Chaste Commit::baa90ac2819b962188b7562f2326be23c47859a7
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#include <WntConcentration.hpp>
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 |
Singleton Wnt concentration object.
Definition at line 66 of file WntConcentration.hpp.
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protected |
Protected constuctor. Not to be called, use Instance() instead.
Definition at line 52 of file WntConcentration.cpp.
References WntConcentration< DIM >::mpInstance.
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Destructor - frees up the singleton instance.
Definition at line 69 of file WntConcentration.cpp.
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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().
double WntConcentration< DIM >::GetCryptLength | ( | ) |
Definition at line 140 of file WntConcentration.cpp.
double WntConcentration< DIM >::GetCryptProjectionParameterA | ( | ) |
Definition at line 299 of file WntConcentration.cpp.
Referenced by CryptProjectionForce::CryptProjectionForce().
double WntConcentration< DIM >::GetCryptProjectionParameterB | ( | ) |
Definition at line 305 of file WntConcentration.cpp.
Referenced by CryptProjectionForce::CryptProjectionForce().
WntConcentrationType WntConcentration< DIM >::GetType | ( | ) |
Definition at line 159 of file WntConcentration.cpp.
Referenced by SimpleWntCellCycleModel::GetWntType().
double WntConcentration< DIM >::GetWntConcentrationParameter | ( | ) |
Definition at line 286 of file WntConcentration.cpp.
c_vector< double, DIM > WntConcentration< DIM >::GetWntGradient | ( | c_vector< double, DIM > & | rLocation | ) |
rLocation | the location at which we want the Wnt gradient |
Definition at line 219 of file WntConcentration.cpp.
References EXCEPTION.
Referenced by CryptProjectionForce::AddForceContribution().
c_vector< double, DIM > WntConcentration< DIM >::GetWntGradient | ( | CellPtr | pCell | ) |
pCell | the cell at which we want the Wnt gradient |
Definition at line 112 of file WntConcentration.cpp.
double WntConcentration< DIM >::GetWntLevel | ( | CellPtr | pCell | ) |
Get the Wnt level at a given cell in the crypt. The crypt must be set for this.
pCell | the cell at which we want the Wnt concentration |
Definition at line 84 of file WntConcentration.cpp.
double WntConcentration< DIM >::GetWntLevel | ( | double | height | ) |
Get the Wnt level at a given height in the crypt.
height | the height of the cell at which we want the Wnt concentration |
Definition at line 176 of file WntConcentration.cpp.
Referenced by AbstractWntOdeBasedCellCycleModel::GetWntLevel(), and SimpleWntCellCycleModel::GetWntLevel().
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Return a pointer to the WntConcentration object. The first time this is called, the object is created.
Definition at line 42 of file WntConcentration.cpp.
Referenced by CryptProjectionForce::CryptProjectionForce(), CryptProjectionForce::AddForceContribution(), CryptVertexBasedDivisionRule< SPACE_DIM >::CalculateCellDivisionVector(), AbstractWntOdeBasedCellCycleModel::GetWntLevel(), SimpleWntCellCycleModel::GetWntLevel(), SimpleWntCellCycleModel::GetWntType(), CryptSimulationBoundaryCondition< DIM >::ImposeBoundaryCondition(), CryptSimulation1d::serialize(), and CryptSimulation2d::serialize().
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.
Definition at line 260 of file WntConcentration.cpp.
Referenced by CryptVertexBasedDivisionRule< SPACE_DIM >::CalculateCellDivisionVector(), CryptSimulationBoundaryCondition< DIM >::ImposeBoundaryCondition(), and WntConcentration< DIM >::serialize().
AbstractCellPopulation< DIM > & WntConcentration< DIM >::rGetCellPopulation | ( | ) |
Definition at line 134 of file WntConcentration.cpp.
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inlineprivate |
Archive the object and its member variables.
archive | the archive |
version | the current version of this class |
Definition at line 146 of file WntConcentration.hpp.
References 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, and WntConcentration< DIM >::mWntType.
void WntConcentration< DIM >::SetCellPopulation | ( | AbstractCellPopulation< DIM > & | rCellPopulation | ) |
Set the crypt. Must be called before GetWntLevel().
rCellPopulation | reference to the cell population |
Definition at line 128 of file WntConcentration.cpp.
void WntConcentration< DIM >::SetConstantWntValueForTesting | ( | double | value | ) |
Force the Wnt concentration to return a given value for all cells. Only for testing.
value | the constant value to set the Wnt concentration to be |
Definition at line 271 of file WntConcentration.cpp.
References EXCEPTION.
void WntConcentration< DIM >::SetCryptLength | ( | double | cryptLength | ) |
Set mCryptLength. Must be called before GetWntLevel().
cryptLength | the new value of mCryptLength |
Definition at line 146 of file WntConcentration.cpp.
References EXCEPTION.
void WntConcentration< DIM >::SetCryptProjectionParameterA | ( | double | cryptProjectionParameterA | ) |
Set mCryptProjectionParameterA.
cryptProjectionParameterA | the new value of mCryptProjectionParameterA |
Definition at line 311 of file WntConcentration.cpp.
void WntConcentration< DIM >::SetCryptProjectionParameterB | ( | double | cryptProjectionParameterB | ) |
Set mCryptProjectionParameterB.
cryptProjectionParameterB | the new value of mCryptProjectionParameterB |
Definition at line 318 of file WntConcentration.cpp.
void WntConcentration< DIM >::SetType | ( | WntConcentrationType | type | ) |
Set the type of Wnt concentration. Must be called before GetWntLevel().
type | the type of Wnt concentration |
Definition at line 165 of file WntConcentration.cpp.
References EXCEPTION.
void WntConcentration< DIM >::SetWntConcentrationParameter | ( | double | wntConcentrationParameter | ) |
Set mWntConcentrationParameter.
wntConcentrationParameter | the new value of mWntConcentrationParameter |
Definition at line 292 of file WntConcentration.cpp.
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Needed for serialization.
Definition at line 138 of file WntConcentration.hpp.
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A value to return for testing purposes.
Definition at line 104 of file WntConcentration.hpp.
Referenced by WntConcentration< DIM >::serialize().
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The length of the crypt.
Definition at line 76 of file WntConcentration.hpp.
Referenced by WntConcentration< DIM >::serialize().
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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().
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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().
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Whether this WntConcentration object has had its crypt length set.
Definition at line 81 of file WntConcentration.hpp.
Referenced by WntConcentration< DIM >::serialize().
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The cell population in which the WntConcentration occurs.
Definition at line 94 of file WntConcentration.hpp.
Referenced by WntConcentration< DIM >::serialize().
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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().
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Whether this WntConcentration object has had its type set.
Definition at line 99 of file WntConcentration.hpp.
Referenced by WntConcentration< DIM >::serialize().
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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().
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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().
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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().