.hpp.

Referenced by WntConcentration< DIM >::Destroy(), and WntConcentration< DIM >::WntConcentration().

template<unsigned DIM>

bool WntConcentration< DIM >::mTypeSet

private

Whether this WntConcentration object has had its type set.

Definition at line 99 of file WntConcentration.hpp.

Referenced by WntConcentration< DIM >::GetWntGradient(), WntConcentration< DIM >::GetWntLevel(), WntConcentration< DIM >::IsWntSetUp(), WntConcentration< DIM >::serialize(), WntConcentration< DIM >::SetConstantWntValueForTesting(), and WntConcentration< DIM >::SetType().

template<unsigned DIM>

bool WntConcentration< DIM >::mUseConstantWntValueForTesting

private

Whether to return the testing value (when false WntConcentration works with CellPopulation).

Definition at line 110 of file WntConcentration.hpp.

Referenced by WntConcentration< DIM >::GetWntGradient(), WntConcentration< DIM >::GetWntLevel(), WntConcentration< DIM >::serialize(), and WntConcentration< DIM >::SetConstantWntValueForTesting().

template<unsigned DIM>

double WntConcentration< DIM >::mWntConcentrationParameter

private

For LINEAR or RADIAL Wnt type: The proportion of the crypt that has a Wnt gradient. The Wnt concentration goes from one at the base to zero at this height up the crypt.

For EXPONENTIAL Wnt type: The parameter lambda in the Wnt concentration Wnt = exp(-height/lambda)

Definition at line 121 of file WntConcentration.hpp.

Referenced by WntConcentration< DIM >::GetWntConcentrationParameter(), WntConcentration< DIM >::GetWntGradient(), WntConcentration< DIM >::GetWntLevel(), WntConcentration< DIM >::serialize(), and WntConcentration< DIM >::SetWntConcentrationParameter().

template<unsigned DIM>

WntConcentrationType WntConcentration< DIM >::mWntType

private

The type of WntConcentration current options are NONE - returns zero everywhere LINEAR - decreases from 1 to zero at height specified by mWntConcentrationParameter RADIAL - decreases from 1 to zero at height specified by mWntConcentrationParameter

Definition at line 89 of file WntConcentration.hpp.

Referenced by WntConcentration< DIM >::GetType(), WntConcentration< DIM >::GetWntGradient(), WntConcentration< DIM >::GetWntLevel(), WntConcentration< DIM >::IsWntSetUp(), WntConcentration< DIM >::serialize(), WntConcentration< DIM >::SetConstantWntValueForTesting(), and WntConcentration< DIM >::SetType().

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

• crypt/src/cell/cycle/WntConcentration.hpp
• crypt/src/cell/cycle/WntConcentration.cpp