WntConcentration< DIM > Class Template Reference

#include <WntConcentration.hpp>

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List of all members.

Public Member Functions

virtual ~WntConcentration ()
double GetWntLevel (double height)
double GetWntLevel (TissueCell *pCell)
c_vector< double, DIM > GetWntGradient (c_vector< double, DIM > location)
c_vector< double, DIM > GetWntGradient (TissueCell *pCell)
void SetTissue (AbstractTissue< DIM > &rTissue)
WntConcentrationType GetType ()
void SetType (WntConcentrationType type)
void SetConstantWntValueForTesting (double value)
bool IsWntSetUp ()

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

TissueConfig * mpTissueConfig
WntConcentrationType mWntType
AbstractTissue< DIM > * mpTissue
bool mTypeSet
double mConstantWntValueForTesting
bool mUseConstantWntValueForTesting

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 59 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 47 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 60 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 107 of file WntConcentration.hpp.

References TissueConfig::Instance(), WntConcentration< DIM >::mConstantWntValueForTesting, WntConcentration< DIM >::mpTissue, WntConcentration< DIM >::mpTissueConfig, WntConcentration< DIM >::mTypeSet, WntConcentration< DIM >::mUseConstantWntValueForTesting, 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 37 of file WntConcentration.cpp.

References WntConcentration< DIM >::mpInstance.

Referenced by CryptSimulation2d::ApplyTissueBoundaryConditions(), SimpleWntCellCycleModel::GetWntLevel(), AbstractWntOdeBasedCellCycleModel::GetWntLevel(), SimpleWntCellCycleModel::GetWntType(), TissueSimulationArchiver< DIM, SIM >::Load(), and TissueSimulationArchiver< 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 CryptSimulation2d::ApplyTissueBoundaryConditions().

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

Get the Wnt level at a given height in the crypt. Note the TissueConfig::CryptLength() is used for this.

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 148 of file WntConcentration.cpp.

References TissueConfig::GetCryptLength(), TissueConfig::GetTopOfLinearWntConcentration(), WntConcentration< DIM >::mpTissueConfig, and WntConcentration< DIM >::mWntType.

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

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

Get the Wnt level at a given cell in the crypt. The crypt must be set for this. Note the TissueConfig::CryptLength() is used for this.

Parameters:
pCell pointer to the cell at which we want the Wnt concentration
Returns:
the Wnt concentration at this cell

Definition at line 77 of file WntConcentration.cpp.

References TissueConfig::GetCryptProjectionParameterA(), TissueConfig::GetCryptProjectionParameterB(), WntConcentration< DIM >::GetWntLevel(), TissueConfig::Instance(), WntConcentration< DIM >::mConstantWntValueForTesting, WntConcentration< DIM >::mpTissue, WntConcentration< DIM >::mTypeSet, WntConcentration< DIM >::mUseConstantWntValueForTesting, and WntConcentration< DIM >::mWntType.

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

Get the Wnt gradient at a given location in the crypt. Note the TissueConfig::CryptLength() is used for this.

Parameters:
location the location at which we want the Wnt gradient

Definition at line 180 of file WntConcentration.cpp.

References TissueConfig::GetCryptLength(), TissueConfig::GetCryptProjectionParameterA(), TissueConfig::GetCryptProjectionParameterB(), TissueConfig::GetTopOfLinearWntConcentration(), TissueConfig::Instance(), WntConcentration< DIM >::mpTissueConfig, and WntConcentration< DIM >::mWntType.

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

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

Get the Wnt gradient at a given cell in the crypt. The crypt must be set for this. Note the TissueConfig::CryptLength() is used for this.

Parameters:
pCell pointer to the cell at which we want the Wnt gradient

Definition at line 105 of file WntConcentration.cpp.

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

template<unsigned DIM>
void WntConcentration< DIM >::SetTissue ( AbstractTissue< DIM > &  rTissue  )  [inline]

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

Parameters:
rTissue reference to the tissue

Definition at line 122 of file WntConcentration.cpp.

References WntConcentration< DIM >::mpTissue.

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

Get the type of Wnt concentration.

Definition at line 129 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 136 of file WntConcentration.cpp.

References 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 233 of file WntConcentration.cpp.

References 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 TissueSimulation 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 221 of file WntConcentration.cpp.

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

Referenced by CryptSimulation2d::ApplyTissueBoundaryConditions(), and TissueSimulationArchiver< DIM, SIM >::Save().

Friends And Related Function Documentation

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

Needed for serialization.

Definition at line 99 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 64 of file WntConcentration.hpp.

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

template<unsigned DIM>
TissueConfig* WntConcentration< DIM >::mpTissueConfig [private]

The cancer parameters

Definition at line 67 of file WntConcentration.hpp.

Referenced by WntConcentration< DIM >::GetWntGradient(), WntConcentration< DIM >::GetWntLevel(), and 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 TissueConfig::mTopOfLinearWntConcentration RADIAL - decreases from 1 to zero at height specified by TissueConfig::mTopOfLinearWntConcentration

Definition at line 75 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>
AbstractTissue<DIM>* WntConcentration< DIM >::mpTissue [private]

The tissue in which the WntConcentration occurs.

Definition at line 80 of file WntConcentration.hpp.

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

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

Whether this WntConcentration object has had its type set.

Definition at line 85 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 90 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 Tissue).

Definition at line 96 of file WntConcentration.hpp.

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

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