EI/VirtualLeaf Changeset - 413a4067bfff · Centrum Wiskunde & Informatica (CWI)

Changeset - 413a4067bfff

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0 17 19

Roeland Merks - 15 years ago 2010-06-03 18:40:26
roeland.merks@cwi.nl

Changed interface for model plugins to make usage of pointers and references consistent.
Added codes for tutorial belonging to VLeaf manuscript.
Something changed in modelcatalogue. I'm not sure what...

user: Roeland Merks <roeland.merks@cwi.nl>
branch 'default'
added src/TutorialCode/Tutorial0/mymodel.cpp
added src/TutorialCode/Tutorial0/mymodel.h
added src/TutorialCode/Tutorial0/mymodel.pro
added src/TutorialCode/Tutorial1/mymodel.cpp
added src/TutorialCode/Tutorial1/mymodel.h
added src/TutorialCode/Tutorial1/mymodel.pro
added src/TutorialCode/Tutorial2/mymodel.cpp
added src/TutorialCode/Tutorial2/mymodel.h
added src/TutorialCode/Tutorial2/mymodel.pro
added src/TutorialCode/Tutorial3/mymodel.cpp
added src/TutorialCode/Tutorial3/mymodel.h
added src/TutorialCode/Tutorial3/mymodel.pro
added src/TutorialCode/Tutorial4/mymodel.cpp
added src/TutorialCode/Tutorial4/mymodel.h
added src/TutorialCode/Tutorial4/mymodel.pro
added src/TutorialCode/Tutorial5/mymodel.cpp
added src/TutorialCode/Tutorial5/mymodel.h
added src/TutorialCode/Tutorial5/mymodel.pro
added src/build_models/translate_plugin.pl
changed src/VirtualLeafpar.tmpl
changed src/build_models/auxingrowthplugin.cpp
changed src/build_models/auxingrowthplugin.h
changed src/build_models/meinhardtplugin.cpp
changed src/build_models/meinhardtplugin.h
changed src/build_models/plugin_auxingrowth.pro
changed src/build_models/plugin_leaf.pro
changed src/build_models/plugin_meinhardt.pro
changed src/build_models/plugin_test.pro
changed src/cell.cpp
changed src/cellbase.cpp
changed src/cellbase.h
changed src/libplugin.pro
changed src/mesh.cpp
changed src/mesh.h
changed src/modelcatalogue.cpp
changed src/simplugin.h

36 files changed with 1397 insertions and 75 deletions:

src/TutorialCode/Tutorial0/mymodel.cpp

src/TutorialCode/Tutorial0/mymodel.h

src/TutorialCode/Tutorial0/mymodel.pro

src/TutorialCode/Tutorial1/mymodel.cpp

src/TutorialCode/Tutorial1/mymodel.h

src/TutorialCode/Tutorial1/mymodel.pro

src/TutorialCode/Tutorial2/mymodel.cpp

src/TutorialCode/Tutorial2/mymodel.h

src/TutorialCode/Tutorial2/mymodel.pro

src/TutorialCode/Tutorial3/mymodel.cpp

src/TutorialCode/Tutorial3/mymodel.h

src/TutorialCode/Tutorial3/mymodel.pro

src/TutorialCode/Tutorial4/mymodel.cpp

src/TutorialCode/Tutorial4/mymodel.h

src/TutorialCode/Tutorial4/mymodel.pro

src/TutorialCode/Tutorial5/mymodel.cpp

120

src/TutorialCode/Tutorial5/mymodel.h

src/TutorialCode/Tutorial5/mymodel.pro

src/VirtualLeafpar.tmpl

src/build_models/auxingrowthplugin.cpp

src/build_models/auxingrowthplugin.h

src/build_models/meinhardtplugin.cpp

src/build_models/meinhardtplugin.h

src/build_models/plugin_auxingrowth.pro

src/build_models/plugin_leaf.pro

src/build_models/plugin_meinhardt.pro

src/build_models/plugin_test.pro

src/build_models/translate_plugin.pl

src/cell.cpp

src/cellbase.cpp

src/cellbase.h

src/libplugin.pro

src/mesh.cpp

src/mesh.h

src/modelcatalogue.cpp

src/simplugin.h

0 comments (0 inline, 0 general)

src/TutorialCode/Tutorial0/mymodel.cpp

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Show inline comments

@@ new file 100644 @@
 /*
+ *
  *  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 "mymodel.h"
 static const std::string _module_id("$Id$");
 QString MyModel::ModelID(void) {
   // specify the name of your model here
   return QString( "My first model in VirtualLeaf" );
+}
 // return the number of chemicals your model uses
 int MyModel::NChem(void) { return 0; }
 // To be executed after cell division
 void MyModel::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) {
   // rules to be executed after cell division go here
   // (e.g., cell differentiation rules)
+}
 void MyModel::SetCellColor(CellBase *c, QColor *color) {
   // add cell coloring rules here
+}
 void MyModel::CellHouseKeeping(CellBase *c) {
   // add cell behavioral rules here
+}
 void MyModel::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) {
   // add biochemical transport rules here
+}
 void MyModel::WallDynamics(Wall *w, double *dw1, double *dw2) {
   // add biochemical networks for reactions occuring at walls here
+}
 void MyModel::CellDynamics(CellBase *c, double *dchem) {
   // add biochemical networks for intracellular reactions here
+}
 Q_EXPORT_PLUGIN2(mymodel, MyModel)

src/TutorialCode/Tutorial0/mymodel.h

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Show inline comments

@@ new file 100644 @@
 /*
  *  $Id$
+ *
  *  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.
+ *
  */
 #include <QObject>
 #include <QtGui>
 #include <QString>
 #include "simplugin.h"
 class MyModel : 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);
 };

src/TutorialCode/Tutorial0/mymodel.pro

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Show inline comments

@@ new file 100644 @@
+#
 # $Id$
+#
 #  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 = mymodel
 VLEAFHOME = ../../..
 CONFIG += release
 CONFIG -= debug
 CONFIG += plugin
 BINDIR = $${VLEAFHOME}/bin
 LIBDIR = $${VLEAFHOME}/lib
 INCDIR = $${VLEAFHOME}/src
 DEFINES = QTGRAPHICS # VLEAFPLUGIN
 DESTDIR = $${BINDIR}/models
 HEADERS = $${TARGET}.h
 INCLUDEPATH += $${INCDIR}
 QMAKE_CXXFLAGS += -fexceptions #-I$${INCDIR}
 QMAKE_CXXFLAGS_DEBUG += -g3
 QMAKE_CXXFLAGS_DEBUG += -DQDEBUG
 QT += qt3support
 SOURCES = $${TARGET}.cpp
 TEMPLATE = lib
 unix {
  LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -fPIC -I/usr/include/libxml2
  QMAKE_LFLAGS += -fPIC
+}
 win32 {
  LIBXML2DIR = C:\libxml2
  LIBICONVDIR = C:\libiconv
  LIBZDIR = C:\libz
  LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -DLIBXML_STATIC
  QMAKE_CXXFLAGS += -I$${LIBXML2DIR}\include -I$${LIBICONVDIR}\include -I$${LIBZDIR}\include
+}
 # finish

src/TutorialCode/Tutorial1/mymodel.cpp

➞

Show inline comments

@@ new file 100644 @@
 /*
+ *
  *  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 "mymodel.h"
 static const std::string _module_id("$Id$");
 QString MyModel::ModelID(void) {
   // specify the name of your model here
   return QString( "Cell growth" );
+}
 // return the number of chemicals your model uses
 int MyModel::NChem(void) { return 0; }
 // To be executed after cell division
 void MyModel::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) {
   // rules to be executed after cell division go here
   // (e.g., cell differentiation rules)
+}
 void MyModel::SetCellColor(CellBase *c, QColor *color) {
   // add cell coloring rules here
+}
 void MyModel::CellHouseKeeping(CellBase *c) {
   // add cell behavioral rules here
 	c->EnlargeTargetArea(par->cell_expansion_rate);
+}
 void MyModel::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) {
   // add biochemical transport rules here
+}
 void MyModel::WallDynamics(Wall *w, double *dw1, double *dw2) {
   // add biochemical networks for reactions occuring at walls here
+}
 void MyModel::CellDynamics(CellBase *c, double *dchem) {
   // add biochemical networks for intracellular reactions here
+}
 Q_EXPORT_PLUGIN2(mymodel, MyModel)

src/TutorialCode/Tutorial1/mymodel.h

➞

Show inline comments

@@ new file 100644 @@
 /*
  *  $Id$
+ *
  *  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.
+ *
  */
 #include <QObject>
 #include <QtGui>
 #include <QString>
 #include "simplugin.h"
 class MyModel : 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);
 };

src/TutorialCode/Tutorial1/mymodel.pro

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Show inline comments

@@ new file 100644 @@
+#
 # $Id$
+#
 #  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 = mymodel
 VLEAFHOME = ../../..
 CONFIG += release
 CONFIG -= debug
 CONFIG += plugin
 BINDIR = $${VLEAFHOME}/bin
 LIBDIR = $${VLEAFHOME}/lib
 INCDIR = $${VLEAFHOME}/src
 DEFINES = QTGRAPHICS # VLEAFPLUGIN
 DESTDIR = $${BINDIR}/models
 HEADERS = $${TARGET}.h
 INCLUDEPATH += $${INCDIR}
 QMAKE_CXXFLAGS += -fexceptions #-I$${INCDIR}
 QMAKE_CXXFLAGS_DEBUG += -g3
 QMAKE_CXXFLAGS_DEBUG += -DQDEBUG
 QT += qt3support
 SOURCES = $${TARGET}.cpp
 TEMPLATE = lib
 unix {
  LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -fPIC -I/usr/include/libxml2
  QMAKE_LFLAGS += -fPIC
+}
 win32 {
  LIBXML2DIR = C:\libxml2
  LIBICONVDIR = C:\libiconv
  LIBZDIR = C:\libz
  LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -DLIBXML_STATIC
  QMAKE_CXXFLAGS += -I$${LIBXML2DIR}\include -I$${LIBICONVDIR}\include -I$${LIBZDIR}\include
+}
 # finish

src/TutorialCode/Tutorial2/mymodel.cpp

➞

Show inline comments

@@ new file 100644 @@
 /*
+ *
  *  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 "mymodel.h"
 static const std::string _module_id("$Id$");
 QString MyModel::ModelID(void) {
   // specify the name of your model here
   return QString( "Cell growth and cell division" );
+}
 // return the number of chemicals your model uses
 int MyModel::NChem(void) { return 0; }
 // To be executed after cell division
 void MyModel::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) {
   // rules to be executed after cell division go here
   // (e.g., cell differentiation rules)
+}
 void MyModel::SetCellColor(CellBase *c, QColor *color) {
   // add cell coloring rules here
+}
 void MyModel::CellHouseKeeping(CellBase *c) {
   // add cell behavioral rules here
 	c->EnlargeTargetArea(par->cell_expansion_rate);
 	if (c->Area() > par->rel_cell_div_threshold * c->BaseArea()) {
 		c->Divide();
+	}
+}
 void MyModel::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) {
   // add biochemical transport rules here
+}
 void MyModel::WallDynamics(Wall *w, double *dw1, double *dw2) {
   // add biochemical networks for reactions occuring at walls here
+}
 void MyModel::CellDynamics(CellBase *c, double *dchem) {
   // add biochemical networks for intracellular reactions here
+}
 Q_EXPORT_PLUGIN2(mymodel, MyModel)

src/TutorialCode/Tutorial2/mymodel.h

➞

Show inline comments

@@ new file 100644 @@
 /*
  *  $Id$
+ *
  *  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.
+ *
  */
 #include <QObject>
 #include <QtGui>
 #include <QString>
 #include "simplugin.h"
 class MyModel : 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);
 };

src/TutorialCode/Tutorial2/mymodel.pro

➞

Show inline comments

@@ new file 100644 @@
+#
 # $Id$
+#
 #  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 = mymodel
 VLEAFHOME = ../../..
 CONFIG += release
 CONFIG -= debug
 CONFIG += plugin
 BINDIR = $${VLEAFHOME}/bin
 LIBDIR = $${VLEAFHOME}/lib
 INCDIR = $${VLEAFHOME}/src
 DEFINES = QTGRAPHICS # VLEAFPLUGIN
 DESTDIR = $${BINDIR}/models
 HEADERS = $${TARGET}.h
 INCLUDEPATH += $${INCDIR}
 QMAKE_CXXFLAGS += -fexceptions #-I$${INCDIR}
 QMAKE_CXXFLAGS_DEBUG += -g3
 QMAKE_CXXFLAGS_DEBUG += -DQDEBUG
 QT += qt3support
 SOURCES = $${TARGET}.cpp
 TEMPLATE = lib
 unix {
  LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -fPIC -I/usr/include/libxml2
  QMAKE_LFLAGS += -fPIC
+}
 win32 {
  LIBXML2DIR = C:\libxml2
  LIBICONVDIR = C:\libiconv
  LIBZDIR = C:\libz
  LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -DLIBXML_STATIC
  QMAKE_CXXFLAGS += -I$${LIBXML2DIR}\include -I$${LIBICONVDIR}\include -I$${LIBZDIR}\include
+}
 # finish

src/TutorialCode/Tutorial3/mymodel.cpp

➞

Show inline comments

@@ new file 100644 @@
 /*
+ *
  *  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 "mymodel.h"
 static const std::string _module_id("$Id$");
 QString MyModel::ModelID(void) {
   // specify the name of your model here
   return QString( "Cell growth and cell division" );
+}
 // return the number of chemicals your model uses
 int MyModel::NChem(void) { return 0; }
 // To be executed after cell division
 void MyModel::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) {
   // rules to be executed after cell division go here
   // (e.g., cell differentiation rules)
+}
 void MyModel::SetCellColor(CellBase *c, QColor *color) {
   // add cell coloring rules here
+}
 void MyModel::CellHouseKeeping(CellBase *c) {
   // add cell behavioral rules here
 	c->EnlargeTargetArea(par->cell_expansion_rate);
 	if (c->Area() > par->rel_cell_div_threshold * c->BaseArea()) {
 		c->DivideOverAxis(Vector(1,0,0));
+	}
+}
 void MyModel::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) {
   // add biochemical transport rules here
+}
 void MyModel::WallDynamics(Wall *w, double *dw1, double *dw2) {
   // add biochemical networks for reactions occuring at walls here
+}
 void MyModel::CellDynamics(CellBase *c, double *dchem) {
   // add biochemical networks for intracellular reactions here
+}
 Q_EXPORT_PLUGIN2(mymodel, MyModel)

src/TutorialCode/Tutorial3/mymodel.h

➞

Show inline comments

@@ new file 100644 @@
 /*
  *  $Id$
+ *
  *  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.
+ *
  */
 #include <QObject>
 #include <QtGui>
 #include <QString>
 #include "simplugin.h"
 class MyModel : 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);
 };

src/TutorialCode/Tutorial3/mymodel.pro

➞

Show inline comments

@@ new file 100644 @@
+#
 # $Id$
+#
 #  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 = mymodel
 VLEAFHOME = ../../..
 CONFIG += release
 CONFIG -= debug
 CONFIG += plugin
 BINDIR = $${VLEAFHOME}/bin
 LIBDIR = $${VLEAFHOME}/lib
 INCDIR = $${VLEAFHOME}/src
 DEFINES = QTGRAPHICS # VLEAFPLUGIN
 DESTDIR = $${BINDIR}/models
 HEADERS = $${TARGET}.h
 INCLUDEPATH += $${INCDIR}
 QMAKE_CXXFLAGS += -fexceptions #-I$${INCDIR}
 QMAKE_CXXFLAGS_DEBUG += -g3
 QMAKE_CXXFLAGS_DEBUG += -DQDEBUG
 QT += qt3support
 SOURCES = $${TARGET}.cpp
 TEMPLATE = lib
 unix {
  LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -fPIC -I/usr/include/libxml2
  QMAKE_LFLAGS += -fPIC
+}
 win32 {
  LIBXML2DIR = C:\libxml2
  LIBICONVDIR = C:\libiconv
  LIBZDIR = C:\libz
  LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -DLIBXML_STATIC
  QMAKE_CXXFLAGS += -I$${LIBXML2DIR}\include -I$${LIBICONVDIR}\include -I$${LIBZDIR}\include
+}
 # finish

src/TutorialCode/Tutorial4/mymodel.cpp

➞

Show inline comments

@@ new file 100644 @@
 /*
+ *
  *  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 "mymodel.h"
 static const std::string _module_id("$Id$");
 QString MyModel::ModelID(void) {
   // specify the name of your model here
   return QString( "Growth, division, coloring" );
+}
 // return the number of chemicals your model uses
 int MyModel::NChem(void) { return 0; }
 // To be executed after cell division
 void MyModel::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) {
   // rules to be executed after cell division go here
   // (e.g., cell differentiation rules)
+}
 void MyModel::SetCellColor(CellBase *c, QColor *color) {
   // add cell coloring rules here
 	if (c->Area()/c->BaseArea()>1.8) { color->setNamedColor("blue"); }
 	else { color->setNamedColor("green"); }
+}
 void MyModel::CellHouseKeeping(CellBase *c) {
   // add cell behavioral rules here
 	c->EnlargeTargetArea(par->cell_expansion_rate);
 	if (c->Area() > par->rel_cell_div_threshold * c->BaseArea()) {
 		c->Divide();
+	}
+}
 void MyModel::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) {
   // add biochemical transport rules here
+}
 void MyModel::WallDynamics(Wall *w, double *dw1, double *dw2) {
   // add biochemical networks for reactions occuring at walls here
+}
 void MyModel::CellDynamics(CellBase *c, double *dchem) {
   // add biochemical networks for intracellular reactions here
+}
 Q_EXPORT_PLUGIN2(mymodel, MyModel)

src/TutorialCode/Tutorial4/mymodel.h

➞

Show inline comments

@@ new file 100644 @@
 /*
  *  $Id$
+ *
  *  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.
+ *
  */
 #include <QObject>
 #include <QtGui>
 #include <QString>
 #include "simplugin.h"
 class MyModel : 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);
 };

src/TutorialCode/Tutorial4/mymodel.pro

➞

Show inline comments

@@ new file 100644 @@
+#
 # $Id$
+#
 #  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 = mymodel
 VLEAFHOME = ../../..
 CONFIG += release
 CONFIG -= debug
 CONFIG += plugin
 BINDIR = $${VLEAFHOME}/bin
 LIBDIR = $${VLEAFHOME}/lib
 INCDIR = $${VLEAFHOME}/src
 DEFINES = QTGRAPHICS # VLEAFPLUGIN
 DESTDIR = $${BINDIR}/models
 HEADERS = $${TARGET}.h
 INCLUDEPATH += $${INCDIR}
 QMAKE_CXXFLAGS += -fexceptions #-I$${INCDIR}
 QMAKE_CXXFLAGS_DEBUG += -g3
 QMAKE_CXXFLAGS_DEBUG += -DQDEBUG
 QT += qt3support
 SOURCES = $${TARGET}.cpp
 TEMPLATE = lib
 unix {
  LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -fPIC -I/usr/include/libxml2
  QMAKE_LFLAGS += -fPIC
+}
 win32 {
  LIBXML2DIR = C:\libxml2
  LIBICONVDIR = C:\libiconv
  LIBZDIR = C:\libz
  LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -DLIBXML_STATIC
  QMAKE_CXXFLAGS += -I$${LIBXML2DIR}\include -I$${LIBICONVDIR}\include -I$${LIBZDIR}\include
+}
 # finish

src/TutorialCode/Tutorial5/mymodel.cpp

➞

Show inline comments

@@ new file 100644 @@
 /*
+ *
  *  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 "mymodel.h"
 static const std::string _module_id("$Id$");
 QString MyModel::ModelID(void) {
   // specify the name of your model here
   return QString( "Growth hormones" );
+}
 // return the number of chemicals your model uses
 int MyModel::NChem(void) { return 1; }
 // To be executed after cell division
 void MyModel::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) {
   // rules to be executed after cell division go here
   // (e.g., cell differentiation rules)
 	// set one cell to source after first division
 	if (CellBase::NCells()==2) {
 		daughter1->SetCellType(1);
 		daughter2->SetCellType(0);
+	}
 	// if a source cells has divided, one of the daughters becomes the new source
 	if (daughter1->CellType()==1) {
 		// if both cells are at the tissue perimeter, choose at random
 		if (daughter1->AtBoundaryP() && daughter2->AtBoundaryP()) {
 			if (qrand()%2){
 				daughter1->SetCellType(1);
 				daughter2->SetCellType(0);
 			} else {
 				daughter1->SetCellType(0);
 				daughter2->SetCellType(1);
+			}
 		} else {
 			// otherwise choose the one that is still at the perimeter
 			if (daughter1->AtBoundaryP()) {
 				daughter1->SetCellType(1);
 				daughter2->SetCellType(0);
 			} else {
 				daughter1->SetCellType(0);
 				daughter2->SetCellType(1);
+			}
+		}
+	}
+}
 void MyModel::SetCellColor(CellBase *c, QColor *color) {
   // add cell coloring rules here
 	// white: high concentration of growth hormone, black low concentration
 	double val = c->Chemical(0)/(1.+c->Chemical(0));
 	color->setRgbF(val, val, val);
+}
 void MyModel::CellHouseKeeping(CellBase *c) {
   // add cell behavioral rules here
 	if (CellBase::NCells()==1)
 		// first cell expands unconditionally
 		c->EnlargeTargetArea(par->cell_expansion_rate);
 	else
 		c->EnlargeTargetArea(c->Chemical(0)*par->cell_expansion_rate);
 	if (c->Area() > par->rel_cell_div_threshold * c->BaseArea()) {
 		c->Divide();
+	}
+}
 void MyModel::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) {
   // add biochemical transport rules here
 	double phi = w->Length() * par->D[0] * ( w->C2()->Chemical(0) - w->C1()->Chemical(0) );
 	dchem_c1[0]+=phi;
 	dchem_c2[0]-=phi;
+}
 void MyModel::WallDynamics(Wall *w, double *dw1, double *dw2) {
   // add biochemical networks for reactions occuring at walls here
+}
 void MyModel::CellDynamics(CellBase *c, double *dchem) {
   // add biochemical networks for intracellular reactions here
 	if (c->CellType()==1) {
 		dchem[0] = par->leaf_tip_source;
+	}
+}
 Q_EXPORT_PLUGIN2(mymodel, MyModel)

src/TutorialCode/Tutorial5/mymodel.h

➞

Show inline comments

@@ new file 100644 @@
 /*
  *  $Id$
+ *
  *  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.
+ *
  */
 #include <QObject>
 #include <QtGui>
 #include <QString>
 #include "simplugin.h"
 class MyModel : 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);
 };

src/TutorialCode/Tutorial5/mymodel.pro

➞

Show inline comments

@@ new file 100644 @@
+#
 # $Id$
+#
 #  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 = mymodel
 VLEAFHOME = ../../..
 CONFIG += release
 CONFIG -= debug
 CONFIG += plugin
 BINDIR = $${VLEAFHOME}/bin
 LIBDIR = $${VLEAFHOME}/lib
 INCDIR = $${VLEAFHOME}/src
 DEFINES = QTGRAPHICS # VLEAFPLUGIN
 DESTDIR = $${BINDIR}/models
 HEADERS = $${TARGET}.h
 INCLUDEPATH += $${INCDIR}
 QMAKE_CXXFLAGS += -fexceptions #-I$${INCDIR}
 QMAKE_CXXFLAGS_DEBUG += -g3
 QMAKE_CXXFLAGS_DEBUG += -DQDEBUG
 QT += qt3support
 SOURCES = $${TARGET}.cpp
 TEMPLATE = lib
 unix {
  LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -fPIC -I/usr/include/libxml2
  QMAKE_LFLAGS += -fPIC
+}
 win32 {
  LIBXML2DIR = C:\libxml2
  LIBICONVDIR = C:\libiconv
  LIBZDIR = C:\libz
  LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -DLIBXML_STATIC
  QMAKE_CXXFLAGS += -I$${LIBXML2DIR}\include -I$${LIBICONVDIR}\include -I$${LIBZDIR}\include
+}
 # finish

src/VirtualLeafpar.tmpl

➞

Show inline comments

@@ @@ -8,7 +8,7 @@ nodenumsize = 1 / int @@
 node_mag = 1.0 / double
 outlinewidth = 1.0 / double
 cell_outline_color = forestgreen / string
-resize_stride = 10 / int
+resize_stride = 0 / int
 label = / label
 label = <b>Cell mechanics</b> / label
 T = 1.0 / double

src/build_models/auxingrowthplugin.cpp

➞

Show inline comments

@@ @@ -37,23 +37,23 @@ bool batch = false; @@
 // To be executed after cell division
-void AuxinGrowthPlugin::OnDivide(ParentInfo &parent_info, CellBase &daughter1, CellBase &daughter2) {
+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 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));
 	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]);
 	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.);
 		w->setTransporter(daughter1, 1, 0.);
+	}
 	//daughter1.LoopWalls(Wall::setTransporter(&daughter1, 1, 0.));
@@ @@ -68,29 +68,29 @@ void AuxinGrowthPlugin::OnDivide(ParentI @@
 	*/
+}
-void AuxinGrowthPlugin::SetCellColor(CellBase &c, QColor &color) {
+void AuxinGrowthPlugin::SetCellColor(CellBase *c, QColor *color) {
 	// Red: PIN1
 	// Green: Auxin
 	if (c.CellType()==1) color = QColor("Blue");
 	else color.setRgb(c.Chemical(1)/(1+c.Chemical(1)) * 255.,(c.Chemical(0)/(1+c.Chemical(0)) * 255.),/* (chem[2]/(1+chem[2]) *255.) */ 0);
 	if (c->CellType()==1) color->setNamedColor("Blue");
 	else color->setRgb(c->Chemical(1)/(1+c->Chemical(1)) * 255.,(c->Chemical(0)/(1+c->Chemical(0)) * 255.),/* (chem[2]/(1+chem[2]) *255.) */ 0);
+}
-void AuxinGrowthPlugin::CellHouseKeeping(CellBase &c) {
+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();
 	if (c->Boundary()==CellBase::None) {
 		if (c->Area() > par->rel_cell_div_threshold * c->BaseArea() ) {
 			c->SetChemical(0,0);
 			c->Divide();
+        }
 		if (c.Chemical(0)>0.6) {
 			c.SetCellType(1);
 		if (c->Chemical(0)>0.6) {
 			c->SetCellType(1);
+		}
 		// 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);
+   		c->EnlargeTargetArea(par->auxin_dependent_growth?(c->Chemical(0)/(1.+c->Chemical(0)))*par->cell_expansion_rate:par->cell_expansion_rate);
+	}
@@ @@ -241,15 +241,15 @@ void AuxinGrowthPlugin::WallDynamics(Wal @@
     dw2[1] = dPijdt2;
+}
-double AuxinGrowthPlugin::complex_PijAj(CellBase &here, CellBase &nb, Wall &w) {
+double AuxinGrowthPlugin::complex_PijAj(CellBase *here, CellBase *nb, Wall *w) {
 	// 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 nb_aux = (nb.BoundaryPolP() && w.AuxinSink()) ? par->sam_auxin : nb.Chemical(0);
+	double nb_aux = (nb->BoundaryPolP() && w->AuxinSink()) ? par->sam_auxin : nb->Chemical(0);
 	double receptor_level = nb_aux * par->r / (par->kr + nb_aux);
-	return here.Chemical(1) * receptor_level / ( par->km + here.Chemical(1));
+	return here->Chemical(1) * receptor_level / ( par->km + here->Chemical(1));
+}

src/build_models/auxingrowthplugin.h

➞

Show inline comments

@@ @@ -37,7 +37,7 @@ public: @@
 	virtual QString ModelID(void) { return QString( "Auxin accumulation and growth" ); }
 	// Executed after the cellular mechanics steps have equillibrized
-	virtual void CellHouseKeeping (CellBase &c);
+	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);
@@ @@ -49,15 +49,15 @@ public: @@
 	virtual void CellDynamics(CellBase *c, double *dchem);
 	// to be executed after a cell division
-	virtual void OnDivide(ParentInfo &parent_info, CellBase &daughter1, CellBase &daughter2);
+	virtual void OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2);
 	// to be executed for coloring a cell
-	virtual void SetCellColor(CellBase &c, QColor &color);
+	virtual void SetCellColor(CellBase *c, QColor *color);
 	// return number of chemicals
 	virtual int NChem(void) { return 2; }
 private:
-	double complex_PijAj(CellBase &here, CellBase &nb, Wall &w);
+	double complex_PijAj(CellBase *here, CellBase *nb, Wall *w);
 };
 #endif

src/build_models/meinhardtplugin.cpp

➞

Show inline comments

@@ @@ -21,7 +21,7 @@ @@
 #include <QObject>
 #include <QtGui>
 #include "simplugin.h"
+#include "../simplugin.h"
 #include "parameter.h"
 #include "warning.h"
@@ @@ -34,24 +34,24 @@ static const std::string _module_id("$Id @@
 bool batch = false;
 // To be executed after cell division
-void MeinhardtPlugin::OnDivide(ParentInfo &parent_info, CellBase &daughter1, CellBase &daughter2) {
+void MeinhardtPlugin::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) {
+}
-void MeinhardtPlugin::SetCellColor(CellBase &c, QColor &color) {
+void MeinhardtPlugin::SetCellColor(CellBase *c, QColor *color) {
-	if (fpclassify(c.Chemical(0))==FP_NAN) {
+	if (fpclassify(c->Chemical(0))==FP_NAN) {
 		// somehow the function isnan doesn't work properly on my system... SuSE Linux
 		// 10.0 64-bits (isnan seems not be implemented using fpclassify).
 		MyWarning::warning("Whoops! Numerical instability!!");
-		color.setNamedColor("red");
+		color->setNamedColor("red");
 	} else {
 		double range_min = 0.;//, range_max = 1.;
-		if (c.Chemical(0)<range_min) {
+		if (c->Chemical(0)<range_min) {
 			MyWarning::warning("Whoops! Numerical instability!!");
-			color.setNamedColor("blue");
+			color->setNamedColor("blue");
 		} else {
-			color.setRgb(c.Chemical(1)/(1+c.Chemical(1)) * 255.,(c.Chemical(0)/(1+c.Chemical(0)) * 255.),(c.Chemical(3)/(1+c.Chemical(3)) *255.) );
+			color->setRgb(c->Chemical(1)/(1+c->Chemical(1)) * 255.,(c->Chemical(0)/(1+c->Chemical(0)) * 255.),(c->Chemical(3)/(1+c->Chemical(3)) *255.) );
+		}
+	}
@@ @@ -59,21 +59,21 @@ void MeinhardtPlugin::SetCellColor(CellB @@
-void MeinhardtPlugin::CellHouseKeeping(CellBase &c) {
+void MeinhardtPlugin::CellHouseKeeping(CellBase *c) {
 	if (c.Area() > par->rel_cell_div_threshold * c.BaseArea() ) {
 		c.Divide();
 	if (c->Area() > par->rel_cell_div_threshold * c->BaseArea() ) {
 		c->Divide();
+	}
     // cell expansion is inhibited by substrate (chem 3)
 	if (!par->constituous_expansion_limit || c.NCells()<par->constituous_expansion_limit) {
 		c.EnlargeTargetArea(par->cell_expansion_rate );
 	if (!par->constituous_expansion_limit || c->NCells()<par->constituous_expansion_limit) {
 		c->EnlargeTargetArea(par->cell_expansion_rate );
 	} else {
-		if (c.Chemical(0)<0.5) {
+		if (c->Chemical(0)<0.5) {
 			double tmp;
-			c.EnlargeTargetArea((tmp=(1.-par->vessel_inh_level*c.Chemical(3))*par->cell_expansion_rate /* + c.Chemical(4)*/)<0?0:tmp);
+			c->EnlargeTargetArea((tmp=(1.-par->vessel_inh_level*c->Chemical(3))*par->cell_expansion_rate /* + c->Chemical(4)*/)<0?0:tmp);
 		} else {
-			c.EnlargeTargetArea(par->vessel_expansion_rate);
+			c->EnlargeTargetArea(par->vessel_expansion_rate);
+		}
+	}

src/build_models/meinhardtplugin.h

➞

Show inline comments

@@ @@ -26,7 +26,7 @@ @@
 #include <QObject>
 #include <QtGui>
 #include <QString>
 #include "simplugin.h"
+#include "../simplugin.h"
 class MeinhardtPlugin : public QObject, SimPluginInterface {
@@ @@ -37,7 +37,7 @@ public: @@
 	virtual QString ModelID(void) { return QString( "Meinhardt 1976, with growth" ); }
 	// Executed after the cellular mechanics steps have equillibrized
-	virtual void CellHouseKeeping (CellBase &c);
+	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);
@@ @@ -49,10 +49,10 @@ public: @@
 	virtual void CellDynamics(CellBase *c, double *dchem);
 	// to be executed after a cell division
-	virtual void OnDivide(ParentInfo &parent_info, CellBase &daughter1, CellBase &daughter2);
+	virtual void OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2);
 	// to be executed for coloring a cell
-	virtual void SetCellColor(CellBase &c, QColor &color);
+	virtual void SetCellColor(CellBase *c, QColor *color);
 	// return number of chemicals
 	virtual int NChem(void) { return 4; }
 };

src/build_models/plugin_auxingrowth.pro

➞

Show inline comments

@@ @@ -24,6 +24,7 @@ CONFIG -= debug @@
 CONFIG += plugin
 BINDIR = ../../bin
 LIBDIR = ../../lib
 DEFINES = QTGRAPHICS # VLEAFPLUGIN
 DESTDIR = $${BINDIR}/models
 TARGET = auxingrowth
@@ @@ -37,7 +38,7 @@ SOURCES = $${TARGET}plugin.cpp @@
 TEMPLATE = lib
 unix {
- LIBS += -Llib -lvleaf
+ LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -fPIC -I/usr/include/libxml2
  QMAKE_LFLAGS += -fPIC
+}
@@ @@ -46,7 +47,7 @@ win32 { @@
  LIBXML2DIR = C:\libxml2
  LIBICONVDIR = C:\libiconv
  LIBZDIR = C:\libz
  LIBS += -Llib -lvleaf
+ LIBS += -L$${LIBDIR} -Llib -lvleaf
  QMAKE_CXXFLAGS += -DLIBXML_STATIC
  QMAKE_CXXFLAGS += -I$${LIBXML2DIR}\include -I$${LIBICONVDIR}\include -I$${LIBZDIR}\include
+}

src/build_models/plugin_leaf.pro

➞

Show inline comments

@@ @@ -24,6 +24,7 @@ CONFIG -= debug @@
 CONFIG += plugin
 BINDIR = ../../bin
 LIBDIR = ../../lib
 DEFINES = QTGRAPHICS # VLEAFPLUGIN
 DESTDIR = $${BINDIR}/models
 TARGET = leaf
@@ @@ -37,7 +38,7 @@ SOURCES = $${TARGET}plugin.cpp @@
 TEMPLATE = lib
 unix {
- LIBS += -Llib -lvleaf
+ LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -fPIC -I/usr/include/libxml2
  QMAKE_LFLAGS += -fPIC
+}
@@ @@ -46,7 +47,7 @@ win32 { @@
  LIBXML2DIR = C:\libxml2
  LIBICONVDIR = C:\libiconv
  LIBZDIR = C:\libz
  LIBS += -Llib -lvleaf
+ LIBS += -L$${LIBDIR} -Llib -lvleaf
  QMAKE_CXXFLAGS += -DLIBXML_STATIC
  QMAKE_CXXFLAGS += -I$${LIBXML2DIR}\include -I$${LIBICONVDIR}\include -I$${LIBZDIR}\include
+}

src/build_models/plugin_meinhardt.pro

➞

Show inline comments

@@ @@ -24,6 +24,7 @@ CONFIG -= debug @@
 CONFIG += plugin
 BINDIR = ../../bin
 LIBDIR = ../../lib
 DEFINES = QTGRAPHICS # VLEAFPLUGIN
 DESTDIR = $${BINDIR}/models
 TARGET = meinhardt
@@ @@ -37,7 +38,7 @@ SOURCES = $${TARGET}plugin.cpp @@
 TEMPLATE = lib
 unix {
- LIBS += -Llib -lvleaf
+ LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -fPIC -I/usr/include/libxml2
  QMAKE_LFLAGS += -fPIC
+}
@@ @@ -46,7 +47,7 @@ win32 { @@
  LIBXML2DIR = C:\libxml2
  LIBICONVDIR = C:\libiconv
  LIBZDIR = C:\libz
  LIBS += -Llib -lvleaf
+ LIBS += -L$${LIBDIR} -Llib -lvleaf
  QMAKE_CXXFLAGS += -DLIBXML_STATIC
  QMAKE_CXXFLAGS += -I$${LIBXML2DIR}\include -I$${LIBICONVDIR}\include -I$${LIBZDIR}\include
+}

src/build_models/plugin_test.pro

➞

Show inline comments

@@ @@ -25,6 +25,7 @@ CONFIG -= debug @@
 CONFIG += plugin
 BINDIR = ../../bin
 LIBDIR = ../../lib
 DEFINES = QTGRAPHICS # VLEAFPLUGIN
 DESTDIR = $${BINDIR}/models
 TARGET = test
@@ @@ -38,7 +39,7 @@ SOURCES = $${TARGET}plugin.cpp @@
 TEMPLATE = lib
 unix {
- LIBS += -Llib -lvleaf
+ LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -fPIC -I/usr/include/libxml2
  QMAKE_LFLAGS += -fPIC
+}
@@ @@ -47,7 +48,7 @@ win32 { @@
  LIBXML2DIR = C:\libxml2
  LIBICONVDIR = C:\libiconv
  LIBZDIR = C:\libz
  LIBS += -Llib -lvleaf
+ LIBS += -L$${LIBDIR} -Llib -lvleaf
  QMAKE_CXXFLAGS += -DLIBXML_STATIC
  QMAKE_CXXFLAGS += -I$${LIBXML2DIR}\include -I$${LIBICONVDIR}\include -I$${LIBZDIR}\include

src/build_models/translate_plugin.pl

➞

Show inline comments

@@ new file 100755 @@
 #!/usr/bin/perl
 $cfilename = shift(@ARGV) || die "Usage: translate_plugin.pl [cfile] [hfile] [profile]\n";
 $hfilename = shift(@ARGV) || die "Usage: translate_plugin.pl [cfile] [hfile] [profile]\n";
 $pfilename = shift(@ARGV) || die "Usage: translate_plugin.pl [cfile] [hfile] [profile]\n";
 $ocfname = $cfilename; $ocfname =~ s/\.cpp/_tl.cpp/g;
 $ohfname = $hfilename; $ohfname =~ s/\.h/_tl.h/g;
 $opfname = $pfilename; $opfname =~ s/\.pro/_tl.pro/g;
 print STDERR "Translating '$cfilename' to '$ocfname', '$hfilename' to '$ohfname', and '$pfilename' to '$opfname'\n";
 open cfile,"<$cfilename";
 open ocfile,">$ocfname";
 while (<cfile>) {
 	#s/$hfilename/$ohfname/g;
 	# translate function definitions
 	if (/[a-zA-Z0-9 ]*::OnDivide/) {
 		s/ParentInfo &parent_info/ParentInfo *parent_info/g;
 		s/CellBase &daughter1/CellBase *daughter1/g;
 		s/CellBase &daughter2/CellBase *daughter2/g;
+	}
 	if (/[a-zA-Z0-9 ]*::SetCellColor/) {
 		s/CellBase &c/CellBase *c/g;
 		s/QColor &color/QColor *color/g;
+	}
 	if (/[a-zA-Z0-9 ]*::CellHouseKeeping/) {
 		s/CellBase &c/CellBase *c/g;
+	}
 	# translate member function calls
 	s/\bparent_info\b\./parent_info->/g;
 	s/\bdaughter1\b\./daughter1->/g;
 	s/\bdaughter2\b\./daughter2->/g;
 	s/\bc\b\./c->/g;
 	s/\bcolor\b\./color->/g;
 	print ocfile;
+}
 open hfile,"<$hfilename";
 open ohfile,">$ohfname";
 while (<hfile>) {
 	if (/[ \t]*virtual[ \t]+void[ \t]+CellHouseKeeping/) {
 		s/CellBase &c/CellBase *c/g;
+	}
 	if (/[ \t]*virtual[ \t]+void[ \t]+OnDivide/) {
 		s/ParentInfo &parent_info/ParentInfo *parent_info/g;
 		s/CellBase &daughter1/CellBase *daughter1/g;
 		s/CellBase &daughter2/CellBase *daughter2/g;
+	}
 	if (/[ \t]*virtual[ \t]+void[ \t]+SetCellColor/) {
 		s/CellBase &c/CellBase *c/g;
 		s/QColor &color/QColor *color/g;
+	}
 	print ohfile;
+}
 open pfile,"<$pfilename";
 open opfile,">$opfname";
 while (<pfile>) {
 	s/\bplugin\b\.h/plugin_tl\.h/g;
 	s/\bplugin\b\.cpp/plugin_tl\.cpp/g;
 	print opfile;
+}
@@ \ No newline at end of file @@

src/cell.cpp

➞

Show inline comments

@@ @@ -415,6 +415,7 @@ void Cell::DivideWalls(ItList new_node_l @@
 		daughter->chem[i]=chem[i];
+	}
 	daughter->cell_type = cell_type;
 	//extern double auxin_account;
 	//auxin_account += daughter->chem[0];
@@ @@ -1093,7 +1094,7 @@ void Cell::DivideWalls(ItList new_node_l @@
 	ConstructNeighborList();
 	daughter->ConstructNeighborList();
-	m->plugin->OnDivide(parent_info,*daughter, *this);
+	m->plugin->OnDivide(&parent_info, daughter, this);
 	// wall->OnWallInsert();
 	//daughter->OnDivide();
@@ @@ -1660,7 +1661,7 @@ void Cell::Draw(QGraphicsScene *c, QStri @@
 	QColor cell_color;
-	m->plugin->SetCellColor(*this,cell_color);
+	m->plugin->SetCellColor(this,&cell_color);
 	p->setPolygon(pa);
 	p->setPen(par.outlinewidth>=0?QPen( QColor(par.cell_outline_color),par.outlinewidth):QPen(Qt::NoPen));

src/cellbase.cpp

➞

Show inline comments

@@ @@ -101,6 +101,7 @@ Vector() @@
 	div_counter=0;
 	cell_type = 0;
 	flag_for_divide = false;
 	division_axis = 0;
+}
@@ @@ -140,6 +141,7 @@ CellBase::CellBase(double x,double y,dou @@
 	div_counter = 0;
 	cell_type = 0;
 	flag_for_divide = false;
 	division_axis = 0;
+}
@@ @@ -180,7 +182,7 @@ CellBase::CellBase(const CellBase &src) @@
 	cell_type = src.cell_type;
 	div_counter = src.div_counter;
 	flag_for_divide = src.flag_for_divide;
-	</i>
+	division_axis = src.division_axis;
+}
@@ @@ -219,6 +221,7 @@ CellBase CellBase::operator=(const CellB @@
 	cell_type = src.cell_type;
 	div_counter = src.div_counter;
 	flag_for_divide = src.flag_for_divide;
 	division_axis = src.division_axis;
 	return *this;
+}

src/cellbase.h

➞

Show inline comments

@@ @@ -96,6 +96,7 @@ class CellBase : public QObject, public @@
   virtual ~CellBase() {
 	  delete[] chem;
 	  delete[] new_chem;
 	  if (division_axis) delete division_axis;
 	  //cerr << "CellBase " << index << " is dying. " << endl;
+  }
@@ @@ -217,7 +218,13 @@ class CellBase : public QObject, public @@
 	inline void Divide(void) {
 		flag_for_divide = true;
+	}
     //Vector Strain(void) const;
 	inline void DivideOverAxis(const Vector &v) {
 		division_axis = new Vector(v);
 		flag_for_divide = true;
+	}
 	//Vector Strain(void) const;
     inline double Circumference(void) const {
       double sum=0.;
@@ @@ -324,9 +331,9 @@ class CellBase : public QObject, public @@
       for (list<Wall *>::const_iterator w=walls.begin();
 	   w!=walls.end();
 	   w++) {
 	sum += (*w)->c1 == this ?
 	  f( *((*w)->c1), *((*w)->c2), **w ) :
 	  f( *((*w)->c2), *((*w)->c1), **w );
 	sum += ((*w)->c1 == this) ?
 	  f( ((*w)->c1), ((*w)->c2), *w ) :
 	  f( ((*w)->c2), ((*w)->c1), *w );
+      }
       return sum;
+    }
@@ @@ -447,6 +454,8 @@ protected: @@
     bool dead;
 	bool flag_for_divide;
 	Vector *division_axis;
 	int cell_type;
     //double length;
@@ @@ -475,8 +484,8 @@ protected: @@
 ostream &operator<<(ostream &os, const CellBase &v);
 inline Vector PINdir(CellBase &here, CellBase &nb, Wall &w) {
 	return w.getTransporter( &here, 1)  *  w.getInfluxVector(&here);
 inline Vector PINdir(CellBase *here, CellBase *nb, Wall *w) {
 	return w->getTransporter( here, 1)  *  w->getInfluxVector(here);
+}

src/libplugin.pro

➞

Show inline comments

@@ @@ -29,7 +29,7 @@ QMAKE_CXXFLAGS_DEBUG += -DQDEBUG @@
 QMAKE_CXXFLAGS_DEBUG -= -finstrument-functions
 DEFINES = QTGRAPHICS # VLEAFPLUGIN
-DESTDIR = build_models/lib
+DESTDIR = ../lib
 PERLDIR = ./perl
 PARTMPL = VirtualLeafpar.tmpl
 QT += qt3support

src/mesh.cpp

➞

Show inline comments

@@ @@ -47,7 +47,7 @@ @@
 #include <iostream>
 #include <iterator>
 static const std::string _module_id("$Id$");
+static const std::string _module_id("$Id: mesh.cpp,v 79f94eaa3b9e 2010/04/14 07:51:02 michael $");
 extern Parameter par;
@@ @@ -1983,9 +1983,21 @@ void Mesh::Derivatives(double *derivs) { @@
    // (*wr)(*w, &(derivs[i]), &(derivs[i+nchems]));
 	  plugin->WallDynamics(*w,  &(derivs[i]), &(derivs[i+nchems]));
     // Transport function adds to derivatives of cell chemicals
 	  plugin->CelltoCellTransport(*w, &(derivs[(*w)->c1->Index() * nchems]),
 								  &(derivs[(*w)->c2->Index() * nchems]));
 	  double *dchem_c1 = &(derivs[(*w)->c1->Index() * nchems]);
 	  double *dchem_c2 = &(derivs[(*w)->c2->Index() * nchems]);
 	  //plugin->CelltoCellTransport(*w, &(derivs[(*w)->c1->Index() * nchems]),
 							//	  &(derivs[(*w)->c2->Index() * nchems]));
 	  // quick fix: dummy values to prevent end user from writing into outer space and causing a crash :-)
 	  // start here if you want to implement chemical input/output into environment over boundaries
 	  double dummy1, dummy2;
 	  if ((*w)->c1->Index()<0) { // tests if c1 is the boundary pol
 		  dchem_c1 = &dummy1;
+	  }
 	  if ((*w)->c2->Index()<0) {
 		  dchem_c2 = &dummy2;
+	  }
 	  plugin->CelltoCellTransport(*w, dchem_c1, dchem_c2);
 	  //(*tf)(*w, &(derivs[(*w)->c1->Index() * nchems]),
       //&(derivs[(*w)->c2->Index() * nchems] ) );
     i+=2*nchems;

src/mesh.h

➞

Show inline comments

@@ @@ -238,11 +238,17 @@ public: @@
 		for (vector<Cell *>::iterator i = current_cells.begin();
 			 i != current_cells.end();
 			 i ++) {
-			plugin->CellHouseKeeping(**i);
 			plugin->CellHouseKeeping(*i);
 			// Call functions of Cell that cannot be called from CellBase, including Division
 			if ((*i)->flag_for_divide) {
 				(*i)->Divide();
 				if ((*i)->division_axis) {
 					(*i)->DivideOverAxis(*(*i)->division_axis);
 					delete (*i)->division_axis;
 					(*i)->division_axis = 0;
 				} else {
 					(*i)->Divide();
+				}
 				(*i)->flag_for_divide=false;
+			}
+		}

src/modelcatalogue.cpp

➞

Show inline comments

@@ @@ -68,9 +68,13 @@ void ModelCatalogue::LoadPlugins() { @@
 			qobject_cast<SimPluginInterface *>(loader.instance())) {
 			models.append(plugin);
 		} else {
 			MyWarning::warning("Could not load plugin %s",fileName.toStdString().c_str());
 			cerr << loader.errorString().toStdString().c_str() << endl;
 			MyWarning::warning("Could not load model %s: %s",fileName.toStdString().c_str(), loader.errorString().toStdString().c_str());
+		}
+	}
 	if (models.size()==0) {
 		MyWarning::error("No models could be loaded.");
+	}
+}
 void ModelCatalogue::LoadPlugin(const char *model) {

src/simplugin.h

➞

Show inline comments

@@ @@ -44,7 +44,7 @@ public: @@
 	virtual ~SimPluginInterface() { }
 	// Executed after the cellular mechanics steps have equillibrized
-	virtual void CellHouseKeeping(CellBase &c) = 0;
+	virtual void CellHouseKeeping(CellBase *c) = 0;
 	// Differential equations describing transport of chemicals from cell to cell
 	virtual void CelltoCellTransport(Wall *, double *dchem_c1, double *dchem_c2) = 0;
@@ @@ -57,10 +57,10 @@ public: @@
 	virtual void CellDynamics(CellBase *c, double *dchem) = 0;
 	// to be executed after a cell division
-	virtual void OnDivide(ParentInfo &parent_info, CellBase &daughter1, CellBase &daughter2) = 0;
+	virtual void OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) = 0;
 	// to be executed for coloring a cell
-	virtual void SetCellColor(CellBase &c, QColor &color) = 0;
+	virtual void SetCellColor(CellBase *c, QColor *color) = 0;
 	// Number of chemicals
 	virtual int NChem(void) = 0;
@@ @@ -75,7 +75,7 @@ protected: @@
 };
 Q_DECLARE_INTERFACE(SimPluginInterface,
-                    "nl.cwi.VirtualLeaf.SimPluginInterface/1.1")
+                    "nl.cwi.VirtualLeaf.SimPluginInterface/1.2")
 Q_DECLARE_METATYPE(SimPluginInterface *)

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