#include <AbstractSrnModel.hpp>

Inheritance diagram for AbstractSrnModel:

Collaboration diagram for AbstractSrnModel:

Public Member Functions
	AbstractSrnModel ()

virtual	~AbstractSrnModel ()

void	SetCell (CellPtr pCell)

virtual void	Initialise ()

virtual void	InitialiseDaughterCell ()

CellPtr	GetCell ()

void	SetSimulatedToTime (double simulatedToTime)

double	GetSimulatedToTime () const

virtual void	SimulateToCurrentTime ()=0

virtual void	ResetForDivision ()

virtual AbstractSrnModel *	CreateSrnModel ()=0

void	OutputSrnModelInfo (out_stream &rParamsFile)

virtual void	OutputSrnModelParameters (out_stream &rParamsFile)

Public Member Functions inherited from Identifiable
virtual	~Identifiable ()

std::string	GetIdentifier () const

Protected Member Functions
	AbstractSrnModel (const AbstractSrnModel &rModel)

Protected Attributes
CellPtr	mpCell

double	mSimulatedToTime

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

AbstractSrnModel &	operator= (const AbstractSrnModel &)

Friends
class	boost::serialization::access

Detailed Description

The AbstractSrnModel contains basic information to all sub-cellular reaction network (SRN) models.

SRN models are noncopyable since cells are noncopyable.

Todo:: #2752 Thoroughly document this class

Definition at line 61 of file AbstractSrnModel.hpp.

Constructor & Destructor Documentation

AbstractSrnModel::AbstractSrnModel ( const AbstractSrnModel & rModel )

protected

Protected copy-constructor for use by CreateSrnModel(). The only way for external code to create a copy of a SRN model is by calling that method, to ensure that a model of the correct subclass is created. This copy-constructor helps subclasses to ensure that all member variables are correctly copied when this happens.

This method is called by child classes to set member variables for a daughter cell upon cell division. Note that the parent SRN model will have had ResetForDivision() called just before CreateSrnModel() is called, so performing an exact copy of the parent is suitable behaviour. Any daughter-cell-specific initialisation can be done in InitialiseDaughterCell().

Parameters

rModel the SRN model to copy.

Definition at line 55 of file AbstractSrnModel.cpp.

AbstractSrnModel::AbstractSrnModel ( )

Sets up a new AbstractSrnModel, gives it a birth time of the current simulation time (which is overwritten by some subclasses)

Definition at line 38 of file AbstractSrnModel.cpp.

AbstractSrnModel::~AbstractSrnModel ( )

virtual

Base class with virtual methods needs a virtual destructor. The destructor does not delete mpCell. Instead, the cell takes responsibility for deleting the SRN model when it is destroyed.

Definition at line 43 of file AbstractSrnModel.cpp.

Member Function Documentation

virtual AbstractSrnModel* AbstractSrnModel::CreateSrnModel ( )

pure virtual

Builder method to create new instances of the SRN model.

As this method is pure virtual, it must be overridden in subclasses.

This method is called by Cell::Divide() to create a SRN model for the daughter cell. Note that the parent SRN model will have had ResetForDivision() called just before CreateSrnModel() is called, so performing an exact copy of the parent is suitable behaviour. Any daughter-cell-specific initialisation can be done in InitialiseDaughterCell().

Copy constructors are used to set all the member variables in the appropriate classes.

Returns: new srn model

Implemented in NullSrnModel, Goldbeter1991SrnModel, and DeltaNotchSrnModel.

Referenced by Cell::Divide().

CellPtr AbstractSrnModel::GetCell ( )

Returns: The cell which plays host to this SRN model.

Definition at line 86 of file AbstractSrnModel.cpp.

References mpCell.

double AbstractSrnModel::GetSimulatedToTime ( ) const

Returns: the time the SRN simulated has run to.

Definition at line 97 of file AbstractSrnModel.cpp.

References mSimulatedToTime.

void AbstractSrnModel::Initialise ( void )

virtual

Initialise the SRN 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(), CreateSrnModel() 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 Goldbeter1991SrnModel, and DeltaNotchSrnModel.

Definition at line 47 of file AbstractSrnModel.cpp.

Referenced by DeltaNotchSrnModel::Initialise(), Goldbeter1991SrnModel::Initialise(), and Cell::InitialiseSrnModel().

void AbstractSrnModel::InitialiseDaughterCell ( )

virtual

Initialise the new daughter cell's SRN 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 SRN 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 CreateSrnModel() (called on the reset parent to create the new cell-cycle model object).

Definition at line 51 of file AbstractSrnModel.cpp.

AbstractSrnModel& AbstractSrnModel::operator= ( const AbstractSrnModel & )

private

Prevent copy-assignment of this class, or its subclasses. Note that we do not define this method, therefore statements like "AbstractSrnModel new = old;" will not compile. We do not inherit from boost::noncopyable because we *do* define a protected copy-constructor, for use by CreateSrnModel.

Returns: the new SRN model.

void AbstractSrnModel::OutputSrnModelInfo ( out_stream & rParamsFile )

Output SRN model used in the simulation to file and then call OutputSrnParameters() to output all relevant parameters.

Parameters

rParamsFile the file stream to which the parameters are output

Definition at line 111 of file AbstractSrnModel.cpp.

References Identifiable::GetIdentifier(), and OutputSrnModelParameters().

void AbstractSrnModel::OutputSrnModelParameters ( out_stream & rParamsFile )

virtual

Output SRN 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

Reimplemented in AbstractOdeSrnModel, DeltaNotchSrnModel, and Goldbeter1991SrnModel.

Definition at line 120 of file AbstractSrnModel.cpp.

Referenced by OutputSrnModelInfo(), and AbstractOdeSrnModel::OutputSrnModelParameters().

void AbstractSrnModel::ResetForDivision ( )

virtual

Each SRN model must be able to be reset 'after' a cell division.

Actually, this method is called from Cell::Divide() to reset the SRN just before the daughter cell is created. CreateSrnModel() can then clone our state to generate a cell-cycle model instance for the daughter cell.

Reimplemented in AbstractOdeSrnModel.

Definition at line 74 of file AbstractSrnModel.cpp.

References SimulationTime::Instance(), mSimulatedToTime, and SimulateToCurrentTime().

Referenced by Cell::Divide(), and AbstractOdeSrnModel::ResetForDivision().

template<class Archive >