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

	* simitembase.cpp: Removed NULL assignments to unused variables.

 *

 *  This file is part of the Virtual Leaf.

 *

 *  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.

 *

 *  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.

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

Neighbor::Neighbor(void):

Neighbor::Neighbor(Cell *c, Node *n1, Node *n2):

  cell(c), nb1(n1), nb2(n2){}

 *

 *  This file is part of the Virtual Leaf.

 *

 *  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.

 *

 *  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.

 *

 *  This file is part of the Virtual Leaf.

 *

 *  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.

 *

 *  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.

 *

 *  This file is part of the Virtual Leaf.

 *

 *  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.

 *

 *  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.

 *

 *  This file is part of the Virtual Leaf.

 *

 *  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.

 *

 *  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.

 *

 *  This file is part of the Virtual Leaf.

 *

 *  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.

 *

 *  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.

 *

 *  This file is part of the Virtual Leaf.

 *

 *  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.

 *

 *  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.

    if (m.ShowBorderCellsP() || c.Boundary()==Cell::None) {

      if (!m.ShowBoundaryOnlyP() && !m.HideCellsP()) {

	if (m.ShowToolTipsP()) {

	  c.Draw(&canvas, info_string);

	} else {

	  c.Draw(&canvas);

  static int count=0;

  if (resize_stride) {

      FitLeafToCanvas();

    }

  }

  if (ShowWallsP())

    mesh.LoopWalls( bind2nd( mem_fun_ref( &Wall::Draw ), &canvas ) );

    mesh.LoopWalls( bind2nd( mem_fun_ref( &Wall::DrawApoplast ), &canvas ) );

  if (ShowMeshP()) 

    mesh.DrawNodes(&canvas);

      mesh.XMLSave(fname.str().c_str(), XMLSettingsTree());

    }

  }

}

CONFIG += qt

QMAKE_CXXFLAGS += -fexceptions

QMAKE_CXXFLAGS_DEBUG += -g3

QMAKE_CXXFLAGS_DEBUG += -DQDEBUG

win32 {

 CONFIG -= console

 GRAPHICS = qt 

 RC_FILE = VirtualLeaf.rc

 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

}

# Input

HEADERS += \

 canvas.h \

 cellbase.h \

 cell.h \

 $${PARTMPL}

SOURCES += \

 canvas.cpp \

 cellbase.cpp \

 cell.cpp \

}

win32 {

 LIBS += -L$${LIBDIR} -Llib -lvleaf

 QMAKE_CXXFLAGS += -DLIBXML_STATIC

 QMAKE_CXXFLAGS += -I$${LIBXML2DIR}\include -I$${LIBICONVDIR}\include -I$${LIBZDIR}\include

}

win32 {

 LIBS += -L$${LIBDIR} -Llib -lvleaf

 QMAKE_CXXFLAGS += -DLIBXML_STATIC

 QMAKE_CXXFLAGS += -I$${LIBXML2DIR}\include -I$${LIBICONVDIR}\include -I$${LIBZDIR}\include

}

win32 {

 LIBS += -L$${LIBDIR} -Llib -lvleaf

 QMAKE_CXXFLAGS += -DLIBXML_STATIC

 QMAKE_CXXFLAGS += -I$${LIBXML2DIR}\include -I$${LIBICONVDIR}\include -I$${LIBZDIR}\include

 *

 *  This file is part of the Virtual Leaf.

 *

 *  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.

 *

 *  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.

  view->setItemChecked(fluxes_id, FALSE);

  cell_walls_id = view->insertItem("Show transporters", this, SLOT(toggleShowWalls()));

  view->setItemChecked(cell_walls_id, FALSE);

  view->insertSeparator();

  only_boundary_id = view->insertItem("Show only leaf &boundary", this, SLOT(toggleLeafBoundary()));

  view->insertSeparator();

  tooltips_id = helpmenu->insertItem("Show Cell&Info", this, SLOT(Refresh()));

  helpmenu->setItemChecked(tooltips_id, true);

  helpmenu->insertSeparator();

  helpmenu->insertItem("&LICENSE", this, SLOT(gpl()) );

  statusBar();

  setCentralWidget(editor);

  printer = 0;

void Main::about()

{

  static QMessageBox* about = new QMessageBox

      "<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>"

      "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>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>.", 

  view->setItemChecked(hide_cells_id, hidecellsp);

  options->setItemChecked(dyn_cells_id, dynamicscellsp);

  view->setItemChecked( cell_walls_id, showwallsp);

  editor->setTransform(viewport);

}

  showfluxesp = view->isItemChecked(fluxes_id);

  dynamicscellsp = options->isItemChecked(dyn_cells_id);

  showwallsp = view->isItemChecked( cell_walls_id);

  hidecellsp = view->isItemChecked( hide_cells_id);

  xmlNode *settings = MainBase::XMLSettingsTree();

 *

 *  This file is part of the Virtual Leaf.

 *

 *  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.

 *

 *  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.

  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 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); }

  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 tooltips_id; // help -> Show Cell Info

  int hide_cells_id; // view->Hide Cells

  double flux_arrow_size;

 *

 *  This file is part of the Virtual Leaf.

 *

 *  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.

 *

 *  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.

 *

 *  This file is part of the Virtual Leaf.

 *

 *  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.

 *

 *  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.

 *

 *  This file is part of the Virtual Leaf.

 *

 *  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.

 *

 *  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.

  division_axis = 0;

}

{

  chem=new double[NChem()];

 *

 *  This file is part of the Virtual Leaf.

 *

 *  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.

 *

 *  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.

// 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.

// has a static pointer to it. After loading the plugin I set a static pointer to the same class 

class CellsStaticDatamembers {

 *

 *  This file is part of the Virtual Leaf.

 *

 *  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.

 *

 *  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.

 *

 *  This file is part of the Virtual Leaf.

 *

 *  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.

 *

 *  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.

 *

 *  This file is part of the Virtual Leaf.

 *

 *  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.

 *

 *  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.

 *

 *  This file is part of the Virtual Leaf.

 *

 *  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.

 *

 *  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.

 *

 *  This file is part of the Virtual Leaf.

 *

 *  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.

 *

 *  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.

  }

  void SetText(QString text) {

  }

 private:

CONFIG += staticlib

QMAKE_CXXFLAGS += -fexceptions

QMAKE_CXXFLAGS_DEBUG += -g3

QMAKE_CXXFLAGS_DEBUG += -DQDEBUG

QMAKE_CXXFLAGS_DEBUG -= -finstrument-functions

}

win32 {

 QMAKE_CXXFLAGS += -I$${LIBXML2DIR}\include -I$${LIBICONVDIR}\include -I$${LIBZDIR}\include

}

 *

 *  This file is part of the Virtual Leaf.

 *

 *  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.

 *

 *  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.

    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");

      if (!xmlStrcmp(name, (const xmlChar *)"show_walls")) {

	showwallsp = strtobool( (const char *)val );

      }

	showapoplastsp = strtobool( (const char *)val );

      if (!xmlStrcmp(name, (const xmlChar *)"save_movie_frames")) {

	movieframesp = strtobool( (const char *)val );

      }

 *

 *  This file is part of the Virtual Leaf.

 *

 *  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.

 *

 *  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.

  virtual bool ShowBoundaryOnlyP(void) {return showboundaryonlyp;}

  virtual bool ShowToolTipsP(void) {return showtooltipsp;}

  virtual bool ShowWallsP(void) {return showwallsp;}

  virtual bool ShowFluxesP(void) { return showfluxesp; }

  virtual bool DynamicCellsP(void) { return dynamicscellsp; }

  virtual void FitCanvasToWindow() {};

  bool movieframesp;

  bool showboundaryonlyp;

  bool showwallsp;

  bool showfluxesp;

  bool dynamicscellsp;

  bool showtooltipsp;

 *

 *  This file is part of the Virtual Leaf.

 *

 *  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.

 *

 *  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.

 *

 *  This file is part of the Virtual Leaf.

 *

 *  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.

 *

 *  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.

 *

 *  This file is part of the Virtual Leaf.

 *

 *  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.

 *

 *  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.

  shuffled_cells.clear();

  shuffled_nodes.clear();

#ifdef QDEBUG

  qDebug() << "cells.size() = " << cells.size() << endl;

  qDebug() << "walls.size() = " << walls.size() << endl;

      for (list<Neighbor>::const_iterator cit=node.owners.begin(); cit!=node.owners.end(); cit++) {

	Cell &c=*((Cell *)(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

	// 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 = *(cit->nb1);

	//Vector i_plus_1 = m->getNode(cit->nb2);

	Vector i_plus_1 = *(cit->nb2);

	      node_insertion_queue.push( Edge(&node, cit->nb2 ) );