Chaste Commit::baa90ac2819b962188b7562f2326be23c47859a7
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#include <TargetAreaLinearGrowthModifier.hpp>
Public Member Functions | |
TargetAreaLinearGrowthModifier () | |
virtual | ~TargetAreaLinearGrowthModifier () |
void | UpdateTargetAreaOfCell (const CellPtr pCell) |
double | GetAgeToStartGrowing () |
void | SetAgeToStartGrowing (double ageToStartGrowing) |
double | GetGrowthRate () |
void | SetGrowthRate (double growthRate) |
void | OutputSimulationModifierParameters (out_stream &rParamsFile) |
Public Member Functions inherited from AbstractTargetAreaModifier< DIM > | |
AbstractTargetAreaModifier () | |
virtual | ~AbstractTargetAreaModifier () |
virtual void | UpdateAtEndOfTimeStep (AbstractCellPopulation< DIM, DIM > &rCellPopulation) |
virtual void | SetupSolve (AbstractCellPopulation< DIM, DIM > &rCellPopulation, std::string outputDirectory) |
double | GetReferenceTargetArea () |
void | SetReferenceTargetArea (double referenceTargetArea) |
void | UpdateTargetAreas (AbstractCellPopulation< DIM, DIM > &rCellPopulation) |
Public Member Functions inherited from AbstractCellBasedSimulationModifier< DIM, DIM > | |
AbstractCellBasedSimulationModifier () | |
virtual | ~AbstractCellBasedSimulationModifier () |
virtual void | UpdateAtEndOfTimeStep (AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &rCellPopulation)=0 |
virtual void | UpdateAtEndOfOutputTimeStep (AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &rCellPopulation) |
virtual void | SetupSolve (AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &rCellPopulation, std::string outputDirectory)=0 |
virtual void | UpdateAtEndOfSolve (AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &rCellPopulation) |
void | OutputSimulationModifierInfo (out_stream &rParamsFile) |
Public Member Functions inherited from Identifiable | |
virtual | ~Identifiable () |
std::string | GetIdentifier () const |
Private Member Functions | |
template<class Archive > | |
void | serialize (Archive &archive, const unsigned int version) |
Private Attributes | |
double | mAgeToStartGrowing |
double | mGrowthRate |
Friends | |
class | boost::serialization::access |
Additional Inherited Members | |
Protected Attributes inherited from AbstractTargetAreaModifier< DIM > | |
double | mReferenceTargetArea |
A target area modifier class in which the target area of a cell grows linearly, starting from mReferenceTargetArea, over a prescribed duration.
If used with a phase-based cell-cycle model (such as FixedG1GenerationalCellCycleModel), the target area of a cell doubles from the value mReferenceTargetArea over the course of the cell's G2 phase. This rule is based on the description of cell growth and division proposed by Farhadifar et al (The influence of cell mechanics, cell-cell interactions, and proliferation on epithelial packing, Current Biology 17(24):2095-2104, 2007, http://dx.doi.org/10.1016/j.cub.2007.11.049).
If used with a non-phase-based cell-cycle model, the target area of a cell increases linearly at a rate mGrowthRate as soon as the cell's age exceeds mAgeToStartGrowing.
Here mReferenceTargetArea, mAgeToStartGrowing and mGrowthRate are settable member variables. The default value of mReferenceTargetArea is 1.0 and the default value of mAgeToStartGrowing and mGrowthRate is DOUBLE_UNSET.
If mAgeToStartGrowing is set by the user, then mGrowthRate must also be set; note that in this case, these values are used to prescribe target area growth as described earlier, regardless of whether a phase-based cell-cycle model is present.
Definition at line 68 of file TargetAreaLinearGrowthModifier.hpp.
TargetAreaLinearGrowthModifier< DIM >::TargetAreaLinearGrowthModifier | ( | ) |
Default constructor.
Definition at line 42 of file TargetAreaLinearGrowthModifier.cpp.
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virtual |
Destructor.
Definition at line 50 of file TargetAreaLinearGrowthModifier.cpp.
double TargetAreaLinearGrowthModifier< DIM >::GetAgeToStartGrowing | ( | ) |
Definition at line 134 of file TargetAreaLinearGrowthModifier.cpp.
double TargetAreaLinearGrowthModifier< DIM >::GetGrowthRate | ( | ) |
Definition at line 147 of file TargetAreaLinearGrowthModifier.cpp.
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virtual |
Overridden OutputSimulationModifierParameters() method. Output any simulation modifier parameters to file.
rParamsFile | the file stream to which the parameters are output |
Reimplemented from AbstractTargetAreaModifier< DIM >.
Definition at line 160 of file TargetAreaLinearGrowthModifier.cpp.
References AbstractTargetAreaModifier< DIM >::OutputSimulationModifierParameters().
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inlineprivate |
Boost Serialization method for archiving/checkpointing. Archives the object and its member variables.
archive | The boost archive. |
version | The current version of this class. |
Definition at line 80 of file TargetAreaLinearGrowthModifier.hpp.
References TargetAreaLinearGrowthModifier< DIM >::mAgeToStartGrowing, and TargetAreaLinearGrowthModifier< DIM >::mGrowthRate.
void TargetAreaLinearGrowthModifier< DIM >::SetAgeToStartGrowing | ( | double | ageToStartGrowing | ) |
Set mAgeToStartGrowing.
ageToStartGrowing | the new value of mAgeToStartGrowing |
Definition at line 140 of file TargetAreaLinearGrowthModifier.cpp.
void TargetAreaLinearGrowthModifier< DIM >::SetGrowthRate | ( | double | growthRate | ) |
Set mGrowthRate.
growthRate | the new value of mGrowthRate |
Definition at line 153 of file TargetAreaLinearGrowthModifier.cpp.
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virtual |
Helper method to update the target area property of an individual cell.
pCell | pointer to a cell |
At division, daughter cells inherit the cell data array from the mother cell. Here, we assign the target area that we want daughter cells to have to cells that we know to divide in this time step.
Implements AbstractTargetAreaModifier< DIM >.
Definition at line 55 of file TargetAreaLinearGrowthModifier.cpp.
References DOUBLE_UNSET, EXCEPTION, AbstractPhaseBasedCellCycleModel::GetG1Duration(), AbstractPhaseBasedCellCycleModel::GetG2Duration(), AbstractPhaseBasedCellCycleModel::GetMDuration(), AbstractPhaseBasedCellCycleModel::GetSDuration(), SimulationTime::GetTime(), and SimulationTime::Instance().
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friend |
Needed for serialization.
Definition at line 71 of file TargetAreaLinearGrowthModifier.hpp.
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private |
The age of a proliferating cell at which its target area should start growing. Defaults to DOUBLE_UNSET. If this variable is set using SetAgeToStartGrowing(), then it is used regardless of whether a phase-based cell-cycle model is used.
Definition at line 92 of file TargetAreaLinearGrowthModifier.hpp.
Referenced by TargetAreaLinearGrowthModifier< DIM >::serialize().
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private |
The growth rate of a proliferating cell's target area, when it is growing. Defaults to DOUBLE_UNSET. This variable must be set if mAgeToStartGrowing is set, otherwise an exception is thrown.
Definition at line 99 of file TargetAreaLinearGrowthModifier.hpp.
Referenced by TargetAreaLinearGrowthModifier< DIM >::serialize().