AbstractCellCycleModel.hpp

00001 /*
00002 
00003 Copyright (C) University of Oxford, 2005-2011
00004 
00005 University of Oxford means the Chancellor, Masters and Scholars of the
00006 University of Oxford, having an administrative office at Wellington
00007 Square, Oxford OX1 2JD, UK.
00008 
00009 This file is part of Chaste.
00010 
00011 Chaste is free software: you can redistribute it and/or modify it
00012 under the terms of the GNU Lesser General Public License as published
00013 by the Free Software Foundation, either version 2.1 of the License, or
00014 (at your option) any later version.
00015 
00016 Chaste is distributed in the hope that it will be useful, but WITHOUT
00017 ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
00018 FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public
00019 License for more details. The offer of Chaste under the terms of the
00020 License is subject to the License being interpreted in accordance with
00021 English Law and subject to any action against the University of Oxford
00022 being under the jurisdiction of the English Courts.
00023 
00024 You should have received a copy of the GNU Lesser General Public License
00025 along with Chaste. If not, see <http://www.gnu.org/licenses/>.
00026 
00027 */
00028 #ifndef ABSTRACTCELLCYCLEMODEL_HPP_
00029 #define ABSTRACTCELLCYCLEMODEL_HPP_
00030 
00031 #include "ChasteSerialization.hpp"
00032 #include "ClassIsAbstract.hpp"
00033 #include "Identifiable.hpp"
00034 
00035 #include <boost/serialization/base_object.hpp>
00036 
00037 #include <vector>
00038 
00039 #include "OutputFileHandler.hpp"
00040 #include "CellProliferativeTypes.hpp"
00041 #include "CellCyclePhases.hpp"
00042 #include "SimulationTime.hpp"
00043 #include "Cell.hpp"
00044 
00045 class Cell; // Circular definition (cells need to know about cycle models and vice-versa)
00046 typedef boost::shared_ptr<Cell> CellPtr;
00047 
00054 class AbstractCellCycleModel : public Identifiable, boost::noncopyable
00055 {
00056 private:
00057 
00059     friend class boost::serialization::access;
00071     template<class Archive>
00072     void serialize(Archive & archive, const unsigned int version)
00073     {
00074         // Make sure the SimulationTime singleton gets saved too
00075         SimulationTime* p_time = SimulationTime::Instance();
00076         archive & *p_time;
00077         archive & p_time;
00078 
00079         // DO NOT archive & mpCell; -- The CellCycleModel is only ever archived from the Cell
00080         // which knows this and it is handled in the load_construct of Cell.
00081         archive & mBirthTime;
00082         archive & mCurrentCellCyclePhase;
00083         archive & mG1Duration;
00084         archive & mReadyToDivide;
00085         archive & mDimension;
00086         archive & mCellProliferativeType;
00087         archive & mMinimumGapDuration;
00088         archive & mStemCellG1Duration;
00089         archive & mTransitCellG1Duration;
00090         archive & mSDuration;
00091         archive & mG2Duration;
00092         archive & mMDuration;
00093     }
00094 
00095 protected:
00096 
00098     CellPtr mpCell;
00099 
00104     double mBirthTime;
00105 
00107     CellCyclePhase mCurrentCellCyclePhase;
00108 
00113     double mG1Duration;
00114 
00118     bool mReadyToDivide;
00119 
00123     unsigned mDimension;
00124 
00128     CellProliferativeType mCellProliferativeType;
00129 
00137     double mMinimumGapDuration;
00138 
00144     double mStemCellG1Duration;
00145 
00150     double mTransitCellG1Duration;
00151 
00155     double mSDuration;
00156 
00160     double mG2Duration;
00161 
00165     double mMDuration;
00166 
00167 public:
00168 
00173     AbstractCellCycleModel();
00174 
00180     virtual ~AbstractCellCycleModel();
00181 
00191     void SetCell(CellPtr pCell);
00192 
00204     virtual void Initialise();
00205 
00218     virtual void InitialiseDaughterCell();
00219 
00223     CellPtr GetCell();
00224 
00233     virtual void SetBirthTime(double birthTime);
00234 
00240     void SetDimension(unsigned dimension);
00241 
00245     unsigned GetDimension();
00246 
00250     double GetBirthTime() const;
00251 
00255     double GetAge();
00256 
00265     virtual bool ReadyToDivide();
00266 
00273     virtual void UpdateCellCyclePhase()=0;
00274 
00283     virtual void ResetForDivision();
00284 
00297     virtual AbstractCellCycleModel* CreateCellCycleModel()=0;
00298 
00302     CellCyclePhase GetCurrentCellCyclePhase();
00303 
00307     virtual double GetG1Duration();
00308 
00312     double GetStemCellG1Duration();
00313 
00317     double GetTransitCellG1Duration();
00318 
00322     double GetSG2MDuration();
00323 
00327     virtual double GetSDuration();
00328 
00332     virtual double GetG2Duration();
00333 
00337     virtual double GetMDuration();
00338 
00344     void SetStemCellG1Duration(double stemCellG1Duration);
00345 
00351     void SetTransitCellG1Duration(double transitCellG1Duration);
00352 
00358     void SetSDuration(double sDuration);
00359 
00365     void SetG2Duration(double g2Duration);
00366 
00372     void SetMDuration(double mDuration);
00373 
00378     virtual double GetAverageTransitCellCycleTime();
00379 
00384     virtual double GetAverageStemCellCycleTime();
00385 
00389     virtual bool CanCellTerminallyDifferentiate();
00390 
00394     CellProliferativeType GetCellProliferativeType() const;
00395 
00401     void SetCellProliferativeType(CellProliferativeType cellType);
00402 
00406     double GetMinimumGapDuration();
00407 
00413     void SetMinimumGapDuration(double minimumGapDuration);
00414 
00421     void OutputCellCycleModelInfo(out_stream& rParamsFile);
00422 
00431     virtual void OutputCellCycleModelParameters(out_stream& rParamsFile)=0;
00432 };
00433 
00434 CLASS_IS_ABSTRACT(AbstractCellCycleModel)
00435 
00436 #endif /*ABSTRACTCELLCYCLEMODEL_HPP_*/

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