Chaste Release::3.1
VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo.cpp
00001 /*
00002 
00003 Copyright (c) 2005-2012, University of Oxford.
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00008 Square, Oxford OX1 2JD, UK.
00009 
00010 This file is part of Chaste.
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00022 
00023 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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00034 */
00035 
00036 #include "VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo.hpp"
00037 
00038 VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo(boost::shared_ptr<AbstractCellCycleModelOdeSolver> pOdeSolver)
00039     : AbstractVanLeeuwen2009WntSwatCellCycleModel(pOdeSolver)
00040 {
00041     if (mpOdeSolver == boost::shared_ptr<AbstractCellCycleModelOdeSolver>())
00042     {
00043 #ifdef CHASTE_CVODE
00044         mpOdeSolver = CellCycleModelOdeSolver<VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo, CvodeAdaptor>::Instance();
00045         mpOdeSolver->Initialise();
00046         // Chaste solvers always check for stopping events, CVODE needs to be instructed to do so
00047         mpOdeSolver->CheckForStoppingEvents();
00048         mpOdeSolver->SetMaxSteps(10000);
00049 #else
00050         mpOdeSolver = CellCycleModelOdeSolver<VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo, RungeKutta4IvpOdeSolver>::Instance();
00051         mpOdeSolver->Initialise();
00052         SetDt(0.00005);
00053 #endif //CHASTE_CVODE
00054     }
00055 }
00056 
00057 void VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::InitialiseOdeSystem(double wntConcentration, boost::shared_ptr<AbstractCellMutationState> pMutationState)
00058 {
00059     mpOdeSystem = new VanLeeuwen2009WntSwatCellCycleOdeSystem(2, wntConcentration,  pMutationState);
00060 }
00061 
00062 AbstractCellCycleModel* VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::CreateCellCycleModel()
00063 {
00064     // Create a new cell-cycle model
00065     VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo* p_model = new VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo(mpOdeSolver);
00066 
00067     /*
00068      * Set each member variable of the new cell-cycle model that inherits
00069      * its value from the parent.
00070      *
00071      * Note 1: some of the new cell-cycle model's member variables (namely
00072      * mBirthTime, mCurrentCellCyclePhase, mReadyToDivide, mDt, mpOdeSolver)
00073      * will already have been correctly initialized in its constructor.
00074      *
00075      * Note 2: one or more of the new cell-cycle model's member variables
00076      * may be set/overwritten as soon as InitialiseDaughterCell() is called on
00077      * the new cell-cycle model.
00078      */
00079     p_model->SetBirthTime(mBirthTime);
00080     p_model->SetDimension(mDimension);
00081     p_model->SetMinimumGapDuration(mMinimumGapDuration);
00082     p_model->SetStemCellG1Duration(mStemCellG1Duration);
00083     p_model->SetTransitCellG1Duration(mTransitCellG1Duration);
00084     p_model->SetSDuration(mSDuration);
00085     p_model->SetG2Duration(mG2Duration);
00086     p_model->SetMDuration(mMDuration);
00087     p_model->SetDivideTime(mDivideTime);
00088     p_model->SetFinishedRunningOdes(mFinishedRunningOdes);
00089     p_model->SetG2PhaseStartTime(mG2PhaseStartTime);
00090     p_model->SetLastTime(mLastTime);
00091 
00092     /*
00093      * Create the new cell-cycle model's ODE system and use the current values
00094      * of the state variables in mpOdeSystem as an initial condition.
00095      */
00096     assert(mpOdeSystem);
00097     double wnt_level = GetWntLevel();
00098     p_model->InitialiseOdeSystem(wnt_level, mpCell->GetMutationState());
00099     p_model->SetStateVariables(mpOdeSystem->rGetStateVariables());
00100 
00101     return p_model;
00102 }
00103 
00104 void VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::OutputCellCycleModelParameters(out_stream& rParamsFile)
00105 {
00106     // No new parameters to output
00107 
00108     // Call method on direct parent class
00109     AbstractVanLeeuwen2009WntSwatCellCycleModel::OutputCellCycleModelParameters(rParamsFile);
00110 }
00111 
00112 // Declare identifier for the serializer
00113 #include "SerializationExportWrapperForCpp.hpp"
00114 CHASTE_CLASS_EXPORT(VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo)
00115 #include "CellCycleModelOdeSolverExportWrapper.hpp"
00116 EXPORT_CELL_CYCLE_MODEL_ODE_SOLVER(VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo)