/*

 *

 *  This file is part of the Virtual Leaf.

 *

 *  The Virtual Leaf is free software: you can redistribute it and/or modify

 *  it under the terms of the GNU General Public License as published by

 *  the Free Software Foundation, either version 3 of the License, or

 *  (at your option) any later version.

 *

 *  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 "../simplugin.h"

#include "parameter.h"

#include "wallbase.h"

#include "cellbase.h"

#include "auxingrowthplugin.h"

#include "far_mem_5.h"

static const std::string _module_id("$Id$");

// To be executed after cell division

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

{

  // Auxin distributes between parent and daughter according to area

  double area1 = daughter1->Area(), area2 = daughter2->Area();

  double tot_area = area1 + area2;

  daughter1->SetChemical(0,daughter1->Chemical(0)*(area1/tot_area));

  daughter2->SetChemical(0,daughter2->Chemical(0)*(area2/tot_area));

  // After divisions, parent and daughter cells get a standard stock of PINs.

  daughter1->SetChemical(1, par->initval[1]);

  daughter2->SetChemical(1, par->initval[1]);

  // Reset transporter values of parent and daughter

  QList<WallBase *> walls;

  foreach(WallBase *w, walls) { 

    w->setTransporter(daughter1, 1, 0.);

  }

}

void AuxinGrowthPlugin::SetCellColor(CellBase *c, QColor *color)

{ 

  // Red: PIN1

  // Green: Auxin

}

void AuxinGrowthPlugin::CellHouseKeeping(CellBase *c)

{

  if (c->Boundary()==CellBase::None) {

    if (c->Area() > par->rel_cell_div_threshold * c->BaseArea() ) {

      c->SetChemical(0,0);

      c->Divide();

    }		

    // expand according to auxin concentration

    c->EnlargeTargetArea(par->auxin_dependent_growth?(c->Chemical(0)/(1.+c->Chemical(0)))*par->cell_expansion_rate:par->cell_expansion_rate);

  }  

}

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

{

  // leaf edge is const source of auxin

  // (Neumann boundary condition: we specify the influx)

  if (w->C2()->BoundaryPolP()) {

    if (w->AuxinSource()) {

      double aux_flux = par->leaf_tip_source * w->Length();

      dchem_c1[0]+= aux_flux;

      return;

    } else {

      return;

    }

  }

  if (w->C1()->BoundaryPolP()) {

    if (w->AuxinSource()) {

      double aux_flux = par->leaf_tip_source * w->Length();

      dchem_c2[0] += aux_flux;

      return;

    } else {

      if (w->AuxinSink()) {

	// efflux into Shoot Apical meristem

	// we assume all PINs are directed towards shoot apical meristem

	dchem_c2[0] -= par->sam_efflux * w->C2()->Chemical(0) / (par->ka + w->C2()->Chemical(0));

	return;

      } else 

	return;

    }

  }

  // Passive fluxes (Fick's law)

  // only auxin flux now

  // flux depends on edge length and concentration difference

  int c=0;

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

  dchem_c1[c] += phi; 

  dchem_c2[c] -= phi;