#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 ()

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 Attributes
CellPtr	mpCell

double	mSimulatedToTime

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

Friends
class	boost::serialization::access

Detailed Description

The AbstractSrnModel contains basic information to all sub-cellular reaction network (SRN) models. It handles assignment of a Cell.

SRN models are noncopyable since cells are noncopyable.

Todo:: #2752 Thoroughly document this class (including, for example, what SRN stands for!)

Definition at line 62 of file AbstractSrnModel.hpp.

Constructor & Destructor Documentation

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 cell-cycle 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. Each concrete subclass must implement this method to create an instance of that subclass.

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().

Returns: new SRN model

Implemented in NullSrnModel, Goldbeter1991SrnModel, and DeltaNotchSrnModel.

Referenced by DeltaNotchSrnModel::CreateSrnModel(), Goldbeter1991SrnModel::CreateSrnModel(), and Cell::Divide().

CellPtr AbstractSrnModel::GetCell ( )

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

Definition at line 67 of file AbstractSrnModel.cpp.

References mpCell.

double AbstractSrnModel::GetSimulatedToTime ( )

Returns: the time the SRN simulated has run to.

Definition at line 78 of file AbstractSrnModel.cpp.

References mSimulatedToTime.

void AbstractSrnModel::Initialise ( void )

virtual

Todo:: #2752 remove in favour of copy-constructors

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(), 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 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 CreateCellCycleModel() (called on the reset parent to create the new cell-cycle model object).

Definition at line 51 of file AbstractSrnModel.cpp.

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 92 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 101 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 55 of file AbstractSrnModel.cpp.

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

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

template<class Archive >