WntConcentration< DIM > Class Template Reference

#include <WntConcentration.hpp>

Collaboration diagram for WntConcentration< DIM >:

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List of all members.

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)
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 57 of file WntConcentration.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>
WntConcentration< DIM >::WntConcentration (  )  [inline, protected]

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

Definition at line 45 of file WntConcentration.cpp.

References WntConcentration< DIM >::mpInstance.

template<unsigned DIM>
WntConcentration< DIM >::~WntConcentration (  )  [inline, virtual]

Destructor - frees up the singleton instance.

Definition at line 61 of file WntConcentration.cpp.

Member Function Documentation

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 137 of file WntConcentration.hpp.

References 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, and WntConcentration< DIM >::mWntType.

template<unsigned DIM>
WntConcentration< DIM > * WntConcentration< DIM >::Instance (  )  [inline, 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 35 of file WntConcentration.cpp.

References WntConcentration< DIM >::mpInstance.

Referenced by CryptProjectionForce::AddForceContribution(), VertexCryptSimulation2d::ApplyCellPopulationBoundaryConditions(), CryptSimulation2d::ApplyCellPopulationBoundaryConditions(), CryptSimulation1d::ApplyCellPopulationBoundaryConditions(), VertexCryptSimulation2d::CalculateCellDivisionVector(), CryptProjectionForce::CryptProjectionForce(), SimpleWntCellCycleModel::GetWntLevel(), AbstractWntOdeBasedCellCycleModel::GetWntLevel(), SimpleWntCellCycleModel::GetWntType(), CryptSimulationArchiver< DIM, SIM >::Load(), and CryptSimulationArchiver< DIM, SIM >::Save().

template<unsigned DIM>
void WntConcentration< DIM >::Destroy (  )  [inline, static]

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

Definition at line 66 of file WntConcentration.cpp.

References WntConcentration< DIM >::mpInstance.

Referenced by VertexCryptSimulation2d::ApplyCellPopulationBoundaryConditions(), CryptSimulation2d::ApplyCellPopulationBoundaryConditions(), CryptSimulation1d::ApplyCellPopulationBoundaryConditions(), and VertexCryptSimulation2d::CalculateCellDivisionVector().

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

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 161 of file WntConcentration.cpp.

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

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

template<unsigned DIM>
double WntConcentration< DIM >::GetWntLevel ( CellPtr  pCell  )  [inline]

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 76 of file WntConcentration.cpp.

References WntConcentration< DIM >::GetCryptProjectionParameterA(), WntConcentration< DIM >::GetCryptProjectionParameterB(), 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>
c_vector< double, DIM > WntConcentration< DIM >::GetWntGradient ( c_vector< double, DIM > &  rLocation  )  [inline]

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 204 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(), and WntConcentration< DIM >::GetWntGradient().

template<unsigned DIM>
c_vector< double, DIM > WntConcentration< DIM >::GetWntGradient ( CellPtr  pCell  )  [inline]

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 104 of file WntConcentration.cpp.

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

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

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

Parameters:
rCellPopulation reference to the cell population

Definition at line 120 of file WntConcentration.cpp.

References WntConcentration< DIM >::mpCellPopulation.

template<unsigned DIM>
double WntConcentration< DIM >::GetCryptLength (  )  [inline]

Returns:
mCryptLength

Definition at line 126 of file WntConcentration.cpp.

References WntConcentration< DIM >::mCryptLength.

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

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

Set mCryptLength. Must be called before GetWntLevel().

Parameters:
cryptLength the new value of mCryptLength

Definition at line 132 of file WntConcentration.cpp.

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

template<unsigned DIM>
WntConcentrationType WntConcentration< DIM >::GetType (  )  [inline]

Get the type of Wnt concentration.

Definition at line 144 of file WntConcentration.cpp.

References WntConcentration< DIM >::mWntType.

Referenced by SimpleWntCellCycleModel::GetWntType().

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

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

Parameters:
type the type of Wnt concentration

Definition at line 150 of file WntConcentration.cpp.

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

template<unsigned DIM>
void WntConcentration< DIM >::SetConstantWntValueForTesting ( double  value  )  [inline]

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 256 of file WntConcentration.cpp.

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

template<unsigned DIM>
bool WntConcentration< DIM >::IsWntSetUp (  )  [inline]

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 245 of file WntConcentration.cpp.

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

Referenced by VertexCryptSimulation2d::ApplyCellPopulationBoundaryConditions(), CryptSimulation2d::ApplyCellPopulationBoundaryConditions(), CryptSimulation1d::ApplyCellPopulationBoundaryConditions(), VertexCryptSimulation2d::CalculateCellDivisionVector(), and CryptSimulationArchiver< DIM, SIM >::Save().

template<unsigned DIM>
double WntConcentration< DIM >::GetWntConcentrationParameter (  )  [inline]

Returns:
mWntConcentrationParameter

Definition at line 271 of file WntConcentration.cpp.

References WntConcentration< DIM >::mWntConcentrationParameter.

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

Set mWntConcentrationParameter.

Parameters:
wntConcentrationParameter the new value of mWntConcentrationParameter

Definition at line 277 of file WntConcentration.cpp.

References WntConcentration< DIM >::mWntConcentrationParameter.

template<unsigned DIM>
double WntConcentration< DIM >::GetCryptProjectionParameterA (  )  [inline]

Returns:
mCryptProjectionParameterA

Definition at line 284 of file WntConcentration.cpp.

References WntConcentration< DIM >::mCryptProjectionParameterA.

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

template<unsigned DIM>
double WntConcentration< DIM >::GetCryptProjectionParameterB (  )  [inline]

Returns:
mCryptProjectionParameterB

Definition at line 290 of file WntConcentration.cpp.

References WntConcentration< DIM >::mCryptProjectionParameterB.

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

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

Set mCryptProjectionParameterA.

Parameters:
cryptProjectionParameterA the new value of mCryptProjectionParameterA

Definition at line 296 of file WntConcentration.cpp.

References WntConcentration< DIM >::mCryptProjectionParameterA.

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

Set mCryptProjectionParameterB.

Parameters:
cryptProjectionParameterB the new value of mCryptProjectionParameterB

Definition at line 303 of file WntConcentration.cpp.

References WntConcentration< DIM >::mCryptProjectionParameterB.

Friends And Related Function Documentation

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

Needed for serialization.

Definition at line 129 of file WntConcentration.hpp.

Member Data Documentation

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

Pointer to the singleton instance of WntConcentration

Pointer to the single instance

Definition at line 62 of file WntConcentration.hpp.

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

template<unsigned DIM>
double WntConcentration< DIM >::mCryptLength [private]

The length of the crypt.

Definition at line 67 of file WntConcentration.hpp.

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

template<unsigned DIM>
bool WntConcentration< DIM >::mLengthSet [private]

Whether this WntConcentration object has had its crypt length set.

Definition at line 72 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>
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 80 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().

template<unsigned DIM>
AbstractCellPopulation<DIM>* WntConcentration< DIM >::mpCellPopulation [private]

The cell population in which the WntConcentration occurs.

Definition at line 85 of file WntConcentration.hpp.

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

template<unsigned DIM>
bool WntConcentration< DIM >::mTypeSet [private]

Whether this WntConcentration object has had its type set.

Definition at line 90 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>
double WntConcentration< DIM >::mConstantWntValueForTesting [private]

A value to return for testing purposes.

Definition at line 95 of file WntConcentration.hpp.

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

template<unsigned DIM>
bool WntConcentration< DIM >::mUseConstantWntValueForTesting [private]

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

Definition at line 101 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 112 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>
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 119 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 126 of file WntConcentration.hpp.

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

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