2010-06-28    <guravage@caterpie.sen.cwi.nl>

	* VirtualLeaf-install.nsi: Grab gpl3.txt from doc directory.

	* VirtualLeaf-install.nsi: Add VirtualLeaf doc directory.

2010-06-25    <guravage@caterpie.sen.cwi.nl>

	* gpl3.txt: Moved gpl3.txt from doc to src directory.

	* VirtualLeaf.pro: Added -Wno-write-strings and -Wno-unused-parameter to QMAKE_CXXFLAGS.

	* libplugin.pro: Ditto.

	* parameter.cpp: Result of adding datadir changes to make_parameter_source.pl.

	* parameter.h: Ditto.

	* output.h: Declared new function (AppendHomeDirIfPathRelative).

	* output.cpp (AppendHomeDirIfPathRelative): Added new function.

	* canvas.cpp (gpl): Moving gpl3.txt from doc to src obviates the need to docDir.cd("../doc").

	* VirtualLeaf-install.nsi: Grab gpl3.txt from src directory.

	Add missing libiconv/bin, libxml2bin and libz/bin directories.

	Copy libiconv-2.dll, libxml2.dll and zlib1.dll from relative paths.

	* VirtualLeaf.pro: copy gpl3.txt as part of QMAKE_POST_LINK.

2010-06-24    <guravage@caterpie.sen.cwi.nl>

	* libplugin.pro: Use correct library path.

	* VirtualLeaf.pro: Ditto.

	* VirtualLeaf.cpp (DrawCell): Iterate over NChem to construct info_string.

2010-06-23    <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().

	* canvas.cpp (mouseReleaseEvent): Replaced qDebug() with cerr since qDebug complains about *node_set.

	* wall.cpp (CorrectWall): Rplaced gDebug() with cerr in transform call and when printing *this.

2010-06-22    <guravage@caterpie.sen.cwi.nl>

	* Makefile (tutorials): Add tutorials target.

2010-06-21    <guravage@caterpie.sen.cwi.nl>

	* parameter.cpp: Added particular reassignment of datadir.

	* canvas.cpp (gpl): Added GPL3 License text. Display detail text only if the source text file exists.

2010-06-18    <guravage@caterpie.sen.cwi.nl>

	* canvas.cpp (gpl): Added gpl slot to display GPL license.

	* VirtualLeaf.pro: Changed default LIBXML2DIR, LIBICONVDIR and LIBZDIR to corresponding distribution lib directories.

	* libplugin.pro: Ditto.

	* Makefile (clean): add if stmt not to `touch` on windows.

2010-06-17    <guravage@caterpie.sen.cwi.nl>

	* VirtualLeaf.pro: Removed perl references.

	* libplugin.pro: Ditto.

2010-06-15    <guravage@caterpie.sen.cwi.nl>

	* VirtualLeaf.pro: Removed xmlwritecode.cpp from SOURCES list.

	* xmlwrite.cpp (XMLSave): Removed references to XMLWriteLeafSourceCode and XMLWriteReactionsCode.

	* xmlwrite.h (XMLIO): Ditto!

	* mesh.cpp (findNextBoundaryNode): Initialize Node *next_boundary_node = NULL;

	* xmlwrite.cpp (XMLReadSimtime): Removed unused variable cur

/*

 *

 *  This file is part of the Virtual Leaf.

 *

 *  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.

 *

 *  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>

#include <qlabel.h>

#include <qimage.h>

#include <q3progressdialog.h>

#include <qtimer.h>

#include <qslider.h>

#include <qpixmap.h>

#include <qfile.h>

#include <qdir.h>

#include <q3filedialog.h>

#include <QGraphicsItem>

#include <QList>

#include <QDir>

#include <QDebug>

#include <set>

//Added by qt3to4:

#include <Q3ValueList>

#include <Q3PopupMenu>

#include <QMouseEvent>

#include <typeinfo>

#include <cstring>

#include <q3process.h>

#include <qlayout.h>

#include <qspinbox.h>

#include <fstream>

#include <sstream>

#include "pardialog.h"

#include "parameter.h"

#include "canvas.h"

#include "node.h"

#include "nodeset.h"

#include "nodeitem.h"

#include "cellitem.h"

#include "wallitem.h"

#include "mesh.h"

#include "xmlwrite.h"

#include "miscq.h"

#include "OptionFileDialog.h"

#include <cstdlib>

#include <cstdio>

#include "modelcatalogue.h"

#include <algorithm>

// Include VIB and PSB logos

#include "psb.xpm"

#include "cwi.xpm"

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

// We use a global variable to save memory - all the brushes and pens in

// the mesh are shared.

#define QUOTE_ME(s) QUOTE_ME_2NDLEV(s)

#define QUOTE_ME_2NDLEV(s) #s

static QColor dark_red("darkRed");

static const int imageRTTI = 984376;

extern Parameter par;

const QString Main::caption("Virtual leaf");

const QString Main::caption_with_file("Virtual leaf: %1");

FigureEditor::FigureEditor(

			   QGraphicsScene& c, Mesh &m, QWidget* parent,

			   const char* name, Qt::WindowFlags f) :

  QGraphicsView(&c,parent), mesh(m)

{

  intersection_line = 0;

  //angle_line = 0;

  setInteractive(true);

  moving = 0;  

  rotation_mode = false;

}

void FigureEditor::clear()

{

  QList<QGraphicsItem *> list = scene()->items();

  QList<QGraphicsItem *>::Iterator it = list.begin();

  for (; it != list.end(); ++it) {

    delete *it;

  }

}

void FigureEditor::wheelEvent(QWheelEvent *event)

{

  scaleView(pow((double)2, -event->delta() / 240.0));

}

void FigureEditor::scaleView (qreal scaleFactor)

{

  qreal factor = matrix().scale(scaleFactor, scaleFactor).mapRect(QRectF(0, 0, 1, 1)). width();

  if (factor < 0.07 || factor > 100) return;

  scale (scaleFactor, scaleFactor);

}

void FigureEditor::Save(const char *fname, const char *format, int sizex, int sizey)

{

  QImage *image = new QImage(sizex, sizey, QImage::Format_RGB32);

  image->fill(QColor(Qt::white).rgb());

  QPainter *painter=new QPainter(image);

  render(painter);

  image->save(QString(fname),format);

  delete painter;

  delete image;

}

void FigureEditor::mousePressEvent(QMouseEvent* e)

{

  static QList<Node*> selected;

  emit MousePressed();

  //QPointF p = matrix().inverted().map(e->pos());

  QPointF p = mapToScene(e->pos());

#ifdef QDEBUG  

  qDebug() << endl << "MousePressEvent location: (" << p.x() << "," << p.y() << ")." << endl;

  qDebug() << "Magnification:  " << Cell::Magnification() << endl;

  qDebug() << "Offsets:  " << Cell::Offset() << endl;

#endif

  QList<QGraphicsItem *> l=scene()->items(p);

#ifdef QDEBUG  

  qDebug() << "MousePressEvents, items: " << l.size() << endl;

  qDebug() << "Mouse button modifier: " << e->modifiers() << endl;

#endif

  if (e->button()==Qt::RightButton || l.size()==0) {

    //cerr << "Drawing an intersection line from " << p.x() << ", " << p.y() << endl;

    intersection_line = new QGraphicsLineItem( 0, scene() );

    intersection_line->setPen( QPen( QColor("red"), 3, Qt::DashLine ) );

    intersection_line->setLine( QLineF(p,p) );

    intersection_line->setZValue( 100 );

    intersection_line->show();

  }

  for (QList<QGraphicsItem *>::Iterator it=l.begin(); it!=l.end(); ++it) {

    QString currentFile_nopath = currentFile.section( '/', -1 );

    QString currentFile_path = currentFile.section( '/', 0, -2 );

    next_file = xml_files.back();

    next_file = currentFile_path+"/"+next_file;

    readStateXML((const char*)next_file);

  }

}

void Main::readFirstStateXML()

{

  // if we have already read a file, read the next file

  if (!currentFile.isEmpty() && working_dir) {

    QString next_file;

    QStringList xml_files = working_dir->entryList("*.xml");

    QString currentFile_nopath = currentFile.section( '/', -1 );

    QString currentFile_path = currentFile.section( '/', 0, -2 );

    next_file = xml_files.front();

    next_file = currentFile_path+"/"+next_file;

    readStateXML((const char*)next_file);

  }

}

void Main::readStateXML()

{

  //  extern Mesh mesh;

  stopSimulation();

#ifdef QDEBUG

  qDebug() << "Trying to open an OptionFileDialog" << endl;

#endif

  OptionFileDialog *fd = new OptionFileDialog( this, "read dialog", TRUE );

  fd->setMode( OptionFileDialog::ExistingFile );

  fd->setFilter( "XML files (*.xml)");

  if (working_dir) {

    fd->setDir(*working_dir);

  }

  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

    ( "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>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());

  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());

    file.seekg(0, std::ios::beg);

    str.assign((std::istreambuf_iterator<char>(file)),

	       std::istreambuf_iterator<char>());

    gpl->setDetailedText(QString(str.c_str()));

  }

  gpl->setText(QString( "<h3>GNU GENERAL PUBLIC LICENSE</h3>"

			"<p>Version 3, 29 June 2007</p>"

			"<p>Copyright &copy; 2007 Free Software Foundation, Inc. "

			"&lt;<a href=\"http://fsf.org/\">http://fsf.org/</a>&gt;</p><p>"

			"Everyone is permitted to copy and distribute verbatim copies "

			"of this license document, but changing it is not allowed.</p>"

			"<h2>GNU GENERAL PUBLIC LICENSE</h2>"));

  gpl->setButtonText( 1, "Dismiss" );

  gpl->show();

}

void Main::aboutQt(){

  QMessageBox::aboutQt( this, "Virtual Leaf" );

}

void Main::toggleShowCellCenters()

{

  Plot();

}

void Main::toggleShowWalls()

{

  Plot();

}

void Main::toggleShowApoplasts()

{

  Plot();

}

void Main::toggleShowNodes()

{

  Plot();

}

void Main::toggleNodeNumbers(void)

{

  Plot();

}

void Main::toggleCellNumbers(void)

{

  Plot();

}

void Main::toggleCellAxes(void)

{

  Plot();

}

void Main::toggleCellStrain(void)

{

  Plot();

}

void Main::toggleShowFluxes(void)

{

  Plot();

}

void Main::toggleShowBorderCells()

{

  Plot();

}

void Main::toggleHideCells(void)

{

  Plot();

  editor->FullRedraw();

}

void Main::toggleMovieFrames(){}

void Main::toggleLeafBoundary(){}

void Main::toggleDynCells() {}

void Main::startSimulation(void)

{

  timer->start( 0 );