# $Id$

# Set an environment varible $(MAKE) to the name of the make command

# on your machine, e.g. 'make' on UNIX and 'mingw32-make' on windows.

# Fallback default is UNIX make.

ifeq ($(MAKE),)

	MAKE=make

endif

PROTOCOLS=\

 MyEmptyModel

all:

	@for p in $(PROTOCOLS); do $(MAKE) -C $$p; done;

clean:

	@for p in $(PROTOCOLS); do $(MAKE) -C $$p clean; done;

# finis

# Set an environment varible $(MAKE) to the name of the make command

# on your machine, e.g. 'make' on UNIX and 'mingw32-make' on windows.

# Fallback default is UNIX make.

ifeq ($(MAKE),)

	MAKE=make

endif

# Ditto for QMAKE

ifeq ($(QMAKE),)

	QMAKE=qmake

endif

all: myemptymodel

myemptymodel: Makefile.myemptymodel

	$(MAKE) -f Makefile.myemptymodel

Makefile.myemptymodel: myemptymodel.pro

	$(QMAKE) -o $@ $< 

clean:

	$(MAKE) -f Makefile.myemptymodel clean

ifeq ($(MAKE),make)

	touch myemptymodel.pro

else

	copy /b myemptymodel.pro +,,

endif

# 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 <QDebug>

#include "simplugin.h"

#include "parameter.h"

#include "wallbase.h"

#include "cellbase.h"

#include "myemptymodel.h"

QString Myemptymodel::ModelID(void) {

  // specify the name of your model here

  return QString( "First Vleaf model" );

}

// return the number of chemicals your model uses

int Myemptymodel::NChem(void) { return 0; }

// To be executed after cell division

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

  // rules to be executed after cell division go here

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

}

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

  // add cell coloring rules here

}

void Myemptymodel::CellHouseKeeping(CellBase *c) {

  // add cell behavioral rules here

}

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

  // add biochemical transport rules here

}

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

  // add biochemical networks for reactions occuring at walls here

}

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

  // add biochemical networks for intracellular reactions here

}

Q_EXPORT_PLUGIN2(myemptymodel, Myemptymodel)

// 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 <QString>

#include "simplugin.h"

class Myemptymodel : public QObject, SimPluginInterface {

  Q_OBJECT

  Q_INTERFACES(SimPluginInterface);

 public:

  virtual QString ModelID(void);

  // Executed after the cellular mechanics steps have equillibrized

  virtual void CellHouseKeeping (CellBase *c);

  // 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

  virtual void OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2);

  // To be executed for coloring a cell

  virtual void SetCellColor(CellBase *c, QColor *color);	

  // Return number of chemicals

  virtual int NChem(void);

};

// finis

#

# $Id$

#

#  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.

#

TARGET = myemptymodel

VLEAFHOME = ../../..

CONFIG += release

CONFIG -= debug

CONFIG += plugin

BINDIR = $${VLEAFHOME}/bin

LIBDIR = $${VLEAFHOME}/lib

INCDIR = $${VLEAFHOME}/src

DEFINES = QTGRAPHICS # VLEAFPLUGIN

DESTDIR = $${BINDIR}/models

HEADERS = $${TARGET}.h $${INCDIR}/simplugin.h

INCLUDEPATH += $${INCDIR}	

QMAKE_CXXFLAGS += -fexceptions #-I$${INCDIR}

QMAKE_CXXFLAGS += -Wno-write-strings

QMAKE_CXXFLAGS += -Wno-unused-parameter

QMAKE_CXXFLAGS_DEBUG += -g3

QMAKE_CXXFLAGS_DEBUG += -DQDEBUG

QT += qt3support

SOURCES = $${TARGET}.cpp

TEMPLATE = lib 

unix {

 LIBS += -L$${LIBDIR} -lvleaf

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

 QMAKE_LFLAGS += -fPIC

}

win32 {

 LIBXML2DIR = $${LIBDIR}\libxml2

 LIBICONVDIR = $${LIBDIR}\libiconv

 LIBZDIR = $${LIBDIR}\libz

 LIBS += -L$${LIBDIR} -lvleaf

 QMAKE_CXXFLAGS += -DLIBXML_STATIC

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

}

# finish