Cell.cpp

/*

Copyright (C) University of Oxford, 2005-2011

University of Oxford means the Chancellor, Masters and Scholars of the
University of Oxford, having an administrative office at Wellington
Square, Oxford OX1 2JD, UK.

This file is part of Chaste.

Chaste is free software: you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License as published
by the Free Software Foundation, either version 2.1 of the License, or
(at your option) any later version.

Chaste is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public
License for more details. The offer of Chaste under the terms of the
License is subject to the License being interpreted in accordance with
English Law and subject to any action against the University of Oxford
being under the jurisdiction of the English Courts.

You should have received a copy of the GNU Lesser General Public License
along with Chaste. If not, see <http://www.gnu.org/licenses/>.

*/

#include "Cell.hpp"
#include "ApoptoticCellProperty.hpp"

unsigned Cell::mMaxCellId = 0;

struct null_deleter
{
    void operator()(void const *) const
    {
    }
};

Cell::Cell(boost::shared_ptr<AbstractCellProperty> pMutationState,
           AbstractCellCycleModel* pCellCycleModel,
           bool archiving,
           CellPropertyCollection cellPropertyCollection)
    : mCanDivide(false),
      mCellPropertyCollection(cellPropertyCollection),
      mpCellCycleModel(pCellCycleModel),
      mAncestor(UNSIGNED_UNSET), // Has to be set by a SetAncestor() call (usually from CellPopulation)
      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()));

    // Set cell identifier
    mCellId = ++ mMaxCellId -1;

    if (!pMutationState->IsSubType<AbstractCellMutationState>())
    {
        EXCEPTION("Attempting to create cell with a cell mutation state is not a subtype of AbstractCellMutationState");
    }

    if (!mCellPropertyCollection.HasProperty(pMutationState))
    {
        mCellPropertyCollection.AddProperty(pMutationState);
    }

    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();
        }
    }
}

Cell::~Cell()
{
    if (!mIsDead)
    {
        Kill();
    }
    delete mpCellCycleModel;
}

void Cell::SetCellCycleModel(AbstractCellCycleModel* pCellCycleModel)
{
    if (mpCellCycleModel != pCellCycleModel)
    {
        delete mpCellCycleModel;
    }
    mpCellCycleModel = pCellCycleModel;
    mpCellCycleModel->SetCell(CellPtr(this, null_deleter()));
}

AbstractCellCycleModel* Cell::GetCellCycleModel() const
{
    return mpCellCycleModel;
}

void Cell::InitialiseCellCycleModel()
{
    mpCellCycleModel->Initialise();
}

double Cell::GetAge() const
{
    return mpCellCycleModel->GetAge();
}

double Cell::GetBirthTime() const
{
    return mpCellCycleModel->GetBirthTime();
}

void Cell::SetBirthTime(double birthTime)
{
    mpCellCycleModel->SetBirthTime(birthTime);
}

void Cell::SetMutationState(boost::shared_ptr<AbstractCellProperty> pMutationState)
{
    if (!pMutationState->IsSubType<AbstractCellMutationState>())
    {
        EXCEPTION("Attempting to give cell a cell mutation state is not a subtype of AbstractCellMutationState");
    }

    boost::shared_ptr<AbstractCellMutationState> p_old_mutation_state = GetMutationState();
    p_old_mutation_state->DecrementCellCount();
    mCellPropertyCollection.RemoveProperty(p_old_mutation_state);

    AddCellProperty(pMutationState);
}

boost::shared_ptr<AbstractCellMutationState> Cell::GetMutationState() const
{
    CellPropertyCollection mutation_state_collection = mCellPropertyCollection.GetPropertiesType<AbstractCellMutationState>();

    /*
     * Note: In its current form the code requires each cell to have exactly
     * one mutation state. This is reflected in the assertion below. If a user
     * wishes to include cells with multiple mutation states, each possible
     * combination must be created as a separate mutation state class.
     */
    assert(mutation_state_collection.GetSize() == 1);

    return boost::static_pointer_cast<AbstractCellMutationState>(mutation_state_collection.GetProperty());
}

CellPropertyCollection& Cell::rGetCellPropertyCollection()
{
    return mCellPropertyCollection;
}

const CellPropertyCollection& Cell::rGetCellPropertyCollection() const
{
    return mCellPropertyCollection;
}

void Cell::AddCellProperty(const boost::shared_ptr<AbstractCellProperty>& rProperty)
{
    // Note: if the cell already has the specified property, no action is taken
    if (!mCellPropertyCollection.HasProperty(rProperty))
    {
        mCellPropertyCollection.AddProperty(rProperty);
        rProperty->IncrementCellCount();
    }
}

void Cell::SetLogged()
{
    mIsLogged = true;
}

bool Cell::IsLogged()
{
    return mIsLogged;
}

void Cell::StartApoptosis(bool setDeathTime)
{
    assert(!IsDead());

    if (mUndergoingApoptosis)
    {
        EXCEPTION("StartApoptosis() called when already undergoing apoptosis");
    }
    mUndergoingApoptosis = true;
    mStartOfApoptosisTime = SimulationTime::Instance()->GetTime();
    if (setDeathTime)
    {
        mDeathTime = mStartOfApoptosisTime + mApoptosisTime;
    }
    else
    {
        mDeathTime = DBL_MAX;
    }
    AddCellProperty(mCellPropertyCollection.GetCellPropertyRegistry()->Get<ApoptoticCellProperty>());
}

bool Cell::HasApoptosisBegun() const
{
    return mUndergoingApoptosis;
}

double Cell::GetStartOfApoptosisTime() const
{
    return mStartOfApoptosisTime;
}

double Cell::GetApoptosisTime() const
{
    return mApoptosisTime;
}

void Cell::SetApoptosisTime(double apoptosisTime)
{
    assert(apoptosisTime > 0.0);
    mApoptosisTime = apoptosisTime;
}

double Cell::GetTimeUntilDeath() const
{
    if (!mUndergoingApoptosis || mDeathTime==DBL_MAX)
    {
        EXCEPTION("Shouldn't be checking time until apoptosis as it isn't set");
    }

    return mDeathTime - SimulationTime::Instance()->GetTime();
}

bool Cell::IsDead()
{
    if (mUndergoingApoptosis && !mIsDead)
    {
        double sloppy_death_time = mDeathTime - DBL_EPSILON * mApoptosisTime;
        if (SimulationTime::Instance()->GetTime() >= sloppy_death_time )
        {
            this->Kill();
        }
    }
    return mIsDead;
}

void Cell::Kill()
{
    // Decrement cell count for each cell property in mCellPropertyCollection
    for (CellPropertyCollection::Iterator property_iter = mCellPropertyCollection.Begin();
         property_iter != mCellPropertyCollection.End();
         ++property_iter)
    {
        (*property_iter)->DecrementCellCount();
    }
    mIsDead = true;
}

void Cell::SetAncestor(unsigned ancestorIndex)
{
    mAncestor = ancestorIndex;
}

unsigned Cell::GetAncestor() const
{
    return mAncestor;
}

unsigned Cell::GetCellId() const
{
    return mCellId;
}

void Cell::ResetMaxCellId()
{
    mMaxCellId = 0;
}

bool Cell::ReadyToDivide()
{
    assert(!IsDead());
    if (mUndergoingApoptosis || HasCellProperty<ApoptoticCellProperty>())
    {
        return false;
    }

    mCanDivide = mpCellCycleModel->ReadyToDivide();

    return mCanDivide;
}

CellPtr Cell::Divide()
{
    // Check we're allowed to divide
    assert(!IsDead());
    assert(mCanDivide);
    mCanDivide = false;

    // Reset properties of parent cell
    mpCellCycleModel->ResetForDivision();

    // Create daughter cell
    CellPtr p_new_cell(new Cell(GetMutationState(), mpCellCycleModel->CreateCellCycleModel(), false, mCellPropertyCollection));

    // Initialise properties of daughter cell
    p_new_cell->GetCellCycleModel()->InitialiseDaughterCell();
    p_new_cell->SetAncestor(GetAncestor());

    return p_new_cell;
}