StochasticDurationGenerationBasedCellCycleModel.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 "StochasticDurationGenerationBasedCellCycleModel.hpp"
00029 #include "PetscTools.hpp"
00030 
00031 StochasticDurationGenerationBasedCellCycleModel::StochasticDurationGenerationBasedCellCycleModel()
00032 {
00033 }
00034 
00035 AbstractCellCycleModel* StochasticDurationGenerationBasedCellCycleModel::CreateCellCycleModel()
00036 {
00037     // Create a new cell-cycle model
00038     StochasticDurationGenerationBasedCellCycleModel* p_model = new StochasticDurationGenerationBasedCellCycleModel();
00039 
00040     /*
00041      * Set each member variable of the new cell-cycle model that inherits
00042      * its value from the parent.
00043      * 
00044      * Note 1: some of the new cell-cycle model's member variables (namely
00045      * mBirthTime, mCurrentCellCyclePhase, mReadyToDivide) will already have been
00046      * correctly initialized in its constructor.
00047      * 
00048      * Note 2: one or more of the new cell-cycle model's member variables
00049      * may be set/overwritten as soon as InitialiseDaughterCell() is called on
00050      * the new cell-cycle model.
00051      * 
00052      * Note 3: the member variable mDimension remains unset, since this cell-cycle
00053      * model does not need to know the spatial dimension, so if we were to call
00054      * SetDimension() on the new cell-cycle model an exception would be triggered;
00055      * hence we do not set this member variable.
00056      */
00057     p_model->SetBirthTime(mBirthTime);
00058     p_model->SetCellProliferativeType(mCellProliferativeType);
00059     p_model->SetMinimumGapDuration(mMinimumGapDuration);
00060     p_model->SetStemCellG1Duration(mStemCellG1Duration);
00061     p_model->SetTransitCellG1Duration(mTransitCellG1Duration);
00062     p_model->SetSDuration(mSDuration);
00063     p_model->SetG2Duration(mG2Duration);
00064     p_model->SetMDuration(mMDuration);
00065     p_model->SetGeneration(mGeneration);
00066     p_model->SetMaxTransitGenerations(mMaxTransitGenerations);
00067 
00068     return p_model;
00069 }
00070 
00071 void StochasticDurationGenerationBasedCellCycleModel::SetG1Duration()
00072 {
00073     assert(mpCell != NULL);
00074 
00075     RandomNumberGenerator* p_gen = RandomNumberGenerator::Instance();
00076 
00077     switch (mCellProliferativeType)
00078     {
00079         case STEM:
00080             mG1Duration = 1 + 4*p_gen->ranf(); // U[1,5] according to Meineke
00081             break;
00082         case TRANSIT:
00083             mG1Duration = 1 + 2*p_gen->ranf(); // U[1,3] according to Meineke
00084             break;
00085         case DIFFERENTIATED:
00086             mG1Duration = DBL_MAX;
00087             break;
00088         default:
00089             NEVER_REACHED;
00090     }
00091 }
00092 
00093 void StochasticDurationGenerationBasedCellCycleModel::OutputCellCycleModelParameters(out_stream& rParamsFile)
00094 {
00095     // No new parameters to output
00096 
00097     // Call method on direct parent class
00098     AbstractSimpleGenerationBasedCellCycleModel::OutputCellCycleModelParameters(rParamsFile);
00099 }
00100 
00101 
00102 // Serialization for Boost >= 1.36
00103 #include "SerializationExportWrapperForCpp.hpp"
00104 CHASTE_CLASS_EXPORT(StochasticDurationGenerationBasedCellCycleModel)

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