EI/VirtualLeaf Changeset - 15d600891648 · Centrum Wiskunde & Informatica (CWI)

Changeset - 15d600891648

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! ! !

Michael Guravage - 15 years ago 2010-06-24 15:22:58
michael.guravage@cwi.nl

In DrawCell class (VirtualLeaf.cpp) - iterate over NChem to construct info_string. Additional cleanup.

--
user: Michael Guravage <michael.guravage@cwi.nl>
branch 'default'
changed src/ChangeLog
changed src/Neighbor.cpp
changed src/Neighbor.h
changed src/OptionFileDialog.cpp
changed src/OptionFileDialog.h
changed src/UniqueMessage.cpp
changed src/UniqueMessage.h
changed src/VirtualLeaf.cpp
changed src/VirtualLeaf.pro
changed src/build_models/plugin_auxingrowth.pro
changed src/build_models/plugin_meinhardt.pro
changed src/build_models/plugin_test.pro
changed src/canvas.cpp
changed src/canvas.h
changed src/cell.cpp
changed src/cell.h
changed src/cellbase.cpp
changed src/cellbase.h
changed src/cellitem.cpp
changed src/cellitem.h
changed src/forwardeuler.cpp
changed src/forwardeuler.h
changed src/infobar.h
changed src/libplugin.pro
changed src/mainbase.cpp
changed src/mainbase.h
changed src/matrix.cpp
changed src/matrix.h
changed src/mesh.cpp
changed src/mesh.h
changed src/miscq.cpp
changed src/miscq.h
changed src/modelcatalogue.cpp
changed src/modelcatalogue.h
changed src/node.cpp
changed src/node.h
changed src/nodeitem.cpp
changed src/nodeitem.h
changed src/nodeset.cpp
changed src/nodeset.h
changed src/output.cpp
changed src/output.h
changed src/parameter.cpp
changed src/parameter.h
changed src/pardialog.cpp
changed src/parse.cpp
changed src/parse.h
changed src/pi.h
changed src/qcanvasarrow.h
changed src/random.cpp
changed src/random.h
changed src/rungekutta.cpp
changed src/rungekutta.h
changed src/simitembase.cpp
changed src/simitembase.h
changed src/simplugin.h
changed src/sqr.h
changed src/tiny.h
changed src/transporterdialog.cpp
changed src/transporterdialog.h
changed src/vector.cpp
changed src/vector.h
changed src/wall.cpp
changed src/wall.h
changed src/wallbase.cpp
changed src/wallbase.h
changed src/wallitem.cpp
changed src/wallitem.h
changed src/warning.cpp
changed src/warning.h
changed src/xmlwrite.cpp
changed src/xmlwrite.h

72 files changed with 231 insertions and 289 deletions:

src/ChangeLog

src/Neighbor.cpp

src/Neighbor.h

src/OptionFileDialog.cpp

src/OptionFileDialog.h

src/UniqueMessage.cpp

src/UniqueMessage.h

src/VirtualLeaf.cpp

src/VirtualLeaf.pro

src/build_models/plugin_auxingrowth.pro

src/build_models/plugin_meinhardt.pro

src/build_models/plugin_test.pro

src/canvas.cpp

src/canvas.h

src/cell.cpp

src/cell.h

src/cellbase.cpp

src/cellbase.h

src/cellitem.cpp

src/cellitem.h

src/forwardeuler.cpp

src/forwardeuler.h

src/infobar.h

src/libplugin.pro

src/mainbase.cpp

src/mainbase.h

src/matrix.cpp

src/matrix.h

src/mesh.cpp

src/mesh.h

src/miscq.cpp

src/miscq.h

src/modelcatalogue.cpp

src/modelcatalogue.h

src/node.cpp

src/node.h

src/nodeitem.cpp

src/nodeitem.h

src/nodeset.cpp

src/nodeset.h

src/output.cpp

src/output.h

src/parameter.cpp

src/parameter.h

src/pardialog.cpp

src/parse.cpp

src/parse.h

src/pi.h

src/qcanvasarrow.h

src/random.cpp

src/random.h

src/rungekutta.cpp

src/rungekutta.h

src/simitembase.cpp

src/simitembase.h

src/simplugin.h

src/sqr.h

src/tiny.h

src/transporterdialog.cpp

src/transporterdialog.h

src/vector.cpp

src/vector.h

src/wall.cpp

src/wall.h

src/wallbase.cpp

src/wallbase.h

src/wallitem.cpp

src/wallitem.h

src/warning.cpp

src/warning.h

src/xmlwrite.cpp

src/xmlwrite.h

0 comments (0 inline, 0 general)

src/ChangeLog

➞

Show inline comments

 -06-24    <guravage@caterpie.sen.cwi.nl>
 	* VirtualLeaf.cpp (DrawCell): Iterate over NChem to construct info_string.
 -06-23    <guravage@caterpie.sen.cwi.nl>
 	* simitembase.cpp: Removed NULL assignments to unused variables.
 	* VirtualLeaf.cpp: Ditto.
 	* apoplastitem.cpp: Ditto.
 	* canvas.cpp: Ditto.
 	* cell.cpp: Ditto.
 	* cellbase.h: Ditto.
 	* forwardeuler.cpp: Ditto.
 	* mainbase.h: Ditto.
 	* nodeitem.cpp: Ditto.
 	* qcanvasarrow.h: Ditto.
 	* simitembase.cpp: Ditto.
 	* Makefile (clean): Add -f Makefile argument to each make invocation.
 	* VirtualLeaf-install.nsi: New gpl license text.
 	* VirtualLeaf.pro: Disabled console mode.
 	* mesh.cpp (Clear): Added parentheses to qDebug statments.
 	(TestIllegalWalls): Replaced qDebug().

src/Neighbor.cpp

➞

Show inline comments

 /*
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 "Neighbor.h"
 #include "cell.h"
 #include <string>
 static const std::string _module_id("$Id$");
 Neighbor::Neighbor(void):
-  cell(NULL), nb1(NULL), nb2(NULL){}
+  cell(0), nb1(0), nb2(0){}
 Neighbor::Neighbor(Cell *c, Node *n1, Node *n2):
   cell(c), nb1(n1), nb2(n2){}
 Neighbor::Neighbor(const Neighbor &src):
   cell(src.cell), nb1(src.nb1), nb2(src.nb2){} // copy constructor
 bool Neighbor::CellEquals(int i) const { return cell->Index() == i; }
 bool Neighbor::Cmp(Neighbor &c) const { return cell->Index() < c.cell->Index(); } // Compare cell indices not pointers.
 bool Neighbor::Eq(Neighbor &c) const { return cell->Index() == c.cell->Index(); }
 Cell* Neighbor::getCell(void) const { return cell; }
 bool neighbor_cell_eq(const Neighbor &n1, const Neighbor &n2) {
   return (n1.getCell())->Index() == (n2.getCell())->Index(); // Compare cell indices not pointers.
+}
 /* finis */

src/Neighbor.h

➞

Show inline comments

 /*
+ *
  *  $Id$
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 _NEIGHBOR_H_
 #define _NEIGHBOR_H_
 #include <iostream>
 #include <libxml/parser.h>
 #include <libxml/tree.h>
 using namespace std;
 class Cell;
 class Node;

src/OptionFileDialog.cpp

➞

Show inline comments

 /*
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 <string>
 #include "OptionFileDialog.h"
 #include <QCheckBox>
 #include <iostream>
 using namespace  std;
 static const std::string _module_id("$Id$");
 OptionFileDialog::OptionFileDialog(QWidget *parent, const char *name, bool modal) : Q3FileDialog(parent, name, modal)
+{
   //cerr << "This is an OptionFileDialog\n";
   geometrycheck = new QCheckBox("geometry",this);
   geometrycheck -> setCheckState(Qt::Checked);

src/OptionFileDialog.h

➞

Show inline comments

 /*
  *  $Id$
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 _OPTIONFILEDIALOG_H_
 #define _OPTIONFILEDIALOG_H_
 #include <Q3FileDialog>
 #include <QCheckBox>
 class OptionFileDialog : public Q3FileDialog {
   Q_OBJECT
  public:
   OptionFileDialog(QWidget *parent = 0, const char *name = 0, bool modal = false);
   OptionFileDialog ( const QString & dirName, const QString & filter = QString(),
 		     QWidget * parent = 0, const char * name = 0, bool modal = false );

src/UniqueMessage.cpp

➞

Show inline comments

 /*
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 <string>
 #include <QMessageBox>
 #include <QCheckBox>
 #include <QPushButton>
 #include <QBoxLayout>
 #include "UniqueMessage.h"
 #include <iostream>
 static const std::string _module_id("$Id$");
 using namespace std;
 UniqueMessageBox::UniqueMessageBox ( /* Icon icon,*/

src/UniqueMessage.h

➞

Show inline comments

 /*
+ *
  *  $Id$
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 _UNIQUEMESSAGE_H_
 #define _UNIQUEMESSAGE_H_
 #include <QDialog>
 #include <QCheckBox>
 #include <QStringList>
 #include <QLabel>
 class UniqueMessageBox : public QDialog {
   Q_OBJECT
  public:

src/VirtualLeaf.cpp

➞

Show inline comments

 /*
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 <string>
 #include <fstream>
 #include <sstream>
 #include <cstring>
 #include <functional>
 #include <getopt.h>
 #include <cerrno>
 #include "mesh.h"
 #include "parameter.h"
 #include "random.h"
 #include "pi.h"
 #include "cellitem.h"
 #include "canvas.h"
@@ @@ -94,141 +94,147 @@ public: @@
 class CellInfo {
 public:
   void operator() (Cell &c,std::ostream &os) const {
     os << "Cell " << c.index << " says: " << endl;
     os << "c.nodes.size() = " << c.nodes.size() << endl;
     for (list<Node *>::iterator i=c.nodes.begin(); i!=c.nodes.end(); i++) {
       cerr << (*i)->Index() << " ";
+    }
     cerr << endl;
+  }
 };
 double PINSum(Cell &c) {
   return c.Chemical(1) + c.SumTransporters(1);// + c.ReduceCellAndWalls<double>( complex_PijAj );
+}
 class DrawCell {
 public:
   void operator() (Cell &c,QGraphicsScene &canvas, MainBase &m) const {
     if (m.ShowBorderCellsP() || c.Boundary()==Cell::None) {
       if (!m.ShowBoundaryOnlyP() && !m.HideCellsP()) {
 	if (m.ShowToolTipsP()) {
 	  QString info_string=QString("Cell %1, chemicals: ( %2, %3, %4, %5, %6)\n %7 of PIN1 at walls.\n Area is %8\n PIN sum is %9\n Circumference is %10\n Boundary type is %11").arg(c.Index()).arg(c.Chemical(0)).arg(c.Chemical(1)).arg(c.Chemical(2)).arg(c.Chemical(3)).arg(c.Chemical(4)).arg(c.SumTransporters(1)).arg(c.Area()).arg(PINSum(c)).arg(c.Circumference()).arg(c.BoundaryStr());
 	  info_string += "\n" + c.printednodelist();
 	  //QString info_string=QString("Cell %1, chemicals: ( %2, %3, %4, %5, %6)\n %7 of PIN1 at walls.\n Area is %8\n PIN sum is %9\n Circumference is %10\n Boundary type is %11").arg(c.Index()).arg(c.Chemical(0)).arg(c.Chemical(1)).arg(c.Chemical(2)).arg(c.Chemical(3)).arg(c.Chemical(4)).arg(c.SumTransporters(1)).arg(c.Area()).arg(PINSum(c)).arg(c.Circumference()).arg(c.BoundaryStr());
 		QString info_string=QString("Cell %1, chemicals(%2): ").arg(c.Index()).arg(Cell::NChem());
 		for (int i=0;i<Cell::NChem();i++) {
 			info_string += QString("%1 ").arg(c.Chemical(i));
+		}
 		info_string += QString("\nArea is %1\n Circumference is %2\n Boundary type is %3").arg(c.Area()).arg(c.Circumference()).arg(c.BoundaryStr());
 	  info_string += "\nNodes: " + c.printednodelist();
 	  c.Draw(&canvas, info_string);
 	} else {
 	  c.Draw(&canvas);
+	}
+      }
       if (m.ShowCentersP()){
 	c.DrawCenter(&canvas);
+      }
       if (m.ShowFluxesP()){
 	c.DrawFluxes(&canvas, par.arrowsize);
+      }
+    }
+  }
 };
 Mesh mesh;
 bool batch=false;
 void MainBase::Plot(int resize_stride)
+{
   clear();
   static int count=0;
   if (resize_stride) {
-    if ( !((++count)%resize_stride) ) {
     if ( !((count)%resize_stride) ) {
       FitLeafToCanvas();
+    }
+  }
   mesh.LoopCells(DrawCell(),canvas,*this);
   if (ShowNodeNumbersP())
     mesh.LoopNodes( bind2nd (mem_fun_ref ( &Node::DrawIndex), &canvas ) ) ;
   if (ShowCellNumbersP())
     mesh.LoopCells( bind2nd (mem_fun_ref ( &Cell::DrawIndex), &canvas ) ) ;
   if (ShowCellAxesP())
     mesh.LoopCells( bind2nd (mem_fun_ref ( &Cell::DrawAxis), &canvas ) );
   if (ShowCellStrainP())
     mesh.LoopCells( bind2nd (mem_fun_ref ( &Cell::DrawStrain), &canvas ) );
   if (ShowWallsP())
     mesh.LoopWalls( bind2nd( mem_fun_ref( &Wall::Draw ), &canvas ) );
   if (ShowApoplastsP())
+/*  if (ShowApoplastsP())
     mesh.LoopWalls( bind2nd( mem_fun_ref( &Wall::DrawApoplast ), &canvas ) );
+*/
   if (ShowMeshP())
     mesh.DrawNodes(&canvas);
   if (ShowBoundaryOnlyP())
     mesh.DrawBoundary(&canvas);
   if ( ( batch || MovieFramesP() )) {
     static int frame = 0;
     // frame numbers are sequential for the most frequently written file type.
     // for the less frequently written file type they match the other type
     if (!(count%par.storage_stride) )  {
       stringstream fname;
       fname << par.datadir << "/leaf.";
       fname.fill('0');
       fname.width(6);
       fname << frame << ".jpg";
       if (par.storage_stride <= par.xml_storage_stride) {
 	frame++;
+      }
       // Write high-res JPG snapshot every plot step
       Save(fname.str().c_str(), "JPEG",1024,768);
+    }
     if (!(count%par.xml_storage_stride)) {
       stringstream fname;
       fname << par.datadir << "/leaf.";
       fname.fill('0');
       fname.width(6);
       fname << frame << ".xml";
       if (par.xml_storage_stride < par.storage_stride) {
 	frame++;
+      }
       // Write XML file every ten plot steps
       mesh.XMLSave(fname.str().c_str(), XMLSettingsTree());
+    }
+  }
  count++;
+}
 INIT {
   //mesh.SetSimPlugin(plugin);
   if (leaffile) {
     xmlNode *settings;
     mesh.XMLRead(leaffile, &settings);
     main_window->XMLReadSettings(settings);
     xmlFree(settings);
     main_window->UserMessage(QString("Ready. Time is %1").arg(mesh.getTimeHours().c_str()));
   } else {
     mesh.StandardInit();
+  }
+}
 TIMESTEP {
   static int i=0;
   static int t=0;

src/VirtualLeaf.pro

➞

Show inline comments

@@ @@ -3,142 +3,143 @@ @@
+#
 #  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.
+#
 CONFIG += release
 CONFIG -= debug
 CONFIG += qt
 QMAKE_CXXFLAGS += -fexceptions
 QMAKE_CXXFLAGS += -Wall
 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
 BINDIR = ../bin
 DESTDIR = $$BINDIR
 TARGET = VirtualLeaf
 TEMPLATE = app
 PARTMPL = $${TARGET}par.tmpl
 MAINSRC = $${TARGET}.cpp
 QT -= network sql xml
 QT += qt3support
 !win32 {
  GRAPHICS = qt #qwt
+}
 win32 {
  CONFIG -= console
  LIBXML2DIR = ..\lib\libxml2
  LIBICONVDIR = ..\lib\libiconv
  LIBZDIR = ..\lib\libz
  LIBXML2DIR = C:
  LIBICONVDIR = C:
  LIBZDIR = C:
  GRAPHICS = qt
  RC_FILE = VirtualLeaf.rc
  QMAKE_CXXFLAGS += -DLIBXML_STATIC
+# QMAKE_CXXFLAGS += -DLIBXML_STATIC
  QMAKE_CXXFLAGS += -I$${LIBXML2DIR}\include -I$${LIBICONVDIR}\include -I$${LIBZDIR}\include
  LIBS += -L$${LIBXML2DIR}\lib -lxml2 -L$${LIBICONVDIR}\lib -L$${LIBZDIR}\lib  -lz -lm -lwsock32 -liconv
+}
 macx:release {
  LIBS+= -dead_strip
+}
 unix {
  CC = /usr/bin/gcc
  QWTDIR = /ufs/guravage/opt/qwt-5.2.1-svn
  QMAKE_LIBDIR += $$QWTDIR/lib
  QMAKE_CXXFLAGS += -fPIC -I/usr/include/libxml2
  QMAKE_LFLAGS += -fPIC
  LIBS += -lxml2 -lz -lm
+}
 # Input
 HEADERS += \
  apoplastitem.h \
+# apoplastitem.h \
  canvas.h \
  cellbase.h \
  cell.h \
  cellitem.h \
  forwardeuler.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 \
+# apoplastitem.cpp \
  canvas.cpp \
  cellbase.cpp \
  cell.cpp \
  cellitem.cpp \
  forwardeuler.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 \

src/build_models/plugin_auxingrowth.pro

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Show inline comments

@@ @@ -23,33 +23,33 @@ CONFIG += release @@
 CONFIG -= debug
 CONFIG += plugin
 BINDIR = ../../bin
 LIBDIR = ../../lib
 DEFINES = QTGRAPHICS # VLEAFPLUGIN
 DESTDIR = $${BINDIR}/models
 TARGET = auxingrowth
 HEADERS = ../simplugin.h $${TARGET}plugin.h
 QMAKE_CXXFLAGS += -fexceptions -I..
 QMAKE_CXXFLAGS_DEBUG += -g3
 QMAKE_CXXFLAGS_DEBUG += -DQDEBUG
 QT += qt3support
 SOURCES = $${TARGET}plugin.cpp
 TEMPLATE = lib
 unix {
  LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -fPIC -I/usr/include/libxml2
  QMAKE_LFLAGS += -fPIC
+}
 win32 {
  LIBXML2DIR = ..\..\lib\libxml2
  LIBICONVDIR = ..\..\lib\libiconv
  LIBZDIR = ..\..\lib\libz
  LIBXML2DIR = $${LIBDIR}\lib\libxml2
  LIBICONVDIR = $${LIBDIR}\lib\libiconv
  LIBZDIR = $${LIBDIR}\lib\libz
  LIBS += -L$${LIBDIR} -Llib -lvleaf
  QMAKE_CXXFLAGS += -DLIBXML_STATIC
  QMAKE_CXXFLAGS += -I$${LIBXML2DIR}\include -I$${LIBICONVDIR}\include -I$${LIBZDIR}\include
+}
 # finis

src/build_models/plugin_meinhardt.pro

➞

Show inline comments

@@ @@ -23,34 +23,34 @@ CONFIG += release @@
 CONFIG -= debug
 CONFIG += plugin
 BINDIR = ../../bin
 LIBDIR = ../../lib
 DEFINES = QTGRAPHICS # VLEAFPLUGIN
 DESTDIR = $${BINDIR}/models
 TARGET = meinhardt
 HEADERS = ../simplugin.h $${TARGET}plugin.h
 QMAKE_CXXFLAGS += -fexceptions -I..
 QMAKE_CXXFLAGS_DEBUG += -g3
 QMAKE_CXXFLAGS_DEBUG += -DQDEBUG
 QT += qt3support
 SOURCES = $${TARGET}plugin.cpp
 TEMPLATE = lib
 unix {
  LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -fPIC -I/usr/include/libxml2
  QMAKE_LFLAGS += -fPIC
+}
 win32 {
  LIBXML2DIR = ..\..\lib\libxml2
  LIBICONVDIR = ..\..\lib\libiconv
  LIBZDIR = ..\..\lib\libz
  LIBXML2DIR = $${LIBDIR}\lib\libxml2
  LIBICONVDIR = $${LIBDIR}\lib\libiconv
  LIBZDIR = $${LIBDIR}\lib\libz
  LIBS += -L$${LIBDIR} -Llib -lvleaf
  QMAKE_CXXFLAGS += -DLIBXML_STATIC
  QMAKE_CXXFLAGS += -I$${LIBXML2DIR}\include -I$${LIBICONVDIR}\include -I$${LIBZDIR}\include
+}
 # finis

src/build_models/plugin_test.pro

➞

Show inline comments

@@ @@ -23,34 +23,34 @@ CONFIG += release @@
 CONFIG -= debug
 CONFIG += plugin
 BINDIR = ../../bin
 LIBDIR = ../../lib
 DEFINES = QTGRAPHICS # VLEAFPLUGIN
 DESTDIR = $${BINDIR}/models
 TARGET = test
 HEADERS = ../simplugin.h $${TARGET}plugin.h
 QMAKE_CXXFLAGS += -fexceptions -I..
 QMAKE_CXXFLAGS_DEBUG += -g3
 QMAKE_CXXFLAGS_DEBUG += -DQDEBUG
 QT += qt3support
 SOURCES = $${TARGET}plugin.cpp
 TEMPLATE = lib
 unix {
  LIBS += -L$${LIBDIR} -lvleaf
  QMAKE_CXXFLAGS += -fPIC -I/usr/include/libxml2
  QMAKE_LFLAGS += -fPIC
+}
 win32 {
  LIBXML2DIR = ..\..\lib\libxml2
  LIBICONVDIR = ..\..\lib\libiconv
  LIBZDIR = ..\..\lib\libz
  LIBXML2DIR = $${LIBDIR}\lib\libxml2
  LIBICONVDIR = $${LIBDIR}\lib\libiconv
  LIBZDIR = $${LIBDIR}\lib\libz
  LIBS += -L$${LIBDIR} -Llib -lvleaf
  QMAKE_CXXFLAGS += -DLIBXML_STATIC
  QMAKE_CXXFLAGS += -I$${LIBXML2DIR}\include -I$${LIBICONVDIR}\include -I$${LIBZDIR}\include
+}
 # finis

src/canvas.cpp

➞

Show inline comments

 /*
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 <string>
 #include <fstream>
 #include <streambuf>
 #include <QGraphicsScene>
 #include <QGraphicsView>
 #include <qdatetime.h>
 #include <q3mainwindow.h>
 #include <qstatusbar.h>
 #include <qmessagebox.h>
 #include <qmenubar.h>
 #include <qapplication.h>
 #include <qpainter.h>
 #include <qprinter.h>
@@ @@ -502,86 +502,87 @@ Main::Main(QGraphicsScene& c, Mesh &m, Q @@
   view = new Q3PopupMenu( menu );
   view->insertItem("&Zoom in", this, SLOT(zoomIn()), Qt::CTRL+Qt::Key_Equal);
   view->insertItem("Zoom &out", this, SLOT(zoomOut()), Qt::CTRL+Qt::Key_Minus);
   view->insertSeparator();
   com_id = view->insertItem("Show cell &centers", this, SLOT(toggleShowCellCenters()));
   view->setItemChecked(com_id, FALSE);
   mesh_id = view->insertItem("Show &nodes", this, SLOT(toggleShowNodes()), Qt::CTRL+Qt::SHIFT+Qt::Key_N);
   view->setItemChecked(mesh_id, TRUE);
   node_number_id = view->insertItem("Show node numbers", this, SLOT(toggleNodeNumbers()), Qt::CTRL+Qt::SHIFT+Qt::Key_M);
   view->setItemChecked(node_number_id, FALSE);
   cell_number_id = view->insertItem("Show cell numbers", this, SLOT(toggleCellNumbers()));
   view->setItemChecked(cell_number_id, FALSE);
   hide_cells_id = view->insertItem("Hide cells", this, SLOT(toggleHideCells()));
   view->setItemChecked(hide_cells_id, FALSE);
   border_id = view->insertItem("Show &border cells", this, SLOT(toggleShowBorderCells()));
   view->setItemChecked(border_id, FALSE);
   cell_axes_id = view->insertItem("Show cell &axes", this, SLOT(toggleCellAxes()));
   cell_strain_id = view->insertItem("Show cell &strain", this, SLOT(toggleCellStrain()));
   view->setItemChecked(cell_axes_id, FALSE);
   fluxes_id = view->insertItem("Show &fluxes", this, SLOT(toggleShowFluxes()));
   view->setItemChecked(fluxes_id, FALSE);
   cell_walls_id = view->insertItem("Show transporters", this, SLOT(toggleShowWalls()));
   view->setItemChecked(cell_walls_id, FALSE);
   apoplasts_id = view->insertItem("Show apoplasts", this, SLOT(toggleShowApoplasts()));
   view->setItemChecked(apoplasts_id, FALSE);
  // apoplasts_id = view->insertItem("Show apoplasts", this, SLOT(toggleShowApoplasts()));
  // view->setItemChecked(apoplasts_id, FALSE);
   view->insertSeparator();
   only_boundary_id = view->insertItem("Show only leaf &boundary", this, SLOT(toggleLeafBoundary()));
   view->insertSeparator();
   movie_frames_id = view->insertItem("Start saving movie &frames", this, SLOT(toggleMovieFrames()));
   view->setItemChecked(movie_frames_id, par.movie);
   view->setItemChecked(only_boundary_id, FALSE);
   menu->insertItem("&View", view);
   options = new Q3PopupMenu( menu );
   dyn_cells_id = options->insertItem("Cell growth", this, SLOT(toggleDynCells()));
   options->setItemChecked(dyn_cells_id, true);
   options->insertItem("Edit &parameters", this, SLOT(EditParameters()), Qt::CTRL+Qt::Key_E);
   rotation_mode_id = options->insertItem("Rotate leaf", this, SLOT(EnterRotationMode()), Qt::CTRL + Qt::SHIFT + Qt::Key_R);
   options->setItemChecked(rotation_mode_id, false);
   menu->insertItem("&Options",options);
   // Menu of models
   modelmenu = new QMenu( menu );
   menu->insertItem("&Models", modelmenu);
   menu->insertSeparator();
   helpmenu = new Q3PopupMenu( menu );
   tooltips_id = helpmenu->insertItem("Show Cell&Info", this, SLOT(Refresh()));
   helpmenu->setItemChecked(tooltips_id, true);
   helpmenu->insertSeparator();
   helpmenu->insertItem("&About", this, SLOT(about()) ); //, Key_F1);
   helpmenu->insertSeparator();
     //helpmenu->insertSeparator();
   helpmenu->insertItem("&LICENSE", this, SLOT(gpl()) );
   menu->insertItem("&Help",helpmenu);
   helpmenu->insertItem("About", this, SLOT(about()) ); //, Key_F1);
 	menu->insertItem("&Help",helpmenu);
   statusBar();
   setCentralWidget(editor);
   printer = 0;
   init();
   // Start timer which repetitively invokes
   // a simulation time step
   timer = new QTimer( this );
   connect( timer, SIGNAL(timeout()), SLOT(TimeStepWrap()) );
   stopSimulation();
   statusBar()->addWidget(new QLabel("Ready."));
   setCaption(caption);
   gifanim = 0;
   infobar = new InfoBar();
   addDockWindow(infobar);
+}
 void Main::RefreshInfoBar(void)
+{
   infobar->SetText(mesh.ModelID());
+}
@@ @@ -907,58 +908,58 @@ void Main::readStateXML() @@
+  }
   QString fileName;
   if ( fd->exec() == QDialog::Accepted ) {
     fileName = fd->selectedFile();
     if (working_dir) {
       delete working_dir;
+    }
     working_dir = fd->dir();
     if (readStateXML((const char *)fileName,fd->readGeometryP(), fd->readParametersP()) )
       return readStateXML(); // user can try again
+  }
+}
 void Main::clear()
+{
   editor->clear();
+}
 void Main::about()
+{
   static QMessageBox* about = new QMessageBox
     ( "Virtual Leaf V1.0",
       "<h3>Virtual Leaf V1.0</h3>"
     ( "VirtualLeaf V1.0",
       "<h3>VirtualLeaf V1.0</h3>"
       "<p>"
       "An Open Source framework for cell-based modeling of plant tissue growth and development <br>"
       "(c) 2005-2008, Roeland Merks <i>et al.</i><br>"
       "    <a href=\"http://www.psb.vib-ugent.be\">VIB Department Plant Systems Biology</a>, "
       "Ghent, Belgium <br>"
       "(c) 2008-2010, <a href=\"http://www.cwi.nl/~merks\">Roeland Merks <i>et al.</i></a> <br>"
       "    <a href=\"http://www.cwi.nl\">Centrum Wiskunde & Informatica</a> and <a href=\"http://www.ncsb.nl\">Netherlands Consortium for Systems Biology</a>, Amsterdam, Netherlands <br>"
-"<br>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.<br>"
+"<br>VirtualLeaf 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.<br>"
       "<br>If you use this code for your projects, please cite our paper:"
 "<br>Merks, Guravage, Inze, and Beemster. An Open Source framework for cell-based modeling of plant tissue growth and development. <i>Plant Physiology,</i> submitted.<br> . <br>"
       "<br>Please share your model plugins and extensions at <a href=\"http://virtualleaf.googlecode.com\">http://virtualleaf.googlecode.com</a>.",
       QMessageBox::Information, 1, 0, 0, this, 0, FALSE );
   about->setButtonText( 1, "Dismiss" );
   about->show();
+}
 void Main::gpl()
+{
   static QMessageBox* gpl = new QMessageBox ( "GPL License", "",
       QMessageBox::Information, 1, 0, 0, this, 0, FALSE );
   QDir docDir(QApplication::applicationDirPath());
   docDir.cd("../doc");
   QString path = docDir.filePath("gpl3.txt");
   std::ifstream file(path.toStdString().c_str());
   std::string str;
   if (file) {
     file.seekg(0, std::ios::end);
     str.reserve(file.tellg());
@@ @@ -1303,54 +1304,54 @@ void Main::RandomizeMesh(void) @@
   mesh.RandomizeChemicals(max_chem, max_transporters);
   Plot();
+}
 void Main::XMLReadSettings(xmlNode *settings)
+{
   MainBase::XMLReadSettings(settings);
   view->setItemChecked(com_id, showcentersp);
   view->setItemChecked(mesh_id, showmeshp);
   view->setItemChecked(border_id, showbordercellp);
   view->setItemChecked(node_number_id, shownodenumbersp);
   view->setItemChecked(cell_number_id, showcellnumbersp);
   view->setItemChecked(cell_axes_id, showcellsaxesp);
   view->setItemChecked(cell_strain_id, showcellstrainp);
   view->setItemChecked(movie_frames_id, movieframesp);
   view->setItemChecked(only_boundary_id, showboundaryonlyp);
   view->setItemChecked(fluxes_id, showfluxesp);
   view->setItemChecked(hide_cells_id, hidecellsp);
   options->setItemChecked(dyn_cells_id, dynamicscellsp);
   view->setItemChecked( cell_walls_id, showwallsp);
   view->setItemChecked( apoplasts_id, showapoplastsp);
+ // view->setItemChecked( apoplasts_id, showapoplastsp);
   editor->setTransform(viewport);
+}
 xmlNode *Main::XMLSettingsTree(void)
+{
   showcentersp = view->isItemChecked(com_id);
   showmeshp = view->isItemChecked(mesh_id);
   showbordercellp =  view->isItemChecked(border_id);
   shownodenumbersp =  view->isItemChecked(node_number_id);
   showcellnumbersp =  view->isItemChecked(cell_number_id);
   showcellsaxesp = view->isItemChecked( cell_axes_id );
   showcellstrainp = view->isItemChecked( cell_strain_id );
   movieframesp = view->isItemChecked(movie_frames_id);;
   showboundaryonlyp =  view->isItemChecked(only_boundary_id);
   showfluxesp = view->isItemChecked(fluxes_id);
   dynamicscellsp = options->isItemChecked(dyn_cells_id);
   showwallsp = view->isItemChecked( cell_walls_id);
   showapoplastsp = view->isItemChecked( apoplasts_id);
+  //showapoplastsp = view->isItemChecked( apoplasts_id);
   hidecellsp = view->isItemChecked( hide_cells_id);
   xmlNode *settings = MainBase::XMLSettingsTree();
   QTransform viewport(editor->transform());
   xmlAddChild(settings, XMLViewportTree(viewport));
   return settings;
+}
 /* finis */

src/canvas.h

➞

Show inline comments

 /*
+ *
  *  $Id$
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 _CANVAS_H_
 #define _CANVAS_H_
 #include <q3popupmenu.h>
 #include <q3mainwindow.h>
 #include <q3intdict.h>
 #include <QGraphicsScene>
 #include <QGraphicsView>
 #include <QList>
 #include <string>
 #include <sstream>
@@ @@ -99,49 +99,49 @@ class FigureEditor : public QGraphicsVie @@
   QGraphicsLineItem *intersection_line;
   bool rotation_mode;
   bool insert_mode;
   double rot_angle;
 };
 class Main : public Q3MainWindow, public MainBase {
   Q_OBJECT
     friend class ModelCatalogue; // needs to populate menu item models
  public:
   Main(QGraphicsScene&, Mesh&, QWidget* parent=0, const char* name=0, Qt::WFlags f=0);
   ~Main();
   virtual bool ShowCentersP(void) {return view->isItemChecked(com_id);}
   virtual bool ShowMeshP(void) {return view->isItemChecked(mesh_id);}
   virtual bool ShowBorderCellsP(void) {return view->isItemChecked(border_id);}
   virtual bool PausedP(void) {return run->isItemChecked(paused_id);}
   virtual bool ShowNodeNumbersP(void) {return view->isItemChecked(node_number_id);}
   virtual bool ShowCellNumbersP(void) {return view->isItemChecked(cell_number_id);}
   virtual bool ShowCellAxesP(void) {return view->isItemChecked(cell_axes_id);}
   virtual bool ShowCellStrainP(void) {return view->isItemChecked(cell_strain_id);}
   virtual bool MovieFramesP(void) {return view->isItemChecked(movie_frames_id);}
   virtual bool ShowBoundaryOnlyP(void) {return view->isItemChecked(only_boundary_id);}
   virtual bool ShowWallsP(void) {return view->isItemChecked(cell_walls_id);}
   virtual bool ShowApoplastsP(void) { return view->isItemChecked(apoplasts_id);}
+ // virtual bool ShowApoplastsP(void) { return view->isItemChecked(apoplasts_id);}
   virtual bool ShowFluxesP(void) { return view->isItemChecked(fluxes_id); }
   virtual bool DynamicCellsP(void) { return options->isItemChecked(dyn_cells_id); }
   virtual bool RotationModeP(void) { return options->isItemChecked(rotation_mode_id); }
   virtual bool InsertModeP(void) { return options->isItemChecked(insert_mode_id); }
   virtual bool ShowToolTipsP(void) { return helpmenu->isItemChecked(tooltips_id); }
   virtual bool HideCellsP(void) { return view->isItemChecked(hide_cells_id); }
   void scale(double factor);
   virtual double getFluxArrowsize(void)
+  {
     return flux_arrow_size;
+  }
   void FitCanvasToWindow();
   void FitLeafToCanvas(void);
   public slots:
   void about();
   void gpl();
   void TimeStepWrap();
   void togglePaused();
   void setFluxArrowSize(int size);
   void RestartSim(void);
@@ @@ -235,45 +235,45 @@ class Main : public Q3MainWindow, public @@
  private:
   NodeSet *node_set;
   FigureEditor *editor;
   Q3PopupMenu* options;
   Q3PopupMenu *view;
   Q3PopupMenu *run;
   QMenu *modelmenu;
   Q3PopupMenu *helpmenu;
   QPrinter* printer;
   const QDir *working_dir;
   QString currentFile;
   //  toggle item states
   int dbf_id; // options->Double Buffer
   int com_id; // view->Show centers
   int mesh_id; // view->Show mesh
   int node_number_id; // view->Show Node numbers
   int cell_number_id; // view->Show Cell numbers
   int border_id; // view->Show border cells
   int paused_id; // run->Simulation paused
   int cell_axes_id; // view->Show cell axes
   int cell_strain_id; // view->Show cell strain
   int only_boundary_id; // view ->Show only leaf boundary
   int cell_walls_id; // view -> Show transporters
   int apoplasts_id; // view -> Show apoplasts
+  //int apoplasts_id; // view -> Show apoplasts
   int tooltips_id; // help -> Show Cell Info
   int hide_cells_id; // view->Hide Cells
   double flux_arrow_size;
   int movie_frames_id;
   int fluxes_id;
   int dyn_cells_id;
   int rotation_mode_id;
   int insert_mode_id;
   QTimer *timer;
   QFile *gifanim;
   bool running;
   virtual xmlNode *XMLSettingsTree(void);
   static const QString caption;
   static const QString caption_with_file;
   InfoBar *infobar;
 };
 #endif
 /* finis*/

src/cell.cpp

➞

Show inline comments

 /*
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 <QDebug>
 #include <string>
 #include "cell.h"
 #include "node.h"
 #include "mesh.h"
 #include "tiny.h"
 #include "nodeset.h"
 #include "cellitem.h"
 #include "nodeitem.h"
 #include "qcanvasarrow.h"
 #include "parameter.h"

src/cell.h

➞

Show inline comments

 /*
+ *
  *  $Id$
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 _CELL_H_
 #define _CELL_H_
 #include <list>
 #include <vector>
 #include <iostream>
 #include <QString>
 #include "vector.h"
 #include "parameter.h"
 #include "wall.h"
 #include "warning.h"
 #include "cellbase.h"
 #include "cell.h"

src/cellbase.cpp

➞

Show inline comments

 /*
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 <cmath>
 #include <string>
 #include <sstream>
 #include <vector>
 #include <algorithm>
 #include <functional>
 #ifdef QTGRAPHICS
 #include <QGraphicsScene>
 #include <qpainter.h>
 #include <qcolor.h>
 #include <qfont.h>
 #include <qwidget.h>
 //Added by qt3to4:
@@ @@ -115,49 +115,49 @@ CellBase::CellBase(double x,double y,dou @@
   boundary=None;
   area=0.;
   target_area=1;
   target_length=0; //par.target_length;
   lambda_celllength=0; // par.lambda_celllength;
   index=(NCells()++);
   intgrl_xx=0.; intgrl_xy=0.; intgrl_yy=0.;
   intgrl_x=0.; intgrl_y=0.;
   source = false;
   fixed = false;
   at_boundary=false;
   pin_fixed = false;
   stiffness = 0;
   marked=false;
   dead  = false;
   div_counter = 0;
   cell_type = 0;
   flag_for_divide = false;
   division_axis = 0;
+}
-CellBase::CellBase(const CellBase &src) :  Vector(src), QObject()
+CellBase::CellBase(const CellBase &src) :  QObject(), Vector(src)
+{
   chem=new double[NChem()];
   for (int i=0;i<NChem();i++) {
     chem[i]=src.chem[i];
+  }
   new_chem=new double[NChem()];
   for (int i=0;i<NChem();i++) {
     new_chem[i]=src.new_chem[i];
+  }
   boundary=src.boundary;
   area=src.area;
   target_length=src.target_length;
   lambda_celllength=src.lambda_celllength;
   intgrl_xx=src.intgrl_xx; intgrl_xy=src.intgrl_xy; intgrl_yy=src.intgrl_yy;
   intgrl_x=src.intgrl_x; intgrl_y=src.intgrl_y;
   target_area=src.target_area;
   index=src.index;
   nodes=src.nodes;
   neighbors=src.neighbors;
   walls=src.walls;
   source = src.source;

src/cellbase.h

➞

Show inline comments

 /*
+ *
  *  $Id$
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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.
+ *
  */
 // CellBase derives from Vector, where Vector is simply used as a Vertex
 #ifndef _CELLBASE_H_
 #define _CELLBASE_H_
 #include <list>
 #include <vector>
 #include <iostream>
 #include <QString>
 #include <QDebug>
 #include "vector.h"
 #include "parameter.h"
 #include "wall.h"
 #include "warning.h"
 #include "assert.h"
 extern Parameter par;
 using namespace std;
 class Mesh;
 class Node;
 class CellBase;
 class NodeSet;
 struct ParentInfo {
   Vector polarization;
   double PINmembrane;
   double PINendosome;
 };
 // We need a little trick here, to make sure the plugin and the main application will see the same static datamembers
 // otherwise each have their own instantation.
-// My solution is as follow. I collect all original statics in a class. The main application instantiates it and
+// My solution is as follows. I collect all original statics in a class. The main application instantiates it and
 // has a static pointer to it. After loading the plugin I set a static pointer to the same class
 class CellsStaticDatamembers {
  public:
   CellsStaticDatamembers(void) {
     ncells = 0;
     nchem = 0;
     base_area = 0.;
+  }
   ~CellsStaticDatamembers() {
 #ifdef QDEBUG
     qDebug() << "Oops! Desctructor of CellsStaticDatamembers called" << endl;
 #endif
+  }
   int ncells;
   int nchem;
   double base_area;
 };
 class CellBase :  public QObject, public Vector
+{
   Q_OBJECT

src/cellitem.cpp

➞

Show inline comments

 /*
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 <string>
 #include<QGraphicsScene>
 #include "cellitem.h"
 static const std::string _module_id("$Id$");
 CellItem::CellItem( Cell *c, QGraphicsScene *canvas )
   : QGraphicsPolygonItem( 0, canvas ), SimItemBase( c, canvas){
+}
 void CellItem::userMove(double dx, double dy)
+{
   QGraphicsPolygonItem::moveBy( dx, dy );

src/cellitem.h

➞

Show inline comments

 /*
  *  VirtualLeaf
+ *
  *  $Id$
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 _CELLITEM_H_
 #define _CELLITEM_H_
 #include <QGraphicsScene>
 #include <QGraphicsPolygonItem>
 #include <QPainter>
 #include "simitembase.h"
 #include "cell.h"
 class CellItem : public QGraphicsPolygonItem, public SimItemBase
+{
  public:

src/forwardeuler.cpp

➞

Show inline comments

 /*
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 <cmath>
 #include <iostream>
 #include "forwardeuler.h"
 #include "warning.h"
 #include "maxmin.h"
 #include <string>
 using namespace std;
 static const string _module_id("$Id$");
 // The value Errcon equals (5/Safety) raised to the power (1/PGrow), see use below.

src/forwardeuler.h

➞

Show inline comments

 /*
  *  VirtualLeaf
+ *
  *  $Id$
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 _FORWARDEULER_H_
 #define _FORWARDEULER_H_
 class ForwardEuler  {
  public:
   ForwardEuler(void) {
     kmax=kount=0;
     dxsav=0.;
     xp=0;
     yp=0;
+  }

src/infobar.h

➞

Show inline comments

 /*
+ *
  *  $Id$
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 _INFOBAR_H_
 #define _INFOBAR_H_
 #include <q3mainwindow.h>
 #include <QLabel>
 #include <QBoxLayout>
 class InfoBar : public Q3DockWindow {
   Q_OBJECT
     public:
   InfoBar(void) : Q3DockWindow() {
     virtleaf = new QLabel();
     SetText("undefined");
     setHorizontalStretchable(true);
     boxLayout()->addStretch();
     boxLayout()->addWidget(virtleaf);//, Qt::AlignHCenter);
     boxLayout()->addStretch();
+  }
   void SetText(QString text) {
-    virtleaf->setText(QString("<h1>The Virtual Leaf</h1>\n<center><b>Model:</b> <i>%1</i></center>").arg(text));
+    virtleaf->setText(QString("<h1>VirtualLeaf</h1>\n<center><b>Model:</b> <i>%1</i></center>").arg(text));
+  }
  private:
   QLabel *virtleaf;
 };
 #endif
 /* finis */

src/libplugin.pro

➞

Show inline comments

@@ @@ -3,76 +3,77 @@ @@
+#
 #  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.
+#
 CONFIG += release
 CONFIG -= debug
 CONFIG += staticlib
 QMAKE_CXXFLAGS += -fexceptions
 win32:QMAKE_CXXFLAGS -= O2
 QMAKE_CXXFLAGS_DEBUG += -g3
 QMAKE_CXXFLAGS_DEBUG += -DQDEBUG
 QMAKE_CXXFLAGS_DEBUG -= -finstrument-functions
 DEFINES = QTGRAPHICS # VLEAFPLUGIN
 DESTDIR = ../lib
 PARTMPL = VirtualLeafpar.tmpl
 QT += qt3support
 TARGET = vleaf
 TEMPLATE = lib
 HEADERS = \
  cellbase.h \
  matrix.h \
  output.h \
  parameter.h \
  parse.h \
  random.h \
  simplugin.h \
  UniqueMessage.h \
  vector.h \
  wallbase.h \
  warning.h
 SOURCES = \
  cellbase.cpp \
  matrix.cpp \
  output.cpp \
  parameter.cpp \
  parse.cpp \
  random.cpp \
  simplugin.cpp \
  UniqueMessage.cpp \
  vector.cpp \
  wallbase.cpp \
  warning.cpp
 unix {
  QMAKE_CXXFLAGS += -fPIC -I/usr/include/libxml2
  QMAKE_LFLAGS += -fPIC
  LIBS += -lxml2 -lz -lm
+}
 win32 {
  LIBXML2DIR = ..\lib\libxml2
  LIBICONVDIR = ..\lib\libiconv
  LIBZDIR = ..\lib\libz
  QMAKE_CXXFLAGS += -DLIBXML_STATIC
  LIBXML2DIR = C:
  LIBICONVDIR = C:
  LIBZDIR = C:
 # QMAKE_CXXFLAGS += -DLIBXML_STATIC
  QMAKE_CXXFLAGS += -I$${LIBXML2DIR}\include -I$${LIBICONVDIR}\include -I$${LIBZDIR}\include
+}
+#

src/mainbase.cpp

➞

Show inline comments

 /*
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 <libxml/xpath.h>
 #include <libxml/xmlreader.h>
 #include "mainbase.h"
 #include "xmlwrite.h"
 #include <sstream>
 #include <string>
 #include <QLocale>
 static const std::string _module_id("$Id$");
@@ @@ -95,55 +95,55 @@ xmlNode *MainBase::XMLSettingsTree(void) @@
     text << bool_name(showcellsaxesp);
     xmlNewProp(xmloption, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmloption = xmlNewChild(xmlsettings, NULL, BAD_CAST "setting", NULL);
     xmlNewProp(xmloption, BAD_CAST "name", BAD_CAST "show_cell_strain");
     ostringstream text;
     text << bool_name(showcellstrainp);
     xmlNewProp(xmloption, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmloption = xmlNewChild(xmlsettings, NULL, BAD_CAST "setting", NULL);
     xmlNewProp(xmloption, BAD_CAST "name", BAD_CAST "show_fluxes");
     ostringstream text;
     text << bool_name(showfluxesp);
     xmlNewProp(xmloption, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmloption = xmlNewChild(xmlsettings, NULL, BAD_CAST "setting", NULL);
     xmlNewProp(xmloption, BAD_CAST "name", BAD_CAST "show_walls");
     ostringstream text;
     text << bool_name(showwallsp);
     xmlNewProp(xmloption, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
+ /* {
     xmlNode *xmloption = xmlNewChild(xmlsettings, NULL, BAD_CAST "setting", NULL);
     xmlNewProp(xmloption, BAD_CAST "name", BAD_CAST "show_apoplasts");
     ostringstream text;
     text << bool_name(showapoplastsp);
     xmlNewProp(xmloption, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  }*/
+  {
     xmlNode *xmloption = xmlNewChild(xmlsettings, NULL, BAD_CAST "setting", NULL);
     xmlNewProp(xmloption, BAD_CAST "name", BAD_CAST "save_movie_frames");
     ostringstream text;
     text << bool_name(movieframesp);
     xmlNewProp(xmloption, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmloption = xmlNewChild(xmlsettings, NULL, BAD_CAST "setting", NULL);
     xmlNewProp(xmloption, BAD_CAST "name", BAD_CAST "show_only_leaf_boundary");
     ostringstream text;
     text << bool_name(showboundaryonlyp);
     xmlNewProp(xmloption, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmloption = xmlNewChild(xmlsettings, NULL, BAD_CAST "setting", NULL);
     xmlNewProp(xmloption, BAD_CAST "name", BAD_CAST "cell_growth");
     ostringstream text;
     text << bool_name(dynamicscellsp);
     xmlNewProp(xmloption, BAD_CAST "val", BAD_CAST text.str().c_str());
+  }
+  {
     xmlNode *xmloption = xmlNewChild(xmlsettings, NULL, BAD_CAST "setting", NULL);
     xmlNewProp(xmloption, BAD_CAST "name", BAD_CAST "hide_cells");
@@ @@ -271,51 +271,51 @@ void MainBase::XMLReadSettings(xmlNode * @@
       if (!xmlStrcmp(name, (const xmlChar *)"show_nodes")) {
 	showmeshp = strtobool( (const char *)val );
+      }
       if (!xmlStrcmp(name, (const xmlChar *)"show_node_numbers")) {
 	shownodenumbersp = strtobool( (const char *)val );
+      }
       if (!xmlStrcmp(name, (const xmlChar *)"show_cell_numbers")) {
 	showcellnumbersp = strtobool( (const char *)val );
+      }
       if (!xmlStrcmp(name, (const xmlChar *)"show_border_cells")) {
 	showbordercellp = strtobool( (const char *)val );
+      }
       if (!xmlStrcmp(name, (const xmlChar *)"show_cell_axes")) {
 	showcellsaxesp = strtobool( (const char *)val );
+      }
       if (!xmlStrcmp(name, (const xmlChar *)"show_cell_strain")) {
 	showcellstrainp = strtobool( (const char *)val );
+      }
       if (!xmlStrcmp(name, (const xmlChar *)"show_fluxes")) {
 	showfluxesp = strtobool( (const char *)val );
+      }
       if (!xmlStrcmp(name, (const xmlChar *)"show_walls")) {
 	showwallsp = strtobool( (const char *)val );
+      }
       if (!xmlStrcmp(name, (const xmlChar *)"show_apoplasts")) {
+     /* if (!xmlStrcmp(name, (const xmlChar *)"show_apoplasts")) {
 	showapoplastsp = strtobool( (const char *)val );
+      }
+      }*/
       if (!xmlStrcmp(name, (const xmlChar *)"save_movie_frames")) {
 	movieframesp = strtobool( (const char *)val );
+      }
       if (!xmlStrcmp(name, (const xmlChar *)"show_only_leaf_boundary")) {
 	showboundaryonlyp = strtobool( (const char *)val );
+      }
       if (!xmlStrcmp(name, (const xmlChar *)"cell_growth")) {
 	dynamicscellsp = strtobool( (const char *)val );
+      }
       if (!xmlStrcmp(name,(const xmlChar *)"hide_cells")) {
 	hidecellsp = strtobool( (const char *)val );
+      }
       xmlFree(name);
       xmlFree(val);
+    }
     cur=cur->next;
+  }
+}
 void MainBase::Save(const char *fname, const char *format, int sizex, int sizey)
+{

src/mainbase.h

➞

Show inline comments

 /*
+ *
  *  $Id$
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 _MAINBASE_H_
 #define _MAINBASE_H_
 #include <QGraphicsScene>
 #include <qpixmap.h>
 #include <q3picture.h>
 #include <qpainter.h>
 #include <qwidget.h>
 #include <iostream>
 #include <QGraphicsItem>
 #include <QPrinter>
 #include "mesh.h"
@@ @@ -56,85 +56,85 @@ class MainBase { @@
     showboundaryonlyp =  false;
     showwallsp =  false;
     showfluxesp = false;
     dynamicscellsp = true;
     showtooltipsp = false;
     hidecellsp = false;
+  }
   virtual ~MainBase() {};
   virtual double TimeStep();
   virtual void Init(char *leaffile=0);
   virtual bool ShowCentersP(void) {return showcentersp;}
   virtual bool ShowMeshP(void) {return showmeshp; }
   virtual bool ShowBorderCellsP(void) {return showbordercellp; }
   virtual bool PausedP(void) {return false; }
   virtual bool ShowNodeNumbersP(void) {return shownodenumbersp; }
   virtual bool ShowCellNumbersP(void) {return showcellnumbersp;}
   virtual bool ShowCellAxesP(void) {return showcellsaxesp;}
   virtual bool ShowCellStrainP(void) {return showcellstrainp;}
   virtual bool MovieFramesP(void) {return movieframesp;}
   virtual bool ShowBoundaryOnlyP(void) {return showboundaryonlyp;}
   virtual bool ShowToolTipsP(void) {return showtooltipsp;}
   virtual bool ShowWallsP(void) {return showwallsp;}
   virtual bool ShowApoplastsP(void) { return showapoplastsp;}
+ // virtual bool ShowApoplastsP(void) { return showapoplastsp;}
   virtual bool ShowFluxesP(void) { return showfluxesp; }
   virtual bool DynamicCellsP(void) { return dynamicscellsp; }
   virtual void FitCanvasToWindow() {};
   virtual void FitLeafToCanvas() {};
   virtual bool HideCellsP(void) { return hidecellsp; }
   virtual void clear(void) {
     QList<QGraphicsItem *> list = canvas.items();
     QList<QGraphicsItem *>::Iterator it = list.begin();
     for (; it != list.end(); ++it) {
       if ( *it )
 	delete *it;
+    }
   };
   virtual void XMLReadSettings(xmlNode *settings);
   virtual void XMLReadViewport(xmlNode *viewport);
   virtual double getFluxArrowsize(void) { return 10.;}
   void Save(const char *fname, const char *format, int sizex=640, int sizey=480);
   void CutSAM(void);
   void Plot(int resize_stride=10);
   virtual void UserMessage(QString message, int timeout = 0) {
     cerr << message.toAscii().constData() << endl;
+  }
   Mesh &mesh;
   QTransform viewport;
  protected:
   QGraphicsScene &canvas;
   virtual xmlNode *XMLSettingsTree(void) const;
   virtual xmlNode *XMLViewportTree(QTransform &transform) const;
  protected:
   bool showcentersp;
   bool showmeshp;
   bool showbordercellp;
   bool shownodenumbersp;
   bool showcellnumbersp;
   bool showcellsaxesp;
   bool showcellstrainp;
   bool movieframesp;
   bool showboundaryonlyp;
   bool showwallsp;
   bool showapoplastsp;
+//  bool showapoplastsp;
   bool showfluxesp;
   bool dynamicscellsp;
   bool showtooltipsp;
   bool hidecellsp;
 };
 //#include <qapplication.h>
 #define TIMESTEP double MainBase::TimeStep(void)
 #define INIT void MainBase::Init(char *leaffile)
 #endif
 /* finis */

src/matrix.cpp

➞

Show inline comments

 /*
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 <string>
 #include <ostream>
 #include <cmath>
 #include "vector.h"
 #include "matrix.h"
 #include "tiny.h"
 static const std::string _module_id("$Id$");
 Matrix::Matrix(const Vector &c1, const Vector &c2, const Vector &c3) {
   Alloc();

src/matrix.h

➞

Show inline comments

 /*
+ *
  *  $Id$
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 _MATRIX_H_
 #define _MATRIX_H_
 // three by three matrix (mostly for changes of basis of the vector object)
 class Vector;
 class Matrix {
  public:
   Matrix(const Vector &v1,const Vector &v2, const Vector &v3); // constructor
   Matrix(void);
   ~Matrix(); // destructor

src/mesh.cpp

➞

Show inline comments

 /*
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 <string>
 #include <algorithm>
 #include <vector>
 #include <sstream>
 #include <cstdlib>
 //#include <cerrno>
 #include <cstring>
 #include <numeric>
 #include <functional>
 #include <fstream>
 #include <QPair>
 #include "mesh.h"
 #include "tiny.h"
@@ @@ -459,61 +459,49 @@ void Mesh::Clear(void) { @@
   time = 0;
   // clear cells
   for (vector<Cell *>::iterator i=cells.begin(); i!=cells.end(); i++) {
     delete *i;
+  }
   cells.clear();
   Cell::NCells() = 0;
   delete boundary_polygon;
   // Clear walls
   for (list<Wall *>::iterator i=walls.begin(); i!=walls.end(); i++) {
     delete *i;
+  }
   walls.clear();
   WallBase::nwalls = 0;
   //tmp_walls->clear();
   shuffled_cells.clear();
   shuffled_nodes.clear();
   //Cell::ncells=0;
   /*    Cell::ClearNCells();
 	Node::nnodes=0;
 	cells.clear();
 	nodes.clear();
 	shuffled_cells.clear();
 	shuffled_nodes.clear();
 	node_insertion_queue.empty();
 	cerr << "Meshed cleared: cells: " << cells.size() << ", nodes: " << nodes.size() << endl;
   */
 #ifdef QDEBUG
   qDebug() << "cells.size() = " << cells.size() << endl;
   qDebug() << "walls.size() = " << walls.size() << endl;
   qDebug() << "nodes.size() = " << nodes.size() << endl;
 #endif
+}
 double Mesh::DisplaceNodes(void) {
   MyUrand r(shuffled_nodes.size());
   random_shuffle(shuffled_nodes.begin(),shuffled_nodes.end(),r);
   double sum_dh=0;
   list<DeltaIntgrl> delta_intgrl_list;
   for_each( node_sets.begin(), node_sets.end(), mem_fun( &NodeSet::ResetDone ) );
   for (vector<Node *>::const_iterator i=shuffled_nodes.begin(); i!=shuffled_nodes.end(); i++) {
     //int n=shuffled_nodes[*i];
     Node &node(**i);
     // Do not allow displacement if fixed
@@ @@ -543,66 +531,65 @@ double Mesh::DisplaceNodes(void) { @@
     if (node.node_set) {
       // move each node set only once
       if (!node.node_set->DoneP())
 	node.node_set->AttemptMove(rx,ry);
     } else {
       // for all cells to which this node belongs:
       //   calculate energy difference
       double area_dh=0.;
       double length_dh=0.;
       double bending_dh=0.;
       double cell_length_dh=0.;
       double alignment_dh=0.;
       double old_l1=0.,old_l2=0.,new_l1=0.,new_l2=0.;
       double sum_stiff=0.;
       double dh=0.;
       for (list<Neighbor>::const_iterator cit=node.owners.begin(); cit!=node.owners.end(); cit++) {
 	//Cell &c=m->getCell(cit->cell);
 	//Cell &c=cit->cell->BoundaryPolP()?*boundary_polygon:*(cit->cell);
 	Cell &c=*((Cell *)(cit->cell));
-	//Cell &c=cells[cit->cell];
 	if (c.MoveSelfIntersectsP(&node,  new_p )) {
 	  // reject if move results in self intersection
 	  //
 	  // I know: using goto's is bad practice... except when jumping out
 	  // of deeply nested loops :-)
 	  //cerr << "Rejecting due to self-intersection\n";
 	  goto next_node;
+	}
 	// summing stiffnesses of cells. Move has to overcome this minimum required energy.
 	sum_stiff += c.stiffness;
 	// area - (area after displacement): see notes for derivation
 	//Vector i_min_1 = m->getNode(cit->nb1);
 	Vector i_min_1 = *(cit->nb1);
 	//Vector i_plus_1 = m->getNode(cit->nb2);
 	Vector i_plus_1 = *(cit->nb2);
 	// We must double the weights for the perimeter (otherwise they start bulging...)
 	double w1, w2;
 	if (node.boundary && cit->nb1->boundary)
 #ifdef FLEMING
 	  w1 = par.rel_perimeter_stiffness;
 #else
 	w1=2;
 #endif
 	else
 	  w1 = 1;
 	if (node.boundary && cit->nb2->boundary)
 #ifdef FLEMING
 	  w2 = par.rel_perimeter_stiffness;
 #else
 	w2 = 2;
 #endif
 	else
 	  w2 = 1;
@@ @@ -756,143 +743,95 @@ double Mesh::DisplaceNodes(void) { @@
 	  } else {
 	    // if we have no length constraint, still need to update area
 	    delta_intgrl_list.push_back(DeltaIntgrl(delta_A,0,0,0,0,0));
+	  }
 	  old_l1=(old_p-i_min_1).Norm();
 	  old_l2=(old_p-i_plus_1).Norm();
 	  new_l1=(new_p-i_min_1).Norm();
 	  new_l2=(new_p-i_plus_1).Norm();
 	  static int count=0;
 	  // Insertion of nodes (cell wall yielding)
 	  if (!node.fixed) {
 	    if (old_l1 > 4*Node::target_length && !cit->nb1->fixed) {
 	      node_insertion_queue.push( Edge(cit->nb1, &node) );
+	    }
 	    if (old_l2 > 4*Node::target_length && !cit->nb2->fixed) {
 	      node_insertion_queue.push( Edge(&node, cit->nb2 ) );
+	    }
 	    count++;
 	    /*length_dh += 2*Node::target_length * (old_l1 + old_l2 - new_l1 - new_l2)
 	      + DSQR(new_l1) - DSQR(old_l1) + DSQR(new_l2) - DSQR(old_l2);*/
+	  }
 	  /* length_dh += 2*Node::target_length * ( w1*(old_l1 - new_l1) +
 	     w2*(old_l2 - new_l2) ) +
 	     w1*(DSQR(new_l1)
 	     - DSQR(old_l1))
 	     + w2*(DSQR(new_l2)
 	     - DSQR(old_l2)); */
 	  /*	if (c.cellvec.ManhattanNorm()!=0) {
 	  // wall element length constraint
 	  double old_aniso1, old_aniso2;
 	  double new_aniso1, new_aniso2;
 	  // anisotropic expansion?
 	  old_aniso1 = 1 + par.lambda_aniso*(1 - fabs(InnerProduct((old_p-i_min_1), c.cellvec))/old_l1);
 	  old_aniso2 = 1 + par.lambda_aniso*(1 - fabs(InnerProduct((old_p-i_plus_1), c.cellvec))/old_l2);
 	  new_aniso1 = 1 + par.lambda_aniso*(1 - fabs(InnerProduct((new_p-i_min_1),  c.cellvec))/new_l1);
 	  new_aniso2 = 1 + par.lambda_aniso*(1 - fabs(InnerProduct((new_p-i_plus_1), c.cellvec))/new_l2);
 	  length_dh += w1 * ( new_aniso1 * DSQR(new_l1 - Node::target_length) -
 	  old_aniso1 * DSQR(old_l1 - Node::target_length) )
 	  +  w2 * ( new_aniso2 * DSQR(new_l2 - Node::target_length) -
 	  old_aniso2 * DSQR(old_l2 - Node::target_length) );
 	  } else {
 	  */
 	  length_dh += 2*Node::target_length * ( w1*(old_l1 - new_l1) +
 						 w2*(old_l2 - new_l2) ) +
 	    w1*(DSQR(new_l1)
 		- DSQR(old_l1))
 	    + w2*(DSQR(new_l2)
 		  - DSQR(old_l2));
 	  //}
+	}
 	// bending energy also holds for outer boundary
 	// first implementation. Can probably be done more efficiently
 	// calculate circumcenter radius (gives local curvature)
 	// the ideal bending state is flat... (K=0)
 	// if (cit->cell==-1 && node.cells.size()>2 /* boundary_pol, cell and a second cell */)  {
+	{
+		  {
 	  // strong bending energy to resist "cleaving" by division planes
 	  double r1, r2, xc, yc;
 	  CircumCircle(i_min_1.x, i_min_1.y, old_p.x, old_p.y, i_plus_1.x, i_plus_1.y,
 		       &xc,&yc,&r1);
 	  CircumCircle(i_min_1.x, i_min_1.y, new_p.x, new_p.y, i_plus_1.x, i_plus_1.y,
 		       &xc,&yc, &r2);
 	  if (r1<0 || r2<0) {
 	    MyWarning::warning("r1 = %f, r2 = %f",r1,r2);
+	  }
 	  bending_dh += DSQR(1/r2 - 1/r1);
 	  //bending_dh += ( DSQR(1/r2) - DSQR(1/r1) );
 	  //cerr << "bending_dh = " << par.bend_lambda*bending_dh << endl;
+	}
 	/*cerr << "Bending = " <<  ( DSQR(1/r2) - DSQR(1/r1))  << endl;
 	  cerr << node.index << ": " << bending_dh << " (" << r1 << ", " << r2 << ") " << cit->nb1 << ", " << cit->nb2 << ")" << endl;
 	  }*/
 	/*else
 	  bending_dh += ( DSQR(1/r2) - DSQR(1/r1) );*/
 	/*if (cit->cell==-1) {
 	  cerr << node.index << ": " << bending_dh << " (" << r1 << ", " << r2 << ") " << cit->nb1 << ", " << cit->nb2 << ")" << endl;
 	  }*/
 	//bending_dh += r1 - r2;
+      }
       //const double bend_lambda = 100000;
       //const double bend_lambda = 0;
       /* double dh = //(area_dev_sum_after - area_dev_sum_before) +
 	 area_dh + par.lambda_celllength * cell_length_dh +
 	 par.lambda_length * length_dh + par.bend_lambda * bending_dh + par.alignment_lambda * alignment_dh;*/
       dh = //(area_dev_sum_after - area_dev_sum_before) +
 	area_dh + cell_length_dh +
       dh = 	area_dh + cell_length_dh +
 	par.lambda_length * length_dh + par.bend_lambda * bending_dh + par.alignment_lambda * alignment_dh;
       //cerr << "cell_length_dh = " << par.lambda_celllength * cell_length_dh << endl;
       //(length_constraint_after - length_constraint_before);
          //(length_constraint_after - length_constraint_before);
       if (node.fixed) {
 	// search the fixed cell to which this node belongs
 	// and displace these cells as a whole
 	// WARNING: undefined things will happen for connected fixed cells...
 	for (list<Neighbor>::iterator c=node.owners.begin(); c!=node.owners.end(); c++) {
 	  if (!c->cell->BoundaryPolP() && c->cell->FixedP()) {
 	    sum_dh+=c->cell->Displace(rx,ry,0);
+	  }
+	}
       } else {
 	if (dh<-sum_stiff || RANDOM()<exp((-dh-sum_stiff)/par.T)) {
 	  // update areas of cells
 	  list<DeltaIntgrl>::const_iterator di_it = delta_intgrl_list.begin();
 	  for (list<Neighbor>::iterator cit=node.owners.begin(); cit!=node.owners.end(); ( cit++) ) {
 	    if (!cit->cell->BoundaryPolP()) {
 	      cit->cell->area -= di_it->area;
 	      if (par.lambda_celllength) {
 		cit->cell->intgrl_x -= di_it->ix;
 		cit->cell->intgrl_y -= di_it->iy;
@@ @@ -992,50 +931,49 @@ void Mesh::InsertNode(Edge &e) { @@
        back_inserter(owners));
   //copy(owners.begin(), owners.end(), ostream_iterator<Neighbor>(cerr, " "));
   //cerr << endl;
   // sort the nodes
   owners.sort( mem_fun_ref( &Neighbor::Cmp ) );
   //  extern ofstream debug_stream;
   //  debug_stream << "Nodes " << e.first << " and " << e.second << endl;
   //  copy(owners.begin(), owners.end(), ostream_iterator<Neighbor>(debug_stream, " "));
   //  debug_stream << endl;
   // the duplicates in this list indicate cells owning this edge
   list<Neighbor>::iterator c=owners.begin();
   while (c!=owners.end()) {
     c=adjacent_find(c,owners.end(),  neighbor_cell_eq);
     if (c!=owners.end()) { // else break;
       //      debug_stream << "Cell " << c->cell << " owns Edge " << e << endl;
       //if (c->cell>=0) {
       //if (!c->cell->BoundaryPolP()) {
       // find the position of the edge's first node in cell c...
       list<Node *>::iterator ins_pos = find
 	(c->cell->nodes.begin(),
 	 c->cell->nodes.end(),
 	 e.first);
       // ... second node comes before or after it ...
       // XXXX probably this test is always false XXXX: No, works okay.
       if (*(++ins_pos!=c->cell->nodes.end()?
 	    ins_pos:c->cell->nodes.begin())!=e.second) {
 	c->cell->nodes.insert(((ins_pos--)!=c->cell->nodes.begin()?ins_pos:(--c->cell->nodes.end())), new_node);
 	//cells[c->cell].nodes.insert(--ins_pos, new_node->index);
 	// .. set the neighbors of the new node ...
 	// in this case e.second and e.first are inverted
 	//  cerr << "Inverted\n";
 	new_node->owners.push_back( Neighbor(c->cell, e.second, e.first ) );
       } else {
 	// insert before second node, so leave ins_pos as it is,
 	// that is incremented
 	c->cell->nodes.insert(ins_pos, new_node);
 	// .. set the neighbors of the new node ...
 	// cerr << "Not inverted\n";
 	new_node->owners.push_back( Neighbor(c->cell, e.first, e.second ) );
+      }
@@ @@ -1061,56 +999,56 @@ void Mesh::InsertNode(Edge &e) { @@
       // - same for Node e.second
       cpos=
 	find_if( e.second->owners.begin(),
 		 e.second->owners.end(),
 		 bind2nd( mem_fun_ref(&Neighbor::CellEquals), c->cell->Index()) );
       // - correct the record
       if (cpos->nb1 == e.first) {
 	cpos->nb1 = new_node;
       } else
 	if (cpos->nb2 == e.first) {
 	  cpos->nb2 = new_node;
+	}
     } else break;
     c++;
+  }
   // Repair neighborhood lists in a second loop, to make sure all
   // `administration' is up to date
   while (c!=owners.end()) {
     c=adjacent_find(c,owners.end(),  neighbor_cell_eq);
     // repair neighborhood lists of cell and Wall lists
-    //if (c->cell>=0) {
     if (!c->cell->BoundaryPolP()) {
       c->cell->ConstructNeighborList();
-      //      debug_stream << "Repairing NeighborList of " << c->cell << endl;
+    }
     c++;
+  }
-  //  debug_stream.flush();
+}
 /*
   Calculate circumcircle of triangle (x1,y1), (x2,y2), (x3,y3)
   The circumcircle centre is returned in (xc,yc) and the radius in r
   NOTE: A point on the edge is inside the circumcircle
 */
 void Mesh::CircumCircle(double x1,double y1,double x2,double y2,double x3,double y3,
 			double *xc,double *yc,double *r)
+{
   double m1,m2,mx1,mx2,my1,my2;
   double dx,dy,rsqr;
   /* Check for coincident points */
   /*if (abs(y1-y2) < TINY && abs(y2-y3) < TINY)
     return(false);*/
   if (abs(y2-y1) < TINY) {
     m2 = - (x3-x2) / (y3-y2);
     mx2 = (x2 + x3) / 2.0;
     my2 = (y2 + y3) / 2.0;
     *xc = (x2 + x1) / 2.0;
     *yc = m2 * (*xc - mx2) + my2;
@@ @@ -1457,49 +1395,49 @@ void Mesh::RepairBoundaryPolygon(void) { @@
   qDebug() << "NODES:" << endl;
   foreach(Node* node, nodes) {
     qDebug() << *node;
+  }
   qDebug() << endl;
   qDebug() << "WALLS:" << endl;
   foreach(Wall* wall, walls) {
     qDebug() << *wall;
+  }
   qDebug() << endl;
   qDebug() << "CELLS:" << endl;
   foreach(Cell* cell, cells) {
     qDebug() << *cell;
+  }
   qDebug() << endl;
 #endif
 #endif
+}
 Node* Mesh::findNextBoundaryNode(Node* boundary_node) {
   bool found_next_boundary_node = false;
-  Node *next_boundary_node = NULL;
+  Node *next_boundary_node = 0;
   set<int> boundary_node_owners; // This is a list of the current boundary node's owners' Ids
   vector<int> neighborIds; // A list of the current boundary node's owners' 2nd neighbor Ids
   vector<set<int> *>  nodeOwners; // A vector of set pointers where each set contains the owner Ids of the nodes in the neighborIds list.
   vector<int> intersection; // set intersection result
   // The next boundary node is that which has only one owner in common with the current boundary node
   for (list<Neighbor>::iterator it=boundary_node->owners.begin(); it!=boundary_node->owners.end(); ++it) {
     if (it->cell->Index() != -1) boundary_node_owners.insert(it->cell->Index()); // Save each of the current boundary node's owners' Ids - except the boundary polygon
     set<int> *owners = new set<int>; // create a set to hold a 2nd neighbor's owners' Ids
     nodeOwners.push_back(owners);
     neighborIds.push_back(it->nb2->Index());
     foreach(Neighbor neighbor, it->nb2->owners){
       if (neighbor.cell->Index() != -1) owners->insert(neighbor.cell->Index()); // Save second neighbors' owners' Ids - except the boundary polygon
+    }
+  }
   vector<int>::iterator itt = neighborIds.begin();
   vector<set<int> *>::iterator it = nodeOwners.begin();
 #ifdef QDEBUG
   qDebug() << "Boundary node: " <<  boundary_node->Index() << " is owned by the following cells: ";
   foreach (int i, boundary_node_owners){
     qDebug() << i << "  ";
+  }
   qDebug() << endl;
@@ @@ -1902,51 +1840,48 @@ double Mesh::CalcProtCellsWalls(int ch) @@
   // At membranes
   for (list<Wall *>::const_iterator w=walls.begin(); w!=walls.end(); w++) {
     sum_prot += (*w)->Transporters1(ch);
     sum_prot += (*w)->Transporters2(ch);
+  }
   // At cells
   for (vector<Cell *>::const_iterator c=cells.begin(); c!=cells.end(); c++) {
     sum_prot += (*c)->Chemical(ch);
+  }
   return sum_prot;
+}
 void Mesh::SettoInitVals(void) {
   vector<double> clean_chem(Cell::NChem());
   vector<double> clean_transporters(Cell::NChem());
   for (int i=0;i<Cell::NChem();i++) {
     clean_transporters[i]=0.;
     clean_chem[i]=par.initval[i];
+  }
   // Amount of PIN1
   //clean_chem[1] = 0.;
   CleanChemicals(clean_chem);
   CleanTransporters(clean_transporters);
+}
 string Mesh::getTimeHours(void) const {
   int hours = (int)(time / 3600);
   int mins = (int)((time - hours * 3600)/60);
   int secs = (int)((time - hours * 3600 - mins * 60));
   ostringstream tstr;
   tstr << hours << " h " << mins << " m " << secs << " s";
   return tstr.str();
+}
 QVector<qreal> Mesh::VertexAngles(void) {
   QVector<qreal> angles;
   for (vector<Node *>::const_iterator n=nodes.begin(); n!=nodes.end(); n++) {
     if ((*n)->Value()>2 && !(*n)->BoundaryP() ) {
       angles+=(*n)->NeighbourAngles();
+    }
+  }
   return angles;
+}
 QVector< QPair<qreal,int> > Mesh::VertexAnglesValues(void) {

src/mesh.h

➞

Show inline comments

 /*
+ *
  *  $Id$
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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.
+ *
  */
 // Cell derives from Vector, where Vector is simply used as a Vertex
 #ifndef _MESH_H_
 #define _MESH_H_
 #include <vector>
 #include <algorithm>
 #include <queue>
 #include <iterator>
 #include <functional>
 #ifdef QTGRAPHICS
 #include <QGraphicsScene>

src/miscq.cpp

➞

Show inline comments

 /*
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 <string>
 #include <QString>
 #include <QStringList>
 static const std::string _module_id("$Id$");
 // Returns the extension of a filename
 QString getExtension(const QString fn)
+{
   // split on dots
   QStringList parts = fn.split(".");
   // return last part, this should be the extension

src/miscq.h

➞

Show inline comments

 /*
+ *
  *  $Id$
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 _MISCQ_h_
 #define _MISCQ_h_
 #include <QString>
 // Miscellaneous helper functions, using Qt
 QString getExtension(const QString fn);
 #endif
 /* finis */

src/modelcatalogue.cpp

➞

Show inline comments

 /*
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 <string>
 #include "modelcatalogue.h"
 #include <QVariant>
 static const std::string _module_id("$Id$");
 ModelCatalogue::ModelCatalogue(Mesh *_mesh, Main *_mainwin, const char *model=0) {
   mesh = _mesh;
   mainwin = _mainwin;
   if (model) {
     cerr << "Loading model: " << model << endl;
     LoadPlugin(model);
   } else {

src/modelcatalogue.h

➞

Show inline comments

 /*
+ *
  *  $Id$
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 _MODELCATALOGUE_H_
 #define _MODELCATALOGUE_H_
 #include "warning.h"
 #include "cell.h"
 #include "mesh.h"
 #include "simplugin.h"
 #include "canvas.h"
 #include <QPluginLoader>
 #include <Q3PopupMenu>
 #include <QAction>
 #include <QDir>
 #include <QApplication>

src/node.cpp

➞

Show inline comments

 /*
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 <string>
 #include <sstream>
 #ifdef QTGRAPHICS
 #include <qstring.h>
 #include <QGraphicsSimpleTextItem>
 #endif
 #include "node.h"
 #include "cell.h"
 #include "mesh.h"
 #include "random.h"
 #include "parameter.h"
 #include "sqr.h"
 #include "pi.h"

src/node.h

➞

Show inline comments

 /*
+ *
  *  $Id$
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 _NODE_H_
 #define _NODE_H_
 #include <list>
 //#include <pair>
 #include <libxml/parser.h>
 #include <libxml/tree.h>
 #ifdef QTGRAPHICS
 #include <QGraphicsScene>
 #include <qcolor.h>

src/nodeitem.cpp

➞

Show inline comments

 /*
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 <string>
 #include <QGraphicsScene>
 #include <QGraphicsItem>
 #include <QPainter>
 #include <QStyleOption>
 #include <Qt>
 #include "nodeitem.h"
 #include "parameter.h"
 static const std::string _module_id("$Id$");
 extern Parameter par;

src/nodeitem.h

➞

Show inline comments

 /*
+ *
  *  $Id$
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 _NODEITEM_H_
 #define _NODEITEM_H_
 #include <QGraphicsScene>
 #include <QGraphicsItem>
 #include "simitembase.h"
 #include "node.h"
 #include "cell.h"
 class NodeItem: public QGraphicsItem, public SimItemBase
+{
  public:

src/nodeset.cpp

➞

Show inline comments

 /*
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 <string>
 #include <ostream>
 #include "nodeset.h"
 static const std::string _module_id("$Id$");
 ostream &operator<<(ostream &os, const NodeSet &ns)  {
   ns.print(os);
   return os;
+}
 /* finis */

src/nodeset.h

➞

Show inline comments

 /*
+ *
  *  $Id$
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 _NODESET_H_
 #define _NODESET_H_
 #include <algorithm>
 #include <numeric>
 #include <list>
 #include <iterator>
 #include "node.h"
 class NodeSet : public list<Node *> {
  public:

src/output.cpp

➞

Show inline comments

 /*
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 <string>
 #include <stdio.h>
 #include <string.h>
 #include <stdlib.h>
 #include <errno.h>
 #include <sys/types.h>
 #include <sys/stat.h>
 #include "warning.h"
 #include "parameter.h"
 #include "output.h"
 #include <QDir>

src/output.h

➞

Show inline comments

 /*
+ *
  *  $Id$
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 _OUTPUT_H_
 #define _OUTPUT_H_
 #ifdef __cplusplus
 extern "C" {
 #endif
   int OpenFileAndCheckExistance(FILE **fp,const char *fname,char *ftype);
   int YesNoP(const char *message);
   FILE *OpenWriteFile(const char *filename);
   FILE *OpenGZippedWriteFile(const char *filename);
   FILE *OpenReadFile(const char *filename);

src/parameter.cpp

➞

Show inline comments

 /*
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 "parameter.h"
 #include <cstdio>
 #include <cstring>
 #include <cstdlib>
 #include <cerrno>
 #include <iostream>
 #include <sstream>
 #include "output.h"
 #include "parse.h"
 #include "xmlwrite.h"
 #include "warning.h"
 #include <QLocale>
 #include <QDir>

src/parameter.h

➞

Show inline comments

 /*
+ *
  *  $Id$
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 _PARAMETER_H_
 #define _PARAMETER_H_
 #include "vector.h"
 #include <vector>
 #include <libxml/parser.h>
 #include <libxml/tree.h>
 class Parameter {
  public:
   Parameter();
   ~Parameter();

src/pardialog.cpp

➞

Show inline comments

 /*
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 "pardialog.h"
 #include "parameter.h"
 #include <cstring>
 #include <qdialog.h>
 #include <qlabel.h>
 #include <qlineedit.h>
 #include <qmessagebox.h>
 static const std::string _module_id("$Id$");
 ParameterDialog::ParameterDialog(QWidget *parent, const char *name, Qt::WindowFlags f) : QDialog(parent,name,false,f) {
   extern Parameter par;
   arrowcolor_edit = new QLineEdit( QString("%1").arg(par.arrowcolor), this, "arrowcolor_edit" );
@@ @@ -118,50 +118,50 @@ ParameterDialog::ParameterDialog(QWidget @@
   c0_edit = new QLineEdit( QString("%1").arg(par.c0), this, "c0_edit" );
   gamma_edit = new QLineEdit( QString("%1").arg(par.gamma), this, "gamma_edit" );
   eps_edit = new QLineEdit( QString("%1").arg(par.eps), this, "eps_edit" );
   QString k_string("%1,%2,%3,%4,%5,%6,%7,%8,%9,%10,%11,%12,%13,%14,%15");
   k_string = k_string.arg(par.k[0]).arg(par.k[1]).arg(par.k[2]).arg(par.k[3]).arg(par.k[4]).arg(par.k[5]).arg(par.k[6]).arg(par.k[7]).arg(par.k[8]).arg(par.k[9]).arg(par.k[10]).arg(par.k[11]).arg(par.k[12]).arg(par.k[13]).arg(par.k[14]);
   k_edit = new QLineEdit( k_string, this, "k_edit" );
   i1_edit = new QLineEdit( QString("%1").arg(par.i1), this, "i1_edit" );
   i2_edit = new QLineEdit( QString("%1").arg(par.i2), this, "i2_edit" );
   i3_edit = new QLineEdit( QString("%1").arg(par.i3), this, "i3_edit" );
   i4_edit = new QLineEdit( QString("%1").arg(par.i4), this, "i4_edit" );
   i5_edit = new QLineEdit( QString("%1").arg(par.i5), this, "i5_edit" );
   s1_edit = new QLineEdit( QString("%1").arg(par.s1), this, "s1_edit" );
   s2_edit = new QLineEdit( QString("%1").arg(par.s2), this, "s2_edit" );
   s3_edit = new QLineEdit( QString("%1").arg(par.s3), this, "s3_edit" );
   b1_edit = new QLineEdit( QString("%1").arg(sbool(par.b1)), this, "b1_edit" );
   b2_edit = new QLineEdit( QString("%1").arg(sbool(par.b2)), this, "b2_edit" );
   b3_edit = new QLineEdit( QString("%1").arg(sbool(par.b3)), this, "b3_edit" );
   b4_edit = new QLineEdit( QString("%1").arg(sbool(par.b4)), this, "b4_edit" );
   dir1_edit = new QLineEdit( QString("%1").arg(par.dir1), this, "dir1_edit" );
   dir2_edit = new QLineEdit( QString("%1").arg(par.dir2), this, "dir2_edit" );
   // make a 1x1 grid; it will auto-expand
   QGridLayout *grid = new QGridLayout( this, 1, 1 );
   // add the first four widgets with (row, column) addressing
   setWindowTitle( QString( " Parameter values for The Virtual Leaf") );
   grid->addWidget( new QLabel( "<h3> Parameter values for The Virtual Leaf</h3>",this), 0, 0, 1, -1, Qt::AlignCenter);
   setWindowTitle( QString( " Parameter values for VirtualLeaf") );
   grid->addWidget( new QLabel( "<h3> Parameter values for VirtualLeaf</h3>",this), 0, 0, 1, -1, Qt::AlignCenter);
   grid->addWidget( new QLabel( "", this), 0+1, 0, 1, -1);
   grid->addWidget( new QLabel( " <b>Visualization</b>", this), 3, 0, 1, 2 );
   grid->addWidget( new QLabel( "arrowcolor", this ),4, 0 );
   grid->addWidget( arrowcolor_edit, 4, 0+1  );
   grid->addWidget( new QLabel( "arrowsize", this ),5, 0 );
   grid->addWidget( arrowsize_edit, 5, 0+1  );
   grid->addWidget( new QLabel( "textcolor", this ),6, 0 );
   grid->addWidget( textcolor_edit, 6, 0+1  );
   grid->addWidget( new QLabel( "cellnumsize", this ),7, 0 );
   grid->addWidget( cellnumsize_edit, 7, 0+1  );
   grid->addWidget( new QLabel( "nodenumsize", this ),8, 0 );
   grid->addWidget( nodenumsize_edit, 8, 0+1  );
   grid->addWidget( new QLabel( "node_mag", this ),9, 0 );
   grid->addWidget( node_mag_edit, 9, 0+1  );
   grid->addWidget( new QLabel( "outlinewidth", this ),10, 0 );
   grid->addWidget( outlinewidth_edit, 10, 0+1  );
   grid->addWidget( new QLabel( "cell_outline_color", this ),11, 0 );
   grid->addWidget( cell_outline_color_edit, 11, 0+1  );
   grid->addWidget( new QLabel( "resize_stride", this ),12, 0 );
   grid->addWidget( resize_stride_edit, 12, 0+1  );
   grid->addWidget( new QLabel( "", this), 13, 0, 1, 2 );
   grid->addWidget( new QLabel( " <b>Cell mechanics</b>", this), 14, 0, 1, 2 );
   grid->addWidget( new QLabel( "T", this ),15, 0 );
   grid->addWidget( T_edit, 15, 0+1  );

src/parse.cpp

➞

Show inline comments

 /*
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 <stdio.h>
 #include <string.h>
 #include <stdlib.h>
 #include <errno.h>
 #include <string.h>
 #include "warning.h"
 #include "parse.h"
 #include "output.h"
 #include <string>
 static const std::string _module_id("$Id$");
 using namespace MyWarning;

src/parse.h

➞

Show inline comments

 /*
+ *
  *  $Id$
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 _PARSE_H_
 #define _PARSE_H_
 char *ParsePar(FILE *fp, char *parameter, bool wrapflag);
 int igetpar(FILE *fp,char *parameter, bool wrapflag);
 int igetpar(FILE *fp,char *parameter, int default_val, bool wrapflag);
 float fgetpar(FILE *fp,char *parameter, bool wrapflag);
 float fgetpar(FILE *fp,char *parameter, double default_val, bool wrapflag);
 /* Get a list of n comma separated doubles */
 double *dgetparlist(FILE *fp,char *parameter, int n, bool wrapflag);
 char *sgetpar(FILE *fp,char *parameter, bool wrapflag);

src/pi.h

➞

Show inline comments

 /*
+ *
  *  $Id$
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 _PI_H_
 #define _PI_H_
 const double Pi=3.1415926535897932384626433832795028841971693993751058209749445923078164062862089986280348253421170676;
 #endif
 /* finis */

src/qcanvasarrow.h

➞

Show inline comments

 /*
+ *
  *  $Id$
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 _QCANVASARROW_H_
 #define _QCANVASARROW_H_
 #include <QGraphicsScene>
 class QGraphicsArrowItem : public QGraphicsLineItem {
  public:
  QGraphicsArrowItem(QGraphicsItem *parent, QGraphicsScene *c) : QGraphicsLineItem(parent, c) {};
   void paint ( QPainter *p, const QStyleOptionGraphicsItem *option,
 	       QWidget *widget ) {

src/random.cpp

➞

Show inline comments

 /*
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 <QDebug>
 #include <string>
 #include <stdio.h>
 #include <stdlib.h>
 #include <sys/timeb.h>
 #include <iostream>
 #include "random.h"
 static const std::string _module_id("$Id$");
 static int idum = -1;
 using namespace std;

src/random.h

➞

Show inline comments

 /*
+ *
  *  $Id$
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 _RANDOM_H_
 #define _RANDOM_H_
 #define MBIG 1000000000
 #define MSEED 161803398
 #define MZ 0
 #define FAC (1.0/MBIG)
 double RANDOM();
 int Seed(int seed);
 long RandomNumber(long max);
 void AskSeed();

src/rungekutta.cpp

➞

Show inline comments

 /*
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 <string>
 #include <math.h>
 #include <iostream>
 #include "rungekutta.h"
 #include "warning.h"
 #include "maxmin.h"
 static const std::string _module_id("$Id$");
 // The value Errcon equals (5/Safety) raised to the power (1/PGrow), see use below.
 /*
   static float maxarg1,maxarg2;

src/rungekutta.h

➞

Show inline comments

 /*
+ *
  *  $Id$
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 _RUNGEKUTTA_H_
 #define _RUNGEKUTTA_H_
 class RungeKutta  {
  public:
   RungeKutta(void) {
     kmax=kount=0;
     dxsav=0.;
     xp=0;
     yp=0;
+  }

src/simitembase.cpp

➞

Show inline comments

 /*
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 <string>
 #include <QBrush>
 #include "simitembase.h"
 static const std::string _module_id("$Id$");
 SimItemBase::SimItemBase( void *v, QGraphicsScene *canvas )
+{
   obj=v;
 };
 SimItemBase::~SimItemBase(void) {};

src/simitembase.h

➞

Show inline comments

 /*
+ *
  *  $Id$
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 _SIMITEMBASE_H_
 #define _SIMITEMBASE_H_
 #include <QGraphicsScene>
 #include <QBrush>
 #include <assert.h>
 class Vector;
 template<class TYPE>
 TYPE class_cast(void * symbol)
+{

src/simplugin.h

➞

Show inline comments

 /*
+ *
  *  $Id$
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 _SIMPLUGIN_H_
 #define _SIMPLUGIN_H_
 #include <QtPlugin>
 #include <QMetaType>
 #include "cellbase.h"
 #include "wallbase.h"
 class Parameter;
 #include <QColor>
 #include <QString>

src/sqr.h

➞

Show inline comments

 /*
+ *
  *  $Id$
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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/>.
+ *
  *  From "Numerical recipes in C"
+ *
  *  Copyright 2010 Roeland Merks.
+ *
  */
 #ifndef _SQR_H_
 #define _SQR_H_
 // redefine these macros as inline functions, to prevent scary
 // behavior.  (According to compiler warnings, the above macros from
 // Numerical Recipes in C are officially undefined...)
 //
 // However, they seem to work, but it seems safer to redefine them.
 // Inline functions will behave like macros anyhow.
 inline double DSQR( double a ) {

src/tiny.h

➞

Show inline comments

 /*
+ *
  *  $Id$
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 _TINY_H_
 #define _TINY_H_
 #define TINY 1e-5
 #endif
 /* finis */

src/transporterdialog.cpp

➞

Show inline comments

 /*
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 <QtGui>
 #include <QDoubleValidator>
 #include <sstream>
 #include "canvas.h"
 #include "transporterdialog.h"
 static const std::string _module_id("$Id$");
 TransporterDialog::TransporterDialog(Wall *w, CellBase *c, int wn, QWidget *parent)
-  : wall(w), cell(c), wall_num(wn), QDialog(parent)
+  :  QDialog(parent), wall(w), cell(c), wall_num(wn)
+{
   int frameStyle = QFrame::Plain | QFrame::NoFrame;
   QPushButton *ok = new QPushButton(tr("Ok"));
   QPushButton *cancel = new QPushButton(tr("Cancel"));
   QGridLayout *t_grid = new QGridLayout; // transporter grid
   // connect the slots
   connect(ok, SIGNAL(clicked()), this, SLOT(setTransporterValues()));
   connect(cancel, SIGNAL(clicked()), this, SLOT(close()));
   // compose a label for the dialog box
   std::stringstream label_text;
   label_text << "C("<< wall->C1()->Index() << "," << wall->C2()->Index() << "), N("
 	     << wall->N1()->Index() << "," << wall->N2()->Index() << ")";
   // retrieve the current transporters
   QVector <double> transporters;  // transporter vector
   ntransporters = cell->NChem(); // size of transporter vector
   for (int i=0; i<ntransporters; ++i){
     transporters << ((wall_num == 1) ? wall->Transporters1(i) : wall->Transporters2(i)); // dependent on the wall number of course.
+  }
   // iterate over the vector of transporter values making a label/edit line for each
   for (int i=0; i<transporters.size(); ++i) {

src/transporterdialog.h

➞

Show inline comments

 /*
+ *
  *  $Id$
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 _TRANSPORTERDIALOG_H_
 #define _TRANSPORTERDIALOG_H_
 #include <QDialog>
 #include <QVector>
 #include <QLineEdit>
 class QLabel;
 class QLineEdit;
 class Wall;
 class CellBase;

src/vector.cpp

➞

Show inline comments

 /*
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 <string>
 #include <stddef.h>
 #include <ostream>
 #include <limits.h>
 #include <stdio.h>
 //#include <math.h>
 #include <stdarg.h>
 #include "sqr.h"
 #include "pi.h"
 #include "vector.h"
 #include "tiny.h"
 static const std::string _module_id("$Id$");

src/vector.h

➞

Show inline comments

 /*
+ *
  *  $Id$
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 _VECTOR_H_
 #define _VECTOR_H_
 #include <iostream>
 #include <cmath>
 #include "sqr.h"
 #ifdef QTGRAPHICS
 #include <QPointF>
 #endif
 // three dimensional vector
 using namespace std;
 class Vector {
  public:
   inline Vector(const double cx=0,const double cy=0,const double cz=0) {
     x=cx;
     y=cy;
     z=cz;
   };
   explicit inline Vector(const double m[3]) {
     x=m[0];
     y=m[1];
     z=m[2];
+  }
   // should be taken over by default arguments of Vector constructor
   /*  inline Vector(void) { */
   /*     x=0.; */
   /*     y=0.; */
   /*     z=0.; */
   /*   } */
   inline Vector(const Vector &source) {
     // copy constructor
     x=source.x;
     y=source.y;
     z=source.z;
+  }
   // type conversion from and to QPointF (2D vector class from Qt library; we throw away "z" here!!)
 #ifdef QTGRAPHICS
   inline operator QPointF() const {
     return QPointF( x, y );
+  }
   inline Vector(const QPointF &p) {
     x = p.x();
     y = p.y();
     z = 0.;
+  }
 #endif
   virtual ~Vector() {
   };

src/wall.cpp

➞

Show inline comments

 /*
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 <string>
 #include "wall.h"
 #include "cell.h"
 #include "wallitem.h"
 #include "node.h"
 #include "apoplastitem.h"
+//#include "apoplastitem.h"
 #include <algorithm>
 #include <QGraphicsScene>
 static const std::string _module_id("$Id$");
 /*! Check if this Wall still belongs to Cell a, otherwise gives it to Cell b.
   \return true: Wall was corrected
   \return false: Wall was still correct
 */
 bool Wall::CorrectWall( void ) {
   // collect all cells to which my nodes are connected on one list
   list<CellBase *> owners;
   transform(n1->owners.begin(),n1->owners.end(), back_inserter(owners), mem_fun_ref(&Neighbor::getCell));
   transform(n2->owners.begin(),n2->owners.end(), back_inserter(owners), mem_fun_ref(&Neighbor::getCell));
   // get the list of duplicates
   list<CellBase *> wall_owners;
   owners.sort();
   //transform(owners.begin(), owners.end(), ostream_iterator<int>(cerr, ", "), mem_fun(&Cell::Index));
   duplicates_copy( owners.begin(), owners.end(), back_inserter(wall_owners) );
   // duplicates are the cells to which the Wall belongs
@@ @@ -141,52 +141,52 @@ bool Wall::CorrectWall( void ) { @@
 	  ((Cell *)c1)->RemoveWall(this);
 	  c1 = cell1;
 	  ((Cell *)c1)->AddWall(this);
 	  //	  cerr << "Block 3\n";
 	} else {
 #ifdef QDEBUG
 	  qDebug() << "Warning, cell wall was not corrected." << endl;
 #endif
 	  return false;
+	}
+      }
+    }
+  }
   return true;
+}
 void Wall::Draw(QGraphicsScene *c) {
   WallItem *wi1 = new WallItem(this, 1, c);
   WallItem *wi2 = new WallItem(this, 2, c);
   wi1->show();
   wi2->show();
+}
 void Wall::DrawApoplast(QGraphicsScene *c) {
+/* void Wall::DrawApoplast(QGraphicsScene *c) {
   ApoplastItem *apo = new ApoplastItem(this, c);
   apo->show();
+}
+}*/
 void Wall::ShowStructure(QGraphicsScene *c) {
   Vector offset = Cell::Offset();
   double factor = Cell::Factor();
   Vector startpoint ( ((offset.x+n1->x)*factor),((offset.y+n1->y)*factor)),
     endpoint (((offset.x+n2->x)*factor),((offset.y+n2->y)*factor));
   Vector linevec = endpoint - startpoint;
   Vector midline = startpoint + linevec/2.;
   Vector perpvec = linevec.Normalised().Perp2D();
   Vector textpos1 = midline + 100 * perpvec;
   Vector textpos2 = midline - 100 * perpvec;
   QGraphicsLineItem *line = new QGraphicsLineItem(0,c);
   line->setPen( QPen(QColor(par.arrowcolor),2) );
   line->setLine(startpoint.x, startpoint.y, endpoint.x, endpoint.y );
   line->setZValue(10);
   line->show();
   QGraphicsSimpleTextItem *text1 = new QGraphicsSimpleTextItem( QString("%1").arg(c2->Index()),0,c);
   QGraphicsSimpleTextItem *text2 = new QGraphicsSimpleTextItem( QString("%1").arg(c1->Index()),0,c);

src/wall.h

➞

Show inline comments

 /*
+ *
  *  $Id$
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 _WALL_H_
 #define _WALL_H_
 #include "wallbase.h"
 #include <libxml/parser.h>
 #include <libxml/tree.h>
 #include<QGraphicsScene>
 class Wall : public WallBase {
  public:
  Wall(Node *sn1, Node *sn2, CellBase *sc1, CellBase *sc2) : WallBase(sn1, sn2, sc1, sc2) {}
   void XMLAdd(xmlNodePtr parent_node) const;
   bool CorrectWall(void);
   // Graphics:
   //! Visualize transport protein concentrations
   void Draw(QGraphicsScene *c);
   //! Visualize contents of the apoplast
   void DrawApoplast(QGraphicsScene *c);
+  //void DrawApoplast(QGraphicsScene *c);
   /*! \brief Visualize the structure of the wall (Cell ID's etc.).
     Used for debugging purposes.
   */
   void ShowStructure(QGraphicsScene *c);
  private:
   string WallTypetoStr(const WallType &wt) const;
 };
 #endif
 /* finis */

src/wallbase.cpp

➞

Show inline comments

 /*
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 <QDebug>
 #include "wall.h"
 #include "wallbase.h"
 #include "node.h"
 #include "mesh.h"
 #include "parameter.h"
 #include <sstream>
 #include <string>
 #include "warning.h"
 #ifdef QTGRAPHICS
 #include <QGraphicsScene>
 #include <QGraphicsLineItem>
 #include "wallitem.h"
 #include "apoplastitem.h"
+//#include "apoplastitem.h"
 #endif
 static const std::string _module_id("$Id$");
 int WallBase::nwalls=0;
 ostream &WallBase::print(ostream &os) const {
   os << "{ " << n1->Index() << "->" << n2->Index()
      << ", " << c1->Index() << " | " << c2->Index() << "} ";
   return os;
+}
 ostream &operator<<(ostream &os, const WallBase &w) {
   w.print(os);
   return os;
+}
 WallBase::WallBase(Node *sn1, Node *sn2, CellBase *sc1, CellBase *sc2)
+{
 #ifdef QDEBUG
   if (sc1==sc2) {
     qDebug() << "Attempting to build a wall between identical cells: " << sc1->Index() << endl;
+  }
 #endif
   c1 = sc1;
   c2 = sc2;
   n1 = sn1;
   n2 = sn2;
   transporters1 = new double[CellBase::NChem()];
   transporters2 = new double[CellBase::NChem()];
   new_transporters1 = new double[CellBase::NChem()];
   new_transporters2 = new double[CellBase::NChem()];
   for (int i=0;i<CellBase::NChem();i++) {
     transporters1[i] = transporters2[i] = new_transporters1[i] = new_transporters2[i] = 0.;
+  }
   apoplast = new double[CellBase::NChem()]; // not yet in use.
+//  apoplast = new double[CellBase::NChem()]; // not yet in use.
   SetLength();
   // to visualize flux through WallBase
   viz_flux=0;
   dead = false;
   wall_type = Normal;
   wall_index = nwalls++;
+}
 void WallBase::CopyWallContents(const WallBase &src)
+{
   for (int i=0; i<CellBase::NChem(); i++) {
     if (transporters1) {
       transporters1[i]=src.transporters1[i];
+    }
     if (transporters2) {
       transporters2[i]=src.transporters2[i];
+    }
     if (new_transporters1) {
       new_transporters1[i]=src.new_transporters1[i];
+    }
     if (new_transporters2) {
       new_transporters2[i]=src.new_transporters2[i];
+    }
     if (apoplast) {
+  /*  if (apoplast) {
       apoplast[i]=src.apoplast[i];
+    }
+    }*/
+  }
   dead = src.dead;
   wall_type = src.wall_type;
+}
 void WallBase::SwapWallContents(WallBase *src)
+{
   for (int i=0; i<CellBase::NChem(); i++) {
     if (transporters1) {
       double tmp;
       tmp=src->transporters1[i];
       src->transporters1[i]=transporters1[i];
       transporters1[i]=tmp;
+    }
     if (transporters2) {
       double tmp;
       tmp=src->transporters2[i];
       src->transporters2[i]=transporters2[i];
       transporters2[i]=tmp;
+    }
     if (new_transporters1) {
       double tmp;
       tmp=src->new_transporters1[i];
       src->new_transporters1[i]=new_transporters1[i];
       new_transporters1[i]=tmp;
+    }
     if (new_transporters2) {
       double tmp;
       tmp=src->new_transporters2[i];
       src->new_transporters2[i]=new_transporters2[i];
       new_transporters2[i]=tmp;
+    }
     if (apoplast) {
+  /*  if (apoplast) {
       double tmp;
       tmp=src->apoplast[i];
       src->apoplast[i]=apoplast[i];
       apoplast[i]=tmp;
+    }
+    }*/
+  }
   bool tmp_bool;
   tmp_bool = src->dead;
   src->dead=dead;
   dead = tmp_bool;
   WallType tmp_wall_type;
   tmp_wall_type = src->wall_type;
   src->wall_type = wall_type;
   wall_type = tmp_wall_type;
+}
 bool WallBase::SAM_P(void)
+{
   return N1()->sam || N2()->sam;
+}
 #include <fstream>
 void WallBase::SetLength(void)
+{
   // Step 1: find the path of nodes leading along the WallBase.
   // A WallBase often represents a curved cell wall: we want the total

src/wallbase.h

➞

Show inline comments

 /*
+ *
  *  $Id$
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 _WALLBASE_H_
 #define _WALLBASE_H_
 #include <list>
 #include <iostream>
 #include "vector.h"
 class Node;
 class CellBase;
 using namespace std;
@@ @@ -45,83 +45,83 @@ template<class In, class Out> Out duplic @@
     i = adjacent_find(++i, last);
+  }
   return res;
+}
 /*! \class WallBase. A cell wall, which runs between cell "corner points",
   and consists of wall elements. */
 class WallBase {
  protected:
   friend class CellBase;
   friend class Cell;
   friend class Mesh;
   //! Cells to which the wall belongs
   CellBase *c1, *c2;
   //! A list of transporter protein concentrations associated with the wall
   double *transporters1, *transporters2;
   double *new_transporters1, *new_transporters2;
   bool IllegalP(void) { return c1 == c2; }
   //! The chemicals in the apoplast at this position
   double *apoplast;
+  //double *apoplast;
   //! Pointers to the wall's corner nodes
   Node *n1, *n2;
   double length;
   double viz_flux;
   //  bool aux_source;
   bool dead;
   // disallow usage of empty constructor
   WallBase(void) {}
   enum WallType {Normal, AuxSource, AuxSink};
   static int nwalls;
  protected:
   int wall_index;
   WallType wall_type;
  public:
   WallBase(Node *sn1, Node *sn2, CellBase *sc1, CellBase *sc2);
   // shallow copy
   WallBase(const WallBase &src) {
     c1 = src.c1;
     c2 = src.c2;
     transporters1 = src.transporters1;
     transporters2 = src.transporters2;
     new_transporters1 = src.new_transporters1;
     new_transporters2 = src.new_transporters2;
     apoplast = src.apoplast;
+    //apoplast = src.apoplast;
     n1 = src.n1;
     n2 = src.n2;
     length = src.length;
     viz_flux = src.viz_flux;
     dead = src.dead;
     wall_index = src.wall_index;
+  }
   inline int Index(void) const { return wall_index;}
   inline bool DeadP(void) const { return dead; }
   inline void Kill(void) { dead = true; }
   // deep copying of chemicals and transporters
   void CopyWallContents(const WallBase &src);
   void SwapWallContents(WallBase *src);
   bool is_wall_of_cell_p ( const CellBase *c ) {
     return (c1==c || c2==c);
+  }
   inline CellBase *C1(void) const { return c1; }
   inline CellBase *C2(void) const { return c2; }
   inline Node *N1(void) const { return n1; }
   inline Node *N2(void) const { return n2; }
   inline void setTransporters1(int ch, double val) { transporters1[ch]=val; }
   inline void setTransporters2(int ch, double val) { transporters2[ch]=val; }
@@ @@ -146,50 +146,50 @@ class WallBase { @@
     else
       if (wall_type == AuxSource)
 	wall_type = AuxSink;
       else
 	if (wall_type == AuxSink) {
 	  wall_type = Normal;
+	}
+  }
   // checked version. Use during debugging stage.
   inline double getTransporter(CellBase *c, int ch) const
+  {
     return c1 == c ? transporters1[ch] : ( c2 == c ? transporters2[ch] : throw "WallBase::getTransporter called with wrong cell") ; }
   inline void setTransporter(CellBase *c, int ch, double val) {
     if ( c1 == c ) {
       transporters1[ch]=val;
     } else
       if (c2 == c ) {
 	transporters2[ch]=val;
       } else {
 	throw "WallBase::setTransporter called with wrong cell";
+      }
+  }
   inline double getApoplast(int ch) const { return apoplast[ch]; }
   inline void setApoplast(int ch, double val) { apoplast[ch] = val; }
   //inline double getApoplast(int ch) const { return apoplast[ch]; }
   //inline void setApoplast(int ch, double val) { apoplast[ch] = val; }
   inline CellBase *getOtherCell(CellBase *c) { return c1 == c ? c2 : c1; }
   Vector getInfluxVector(CellBase *c);
   Vector getWallVector(CellBase *c);
   void CorrectTransporters(double orig_length);
   inline double Length(void) { return length; }
   //double Length(void);
   ostream &print(ostream &os) const;
   void SetLength(void);
   void Transport(void);
   inline void setVizFlux( double value ) { viz_flux = value; }
   /*! Return vector containing the directional flux through the wall.
     as defined by the value "viz_flux" which is supplied by the end-user
     in the TransportFunction.
   */
   Vector VizFlux(void);
   bool IntersectsWithDivisionPlaneP(const Vector &p1, const Vector &p2);
   void SetTransToNewTrans( void );
  private:

src/wallitem.cpp

➞

Show inline comments

 /*
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 <QDebug>
 #include <string>
 #include <QGraphicsScene>
 #include <QVector>
 #include "canvas.h"
 #include "wallitem.h"
 #include "parameter.h"
 #include "node.h"
 #include "transporterdialog.h"
 static const std::string _module_id("$Id$");
 WallItem::WallItem( Wall *w, int wallnumber, QGraphicsScene *canvas )

src/wallitem.h

➞

Show inline comments

 /*
+ *
  *  $Id$
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 _WALLITEM_H_
 #define _WALLITEM_H_
 #include <QGraphicsScene>
 #include <QGraphicsLineItem>
 #include <QPainter>
 #include <qpainter.h>
 #include <QMouseEvent>
 #include "simitembase.h"
 #include "wall.h"
 //! Shows transporter concentrations at one side of the wall

src/warning.cpp

➞

Show inline comments

 /*
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 <string>
 #include <stdarg.h>
 #include <stdio.h>
 #include <stdlib.h>
 #include <iostream>
 #include "warning.h"
 #ifdef QTGRAPHICS
 #include <qapplication.h>
 #include "canvas.h"
 #endif
 #include <QMessageBox>
 static const std::string _module_id("$Id$");

src/warning.h

➞

Show inline comments

 /*
+ *
  *  $Id$
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 _WARNING_H_
 #define _WARNING_H_
 #define MEMORYCHECK(x) if ((x)==NULL) {   fprintf(stderr, "Out of Memory error in "#x" \n");  exit(0); }
 #define UNIDENTIFIED 2353996
 #ifdef __cplusplus
 extern "C" {
 #endif
   // namespace MyWarning needed because libxml2 also defines a warning token.

src/xmlwrite.cpp

➞

Show inline comments

 /*
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 "mesh.h"
 #include "parameter.h"
 #include <ctime>
 #include <cstring>
 #include <string>
 #include <sstream>
 #include <QString>
 #include <libxml/parser.h>
 #include <libxml/tree.h>
 #include <libxml/xpath.h>
 #include <libxml/xmlreader.h>
 #include <QLocale>
@@ @@ -634,60 +634,60 @@ void Wall::XMLAdd(xmlNode *parent) const @@
   if (transporters1) {
     for (int i=0;i<Cell::NChem();i++) {
       xmlNodePtr tr1_val_xml = xmlNewChild(tr1_xml, NULL, BAD_CAST "val", NULL);
+      {
 	ostringstream text;
 	text << transporters1[i];
 	xmlNewProp(tr1_val_xml, BAD_CAST "v", BAD_CAST text.str().c_str());
+      }
+    }
+  }
   if (transporters2) {
     xmlNodePtr tr2_xml = xmlNewChild(xmlwall, NULL, BAD_CAST "transporters2", NULL);
     for (int i=0;i<Cell::NChem();i++) {
       xmlNodePtr tr2_val_xml = xmlNewChild(tr2_xml, NULL, BAD_CAST "val", NULL);
+      {
 	ostringstream text;
 	text << transporters2[i];
 	xmlNewProp(tr2_val_xml, BAD_CAST "v", BAD_CAST text.str().c_str());
+      }
+    }
+  }
   if (apoplast) {
+/*  if (apoplast) {
     xmlNodePtr apo_xml = xmlNewChild(xmlwall, NULL, BAD_CAST "apoplast", NULL);
     for (int i=0;i<Cell::NChem();i++) {
       xmlNodePtr apo_val_xml = xmlNewChild(apo_xml, NULL, BAD_CAST "val", NULL);
+      {
 	ostringstream text;
 	text << transporters2[i];
 	xmlNewProp(apo_val_xml, BAD_CAST "v", BAD_CAST text.str().c_str());
+      }
+    }
+  }
+  } */
+}
 vector<double> XMLIO::XMLReadValArray(xmlNode *cur)
+{
   vector<double> result;
   QLocale standardlocale(QLocale::C);
   bool ok;
   xmlNode *valarray_node = cur->xmlChildrenNode;
   while (valarray_node!=NULL) {
     if (!xmlStrcmp(valarray_node->name, (const xmlChar *)"val")) {
       xmlChar *vc = xmlGetProp(valarray_node, BAD_CAST "v");
       if (vc) {
 	//result.push_back(strtod( (const char *)vc, 0));
 	result.push_back(standardlocale.toDouble((char *)vc, &ok));
 	if (!ok) MyWarning::error("Could not convert \"%s\" to double in XMLRead.",(char *)vc);
 	xmlFree(vc);
+      }
+    }
     valarray_node = valarray_node->next;
+  }
@@ @@ -1258,79 +1258,79 @@ void Mesh::XMLReadWalls(xmlNode *root, v @@
+		  {
 		    stringstream text;
 		    text << "Exception in Mesh::XMLRead: Too many transporter values given for wall(s). Ignoring remaining values.";
 		    unique_warning(text.str().c_str());
 		    break;
+		  }
+		}
 		xmlChar *nc = xmlGetProp(v_node, (const xmlChar *) "v");
 		if (nc==0) {
 		  unique_warning("Token \"v\" not found in xmlwrite.cpp at or around line no. 861");
+		}
 		double v = standardlocale.toDouble((const char *)nc, &ok);
 		if (!ok) MyWarning::error("Could not convert \"%s\" to double in XMLRead.",(const char *)nc);
 		w->transporters2[nv++]=v;
 		xmlFree(nc);
+	      }
 	      v_node = v_node->next;
+	    }
+	  }
 	  if ((!xmlStrcmp(w_node->name, (const xmlChar *)"apoplast"))) {
+	/*  if ((!xmlStrcmp(w_node->name, (const xmlChar *)"apoplast"))) {
 	    xmlNode *v_node = w_node->xmlChildrenNode;
 	    int nv=0;
 	    while (v_node!=NULL) {
 	      if ((!xmlStrcmp(v_node->name, (const xmlChar *)"val"))) {
 		if (nv>=Cell::NChem()) {
+		  {
 		    stringstream text;
 		    text << "Exception in Mesh::XMLRead: Too many transporter values given for wall(s). Ignoring remaining values.";
 		    unique_warning(text.str().c_str());
 		    break;
+		  }
+		}
 		xmlChar *nc = xmlGetProp(v_node, (const xmlChar *) "v");
 		if (nc==0) {
 		  unique_warning("Token \"v\" not found in xmlwrite.cpp at or around line no. 887");
+		}
 		double v = standardlocale.toDouble((const char *)nc, &ok);
 		if (!ok) MyWarning::error("Could not convert \"%s\" to double in XMLRead.",(const char *)nc);
 		w->apoplast[nv++]=v;
 		xmlFree(nc);
+	      }
 	      v_node = v_node->next;
+	    }
+	  }
+	  }*/
 	  w_node=w_node->next;
+	}
+      }
       cur = cur->next;
+    }
+  }
+}
 void Mesh::XMLReadWallsToCells(xmlNode *root, vector<Wall *> *tmp_walls)
+{
   // Add the walls to the cells (do this after reading the walls; read walls after reading cells...)
   // 1. Read Nodes
   // 2. Read Cells
   // 3. Read Walls
   // 4. Read Walls into Cells
   xmlNode *cur = root->xmlChildrenNode;
   int ci=0; // cell index
   while (cur!=NULL) {
     if ((!xmlStrcmp(cur->name, (const xmlChar *)"cell")) ||

src/xmlwrite.h

➞

Show inline comments

 /*
+ *
  *  $Id$
+ *
  *  This file is part of the Virtual Leaf.
+ *
- *  The Virtual Leaf is free software: you can redistribute it and/or modify
+ *  VirtualLeaf 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,
+ *  VirtualLeaf 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 _XML_WRITE_H_
 #define _XML_WRITE_H_
 #include <vector>
 #include <libxml/tree.h>
 #include <cstring>
 namespace XMLIO {
   std::vector <double> XMLReadValArray(xmlNode *cur);
   template<class For, class E> long list_index (For beg, For end, E *elem) {

0 comments (0 inline, 0 general)