Chaste Commit::baa90ac2819b962188b7562f2326be23c47859a7
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 WntConcentrationInstance ()
 
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 WntConcentrationmpInstance = 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

◆ WntConcentration()

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.

◆ ~WntConcentration()

template<unsigned DIM>
WntConcentration< DIM >::~WntConcentration ( )
virtual

Destructor - frees up the singleton instance.

Definition at line 69 of file WntConcentration.cpp.

Member Function Documentation

◆ Destroy()

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 CryptVertexBasedDivisionRule< SPACE_DIM >::CalculateCellDivisionVector(), and CryptSimulationBoundaryCondition< DIM >::ImposeBoundaryCondition().

◆ GetCryptLength()

template<unsigned DIM>
double WntConcentration< DIM >::GetCryptLength ( )
Returns
mCryptLength

Definition at line 140 of file WntConcentration.cpp.

◆ GetCryptProjectionParameterA()

template<unsigned DIM>
double WntConcentration< DIM >::GetCryptProjectionParameterA ( )
Returns
mCryptProjectionParameterA

Definition at line 299 of file WntConcentration.cpp.

Referenced by CryptProjectionForce::CryptProjectionForce().

◆ GetCryptProjectionParameterB()

template<unsigned DIM>
double WntConcentration< DIM >::GetCryptProjectionParameterB ( )
Returns
mCryptProjectionParameterB

Definition at line 305 of file WntConcentration.cpp.

Referenced by CryptProjectionForce::CryptProjectionForce().

◆ GetType()

template<unsigned DIM>
WntConcentrationType WntConcentration< DIM >::GetType ( )
Returns
the type of Wnt concentration.

Definition at line 159 of file WntConcentration.cpp.

Referenced by SimpleWntCellCycleModel::GetWntType().

◆ GetWntConcentrationParameter()

template<unsigned DIM>
double WntConcentration< DIM >::GetWntConcentrationParameter ( )
Returns
mWntConcentrationParameter

Definition at line 286 of file WntConcentration.cpp.

◆ GetWntGradient() [1/2]

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
rLocationthe location at which we want the Wnt gradient

Definition at line 219 of file WntConcentration.cpp.

References EXCEPTION.

Referenced by CryptProjectionForce::AddForceContribution().

◆ GetWntGradient() [2/2]

template<unsigned DIM>
c_vector< double, DIM > WntConcentration< DIM >::GetWntGradient ( CellPtr  pCell)
Returns
the Wnt gradient at a given cell in the crypt.
Parameters
pCellthe cell at which we want the Wnt gradient

Definition at line 112 of file WntConcentration.cpp.

◆ GetWntLevel() [1/2]

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
pCellthe cell at which we want the Wnt concentration
Returns
the Wnt concentration at this cell

Definition at line 84 of file WntConcentration.cpp.

◆ GetWntLevel() [2/2]

template<unsigned DIM>
double WntConcentration< DIM >::GetWntLevel ( double  height)

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

Parameters
heightthe 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 AbstractWntOdeBasedCellCycleModel::GetWntLevel(), and SimpleWntCellCycleModel::GetWntLevel().

◆ Instance()

◆ IsWntSetUp()

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

◆ rGetCellPopulation()

template<unsigned DIM>
AbstractCellPopulation< DIM > & WntConcentration< DIM >::rGetCellPopulation ( )
Returns
reference to the CellPopulation.

Definition at line 134 of file WntConcentration.cpp.

◆ serialize()

◆ SetCellPopulation()

template<unsigned DIM>
void WntConcentration< DIM >::SetCellPopulation ( AbstractCellPopulation< DIM > &  rCellPopulation)

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

Parameters
rCellPopulationreference to the cell population

Definition at line 128 of file WntConcentration.cpp.

◆ SetConstantWntValueForTesting()

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
valuethe constant value to set the Wnt concentration to be

Definition at line 271 of file WntConcentration.cpp.

References EXCEPTION.

◆ SetCryptLength()

template<unsigned DIM>
void WntConcentration< DIM >::SetCryptLength ( double  cryptLength)

Set mCryptLength. Must be called before GetWntLevel().

Parameters
cryptLengththe new value of mCryptLength

Definition at line 146 of file WntConcentration.cpp.

References EXCEPTION.

◆ SetCryptProjectionParameterA()

template<unsigned DIM>
void WntConcentration< DIM >::SetCryptProjectionParameterA ( double  cryptProjectionParameterA)

Set mCryptProjectionParameterA.

Parameters
cryptProjectionParameterAthe new value of mCryptProjectionParameterA

Definition at line 311 of file WntConcentration.cpp.

◆ SetCryptProjectionParameterB()

template<unsigned DIM>
void WntConcentration< DIM >::SetCryptProjectionParameterB ( double  cryptProjectionParameterB)

Set mCryptProjectionParameterB.

Parameters
cryptProjectionParameterBthe new value of mCryptProjectionParameterB

Definition at line 318 of file WntConcentration.cpp.

◆ SetType()

template<unsigned DIM>
void WntConcentration< DIM >::SetType ( WntConcentrationType  type)

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

Parameters
typethe type of Wnt concentration

Definition at line 165 of file WntConcentration.cpp.

References EXCEPTION.

◆ SetWntConcentrationParameter()

template<unsigned DIM>
void WntConcentration< DIM >::SetWntConcentrationParameter ( double  wntConcentrationParameter)

Set mWntConcentrationParameter.

Parameters
wntConcentrationParameterthe new value of mWntConcentrationParameter

Definition at line 292 of file WntConcentration.cpp.

Friends And Related Symbol Documentation

◆ boost::serialization::access

template<unsigned DIM>
friend class boost::serialization::access
friend

Needed for serialization.

Definition at line 138 of file WntConcentration.hpp.

Member Data Documentation

◆ mConstantWntValueForTesting

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().

◆ mCryptLength

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().

◆ mCryptProjectionParameterA

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().

◆ mCryptProjectionParameterB

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().

◆ mLengthSet

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().

◆ mpCellPopulation

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().

◆ mpInstance

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 >::WntConcentration().

◆ mTypeSet

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().

◆ mUseConstantWntValueForTesting

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().

◆ mWntConcentrationParameter

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().

◆ mWntType

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: