AbstractWntOdeBasedCellCycleModel.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 "AbstractWntOdeBasedCellCycleModel.hpp"
00029 #include "PetscTools.hpp"
00030 
00031 AbstractWntOdeBasedCellCycleModel::AbstractWntOdeBasedCellCycleModel(boost::shared_ptr<AbstractCellCycleModelOdeSolver> pOdeSolver)
00032     : AbstractOdeBasedCellCycleModel(SimulationTime::Instance()->GetTime(), pOdeSolver)
00033 {
00034 }
00035 
00036 AbstractWntOdeBasedCellCycleModel::~AbstractWntOdeBasedCellCycleModel()
00037 {
00038 }
00039 
00040 double AbstractWntOdeBasedCellCycleModel::GetWntLevel()
00041 {
00042     assert(mpCell != NULL);
00043     double level = 0;
00044 
00045     switch (mDimension)
00046     {
00047         case 1:
00048         {
00049             const unsigned DIM = 1;
00050             level = WntConcentration<DIM>::Instance()->GetWntLevel(mpCell);
00051             break;
00052         }
00053         case 2:
00054         {
00055             const unsigned DIM = 2;
00056             level = WntConcentration<DIM>::Instance()->GetWntLevel(mpCell);
00057             break;
00058         }
00059         case 3:
00060         {
00061             const unsigned DIM = 3;
00062             level = WntConcentration<DIM>::Instance()->GetWntLevel(mpCell);
00063             break;
00064         }
00065         default:
00066             NEVER_REACHED;
00067     }
00068 
00069     return level;
00070 }
00071 
00072 void AbstractWntOdeBasedCellCycleModel::ResetForDivision()
00073 {
00074     AbstractOdeBasedCellCycleModel::ResetForDivision();
00075 
00076     assert(mpOdeSystem != NULL);
00077 
00078     // This model needs the protein concentrations and phase resetting to G0/G1.
00079     // Keep the Wnt pathway in the same state but reset the cell cycle part
00080     // Cell cycle is proteins 0 to 4 (first 5 ODEs)
00081     std::vector<double> init_conds = mpOdeSystem->GetInitialConditions();
00082     for (unsigned i=0; i<5; i++)
00083     {
00084        mpOdeSystem->rGetStateVariables()[i] = init_conds[i];
00085     }
00086 }
00087 
00088 void AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase()
00089 {
00090     AbstractOdeBasedCellCycleModel::UpdateCellCyclePhase();
00091     if (SimulationTime::Instance()->GetTime() == mLastTime
00092         || GetOdeStopTime() == mLastTime)
00093     {
00094         // Should only be called if we're still running ODEs
00095         UpdateCellProliferativeType();
00096     }
00097 }
00098 
00099 void AbstractWntOdeBasedCellCycleModel::UpdateCellProliferativeType()
00100 {
00101     assert(mpOdeSystem != NULL);
00102     assert(mpCell != NULL);
00103     ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel();
00104 }
00105 
00106 double AbstractWntOdeBasedCellCycleModel::GetAverageTransitCellCycleTime()
00107 {
00108     return 16.0;
00109 }
00110 
00111 double AbstractWntOdeBasedCellCycleModel::GetAverageStemCellCycleTime()
00112 {
00113     return 16.0;
00114 }
00115 
00116 bool AbstractWntOdeBasedCellCycleModel::CanCellTerminallyDifferentiate()
00117 {
00118     return false;
00119 }
00120 
00121 void AbstractWntOdeBasedCellCycleModel::OutputCellCycleModelParameters(out_stream& rParamsFile)
00122 {
00123     // No new parameters to output
00124 
00125     // Call method on direct parent class
00126     AbstractOdeBasedCellCycleModel::OutputCellCycleModelParameters(rParamsFile);
00127 }
00128 

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