2010-10-14    <merks@cwi.nl>

	* cell.cpp (DivideWalls): accomodated for rename of Circumference -> WallCircumference

	* hull.h: added an operator< to sort Points

	* hull.cpp: added an operator< to sort Points

2010-10-14    <guravage@caterpie.sen.cwi.nl>

	* VirtualLeafpar.tmpl (export_fn_prefix): changed to 'cell.'

	* canvas.cpp (TimeStepWrap): Removed TimeStamp(). Cell data

	filename now incorporates iteration number.

	* canvas.h (MainBase): Removed TimeStamp().

2010-10-08    <guravage@caterpie.sen.cwi.nl>

	* pardialog.h:

	* pardialog.cpp:

	* parameter.h:

	* parameter.cpp: Regenerated to include export_interval and export_fn_prefix.

	* VirtualLeafpar.tmpl: Appended export_interval and export_fn_prefix.

	* canvas.h (MainBase): Declared polymorphic exportCellData() functions.

	* canvas.cpp:

	(TimeStamp): New private TimeStamp() function.

	(TimeStepWrap): Added invocation of exportCellData().

	(exportCellData): Created two polymorphic functions: one with a

	single QString argument, the other with no argument. The former is

	called from TimeStepWrap() while the latter is called from the

	"Export cell areas" item in the file menu.

2010-10-07    <guravage@caterpie.sen.cwi.nl>

	* canvas.cpp (exportCellData): Added a Q3FileDialog to inquire

	where to write the exportCellData.

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

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

	* canvas.cpp (gpl): gpl3.txt can be either in an ancestor doc

	directory (Linux) or a decedent doc directory (Windows, via the

	binary installer).

	* 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

	(XMLReadWalls): viz_flux need not be declared twice; default value of 0.0.

	(XMLReadCells): Removed unused count variable.

	(XMLReadSimtime): Removed unused cur variable.

	(XMLRead): Removed unused v_str variable.

	* simitembase.cpp (userMove): Use assignment merely to obviate compilation warning.

	(SimItemBase) Ditto.

	* qcanvasarrow.h (QGraphicsLineItem): Use assignment merely to obviate compilation warning.

	* output.cpp (OpenWriteFile): Removed unused par variable.

	* nodeitem.cpp (paint): Use assignment merely to obviate compilation warning.

	* forwardeuler.cpp (odeint): Use assignment merely to obviate compilation warning.

	* cell.cpp (DivideOverGivenLine): Use assignment merely to obviate compilation warning.

	* canvas.cpp (FigureEditor): Use assignments merely to obviate compilation errors.

	(mousePressEvent): Removed unused item variable.

	* apoplastitem.cpp

	(ApoplastItem): Removed unused par variable.

	(OnClick): Use NULL assignment merely to obviate compilation warning.

	* mainbase.h (MainBase): Use assignment merely to obviate compilation warning.

	* cellbase.h (CellsStaticDatamembers): Use assignment merely to obviate compilation warning.

	* cell.cpp: Wrapped diagnostic output in QDEBUG blocks.

	* VirtualLeaf.cpp ditto.

	* canvas.cpp ditto.

	* cell.cpp ditto.

	* data_plot.cpp ditto.

	* forwardeuler.cpp ditto.

	* mesh.cpp ditto.

	* mesh.h

	* random.cpp ditto.

	* wall.cpp ditto.

	* wallbase.cpp ditto.

	* wallitem.cpp ditto.

2010-06-07    <guravage@caterpie.sen.cwi.nl>

	* VirtualLeaf.pro: Removed explicit perl invocation to regerenerate parameter files.

	* libplugin.pro: ditto.

2010-06-03    <guravage@caterpie.sen.cwi.nl>

	* pardialog.h: Added default versions of this automatically generated file.

	* pardialog.cpp: ditto.

	* parameter.h: ditto.

	* parameter.cpp: ditto.

	* VirtualLeaf.pro: delete/generate  parameter.{h,cpp}and pardialog.{h,cpp} only if perl is installed.

 	* libplugin.pro: dito.

	* Makefile: Added top-level Makefile

2010-05-10    <guravage@caterpie.sen.cwi.nl>

	* VirtualLeaf.pro: Added -fPIC option to QMAKE_CXXFLAGS.

}

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 );

  statusBar()->message("Simulation started");

  running = true;

}

void Main::stopSimulation(void)

{

  timer->stop();

  cerr << "Stopping simulation" << endl;

  statusBar()->message("Simulation paused");

  running = false;

}

void Main::togglePaused()

{

  bool s = run->isItemChecked(paused_id);

  if (s) {

    cerr << "Calling start simulation" << endl;

    startSimulation();

  } else {

    cerr << "Calling stop simulation" << endl;

    stopSimulation();

  }

}

void Main::setFluxArrowSize(int size)

{

  flux_arrow_size = size/100.;

}

void Main::enlarge()

{

  canvas.setSceneRect( QRectF( 0,0, canvas.width()*4./3., canvas.height()*4./3.) );

}

void Main::shrink()

{

  canvas.setSceneRect( QRectF( 0,0, canvas.width()*3/4, canvas.height()*3/4) );

}

void Main::scale(double factor)

{

  QMatrix m = editor->matrix();

  m.scale(factor, factor);

  editor->setMatrix( m );

}

void Main::zoomIn()

{

  QMatrix m = editor->matrix();

  m.scale( 1.1, 1.1 );

  editor->setMatrix( m );

}

void Main::zoomOut()

{

  QMatrix m = editor->matrix();

  m.scale( 0.9, 0.9 );

  editor->setMatrix( m );

}

void Main::print()

{

  if ( !printer ) printer = new QPrinter;

  if ( printer->setup(this) ) {

    //    extern Mesh mesh;

    Vector bbll,bbur;

    mesh.BoundingBox(bbll,bbur);

#ifdef QDEBUG

    qDebug() << "bbll = " << bbll << endl;

    qDebug() << "bbur = " << bbur << endl;

#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;

  stringstream fname;

  TimeStep();

  t++;

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

    fname << par.datadir << "/" << par.export_fn_prefix;

    fname.fill('0');

    fname.width(6);

    fname << t << ".csv";

    this->exportCellData(QString(fname.str().c_str()));

  }

  // 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)

{

  double scale_factor_x = (double)editor->width()/(double)canvas.width();

  double scale_factor_y = (double)editor->height()/(double)canvas.height();

  double scale_factor = scale_factor_x > scale_factor_y ? scale_factor_x : scale_factor_y;

  QMatrix m = editor->matrix();

#ifdef QDEBUG  

  qDebug() << "editor->width() = " << editor->width() << endl;

  qDebug() << "editor->height() = " << editor->height() << endl;

  qDebug() << "scale_factor = " << scale_factor << endl;

  qDebug() << "scale_factor_x = " << scale_factor_x << endl;

  qDebug() << "scale_factor_y = " << scale_factor_y << endl;

#endif

  m.scale( scale_factor, scale_factor );

  editor->setMatrix( m );

  editor->show();

}

void Main::PauseIfRunning(void)

{

  if (running) {

    timer->stop();

  }

}

void Main::ContIfRunning(void)

{

  if (running) {

    timer->start( 0 );

  }

}

void Main::FitLeafToCanvas(void) 

{

  Vector ll,ur;

  mesh.BoundingBox(ll, ur);

  ll*=Cell::Magnification(); ur*=Cell::Magnification();

  // give the leaf some space

  Vector border = ((ur-ll)/5.);

  QRectF bb( ll.x - border.x, ll.y - border.y, ur.x-ll.x + 2*border.x, ur.y-ll.y + 2*border.y );

  // cerr << ur << ", " << ll << endl;

  // editor->fitInView(bb, Qt::KeepAspectRatio);

  editor->ensureVisible(bb);

  //editor->setTransform(viewport);

}

void Main::CleanMesh(void) 

{

  vector<double> clean_chem(Cell::NChem());

  vector<double> clean_transporters(Cell::NChem());

  for (int i=0;i<Cell::NChem();i++) {

    clean_chem[i]=par.initval[i];

    clean_transporters[i]=0.;		

  }

  mesh.CleanChemicals(clean_chem);

  mesh.CleanTransporters(clean_transporters);

  mesh.setTime(0);

  Plot();

  editor->FullRedraw();

}

void Main::CleanMeshChemicals(void) 

{

  vector<double> clean_chem(Cell::NChem());

  for (int i=0;i<Cell::NChem();i++) {

    clean_chem[i]=par.initval[i];

  }

  mesh.CleanChemicals(clean_chem);

  mesh.setTime(0);

  Plot();

  editor->FullRedraw();

}

void Main::CleanMeshTransporters(void) 

{

  vector<double> clean_transporters(Cell::NChem());

  for (int i=0;i<Cell::NChem();i++) {

    clean_transporters[i]=0.;

  }

  mesh.CleanTransporters(clean_transporters);

  mesh.setTime(0);

  Plot();

  editor->FullRedraw();

}

void Main::RandomizeMesh(void) 

{

  vector<double> max_chem(Cell::NChem());

  vector<double> max_transporters(Cell::NChem());

  for (int i=0;i<Cell::NChem();i++) {

    max_transporters[i]=0.;

    max_chem[i]=par.initval[i];

  }

  // Amount of PIN1 at walls

  max_transporters[1] = 0.01;

  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);

  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);

  hidecellsp = view->isItemChecked( hide_cells_id);

  xmlNode *settings = MainBase::XMLSettingsTree();

  QTransform viewport(editor->transform());

  xmlAddChild(settings, XMLViewportTree(viewport));

  return settings;

}

void Main::exportCellData(QString fileName) {

#ifdef QDEBUG  

  qDebug() << "exportCellData fileName: " << fileName << endl;

#endif

  QFile file(fileName);

  if ( file.open( IO_WriteOnly ) ) {

    QTextStream stream( &file );

    mesh.CSVExportCellData(stream);

    mesh.CSVExportMeshData(stream);

    file.close();

  }

}

void Main::exportCellData() {

  QString fileName;

  Q3FileDialog *fd = new Q3FileDialog( this, "file dialog", TRUE );

  stopSimulation();

  fd->setMode( Q3FileDialog::AnyFile );

  if ( fd->exec() == QDialog::Accepted ) {

    fileName = fd->selectedFile();

  }

}

/* finis */