CellSrnModel Class Reference

#include <CellSrnModel.hpp>

Inheritance diagram for CellSrnModel:

Collaboration diagram for CellSrnModel:

Public Types
using	iterator = abstractsrnmodel_t::iterator
using	const_iterator = abstractsrnmodel_t::const_iterator

Public Member Functions
iterator	begin ()
iterator	end ()
const_iterator	begin () const
const_iterator	end () const
const_iterator	cbegin () const
const_iterator	cend () const
	CellSrnModel ()
	~CellSrnModel ()
virtual void	Initialise ()
virtual void	ResetForDivision ()
virtual void	SimulateToCurrentTime ()
virtual AbstractSrnModel *	CreateSrnModel ()
void	AddEdgeSrn (std::vector< AbstractSrnModelPtr > edgeSrns)
void	AddEdgeSrnModel (AbstractSrnModelPtr pEdgeSrn)
unsigned	GetNumEdgeSrn () const
AbstractSrnModelPtr	GetEdgeSrn (unsigned index) const
const std::vector< AbstractSrnModelPtr > &	GetEdges () const
void	SetInteriorSrnModel (AbstractSrnModelPtr pInteriorSrn)
AbstractSrnModelPtr	GetInteriorSrn () const
virtual void	SetCell (CellPtr pCell)
Public Member Functions inherited from AbstractSrnModel
	AbstractSrnModel ()
virtual	~AbstractSrnModel ()
virtual void	InitialiseDaughterCell ()
CellPtr	GetCell ()
void	SetSimulatedToTime (double simulatedToTime)
double	GetSimulatedToTime () const
void	OutputSrnModelInfo (out_stream &rParamsFile)
virtual void	OutputSrnModelParameters (out_stream &rParamsFile)
void	SetEdgeLocalIndex (unsigned index)
unsigned	GetEdgeLocalIndex ()
bool	HasEdgeModel () const
void	SetEdgeModelIndicator (const bool isEdgeModel)
virtual void	ScaleSrnVariables (const double theta)
virtual void	AddSrnQuantities (AbstractSrnModel *pOtherSrn, const double scale=1.0)
virtual void	AddShrunkEdgeSrn (AbstractSrnModel *pShrunkEdgeSrn)
virtual void	AddMergedEdgeSrn (AbstractSrnModel *pMergedEdgeSrn)
virtual void	AddShrunkEdgeToInterior (AbstractSrnModel *pShrunkEdgeSrn)
virtual void	SplitEdgeSrn (const double relativePosition)
Public Member Functions inherited from Identifiable
virtual	~Identifiable ()
std::string	GetIdentifier () const

Protected Member Functions
	CellSrnModel (const CellSrnModel &rModel)
Protected Member Functions inherited from AbstractSrnModel
	AbstractSrnModel (const AbstractSrnModel &rModel)

Private Types
using	abstractsrnmodel_t = std::vector< AbstractSrnModelPtr >

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

Private Attributes
std::vector< boost::shared_ptr< AbstractSrnModel > >	mEdgeSrnModels
boost::shared_ptr< AbstractSrnModel >	mpInteriorSrnModel

Friends
class	boost::serialization::access

Additional Inherited Members
Protected Attributes inherited from AbstractSrnModel
CellPtr	mpCell
double	mSimulatedToTime
unsigned	mEdgeLocalIndex = UNSIGNED_UNSET
bool	mIsEdgeBasedModel = false

Detailed Description

SRN model at the cell level, has representation for edges internally. Also contains cell interior (cytoplasmic) SRN. Mostly serves to coordinate between interior/edge SRNs, in case these are specified. Functionality of SRNs is defined in AbstractSrnModel class and user-defined SRN models.

Definition at line 56 of file CellSrnModel.hpp.

Member Typedef Documentation

abstractsrnmodel_t

CellSrnModel::abstractsrnmodel_t

private

Type alias for a vector storing pointers to AbstractSrnModel.

Definition at line 84 of file CellSrnModel.hpp.

const_iterator

CellSrnModel::const_iterator

Type alias for constant iterator in the SRN model.

Definition at line 109 of file CellSrnModel.hpp.

iterator

CellSrnModel::iterator

Type alias for non-constant iterator in the SRN model.

Definition at line 103 of file CellSrnModel.hpp.

Constructor & Destructor Documentation

CellSrnModel() [1/2]

CellSrnModel::CellSrnModel ( const CellSrnModel &  rModel )

protected

Copy constructor. Called ONLY when a cell division occurs. See parent class comment for details

Parameters

rModel

SRN model to be copied

Definition at line 38 of file CellSrnModel.cpp.

References GetInteriorSrn(), AbstractSrnModel::HasEdgeModel(), mEdgeSrnModels, AbstractSrnModel::mIsEdgeBasedModel, mpInteriorSrnModel, and SetInteriorSrnModel().

CellSrnModel() [2/2]

CellSrnModel::CellSrnModel

(

)

Default constuctor.

Definition at line 60 of file CellSrnModel.cpp.

References mpInteriorSrnModel.

Referenced by CreateSrnModel().

~CellSrnModel()

CellSrnModel::~CellSrnModel

(

)

Destructor.

Definition at line 65 of file CellSrnModel.cpp.

Member Function Documentation

AddEdgeSrn()

void CellSrnModel::AddEdgeSrn

(

std::vector< AbstractSrnModelPtr >

edgeSrns

)

Adds a vector of SRN models to this cell.

Parameters

edgeSrns

vector of SRN models. Index of each SRN corresponds to the local edge index

Definition at line 126 of file CellSrnModel.cpp.

References mEdgeSrnModels, and AbstractSrnModel::mIsEdgeBasedModel.

Referenced by VertexBasedPopulationSrn< DIM >::RemapCellSrn().

AddEdgeSrnModel()

void CellSrnModel::AddEdgeSrnModel

(

AbstractSrnModelPtr

pEdgeSrn

)

Inserts edge SRN at the end of the list.

Parameters

pEdgeSrn

the edge SRN to be inserted

Definition at line 137 of file CellSrnModel.cpp.

References mEdgeSrnModels, and AbstractSrnModel::mIsEdgeBasedModel.

begin() [1/2]

iterator CellSrnModel::begin ( )

inline

Returns an iterator pointing to the first element.

Returns

Iterator to the beginning.

Definition at line 115 of file CellSrnModel.hpp.

References mEdgeSrnModels.

begin() [2/2]

const_iterator CellSrnModel::begin ( ) const

inline

Returns a constant iterator pointing to the first element.

Returns

Constant iterator to the beginning.

Definition at line 127 of file CellSrnModel.hpp.

References mEdgeSrnModels.

cbegin()

const_iterator CellSrnModel::cbegin ( ) const

inline

Returns a constant iterator pointing to the first element.

Returns

Constant iterator to the beginning.

Definition at line 139 of file CellSrnModel.hpp.

References mEdgeSrnModels.

cend()

const_iterator CellSrnModel::cend ( ) const

inline

Returns a constant iterator pointing one past the last element.

Returns

Constant iterator to the end.

Definition at line 145 of file CellSrnModel.hpp.

References mEdgeSrnModels.

CreateSrnModel()

AbstractSrnModel * CellSrnModel::CreateSrnModel ( )

virtual

Called in Cell::Divide()

Returns

Implements AbstractSrnModel.

Definition at line 121 of file CellSrnModel.cpp.

References CellSrnModel().

end() [1/2]

iterator CellSrnModel::end ( )

inline

Returns an iterator pointing one past the last element.

Returns

Iterator to the end.

Definition at line 121 of file CellSrnModel.hpp.

References mEdgeSrnModels.

end() [2/2]

const_iterator CellSrnModel::end ( ) const

inline

Returns a constant iterator pointing one past the last element.

Returns

Constant iterator to the end.

Definition at line 133 of file CellSrnModel.hpp.

References mEdgeSrnModels.

GetEdges()

const std::vector< AbstractSrnModelPtr > & CellSrnModel::GetEdges

(

)

const

Return all edge SRNs.

Returns

vector of SRNs associated to this cell

Definition at line 156 of file CellSrnModel.cpp.

References mEdgeSrnModels.

Referenced by VertexBasedPopulationSrn< DIM >::UpdateSrnAfterBirthOrDeath().

GetEdgeSrn()

AbstractSrnModelPtr CellSrnModel::GetEdgeSrn

(

unsigned

index

)

const

Get edge SRN at an index.

Parameters

index

of the SRN to return

Returns

SRN to be returned

Definition at line 150 of file CellSrnModel.cpp.

References mEdgeSrnModels.

GetInteriorSrn()

AbstractSrnModelPtr CellSrnModel::GetInteriorSrn

(

)

const

Returns interior SRN.

Returns

interior SRN

Definition at line 166 of file CellSrnModel.cpp.

References mpInteriorSrnModel.

Referenced by CellSrnModel(), and VertexBasedPopulationSrn< DIM >::RemapCellSrn().

GetNumEdgeSrn()

unsigned CellSrnModel::GetNumEdgeSrn

(

)

const

Get number of edge SRNs.

Returns

the number of edge SRNs

Definition at line 145 of file CellSrnModel.cpp.

References mEdgeSrnModels.

Referenced by VertexBasedPopulationSrn< DIM >::RemapCellSrn(), DeltaNotchEdgeInteriorTrackingModifier< DIM >::UpdateCellData(), and DeltaNotchEdgeTrackingModifier< DIM >::UpdateCellData().

Initialise()

void CellSrnModel::Initialise ( )

virtual

Initialize constituent SRN models.

Reimplemented from AbstractSrnModel.

Definition at line 69 of file CellSrnModel.cpp.

References mEdgeSrnModels, and mpInteriorSrnModel.

ResetForDivision()

void CellSrnModel::ResetForDivision ( )

virtual

Calls SRN model specific behaviour at the time of cell division. All constituent SRNs models (edge and/or interior, if there are any) call their implementation of this method.

Reimplemented from AbstractSrnModel.

Definition at line 82 of file CellSrnModel.cpp.

References SimulationTime::Instance(), mEdgeSrnModels, mpInteriorSrnModel, and AbstractSrnModel::mSimulatedToTime.

serialize()

template<class Archive >

void CellSrnModel::serialize ( Archive &  archive, const unsigned int  version  )

inlineprivate

Archive the SRN model and member variables.

Parameters

archive	the archive
version	the current version of this class

Definition at line 70 of file CellSrnModel.hpp.

References mEdgeSrnModels, and mpInteriorSrnModel.

SetCell()

void CellSrnModel::SetCell ( CellPtr  pCell )

virtual

Overriden method. We Set mpCell for each SRN contained in this cell.

Parameters

pCell

pointer to a Cell

Reimplemented from AbstractSrnModel.

Definition at line 171 of file CellSrnModel.cpp.

References mEdgeSrnModels, mpInteriorSrnModel, and AbstractSrnModel::SetCell().

SetInteriorSrnModel()

void CellSrnModel::SetInteriorSrnModel

(

AbstractSrnModelPtr

pInteriorSrn

)

Set interior SRN.

Parameters

pInteriorSrn

poiner to an interior SRN model

Definition at line 161 of file CellSrnModel.cpp.

References mpInteriorSrnModel.

Referenced by CellSrnModel().

SimulateToCurrentTime()

void CellSrnModel::SimulateToCurrentTime ( )

virtual

Simulate SRN models.

Implements AbstractSrnModel.

Definition at line 107 of file CellSrnModel.cpp.

References mEdgeSrnModels, mpInteriorSrnModel, and AbstractSrnModel::mSimulatedToTime.

Friends And Related Symbol Documentation

boost::serialization::access

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 62 of file CellSrnModel.hpp.

Member Data Documentation

mEdgeSrnModels

std::vector<boost::shared_ptr<AbstractSrnModel> > CellSrnModel::mEdgeSrnModels

private

Vector of pointers to edge SRN models.

Definition at line 78 of file CellSrnModel.hpp.

Referenced by CellSrnModel(), AddEdgeSrn(), AddEdgeSrnModel(), begin(), begin(), cbegin(), cend(), end(), end(), GetEdges(), GetEdgeSrn(), GetNumEdgeSrn(), Initialise(), ResetForDivision(), serialize(), SetCell(), and SimulateToCurrentTime().

mpInteriorSrnModel

boost::shared_ptr<AbstractSrnModel> CellSrnModel::mpInteriorSrnModel

private

Pointer to interior SRN model.

Definition at line 87 of file CellSrnModel.hpp.

Referenced by CellSrnModel(), CellSrnModel(), GetInteriorSrn(), Initialise(), ResetForDivision(), serialize(), SetCell(), SetInteriorSrnModel(), and SimulateToCurrentTime().

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

• cell_based/src/cell/srn/CellSrnModel.hpp
• cell_based/src/cell/srn/CellSrnModel.cpp