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.
  
  */
  
  #ifndef RANDOMCASWITCHINGUPDATERULE_HPP_
  #define RANDOMCASWITCHINGUPDATERULE_HPP_
  
  #include "ChasteSerialization.hpp"
  #include <boost/serialization/base_object.hpp>
  
  #include "AbstractCaSwitchingUpdateRule.hpp"
  #include "CaBasedCellPopulation.hpp"
  
  /**
   * A random switching update rule for use in cell-based simulations
   * using the cellular CA model.
   *
   * The probability of performing a switch is
   *
   * P* delta_t
   *
   * Where P is the mSwitchingParameter.
   * delta_t is the timestep.
   */
  template<unsigned DIM>
  class RandomCaSwitchingUpdateRule : public AbstractCaSwitchingUpdateRule<DIM>
  {
  friend class TestCaUpdateRules;
  
  private:
  
      /**
       * Switching parameter for update rule.
       * Set to the default value 0.5 in the constructor.
       * \todo provide units
       */
      double mSwitchingParameter;
  
      friend class boost::serialization::access;
      /**
       * Boost Serialization method for archiving/checkpointing.
       * Archives the object and its member variables.
       *
       * @param archive  The boost archive.
       * @param version  The current version of this class.
       */
      template<class Archive>
      void serialize(Archive & archive, const unsigned int version)
      {
          archive & boost::serialization::base_object<AbstractCaSwitchingUpdateRule<DIM> >(*this);
          archive & mSwitchingParameter;
      }
  
  public:
  
      /**
       * Constructor.
       */
      RandomCaSwitchingUpdateRule();
  
      /**
       * Destructor.
       */
      ~RandomCaSwitchingUpdateRule();
  
      /**
        * Calculate the probability of a given switch. Here this is hust
        *
        * mSwitchingParameter * dt
        *
        * @param currentNodeIndex The index of the current node/lattice site
        * @param neighbourNodeIndex The index of the neighbour node/lattice site
        * @param rCellPopulation The cell population
        * @param dt is the time interval
        * @param deltaX defines the size of the lattice site
        * @return The probability of the cells associated to the current node and the target node switching.
        */
       double EvaluateSwitchingProbability(unsigned currentNodeIndex,
                                          unsigned neighbourNodeIndex,
                                          CaBasedCellPopulation<DIM>& rCellPopulation,
                                          double dt,
                                          double deltaX);
  
      /**
        * @return mSwitchingParameter
        */
      double GetSwitchingParameter();
  
      /**
       * Set mSwitchingParameter.
       *
       * @param switchingParameter the new value of mSwitchingParameter
       */
      void SetSwitchingParameter(double switchingParameter);
  
      /**
       * Overridden OutputSwitchingUpdateRuleParameters() method.
       *
       * @param rParamsFile the file stream to which the parameters are output
       */
      void OutputSwitchingUpdateRuleParameters(out_stream& rParamsFile);
  };
  
  #include "SerializationExportWrapper.hpp"
  EXPORT_TEMPLATE_CLASS_SAME_DIMS(RandomCaSwitchingUpdateRule)
  
  #endif /*RANDOMCASWITCHINGUPDATERULE_HPP_*/
  