#

CONFIG += release

CONFIG -= debug

CONFIG += qt

QMAKE_CXXFLAGS += -fexceptions

QMAKE_CXXFLAGS_DEBUG += -g3

QMAKE_CXXFLAGS_DEBUG += -DQDEBUG

#REACTIONS = reactions_auxin_growth.h 

#REACTIONS = reactions_meinhardt.h

#REACTIONS = reactions_pce_growth.h

DEFINES += QTGRAPHICS

DEFINES += REACTIONS_HEADER=$${REACTIONS}

DEFINES += REACTIONS_HEADER_STRING=\"$${REACTIONS}\"

DEFINES += FLEMING

PERLDIR = ./perl

BINDIR = ../bin

DESTDIR = $$BINDIR

TARGET = VirtualLeaf

TEMPLATE = app

PARTMPL = $${TARGET}par.tmpl

MAINSRC = $${TARGET}.cpp

QT -= network sql xml

QT += qt3support

!win32 {

 GRAPHICS = qt #qwt

}

win32 {

 CONFIG += console

 LIBXML2DIR = C:\libxml2

 LIBICONVDIR = C:\libiconv

 LIBZDIR = C:\libz

 system(DEL parameter.cpp parameter.h) 

 GRAPHICS = qt 

 RC_FILE = VirtualLeaf.rc

 QMAKE_CXXFLAGS += -DLIBXML_STATIC

 QMAKE_CXXFLAGS += -I$${LIBXML2DIR}\include -I$${LIBICONVDIR}\include -I$${LIBZDIR}\include

 QMAKE_POST_LINK = "\

  C:\Bin\cp release\VirtualLeaf.exe \

  C:\Qt\4.5.3\bin\Qt3Support4.dll \

  C:\Qt\4.5.3\bin\QtGui4.dll \

  C:\Qt\4.5.3\bin\QtSql4.dll \

  C:\Qt\4.5.3\bin\QtXml4.dll \

  C:\Qt\4.5.3\bin\QtCore4.dll \

  C:\Qt\4.5.3\bin\QtNetwork4.dll \

  C:\Qt\4.5.3\bin\QtSvg4.dll \

  C:\bin\iconv.dll \

  C:\bin\libxml2.dll \

  C:\bin\zlib1.dll \

  C:\MinGW\bin\mingwm10.dll \

  $${DESTDIR}"

 LIBS += -L$${LIBXML2DIR}\lib -lxml2 -L$${LIBICONVDIR}\lib -L$${LIBZDIR}\lib  -lz -lm -lwsock32 -liconv

}

# Application icons

macx {

 ICON = leaficon.icns

 # make sure that the executable can find the libqwt share library

 QMAKE_POST_LINK = "mkdir $${DESTDIR}/$${TARGET}.app/Contents/Frameworks; \

  cp /usr/local/qwt/lib/libqwt.dylib $${DESTDIR}/$${TARGET}.app/Contents/Frameworks/.; \

  #install_name_tool -change libqwt.5.dylib $$QWTDIR/lib/libqwt.dylib $${DESTDIR}/$${TARGET}.app/Contents/MacOS/$${TARGET}; \

  install_name_tool -id @executable_path/../Frameworks/libqwt.dylib $${DESTDIR}/$${TARGET}.app/Contents/Frameworks/libqwt.dylib; \

  install_name_tool -change libqwt.5.dylib @executable_path/../Frameworks/libqwt.dylib $${DESTDIR}/$${TARGET}.app/Contents/MacOS/$${TARGET};\

  cp leaficon.icns $${DESTDIR}/$${TARGET}.app; "

}

macx:release {

 LIBS+= -dead_strip

}

unix {

 system(rm -f parameter.cpp parameter.h) 

 CC = /usr/bin/gcc 

 QWTDIR = /ufs/guravage/opt/qwt-5.2.1-svn

 QMAKE_LIBDIR += $$QWTDIR/lib 

 QMAKE_CXXFLAGS += -fPIC -I/usr/include/libxml2

 QMAKE_LFLAGS += -fPIC

 LIBS += -lxml2 -lz -lm 

}

system(perl $$PERLDIR/make_parameter_source.pl $$PARTMPL)

system(perl $$PERLDIR/make_pardialog_source.pl $$PARTMPL)

#system(perl $$PERLDIR/make_xmlwritecode.pl -h $$REACTIONS)

# Input

HEADERS += \

 apoplastitem.h \

 canvas.h \

 cellbase.h \

 cell.h \

 cellitem.h \

 infobar.h \

 mainbase.h \

 mainbase.h \

 matrix.h \

 mesh.h \

 miscq.h \

 modelcatalogue.h \

 Neighbor.h \

 node.h \

 nodeitem.h \

 nodeset.h \

 OptionFileDialog.h \

 output.h \

 parameter.h \

 pardialog.h \

 parse.h \

 pi.h \

 qcanvasarrow.h \

 random.h \

 rungekutta.h \

 simitembase.h \

 simplugin.h \

 sqr.h \

 tiny.h \

 transporterdialog.h \

 UniqueMessage.h \

 vector.h \

 wallbase.h \

 wall.h \

 wallitem.h \

 warning.h \

 xmlwrite.h \

 $${PARTMPL}

SOURCES += \

 apoplastitem.cpp \

 canvas.cpp \

 cellbase.cpp \

 cell.cpp \

 cellitem.cpp \

 mainbase.cpp \

 matrix.cpp \

 mesh.cpp \

 miscq.cpp \

 modelcatalogue.cpp \

 Neighbor.cpp \

 node.cpp \

 nodeitem.cpp \

 nodeset.cpp \

 OptionFileDialog.cpp \

 output.cpp \

 parameter.cpp \

 pardialog.cpp \

 parse.cpp \

 random.cpp \

 rungekutta.cpp \

 simitembase.cpp \

 transporterdialog.cpp \

 UniqueMessage.cpp \

 vector.cpp \

 wallbase.cpp \

 wall.cpp \

 wallitem.cpp \

 warning.cpp \

 xmlwritecode.cpp \

 xmlwrite.cpp \

 $$MAINSRC

contains( TARGET, leaf_fleming ) {

 DEFINES += FLEMING	

}

contains(GRAPHICS, qwt) {

 #macx:LIBS += -L$$QWTDIR/lib -lqwt

 #win32:LIBS += -L$$QWTDIR/lib -lqwt5

 #LIBS += -L$$QWTDIR/lib -lqwt

 INCLUDEPATH += $$QWTDIR/include

 DEFINES += HAVE_QWT

 HEADERS += data_plot.h

 SOURCES += data_plot.cpp

}

contains( GRAPHICS, qt ) {

 message( "Building Qt executable" )

 QMAKE_CXXFLAGS += -DQTGRAPHICS # -fpermissive

}

contains( GRAPHICS, xfig ) {

 message("Building Xfig executable (background runnable).")

 QMAKE_CXXFLAGS += -DXFIGGRAPHICS

}

contains( GRAPHICS, x11 ) {

 !unix {

  error("X11 graphics only available on Unix systems.")

 }

 message("Building X11 executable")

 SOURCES += x11graph.cpp

 HEADERS += x11graph.h

 QMAKE_CXXFLAGS += -DX11GRAPHICS

 CONFIG -= qt

 CONFIG += x11

 unix:LIBS += -lpng

}

# finis

/*

 *

 *  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 "leafplugin.h"

#include "far_mem_5.h"

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

bool batch = false;

// To be executed after cell division

		// PIN1 distributes between parent and daughter according to area

  double tot_area = area + daughter_area;

  //chem[1]*=(area/tot_area);

  //daughter.chem[1]*=(daughter_area/tot_area);

  // For lack of detailed data, or a better rule, we assume that cells remain polarized

  // after division

  // So the PIN1 is redistributed according to the original polarization over the walls

  // parent_info contains info about the parent 

  // redistribute the PIN in the endosome according to area

	// "Fudge" rule: if one of the cells is at the boundary, remove all AUX1 in the other cell

		//daughter.new_chem[0]=daughter.chem[0]=0.;

		//cerr << "Clearing daughter\n";

		//for (list<Wall *>::const_iterator w=daughter.walls.begin();

		//	 w!=daughter.walls.end();

		//	 w++) {

		//	(*w)->setTransporter(&daughter, 1, 0.);

		//}

	} else {

		  //new_chem[2]=chem[2]=0.;

			/*new_chem[0]=chem[0]=0.;

			for (list<Wall *>::const_iterator w=walls.begin();

				 w!=walls.end();

				 w++) {

				(*w)->setTransporter(this, 1, 0.);

			}*/

		  //cerr << "Clearing parent\n";

		} else {

		}

	}

	/*

	  // NB: Code commented out; not yet adapted to plugin format... RM 18/12/2009

	// Now redistribute the membrane PINs according to the original polarization in the parent

	// mmm... I'd like to have a better, biologically motivated rule for this, 

	// but for lack of something better... I hope I'm excused :-). Let's say the overall

	// organization of the actin fibres is not completely destroyed after division...

	// distribute wallPINs according to the circumference of the parent and daughter

	double circ = Circumference( );

	double daughter_circ = daughter.Circumference();

	double tot_circ = circ + daughter_circ;

	// distrubute it according to the overall polarity

	double sum=0.;

	for (list<Wall *>::const_iterator w=walls.begin();

		 w!=walls.end();

		 w++) {

		// distribute according to angle (0 degrees: maximum, 180 degrees minimum)

		double tmp=InnerProduct((*w)->getWallVector(this),polarization); // move domain from [-1,1] to [0,1]

		cerr << "[" << tmp << "]";

		sum+=tmp;

		//(*w)->setTransporter(this, 1, 

	}

	//cerr << "Sum is " << sum << endl;

	//double sum_wall_Pi = SumTransporters(1);

	// After division, cells produce PIN1 (in intracellular storage) until total amount becomes Pi_tot

	//SetChemical(1, par.Pi_tot - sum_wall_Pi  );

	//SetNewChem(1, Chemical(1));

	//cerr << "[ "  << sum_wall_Pi + Chemical(1) << "]";

	*/

}

	// Red: AUX1

	// Green: Auxin

	// Blue: van-3

}

    }		

    // expand if this is not a provascular cell

    } 

  }  

}

void LeafPlugin::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;

      // dchem_c2 is undefined..!

      return;

    } else {

      if (w->AuxinSink()) {

	// efflux into Shoot Apical meristem

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

	dchem_c1[0] -= par->sam_efflux * w->C1()->Chemical(0) / (par->ka + w->C1()->Chemical(0));

	return;

      } else {

	// Active fluxes (PIN1 and AUX1 mediated transport)

	// (Transporters measured in moles, here)

	// efflux from cell 1 to cell 2

	double trans12 = ( par->transport * w->Transporters1(1) * w->C1()->Chemical(0) / (par->ka + w->C1()->Chemical(0)) 

			   + par->aux1transport * w->C2()->Chemical(2) * w->C1()->Chemical(0) / (par->kaux1 + w->C1()->Chemical(0)) );

	// efflux from cell 2 to cell 1

	double trans21 = ( par->transport * w->Transporters2(1) * w->C2()->Chemical(0) / (par->ka + w->C2()->Chemical(0)) 

			   + par->aux1transport * w->C1()->Chemical(2) * w->C2()->Chemical(0) / (par->kaux1 + w->C2()->Chemical(0)) );

	dchem_c1[0] += trans21 - trans12;

	dchem_c2[0] += trans12 - trans21;

	return;

      }

    }

  }

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

    if (w->AuxinSource()) {

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

      dchem_c2[0] += aux_flux;

      // dchem_c1 is undefined...!

      return;

    } else {

      if (w->AuxinSink()) {

	// efflux into Shoot Apical meristem

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

	// no passive fluxes: outside is impermeable

	// Active fluxes (PIN1 and AUX1 mediated transport)

	// (Transporters measured in moles, here)

	// efflux from cell 1 to cell 2

	// assumption: no AUX1 in shoot apical meristem

	double trans12 = ( par->transport * w->Transporters1(1) * w->C1()->Chemical(0) / (par->ka + w->C1()->Chemical(0)));

	dchem_c1[0] +=  - trans12;

	return;

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

	// return;

      }  else {

      }

    }

  }

  // Passive fluxes (Fick's law)

  // only auxin flux now

  // flux depends on edge length and concentration difference

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

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

    dchem_c1[c] += phi; 

    dchem_c2[c] -= phi;

  }

  // Active fluxes (PIN1 and AUX1 mediated transport)

  // (Transporters measured in moles, here)

  // efflux from cell 1 to cell 2

  double trans12 = ( par->transport * w->Transporters1(1) * w->C1()->Chemical(0) / (par->ka + w->C1()->Chemical(0)) 

		     + par->aux1transport * w->C2()->Chemical(2) * w->C1()->Chemical(0) / (par->kaux1 + w->C1()->Chemical(0)) );

  // efflux from cell 2 to cell 1

  double trans21 = ( par->transport * w->Transporters2(1) * w->C2()->Chemical(0) / (par->ka + w->C2()->Chemical(0)) 

		     + par->aux1transport * w->C1()->Chemical(2) * w->C2()->Chemical(0) / (par->kaux1 + w->C2()->Chemical(0)) );

  dchem_c1[0] += trans21 - trans12;

  dchem_c2[0] += trans12 - trans21;

}

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

  // Cells polarize available PIN1 to Shoot Apical Meristem

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

    if (w->AuxinSink()) {

      dw1[0] = 0.; dw2[0] = 0.;

      dw1[2] = 0.; dw2[2] = 0.;

      // assume high auxin concentration in SAM, to convince PIN1 to polarize to it

      // exocytosis regulated0

      double nb_auxin = par->sam_auxin;

      double receptor_level = nb_auxin * par->r / (par->kr + nb_auxin);

      dw1[1] = par->k1 * w->C1()->Chemical(1) * receptor_level /( par->km + w->C1()->Chemical(1) ) - par->k2 * w->Transporters1(1);

      dw2[1] = 0.;

      return;

    } else {

      dw1[0]=dw2[0]=dw1[1]=dw2[1]=dw1[2]=dw2[2];

      return;

    }

  }

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

    if (w->AuxinSink())  {

      dw1[0] = 0.; dw2[0] = 0.;

      dw1[2] = 0.; dw2[2] = 0.;

      // assume high auxin concentration in SAM, to convince PIN1 to polarize to it

      // exocytosis regulated

      double nb_auxin = par->sam_auxin;

      double receptor_level = nb_auxin * par->r / (par->kr + nb_auxin);

      dw2[1] = par->k1 * w->C2()->Chemical(1) * receptor_level /( par->km + w->C2()->Chemical(1) ) - par->k2 * w->Transporters2(1);

      dw1[1] = 0.;

      return;

    }  else {

      dw1[0]=dw2[0]=dw1[1]=dw2[1]=dw1[2]=dw2[2];

      return;

    }

  }

  // PIN1 localization at wall 1

  // Note: chemical 0 is Auxin (intracellular storage only)

  // Chemical 1 is PIN1 (walls and intracellular storage)

  //! \f$ \frac{d Pij/dt}{dt} = k_1 A_j \frac{P_i}{L_ij} - k_2 P_{ij} \f$

  // Note that Pij is measured in term of concentration (mol/L)

  // Pi in terms of quantity (mol)

  double dPijdt1=0., dPijdt2=0.;

  // normal cell

  double  auxin2 = w->C2()->Chemical(0);

  double receptor_level1 = auxin2 * par->r / (par->kr + auxin2);

  dPijdt1 = 

    // exocytosis regulated

    par->k1 * w->C1()->Chemical(1) * receptor_level1 / ( par->km + w->C1()->Chemical(1) ) - par->k2 * w->Transporters1(1);

  double  auxin1 = w->C1()->Chemical(0);

  double receptor_level2 = auxin1 * par->r / (par->kr + auxin1);

  // normal cell

  dPijdt2 = 

    // exocytosis regulated

    par->k1 * w->C2()->Chemical(1) * receptor_level2 / ( par->km + w->C2()->Chemical(1) ) - par->k2 * w->Transporters2(1);

  /* PIN1 of neighboring vascular cell inhibits PIN1 endocytosis */

  dw1[0] = 0.; dw2[0] = 0.;

  dw1[2] = 0.; dw2[2] = 0.;

  dw1[1] = dPijdt1;

  dw2[1] = dPijdt2;

}

  // gives the amount of complex "auxinreceptor-Pin1"  at the wall (at QSS) 

  //return here.Chemical(1) * nb.Chemical(0) / ( par->km + here.Chemical(1));

  double receptor_level = nb_aux * par->r / (par->kr + nb_aux);

}

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

  double dPidt = 0.;

  double sum_Pij = c->SumTransporters( 1 );

  // exocytosis regulated: 

  // van3 expression reduces rate of PIN1 endocytosis 

  dPidt = -par->k1 * c->ReduceCellAndWalls<double>( far_3_arg_mem_fun( *this, &LeafPlugin::complex_PijAj ) ) + 

    (c->Chemical(3) < 0.5 ? par->k2 : par->k2van3) * sum_Pij;

  // production of PIN depends on auxin concentration

  dPidt +=  (c->AtBoundaryP()?par->pin_prod_in_epidermis:par->pin_prod) * c->Chemical(0) - c->Chemical(1) * par->pin_breakdown;

  /*if (c->AtBoundaryP()) {

    dchem[2] = 0.01;

    //cerr << "Making cell blue.\n";

    } else {

    dchem[2] = -0.1 * c->Chemical(2);

    }*/

  // no PIN production in SAM

  if (c->Boundary() == CellBase::SAM) {

    dchem[1]=0.;

    dchem[0]= - par->sam_auxin_breakdown * c->Chemical(0);

    dchem[2]=0.;

  } else {

    dchem[1] = dPidt;

    // source of auxin

    dchem[0] = par->aux_cons;

    // auxin-induced AUX1 production, in the epidermis

    dchem[2] = ( c->AtBoundaryP() ? par->aux1prod : par->aux1prodmeso ) * ( c->Chemical(0)  / ( 1. + par->kap * c->Chemical(0) ) ) - ( par->aux1decay ) * c->Chemical(2) ;//: 0.;

    // auxin-induced production of VAN-3? Autokatalysis?

    //dchem[3] = par->van3prod * (c->Chemical(0) / (1. + par->kvp * c-> Chemical(0) ) )

    double A = c->Chemical(0);

    double van3 = c->Chemical(3);

    dchem[3] = par->van3prod * A - par->van3autokat * van3 + van3*van3/(1 + par->van3sat * van3*van3 ); 

  }

}

Q_EXPORT_PLUGIN2(leafplugin, LeafPlugin)

/*

 *  $Id$

 *

 *  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.

 *

 */

#ifndef _LEAFPLUGIN_H_

#define _LEAFPLUGIN_H_

#include <QObject>

#include <QtGui>

#include <QString>

#include "../simplugin.h"

class LeafPlugin : public QObject, SimPluginInterface {

	Q_OBJECT

	Q_INTERFACES(SimPluginInterface);

public:

	virtual QString ModelID(void) { return QString( "Traveling wave model with influx carriers - Merks and Beemster, 2006-2008" ); }

	// Executed after the cellular mechanics steps have equillibrized

	// Differential equations describing transport of chemicals from cell to cell

	virtual void CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2);

	// Differential equations describing chemical reactions taking place at or near the cell walls

	// (e.g. PIN accumulation)

	virtual void WallDynamics(Wall *w, double *dw1, double *dw2);

	// Differential equations describing chemical reactions inside the cells

	virtual void CellDynamics(CellBase *c, double *dchem);

	// to be executed after a cell division

	// to be executed for coloring a cell

	// return number of chemicals

	virtual int NChem(void) { return 4; }

 private:

};