#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)
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 = NULL
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.

template<unsigned DIM>

WntConcentration< DIM >::~WntConcentration ( ) [virtual]

Destructor - frees up the singleton instance.

Definition at line 69 of file WntConcentration.cpp.

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.

Referenced by CryptSimulationBoundaryCondition< DIM >::ImposeBoundaryCondition().

template<unsigned DIM>

double WntConcentration< DIM >::GetCryptLength ( )

Returns:: mCryptLength

Definition at line 140 of file WntConcentration.cpp.

template<unsigned DIM>

double WntConcentration< DIM >::GetCryptProjectionParameterA ( )

Returns:: mCryptProjectionParameterA

Definition at line 299 of file WntConcentration.cpp.

Referenced by CryptProjectionForce::CryptProjectionForce().

template<unsigned DIM>

double WntConcentration< DIM >::GetCryptProjectionParameterB ( )

Returns:: mCryptProjectionParameterB

Definition at line 305 of file WntConcentration.cpp.

Referenced by CryptProjectionForce::CryptProjectionForce().

template<unsigned DIM>

WntConcentrationType WntConcentration< DIM >::GetType ( )

Get the type of Wnt concentration.

Definition at line 159 of file WntConcentration.cpp.

Referenced by SimpleWntCellCycleModel::GetWntType().

template<unsigned DIM>

double WntConcentration< DIM >::GetWntConcentrationParameter ( )

Returns:: mWntConcentrationParameter

Definition at line 286 of file WntConcentration.cpp.

template<unsigned DIM>

c_vector< double, DIM > WntConcentration< DIM >::GetWntGradient ( c_vector< double, DIM > & rLocation )

Get 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.

Referenced by CryptProjectionForce::AddForceContribution().

template<unsigned DIM>

c_vector< double, DIM > WntConcentration< DIM >::GetWntGradient ( CellPtr pCell )

Get 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.

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.

Referenced by SimpleWntCellCycleModel::GetWntLevel(), and AbstractWntOdeBasedCellCycleModel::GetWntLevel().

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.

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 CryptSimulationBoundaryCondition< DIM >::ImposeBoundaryCondition().

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.

Referenced by CryptSimulation2d::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.

template<unsigned DIM>

template<class Archive >

void WntConcentration< DIM >::serialize	(	Archive &	archive,
		const unsigned int	version
	)		`[inline, private]`

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.

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.

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.

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.

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.

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.

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.

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.

Friends And Related Function Documentation

template<unsigned DIM>

friend class boost::serialization::access [friend]

Needed for serialization.

Reimplemented from SerializableSingleton< WntConcentration< DIM > >.

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 >::serialize().

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 >::serialize().

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 >::serialize().

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 >::serialize().

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 >::serialize().

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 >::serialize().

template<unsigned DIM>

WntConcentration< DIM > * WntConcentration< DIM >::mpInstance = NULL [static, private]

Pointer to the singleton instance of WntConcentration

Pointer to the single instance

Definition at line 71 of file WntConcentration.hpp.

Referenced by 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 >::serialize().

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 >::serialize().

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 >::serialize().

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 >::serialize().

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

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

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Static Private Attributes

Friends

Detailed Description

template<unsigned DIM> class WntConcentration< DIM >

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation

template<unsigned DIM>
class WntConcentration< DIM >