void Cell::SetCellCycleModel(AbstractCellCycleModel* pCellCycleModel)
{
if (mpCellCycleModel != pCellCycleModel)
{
delete mpCellCycleModel;
}
mpCellCycleModel = pCellCycleModel;
mpCellCycleModel->SetCell(CellPtr(this, null_deleter()));
}
void Cell::SetSrnModel(AbstractSrnModel* pSrnModel)
{
if (mpSrnModel != pSrnModel)
{
delete mpSrnModel;
}
mpSrnModel = pSrnModel;
mpSrnModel->SetCell(CellPtr(this, null_deleter()));
}
void MulRk::readFields(CFRecord& record)
{
global_info_ = record.getGlobalWorkbookInfo();
// A little hack to extract colLast before it is used
record.skipNunBytes(record.getDataSize() - sizeof(unsigned short));
record >> colLast;
record.resetPointerToBegin();
//------------------
record >> rw >> colFirst;
for(unsigned short i = colFirst; i <= colLast; ++i)
{
RkRec rec;
record >> rec;
rgrkrec.push_back(RkRecPtr(new RkRec(rec)));
cells.push_back(CellPtr(new Cell(rw, i, rec.get_ixfe())));
}
record.skipNunBytes(sizeof(unsigned short));
}
Cell::Cell(boost::shared_ptr<AbstractCellProperty> pMutationState,
AbstractCellCycleModel* pCellCycleModel,
bool archiving,
CellPropertyCollection cellPropertyCollection)
: mCanDivide(false),
mCellPropertyCollection(cellPropertyCollection),
mpCellCycleModel(pCellCycleModel),
mDeathTime(DBL_MAX), // This has to be initialised for archiving
mStartOfApoptosisTime(DBL_MAX),
mApoptosisTime(0.25), // cell takes 15 min to fully undergo apoptosis
mUndergoingApoptosis(false),
mIsDead(false),
mIsLogged(false)
{
if (SimulationTime::Instance()->IsStartTimeSetUp()==false)
{
EXCEPTION("Cell is setting up a cell-cycle model but SimulationTime has not been set up");
}
if (pCellCycleModel == NULL)
{
EXCEPTION("Cell-cycle model is null");
}
mpCellCycleModel->SetCell(CellPtr(this, null_deleter()));
if (!mCellPropertyCollection.HasPropertyType<CellId>())
{
// Set cell identifier this will be called all the time unless the constructor is called through archiving
MAKE_PTR(CellId, p_cell_id);
p_cell_id->AssignCellId();
mCellPropertyCollection.AddProperty(p_cell_id);
}
if (!pMutationState->IsSubType<AbstractCellMutationState>())
{
EXCEPTION("Attempting to create cell with a cell mutation state that is not a subtype of AbstractCellMutationState");
}
if (!mCellPropertyCollection.HasProperty(pMutationState))
{
mCellPropertyCollection.AddProperty(pMutationState);
}
if (!mCellPropertyCollection.HasPropertyType<CellData>())
{
// Add empty cell data
MAKE_PTR(CellData, p_cell_data);
mCellPropertyCollection.AddProperty(p_cell_data);
}
/*
* If a cell proliferative type was not passed in via the input
* argument cellPropertyCollection (for example as in the case
* of a daughter cell being created following division) then add
* add a 'default' cell proliferative type to the cell property
* collection. This ensures that the method GetCellProliferativeType()
* always returns a valid proliferative type.
*/
if (!mCellPropertyCollection.HasPropertyType<AbstractCellProliferativeType>())
{
mCellPropertyCollection.AddProperty(CellPropertyRegistry::Instance()->Get<DefaultCellProliferativeType>());
}
if (!archiving)
{
// Increment cell count for each cell property in mCellPropertyCollection
for (CellPropertyCollection::Iterator property_iter = mCellPropertyCollection.Begin();
property_iter != mCellPropertyCollection.End();
++property_iter)
{
(*property_iter)->IncrementCellCount();
}
}
}
CellPtr make_cell(ExprPtr car, ExprPtr cdr)
{
return CellPtr(new Cell(car, cdr));
}
