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

    c->Divide();

  }

}

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

  // add biochemical transport rules here

  // Passive fluxes (Fick's law)

  for (int c=0;c<NChem();c++) {

    if (w->C1()->BoundaryPolP() || w->C2()->BoundaryPolP()) return;

    double phi = w->Length() * ( par->D[c] ) * ( w->C2()->Chemical(c) - w->C1()->Chemical(c) );

    dchem_c1[c] += phi;

    dchem_c2[c] -= phi;

  }

}

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