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

	* tutorial3.pro: Added -Wno-write-strings and -Wno-unused-parameter to QMAKE_CXXFLAGS.

2010-06-23    <guravage@caterpie.sen.cwi.nl>

	* tutorial3.pro: Corrected windows library path.

	Q_INTERFACES(SimPluginInterface);

public:

	virtual QString ModelID(void);

	// Executed after the cellular mechanics steps have equillibrized

	virtual void CellHouseKeeping (CellBase *c);

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

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

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

	// (e.g. PIN accumulation)

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

	// Differential equations describing chemical reactions inside the cells

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

	// to be executed after a cell division

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

	// to be executed for coloring a cell

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

	// return number of chemicals

	virtual int NChem(void);

};

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

	* tutorial4.pro: Added -Wno-write-strings and -Wno-unused-parameter to QMAKE_CXXFLAGS.

2010-06-23    <guravage@caterpie.sen.cwi.nl>

	* tutorial4.pro: Corrected windows library path.

public:

	virtual QString ModelID(void);

	// Executed after the cellular mechanics steps have equillibrized

	virtual void CellHouseKeeping (CellBase *c);

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

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

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

	// (e.g. PIN accumulation)

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

	// Differential equations describing chemical reactions inside the cells

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

	// to be executed after a cell division

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

	// to be executed for coloring a cell

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

	// return number of chemicals

	virtual int NChem(void);

	virtual double PINflux(CellBase *this_cell, CellBase *adjacent_cell, Wall *w); 

};

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

	* tutorial5.pro: Added -Wno-write-strings and -Wno-unused-parameter to QMAKE_CXXFLAGS.

2010-06-23    <guravage@caterpie.sen.cwi.nl>

	* tutorial5.pro: Corrected windows library path.

public:

	virtual QString ModelID(void);

	// Executed after the cellular mechanics steps have equillibrized

	virtual void CellHouseKeeping (CellBase *c);

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

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

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

	// (e.g. PIN accumulation)

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

	// Differential equations describing chemical reactions inside the cells

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

	// to be executed after a cell division

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

	// to be executed for coloring a cell

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

	// return number of chemicals

	virtual int NChem(void);

	virtual double PINflux(CellBase *this_cell, CellBase *adjacent_cell, Wall *w); 

};

nu = 0. / double

rho0 = 0. / double

rho1 = 0. / double

c0 = 0. / double

gamma = 0. / double

eps = 0. / double

label = / label

label = <b>User-defined parameters</b> / label

k = 0., 0.0, 0.0, 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0. / doublelist

i1 = 0 / int

i2 = 0 / int

i3 = 0 / int

i4 = 0 / int

i5 = 0 / int

s1 =  / string

s2 =  / string

s3 =  / string

b1 = false / bool

b2 = false / bool

b3 = false / bool

b4 = false / bool

dir1 = . / directory

dir2 = . / directory

export_interval = 0 / int

#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("$Id$");

using namespace std;

// 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;

}

  mesh(m)

{

  editor = new FigureEditor(canvas,mesh, this);

#ifdef QDEBUG

  qDebug() << "Interactive = " << editor->isEnabled();

#endif

  working_dir = 0;

  QObject::connect( editor, SIGNAL(MousePressed()), this, SLOT(PauseIfRunning()));

  QObject::connect( editor, SIGNAL(MouseReleased()), this, SLOT(ContIfRunning()));

  QMenuBar* menu = menuBar();

  Q3PopupMenu* file = new Q3PopupMenu( menu );

  file->insertItem("&Read leaf", this, SLOT(readStateXML()));

  file->insertItem("&Save leaf", this, SLOT(saveStateXML()));

  file->insertItem("Snapshot", this, SLOT(snapshot()), Qt::CTRL+Qt::SHIFT+Qt::Key_S);

  file->insertSeparator();

  file->insertItem("Read next leaf", this, SLOT(readNextStateXML()), Qt::Key_PageDown);

  file->insertItem("Read previous leaf", this, SLOT(readPrevStateXML()), Qt::Key_PageUp);

  file->insertItem("Read last leaf", this, SLOT(readLastStateXML()), Qt::Key_End);

  file->insertItem("Read first leaf", this, SLOT(readFirstStateXML()), Qt::Key_Home);

  file->insertSeparator();

  file->insertItem("&Print...", this, SLOT(print()), Qt::CTRL+Qt::Key_P);

  file->insertSeparator();

  file->insertItem("E&xit", qApp, SLOT(quit()), Qt::CTRL+Qt::Key_Q);

  menu->insertItem("&File", file);

  Q3PopupMenu* edit = new Q3PopupMenu( menu );

  edit->insertItem("Reset Chemicals and Transporters", this, SLOT( CleanMesh()), Qt::CTRL+Qt::Key_R );

  edit->insertItem("Reset Chemicals", this, SLOT( CleanMeshChemicals()) );

  edit->insertItem("Reset Transporters", this, SLOT( CleanMeshTransporters()) );

  edit->insertItem("Randomize PIN1 Transporters", this, SLOT( RandomizeMesh()) );

  edit->insertItem("Cut away SAM", this, SLOT( CutSAM() ));

  menu->insertItem("&Edit", edit);

  run = new Q3PopupMenu( menu );

  running = false;

  paused_id = run->insertItem("&Simulation paused", this, SLOT(togglePaused()), Qt::Key_S);

  run->setItemChecked(paused_id, FALSE);

  menu->insertItem("&Run", run);

  view = new Q3PopupMenu( menu );

  view->insertItem("&Zoom in", this, SLOT(zoomIn()), Qt::CTRL+Qt::Key_Equal);

#endif

    double cw = (bbur.x - bbll.x);

    double ch = (bbur.y - bbll.y);

    QPainter pp(printer);

    QRect vp=pp.viewport();

#ifdef QDEBUG

    qDebug() << "Paper width = " << vp.width() << " x " << vp.height() << endl;

#endif

    // Note that Cell is also translated...

    pp.translate(-bbur.x,-bbur.y);

    if (cw>ch) {

      pp.scale(vp.width()/(2*cw*Cell::Magnification()), vp.width()/(2*cw*Cell::Magnification()));

    } else {

      pp.scale(vp.height()/(2*ch*Cell::Magnification()), vp.height()/(2*ch*Cell::Magnification()));

    }

    canvas.render(&pp, QRectF(), QRectF(0.,0.,canvas.width(),canvas.height()));

  }

}

void Main::TimeStepWrap(void)

{

  static int t=0;

  TimeStep();

  t++;

  if ((par.export_interval > 0) && ((t % par.export_interval) == 0)){

  }

  // check number of timesteps

  if (t==par.nit) {

    emit SimulationDone();

  }

}

void Main::RestartSim(void)

{

  stopSimulation();

  if ( QMessageBox::question(

			     this,

			     tr("Restart simulation?"),

			     tr("Restart simulation.\n"

				"Are you sure?"),

			     QMessageBox::Yes | QMessageBox::No, QMessageBox::NoButton ) == QMessageBox::Yes ) {

    cerr << "Restarting simulation" << endl;

    //    extern Mesh mesh;

    mesh.Clear();

    Init();

    Plot();

    editor->FullRedraw();

  } 

  //startSimulation();

}

void Main::FitCanvasToWindow(void)

{

  void readPrevStateXML();

  void readFirstStateXML();

  void readLastStateXML();

  void exportCellData();

  void exportCellData(QString);

  void saveStateXML();

  void snapshot();

  void savePars();

  void readPars();

  void clear();

  void init();

  virtual void CutSAM() { MainBase::CutSAM(); Refresh();}

  void enlarge();

  void shrink();

  void zoomIn();

  void zoomOut();

  void CleanMesh();

  void CleanMeshChemicals(void);

  void CleanMeshTransporters(void);

  void RandomizeMesh();

 signals:

  void SimulationDone(void);

  void ParsChanged(void);

 protected:

  Mesh &mesh;

 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

/*

 *

 *  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.

 *

 */

// Do not edit. All edits will be discarded.

#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>

#include <QStringList>

using namespace std;

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

Parameter::Parameter() {

  arrowcolor = strdup("white");

  arrowsize = 100;

  textcolor = strdup("red");

  cellnumsize = 1;

  k[5] = 0.;

  k[6] = 0.;

  k[7] = 0.;

  k[8] = 0.;

  k[9] = 0.;

  k[10] = 0.;

  k[11] = 0.;

  k[12] = 0.;

  k[13] = 0.;

  k[14] = 0.;

  i1 = 0;

  i2 = 0;

  i3 = 0;

  i4 = 0;

  i5 = 0;

  s1 = strdup("");

  s2 = strdup("");

  s3 = strdup("");

  b1 = false;

  b2 = false;

  b3 = false;

  b4 = false;

  dir1 = strdup(".");

  dir2 = strdup(".");

}

Parameter::~Parameter() {

// destruct parameter object

// free string parameter

CleanUp();

}

void Parameter::CleanUp(void) {

  if (arrowcolor) 

     free(arrowcolor);

  if (textcolor) 

     free(textcolor);

  if (cell_outline_color) 

     free(cell_outline_color);

  if (D) 

     free(D);

  if (initval) 

     free(initval);

  if (datadir) 

     free(datadir);

  if (k) 

     free(k);

  rho0 = fgetpar(fp, "rho0", 0., true);

  rho1 = fgetpar(fp, "rho1", 0., true);

  c0 = fgetpar(fp, "c0", 0., true);

  gamma = fgetpar(fp, "gamma", 0., true);

  eps = fgetpar(fp, "eps", 0., true);

  k = dgetparlist(fp, "k", 15, true);

  i1 = igetpar(fp, "i1", 0, true);

  i2 = igetpar(fp, "i2", 0, true);

  i3 = igetpar(fp, "i3", 0, true);

  i4 = igetpar(fp, "i4", 0, true);

  i5 = igetpar(fp, "i5", 0, true);

  s1 = sgetpar(fp, "s1", "", true);

  s2 = sgetpar(fp, "s2", "", true);

  s3 = sgetpar(fp, "s3", "", true);

  b1 = bgetpar(fp, "b1", false, true);

  b2 = bgetpar(fp, "b2", false, true);

  b3 = bgetpar(fp, "b3", false, true);

  b4 = bgetpar(fp, "b4", false, true);

  dir1 = sgetpar(fp, "dir1", ".", true);

  if (strcmp(dir1, "."))

    MakeDir(dir1);

  dir2 = sgetpar(fp, "dir2", ".", true);

  if (strcmp(dir2, "."))

    MakeDir(dir2);

}

const char *sbool(const bool &p) {

  const char *true_str="true";

  const char *false_str="false";

  if (p)

    return true_str;

  else

    return false_str;

}

void Parameter::Write(ostream &os) const {

  if (arrowcolor) 

  os << " arrowcolor = " << arrowcolor << endl;

  os << " arrowsize = " << arrowsize << endl;

  if (textcolor) 

  os << " textcolor = " << textcolor << endl;

  os << " cellnumsize = " << cellnumsize << endl;

  os << " nodenumsize = " << nodenumsize << endl;

  os << " node_mag = " << node_mag << endl;

     D[i++]=*(v++);

  }

}

if (!strcmp(namec, "initval")) {

  int i=0;

  vector<double>::const_iterator v=valarray.begin();

  while (v!=valarray.end() && i <= 14 ) {

     initval[i++]=*(v++);

  }

}

if (!strcmp(namec, "k")) {

  int i=0;

  vector<double>::const_iterator v=valarray.begin();

  while (v!=valarray.end() && i <= 14 ) {

     k[i++]=*(v++);

  }

}

}

ostream &operator<<(ostream &os, Parameter &p) {

    p.Write(os);

    return os;

}

/*

 *

 *  $Id$

 *

 *  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.

 *

 */

// WARNING: This file is automatically generated by make_parameter_source.pl. Do not edit.

#ifndef _PARAMETER_H_

#define _PARAMETER_H_

#include "vector.h"

#include <vector>

#include <libxml/parser.h>

#include <libxml/tree.h>

 class Parameter {

 public: 

   Parameter();

   ~Parameter();

   void CleanUp(void);

   void Read(const char *filename);

   void Write(ostream &os) const;

   void XMLAdd(xmlNode *root) const;

   void XMLRead(xmlNode *root);

   void AssignValToPar(const char *namec, const char *valc);

   void AssignValArrayToPar(const char *namec, vector<double> valarray);

  char * arrowcolor;

  double arrowsize;

  char * textcolor;

/*

 *

 *  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.

 *

 */

// Do not edit. All edits will be discarded.

#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" );

  arrowsize_edit = new QLineEdit( QString("%1").arg(par.arrowsize), this, "arrowsize_edit" );

  textcolor_edit = new QLineEdit( QString("%1").arg(par.textcolor), this, "textcolor_edit" );

  cellnumsize_edit = new QLineEdit( QString("%1").arg(par.cellnumsize), this, "cellnumsize_edit" );

  nodenumsize_edit = new QLineEdit( QString("%1").arg(par.nodenumsize), this, "nodenumsize_edit" );

  node_mag_edit = new QLineEdit( QString("%1").arg(par.node_mag), this, "node_mag_edit" );

  outlinewidth_edit = new QLineEdit( QString("%1").arg(par.outlinewidth), this, "outlinewidth_edit" );

  cell_outline_color_edit = new QLineEdit( QString("%1").arg(par.cell_outline_color), this, "cell_outline_color_edit" );

  resize_stride_edit = new QLineEdit( QString("%1").arg(par.resize_stride), this, "resize_stride_edit" );

  T_edit = new QLineEdit( QString("%1").arg(par.T), this, "T_edit" );

  c0_edit->setText( QString("%1").arg(par.c0) );

  gamma_edit->setText( QString("%1").arg(par.gamma) );

  eps_edit->setText( QString("%1").arg(par.eps) );

  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->setText( k_string );

  i1_edit->setText( QString("%1").arg(par.i1) );

  i2_edit->setText( QString("%1").arg(par.i2) );

  i3_edit->setText( QString("%1").arg(par.i3) );

  i4_edit->setText( QString("%1").arg(par.i4) );

  i5_edit->setText( QString("%1").arg(par.i5) );

  s1_edit->setText( QString("%1").arg(par.s1) );

  s2_edit->setText( QString("%1").arg(par.s2) );

  s3_edit->setText( QString("%1").arg(par.s3) );

  b1_edit->setText( QString("%1").arg(sbool(par.b1)));

  b2_edit->setText( QString("%1").arg(sbool(par.b2)));

  b3_edit->setText( QString("%1").arg(sbool(par.b3)));

  b4_edit->setText( QString("%1").arg(sbool(par.b4)));

  dir1_edit->setText( QString("%1").arg(par.dir1) );

  dir2_edit->setText( QString("%1").arg(par.dir2) );

  export_interval_edit->setText( QString("%1").arg(par.export_interval) );

  export_fn_prefix_edit->setText( QString("%1").arg(par.export_fn_prefix) );

}

/*

 *

 *  $Id$

 *

 *  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.

 *

 */

// WARNING: This file is automatically generated by make_parameter_source.pl. Do not edit.

#ifndef PARAMETER_DIALOG_H

#define PARAMETER_DIALOG_H

#include <qdialog.h>

#include <qspinbox.h>

#include <qlineedit.h>

#include <qlayout.h>

#include <qpushbutton.h>

#include <iostream>

class ParameterDialog : public QDialog {

    Q_OBJECT

      public:

	ParameterDialog(QWidget *parent=0, const char *name = 0, Qt::WindowFlags f = 0);

    virtual ~ParameterDialog(void);

    public slots:

    void Reset(void);

    private slots:

    void write(void);

  private:

  QLineEdit *arrowcolor_edit;

  QLineEdit *rho0_edit;

  QLineEdit *rho1_edit;

  QLineEdit *c0_edit;

  QLineEdit *gamma_edit;

  QLineEdit *eps_edit;

  QLineEdit *k_edit;

  QLineEdit *i1_edit;

  QLineEdit *i2_edit;

  QLineEdit *i3_edit;

  QLineEdit *i4_edit;

  QLineEdit *i5_edit;

  QLineEdit *s1_edit;

  QLineEdit *s2_edit;

  QLineEdit *s3_edit;

  QLineEdit *b1_edit;

  QLineEdit *b2_edit;

  QLineEdit *b3_edit;

  QLineEdit *b4_edit;

  QLineEdit *dir1_edit;

  QLineEdit *dir2_edit;

  QLineEdit *export_interval_edit;

  QLineEdit *export_fn_prefix_edit;

};

#endif