SimpleWntCellCycleModel Class Reference

#include <SimpleWntCellCycleModel.hpp>

Inheritance diagram for SimpleWntCellCycleModel:

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List of all members.

Public Member Functions

 SimpleWntCellCycleModel ()
virtual void UpdateCellCyclePhase ()
virtual void InitialiseDaughterCell ()
virtual AbstractCellCycleModel * CreateCellCycleModel ()
void SetUseCellProliferativeTypeDependentG1Duration (bool useCellProliferativeTypeDependentG1Duration=true)
virtual bool CanCellTerminallyDifferentiate ()
double GetWntStemThreshold ()
void SetWntStemThreshold (double wntStemThreshold)
double GetWntTransitThreshold ()
void SetWntTransitThreshold (double wntTransitThreshold)
double GetWntLabelledThreshold ()
void SetWntLabelledThreshold (double wntLabelledThreshold)
virtual void OutputCellCycleModelParameters (out_stream &rParamsFile)

Protected Member Functions

double GetWntLevel ()
WntConcentrationType GetWntType ()
void SetG1Duration ()

Protected Attributes

bool mUseCellProliferativeTypeDependentG1Duration
double mWntStemThreshold
double mWntTransitThreshold
double mWntLabelledThreshold

Private Member Functions

template<class Archive>
void serialize (Archive &archive, const unsigned int version)

Friends

class boost::serialization::access

Detailed Description

Simple Wnt-dependent cell-cycle model

Definition at line 46 of file SimpleWntCellCycleModel.hpp.

Constructor & Destructor Documentation

SimpleWntCellCycleModel::SimpleWntCellCycleModel (  ) 

Constructor - just a default, mBirthTime is now set in the AbstractCellCycleModel class. mG1Duration is set very high, it is set for the individual cells when InitialiseDaughterCell is called.

Definition at line 31 of file SimpleWntCellCycleModel.cpp.

Referenced by CreateCellCycleModel().

Member Function Documentation

template<class Archive>
void SimpleWntCellCycleModel::serialize ( Archive &  archive,
const unsigned int  version 
) [inline, private]

Archive the cell-cycle model, never used directly - boost uses this.

Parameters:
archive the archive
version the current version of this class

Reimplemented from AbstractSimpleCellCycleModel.

Reimplemented in SingleOdeWntCellCycleModel.

Definition at line 59 of file SimpleWntCellCycleModel.hpp.

References RandomNumberGenerator::Instance(), mUseCellProliferativeTypeDependentG1Duration, mWntLabelledThreshold, mWntStemThreshold, and mWntTransitThreshold.

double SimpleWntCellCycleModel::GetWntLevel (  )  [protected]

Get the Wnt level experienced by the cell.

Definition at line 118 of file SimpleWntCellCycleModel.cpp.

References WntConcentration< DIM >::GetWntLevel(), WntConcentration< DIM >::Instance(), AbstractCellCycleModel::mDimension, AbstractCellCycleModel::mpCell, and NEVER_REACHED.

Referenced by SingleOdeWntCellCycleModel::AdjustOdeParameters(), SingleOdeWntCellCycleModel::CreateCellCycleModel(), SingleOdeWntCellCycleModel::Initialise(), and UpdateCellCyclePhase().

WntConcentrationType SimpleWntCellCycleModel::GetWntType (  )  [protected]

Get the type of Wnt concentration (LINEAR, RADIAL, or NONE). This affects how the cell cycle phase is updated.

Definition at line 150 of file SimpleWntCellCycleModel.cpp.

References WntConcentration< DIM >::GetType(), WntConcentration< DIM >::Instance(), AbstractCellCycleModel::mDimension, and NEVER_REACHED.

Referenced by InitialiseDaughterCell(), and UpdateCellCyclePhase().

void SimpleWntCellCycleModel::SetG1Duration (  )  [protected, virtual]

Stochastically set the G1 duration. The G1 duration is taken from a normal distribution whose mean is the G1 duration given in AbstractCellCycleModel for the cell type and whose standard deviation is 1.

Called on cell creation at the start of a simulation, and for both parent and daughter cells at cell division.

Reimplemented from AbstractSimpleCellCycleModel.

Definition at line 81 of file SimpleWntCellCycleModel.cpp.

References AbstractCellCycleModel::GetStemCellG1Duration(), AbstractCellCycleModel::GetTransitCellG1Duration(), RandomNumberGenerator::Instance(), AbstractCellCycleModel::mCellProliferativeType, AbstractCellCycleModel::mG1Duration, AbstractCellCycleModel::mMinimumGapDuration, AbstractCellCycleModel::mpCell, mUseCellProliferativeTypeDependentG1Duration, NEVER_REACHED, and RandomNumberGenerator::NormalRandomDeviate().

void SimpleWntCellCycleModel::UpdateCellCyclePhase (  )  [virtual]

Overridden UpdateCellCyclePhase() method.

Reimplemented from AbstractSimpleCellCycleModel.

Reimplemented in SingleOdeWntCellCycleModel.

Definition at line 180 of file SimpleWntCellCycleModel.cpp.

References GetWntLevel(), GetWntType(), AbstractCellCycleModel::mCellProliferativeType, AbstractCellCycleModel::mpCell, mWntLabelledThreshold, mWntStemThreshold, mWntTransitThreshold, NEVER_REACHED, and AbstractSimpleCellCycleModel::UpdateCellCyclePhase().

void SimpleWntCellCycleModel::InitialiseDaughterCell (  )  [virtual]

Overridden InitialiseDaughterCell() method.

Reimplemented from AbstractSimpleCellCycleModel.

Definition at line 242 of file SimpleWntCellCycleModel.cpp.

References GetWntType(), AbstractSimpleCellCycleModel::InitialiseDaughterCell(), and AbstractCellCycleModel::mCellProliferativeType.

AbstractCellCycleModel * SimpleWntCellCycleModel::CreateCellCycleModel (  )  [virtual]

Overridden builder method to create new copies of this cell-cycle model.

Implements AbstractCellCycleModel.

Reimplemented in SingleOdeWntCellCycleModel.

Definition at line 40 of file SimpleWntCellCycleModel.cpp.

References AbstractCellCycleModel::mBirthTime, AbstractCellCycleModel::mCellProliferativeType, AbstractCellCycleModel::mDimension, AbstractCellCycleModel::mG2Duration, AbstractCellCycleModel::mMDuration, AbstractCellCycleModel::mMinimumGapDuration, AbstractCellCycleModel::mSDuration, AbstractCellCycleModel::mStemCellG1Duration, AbstractCellCycleModel::mTransitCellG1Duration, mUseCellProliferativeTypeDependentG1Duration, mWntLabelledThreshold, mWntStemThreshold, mWntTransitThreshold, AbstractCellCycleModel::SetBirthTime(), AbstractCellCycleModel::SetCellProliferativeType(), AbstractCellCycleModel::SetDimension(), AbstractCellCycleModel::SetG2Duration(), AbstractCellCycleModel::SetMDuration(), AbstractCellCycleModel::SetMinimumGapDuration(), AbstractCellCycleModel::SetSDuration(), AbstractCellCycleModel::SetStemCellG1Duration(), AbstractCellCycleModel::SetTransitCellG1Duration(), SetUseCellProliferativeTypeDependentG1Duration(), SetWntLabelledThreshold(), SetWntStemThreshold(), SetWntTransitThreshold(), and SimpleWntCellCycleModel().

void SimpleWntCellCycleModel::SetUseCellProliferativeTypeDependentG1Duration ( bool  useCellProliferativeTypeDependentG1Duration = true  ) 

Set whether Whether the duration of the G1 phase is dependent on cell type

Parameters:
useCellProliferativeTypeDependentG1Duration - boolean, defaults to true.

Definition at line 75 of file SimpleWntCellCycleModel.cpp.

References mUseCellProliferativeTypeDependentG1Duration.

Referenced by SingleOdeWntCellCycleModel::CreateCellCycleModel(), and CreateCellCycleModel().

bool SimpleWntCellCycleModel::CanCellTerminallyDifferentiate (  )  [virtual]

Overridden CanCellTerminallyDifferentiate() method.

Reimplemented from AbstractCellCycleModel.

Definition at line 254 of file SimpleWntCellCycleModel.cpp.

double SimpleWntCellCycleModel::GetWntStemThreshold (  ) 

Returns:
mWntStemThreshold

Definition at line 259 of file SimpleWntCellCycleModel.cpp.

References mWntStemThreshold.

void SimpleWntCellCycleModel::SetWntStemThreshold ( double  wntStemThreshold  ) 

Set mWntStemThreshold.

Parameters:
wntStemThreshold the value of mWntStemThreshold

Definition at line 264 of file SimpleWntCellCycleModel.cpp.

References mWntStemThreshold.

Referenced by SingleOdeWntCellCycleModel::CreateCellCycleModel(), and CreateCellCycleModel().

double SimpleWntCellCycleModel::GetWntTransitThreshold (  ) 

Returns:
mWntTransitThreshold

Definition at line 271 of file SimpleWntCellCycleModel.cpp.

References mWntTransitThreshold.

void SimpleWntCellCycleModel::SetWntTransitThreshold ( double  wntTransitThreshold  ) 

Set mWntTransitThreshold.

Parameters:
wntTransitThreshold the value of mWntTransitThreshold

Definition at line 276 of file SimpleWntCellCycleModel.cpp.

References mWntTransitThreshold.

Referenced by SingleOdeWntCellCycleModel::CreateCellCycleModel(), and CreateCellCycleModel().

double SimpleWntCellCycleModel::GetWntLabelledThreshold (  ) 

Returns:
mWntLabelledThreshold

Definition at line 283 of file SimpleWntCellCycleModel.cpp.

References mWntLabelledThreshold.

void SimpleWntCellCycleModel::SetWntLabelledThreshold ( double  wntLabelledThreshold  ) 

Set mWntLabelledThreshold.

Parameters:
wntLabelledThreshold the value of mWntLabelledThreshold

Definition at line 288 of file SimpleWntCellCycleModel.cpp.

References mWntLabelledThreshold.

Referenced by SingleOdeWntCellCycleModel::CreateCellCycleModel(), and CreateCellCycleModel().

void SimpleWntCellCycleModel::OutputCellCycleModelParameters ( out_stream &  rParamsFile  )  [virtual]

Outputs cell-cycle model parameters to file.

Parameters:
rParamsFile the file stream to which the parameters are output

Reimplemented from AbstractSimpleCellCycleModel.

Reimplemented in SingleOdeWntCellCycleModel.

Definition at line 295 of file SimpleWntCellCycleModel.cpp.

References mUseCellProliferativeTypeDependentG1Duration, mWntLabelledThreshold, mWntStemThreshold, mWntTransitThreshold, and AbstractSimpleCellCycleModel::OutputCellCycleModelParameters().

Referenced by SingleOdeWntCellCycleModel::OutputCellCycleModelParameters().

Friends And Related Function Documentation

friend class boost::serialization::access [friend]

Needed for serialization.

Reimplemented from AbstractSimpleCellCycleModel.

Reimplemented in SingleOdeWntCellCycleModel.

Definition at line 51 of file SimpleWntCellCycleModel.hpp.

Member Data Documentation

bool SimpleWntCellCycleModel::mUseCellProliferativeTypeDependentG1Duration [protected]

Whether to use different mean G1 durations for different cell types. For use in SetG1Duration().

Definition at line 78 of file SimpleWntCellCycleModel.hpp.

Referenced by SingleOdeWntCellCycleModel::CreateCellCycleModel(), CreateCellCycleModel(), OutputCellCycleModelParameters(), serialize(), SetG1Duration(), and SetUseCellProliferativeTypeDependentG1Duration().

double SimpleWntCellCycleModel::mWntStemThreshold [protected]

Non-dimensionalized Wnt threshold, above which cells behave as stem cells.

Definition at line 83 of file SimpleWntCellCycleModel.hpp.

Referenced by SingleOdeWntCellCycleModel::CreateCellCycleModel(), CreateCellCycleModel(), GetWntStemThreshold(), OutputCellCycleModelParameters(), serialize(), SetWntStemThreshold(), and UpdateCellCyclePhase().

double SimpleWntCellCycleModel::mWntTransitThreshold [protected]

Non-dimensionalized Wnt threshold, above which cells progress through the cell cycle.

Definition at line 88 of file SimpleWntCellCycleModel.hpp.

Referenced by SingleOdeWntCellCycleModel::CreateCellCycleModel(), CreateCellCycleModel(), GetWntTransitThreshold(), OutputCellCycleModelParameters(), serialize(), SetWntTransitThreshold(), and UpdateCellCyclePhase().

double SimpleWntCellCycleModel::mWntLabelledThreshold [protected]

Non-dimensionalized Wnt threshold, above which labelled cells progress through the cell cycle.

Definition at line 93 of file SimpleWntCellCycleModel.hpp.

Referenced by SingleOdeWntCellCycleModel::CreateCellCycleModel(), CreateCellCycleModel(), GetWntLabelledThreshold(), OutputCellCycleModelParameters(), serialize(), SetWntLabelledThreshold(), and UpdateCellCyclePhase().

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