text: /*
  
  Copyright (c) 2005-2016, University of Oxford.
  All rights reserved.
  
  University of Oxford means the Chancellor, Masters and Scholars of the
  University of Oxford, having an administrative office at Wellington
  Square, Oxford OX1 2JD, UK.
  
  This file is part of Chaste.
  
  Redistribution and use in source and binary forms, with or without
  modification, are permitted provided that the following conditions are met:
   * Redistributions of source code must retain the above copyright notice,
     this list of conditions and the following disclaimer.
   * Redistributions in binary form must reproduce the above copyright notice,
     this list of conditions and the following disclaimer in the documentation
     and/or other materials provided with the distribution.
   * Neither the name of the University of Oxford nor the names of its
     contributors may be used to endorse or promote products derived from this
     software without specific prior written permission.
  
  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
  AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
  IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
  ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
  LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
  CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
  GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
  HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
  LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
  OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  
  */
  
  #include "DeltaNotchSrnModel.hpp"
  
  #include <cassert>
  
  DeltaNotchSrnModel::DeltaNotchSrnModel(boost::shared_ptr<AbstractCellCycleModelOdeSolver> pOdeSolver)
      : AbstractOdeSrnModel(2, pOdeSolver)
  {
      if (mpOdeSolver == boost::shared_ptr<AbstractCellCycleModelOdeSolver>())
      {
  #ifdef CHASTE_CVODE
          mpOdeSolver = CellCycleModelOdeSolver<DeltaNotchSrnModel, CvodeAdaptor>::Instance();
          mpOdeSolver->Initialise();
          mpOdeSolver->SetMaxSteps(10000);
  #else
          mpOdeSolver = CellCycleModelOdeSolver<DeltaNotchSrnModel, RungeKutta4IvpOdeSolver>::Instance();
          mpOdeSolver->Initialise();
          SetDt(0.001);
  #endif //CHASTE_CVODE
      }
      assert(mpOdeSolver->IsSetUp());
  }
  
  DeltaNotchSrnModel::DeltaNotchSrnModel(const DeltaNotchSrnModel& rModel)
      : AbstractOdeSrnModel(rModel)
  {
      /*
       * Set each member variable of the new SRN model that inherits
       * its value from the parent.
       *
       * Note 1: some of the new SRN model's member variables
       * will already have been correctly initialized in its constructor.
       *
       * Note 2: one or more of the new SRN model's member variables
       * may be set/overwritten as soon as InitialiseDaughterCell() is called on
       * the new SRN model.
       *
       * Note 3: Only set the variables defined in this class. Variables defined
       * in parent classes will be defined there.
       */
  
      assert(rModel.GetOdeSystem());
      SetOdeSystem(new DeltaNotchOdeSystem(rModel.GetOdeSystem()->rGetStateVariables()));
  }
  
  AbstractSrnModel* DeltaNotchSrnModel::CreateSrnModel()
  {
      return new DeltaNotchSrnModel(*this);
  }
  
  void DeltaNotchSrnModel::SimulateToCurrentTime()
  {
      // Custom behaviour
      UpdateDeltaNotch();
  
      // Run the ODE simulation as needed
      AbstractOdeSrnModel::SimulateToCurrentTime();
  }
  
  void DeltaNotchSrnModel::Initialise()
  {
      AbstractOdeSrnModel::Initialise(new DeltaNotchOdeSystem);
  }
  
  void DeltaNotchSrnModel::UpdateDeltaNotch()
  {
      assert(mpOdeSystem != NULL);
      assert(mpCell != NULL);
  
      double mean_delta = mpCell->GetCellData()->GetItem("mean delta");
      mpOdeSystem->SetParameter("Mean Delta", mean_delta);
  }
  
  double DeltaNotchSrnModel::GetNotch()
  {
      assert(mpOdeSystem != NULL);
      double notch = mpOdeSystem->rGetStateVariables()[0];
      return notch;
  }
  
  double DeltaNotchSrnModel::GetDelta()
  {
      assert(mpOdeSystem != NULL);
      double delta = mpOdeSystem->rGetStateVariables()[1];
      return delta;
  }
  
  double DeltaNotchSrnModel::GetMeanNeighbouringDelta()
  {
      assert(mpOdeSystem != NULL);
      double mean_neighbouring_delta = mpOdeSystem->GetParameter("Mean Delta");
      return mean_neighbouring_delta;
  }
  
  void DeltaNotchSrnModel::OutputSrnModelParameters(out_stream& rParamsFile)
  {
      // No new parameters to output, so just call method on direct parent class
      AbstractOdeSrnModel::OutputSrnModelParameters(rParamsFile);
  }
  
  // Declare identifier for the serializer
  #include "SerializationExportWrapperForCpp.hpp"
  CHASTE_CLASS_EXPORT(DeltaNotchSrnModel)
  #include "CellCycleModelOdeSolverExportWrapper.hpp"
  EXPORT_CELL_CYCLE_MODEL_ODE_SOLVER(DeltaNotchSrnModel)
  