#include <Cell.hpp>
Inheritance diagram for Cell:
Collaboration diagram for Cell:
Detailed Description
Cell is the basic container for all the biological information about a cell. It contains the cell-cycle model and all other biological properties such as mutation state, cell type, whether it is undergoing apoptosis or not.
This class should not store any spatial information - cells are linked to space by the AbstractCellPopulation subclasses.
Constructor & Destructor Documentation
| Cell::Cell | ( | boost::shared_ptr< AbstractCellProperty > | pMutationState, |
| AbstractCellCycleModel * | pCellCycleModel, | ||
| bool | archiving = false, |
||
| CellPropertyCollection | cellPropertyCollection = CellPropertyCollection() |
||
| ) |
Create a new cell.
- Parameters:
-
pMutationState the mutation state of the cell pCellCycleModel the cell-cycle model to use to decide when the cell divides. This MUST be allocated using new, and will be deleted when the cell is destroyed. archiving whether this constructor is being called by the archiver - do things slightly differently! (defaults to false) cellPropertyCollection the cell property collection (defaults to NULL)
Definition at line 59 of file Cell.cpp.
References CellPropertyCollection::AddProperty(), CellPropertyCollection::Begin(), CellPropertyCollection::End(), EXCEPTION, CellPropertyCollection::HasProperty(), CellPropertyCollection::HasPropertyType(), SimulationTime::Instance(), MAKE_PTR, mCellPropertyCollection, mpCellCycleModel, and AbstractCellCycleModel::SetCell().
Referenced by Divide().
| Cell::~Cell | ( | ) |
Destructor, which frees the memory allocated for our cell-cycle model.
Definition at line 123 of file Cell.cpp.
References Kill(), mIsDead, and mpCellCycleModel.
Member Function Documentation
| void Cell::AddCellProperty | ( | const boost::shared_ptr< AbstractCellProperty > & | rProperty | ) |
Add a cell property to the cell. Use this method instead of calling rGetCellPropertyCollection().AddProperty() directly, to ensure that the cell property keeps correct track of the number of cells with it (if this is done).
- Parameters:
-
rProperty the property to add
Definition at line 229 of file Cell.cpp.
References CellPropertyCollection::AddProperty(), CellPropertyCollection::HasProperty(), and mCellPropertyCollection.
Referenced by SetAncestor(), SetMutationState(), and StartApoptosis().
| CellPtr Cell::Divide | ( | ) |
Divide this cell to produce a daughter cell. ReadyToDivide MUST have been called at the current time, and returned true.
- Returns:
- the new daughter cell
Definition at line 388 of file Cell.cpp.
References CellPropertyCollection::AddProperty(), Cell(), AbstractCellCycleModel::CreateCellCycleModel(), GetCellData(), GetMutationState(), CellPropertyCollection::HasPropertyType(), IsDead(), MAKE_PTR_ARGS, mCanDivide, mCellProliferativeType, mCellPropertyCollection, mpCellCycleModel, CellPropertyCollection::RemoveProperty(), and AbstractCellCycleModel::ResetForDivision().
| double Cell::GetAge | ( | ) | const |
Get the cell's age from its cell-cycle model.
Definition at line 162 of file Cell.cpp.
References AbstractCellCycleModel::GetAge(), and mpCellCycleModel.
| unsigned Cell::GetAncestor | ( | ) | const |
- Returns:
- The ancestor object, inherited from parents or set using the method above, used for monoclonality experiments.
Definition at line 348 of file Cell.cpp.
References CellAncestor::GetAncestor(), CellPropertyCollection::GetPropertiesType(), CellPropertyCollection::GetProperty(), CellPropertyCollection::GetSize(), mCellPropertyCollection, and UNSIGNED_UNSET.
| double Cell::GetApoptosisTime | ( | ) | const |
| double Cell::GetBirthTime | ( | ) | const |
Get the cell's birth time from its cell-cycle model.
Definition at line 167 of file Cell.cpp.
References AbstractCellCycleModel::GetBirthTime(), and mpCellCycleModel.
| AbstractCellCycleModel * Cell::GetCellCycleModel | ( | ) | const |
Returns a pointer to the Cell's cell-cycle model.
Definition at line 152 of file Cell.cpp.
References mpCellCycleModel.
| boost::shared_ptr< CellData > Cell::GetCellData | ( | ) | const |
Get the CellData associated with the cell.
- Returns:
- a pointer to the cell data
Definition at line 206 of file Cell.cpp.
References CellPropertyCollection::GetPropertiesType(), CellPropertyCollection::GetProperty(), CellPropertyCollection::GetSize(), and mCellPropertyCollection.
Referenced by Divide().
| unsigned Cell::GetCellId | ( | ) | const |
- Returns:
- The cell identifier.
Definition at line 364 of file Cell.cpp.
References CellId::GetCellId(), CellPropertyCollection::GetPropertiesType(), CellPropertyCollection::GetProperty(), CellPropertyCollection::GetSize(), and mCellPropertyCollection.
| CellProliferativeType Cell::GetCellProliferativeType | ( | ) | const |
Get method for mCellProliferativeType.
Definition at line 137 of file Cell.cpp.
References mCellProliferativeType.
| boost::shared_ptr< AbstractCellMutationState > Cell::GetMutationState | ( | ) | const |
Get the cell's current mutation state.
Definition at line 191 of file Cell.cpp.
References CellPropertyCollection::GetPropertiesType(), CellPropertyCollection::GetProperty(), CellPropertyCollection::GetSize(), and mCellPropertyCollection.
Referenced by Divide(), and SetMutationState().
| double Cell::GetStartOfApoptosisTime | ( | ) | const |
Get the time at which apoptosis was commanded to start.
Definition at line 275 of file Cell.cpp.
References mStartOfApoptosisTime.
| double Cell::GetTimeUntilDeath | ( | ) | const |
- Returns:
- How long until the cell dies (if it is in apoptosis, throws an exception if not)
Definition at line 291 of file Cell.cpp.
References EXCEPTION, SimulationTime::GetTime(), SimulationTime::Instance(), mDeathTime, and mUndergoingApoptosis.
| bool Cell::HasApoptosisBegun | ( | ) | const |
Returns whether the cell is undergoing apoptosis or not.
Definition at line 270 of file Cell.cpp.
References mUndergoingApoptosis.
| bool Cell::HasCellProperty | ( | ) | const [inline] |
Test whether the cell property collection contains a property that has the exact type CLASS. Just calls mCellPropertyCollection.HasProperty().
Definition at line 294 of file Cell.hpp.
References CellPropertyCollection::HasProperty(), and mCellPropertyCollection.
| void Cell::InitialiseCellCycleModel | ( | ) |
Calls Initialise on the cell-cycle model associated with this cell.
Definition at line 157 of file Cell.cpp.
References AbstractCellCycleModel::Initialise(), and mpCellCycleModel.
| bool Cell::IsDead | ( | ) |
Return whether the cell is dead or undergoing apoptosis.
Definition at line 301 of file Cell.cpp.
References SimulationTime::Instance(), Kill(), mApoptosisTime, mDeathTime, mIsDead, and mUndergoingApoptosis.
Referenced by Divide(), ReadyToDivide(), and StartApoptosis().
| bool Cell::IsLogged | ( | ) |
| void Cell::Kill | ( | ) |
This labels the cell as dead, it does not delete the cell, it remains in the CellPopulation until AbstractCellPopulation::RemoveDeadCells() is called.
Definition at line 314 of file Cell.cpp.
References CellPropertyCollection::Begin(), CellPropertyCollection::End(), mCellPropertyCollection, and mIsDead.
| bool Cell::ReadyToDivide | ( | ) |
Determine if this cell is ready to divide at the current simulation time. MUST be called before calling Divide().
Definition at line 375 of file Cell.cpp.
References IsDead(), mCanDivide, mpCellCycleModel, mUndergoingApoptosis, and AbstractCellCycleModel::ReadyToDivide().
| void Cell::RemoveCellProperty | ( | ) | [inline] |
Remove a cell property of the given type. Use this method instead of calling rGetCellPropertyCollection().AddProperty() directly, to ensure that the cell property keeps correct track of the number of cells with it (if this is done).
Definition at line 267 of file Cell.hpp.
References CellPropertyCollection::Begin(), CellPropertyCollection::End(), mCellPropertyCollection, and CellPropertyCollection::RemoveProperty().
| CellPropertyCollection & Cell::rGetCellPropertyCollection | ( | ) |
- Returns:
- reference to mCellPropertyCollection.
Definition at line 219 of file Cell.cpp.
References mCellPropertyCollection.
| const CellPropertyCollection & Cell::rGetCellPropertyCollection | ( | ) | const |
- Returns:
- reference to mCellPropertyCollection (used in archiving).
Definition at line 224 of file Cell.cpp.
References mCellPropertyCollection.
| void Cell::serialize | ( | Archive & | archive, |
| const unsigned int | version | ||
| ) | [inline, private] |
Archive the member variables.
- Parameters:
-
archive the archive version the current version of this class
Definition at line 90 of file Cell.hpp.
References mApoptosisTime, mCanDivide, mCellProliferativeType, mDeathTime, mIsDead, mIsLogged, mpCellCycleModel, mStartOfApoptosisTime, and mUndergoingApoptosis.
| void Cell::SetAncestor | ( | boost::shared_ptr< AbstractCellProperty > | pCellAncestor | ) |
Give the Cell an index which it passes to its children.
- Parameters:
-
pCellAncestor the cell's ancestor
Definition at line 326 of file Cell.cpp.
References AddCellProperty(), EXCEPTION, CellPropertyCollection::GetPropertiesType(), CellPropertyCollection::GetSize(), and mCellPropertyCollection.
| void Cell::SetApoptosisTime | ( | double | apoptosisTime | ) |
Set mApoptosisTime.
- Parameters:
-
apoptosisTime the new value of mApoptosisTime
Definition at line 285 of file Cell.cpp.
References mApoptosisTime.
| void Cell::SetBirthTime | ( | double | birthTime | ) |
Set the birth time of the cell - can be negative so that your cells have an age when a simulation begins
- Parameters:
-
birthTime The time the cell was born (in hours)
Definition at line 172 of file Cell.cpp.
References mpCellCycleModel, and AbstractCellCycleModel::SetBirthTime().
| void Cell::SetCellCycleModel | ( | AbstractCellCycleModel * | pCellCycleModel | ) |
Change the cell-cycle model used. This takes effect immediately.
- Parameters:
-
pCellCycleModel pointer to the cell-cycle model to use
Definition at line 142 of file Cell.cpp.
References mpCellCycleModel, and AbstractCellCycleModel::SetCell().
| void Cell::SetCellProliferativeType | ( | CellProliferativeType | cellType | ) |
Set method for mCellProliferativeType.
- Parameters:
-
cellType the cell's type
Definition at line 132 of file Cell.cpp.
References mCellProliferativeType.
| void Cell::SetLogged | ( | ) |
| void Cell::SetMutationState | ( | boost::shared_ptr< AbstractCellProperty > | pMutationState | ) |
Set the cell's current mutation state.
- Parameters:
-
pMutationState the cell's new mutation state
Definition at line 177 of file Cell.cpp.
References AddCellProperty(), EXCEPTION, GetMutationState(), mCellPropertyCollection, and CellPropertyCollection::RemoveProperty().
| void Cell::StartApoptosis | ( | bool | setDeathTime = true | ) |
Make the cell enter apoptosis and sets mDeathTime using the apoptosis time as defined by mApoptosisTime.
- Parameters:
-
setDeathTime whether we tell the cell exactly when to die (defaults to true)
Definition at line 249 of file Cell.cpp.
References AddCellProperty(), EXCEPTION, CellPropertyRegistry::Get(), CellPropertyCollection::GetCellPropertyRegistry(), SimulationTime::GetTime(), SimulationTime::Instance(), IsDead(), mApoptosisTime, mCellPropertyCollection, mDeathTime, mStartOfApoptosisTime, and mUndergoingApoptosis.
Friends And Related Function Documentation
friend class boost::serialization::access [friend] |
Member Data Documentation
double Cell::mApoptosisTime [protected] |
The time it takes for a cell to fully undergo apoptosis. Has units of hours.
Definition at line 122 of file Cell.hpp.
Referenced by GetApoptosisTime(), IsDead(), serialize(), SetApoptosisTime(), and StartApoptosis().
bool Cell::mCanDivide [private] |
Caches the result of ReadyToDivide() so Divide() can look at it.
Definition at line 79 of file Cell.hpp.
Referenced by Divide(), ReadyToDivide(), and serialize().
CellProliferativeType Cell::mCellProliferativeType [protected] |
The cell type - defined in CellProliferativeTypes.hpp.
Definition at line 107 of file Cell.hpp.
Referenced by Divide(), GetCellProliferativeType(), serialize(), and SetCellProliferativeType().
CellPropertyCollection Cell::mCellPropertyCollection [protected] |
The cell's property collection.
Definition at line 110 of file Cell.hpp.
Referenced by AddCellProperty(), Cell(), Divide(), GetAncestor(), GetCellData(), GetCellId(), GetMutationState(), HasCellProperty(), Kill(), RemoveCellProperty(), rGetCellPropertyCollection(), SetAncestor(), SetMutationState(), and StartApoptosis().
double Cell::mDeathTime [protected] |
When the cell will/did die.
Definition at line 116 of file Cell.hpp.
Referenced by GetTimeUntilDeath(), IsDead(), serialize(), and StartApoptosis().
bool Cell::mIsDead [protected] |
Whether the cell is dead or not (they exist in the CellPopulation until they are removed by AbstractCellPopulation::RemoveDeadCells().
Definition at line 131 of file Cell.hpp.
Referenced by IsDead(), Kill(), serialize(), and ~Cell().
bool Cell::mIsLogged [protected] |
Whether the cell is being tracked specially.
Definition at line 134 of file Cell.hpp.
Referenced by IsLogged(), serialize(), and SetLogged().
AbstractCellCycleModel* Cell::mpCellCycleModel [protected] |
The cell's cell-cycle model.
Definition at line 113 of file Cell.hpp.
Referenced by Cell(), Divide(), GetAge(), GetBirthTime(), GetCellCycleModel(), InitialiseCellCycleModel(), ReadyToDivide(), serialize(), SetBirthTime(), SetCellCycleModel(), and ~Cell().
double Cell::mStartOfApoptosisTime [protected] |
When the cell was commanded to start apoptosis.
Definition at line 119 of file Cell.hpp.
Referenced by GetStartOfApoptosisTime(), serialize(), and StartApoptosis().
bool Cell::mUndergoingApoptosis [protected] |
Whether the cell is currently in apoptosis - don't divide.
Definition at line 125 of file Cell.hpp.
Referenced by GetTimeUntilDeath(), HasApoptosisBegun(), IsDead(), ReadyToDivide(), serialize(), and StartApoptosis().
The documentation for this class was generated from the following files:
