StochasticOxygenBasedCellCycleModel.cpp

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 #include "StochasticOxygenBasedCellCycleModel.hpp"
00029 #include "ApoptoticCellProperty.hpp"
00030 #include "CellPropertyRegistry.hpp"
00031 
00032 StochasticOxygenBasedCellCycleModel::StochasticOxygenBasedCellCycleModel()
00033     : SimpleOxygenBasedCellCycleModel()
00034 {
00035 }
00036 
00037 void StochasticOxygenBasedCellCycleModel::GenerateStochasticG2Duration()
00038 {
00039     RandomNumberGenerator* p_gen = RandomNumberGenerator::Instance();
00040 
00041     double mean = AbstractCellCycleModel::GetG2Duration();
00042     double standard_deviation = 1.0;
00043 
00044     mStochasticG2Duration = p_gen->NormalRandomDeviate(mean, standard_deviation);
00045 
00046     // Check that the normal random deviate has not returned a small or negative G2 duration
00047     if (mStochasticG2Duration < mMinimumGapDuration)
00048     {
00049         mStochasticG2Duration = mMinimumGapDuration;
00050     }
00051 }
00052 
00053 void StochasticOxygenBasedCellCycleModel::InitialiseDaughterCell()
00054 {
00055     SimpleOxygenBasedCellCycleModel::InitialiseDaughterCell();
00056     GenerateStochasticG2Duration();
00057 }
00058 
00059 void StochasticOxygenBasedCellCycleModel::Initialise()
00060 {
00061     AbstractSimpleCellCycleModel::Initialise();
00062     GenerateStochasticG2Duration();
00063 }
00064 
00065 void StochasticOxygenBasedCellCycleModel::ResetForDivision()
00066 {
00067     SimpleOxygenBasedCellCycleModel::ResetForDivision();
00068     GenerateStochasticG2Duration();
00069 }
00070 
00071 double StochasticOxygenBasedCellCycleModel::GetG2Duration()
00072 {
00073     return mStochasticG2Duration;
00074 }
00075 
00076 AbstractCellCycleModel* StochasticOxygenBasedCellCycleModel::CreateCellCycleModel()
00077 {
00078     // Create a new cell-cycle model
00079     StochasticOxygenBasedCellCycleModel* p_model = new StochasticOxygenBasedCellCycleModel();
00080 
00081     /*
00082      * Set each member variable of the new cell-cycle model that inherits
00083      * its value from the parent.
00084      * 
00085      * Note 1: some of the new cell-cycle model's member variables (namely
00086      * mBirthTime, mCurrentCellCyclePhase, mReadyToDivide, mTimeSpentInG1Phase,
00087      * mCurrentHypoxicDuration, mCurrentHypoxiaOnsetTime) will already have been
00088      * correctly initialized in its constructor.
00089      * 
00090      * Note 2: one or more of the new cell-cycle model's member variables
00091      * may be set/overwritten as soon as InitialiseDaughterCell() is called on
00092      * the new cell-cycle model.
00093      */
00094     p_model->SetBirthTime(mBirthTime);
00095     p_model->SetDimension(mDimension);
00096     p_model->SetCellProliferativeType(mCellProliferativeType);
00097     p_model->SetMinimumGapDuration(mMinimumGapDuration);
00098     p_model->SetStemCellG1Duration(mStemCellG1Duration);
00099     p_model->SetTransitCellG1Duration(mTransitCellG1Duration);
00100     p_model->SetSDuration(mSDuration);
00101     p_model->SetG2Duration(mG2Duration);
00102     p_model->SetMDuration(mMDuration);
00103     p_model->SetHypoxicConcentration(mHypoxicConcentration);
00104     p_model->SetQuiescentConcentration(mQuiescentConcentration);
00105     p_model->SetCriticalHypoxicDuration(mCriticalHypoxicDuration);
00106     p_model->SetCurrentHypoxiaOnsetTime(mCurrentHypoxiaOnsetTime);
00107 
00108     return p_model;
00109 }
00110 
00111 void StochasticOxygenBasedCellCycleModel::OutputCellCycleModelParameters(out_stream& rParamsFile)
00112 {
00113     // No new parameters to output
00114 
00115     // Call method on direct parent class
00116     SimpleOxygenBasedCellCycleModel::OutputCellCycleModelParameters(rParamsFile);
00117 }
00118 
00119 // Serialization for Boost >= 1.36
00120 #include "SerializationExportWrapperForCpp.hpp"
00121 CHASTE_CLASS_EXPORT(StochasticOxygenBasedCellCycleModel)

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