*  The Virtual Leaf is distributed in the hope that it will be useful,

 *  but WITHOUT ANY WARRANTY; without even the implied warranty of

 *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the

 *  GNU General Public License for more details.

 *

 *  You should have received a copy of the GNU General Public License

 *  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.

 *

 *  Copyright 2010 Roeland Merks.

 *

 */

#include <QObject>

#include <QtGui>

#include <QDebug>

#include "simplugin.h"

#include "parameter.h"

#include "wallbase.h"

#include "cellbase.h"

#include "mydiffusionmodel.h"

QString Mydiffusionmodel::ModelID(void) {

  // specify the name of your model here

}

// return the number of chemicals your model uses

int Mydiffusionmodel::NChem(void) { return 4; }

// To be executed after cell division

void Mydiffusionmodel::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) {

  // rules to be executed after cell division go here

  // (e.g., cell differentiation rules)

}

void Mydiffusionmodel::SetCellColor(CellBase *c, QColor *color) { 

  // add cell coloring rules here

  double red=c->Chemical(1)/(1.+c->Chemical(1));

  double green=c->Chemical(0)/(1.+c->Chemical(0));

  double blue=c->Chemical(3)/(1.+c->Chemical(3));

  color->setRgbF(red,green,blue);

}

void Mydiffusionmodel::CellHouseKeeping(CellBase *c) {

  // add cell behavioral rules here

  if (c->Chemical(0) < 0.5){

    c->EnlargeTargetArea(par->cell_expansion_rate);

  }

  if(c->Area() > 2*c->BaseArea()){

    c->Divide();

  }

}

void Mydiffusionmodel::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) {

  // add biochemical transport rules here

}

void Mydiffusionmodel::WallDynamics(Wall *w, double *dw1, double *dw2) {

  // add biochemical networks for reactions occuring at walls here

}

void Mydiffusionmodel::CellDynamics(CellBase *c, double *dchem) {

  // add biochemical networks for intracellular reactions here

  double Y = c->Chemical(0), 

         A = c->Chemical(1), 

         H = c->Chemical(2), 

         S = c->Chemical(3);

  dchem[0] = ( par->d * A - par->e * Y + Y*Y/(1 + par->f * Y*Y ) );

  dchem[1] = ( par->c * A*A*S/H - par->mu * A + par->rho0*Y );

  dchem[2] = ( par->c * A*A*S - par->nu*H + par->rho1*Y );

  dchem[3] = ( par->c0 - par->gamma*S - par->eps * Y * S );

}

Q_EXPORT_PLUGIN2(mydiffusionmodel, Mydiffusionmodel)

// finis