#include <AbstractCellCycleModel.hpp>
Inheritance diagram for AbstractCellCycleModel:
Collaboration diagram for AbstractCellCycleModel:
Detailed Description
The AbstractCellCycleModel contains basic information to all cell-cycle models. It handles assignment of birth time, cell cycle phase and a Cell.
Cell-cycle models are noncopyable since cells are noncopyable.
Definition at line 62 of file AbstractCellCycleModel.hpp.
Constructor & Destructor Documentation
| AbstractCellCycleModel::AbstractCellCycleModel | ( | ) |
Sets up a new AbstractCellCycleModel, gives it a birth time of the current simulation time (which is overwritten by some subclasses)
Definition at line 38 of file AbstractCellCycleModel.cpp.
| AbstractCellCycleModel::~AbstractCellCycleModel | ( | ) | [virtual] |
Base class with virtual methods needs a virtual destructor. The destructor does not delete mpCell. Instead, the cell takes responsibility for deleting the cell-cycle model when it is destroyed.
Definition at line 54 of file AbstractCellCycleModel.cpp.
Member Function Documentation
| bool AbstractCellCycleModel::CanCellTerminallyDifferentiate | ( | ) | [virtual] |
Whether a cell with this cell-cycle model is able to fully (terminally) differentiate.
Reimplemented in TysonNovakCellCycleModel, AbstractWntOdeBasedCellCycleModel, and SimpleWntCellCycleModel.
Definition at line 213 of file AbstractCellCycleModel.cpp.
| virtual AbstractCellCycleModel* AbstractCellCycleModel::CreateCellCycleModel | ( | ) | [pure virtual] |
Builder method to create new instances of the cell-cycle model. Each concrete subclass must implement this method to create an instance of that subclass.
This method is called by Cell::Divide() to create a cell cycle model for the daughter cell. Note that the parent cell cycle model will have had ResetForDivision() called just before CreateCellCycleModel() is called, so performing an exact copy of the parent is suitable behaviour. Any daughter-cell-specific initialisation can be done in InitialiseDaughterCell().
Implemented in Alarcon2004OxygenBasedCellCycleModel, ContactInhibitionCellCycleModel, DeltaNotchCellCycleModel, FixedDurationGenerationBasedCellCycleModel, SimpleOxygenBasedCellCycleModel, StochasticDurationCellCycleModel, StochasticDurationGenerationBasedCellCycleModel, StochasticOxygenBasedCellCycleModel, TysonNovakCellCycleModel, SimpleWntCellCycleModel, SingleOdeWntCellCycleModel, StochasticWntCellCycleModel, VanLeeuwen2009WntSwatCellCycleModelHypothesisOne, VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo, and WntCellCycleModel.
Referenced by Cell::Divide().
| double AbstractCellCycleModel::GetAge | ( | ) |
Returns the cell's age.
Definition at line 87 of file AbstractCellCycleModel.cpp.
References SimulationTime::GetTime(), SimulationTime::Instance(), and mBirthTime.
Referenced by Cell::GetAge(), ReadyToDivide(), ContactInhibitionCellCycleModel::UpdateCellCyclePhase(), AbstractSimpleCellCycleModel::UpdateCellCyclePhase(), and AbstractOdeBasedCellCycleModel::UpdateCellCyclePhase().
| double AbstractCellCycleModel::GetAverageStemCellCycleTime | ( | ) | [virtual] |
Return the typical cell cycle duration for a stem cell, in hours. This method is overridden in some subclasses.
Reimplemented in TysonNovakCellCycleModel, and AbstractWntOdeBasedCellCycleModel.
Definition at line 208 of file AbstractCellCycleModel.cpp.
References GetSG2MDuration(), and mStemCellG1Duration.
| double AbstractCellCycleModel::GetAverageTransitCellCycleTime | ( | ) | [virtual] |
Return the typical cell cycle duration for a transit cell, in hours. This method is overridden in some subclasses.
Reimplemented in TysonNovakCellCycleModel, and AbstractWntOdeBasedCellCycleModel.
Definition at line 203 of file AbstractCellCycleModel.cpp.
References GetSG2MDuration(), and mTransitCellG1Duration.
| double AbstractCellCycleModel::GetBirthTime | ( | ) | const |
- Returns:
- the time at which the cell was born.
Definition at line 82 of file AbstractCellCycleModel.cpp.
References mBirthTime.
Referenced by Cell::GetBirthTime().
| CellPtr AbstractCellCycleModel::GetCell | ( | ) |
- Returns:
- The cell which plays host to this cell-cycle model.
Definition at line 71 of file AbstractCellCycleModel.cpp.
References mpCell.
Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::CheckCellPointers().
| CellCyclePhase AbstractCellCycleModel::GetCurrentCellCyclePhase | ( | ) |
- Returns:
- the current cell cycle phase
Definition at line 92 of file AbstractCellCycleModel.cpp.
References mCurrentCellCyclePhase.
Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteVtkResultsToFile().
| unsigned AbstractCellCycleModel::GetDimension | ( | ) |
Get the dimension this cell-cycle model thinks the simulation is in.
Definition at line 198 of file AbstractCellCycleModel.cpp.
References mDimension.
| double AbstractCellCycleModel::GetG1Duration | ( | ) | [virtual] |
- Returns:
- the duration of the G1 phase of the cell cycle
Definition at line 104 of file AbstractCellCycleModel.cpp.
References mG1Duration.
Referenced by ReadyToDivide().
| double AbstractCellCycleModel::GetG2Duration | ( | ) | [virtual] |
- Returns:
- the duration of the G2 phase of the cell cycle mG2Duration
Reimplemented in StochasticOxygenBasedCellCycleModel, TysonNovakCellCycleModel, and StochasticWntCellCycleModel.
Definition at line 133 of file AbstractCellCycleModel.cpp.
References mG2Duration.
Referenced by ReadyToDivide(), ContactInhibitionCellCycleModel::UpdateCellCyclePhase(), AbstractSimpleCellCycleModel::UpdateCellCyclePhase(), and AbstractOdeBasedCellCycleModel::UpdateCellCyclePhase().
| double AbstractCellCycleModel::GetMDuration | ( | ) | [virtual] |
- Returns:
- the duration of the M phase of the cell cycle mMDuration
Reimplemented in TysonNovakCellCycleModel.
Definition at line 138 of file AbstractCellCycleModel.cpp.
References mMDuration.
Referenced by ReadyToDivide(), ContactInhibitionCellCycleModel::UpdateCellCyclePhase(), AbstractSimpleCellCycleModel::UpdateCellCyclePhase(), and AbstractOdeBasedCellCycleModel::UpdateCellCyclePhase().
| double AbstractCellCycleModel::GetMinimumGapDuration | ( | ) |
- Returns:
- mMinimumGapDuration
Definition at line 224 of file AbstractCellCycleModel.cpp.
References mMinimumGapDuration.
| double AbstractCellCycleModel::GetSDuration | ( | ) | [virtual] |
- Returns:
- the duration of the S phase of the cell cycle mSDuration
Reimplemented in TysonNovakCellCycleModel.
Definition at line 128 of file AbstractCellCycleModel.cpp.
References mSDuration.
Referenced by ReadyToDivide(), ContactInhibitionCellCycleModel::UpdateCellCyclePhase(), AbstractSimpleCellCycleModel::UpdateCellCyclePhase(), and AbstractOdeBasedCellCycleModel::UpdateCellCyclePhase().
| double AbstractCellCycleModel::GetSG2MDuration | ( | ) |
- Returns:
- mSDuration + mG2Duration + mMDuration
Definition at line 123 of file AbstractCellCycleModel.cpp.
References mG2Duration, mMDuration, and mSDuration.
Referenced by GetAverageStemCellCycleTime(), and GetAverageTransitCellCycleTime().
| double AbstractCellCycleModel::GetStemCellG1Duration | ( | ) |
- Returns:
- mStemCellG1Duration
Definition at line 113 of file AbstractCellCycleModel.cpp.
References mStemCellG1Duration.
Referenced by SimpleWntCellCycleModel::SetG1Duration(), StochasticDurationGenerationBasedCellCycleModel::SetG1Duration(), StochasticDurationCellCycleModel::SetG1Duration(), and AbstractSimpleCellCycleModel::SetG1Duration().
| double AbstractCellCycleModel::GetTransitCellG1Duration | ( | ) |
- Returns:
- mTransitCellG1Duration
Definition at line 118 of file AbstractCellCycleModel.cpp.
References mTransitCellG1Duration.
Referenced by SimpleWntCellCycleModel::SetG1Duration(), StochasticDurationGenerationBasedCellCycleModel::SetG1Duration(), StochasticDurationCellCycleModel::SetG1Duration(), and AbstractSimpleCellCycleModel::SetG1Duration().
| void AbstractCellCycleModel::Initialise | ( | void | ) | [virtual] |
Initialise the cell-cycle model at the start of a simulation.
This method will be called precisely once per cell set up in the initial cell population. It is not called on cell division; use ResetForDivision(), CreateCellCycleModel() and InitialiseDaughterCell() for that.
By the time this is called, a CellPopulation will have been set up, so the model can know where its cell is located in space. If relevant to the simulation, any singletons will also have been initialised.
Reimplemented in AbstractSimpleCellCycleModel, Alarcon2004OxygenBasedCellCycleModel, DeltaNotchCellCycleModel, StochasticOxygenBasedCellCycleModel, TysonNovakCellCycleModel, AbstractVanLeeuwen2009WntSwatCellCycleModel, SingleOdeWntCellCycleModel, StochasticWntCellCycleModel, and WntCellCycleModel.
Definition at line 58 of file AbstractCellCycleModel.cpp.
Referenced by Cell::InitialiseCellCycleModel().
| void AbstractCellCycleModel::InitialiseDaughterCell | ( | ) | [virtual] |
Initialise the new daughter cell's cycle model after a cell division.
This is called by Cell::Divide once the new cell object has been fully created, to perform any initialisation of the cell cycle which requires access to the cell.
Note that much initialisation can be performed using the combination of ResetForDivision() (called on the parent prior to division) and CreateCellCycleModel() (called on the reset parent to create the new cell-cycle model object).
Reimplemented in AbstractSimpleCellCycleModel, AbstractSimpleGenerationBasedCellCycleModel, StochasticOxygenBasedCellCycleModel, TysonNovakCellCycleModel, SimpleWntCellCycleModel, and StochasticWntCellCycleModel.
Definition at line 62 of file AbstractCellCycleModel.cpp.
| void AbstractCellCycleModel::OutputCellCycleModelInfo | ( | out_stream & | rParamsFile | ) |
Outputs cell-cycle model used in the simulation to file and then calls OutputCellCyclemodelParameters to output all relevant parameters.
- Parameters:
-
rParamsFile the file stream to which the parameters are output
Definition at line 229 of file AbstractCellCycleModel.cpp.
References Identifiable::GetIdentifier(), and OutputCellCycleModelParameters().
| void AbstractCellCycleModel::OutputCellCycleModelParameters | ( | out_stream & | rParamsFile | ) | [pure virtual] |
Outputs cell cycle model parameters to file.
As this method is pure virtual, it must be overridden in subclasses.
- Parameters:
-
rParamsFile the file stream to which the parameters are output
Implemented in AbstractOdeBasedCellCycleModel, AbstractSimpleCellCycleModel, AbstractSimpleGenerationBasedCellCycleModel, Alarcon2004OxygenBasedCellCycleModel, ContactInhibitionCellCycleModel, DeltaNotchCellCycleModel, FixedDurationGenerationBasedCellCycleModel, SimpleOxygenBasedCellCycleModel, StochasticDurationCellCycleModel, StochasticDurationGenerationBasedCellCycleModel, StochasticOxygenBasedCellCycleModel, TysonNovakCellCycleModel, AbstractVanLeeuwen2009WntSwatCellCycleModel, AbstractWntOdeBasedCellCycleModel, SimpleWntCellCycleModel, SingleOdeWntCellCycleModel, StochasticWntCellCycleModel, VanLeeuwen2009WntSwatCellCycleModelHypothesisOne, VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo, and WntCellCycleModel.
Definition at line 238 of file AbstractCellCycleModel.cpp.
References mG2Duration, mMDuration, mSDuration, mStemCellG1Duration, and mTransitCellG1Duration.
Referenced by OutputCellCycleModelInfo().
| bool AbstractCellCycleModel::ReadyToDivide | ( | ) | [virtual] |
Determine whether the cell is ready to divide (enter M phase).
The intention is that this method is called precisely once at each timestep of the simulation. However this does not appear to always be the case at present, and so it can cope with more unusual usage patterns.
Definition at line 173 of file AbstractCellCycleModel.cpp.
References GetAge(), GetG1Duration(), GetG2Duration(), GetMDuration(), GetSDuration(), mCurrentCellCyclePhase, mpCell, mReadyToDivide, and UpdateCellCyclePhase().
Referenced by Cell::ReadyToDivide().
| void AbstractCellCycleModel::ResetForDivision | ( | ) | [virtual] |
Each cell-cycle model must be able to be reset 'after' a cell division.
Actually, this method is called from Cell::Divide() to reset the cell cycle just before the daughter cell is created. CreateCellCycleModel() can then clone our state to generate a cell-cycle model instance for the daughter cell.
Reimplemented in AbstractOdeBasedCellCycleModel, AbstractSimpleCellCycleModel, AbstractSimpleGenerationBasedCellCycleModel, Alarcon2004OxygenBasedCellCycleModel, StochasticOxygenBasedCellCycleModel, TysonNovakCellCycleModel, AbstractWntOdeBasedCellCycleModel, and StochasticWntCellCycleModel.
Definition at line 97 of file AbstractCellCycleModel.cpp.
References mCurrentCellCyclePhase, and mReadyToDivide.
Referenced by Cell::Divide().
| void AbstractCellCycleModel::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
Reimplemented in AbstractOdeBasedCellCycleModel, AbstractSimpleCellCycleModel, AbstractSimpleGenerationBasedCellCycleModel, Alarcon2004OxygenBasedCellCycleModel, ContactInhibitionCellCycleModel, DeltaNotchCellCycleModel, FixedDurationGenerationBasedCellCycleModel, SimpleOxygenBasedCellCycleModel, StochasticDurationCellCycleModel, StochasticDurationGenerationBasedCellCycleModel, StochasticOxygenBasedCellCycleModel, TysonNovakCellCycleModel, AbstractVanLeeuwen2009WntSwatCellCycleModel, AbstractWntOdeBasedCellCycleModel, SimpleWntCellCycleModel, SingleOdeWntCellCycleModel, StochasticWntCellCycleModel, VanLeeuwen2009WntSwatCellCycleModelHypothesisOne, VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo, and WntCellCycleModel.
Definition at line 75 of file AbstractCellCycleModel.hpp.
References SerializableSingleton< SINGLETON_CLASS >::GetSerializationWrapper(), SimulationTime::Instance(), mBirthTime, mCurrentCellCyclePhase, mDimension, mG1Duration, mG2Duration, mMDuration, mMinimumGapDuration, mReadyToDivide, mSDuration, mStemCellG1Duration, and mTransitCellG1Duration.
| void AbstractCellCycleModel::SetBirthTime | ( | double | birthTime | ) | [virtual] |
Set the cell's time of birth (usually not required as it should be inside the indivdual cell-cycle-model-constructor, but useful for tests).
- Parameters:
-
birthTime the simulation time at this cell's birth.
(This function is overridden in AbstractOdeBasedCellCycleModel).
Reimplemented in AbstractOdeBasedCellCycleModel.
Definition at line 77 of file AbstractCellCycleModel.cpp.
References mBirthTime.
Referenced by SingleOdeWntCellCycleModel::CreateCellCycleModel(), SimpleWntCellCycleModel::CreateCellCycleModel(), StochasticOxygenBasedCellCycleModel::CreateCellCycleModel(), StochasticDurationGenerationBasedCellCycleModel::CreateCellCycleModel(), StochasticDurationCellCycleModel::CreateCellCycleModel(), SimpleOxygenBasedCellCycleModel::CreateCellCycleModel(), FixedDurationGenerationBasedCellCycleModel::CreateCellCycleModel(), DeltaNotchCellCycleModel::CreateCellCycleModel(), ContactInhibitionCellCycleModel::CreateCellCycleModel(), and Cell::SetBirthTime().
| void AbstractCellCycleModel::SetCell | ( | CellPtr | pCell | ) |
Gives the cell-cycle model a pointer to its host cell.
Some cell-cycle models pass this pointer to other classes, which use this information to determine other information based upon the location of the cell (e.g. the Wnt concentration at this location).
- Parameters:
-
pCell pointer to the cell
Definition at line 66 of file AbstractCellCycleModel.cpp.
References mpCell.
Referenced by Cell::Cell(), and Cell::SetCellCycleModel().
| void AbstractCellCycleModel::SetDimension | ( | unsigned | dimension | ) |
Set the spatial dimension.
- Parameters:
-
dimension
Definition at line 189 of file AbstractCellCycleModel.cpp.
References EXCEPTION, and mDimension.
Referenced by WntCellCycleModel::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::CreateCellCycleModel(), StochasticWntCellCycleModel::CreateCellCycleModel(), SingleOdeWntCellCycleModel::CreateCellCycleModel(), SimpleWntCellCycleModel::CreateCellCycleModel(), StochasticOxygenBasedCellCycleModel::CreateCellCycleModel(), SimpleOxygenBasedCellCycleModel::CreateCellCycleModel(), DeltaNotchCellCycleModel::CreateCellCycleModel(), ContactInhibitionCellCycleModel::CreateCellCycleModel(), and Alarcon2004OxygenBasedCellCycleModel::CreateCellCycleModel().
| void AbstractCellCycleModel::SetG2Duration | ( | double | g2Duration | ) |
Set mG2Duration.
- Parameters:
-
g2Duration the new value of mG2Duration
Definition at line 162 of file AbstractCellCycleModel.cpp.
References mG2Duration.
Referenced by WntCellCycleModel::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::CreateCellCycleModel(), StochasticWntCellCycleModel::CreateCellCycleModel(), SingleOdeWntCellCycleModel::CreateCellCycleModel(), SimpleWntCellCycleModel::CreateCellCycleModel(), TysonNovakCellCycleModel::CreateCellCycleModel(), StochasticOxygenBasedCellCycleModel::CreateCellCycleModel(), StochasticDurationGenerationBasedCellCycleModel::CreateCellCycleModel(), StochasticDurationCellCycleModel::CreateCellCycleModel(), SimpleOxygenBasedCellCycleModel::CreateCellCycleModel(), FixedDurationGenerationBasedCellCycleModel::CreateCellCycleModel(), ContactInhibitionCellCycleModel::CreateCellCycleModel(), and Alarcon2004OxygenBasedCellCycleModel::CreateCellCycleModel().
| void AbstractCellCycleModel::SetMDuration | ( | double | mDuration | ) |
Set mMDuration.
- Parameters:
-
mDuration the new value of mMDuration
Definition at line 167 of file AbstractCellCycleModel.cpp.
References mMDuration.
Referenced by WntCellCycleModel::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::CreateCellCycleModel(), StochasticWntCellCycleModel::CreateCellCycleModel(), SingleOdeWntCellCycleModel::CreateCellCycleModel(), SimpleWntCellCycleModel::CreateCellCycleModel(), TysonNovakCellCycleModel::CreateCellCycleModel(), StochasticOxygenBasedCellCycleModel::CreateCellCycleModel(), StochasticDurationGenerationBasedCellCycleModel::CreateCellCycleModel(), StochasticDurationCellCycleModel::CreateCellCycleModel(), SimpleOxygenBasedCellCycleModel::CreateCellCycleModel(), FixedDurationGenerationBasedCellCycleModel::CreateCellCycleModel(), ContactInhibitionCellCycleModel::CreateCellCycleModel(), and Alarcon2004OxygenBasedCellCycleModel::CreateCellCycleModel().
| void AbstractCellCycleModel::SetMinimumGapDuration | ( | double | minimumGapDuration | ) |
Set mMinimumGapDuration.
- Parameters:
-
minimumGapDuration the new value of mMinimumGapDuration
Definition at line 218 of file AbstractCellCycleModel.cpp.
References mMinimumGapDuration.
Referenced by WntCellCycleModel::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::CreateCellCycleModel(), StochasticWntCellCycleModel::CreateCellCycleModel(), SingleOdeWntCellCycleModel::CreateCellCycleModel(), SimpleWntCellCycleModel::CreateCellCycleModel(), TysonNovakCellCycleModel::CreateCellCycleModel(), StochasticOxygenBasedCellCycleModel::CreateCellCycleModel(), StochasticDurationGenerationBasedCellCycleModel::CreateCellCycleModel(), StochasticDurationCellCycleModel::CreateCellCycleModel(), SimpleOxygenBasedCellCycleModel::CreateCellCycleModel(), FixedDurationGenerationBasedCellCycleModel::CreateCellCycleModel(), ContactInhibitionCellCycleModel::CreateCellCycleModel(), and Alarcon2004OxygenBasedCellCycleModel::CreateCellCycleModel().
| void AbstractCellCycleModel::SetSDuration | ( | double | sDuration | ) |
Set mSDuration.
- Parameters:
-
sDuration the new value of mSDuration
Definition at line 157 of file AbstractCellCycleModel.cpp.
References mSDuration.
Referenced by WntCellCycleModel::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::CreateCellCycleModel(), StochasticWntCellCycleModel::CreateCellCycleModel(), SingleOdeWntCellCycleModel::CreateCellCycleModel(), SimpleWntCellCycleModel::CreateCellCycleModel(), TysonNovakCellCycleModel::CreateCellCycleModel(), StochasticOxygenBasedCellCycleModel::CreateCellCycleModel(), StochasticDurationGenerationBasedCellCycleModel::CreateCellCycleModel(), StochasticDurationCellCycleModel::CreateCellCycleModel(), SimpleOxygenBasedCellCycleModel::CreateCellCycleModel(), FixedDurationGenerationBasedCellCycleModel::CreateCellCycleModel(), ContactInhibitionCellCycleModel::CreateCellCycleModel(), and Alarcon2004OxygenBasedCellCycleModel::CreateCellCycleModel().
| void AbstractCellCycleModel::SetStemCellG1Duration | ( | double | stemCellG1Duration | ) |
Set mStemCellG1Duration.
- Parameters:
-
stemCellG1Duration the new value of mStemCellG1Duration
Definition at line 147 of file AbstractCellCycleModel.cpp.
References mStemCellG1Duration.
Referenced by WntCellCycleModel::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::CreateCellCycleModel(), StochasticWntCellCycleModel::CreateCellCycleModel(), SingleOdeWntCellCycleModel::CreateCellCycleModel(), SimpleWntCellCycleModel::CreateCellCycleModel(), TysonNovakCellCycleModel::CreateCellCycleModel(), StochasticOxygenBasedCellCycleModel::CreateCellCycleModel(), StochasticDurationGenerationBasedCellCycleModel::CreateCellCycleModel(), StochasticDurationCellCycleModel::CreateCellCycleModel(), SimpleOxygenBasedCellCycleModel::CreateCellCycleModel(), FixedDurationGenerationBasedCellCycleModel::CreateCellCycleModel(), ContactInhibitionCellCycleModel::CreateCellCycleModel(), and Alarcon2004OxygenBasedCellCycleModel::CreateCellCycleModel().
| void AbstractCellCycleModel::SetTransitCellG1Duration | ( | double | transitCellG1Duration | ) |
Set mTransitCellG1Duration.
- Parameters:
-
transitCellG1Duration the new value of mTransitCellG1Duration
Definition at line 152 of file AbstractCellCycleModel.cpp.
References mTransitCellG1Duration.
Referenced by WntCellCycleModel::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::CreateCellCycleModel(), StochasticWntCellCycleModel::CreateCellCycleModel(), SingleOdeWntCellCycleModel::CreateCellCycleModel(), SimpleWntCellCycleModel::CreateCellCycleModel(), TysonNovakCellCycleModel::CreateCellCycleModel(), StochasticOxygenBasedCellCycleModel::CreateCellCycleModel(), StochasticDurationGenerationBasedCellCycleModel::CreateCellCycleModel(), StochasticDurationCellCycleModel::CreateCellCycleModel(), SimpleOxygenBasedCellCycleModel::CreateCellCycleModel(), FixedDurationGenerationBasedCellCycleModel::CreateCellCycleModel(), ContactInhibitionCellCycleModel::CreateCellCycleModel(), and Alarcon2004OxygenBasedCellCycleModel::CreateCellCycleModel().
| virtual void AbstractCellCycleModel::UpdateCellCyclePhase | ( | ) | [pure virtual] |
This method must be implemented by subclasses in order to set the phase the cell-cycle model is currently in. It is called from ReadyToDivide() just prior to deciding whether to divide the cell based on how far through the cell cycle it is, i.e. whether it has completed M, G1, S and G2 phases.
Implemented in AbstractOdeBasedCellCycleModel, AbstractSimpleCellCycleModel, ContactInhibitionCellCycleModel, DeltaNotchCellCycleModel, SimpleOxygenBasedCellCycleModel, AbstractWntOdeBasedCellCycleModel, SimpleWntCellCycleModel, and SingleOdeWntCellCycleModel.
Referenced by ReadyToDivide().
Friends And Related Function Documentation
friend class boost::serialization::access [friend] |
Needed for serialization.
Reimplemented in AbstractOdeBasedCellCycleModel, AbstractSimpleCellCycleModel, AbstractSimpleGenerationBasedCellCycleModel, Alarcon2004OxygenBasedCellCycleModel, ContactInhibitionCellCycleModel, DeltaNotchCellCycleModel, FixedDurationGenerationBasedCellCycleModel, SimpleOxygenBasedCellCycleModel, StochasticDurationCellCycleModel, StochasticDurationGenerationBasedCellCycleModel, StochasticOxygenBasedCellCycleModel, TysonNovakCellCycleModel, AbstractVanLeeuwen2009WntSwatCellCycleModel, AbstractWntOdeBasedCellCycleModel, SimpleWntCellCycleModel, SingleOdeWntCellCycleModel, StochasticWntCellCycleModel, VanLeeuwen2009WntSwatCellCycleModelHypothesisOne, VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo, and WntCellCycleModel.
Definition at line 67 of file AbstractCellCycleModel.hpp.
Member Data Documentation
double AbstractCellCycleModel::mBirthTime [protected] |
The time that the cell began to split from its parent (i.e. beginning of M phase NOT the end)
Definition at line 105 of file AbstractCellCycleModel.hpp.
Referenced by WntCellCycleModel::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::CreateCellCycleModel(), StochasticWntCellCycleModel::CreateCellCycleModel(), SingleOdeWntCellCycleModel::CreateCellCycleModel(), SimpleWntCellCycleModel::CreateCellCycleModel(), TysonNovakCellCycleModel::CreateCellCycleModel(), StochasticOxygenBasedCellCycleModel::CreateCellCycleModel(), StochasticDurationGenerationBasedCellCycleModel::CreateCellCycleModel(), StochasticDurationCellCycleModel::CreateCellCycleModel(), SimpleOxygenBasedCellCycleModel::CreateCellCycleModel(), FixedDurationGenerationBasedCellCycleModel::CreateCellCycleModel(), DeltaNotchCellCycleModel::CreateCellCycleModel(), ContactInhibitionCellCycleModel::CreateCellCycleModel(), Alarcon2004OxygenBasedCellCycleModel::CreateCellCycleModel(), GetAge(), GetBirthTime(), SingleOdeWntCellCycleModel::Initialise(), DeltaNotchCellCycleModel::Initialise(), AbstractSimpleCellCycleModel::ResetForDivision(), AbstractOdeBasedCellCycleModel::ResetForDivision(), serialize(), SetBirthTime(), and AbstractOdeBasedCellCycleModel::UpdateCellCyclePhase().
CellCyclePhase AbstractCellCycleModel::mCurrentCellCyclePhase [protected] |
The phase of the cell cycle that this model is in (specified in CellCyclePhases.hpp)
Definition at line 108 of file AbstractCellCycleModel.hpp.
Referenced by GetCurrentCellCyclePhase(), ReadyToDivide(), ResetForDivision(), serialize(), SimpleOxygenBasedCellCycleModel::UpdateCellCyclePhase(), ContactInhibitionCellCycleModel::UpdateCellCyclePhase(), AbstractSimpleCellCycleModel::UpdateCellCyclePhase(), and AbstractOdeBasedCellCycleModel::UpdateCellCyclePhase().
unsigned AbstractCellCycleModel::mDimension [protected] |
Spatial dimension being used in simulation (defaults to 0, set with SetDimension).
Definition at line 124 of file AbstractCellCycleModel.hpp.
Referenced by WntCellCycleModel::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::CreateCellCycleModel(), StochasticWntCellCycleModel::CreateCellCycleModel(), SingleOdeWntCellCycleModel::CreateCellCycleModel(), SimpleWntCellCycleModel::CreateCellCycleModel(), StochasticOxygenBasedCellCycleModel::CreateCellCycleModel(), SimpleOxygenBasedCellCycleModel::CreateCellCycleModel(), DeltaNotchCellCycleModel::CreateCellCycleModel(), ContactInhibitionCellCycleModel::CreateCellCycleModel(), Alarcon2004OxygenBasedCellCycleModel::CreateCellCycleModel(), GetDimension(), SimpleWntCellCycleModel::GetWntLevel(), AbstractWntOdeBasedCellCycleModel::GetWntLevel(), SimpleWntCellCycleModel::GetWntType(), serialize(), and SetDimension().
double AbstractCellCycleModel::mG1Duration [protected] |
How long the G1 phase lasts for. Not necessarily a fixed value.
Definition at line 114 of file AbstractCellCycleModel.hpp.
Referenced by GetG1Duration(), AbstractOdeBasedCellCycleModel::ResetForDivision(), serialize(), SimpleWntCellCycleModel::SetG1Duration(), StochasticDurationGenerationBasedCellCycleModel::SetG1Duration(), StochasticDurationCellCycleModel::SetG1Duration(), AbstractSimpleCellCycleModel::SetG1Duration(), SimpleOxygenBasedCellCycleModel::UpdateCellCyclePhase(), ContactInhibitionCellCycleModel::UpdateCellCyclePhase(), AbstractSimpleCellCycleModel::UpdateCellCyclePhase(), and AbstractOdeBasedCellCycleModel::UpdateCellCyclePhase().
double AbstractCellCycleModel::mG2Duration [protected] |
Duration of G2 phase for all cell types.
Definition at line 156 of file AbstractCellCycleModel.hpp.
Referenced by WntCellCycleModel::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::CreateCellCycleModel(), StochasticWntCellCycleModel::CreateCellCycleModel(), SingleOdeWntCellCycleModel::CreateCellCycleModel(), SimpleWntCellCycleModel::CreateCellCycleModel(), TysonNovakCellCycleModel::CreateCellCycleModel(), StochasticOxygenBasedCellCycleModel::CreateCellCycleModel(), StochasticDurationGenerationBasedCellCycleModel::CreateCellCycleModel(), StochasticDurationCellCycleModel::CreateCellCycleModel(), SimpleOxygenBasedCellCycleModel::CreateCellCycleModel(), FixedDurationGenerationBasedCellCycleModel::CreateCellCycleModel(), ContactInhibitionCellCycleModel::CreateCellCycleModel(), Alarcon2004OxygenBasedCellCycleModel::CreateCellCycleModel(), GetG2Duration(), GetSG2MDuration(), OutputCellCycleModelParameters(), serialize(), and SetG2Duration().
double AbstractCellCycleModel::mMDuration [protected] |
Duration of M phase for all cell types.
Definition at line 161 of file AbstractCellCycleModel.hpp.
Referenced by WntCellCycleModel::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::CreateCellCycleModel(), StochasticWntCellCycleModel::CreateCellCycleModel(), SingleOdeWntCellCycleModel::CreateCellCycleModel(), SimpleWntCellCycleModel::CreateCellCycleModel(), TysonNovakCellCycleModel::CreateCellCycleModel(), StochasticOxygenBasedCellCycleModel::CreateCellCycleModel(), StochasticDurationGenerationBasedCellCycleModel::CreateCellCycleModel(), StochasticDurationCellCycleModel::CreateCellCycleModel(), SimpleOxygenBasedCellCycleModel::CreateCellCycleModel(), FixedDurationGenerationBasedCellCycleModel::CreateCellCycleModel(), ContactInhibitionCellCycleModel::CreateCellCycleModel(), Alarcon2004OxygenBasedCellCycleModel::CreateCellCycleModel(), GetMDuration(), GetSG2MDuration(), OutputCellCycleModelParameters(), serialize(), and SetMDuration().
double AbstractCellCycleModel::mMinimumGapDuration [protected] |
Minimum possible duration of either of the gap phases (G1 or G2). Has units of hours.
Used to guarantee a strictly positive duration in cell-cycle models that use normal random deviates for G1 or G2 phases.
Definition at line 133 of file AbstractCellCycleModel.hpp.
Referenced by WntCellCycleModel::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::CreateCellCycleModel(), StochasticWntCellCycleModel::CreateCellCycleModel(), SingleOdeWntCellCycleModel::CreateCellCycleModel(), SimpleWntCellCycleModel::CreateCellCycleModel(), TysonNovakCellCycleModel::CreateCellCycleModel(), StochasticOxygenBasedCellCycleModel::CreateCellCycleModel(), StochasticDurationGenerationBasedCellCycleModel::CreateCellCycleModel(), StochasticDurationCellCycleModel::CreateCellCycleModel(), SimpleOxygenBasedCellCycleModel::CreateCellCycleModel(), FixedDurationGenerationBasedCellCycleModel::CreateCellCycleModel(), ContactInhibitionCellCycleModel::CreateCellCycleModel(), Alarcon2004OxygenBasedCellCycleModel::CreateCellCycleModel(), StochasticWntCellCycleModel::GenerateStochasticG2Duration(), StochasticOxygenBasedCellCycleModel::GenerateStochasticG2Duration(), GetMinimumGapDuration(), serialize(), SimpleWntCellCycleModel::SetG1Duration(), and SetMinimumGapDuration().
CellPtr AbstractCellCycleModel::mpCell [protected] |
The cell that this model is associated with.
Definition at line 99 of file AbstractCellCycleModel.hpp.
Referenced by WntCellCycleModel::AdjustOdeParameters(), SingleOdeWntCellCycleModel::AdjustOdeParameters(), AbstractVanLeeuwen2009WntSwatCellCycleModel::AdjustOdeParameters(), Alarcon2004OxygenBasedCellCycleModel::AdjustOdeParameters(), WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel(), SingleOdeWntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel(), AbstractVanLeeuwen2009WntSwatCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel(), WntCellCycleModel::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::CreateCellCycleModel(), StochasticWntCellCycleModel::CreateCellCycleModel(), SingleOdeWntCellCycleModel::CreateCellCycleModel(), Alarcon2004OxygenBasedCellCycleModel::CreateCellCycleModel(), GetCell(), SimpleWntCellCycleModel::GetWntLevel(), AbstractWntOdeBasedCellCycleModel::GetWntLevel(), WntCellCycleModel::Initialise(), SingleOdeWntCellCycleModel::Initialise(), AbstractVanLeeuwen2009WntSwatCellCycleModel::Initialise(), DeltaNotchCellCycleModel::Initialise(), Alarcon2004OxygenBasedCellCycleModel::Initialise(), SimpleWntCellCycleModel::InitialiseDaughterCell(), TysonNovakCellCycleModel::InitialiseDaughterCell(), AbstractSimpleGenerationBasedCellCycleModel::InitialiseDaughterCell(), ReadyToDivide(), AbstractSimpleGenerationBasedCellCycleModel::ResetForDivision(), SetCell(), SimpleWntCellCycleModel::SetG1Duration(), StochasticDurationGenerationBasedCellCycleModel::SetG1Duration(), StochasticDurationCellCycleModel::SetG1Duration(), AbstractSimpleCellCycleModel::SetG1Duration(), SimpleWntCellCycleModel::UpdateCellCyclePhase(), SimpleOxygenBasedCellCycleModel::UpdateCellCyclePhase(), ContactInhibitionCellCycleModel::UpdateCellCyclePhase(), AbstractSimpleCellCycleModel::UpdateCellCyclePhase(), AbstractWntOdeBasedCellCycleModel::UpdateCellProliferativeType(), DeltaNotchCellCycleModel::UpdateDeltaNotch(), and SimpleOxygenBasedCellCycleModel::UpdateHypoxicDuration().
bool AbstractCellCycleModel::mReadyToDivide [protected] |
Whether the cell is currently ready to undergo division.
Definition at line 119 of file AbstractCellCycleModel.hpp.
Referenced by ReadyToDivide(), ResetForDivision(), and serialize().
double AbstractCellCycleModel::mSDuration [protected] |
Duration of S phase for all cell types.
Definition at line 151 of file AbstractCellCycleModel.hpp.
Referenced by WntCellCycleModel::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::CreateCellCycleModel(), StochasticWntCellCycleModel::CreateCellCycleModel(), SingleOdeWntCellCycleModel::CreateCellCycleModel(), SimpleWntCellCycleModel::CreateCellCycleModel(), TysonNovakCellCycleModel::CreateCellCycleModel(), StochasticOxygenBasedCellCycleModel::CreateCellCycleModel(), StochasticDurationGenerationBasedCellCycleModel::CreateCellCycleModel(), StochasticDurationCellCycleModel::CreateCellCycleModel(), SimpleOxygenBasedCellCycleModel::CreateCellCycleModel(), FixedDurationGenerationBasedCellCycleModel::CreateCellCycleModel(), ContactInhibitionCellCycleModel::CreateCellCycleModel(), Alarcon2004OxygenBasedCellCycleModel::CreateCellCycleModel(), GetSDuration(), GetSG2MDuration(), OutputCellCycleModelParameters(), serialize(), and SetSDuration().
double AbstractCellCycleModel::mStemCellG1Duration [protected] |
Duration of G1 phase for stem cells. May be used as a mean duration for stochastic cell-cycle models.
Definition at line 140 of file AbstractCellCycleModel.hpp.
Referenced by WntCellCycleModel::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::CreateCellCycleModel(), StochasticWntCellCycleModel::CreateCellCycleModel(), SingleOdeWntCellCycleModel::CreateCellCycleModel(), SimpleWntCellCycleModel::CreateCellCycleModel(), TysonNovakCellCycleModel::CreateCellCycleModel(), StochasticOxygenBasedCellCycleModel::CreateCellCycleModel(), StochasticDurationGenerationBasedCellCycleModel::CreateCellCycleModel(), StochasticDurationCellCycleModel::CreateCellCycleModel(), SimpleOxygenBasedCellCycleModel::CreateCellCycleModel(), FixedDurationGenerationBasedCellCycleModel::CreateCellCycleModel(), ContactInhibitionCellCycleModel::CreateCellCycleModel(), Alarcon2004OxygenBasedCellCycleModel::CreateCellCycleModel(), GetAverageStemCellCycleTime(), GetStemCellG1Duration(), OutputCellCycleModelParameters(), serialize(), and SetStemCellG1Duration().
double AbstractCellCycleModel::mTransitCellG1Duration [protected] |
Duration of G1 phase for transit cells. May be used as a mean duration for stochastic cell-cycle models.
Definition at line 146 of file AbstractCellCycleModel.hpp.
Referenced by WntCellCycleModel::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::CreateCellCycleModel(), StochasticWntCellCycleModel::CreateCellCycleModel(), SingleOdeWntCellCycleModel::CreateCellCycleModel(), SimpleWntCellCycleModel::CreateCellCycleModel(), TysonNovakCellCycleModel::CreateCellCycleModel(), StochasticOxygenBasedCellCycleModel::CreateCellCycleModel(), StochasticDurationGenerationBasedCellCycleModel::CreateCellCycleModel(), StochasticDurationCellCycleModel::CreateCellCycleModel(), SimpleOxygenBasedCellCycleModel::CreateCellCycleModel(), FixedDurationGenerationBasedCellCycleModel::CreateCellCycleModel(), ContactInhibitionCellCycleModel::CreateCellCycleModel(), Alarcon2004OxygenBasedCellCycleModel::CreateCellCycleModel(), GetAverageTransitCellCycleTime(), GetTransitCellG1Duration(), OutputCellCycleModelParameters(), serialize(), and SetTransitCellG1Duration().
The documentation for this class was generated from the following files:
- cell_based/src/population/cell/cycle/AbstractCellCycleModel.hpp
- cell_based/src/population/cell/cycle/AbstractCellCycleModel.cpp
