EI/VirtualLeaf Changeset - a58b80c85b6f · Centrum Wiskunde & Informatica (CWI)

Changeset - a58b80c85b6f

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0 46 0

Michael Guravage - 15 years ago 2010-06-17 12:25:40
michael.guravage@cwi.nl

Cleanup: e.g. removed commented out and otherwise disabled code.
--
user: Michael Guravage <michael.guravage@cwi.nl>
branch 'default'

changed src/OptionFileDialog.cpp
changed src/OptionFileDialog.h
changed src/UniqueMessage.cpp
changed src/VirtualLeaf.cpp
changed src/apoplastitem.cpp
changed src/apoplastitem.h
changed src/build_models/auxingrowthplugin.cpp
changed src/build_models/meinhardtplugin.cpp
changed src/build_models/testplugin.h
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/data_plot.cpp
changed src/data_plot.h
changed src/flux_function.h
changed src/forwardeuler.cpp
changed src/infobar.h
changed src/mainbase.cpp
changed src/mainbase.h
changed src/matrix.cpp
changed src/mesh.h
changed src/modelcatalogue.cpp
changed src/node.cpp
changed src/node.h
changed src/nodeitem.cpp
changed src/nodeset.h
changed src/output.cpp
changed src/output.h
changed src/parse.cpp
changed src/parse.h
changed src/random.cpp
changed src/random.h
changed src/sqr.h
changed src/vector.h
changed src/vleafmodel.h
changed src/wall.cpp
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

46 files changed with 332 insertions and 1831 deletions:

src/OptionFileDialog.cpp

src/OptionFileDialog.h

src/UniqueMessage.cpp

src/VirtualLeaf.cpp

src/apoplastitem.cpp

src/apoplastitem.h

src/build_models/auxingrowthplugin.cpp

src/build_models/meinhardtplugin.cpp

src/build_models/testplugin.h

src/canvas.cpp

304

src/canvas.h

src/cell.cpp

191

src/cell.h

src/cellbase.cpp

382

src/cellbase.h

src/data_plot.cpp

src/data_plot.h

src/flux_function.h

src/forwardeuler.cpp

src/infobar.h

src/mainbase.cpp

src/mainbase.h

src/matrix.cpp

src/mesh.h

src/modelcatalogue.cpp

src/node.cpp

src/node.h

src/nodeitem.cpp

src/nodeset.h

src/output.cpp

124

src/output.h

src/parse.cpp

src/parse.h

src/random.cpp

src/random.h

src/sqr.h

src/vector.h

src/vleafmodel.h

src/wall.cpp

src/wallbase.cpp

src/wallbase.h

src/wallitem.cpp

src/wallitem.h

src/warning.cpp

src/warning.h

src/xmlwrite.cpp

0 comments (0 inline, 0 general)

src/OptionFileDialog.cpp

➞

Show inline comments

@@ @@ -27,27 +27,23 @@ 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);
 	parcheck = new QCheckBox("parameters", this);
 	parcheck -> setCheckState(Qt::Checked);
 	//timecheck = new QCheckBox("time",this);
 	//timecheck -> setCheckState(Qt::Checked);
 	addToolButton(geometrycheck);
 	//addToolButton(timecheck);
 	addToolButton(parcheck);
 };
 OptionFileDialog::OptionFileDialog ( const QString & dirName, const QString & filter , QWidget * parent, const char * name , bool modal  ) :
 		Q3FileDialog(dirName, filter, parent, name, modal) {
 			cerr << "This is an OptionFileDialog\n";
 	};

src/OptionFileDialog.h

➞

Show inline comments

@@ @@ -11,31 +11,33 @@ @@
  *  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.
+ *
  */
 #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 );
 	bool readGeometryP(void) const { return geometrycheck->checkState()==Qt::Checked; }
 	bool readParametersP(void) const { return parcheck->checkState()==Qt::Checked; }
 private:
 	QCheckBox *geometrycheck;
 	QCheckBox *parcheck;
 	//QCheckBox *timecheck;
 };
-};
+#endif

src/UniqueMessage.cpp

➞

Show inline comments

@@ @@ -33,35 +33,31 @@ static const std::string _module_id("$Id @@
 using namespace std;
 UniqueMessageBox::UniqueMessageBox ( /* Icon icon,*/
 									 const QString & title,
 									 const QString & text,
 									 QWidget * parent ,
 									 Qt::WindowFlags f ) :
 QDialog(parent, f) {
 	label = new QLabel(text);
 	boxtext = text;
 	show_again = new QCheckBox(tr("Do not show this message again"));
 	//addButton(show_again, QMessageBox::ActionRole);
 	//addButton(QMessageBox::Ok);
 	okButton = new QPushButton(tr("Ok"));
 	if (issued_messages.contains(boxtext) ) {
 		cerr << "Saw message before\n";
 		display = false;
 	} else {
 		//cerr << "First time message\n";
 		//issued_messages << text;
 		display=true;
+	}
 	connect(okButton, SIGNAL(clicked()), this, SLOT(close()) );
 	QHBoxLayout *hlayout = new QHBoxLayout;
 	hlayout->addWidget(label);
 	hlayout->addWidget(okButton);
 	QVBoxLayout *layout = new QVBoxLayout;
 	layout->addLayout(hlayout);
 	layout->addWidget(show_again);
 	setLayout(layout);
 	setWindowTitle(title);

src/VirtualLeaf.cpp

➞

Show inline comments

@@ @@ -48,36 +48,29 @@ @@
 #ifdef HAVE_QWT
 #include "data_plot.h"
 #endif
 #include <QPalette>
 #include <QBrush>
 #include <QToolTip>
 #include "simplugin.h"
 #include <QPluginLoader>
 #include <QDir>
 #include "modelcatalogue.h"
 /* #define _xstr_(s) _str_(s)
    #define _str_(s) #s
    #include _xstr_(REACTIONS_HEADER)
 */
 static const std::string _module_id("$Id$");
 extern Parameter par;
 MainBase *main_window = 0;
 //double auxin_account = 0.;
 #ifdef XFIGGRAPHICS
 #define TIMESTEP double Graphics::TimeStep(void)
 #endif
 class PrintNode {
 public:
   void operator() (const Node &n) const
+  {
     cerr << n.Index() << ": " << n <<  endl;
+  }
 };
@@ @@ -183,34 +176,24 @@ void MainBase::Plot(int resize_stride) { @@
   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 << ".pdf";
 	 if (par.storage_stride <= par.xml_storage_stride) {
 	 frame++;
+	 }
 	 // Write high-res JPG snapshot every plot step
 	 Save(fname.str().c_str(), "PDF");
       */
       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.";
@@ @@ -268,84 +251,50 @@ TIMESTEP { @@
     // i.e. cell wall tension equillibrization is much faster
     // than biological processes, including division, cell wall yielding
     // and cell expansion
     mesh.InsertNodes(); // (this amounts to cell wall yielding)
     if ( (-dh) < par.energy_threshold) {
       mesh.IncreaseCellCapacityIfNecessary();
       mesh.DoCellHouseKeeping();
       //mesh.LoopCurrentCells(mem_fun(&plugin->CellHouseKeeping)); // this includes cell division
       // Reaction diffusion
       /*CelltoCellTransport *transport_f = &TestPlugin::CelltoCellTransport;
 	CellReaction *cellreaction_f = new plugin->CellDynamics();
 	WallReaction *wall_f = new WallDynamics();*/
       mesh.ReactDiffuse(par.rd_dt);
       t++;
       Plot(par.resize_stride);
       /*QVector< QPair<double, int> > angles=mesh.VertexAnglesValues();
 	QString afname=QString("Angles/anglesvalues%1.dat").arg(t,6,10,QChar('0'));
 	ofstream af(afname.toStdString().c_str());
       */
       /*for (QVector< QPair<qreal, int> >::const_iterator v=angles.begin();
 	v!=angles.end();
 	v++) {
 	af << v->first << " " << v->second << endl;
+	}
       */
+    }
   } else {
     /*  TransportFunction *transport_f = new CelltoCellTransport();
 	CellReaction *cellreaction_f = new CellDynamics();
 	WallReaction *wall_f = new WallDynamics();
 	mesh.ReactDiffuse_New(transport_f, cellreaction_f, wall_f, par.rd_dt);*/
     mesh.ReactDiffuse(par.rd_dt);
     Plot(par.resize_stride);
+  }
   i++;
   return mesh.getTime();
+}
 /* Called if a cell is clicked */
 void Cell::OnClick(QMouseEvent *e) {
   e = NULL; // use assignment merely to obviate compilation warning
   /* #ifdef HAVE_QWT
   // Launch DataPlot window
   QStringList curvenames;
   for (int i=0;i<NChem();i++) {
   curvenames += QString("Chem #%1").arg(i);
+  }
   PlotDialog *plot = new PlotDialog((Main *)main_window, QString("Monitor for Cell %1").arg(Index()), curvenames);
   QObject::connect(this, SIGNAL(ChemMonValue(double, double *)),
   plot, SLOT(AddValue(double,double *)));
   #endif
   */
   //getMesh().plugin->OnClick(*this);
+}
 /* Custom message handler - Default appends a newline character to the end of each line. */
 void vlMessageOutput(QtMsgType type, const char *msg)
+{
   switch (type) {
   case QtDebugMsg:
     //fprintf(stderr, "Debug: %s\n", msg);
     cerr << msg << flush;
     break;
   case QtWarningMsg:
@@ @@ -469,35 +418,24 @@ int main(int argc,char **argv) { @@
     } else {
       main_window=new MainBase(canvas, mesh);
+    }
     canvas.setSceneRect(QRectF());
     if (!batch) {
       QObject::connect( qApp, SIGNAL(lastWindowClosed()), qApp, SLOT(quit()) );
+    }
     // Load plugins
     /*QVector<SimPluginInterface *> plugins = LoadPlugins();
       InstallPlugin(plugins[0], main_window);
       cerr << "List of models:" << endl;
       foreach (SimPluginInterface *p, plugins) {
       cerr << p->ModelID().toStdString() << endl;
+      }
     */
     // Install model or read catalogue of models
     ModelCatalogue model_catalogue(&mesh, useGUI?(Main *)main_window:0,modelfile);
     if (useGUI)
       model_catalogue.PopulateModelMenu();
     model_catalogue.InstallFirstModel();
     if (leaffile)
       main_window->Init(leaffile);
     Cell::SetMagnification(1);
     Cell::setOffset(0,0);

src/apoplastitem.cpp

➞

Show inline comments

@@ @@ -34,26 +34,26 @@ static const std::string _module_id("$Id @@
 ApoplastItem::ApoplastItem( Wall *w, QGraphicsScene *canvas )
 : QGraphicsLineItem( 0, canvas ), SimItemBase( w, canvas){
 	setColor();
 	// line with "PIN1"is a bit inside the cell wall
 	Vector edgevec = (*(w->N2())) - (*(w->N1()));
 	Vector perp = edgevec.Normalised().Perp2D();
 	Vector offs = Cell::Offset();
 	double factor = Cell::Factor();
 	Vector from = ( offs + *(w->N1()) ) * factor;// + (wn==1?-1:1) * par.outlinewidth;// * 0.2 * factor * perp;
 	Vector to = ( offs + *(w->N2()) ) *factor;// + (wn==1?-1:1) * par.outlinewidth;// * 0.2 * factor * perp;
 	Vector from = ( offs + *(w->N1()) ) * factor;
 	Vector to = ( offs + *(w->N2()) ) *factor;
 	setLine(( from.x ),
 			( from.y ),
 			( to.x ),
 			( to.y ) );
 	setZValue(12);
+}
 void ApoplastItem::setColor(void) {
@@ @@ -61,15 +61,15 @@ void ApoplastItem::setColor(void) { @@
 	static const QColor purple("Purple");
 	static const QColor blue("blue");
 	Wall *w=&getWall();
 	double val = w->getApoplast(2);
 	diffcolor.setRgb( 0,0,(int)( ( val / (1 + val) )*255.));
 	setPen (QPen(diffcolor, 20) );
+}
 void ApoplastItem::OnClick(QMouseEvent *e) {
-  e = NULL; // merely to obviate compile time warning
+  e = NULL; // merely to obviate compilation warnings
+}

src/apoplastitem.h

➞

Show inline comments

@@ @@ -31,20 +31,18 @@ @@
 #include "simitembase.h"
 #include "wall.h"
 //! Shows transporter concentrations at one side of the wall
 class ApoplastItem : public QGraphicsLineItem, public SimItemBase
+{
 public:
 	ApoplastItem( Wall *n, QGraphicsScene *canvas );
 	virtual ~ApoplastItem() {}
 	Wall &getWall(void) const { return *class_cast<Wall*>(obj); }
 	void OnClick(QMouseEvent *e);
 	//virtual void userMove(double dx, double dy);
 	//virtual void paint( QPainter * painter, const QStyleOptionGraphicsItem * option, QWidget * widget = 0);
 	void setColor(void);
 private:
 	int wn;
 };
 #endif

src/build_models/auxingrowthplugin.cpp

➞

Show inline comments

@@ @@ -49,34 +49,24 @@ void AuxinGrowthPlugin::OnDivide(ParentI @@
 	// After divisions, parent and daughter cells get a standard stock of PINs.
 	daughter1->SetChemical(1, par->initval[1]);
 	daughter2->SetChemical(1, par->initval[1]);
 	// Reset transporter values of parent and daughter
 	QList<WallBase *> walls;
 	foreach(WallBase *w, walls) {
 		w->setTransporter(daughter1, 1, 0.);
+	}
 	//daughter1.LoopWalls(Wall::setTransporter(&daughter1, 1, 0.));
 	/* for (list<Wall *>::const_iterator w=daughter2.walls.begin();
 		 w!=daughter2.walls.end();
 		 w++) {
 		// reset transporter value
 		(*w)->setTransporter(&daughter2, 1, 0.);
+	}
 	*/
+}
 void AuxinGrowthPlugin::SetCellColor(CellBase *c, QColor *color) {
 	// Red: PIN1
 	// Green: Auxin
 	if (c->CellType()==1) color->setNamedColor("Blue");
 	else color->setRgb(c->Chemical(1)/(1+c->Chemical(1)) * 255.,(c->Chemical(0)/(1+c->Chemical(0)) * 255.),/* (chem[2]/(1+chem[2]) *255.) */ 0);
+}
@@ @@ -97,38 +87,36 @@ void AuxinGrowthPlugin::CellHouseKeeping @@
+}
 void AuxinGrowthPlugin::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) {
 	// leaf edge is const source of auxin
     // (Neumann boundary condition: we specify the influx)
     if (w->C2()->BoundaryPolP()) {
 		if (w->AuxinSource()) {
 			double aux_flux = par->leaf_tip_source * w->Length();
 			dchem_c1[0]+= aux_flux;
 			// dchem_c2 is undefined..!
 			return;
 		} else {
 			return;
+		}
+	}
 	if (w->C1()->BoundaryPolP()) {
 		if (w->AuxinSource()) {
 			double aux_flux = par->leaf_tip_source * w->Length();
 			dchem_c2[0] += aux_flux;
 			// dchem_c1 is undefined...!
 			return;
 		} else {
 			if (w->AuxinSink()) {
 				// efflux into Shoot Apical meristem
 				// we assume all PINs are directed towards shoot apical meristem
 				dchem_c2[0] -= par->sam_efflux * w->C2()->Chemical(0) / (par->ka + w->C2()->Chemical(0));
 				return;
 			} else
 				return;
@@ @@ -158,59 +146,57 @@ void AuxinGrowthPlugin::CelltoCellTransp @@
+}
 void AuxinGrowthPlugin::WallDynamics(Wall *w, double *dw1, double *dw2) {
     // Cells polarize available PIN1 to Shoot Apical Meristem
     if (w->C2()->BoundaryPolP()) {
 		if (w->AuxinSink()) {
 			dw1[0] = 0.; dw2[0] = 0.;
 			//dw1[2] = 0.; dw2[2] = 0.;
 			// assume high auxin concentration in SAM, to convince PIN1 to polarize to it
 			// exocytosis regulated0
 			double nb_auxin = par->sam_auxin;
 			double receptor_level = nb_auxin * par->r / (par->kr + nb_auxin);
 			dw1[1] = par->k1 * w->C1()->Chemical(1) * receptor_level /( par->km + w->C1()->Chemical(1) ) - par->k2 * w->Transporters1(1);
 			dw2[1] = 0.;
 			return;
 		} else {
-			dw1[0]=dw2[0]=dw1[1]=dw2[1];//=dw1[2]=dw2[2];
 			dw1[0]=dw2[0]=dw1[1]=dw2[1];
 			return;
+		}
+    }
     if (w->C1()->BoundaryPolP()) {
 		if (w->AuxinSink())  {
 			dw1[0] = 0.; dw2[0] = 0.;
 			//dw1[2] = 0.; dw2[2] = 0.;
 			// assume high auxin concentration in SAM, to convince PIN1 to polarize to it
 			// exocytosis regulated
 			double nb_auxin = par->sam_auxin;
 			double receptor_level = nb_auxin * par->r / (par->kr + nb_auxin);
 			dw2[1] = par->k1 * w->C2()->Chemical(1) * receptor_level /( par->km + w->C2()->Chemical(1) ) - par->k2 * w->Transporters2(1);
 			dw1[1] = 0.;
 			return;
 		}  else {
-			dw1[0]=dw2[0]=dw1[1]=dw2[1];//=dw1[2]=dw2[2];
 			dw1[0]=dw2[0]=dw1[1]=dw2[1];
 			return;
+		}
+    }
     // PIN1 localization at wall 1
     // Note: chemical 0 is Auxin (intracellular storage only)
     // Chemical 1 is PIN1 (walls and intracellular storage)
     //! \f$ \frac{d Pij/dt}{dt} = k_1 A_j \frac{P_i}{L_ij} - k_2 P_{ij} \f$
     // Note that Pij is measured in term of concentration (mol/L)
     // Pi in terms of quantity (mol)
@@ @@ -228,26 +214,24 @@ void AuxinGrowthPlugin::WallDynamics(Wal @@
     double  auxin1 = w->C1()->Chemical(0);
     double receptor_level2 = auxin1 * par->r / (par->kr + auxin1);
     // normal cell
     dPijdt2 =
 	// exocytosis regulated
 	par->k1 * w->C2()->Chemical(1) * receptor_level2 / ( par->km + w->C2()->Chemical(1) ) - par->k2 * w->Transporters2(1);
     /* PIN1 of neighboring vascular cell inhibits PIN1 endocytosis */
     dw1[0] = 0.; dw2[0] = 0.;
     //dw1[2] = 0.; dw2[2] = 0.;
     dw1[1] = dPijdt1;
     dw2[1] = dPijdt2;
+}
 double AuxinGrowthPlugin::complex_PijAj(CellBase *here, CellBase *nb, Wall *w) {
 	// gives the amount of complex "auxinreceptor-Pin1"  at the wall (at QSS)
 	//return here.Chemical(1) * nb.Chemical(0) / ( par->km + here.Chemical(1));
 	double nb_aux = (nb->BoundaryPolP() && w->AuxinSink()) ? par->sam_auxin : nb->Chemical(0);
 	double receptor_level = nb_aux * par->r / (par->kr + nb_aux);
@@ @@ -255,32 +239,24 @@ double AuxinGrowthPlugin::complex_PijAj( @@
+}
 void AuxinGrowthPlugin::CellDynamics(CellBase *c, double *dchem) {
 	// Note: Pi and Pij measured in numbers of molecules, not concentrations
 		double dPidt = 0.;
 		double sum_Pij = c->SumTransporters( 1 );
 		// exocytosis regulated:
 	dPidt = -par->k1 * c->ReduceCellAndWalls<double>( far_3_arg_mem_fun( *this, &AuxinGrowthPlugin::complex_PijAj ) ) + par->k2 * sum_Pij;
 	/*for ( list<Wall *>::const_iterator w = c->walls.begin();
 		 w!=walls.end();
 		 w++) {
 		if ((*w)->C1() == c)
 			dPidt +=  complex_PijAj( (*w)->C1(), (*w)->C2(), *w );
 		else
 			dPidt +=  complex_PijAj( (*w)->C2(), (*w)->C1(), *w );
 	}*/
 	// production of PIN depends on auxin concentration
 	dPidt +=  (c->AtBoundaryP()?par->pin_prod_in_epidermis:par->pin_prod) * c->Chemical(0) - c->Chemical(1) * par->pin_breakdown;
 	// no PIN production in SAM
 	if (c->Boundary() == CellBase::SAM) {
 			dchem[1]=0.;
 		dchem[0]= - par->sam_auxin_breakdown * c->Chemical(0);
 	} else {
 		dchem[1] = dPidt;

src/build_models/meinhardtplugin.cpp

➞

Show inline comments

@@ @@ -108,29 +108,23 @@ void MeinhardtPlugin::WallDynamics(Wall @@
   w = NULL;
 	for (int c = 0;c<NChem();c++) {
 		dw1[c] = 0.; dw2[c] = 0.;
+    }
+}
 void MeinhardtPlugin::CellDynamics(CellBase *c, double *dchem) {
 	double Y = c->Chemical(0);
 	double A = c->Chemical(1);
 	double H = c->Chemical(2);
 	double S = c->Chemical(3);
-	//double expansin = c->Chemical(4);
     dchem[0] = ( par->d * A - par->e * Y + Y*Y/(1 + par->f * Y*Y ) );
 	dchem[1] = ( par->c * A*A*S/H - par->mu * A + par->rho0*Y );
 	dchem[2] = ( par->c * A*A*S - par->nu*H + par->rho1*Y );
 	dchem[3] = ( par->c0 - par->gamma*S - par->eps * Y * S );
 	//dchem[4] = ( -par->expansindecay * expansin );
 	//for (int i=0;i<4;i++) { cerr << "[ " << dchem[i] << " ]"; } cerr << endl;
 //	cerr << "Chemicals: "; for (int i=0;i<NChem();i++) { cerr << c->Chemical(i) << " "; } cerr << endl;
 // test:	dchem[0] = 0.01 * c->Chemical(0) * ( 1. - c->Chemical(0));
+}
 Q_EXPORT_PLUGIN2(meinhardtplugin, MeinhardtPlugin)

src/build_models/testplugin.h

➞

Show inline comments

@@ @@ -11,24 +11,26 @@ @@
  *  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.
+ *
  */
 #ifndef _TESTPLUGIN_H_
 #define _TESTPLUGIN_H_
 #include <QObject>
 #include <QtGui>
 #include <QString>
 #include "../simplugin.h"
 class TestPlugin : public QObject, SimPluginInterface {
 	Q_OBJECT
 	Q_INTERFACES(SimPluginInterface);
 public:
@@ @@ -46,15 +48,13 @@ public: @@
 	// 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) { return 0; }
 };
 #endif

src/canvas.cpp

➞

Show inline comments

@@ @@ -154,123 +154,58 @@ void FigureEditor::mousePressEvent(QMous @@
   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
   /*  if (dynamic_cast<Main *>(parent())->RotationModeP()) {
   // if in rotation mode, exit it upon a mouse click
   dynamic_cast<Main *>(parent())->ExitRotationMode();
   }*/
   QList<QGraphicsItem *> l=scene()->items(p);
 #ifdef QDEBUG
   qDebug() << "MousePressEvents, items: " << l.size() << endl;
   qDebug() << "Mouse button modifier: " << e->modifiers() << endl;
 #endif
     /*  if (rotation_mid_point) {
     // calculate rotation angle alpha
     QPointF q_v1 = intersection_line->line().p2();
     - intersection_line->line().p1();
     QPointF q_v2 = angle_line->line().p2();
     - angle_line->line().p1();
     Vector v1(q_v1.x(),q_v1.y());
     Vector v2(q_v2.x(),q_v2.y());
     cerr << "v1 = " << v1 << endl;
     cerr << "v2 = " << v2 << endl;
     rot_angle = v1.SignedAngle(v2);
     cerr << "Angle is " << rot_angle << endl;
     const QPointF &q_c(angle_line->line().p1());
     Vector center = Vector(q_c.x(), q_c.y()) / Cell::Factor() - Cell::Offset();
     cerr << "Center is " << center << endl;
     mesh.Rotate(rot_angle, center);
     delete angle_line;
     angle_line=0;
     delete intersection_line;
     intersection_line=0;
     viewport()->setMouseTracking( FALSE );
     dynamic_cast<Main *>(parent())->Plot();
     return;
     }*/
     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) {
       /*if ( (*it)->rtti() == imageRTTI ) {
 	ImageItem *item= (ImageItem*)(*it);
 	if ( !item->hit( p ) )
 	continue;
 	}*/
       #ifdef QDEBUG
       qDebug() << typeid(**it).name() << endl;
       #endif
       if ( !strcmp(typeid(**it).name(),"8NodeItem")) {
 	//moving = dynamic_cast<NodeItem*>(*it);
 	//moving = *it;
 	//moving_start = p;
 	stringstream data_strstream;
 	data_strstream << (dynamic_cast<NodeItem*>(*it))->getNode();
 	dynamic_cast<Main *>(parent())->UserMessage(QString(data_strstream.str().c_str()));
 	(dynamic_cast<NodeItem*>(*it))->OnClick(e->button());
+      }
       else
 	if ( !strcmp(typeid(**it).name(),"8CellItem") ) {
 	  Cell &c=((dynamic_cast<CellItem *>(*it))->getCell());
 	  //static int old_stride=100;
 	  //if (!c.Source()) {
 	  /* if (!c.Source()) {
 	     c.SetChemical(0,par.cellsource);
 	     //flag=true;
 	     //c.SetSource(0,par.cellsource);
 	     //c.Fix();
 	     //cerr << "Setting source\n";
 	     } else {
 	     //c.UnsetSource();
 	     cerr << "Unsetting source\n";
 	     } */
 	  // OnClick to be defined in end-user code
 	  c.OnClick(e);
 	} else {
 	  if ( !strcmp(typeid(**it).name(),"8WallItem") ) {
 	    (dynamic_cast<WallItem *>(*it))->OnClick(e);
+	  }
+	}
+    }
   FullRedraw();
   moving = 0;
+}
@@ @@ -291,108 +226,91 @@ void FigureEditor::mouseMoveEvent(QMouse @@
     QPointF rotation_midpoint = mesh.Centroid()*Cell::Factor() - Cell::Offset();
     // calculate rotation angle
     double dy = (rotation_midpoint.y() - p.y());
     double dx = (rotation_midpoint.x() - p.x());
     double new_rot_angle = atan2(dx, dy);
     double d_alpha = new_rot_angle - rot_angle;
     rot_angle = new_rot_angle;
     mesh.Rotate(d_alpha, ( Vector(rotation_midpoint) + Cell::Offset() ) / Cell::Factor() );
     //viewport()->setMouseTracking( FALSE );
     dynamic_cast<Main *>(parent())->Plot(0);
 	  FullRedraw();
     return;
+  }
   if ( moving ) {
-    //QPoint p = matrix().inverted().map(e->pos());
     QPointF p = mapToScene(e->pos());
     moving->userMove(p.x() - moving_start.x(),
 		     p.y() - moving_start.y());
     moving_start = p;
     scene()->update();
+  }
   //cerr << "event";
   // keep track of intersection line to interactively cut a growing leaf
   /* if (angle_line) {
     QPointF sp = angle_line -> line().p1(); // startpoint
     //QPointF ep = matrix().inverted().map(e->pos()); // endpoint
     QPointF ep = mapToScene(e->pos()); // endpoint
     angle_line -> setLine( QLineF(sp, ep) );
     scene()->update();
     } else { */
   if ( intersection_line ) {
     QPointF sp = intersection_line -> line().p1(); // startpoint
     //QPointF ep = matrix().inverted().map(e->pos()); // endpoint
     QPointF ep = mapToScene(e->pos()); // endpoint
     intersection_line -> setLine( QLineF(sp, ep) );
     scene()->update();
     // Need this for Mac
     FullRedraw();
+    }
   /* } */
+}
 //void FigureEditor::contentsMouseReleaseEvent(QMouseEvent* e)
 void FigureEditor::mouseReleaseEvent(QMouseEvent* e)
+{
   emit MouseReleased();
   // intersection line for leaf was finished now.
   if (e->button()==Qt::LeftButton) {
     if (intersection_line ) {
       #ifdef QDEBUG
       qDebug() << "Trying to cut leaf" << endl;
       #endif
       QPointF sp = intersection_line -> line().p1(); // startpoint
       //QPointF ep = matrix().inverted().map(e->pos()); // endpoint
       QPointF ep = mapToScene(e->pos());
       intersection_line -> setLine( QLineF(sp, ep) );
       intersection_line -> show();
       vector <CellItem *> intersected_cells = getIntersectedCells();
       // no cells selected, do nothing
       if (intersected_cells.size()==0) {
         #ifdef QDEBUG
 	qDebug() << "No cells detected :-(" << endl;
 	#endif
 	return;
+      }
       Vector startpoint = Vector(sp.x(), sp.y()) / Cell::Factor() - Cell::Offset();
       Vector endpoint = Vector(ep.x(), ep.y()) / Cell::Factor() - Cell::Offset();
       // Mesh &m(intersected_cells.front()->getCell().getMesh());
       NodeSet *node_set = new NodeSet;
       for (vector<CellItem *>::iterator it = intersected_cells.begin();
 	   it != intersected_cells.end();
 	   it++) {
 	//(*it)->Mark();
 	(*it)->setBrush(QBrush("purple"));
 	Cell &c=(*it)->getCell();
 	// sometimes the cell hasn't properly divided yet before the
 	// next division is called?  so check for it?  let's find a way
 	// to do this later. Note that this functionality currently
 	// might result in a segmentation fault for users who are
 	// quickly dragging and releasing division lines...
 	scene()->update();
 	#ifdef QDEBUG
@@ @@ -403,25 +321,24 @@ void FigureEditor::mouseReleaseEvent(QMo @@
+      }
       node_set->CleanUp();
       mesh.AddNodeSet(node_set);
       #ifdef QDEBUG
       qDebug() << "Done DivideOverGivenLine" << endl;
       #endif
       mesh.TestIllegalWalls();
       // Do the actual cutting and removing
       if (intersected_cells.size()) {
 	//      Mesh &m(intersected_cells.front()->getCell().getMesh());
 	mesh.CutAwayBelowLine( startpoint, endpoint );
 	// Correct flags of nodeset
 	for (
 	     NodeSet::iterator i = node_set->begin();
 	     i != node_set->end();
 	     i++) {
 	  (*i)->SetSAM();
 	  (*i)->SetBoundary();
+	}
 	// Make cells attached to nodeset part of the boundary
@@ @@ -456,62 +373,52 @@ void FigureEditor::mouseReleaseEvent(QMo @@
       dynamic_cast<Main *>(parent())->Plot();
         #ifdef QDEBUG
 	qDebug() << "NodeSet of cutting line: " << *node_set << endl;
 	#endif
+    }
   } else
     if (e->button()==Qt::RightButton) {
       if (intersection_line /* && !angle_line*/) {
 	//QPointF p = matrix().inverted().map(e->pos());
 	QPointF p = mapToScene(e->pos());
 	QPointF sp = intersection_line->line().p1();
 	viewport()->setMouseTracking( TRUE );
 	/* angle_line = new QGraphicsLineItem( 0, scene() );
 	angle_line->setPen( QPen( QColor("Blue"), 3, Qt::DashLine ) );
 	angle_line->setLine( QLineF(sp, p) );
 	angle_line->setZValue( 100 );
 	angle_line->show();
 	*/
+      }
+    }
+}
 // returns a vector of pointer to cells colliding with intersection line
 vector <CellItem *> FigureEditor::getIntersectedCells(void) {
   vector <CellItem *> colliding_cells;
   QList<QGraphicsItem *> l = intersection_line->collidingItems( );
   #ifdef QDEBUG
   qDebug() <<  "l.size() = " << l.size() << endl;
   #endif
   for (QList<QGraphicsItem *>::Iterator it=l.begin(); it!=l.end(); ++it) {
     #ifdef QDEBUG
     qDebug() << typeid(**it).name() << endl;
     #endif
     if ( !strcmp(typeid(**it).name(),"8CellItem") ) {
       colliding_cells.push_back(dynamic_cast<CellItem *>(*it));
+    }
+  }
   delete intersection_line;
   intersection_line = 0;
   return colliding_cells;
+}
 void FigureEditor::FullRedraw(void) {
 	QList<QRectF> rl;
 	rl << sceneRect();
@@ @@ -546,192 +453,145 @@ void FigureEditor::insertNode(QPointF p) @@
   FullRedraw();
 #ifdef QDEBUG
   qDebug() << "Node: " << p << endl;
 #endif
+}
 static uint mainCount = 0;
 Main::Main(QGraphicsScene& c, Mesh &m, QWidget* parent, const char* name, Qt::WindowFlags f) :
   Q3MainWindow(parent,name,f),
   MainBase(c,m),
   mesh(m)
 	  //canvas(c)
+{
   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("&Fill canvas", this, SLOT(init()), Qt::CTRL+Qt::Key_F);
 	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->insertItem("&New view", this, SLOT(newView()), Qt::CTRL+Qt::Key_N);
    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->insertItem("Read &parameters", this, SLOT(readPars()));
   //file->insertItem("&Write parameters", this, SLOT(savePars()));
 	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 );
   //  edit->insertItem("Add &Polygon", this, SLOT(addPolygon()), ALT+Key_P);
   //edit->insertItem("Add &Line", this, SLOT(addLine()), ALT+Key_L);
   running = false;
 	paused_id = run->insertItem("&Simulation paused", this, SLOT(togglePaused()), Qt::Key_S);
   run->setItemChecked(paused_id, FALSE);
   //run->insertItem("&Divide Cell", this, SLOT(Divide()), Qt::CTRL+Qt::Key_D);
  // run->insertItem("&Restart Simulation", this, SLOT(RestartSim()));
   menu->insertItem("&Run", run);
   view = new Q3PopupMenu( menu );
   //view->insertItem("&Enlarge", this, SLOT(enlarge()), SHIFT+CTRL+Key_Plus);
   //view->insertItem("Shr&ink", this, SLOT(shrink()), SHIFT+CTRL+Key_Minus);
 	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);
-  //view->insertItem("Cell monitor", this, SLOT(cellmonitor()));
   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);
  	view->insertSeparator();
 	  only_boundary_id = view->insertItem("Show only leaf &boundary", this, SLOT(toggleLeafBoundary()));
   //only_boundary_id = view->insertItem("Show only leaf &boundary", 0,0);
 	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 );
   /* dbf_id = options->insertItem("Double buffer", this, SLOT(toggleDoubleBuffer()));
      options->setItemChecked(dbf_id, TRUE);*/
   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(help()) ); //, Key_F1);
   //help->insertItem( "What's &This", this , SLOT(whatsThis()), SHIFT+Key_F1);
   menu->insertItem("&Help",helpmenu);
   //QSlider *flux_arrow_slider = new QSlider( 0, 10000, 1, 100, Qt::Horizontal, this, "flux arrow size");
   //QSpinBox *stride  = new QSpinBox( 1, 1000, 1, this, "stride");
   //QGridLayout *controlgrid = new QGridLayout( this, 1, 2, 10);
   // 2x1, 10 pixel border
   //controlgrid->addWidget( stride, 0, 0);
   //controlgrid->addWidget( flux_arrow_slider, 0, 1);
   //controlgrid->setColStretch( 1, 10 );
   //flux_arrow_size = 1.;
   //flux_arrow_slider -> setMinimumSize( 200,50);
   //connect( flux_arrow_slider, SIGNAL( valueChanged( int ) ), this, SLOT( setFluxArrowSize(int) ) );
   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;
 	// A little bit of PSB/CWI decoration ;-)
 	/*dockwindow = new Q3DockWindow();
 	addDockWindow(dockwindow);
 	QLabel *viblab = new QLabel; viblab->setPixmap(QPixmap(cwi_xpm));
 	QString virtleafstring("<h1>The Virtual Leaf</h1>\n<center><b>Model:</b> <i>%1</i></center>");
 	QLabel *virtleaf = new QLabel(virtleafstring.arg(mesh.ModelID()));
 	QLabel *psblab = new QLabel; psblab->setPixmap(QPixmap(PSB_xpm));
 	dockwindow->setHorizontalStretchable(true);
 	dockwindow->boxLayout()->addWidget(viblab);//,Qt::AlignLeft);
 	dockwindow->boxLayout()->addStretch();
 	dockwindow->boxLayout()->addWidget(virtleaf);//, Qt::AlignHCenter);
 	dockwindow->boxLayout()->addStretch();
 	dockwindow->boxLayout()->addWidget(psblab);//, Qt::AlignRight);*/
 	//QString virtleafstring("<h1>The Virtual Leaf</h1>\n<center><b>Model:</b> <i>%1</i></center>");
 	infobar = new InfoBar();
 	addDockWindow(infobar);
+}
 void Main::RefreshInfoBar(void) {
 	infobar->SetText(mesh.ModelID());
+}
 void Main::UserMessage(QString message, int timeout) {
@@ @@ -774,27 +634,24 @@ void Main::EditParameters() { @@
   ParameterDialog *pardial = new ParameterDialog(this, "stridediag");
   // Make sure the values in the parameter dialog are updated after a file is read
   // each method changing the parameters (reading XML or PAR files) should
   // emit this signal
   QObject::connect(   this, SIGNAL( ParsChanged() ), pardial, SLOT( Reset() ) );
+}
 void Main::savePars() {
   // bool timer_active;
   /* if (timer_active=timer->isActive())
      imer->stop();*/
   stopSimulation();
   Q3FileDialog *fd = new Q3FileDialog( this, "file dialog", TRUE );
   fd->setMode( Q3FileDialog::AnyFile );
   fd->setFilter( "Parameter files (*.par)");
   QString fileName;
   if ( fd->exec() == QDialog::Accepted ) {
     fileName = fd->selectedFile();
     ofstream parfile((const char *)fileName);
     par.Write(parfile);
+  }
@@ @@ -817,28 +674,24 @@ void Main::readPars() { @@
     par.Read((const char *)fileName);
+  }
   emit ParsChanged();
   /* if (timer_active)
      timer->start( 0 );*/
+}
 void Main::saveStateXML() {
   //   bool timer_active;
   //   if (timer_active=timer->isActive())
   //     timer->stop();
   stopSimulation();
   Q3FileDialog *fd = new Q3FileDialog( this, "file dialog", TRUE );
   fd->setMode( Q3FileDialog::AnyFile );
   fd->setFilter( "XML (*.xml)");
   QString fileName;
   if ( fd->exec() == QDialog::Accepted ) {
     fileName = fd->selectedFile();
     if ( QFile::exists( fileName ) &&
 	 QMessageBox::question(
 			       this,
 			       tr("Overwrite File? -- Leaf Growth"),
@@ @@ -854,27 +707,24 @@ void Main::saveStateXML() { @@
       mesh.XMLSave((const char *)fileName, XMLSettingsTree());
+    }
+  }
+}
 void Main::snapshot() {
   //   bool timer_active;
   //   if (timer_active=timer->isActive())
   //     timer->stop();
   stopSimulation();
   Q3FileDialog *fd = new Q3FileDialog( this, "Save snapshot", TRUE );
   fd->setMode( Q3FileDialog::AnyFile );
   QString fileName;
   if ( fd->exec() == QDialog::Accepted ) {
     fileName = fd->selectedFile();
     if ( QFile::exists( fileName ) &&
 	 QMessageBox::question(
 			       this,
 			       tr("Overwrite File? -- Leaf Growth"),
@@ @@ -922,47 +772,45 @@ void Main::readPrevStateXML() { @@
 		      QMessageBox::Ok | QMessageBox::Default,
 		      QMessageBox::NoButton,
 		      QMessageBox::NoButton);
       mb.exec();
       return;
+    }
     next_file = *(--f);
     next_file = currentFile_path+"/"+next_file;
     readStateXML((const char *)next_file);
+  }
+}
 int Main::readStateXML(const char *filename, bool geometry, bool pars, bool simtime) {
   try {
     xmlNode *settings;
     mesh.XMLRead((const char *)filename, &settings, geometry, pars, simtime);
     #ifdef QDEBUG
     qDebug() << "Reading done."<< endl;
     #endif
     XMLReadSettings(settings);
     xmlFree(settings);
     Cell::SetMagnification(1);
     Cell::setOffset(0,0);
     FitLeafToCanvas();
     currentFile =  QString(filename);
     Plot();
-    QString status_message = QString("Succesfully read leaf from file %1. Time is %2 h.\n").arg(currentFile).arg(mesh.getTimeHours().c_str());
+    QString status_message = QString("Successfully read leaf from file %1. Time is %2 h.").arg(currentFile).arg(mesh.getTimeHours().c_str());
     cerr << status_message.toStdString() << endl;
 	setCaption(caption_with_file.arg(filename));
     statusBar()->message(status_message);
     emit ParsChanged();
     #ifdef QDEBUG
     qDebug() << "Done. Returning 0." << endl;
     #endif
     return 0;
   } catch (const char *error_message) {
     QMessageBox mb( "Read leaf from XML file",
 		    QString(error_message),
 		    QMessageBox::Critical,
@@ @@ -1072,44 +920,24 @@ 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
 //     try {
 //       mesh.XMLRead((const char *)fileName);
 //       currentFile =  fileName;
 //     } catch (const char *error_message) {
 //       QMessageBox mb( "Read leaf from XML file",
 // 		      QString(error_message),
 // 		      QMessageBox::Critical,
 // 		      QMessageBox::Ok | QMessageBox::Default,
 // 		      QMessageBox::NoButton,
 // 		      QMessageBox::NoButton);
 //       mb.exec();
 //       return readStateXML(); // user can try again
 //     }
 //     Vector bbll,bbur;
 //     mesh.BoundingBox(bbll,bbur);
 //     //FitLeafToCanvas();
 //     Plot();
+  }
+}
 void Main::clear()
+{
   editor->clear();
+}
 void Main::help()
+{
   static QMessageBox* about = new QMessageBox
@@ @@ -1124,129 +952,83 @@ void Main::help() @@
       "CWI/NCSB, Amsterdam, Netherlands <br>"
       "Pilot release for WUR/Biometris, 21-10-2009 <br>",
       QMessageBox::Information, 1, 0, 0, this, 0, FALSE );
   about->setButtonText( 1, "Dismiss" );
   about->show();
+}
   void Main::aboutQt()
+  {
     QMessageBox::aboutQt( this, "Virtual Leaf" );
+  }
 /* void Main::toggleDoubleBuffer()
+{
   bool s = !options->isItemChecked(dbf_id);
   options->setItemChecked(dbf_id,s);
   canvas.setDoubleBuffering(s);
+}
 */
   void Main::toggleShowCellCenters()
+  {
     //bool s = !view->isItemChecked(com_id);
     //view->setItemChecked(com_id,s);
     Plot();
+  }
   void Main::toggleShowWalls()
+  {
     //bool s = !view->isItemChecked(cell_walls_id);
     //view->setItemChecked(cell_walls_id,s);
     Plot();
+  }
 void Main::toggleShowApoplasts()
+{
     Plot();
+}
   void Main::toggleShowNodes()
+  {
     //bool s = !view->isItemChecked(mesh_id);
     //view->setItemChecked(mesh_id,s);
     Plot();
+  }
   void Main::toggleNodeNumbers(void) {
     //bool s = !view->isItemChecked(node_number_id);
     //view->setItemChecked(node_number_id,s);
     Plot();
+  }
   void Main::toggleCellNumbers(void) {
     //bool s = !view->isItemChecked(cell_number_id);
     //view->setItemChecked(cell_number_id,s);
     Plot();
+  }
   void Main::toggleCellAxes(void) {
     //bool s = !view->isItemChecked(cell_axes_id);
     //view->setItemChecked(cell_axes_id,s);
     Plot();
+  }
   void Main::toggleCellStrain(void) {
     //bool s = !view->isItemChecked(cell_strain_id);
     //view->setItemChecked(cell_strain_id,s);
     Plot();
+  }
   void Main::toggleShowFluxes(void) {
     //bool s = !view->isItemChecked(fluxes_id);
     //view->setItemChecked(fluxes_id,s);
     Plot();
+  }
   void Main::toggleShowBorderCells()
+  {
     //bool s = !view->isItemChecked(border_id);
     //view->setItemChecked(border_id,s);
   void Main::toggleShowBorderCells(){
     Plot();
+  }
 void Main::toggleHideCells(void) {
 	Plot();
 	editor->FullRedraw();
+}
   void Main::toggleMovieFrames()
+  {
     //bool s = !view->isItemChecked(movie_frames_id);
     //view->setItemChecked(movie_frames_id,s);
+  }
   void Main::toggleMovieFrames(){}
   void Main::toggleLeafBoundary(){}
   void Main::toggleLeafBoundary()
+  {
     //bool s = !view->isItemChecked(only_boundary_id);
     //view->setItemChecked(only_boundary_id,s);
+  }
   void Main::toggleDynCells()
+  {
     //bool s = !options->isItemChecked(dyn_cells_id);
     //options->setItemChecked(dyn_cells_id,s);
+  }
   void Main::toggleDynCells() {}
   void Main::startSimulation(void) {
     //run->setItemChecked(paused_id, false);
     timer->start( 0 );
     statusBar()->message("Simulation started");
     running = true;
+  }
   void Main::stopSimulation(void) {
     //run->setItemChecked(paused_id, true);
     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();
@@ @@ -1255,37 +1037,32 @@ void Main::toggleHideCells(void) { @@
       stopSimulation();
+    }
+  }
   void Main::setFluxArrowSize(int size) {
     flux_arrow_size = size/100.;
+  }
   void Main::enlarge()
+  {
     //canvas.resize(canvas.width()*4/3, canvas.height()*4/3);
     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::scrollBy(int dx, int dy) {
     editor->scrollBy(dx,dy);
     }*/
   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 );
@@ @@ -1356,88 +1133,24 @@ void Main::toggleHideCells(void) { @@
 							   QMessageBox::Yes | QMessageBox::No, QMessageBox::NoButton ) == QMessageBox::Yes ) {
       cerr << "Restarting simulation" << endl;
       //    extern Mesh mesh;
       mesh.Clear();
       Init();
 		Plot();
 		editor->FullRedraw();
+    }
     //startSimulation();
+  }
   /*
     void Main::SaveToGifAnim(void) {
     if (gifanim) {
     QPixmap image(canvas.width(), canvas.height());
     QPainter im(&image);
     canvas.drawArea(QRect(0,0,canvas.width(),canvas.height()),&im,FALSE);
     QFile conversionpipe;
     conversionpipe.open ( IO_WriteOnly, popen("pngtopnm | ppmtogif > tmp.gif", "w") );
     image.save( &conversionpipe, "PNG");
     conversionpipe.close();
     QFile readconvertedimage("tmp.gif");
     readconvertedimage.open(IO_ReadOnly);
     int c;
     while ( (c=readconvertedimage.getch())!=-1) {
     gifanim->putch(c);
+    }
+    }
     }*/
   /* void Main::StartGifAnim(QString fname) {
   if (gifanim) {
   QMessageBox::information( this, "Animation",
   "Already making another animation."
   "Please end it and try again.",
   QMessageBox::Ok );
   } else {
   QString cmdline("gifsicle --multifile - > ");
   cmdline += fname;
   gifanim = new QFile;
   gifanim->open( IO_WriteOnly,
   popen((const char *)cmdline, "w") );
   */   /* QStringList cmdline;
 	  cmdline << "gifsicle" << "--multifile" << "-";
 	  gifanim = new QProcess( cmdline );
 	  cmdline.clear();
 	  cmdline << "pngtopnm";
 	  pngtopnm = new QProcess( cmdline );
 	  pngtopnm->start();
 	  cmdline.clear();
 	  cmdline << "ppmtogif";
 	  ppmtogif = new QProcess( cmdline );
 	  ppmtogif->start();*/
        /*  }
        }*/
        /*void Main::EndGifAnim(void) {
        if (gifanim)
        gifanim->close();
        }*/
 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;
@@ @@ -1486,59 +1199,53 @@ void Main::CleanMesh(void) { @@
 	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();
   //  repaint();
+}
 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();
 	//  repaint();
+}
 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();
 	//  repaint();
+}
 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];
+  }

src/canvas.h

➞

Show inline comments

@@ @@ -66,27 +66,24 @@ class InfoBar; @@
 class FigureEditor : public QGraphicsView {
   Q_OBJECT
     friend class Main;
     public:
   FigureEditor(QGraphicsScene&, Mesh&, QWidget* parent=0, const char* name=0, Qt::WFlags f=0);
   void clear();
   void Save(const char *fname, const char *format, int sizex=640, int sizey=480);
   void FullRedraw(void);
 protected:
   /* void contentsMousePressEvent(QMouseEvent*);
   void contentsMouseMoveEvent(QMouseEvent*);
   void contentsMouseReleaseEvent(QMouseEvent*);*/
   void mousePressEvent(QMouseEvent*);
   void mouseMoveEvent(QMouseEvent*);
   void mouseReleaseEvent(QMouseEvent*);
   void wheelEvent(QWheelEvent *event);
   void scaleView(qreal scaleFactor);
   vector <CellItem *> getIntersectedCells(void);
   void insertNode(QPointF p);
   NodeItem *selectedNodeItem(QList<QGraphicsItem *> l) const;
  signals:
   void status(const QString&);
@@ @@ -125,53 +122,46 @@ class Main : public Q3MainWindow, public @@
   virtual bool ShowWallsP(void) {return view->isItemChecked(cell_walls_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 Save(const char *fname, const char *format);
   /*void StartGifAnim(QString fname);
     void SaveToGifAnim(void);
     void EndGifAnim(void);*/
   void FitCanvasToWindow();
   void FitLeafToCanvas(void);
   public slots:
   void help();
   void TimeStepWrap();
   //void scrollBy(int dx, int dy);
   void togglePaused();
   void setFluxArrowSize(int size);
   //void Divide(void);
   void RestartSim(void);
   //void toggleDoubleBuffer(void);
   void toggleShowCellCenters(void);
   void toggleShowNodes(void);
   void toggleShowBorderCells(void);
   void toggleShowFluxes(void);
   void toggleNodeNumbers(void);
   void toggleCellNumbers(void);
   void toggleCellAxes(void);
   void toggleCellStrain(void);
   void toggleShowWalls(void);
-	void toggleShowApoplasts(void);
+  void toggleShowApoplasts(void);
   void toggleDynCells(void);
   void toggleMovieFrames(void);
   void toggleLeafBoundary(void);
   void toggleHideCells(void);
   void print();
   void startSimulation(void);
   void stopSimulation(void);
   void RefreshInfoBar(void);
   void EnterRotationMode(void) {
     UserMessage("Rotation mode. Click mouse to exit.");
@@ @@ -205,54 +195,46 @@ class Main : public Q3MainWindow, public @@
   int readStateXML(const char *filename, bool geometry = true, bool pars=true, bool simtime = true);
   void readNextStateXML();
   void readPrevStateXML();
   void readFirstStateXML();
   void readLastStateXML();
   void saveStateXML();
   void snapshot();
   void savePars();
   void readPars();
   void clear();
   void init();
   virtual void CutSAM() { MainBase::CutSAM(); Refresh();}
 /*   void cellmonitor() { */
 /*     PlotDialog *plot = new PlotDialog(this); */
 /*     cerr << "Attempting to launch a cell monitor\n"; */
 /*   } */
   //void addPolygon();
   //void addLine();
   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;
   //QCanvas& canvas;
   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

src/cell.cpp

➞

Show inline comments

@@ @@ -85,28 +85,25 @@ void Cell::DivideOverAxis(Vector axis) { @@
 	for (list<Node *>::iterator i=nodes.begin();
 		 i!=nodes.end();
 		 i++) {
 		// cross product to detect position of division
 		Vector cross = axis * (centroid - *(*i));
 		if (cross.z * prev_cross_z < 0 ) {
 			new_node_locations.push_back(i);
 		} // else {
 		//       //cerr << "cross.z * prev_cross_z = " << cross.z * prev_cross_z << endl;
 		//     }
+		}
 		prev_cross_z=cross.z;
+	}
 	DivideWalls(new_node_locations, centroid, centroid+axis);
+}
 double Cell::MeanArea(void) {
 	return m->MeanArea();
+}
 void Cell::Apoptose(void) {
@@ @@ -211,70 +208,24 @@ void Cell::Apoptose(void) { @@
 			// register node with outside world
 			if (find_if( no.owners.begin(), no.owners.end(),
 				     bind2nd ( mem_fun_ref(&Neighbor::CellEquals), m->boundary_polygon->Index() ) ) == no.owners.end() ) {
 				tmp.cell = m->boundary_polygon;
 				no.owners.push_back(tmp);
+			}
+		}
+	}
 	/*
 	 // correct boundary polygon if this cell touches the boundary
 	 // find the first living boundary node after a dead node
 	 bool node_found = false;
 	 for (list<Node *>::iterator n=nodes.begin();
 	 n!=nodes.end();
 	 n++) {
 	 Node &no(*(*n));
 	 if (no.DeadP()) {
 	 list<Node *>::iterator first_node = n;
 	 if (++next_node == nodes.end()) first_node=nodes.begin();
 	 if (!(*(*first_node)).DeadP() && ((*first_node)->boundary)) {
 	 node_found=true;
 	 break;
+	 }
+	 }
+	 }
 	 // locate it in the boundary_polygon
 	 if (node_found) {
 	 list<Node *>::iterator insert_it = find(mesh->boundary_polygon->nodes.begin(),
 	 mesh->boundary_polygon->nodes.end(),
 	 ++first_node);
 	 if (insert_it!=owners.end()) {
 	 if (insert_it==owners.end()) insert_it=owners.begin();
 	 for (list<Node *>::iterator n=insert_it;
 	 n!=nodes.end();
 	 n++) {
 	 Node &no(*(*n));
 	 mesh->boundary_polygon->nodes.insert(
+	 }
+	 }
 	 } */
 	// mark cell as dead
 	MarkDead();
+}
 void Cell::ConstructConnections(void) {
     // Tie up the nodes of this cell, assuming they are correctly ordered
     //cerr << "Constructing connections of cell " << index << endl;
     for (list<Node *>::iterator i=nodes.begin();
 		 i!=nodes.end();
@@ @@ -355,26 +306,24 @@ bool Cell::DivideOverGivenLine(const Vec @@
 			nb = nodes.begin();
+		}
 		Vector v4 = *(*nb);
 		double denominator =
 		(v4.y - v3.y)*(v2.x - v1.x) - (v4.x - v3.x)*(v2.y - v1.y);
 		double ua =
 		((v4.x - v3.x)*(v1.y - v3.y) - (v4.y - v3.y)*(v1.x -v3.x))/denominator;
 		double ub =
 		((v2.x - v1.x)*(v1.y-v3.y) - (v2.y- v1.y)*(v1.x - v3.x))/denominator;
 		/* double intersec_x = v1.x + ua*(v2.x-v1.x);
 		 double intersec_y = v1.y + ua*(v2.y-v1.y);*/
 		//cerr << "Edge " << *i << " to " << *nb << ": ua = " << ua << ", ub = " << ub << ":  ";
 		// this construction with "TINY" should simulate open/closed interval <0,1]
 		if ( ( TINY < ua && ua < 1.+TINY ) && ( TINY < ub && ub < 1.+TINY ) ) {
 			// yes, intersection detected. Push the location to the list of iterators
 			new_node_locations.push_back(nb);
+		}
+	}
         #ifdef QDEBUG
 	if (new_node_locations.size()<2) {
@@ @@ -424,40 +373,37 @@ void Cell::DivideWalls(ItList new_node_l @@
 	//cerr << "Parent polarization before division: " << parent_info.polarization << endl;
 	// Step 1: create a daughter cell
 	Cell *daughter=m->AddCell(new Cell());
 	// Step 2: Copy the basics of parent cell to daughter
 	for (int i=0;i<NChem();i++) {
 		daughter->chem[i]=chem[i];
+	}
 	daughter->cell_type = cell_type;
 	//extern double auxin_account;
 	//auxin_account += daughter->chem[0];
 	for (int i=0;i<NChem();i++) {
 		daughter->new_chem[i]=new_chem[i];
+	}
 	daughter->boundary=boundary;
 	daughter->m=m;
 	daughter->target_area=target_area/2.;
 	target_area/=2;
 	daughter->cellvec=cellvec;
 //	daughter->BaseArea()  = base_area;
 	// Division currently only works for convex cells: i.e. if the division line
 	// intersects the cells at two points only.
 	if (new_node_locations.size()!=2) {
 		// Note: if you would add the possibility of dividing non-convex
 		// cells, remember to update the code below. There are some
 		// fixed-size arrays over there!
 		cerr << "Warning in Cell::Division: division of non-convex cells not fully implemented" << endl;
@@ @@ -608,29 +554,24 @@ void Cell::DivideWalls(ItList new_node_l @@
 				div_edges[i].first->node_set->AddNode( new_node_ind[i] );
+			}
 			// if the new wall should be fixed (i.e. immobile, or moving as
 			// solid body), make it so, and make it part of the boundary. Using
 			// this to make a nice initial condition by cutting off part of a
 			// growing leaf.
 			if (fix_cellwall) {
 				(new_node_ind[i])->fixed = true;
 				// All this we'll do later for the node set only
 				/* (new_node_ind[i])->boundary = true;
 				 (new_node_ind[i])->sam = true;
 				 boundary_touched_flag = true;
 				 boundary = SAM;
 				 daughter->boundary = SAM;*/
+			}
 			// if new node is inserted into the boundary
 			// it will be part of the boundary, too
 			new_node_ind[i]->UnsetBoundary();
 			if ((div_edges[i].first->BoundaryP() && div_edges[i].second->BoundaryP()) && // Both edge nodes are boundary nodes AND
 			     ((m->findNextBoundaryNode(div_edges[i].first))->Index() == div_edges[i].second->Index())){ // The boundary proceeds from first to second.
                                 #ifdef QDEBUG
 			        qDebug() << "Index of the first node: " << div_edges[i].first->Index() << endl;
 			        qDebug() << "Index of the second node: " << div_edges[i].second->Index() << endl;
@@ @@ -797,25 +738,25 @@ void Cell::DivideWalls(ItList new_node_l @@
 			/*************** 1. Find the correct wall element  ********************/
 			list<Wall *>::iterator w, start_search;
 			w = start_search = walls.begin();
 			do {
 				// Find wall between this cell and neighbor cell
 				w = find_if( start_search, walls.end(), bind2nd (mem_fun( &Wall::is_wall_of_cell_p ), neighbor_cell ) );
 				start_search = w; start_search++; // continue searching at next element
 			} while ( w!=walls.end() && !(*w)->IntersectsWithDivisionPlaneP( from, to ) ); // go on until we find the right one.
 			if (w == walls.end()) {
 			        #ifdef QDEBUG
 			  qDebug() << "Whoops, wall element not found...!" << endl;
+			        qDebug() << "Whoops, wall element not found...!" << endl;
 			        qDebug() << "Cell ID: " << neighbor_cell->Index() << endl;
 				qDebug() << "My cell ID: " << Index() << endl;
                                 #endif
 			} else {
 				// 2. Split it up, if we should (sometimes, the new node coincides with an existing node so
 				// we should not split up the Wall)
 				if (new_node_ind[i]!=(*w)->n1 && new_node_ind[i]!=(*w)->n2) {
 					Wall *new_wall;
@@ @@ -830,36 +771,24 @@ void Cell::DivideWalls(ItList new_node_l @@
 						new_wall = new Wall( (*w)->n1, new_node_ind[i], this, neighbor_cell);
 						(*w)->n1 = new_node_ind[i];
 						//  cerr << "wall " << *(*w) << ", and new wall " << *new_wall << endl;
 					} else {
 						new_wall = new Wall( (*w)->n1, new_node_ind[i], neighbor_cell, this);
 						(*w)->n1 = new_node_ind[i];
+					}
 					//new_wall->ResetTransporterConcentrations(orig_length);
 					//(*w)->ResetTransporterConcentrations(orig_length);
 					// reset the transporter concentrations
 					/*	  new_wall->SetLength();
 					 new_wall->CorrectLength(orig_length);
 					 (*w)->SetLength();
 					 (*w)->CorrectLength(orig_length);*/
 					// 3. Give wall elements to appropriate cells
 					if (new_wall->n1 != new_wall->n2) {
 						if (par.copy_wall)
 							new_wall->CopyWallContents(**w);
 						else {
 							// If wall contents are not copied, decide randomly which wall will be the "parent"
 							// otherwise we will get biases (to the left), for example in the meristem growth model
 							if (RANDOM()<0.5) {
 								new_wall->SwapWallContents(*w);
+							}
+						}
@@ @@ -992,29 +921,26 @@ void Cell::DivideWalls(ItList new_node_l @@
 	double element_length = dist/(double)(n+1);
 	// note that wall nodes need to run in inverse order in parent
 	list<Node *>::iterator ins_pos = daughter->nodes.end();
 	for (int i=1;i<=n;i++) {
 		Node *node=
 		m->AddNode( new Node( new_node[0] + i*element_length*nodevec ) );
 		node->fixed=fixed_wall;
 		if (!fix_cellwall)
 			node->boundary = false;
 		else { // if fix_cellwall is true, that is if we are cutting off
 			// part of a leaf to make a nice initial condition, we also want to make it part of the boundary
 			//node->boundary = true;
 		else {
 			node->fixed = true;
 			//node->sam = true;
+		}
 		ins_pos=daughter->nodes.insert(ins_pos, node );
 		new_nodes_parent.push_back( node );
 		// optionally add the new node to the nodeset (passed by pointer)
 		// (in this way we can move the NodeSet as a whole; useful for a fixed cutting line)
 		if (node_set) {
 			node_set->AddNode( node );
+		}
+	}
@@ @@ -1091,44 +1017,38 @@ void Cell::DivideWalls(ItList new_node_l @@
+	}
 	// Correct tranporterconcentrations of divided walls
 	for (int i=0;i<4;i++) {
 		if (div_wall[i]) {
 			div_wall[i]->SetLength();
 			div_wall[i]->CorrectTransporters(orig_length[i/2]);
+		}
+	}
 	//neighbors.push_back( daughter );
 	//daughter->neighbors.push_back( this );
 	//cerr << "Cell " << index << " has been dividing, and gave birth to Cell " << daughter->index << endl;
 	// now reconstruct neighbor list for all "broken" neighbors
 	for (list<CellBase *>::iterator i=broken_neighbors.begin();
 		 i!=broken_neighbors.end();i++) {
 		((Cell *)(*i))->ConstructNeighborList();
+	}
 	ConstructNeighborList();
 	daughter->ConstructNeighborList();
 	m->plugin->OnDivide(&parent_info, daughter, this);
 	// wall->OnWallInsert();
 	//daughter->OnDivide();
 	daughter->div_counter=(++div_counter);
+}
 // Move the whole cell
 void Cell::Move(const Vector T) {
     for (list<Node *>::const_iterator i=nodes.begin();
 		 i!=nodes.end();
 		 i++) {
@@ @@ -1157,37 +1077,35 @@ double Cell::Displace(double dx, double @@
 	vector<double> cellareas;
 	cellareas.reserve(neighbors.size());
 	// for the length constraint, collect all edges to this cell's nodes,
 	// which are not part of the cell
 	// the length of these edges will change
 	double old_length=0.;
 	for (list<Node *>::const_iterator i=nodes.begin();
 		 i!=nodes.end();
 		 i++) {
-		//if ((*i)->Fixed()) return; // commented out 01/12/05
 		for (list<Neighbor>::const_iterator n=(*i)->owners.begin();
 			 n!=(*i)->owners.end();
 			 n++) {
 			if (n->getCell()!=this) {
 				//if (!(m->getNode(n->nb1).Fixed() && m->getNode(n->nb2).Fixed())) {
 				length_edges.push_back( pair <Node *,Node *> (*i, n->nb1) );
 				length_edges.push_back( pair <Node *,Node *> (*i, n->nb2) );
 				old_length +=
 				DSQR(Node::target_length-(*(*i)-*(n->nb1)).Norm())+
 				DSQR(Node::target_length-(*(*i)-*(n->nb2)).Norm());
 				//}
+			}
+		}
+	}
 	// calculate area energy difference of neighboring cells
 	// (this cells' shape remains unchanged)
 	double old_area_energy=0., old_length_energy=0.;
 	for (list<CellBase *>::const_iterator i=neighbors.begin();
 		 i!=neighbors.end();
 		 i++) {
 		old_area_energy += DSQR((*i)->Area()-(*i)->TargetArea());
 		old_length_energy += DSQR((*i)->Length()-(*i)->TargetLength());
@@ @@ -1221,40 +1139,24 @@ double Cell::Displace(double dx, double @@
 		// update areas of cells
 		//cerr << "neighbors: ";
 		list<CellBase *>::const_iterator nb_it = neighbors.begin();
 		for (vector<double>::const_iterator ar_it = cellareas.begin();
 			 ar_it!=cellareas.end();
 			 ( ar_it++, nb_it++) ) {
 			((Cell *)(*nb_it))->area = *ar_it;
 			(*nb_it)->SetIntegrals();
+		}
 		//cerr << endl;
 		/*vector<double> area1;
 		 vector<double> area2;
 		 m->ExtractFromCells( mem_fun_ref(&Cell::Area), back_inserter(area1) );
 		 m->ExtractFromCells( mem_fun_ref(&Cell::CalcArea), back_inserter(area2));
 		 vector<double>::iterator i=area1.begin();
 		 vector<double>::iterator j=area2.begin();
 		 int c=0;
 		 for (;
 		 i!=area1.end();
 		 (i++, j++)) {
 		 if ( (*i-*j) > 1e-10) {
 		 cerr << c++ << " " << *i << " " << *j << endl;
 		 abort();
+		 }
 		 }*/
 	} else {
 		Move ( -1*movement);
+	}
 	return dh;
+}
 void Cell::Displace (void) {
 	Displace(par.mc_cell_stepsize*(RANDOM()-0.5),par.mc_cell_stepsize*(RANDOM()-0.5),0);
@@ @@ -1342,26 +1244,24 @@ bool Cell::SelfIntersect(void) { @@
 				nb = nodes.begin();
+			}
 			Vector v4=*( *nb );
 			double denominator =
 			(v4.y - v3.y)*(v2.x - v1.x) - (v4.x - v3.x)*(v2.y - v1.y);
 			double ua =
 			((v4.x - v3.x)*(v1.y - v3.y) - (v4.y - v3.y)*(v1.x -v3.x))/denominator;
 			double ub =
 			((v2.x - v1.x)*(v1.y-v3.y) - (v2.y- v1.y)*(v1.x - v3.x))/denominator;
 			/* double intersec_x = v1.x + ua*(v2.x-v1.x);
 			 double intersec_y = v1.y + ua*(v2.y-v1.y);*/
 			if ( ( TINY < ua && ua < 1.-TINY ) && ( TINY < ub && ub < 1.-TINY ) ) {
 				//cerr << "ua = " << ua << ", ub = " << ub << endl;
 				return true;
+			}
+		}
+    }
     return false;
+}
@@ @@ -1417,27 +1317,24 @@ bool Cell::MoveSelfIntersectsP(Node *mov @@
 			Vector v3 = *(*i);
 			Vector v4 = *(*nb);
 			double denominator =
 			(v4.y - v3.y)*(neighbor_of_moving_node[j].x - new_pos.x) - (v4.x - v3.x)*(neighbor_of_moving_node[j].y - new_pos.y);
 			double ua =
 			((v4.x - v3.x)*(new_pos.y - v3.y) - (v4.y - v3.y)*(new_pos.x -v3.x))/denominator;
 			double ub =
 			((neighbor_of_moving_node[j].x - new_pos.x)*(new_pos.y-v3.y) - (neighbor_of_moving_node[j].y- new_pos.y)*(new_pos.x - v3.x))/denominator;
 			/* double intersec_x = new_pos.x + ua*(neighbor_of_moving_node[j].x-new_pos.x);
 			 double intersec_y = new_pos.y + ua*(neighbor_of_moving_node[j].y-new_pos.y);*/
 			if ( ( TINY < ua && ua < 1.-TINY ) && ( TINY < ub && ub < 1.-TINY ) ) {
 				//cerr << "ua = " << ua << ", ub = " << ub << endl;
 				return true;
+			}
+		}
+	}
 	return false;
+}
 /*! \brief Test if this cell intersects with the given line.
@@ @@ -1463,27 +1360,24 @@ bool Cell::IntersectsWithLineP(const Vec @@
 			nb = nodes.begin();
+		}
 		Vector v4 = *(*nb);
 		double denominator =
 		(v4.y - v3.y)*(v2.x - v1.x) - (v4.x - v3.x)*(v2.y - v1.y);
 		double ua =
 		((v4.x - v3.x)*(v1.y - v3.y) - (v4.y - v3.y)*(v1.x -v3.x))/denominator;
 		double ub =
 		((v2.x - v1.x)*(v1.y-v3.y) - (v2.y- v1.y)*(v1.x - v3.x))/denominator;
 		/* double intersec_x = v1.x + ua*(v2.x-v1.x);
 		 double intersec_y = v1.y + ua*(v2.y-v1.y);*/
 		if ( ( TINY < ua && ua < 1.-TINY ) && ( TINY < ub && ub < 1.-TINY ) ) {
 			return true;
+		}
+    }
 	return false;
+}
 /*! \brief Constructs Walls, but only one per cell boundary.
  Standard method constructs a Wall for each cell wall element,
@@ @@ -1562,32 +1456,30 @@ void Cell::ConstructWalls(void) { @@
 			vector<Cell *>::iterator dup_it = find_if(duplicates.begin(),duplicates.end(),mem_fun(&Cell::BoundaryPolP) );
 			if (dup_it!=duplicates.end())
 				duplicates.erase(dup_it);
 			else {
 				return;
+			}
+		}
 		// One Wall for each neighbor, so we should be able to correctly construct neighbor lists here.
 		if (duplicates[0]==this) {
 			//walls. new Wall(*nb,*i,duplicates[0],duplicates[1]) );
 			AddWall(  new Wall(*nb,*i,duplicates[0],duplicates[1]) );
 			if (!duplicates[1]->BoundaryPolP()) {
 				neighbors.push_back(duplicates[1]);
+			}
 		} else {
 			//walls.push_back( new Wall(*nb,*i,duplicates[1],duplicates[0]) );
 			AddWall ( new Wall(*nb,*i,duplicates[1],duplicates[0]) );
 			if (!duplicates[0]->BoundaryPolP()) {
 				neighbors.push_back(duplicates[0]);
+			}
+		}
+	}
+}
 void BoundaryPolygon::Draw(QGraphicsScene *c, QString tooltip) {
@@ @@ -1715,76 +1607,48 @@ void Cell::DrawCenter(QGraphicsScene *c) @@
 	disk->show();
 	Vector centroid=Centroid();
 	disk -> setPos((offset[0]+centroid.x)*factor,(offset[1]+centroid.y)*factor);
+}
 void Cell::DrawNodes(QGraphicsScene *c) const {
 	for (list<Node *>::const_iterator n=nodes.begin();
 		 n!=nodes.end();
 		 n++) {
 		Node *i=*n;
-		//QCanvasEllipse *item = new QCanvasEllipse( 10, 10, c);
 		NodeItem *item = new NodeItem ( &(*i), c );
 		//QGraphicsRectItem *item = new QGraphicsRectItem(-50, -50, 50, 50, 0, c);
 		//disk->setBrush( QColor("IndianRed") );
 		/*if (i->sam) {
 		 item->setBrush( purple );
 		 } else {
 		 if (i->boundary) {
 		 item->setBrush( deep_sky_blue );
+		 }
 		 else {
 		 item->setBrush( indian_red );
+		 }
 		 }*/
 		item->setColor();
 		/*(if (item->getNode().DeadP()) {
 		 item->setBrush( QBrush (Qt::Dense6Pattern) );
 		 }*/
 		item->setZValue(5);
 		item->show();
 		item ->setPos(((offset[0]+i->x)*factor),
 					  ((offset[1]+i->y)*factor) );
+	}
+}
 void Cell::DrawIndex(QGraphicsScene *c) const {
 	//  stringstream text;
 	//     text << index;
 	//     Vector centroid = Centroid();
 	//     QCanvasText *number = new QCanvasText ( QString (text.str()), c );
 	//     number->setColor( QColor(par.textcolor) );
 	//     number->setZ(20);
 	//     number->setFont( QFont( "Helvetica", par.cellnumsize, QFont::Bold) );
 	//     number->show();
 	//     number -> move((int)((offset[0]+centroid.x)*factor),
 	// 		   (int)((offset[1]+centroid.y)*factor) );
 	DrawText( c, QString("%1").arg(index));
+}
 // Draw any text in the cell's center
 void Cell::DrawText(QGraphicsScene *c, const QString &text) const {
 	Vector centroid = Centroid();
 	QGraphicsSimpleTextItem *ctext = new QGraphicsSimpleTextItem ( text, 0, c );
 	ctext->setPen( QPen(QColor(par.textcolor)) );
 	ctext->setZValue(20);
 	ctext->setFont( QFont( "Helvetica", par.cellnumsize, QFont::Bold) );
 	//ctext->setTextFlags(Qt::AlignCenter);
 	ctext->show();
 	ctext ->setPos(((offset[0]+centroid.x)*factor),
 				   ((offset[1]+centroid.y)*factor) );
+}
 void Cell::DrawAxis(QGraphicsScene *c) const {
 	Vector long_axis;
 	double width;
 	Length(&long_axis, &width);
@@ @@ -1806,79 +1670,30 @@ void Cell::DrawAxis(QGraphicsScene *c) c @@
 	line->setLine( ( (offset[0]+from.x)*factor ),
 				  ( (offset[1]+from.y)*factor ),
 				  ( (offset[0]+to.x)*factor ),
 				  ( (offset[1]+to.y)*factor ) );
 	line->setZValue(10);
 	line->show();
+}
 void Cell::DrawStrain(QGraphicsScene *c) const {
   c = NULL; // assignment merely to obviate compilation warning
 	MyWarning::warning("Sorry, Cell::DrawStrain temporarily not implemented.");
 	/* Vector long_axis;
 	double width;
 	Length(&long_axis, &width);
 	//cerr << "Length is "  << length << endl;
 	long_axis.Normalise();
 	Vector short_axis=long_axis.Perp2D();
 	//  To test method "Strain" temporarily substitute "short_axis" for "strain"
 	Vector strain = Strain();
 	//strain.Normalise();
 	//static ofstream strainf("strain.dat");
 	//strainf << strain.Norm() << endl;
 	Vector centroid = Centroid();
 	// Vector from = centroid - 0.5 * width * short_axis;
     // Vector to = centroid + 0.5 * width *short_axis;
 	Vector from = centroid - 0.5 * strain;
 	Vector to = centroid + 0.5 * strain;
 	QGraphicsArrowItem *arrow = new QGraphicsArrowItem(0, c);
 	arrow->setPen( QPen(QColor(par.arrowcolor),100) );
 	arrow->setLine( ( (offset[0]+from.x)*factor ),
 				   ( (offset[1]+from.y)*factor ),
 				   ( (offset[0]+to.x)*factor ),
 				   ( (offset[1]+to.y)*factor ) );
 	arrow->setZValue(10.);
 	arrow->show();
 	*/
+}
 // Draw connecting lines to neighbors
 /*void Cell::DrawTriangles(QCanvas &c) {
  for (list<Neighbor>::const_iterator nb=nb_list.begin();
  nb!=nb_list.end();
  nb++) {
  QCanvasLine *line = new QCanvasLine(&c);
  line->setPen( QPen(QColor("black"),2) );
  line->setZ(2);
  line->setPoints((offset[0]+x)*factor,(offset[1]+y)*factor,
  (offset[0]+nb->c->x)*factor,(offset[1]+nb->c->y)*factor);
  line->setZ(10);
  line->show();
+ }
  }*/
 void Cell::DrawFluxes(QGraphicsScene *c, double arrowsize)  {
 	// get the mean flux through this cell
 	//Vector vec_flux = ReduceWalls( mem_fun_ref( &Wall::VizFlux ), Vector() );
 	Vector vec_flux = ReduceCellAndWalls<Vector>( PINdir );
 	vec_flux.Normalise();
 	vec_flux *= arrowsize;
 	QGraphicsArrowItem *arrow = new QGraphicsArrowItem(0,c);
 	Vector centroid = Centroid();
 	Vector from = centroid - vec_flux/2.;
 	Vector to = centroid + vec_flux/2.;
@@ @@ -2003,16 +1818,15 @@ list<Wall *>::iterator Cell::RemoveWall( @@
 				 find(
 					  walls.begin(), walls.end(),
 					  w )
 				 );
+}
 void Cell::EmitValues(double t) {
 	//  cerr << "Attempting to emit " << t << ", " << chem[0] << ", " << chem[1] << endl;
 	//chem[3] = SumTransporters( 1 );
 	emit ChemMonValue(t, chem);
+}

src/cell.h

➞

Show inline comments

@@ @@ -82,28 +82,24 @@ public: @@
 		offset[0]=ox;
 		offset[1]=oy;
+    }
     static double Magnification(void) {
 		return factor;
+    }
     static double Scale(const double scale) {
 		factor*=scale;
 		return factor;
+    }
     // return node "i"
     // wrapped around, i.e. node n==node 0
     // will not work if i < -nodes.size()
     //Node &getNode(int i) const;
     void DivideOverAxis(Vector axis); // divide cell over axis
     bool DivideOverGivenLine(const Vector v1, const Vector v2, bool wall_fixed = false, NodeSet *node_set = 0); // divide over the line (if line and cell intersect)
     void Divide(void) { // Divide cell over short axis
 		Vector long_axis;
 		Length(&long_axis);
 		DivideOverAxis(long_axis.Perp2D());
+    }
 	//void CheckForGFDrivenDivision(void);

src/cellbase.cpp

➞

Show inline comments

@@ @@ -31,46 +31,38 @@ @@
 #include <qcolor.h>
 #include <qfont.h>
 #include <qwidget.h>
 //Added by qt3to4:
 #include <Q3PointArray>
 #include <fstream>
 #include "nodeitem.h"
 #include "cellitem.h"
 #include "qcanvasarrow.h"
 #endif
 #include "nodeset.h"
 //#include "cond_operator.h"
 #include "cellbase.h"
 //#include "node.h"
 #include "wall.h"
 #include "random.h"
 #include "parameter.h"
 #include "mesh.h"
 #include "sqr.h"
 #include "tiny.h"
 static const std::string _module_id("$Id$");
 extern Parameter par;
 const char* CellBase::boundary_type_names[4] = {"None", "NoFlux", "SourceSink", "SAM"};
 // These statics have moved to class "CellsStaticDatamembers"
 //double CellBase::static_base_area = 0.;
 //int CellBase::ncells=0;
 //int CellBase::NChem()=0;
 #ifndef VLEAFPLUGIN
 CellsStaticDatamembers *CellBase::static_data_members = new CellsStaticDatamembers();
 #else
 CellsStaticDatamembers *CellBase::static_data_members = 0;
 #endif
 CellBase::CellBase(QObject *parent) :
 QObject(parent),
 Vector()
+{
 	chem=new double[NChem()];
@@ @@ -179,25 +171,25 @@ CellBase::CellBase(const CellBase &src) @@
 	stiffness = src.stiffness;
 	marked = src.marked;
 	dead = src.dead;
 	cell_type = src.cell_type;
 	div_counter = src.div_counter;
 	flag_for_divide = src.flag_for_divide;
 	division_axis = src.division_axis;
+}
 CellBase CellBase::operator=(const CellBase &src) {
 	Vector::operator=(src);
-	//  QObject::operator=(src);
 	for (int i=0;i<NChem();i++) {
 		chem[i]=src.chem[i];
+	}
 	for (int i=0;i<NChem();i++) {
 		new_chem[i]=src.chem[i];
+	}
 	boundary=src.boundary;
 	area=src.area;
 	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;
 	target_length=src.target_length;
@@ @@ -342,31 +334,24 @@ Vector CellBase::Centroid(void) const { @@
 	//area/=2.0;
 	area = fabs(area)/2.0;
 	integral_x_dxdy/=6.;
 	integral_y_dxdy/=6.;
 	Vector centroid(integral_x_dxdy,integral_y_dxdy,0);
 	centroid/=area;
 	return centroid;
+}
 /*Node &CellBase::getNode(list<Node *>::const_iterator i) const {
 if (i==
 	return m->getNode(i);
   }*/
 void CellBase::SetIntegrals(void) const {
 	// Set the initial values for the integrals over x^2,
 	// xy, yy, x, and y
 	// these values will be updated after each move of the CellBase wall
 	intgrl_xx=0.; intgrl_xy=0.; intgrl_yy=0.;
 	intgrl_x=0.; intgrl_y=0.;
 	area=0.;
@@ @@ -399,35 +384,27 @@ void CellBase::SetIntegrals(void) const @@
 			 (*nb)->y*(*i)->y+
 			 (*nb)->y*(*nb)->y );
 		intgrl_x+=
 			((*nb)->x+(*i)->x)*
 			((*i)->x*(*nb)->y-
 			 (*nb)->x*(*i)->y);
 		intgrl_y+=
 			((*nb)->y+(*i)->y)*
 			((*i)->x*(*nb)->y-
 			 (*nb)->x*(*i)->y);
+	}
-	//area/=2.0;
 	area = fabs(area)/2.0;
 	/* intgrl_x/=6.;
 	intgrl_y/=6.;
 	intgrl_xx/=12.;
 	intgrl_xy/=24.;
 	intgrl_yy/=12.;*/
+}
 double CellBase::Length(Vector *long_axis, double *width)  const {
 	// Calculate length and axes of CellBase
 	// Calculate inertia tensor
 	// see file inertiatensor.nb for explanation of this method
 	if (!lambda_celllength) {
 		// Without length constraint we do not keep track of the cells'
 		// moments of inertia. So we must calculate them here.
@@ @@ -438,27 +415,24 @@ double CellBase::Length(Vector *long_axi @@
 	double intry=intgrl_y/6.;
 	double ixx=(intgrl_xx/12.)-(intrx*intrx)/area;
 	double ixy=(intgrl_xy/24.)+(intrx*intry)/area;
 	double iyy=(intgrl_yy/12.)-(intry*intry)/area;
 	double rhs1=(ixx+iyy)/2., rhs2=sqrt( (ixx-iyy)*(ixx-iyy)+4*ixy*ixy )/2.;
 	double lambda_b=rhs1+rhs2;
 	// see: http://scienceworld.wolfram.com/physics/MomentofInertiaEllipse.html
 	//    cerr << "n = " << n << "\n";
 	// Vector eigenvectors[2];
 	// eigenvectors[0] = Vector(-(-ixx + iyy ) + rhs2, ixy, 0);
 	// eigenvectors[1] = Vector(-(-ixx + iyy ) - rhs2, ixy, 0);
 	if (long_axis) {
 		*long_axis = Vector(-ixy, lambda_b - ixx, 0);
 		//   cerr << "ixx = " << ixx << ", ixy = " << ixy << ", iyy = " << iyy << ", area = " << area << endl;
+	}
 	if (width) {
 		*width = 4*sqrt((rhs1-rhs2)/area);
+	}
 	return 4*sqrt(lambda_b/area);
@@ @@ -522,435 +496,82 @@ double CellBase::CalcLength(Vector *long @@
 	double intry=my_intgrl_y/6.;
 	double ixx=(my_intgrl_xx/12.)-(intrx*intrx)/my_area;
 	double ixy=(my_intgrl_xy/24.)+(intrx*intry)/my_area;
 	double iyy=(my_intgrl_yy/12.)-(intry*intry)/my_area;
 	double rhs1=(ixx+iyy)/2., rhs2=sqrt( (ixx-iyy)*(ixx-iyy)+4*ixy*ixy )/2.;
 	double lambda_b=rhs1+rhs2;
 	// see: http://scienceworld.wolfram.com/physics/MomentofInertiaEllipse.html
 	//    cerr << "n = " << n << "\n";
 	// Vector eigenvectors[2];
 	// eigenvectors[0] = Vector(-(-ixx + iyy ) + rhs2, ixy, 0);
 	// eigenvectors[1] = Vector(-(-ixx + iyy ) - rhs2, ixy, 0);
 	if (long_axis) {
 		*long_axis = Vector(-ixy, lambda_b - ixx, 0);
 		//   cerr << "ixx = " << ixx << ", ixy = " << ixy << ", iyy = " << iyy << ", my_area = " << my_area << endl;
+	}
 	if (width) {
 		*width = 4*sqrt((rhs1-rhs2)/my_area);
+	}
 	return 4*sqrt(lambda_b/my_area);
+}
 // void CellBase::NodeRemoved(int n) {
 //   for (list<Node *>::iterator i=nodes.begin();
 //        i!=nodes.end();
 //        i++) {
 //     if ((*i)->Index()>n) {
 //       (*i)->index--;
 //     }
 //   }
 // }
 void CellBase::ConstructNeighborList(void) {
 	neighbors.clear();
 	for (//list<Wall *>::const_reverse_iterator wit=walls.rbegin();
 		 list<Wall *>::const_iterator wit=walls.begin();
 		 // somehow the reverse_iterator returns by walls needs to be casted to const to let this work.
 		 // it seems to me it is a bug in the STL implementation...
-		 //wit!=(list<Wall *>::const_reverse_iterator)walls.rend();
 		 wit!=walls.end();
 		 wit++) {
 		if ((*wit)->C1() != this) {
 			neighbors.push_back((*wit)->C1());
 		} else {
 			neighbors.push_back((*wit)->C2());
+		}
+	}
 	/*
 	 for (list<CellBase *>::iterator e=neighbors.begin();
 		  e!=neighbors.end();
 		  e++) {
 		 cerr << (*e)->Index() << " ";
 		 if ((*e)->CellBase::BoundaryPolP()) {
 			 cerr << " b ";
+		 }
+	 }
 	 */
 	// remove all boundary_polygons from the list
 	list <CellBase *>::iterator e=neighbors.begin();
 	at_boundary=false;
 	do {
 		// Code crashes here after cutting off part of the leaf. I can't find the problem.
 		// Leaving the "Illegal" walls in the simulation helps. (c1=-1 && c2=-1)
 		// Work-around: define leaf primordium. Save to XML. Restart. Read XML file.
 		// Sorry about this; I hope to solve this annoying issue later. RM :-).
 		// All cells in neighbors seem to be okay (I might be messing some part of the memory elsewhere
 		// during the cutting operation?).
 		e = find_if(neighbors.begin(),neighbors.end(),mem_fun(&CellBase::BoundaryPolP));
 		if (e!=neighbors.end()) {
 			e=neighbors.erase(e);
 			at_boundary=true;
 		} else {
 			break;
+		}
   } while(1);
+}
 // CellBase constructs its neighbor list from its node lists
 // Assumes, obviously, that the node lists are up to date
 // (i.e. call ConstructConnections before calling this method)
 // We'll keep this one private, anyway.
 /* void CellBase::ConstructNeighborList(void) {
 //  extern ofstream debug_stream;
 neighbors.clear();
 //  debug_stream << "Nodes: ";
 //  copy(nodes.begin(),nodes.end(),ostream_iterator<Node>(debug_stream, " "));
 //debug_stream << endl;
 for (list<Node *>::const_iterator i=nodes.begin();
 	 i!=nodes.end();
 	 i++) {
     // collect all cells to which my nodes are connected on one list
     //transform((*i)->cells.begin(),(*i)->cells.end(), back_inserter(neighbors), mem_fun_ref(&Neighbor::CellBase));
     // index of next node
     list<Node *>::const_iterator nn=i;
     ++nn;
     if (nn==nodes.end())
 		nn=nodes.begin();
     //    debug_stream << "Node " << *i << ", Neighbor " << *nn << endl;
     // debug_stream << "Owners: ";
     //    copy((*i)->cells.begin(),(*i)->cells.end(),ostream_iterator<Neighbor>(debug_stream, " "));
     // debug_stream << endl;
     for (list<Neighbor>::const_iterator nb=(*i)->owners.begin();
 		 nb!=(*i)->owners.end();
 		 nb++) {
 		// collect info about neighboring cells, not about myself
 		if (nb->CellBase!=this) {
 			// make sure the whole edge touches this putative neighbor
 			// if (*nn == nb->nb1 || *nn == nb->nb2) {
 			//walls.push_back( new Wall(*i,*nn,this,nb->CellBase) );
 			//debug_stream << "Adding edge " << walls.back() << " to CellBase " << index << endl;
 			//}
 			neighbors.push_back( nb->CellBase );
+		}
+    }
+}
 neighbors.sort();
 list<CellBase *>::iterator e=unique(neighbors.begin(),neighbors.end());
 // iterator e point to the end of the subsequence of unique elements
 // remove every thing that comes after it
 neighbors.erase(e, neighbors.end());
 // okay, now neighbors contains all neighbors of this CellBase, including itself
 // A future optimization for the diffusion algorithm: now we list
 // each of the edges of a (curved) CellBase boundary separately.  We
 // could keep track just of the total length per CellBase boundary
 // the following is not necessary anymore. Is
 // checked at earlier stage
 // // remove myself from the list
 //   e = find(neighbors.begin(),neighbors.end(),index);
 //   if (e!=neighbors.end())
 //   neighbors.erase(e);
 //
 // remove boundary_polygon from the list (CellBase identity <0 )
 e=neighbors.begin();
 at_boundary=false;
 do {
     e = find_if(neighbors.begin(),neighbors.end(),mem_fun(&CellBase::BoundaryPolP));
     if (e!=neighbors.end()) {
 		e=neighbors.erase(e);
 		at_boundary=true;
     } else {
 		break;
+    }
 } while(1);
 }*/
 /*void Cell::print_nblist(void) const {
 //  cerr << "{ ";
 for (list<Neighbor>::const_iterator i=nb_list.begin();
 	 i!=nb_list.end();
 	 i++) {
 	//    cerr << "(" << i->c->index << " " << i->Dij << ")";
+}
 //  cerr << "}" << endl;
+}
 */
 // Tests whether Cell p (given as Vector, remember that Cell is a
 // Vector) is within polygon formed by nearest neighbor cells
 //
 // Based on algorithm and code by Paul Bourke, see
 // http://astronomy.swin.edu.au/~pbourke/geometry/insidepoly/
 //
 // Note: works for 2D only; projects everything on z=0;
 /*
 #define MIN(x,y) (x < y ? x : y)
 #define MAX(x,y) (x > y ? x : y)
  */
 /*bool Cell::CellInsidePolygonP(Vector &p)
+{
     int counter = 0;
     double xinters;
     Vector p1,p2;
     //p1 = polygon[0];
     p1 = *(nb_list.begin()->c);
     int N=nb_list.size();
     list<Neighbor>::const_iterator nb=nb_list.begin();
     for (int i=1;i<=N;i++) {
 		nb++;
 		if (nb!=nb_list.end()) {
 			p2 = *(nb->c);
 		} else {
 			p2 = *(nb_list.begin()->c);
+		}
 		if (p.y > MIN(p1.y,p2.y)) {
 			if (p.y <= MAX(p1.y,p2.y)) {
 				if (p.x <= MAX(p1.x,p2.x)) {
 					if (p1.y != p2.y) {
 						xinters = (p.y-p1.y)*(p2.x-p1.x)/(p2.y-p1.y)+p1.x;
 						if (p1.x == p2.x || p.x <= xinters)
 							counter++;
+					}
+				}
+			}
+		}
 		p1 = p2;
+    }
     if (counter % 2 == 0)
 		return false;
     else
 		return true;
 }*/
 /* // at new position cell should be able to "see" all polygon sides
 bool Cell::NewPointValidP(Vector &p) {
 	//int ninvtri=0;
 	for (list<Neighbor>::const_iterator nb=nb_list.begin();
 		 nb!=nb_list.end();
 		 nb++) {
 		Vector p1=*(nb->c); // first neighbor
 		list<Neighbor>::const_iterator nextv=nb; nextv++;
 		if (nextv==nb_list.end()) {
 			if (Boundary()==None) {
 				nextv=nb_list.begin();
 			} else continue;
+		}
 		Vector p2=*(nextv->c);
 		Vector v1=(p1-p);
 		Vector v2=(p2-p1);
 		Vector cross=v1*v2;
 		//    //cerr << "[" << cross << "]" << endl;
 		if (cross.z<0) {
 			// One of the triangles has "inverted".
 			//if (Boundary()==None || ninvtri)
 			return false;
 			//else
 			// accept one "inverted" triangle
 			//ninvtri++;
+		}
+	}
 	return true;
 }*/
 // void Cell::CheckForDivision(void) {
 //  //  if (/* Chemical(0)<0.4 && */ /* differentiated cells do not divide */ area > 2*base_area /* || Length()>50 */) {
 //  if (area > par.rel_cell_div_threshold * base_area ) {
 //    /* remark no longer valid? //m->IncreaseCellCapacityIfNecessary();
 //      // Note that calling Divide as follows prevents trouble if cell
 //      // vector is relocated */
 //      Divide();
 //  }
 //}
 /* void Cell::CheckForGFDrivenDivision(void) {
 if (area > base_area && chem[0]>par.gf_div_threshold) {
     //int ind=index;
     if (index==1) return; // petiole does not divide
     // remark no longer valid?
     //m->IncreaseCellCapacityIfNecessary();
     // Note that calling Divide as follows prevents trouble if cell
     // vector is relocated
     Vector horizontal(1,0,0);
     Vector vertical(0,1,0);
     double r;
     if ((r=RANDOM())>par.vertdivprob) {
 		DivideOverAxis(horizontal);
     } else {
 		cerr << "[" << r << "]";
 		DivideOverAxis(vertical);
+    }
+}
+}
 */
 // return (a measure of) the strain of this cell
 /*Vector CellBase::Strain(void) const {
 	cerr << "Sorry, CellBase::strain currently not implemented" << endl;
 	std::exit(1);
 	// Reason: we do not want to include "Node" in the plugins (Node::target_length below), and we do need Strain anyway...
 	// go over all wall elements of the cell
 	 Vector Fvec;
 	for (list<Node *>::const_iterator n=nodes.begin();
 		 n!=nodes.end();
 		 n++) {
 		list<Node *>::const_iterator nn=n; nn++;
 		if (nn==nodes.end()) nn=nodes.begin();
 		Vector wall_element = *(*n) - *(*nn);
 		// assume k=1 (Hooke's constant), for now
 		double Fscal  = (Node::target_length - wall_element.Norm())/Node::target_length;
 		Fvec += Fscal * wall_element.Normalised();
+	}
 	return Fvec;
 } */
 /* void Cell::Flux(double *flux, double D)  {
 // Algorithm according to Rudge & Haseloff 2005
 // (will we need to take cell area into account?)
 // For the time being, we don't: assume cell area is
 // mainly determined by vacuole.
 // Currently implements Rolland-Lagan-Mitchison algorithm
 // Rolland-Lagan and Prusinkiewicz, The Plant Journal (2005), 44, 854-865
 // currently I only implemented passive, diffusive transport
 // active transport will be added later
 // loop over cell edges
 for (int c=0;c<Cell::NChem();c++) flux[c]=0.;
 for (list<Wall>::iterator i=walls.begin();
 	 i!=walls.end();
 	 i++) {
 	// leaf cannot take up chemicals from environment ("no flux boundary")
 	if (i->c2 < 0) continue;
 	// calculate edge length
 	// (will later be updated during node displacement for efficiency)
 	double edge_length = (m->nodes[i->n1]-m->nodes[i->n2]).Norm();
 	// D is "background diffusion coefficient" (Rolland-Lagan)
 	// flux depends on edge length and concentration difference */
 	// i->phi = edge_length * ( /* i->D +*/ D ) * ( m->cells[i->c2].chem[0] - chem[0] );
 	/*
 	 if (m->cells[i->c1].index!=index) {
 		 cerr << "Warning, bad cells boundary: " << m->cells[i->c1].index << ", " << index << endl;
+	 }
 	 flux[0] += i->phi;
 	 //double deltaD = par.alpha * (i->phi*i->phi) - par.gamma * i->D; // Note beta=0
 	 //i->D += par.dt*deltaD;
 	 //cerr << "[ i->D = " << i->D << ", deltaD = " << deltaD << "]";
 	 //if (i->D > par.Dmax) i->D=par.Dmax;
 	 // first calculate all fluxes, we update diffusion coefficient afterwards.
 	 // cerr << "[ " << edge_length << ", " << m->cells[i->c2].chem[0] << " - " << chem[0] << "]";
+}
+}
 */
 	// Save the cell to a stream so we can reconstruct its state later
 	void CellBase::Dump(ostream &os) const {
 		os << index << " " << nodes.size() << endl;
 		Vector::Dump(os);
 		os << endl;
 		for (list<Node *>::const_iterator i=nodes.begin();i!=nodes.end();i++) {
 			os << *i << " ";

src/cellbase.h

➞

Show inline comments

@@ @@ -99,26 +99,24 @@ class CellBase : public QObject, public @@
   virtual ~CellBase() {
 	  delete[] chem;
 	  delete[] new_chem;
 	  if (division_axis) delete division_axis;
 	  //cerr << "CellBase " << index << " is dying. " << endl;
+  }
 	CellBase(const CellBase &src); // copy constructor
 	virtual bool BoundaryPolP(void) const { return false; }
 	//  CellBase(const Vector &src); // not allowed (we cannot know to which mesh
 	/// the CellBase will belong...)
     CellBase operator=(const CellBase &src); // assignment operator
     CellBase operator=(const Vector &src);
     void SetChemical(int chem, double conc);
     inline void SetNewChem(int chem, double conc) {
       new_chem[chem] = conc;
+    }
     void SetSource(int chem, double conc) {
       source=true;
       source_chem = chem;
       source_conc = conc;
+	}
@@ @@ -149,26 +147,24 @@ class CellBase : public QObject, public @@
       if ((c<0) || (c>=nchem))
 	MyWarning::warning("CellBase::Chemical says: index c is: %d, but nchem is: %d. Merely return zero", c, nchem);
       #endif
       return ((c<0) || (c>=nchem)) ? 0 : chem[c];
+    }
     //void print_nblist(void) const;
     boundary_type SetBoundary(boundary_type bound) {
       if (bound!=None) {
 	//area=0.;
 	//length=0.;
+      }
       return boundary=bound;
+    }
     boundary_type ResetBoundary(void) {
       return boundary=None;
+    }
     boundary_type Boundary(void) const {
       return boundary;
+    }
     static int &NChem(void) {
       return static_data_members->nchem;
@@ @@ -220,53 +216,50 @@ class CellBase : public QObject, public @@
       return area;
+    }
 	inline void Divide(void) {
 		flag_for_divide = true;
+	}
 	inline void DivideOverAxis(const Vector &v) {
 		division_axis = new Vector(v);
 		flag_for_divide = true;
+	}
 	//Vector Strain(void) const;
     inline double Circumference(void) const {
       double sum=0.;
       for (list<Wall *>::const_iterator w=walls.begin();
 	   w!=walls.end();
 	   w++) {
 	sum +=  (*w)->Length();
+      }
       return sum;
+    }
 	QList<WallBase *> getWalls(void) {
 		QList<WallBase *> wall_list;
 		for (list<Wall *>::iterator i=walls.begin();
 			 i!=walls.end();
 			 i++) {
 			wall_list << *i;
+		}
 		return wall_list;
+	}
   //  void XFigPrint(std::ostream &os) const;
     void Dump(ostream &os) const;
 	QString printednodelist(void);
    // void OnDivide(ParentInfo &parent_info, CellBase &daughter);
     inline bool DeadP(void) { return dead; }
     inline void MarkDead(void) { dead  = true; }
 	static double &BaseArea(void) {
 		return static_data_members->base_area;
+	}
     void CheckForDivision(void);
@@ @@ -334,31 +327,24 @@ class CellBase : public QObject, public @@
     template<class P, class Op> P ReduceCellAndWalls(Op f) {
       P sum = 0;
       for (list<Wall *>::const_iterator w=walls.begin();
 	   w!=walls.end();
 	   w++) {
 	sum += ((*w)->c1 == this) ?
 	  f( ((*w)->c1), ((*w)->c2), *w ) :
 	  f( ((*w)->c2), ((*w)->c1), *w );
+      }
       return sum;
+    }
 	/* template<class Op> void LoopWalls(Op f) {
 		for (list<Wall *>::const_iterator w=walls.begin();
 			 w!=walls.end();
 			 w++) {
 			( **w)->f;
+		}
 	}*/
     //! Sum transporters at this CellBase's side of the walls
     double SumTransporters(int ch) {
       double sum=0.;
       for (list<Wall *>::const_iterator w=walls.begin();
 	   w!=walls.end();
 	   w++) {
 	sum += (*w)->getTransporter(this, ch);
+      }
       return sum;
@@ @@ -454,27 +440,24 @@ protected: @@
     double stiffness; // stiffness like in Hogeweg (2000)
     bool fixed;
     bool pin_fixed;
     bool at_boundary;
     bool dead;
 	bool flag_for_divide;
 	Vector *division_axis;
 	int cell_type;
     //double length;
     //Vector meanflux;
     //int valence;
     // for length constraint
     mutable double intgrl_xx, intgrl_xy, intgrl_yy, intgrl_x, intgrl_y;
     bool source;
     Vector cellvec;
 	// STATIC DATAMEMBERS MOVED TO CLASS
 	static CellsStaticDatamembers *static_data_members;
 	double source_conc;
     int source_chem;

src/data_plot.cpp

➞

Show inline comments

@@ @@ -54,28 +54,24 @@ DataPlot::DataPlot(QWidget *parent, cons @@
   // allocate data and curves
   d_t = new double[PLOT_SIZE];
   d_x = new double *[ncurves];
   d_x[0] = new double[ncurves*PLOT_SIZE];
   for (int i=1;i<ncurves;i++) {
     d_x[i]=d_x[i-1]+PLOT_SIZE;
+  }
   // Disable polygon clipping
   QwtPainter::setDeviceClipping(false);
   // We don't need the cache here
   //canvas()->setPaintAttribute(QwtPlotCanvas::PaintCached, false);
   //canvas()->setPaintAttribute(QwtPlotCanvas::PaintPacked, false);
   alignScales();
   //  Initialize data
   for (int i = 0; i< PLOT_SIZE; i++) {
     d_t[i] = 0.;     // time axis
+  }
   for (int i=0;i<ncurves * PLOT_SIZE;i++) {
     d_x[0][i]=0.;
+  }
@@ @@ -96,42 +92,26 @@ DataPlot::DataPlot(QWidget *parent, cons @@
     #ifdef QDEBUG
     qDebug() << "Curvecolor " << col.toStdString() << endl;
     #endif
     curves[i].setRawData(d_t, d_x[i], PLOT_SIZE);
+  }
   // Axis
   setAxisTitle(QwtPlot::xBottom, "Time");
   setAxisTitle(QwtPlot::yLeft, "Level");
   setAxisScale(QwtPlot::yLeft, 0, 10);
   //    setTimerInterval(0.0);
   data_pos = 0;
   // open file for writing
   /* QString fname(title);
   fname.replace(QString(" "),QString());
   fname.append(".dat");
   std::cerr << "Writing to file " << fname.toStdString() << std::endl;
   datfile = new QFile(fname);
   if (!datfile->open(QIODevice::WriteOnly | QIODevice::Text))
     return;
   datstream.setDevice(datfile);
   */
+}
 DataPlot::~DataPlot(void) {
   delete[] d_t ;
   delete[] d_x[0];
   delete[] d_x;
   delete[] curves;
+}
 //
 //  Set a plain canvas frame and align the scales to it
 //
@@ @@ -147,70 +127,52 @@ void DataPlot::alignScales() @@
     for ( int i = 0; i < QwtPlot::axisCnt; i++ )
+    {
         QwtScaleWidget *scaleWidget = (QwtScaleWidget *)axisWidget(i);
         if ( scaleWidget )
             scaleWidget->setMargin(0);
         QwtScaleDraw *scaleDraw = (QwtScaleDraw *)axisScaleDraw(i);
         if ( scaleDraw )
             scaleDraw->enableComponent(QwtAbstractScaleDraw::Backbone, false);
+    }
+}
 /* void DataPlot::setTimerInterval(double ms)
+{
     d_interval = qRound(ms);
     if ( d_timerId >= 0 )
+    {
         killTimer(d_timerId);
         d_timerId = -1;
+    }
     if (d_interval >= 0 )
         d_timerId = startTimer(d_interval);
+}
 */
 //  Generate new values
 void DataPlot::AddValue(double t,double *x)
+{
   //  std::cerr << "AddValue receives: " << t << ", " << y << ", " << z << std::endl;
   // Plot slowly fills up, then shifts to the left
   if ( data_pos >= PLOT_SIZE ) {
     for ( int j = 0; j < PLOT_SIZE - 1; j++ )
       d_t[j] = d_t[j+1];
     for ( int i=0;i<ncurves;i++) {
       for ( int j = 0; j < PLOT_SIZE - 1; j++ )
 	d_x[i][j] = d_x[i][j+1];
+    }
     data_pos = PLOT_SIZE - 1;
+  }
   d_t[data_pos] = t;
   // datstream << t;
   for ( int i=0;i<ncurves;i++) {
     curves[i].setRawData(d_t, d_x[i], data_pos);
     d_x[i][data_pos] = x[i];
     //datstream << " " << x[i];
+  }
   //datstream << "\n";
   setAxisScale(QwtPlot::xBottom, d_t[0], t);
   data_pos++;
   // update the display
   replot();
+}
 PlotDialog::PlotDialog(QWidget *parent, const QString title, const QStringList curvenames):
   QDialog(parent)

src/data_plot.h

➞

Show inline comments

@@ @@ -33,25 +33,24 @@ @@
 #include "curvecolors.h"
 const int PLOT_SIZE = 1000;
 class DataPlot : public QwtPlot
+{
     Q_OBJECT
 public:
   DataPlot(QWidget *parent, const QString title, const QStringList curvenames);
   virtual ~DataPlot(void);
 public slots:
     //    void setTimerInterval(double interval);
     void AddValue(double t, double *x);
 private:
     void alignScales();
     double *d_t;
     double **d_x;
     int d_interval; // timer in ms
     int d_timerId;
     QwtPlotCurve *curves;
@@ @@ -65,22 +64,21 @@ private: @@
     QFile *datfile;
     QTextStream datstream;
 };
 class PlotDialog : public QDialog {
 Q_OBJECT
  public:
   PlotDialog(QWidget *parent, const QString title, const QStringList curvenames);
   ~PlotDialog(void);
   public slots:
     //    void setTimerInterval(double interval);
   void AddValue(double t, double *x) {
     //std::cerr << "AddValue receives: " << t << ", " << y << ", " << z << std::endl;
     plot->AddValue(t,x);
+  }
  private:
   DataPlot *plot;
 };
 #endif

src/flux_function.h

➞

Show inline comments

 /*
  *  flux_function.h
  *  VirtualLeaf
+ *
  *  $Id$
+ *
  *  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.
+ *
  *  Created by Roeland Merks on 07-06-10.
  *  Copyright 2010 __MyCompanyName__. All rights reserved.
  *  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.
+ *
  */
 #ifndef _FLUX_FUNCTION_h_
 #define _FLUX_FUNCTION_h_
 // This header file defines a macro "SumFluxFromWalls" that attempts to hide this
 // horrendously confusing member function wrapper construct from VirtualLeaf's end users
 // required format of flux_function is:
 // double [model class name]::[function name](CellBase *this_cell, CellBase *adjacent_cell, Wall *w)
 // e.g.:
 // double MyModel::PINflux(CellBase *this_cell, CellBase *adjacent_cell, Wall *w)
 #include "far_mem_5.h"
 #define SumFluxFromWalls( _vleafcellp_, _flux_function_ ) \
 (( _vleafcellp_->ReduceCellAndWalls<double>( far_3_arg_mem_fun( *this, &_flux_function_ ) ) ))
 #endif

src/forwardeuler.cpp

➞

Show inline comments

@@ @@ -23,34 +23,24 @@ @@
 #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.
 /* static float maxarg1,maxarg2;
    #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1) > (maxarg2) ?	\
    (maxarg1) : (maxarg2))
    static float minarg1,minarg2;
    #define FMIN(a,b) (minarg1=(a),minarg2=(b),(minarg1) < (minarg2) ?	\
    (minarg1) : (minarg2))
    #define SIGN(a,b) ((b) >= 0.0 ? fabs(a) : -fabs(a))
 */
 const double ForwardEuler::Safety  = 0.9;
 const double ForwardEuler::PGrow = -0.2;
 const double ForwardEuler::Pshrnk = -0.25;
 const double ForwardEuler::Errcon = 1.89e-4;
 const double ForwardEuler::Maxstp = 10000000;
 const double ForwardEuler::Tiny = 1.0e-30;
 /* User storage for intermediate results. Preset kmax and dxsav in the calling program. If kmax =
 results are stored at approximate intervals dxsav in the arrays xp[1..kount], yp[1..nvar]
    [1..kount], where kount is output by odeint. Defining declarations for these variables, with

src/infobar.h

➞

Show inline comments

@@ @@ -32,30 +32,26 @@ @@
 class InfoBar : public Q3DockWindow {
 	Q_OBJECT
 public:
 	InfoBar(void) : Q3DockWindow() {
 		virtleaf = new QLabel();
 		SetText("undefined");
 		setHorizontalStretchable(true);
 		//dockwindow->boxLayout()->addWidget(viblab);//,Qt::AlignLeft);
 		boxLayout()->addStretch();
 		boxLayout()->addWidget(virtleaf);//, Qt::AlignHCenter);
 		boxLayout()->addStretch();
 		//dockwindow->boxLayout()->addWidget(psblab);//, Qt::AlignRight);
+	}
 	void SetText(QString text) {
 		virtleaf->setText(QString("<h1>The Virtual Leaf</h1>\n<center><b>Model:</b> <i>%1</i></center>").arg(text));
+	}
 private:
 	//Q3DockWindow *dockwindow;
 	QLabel *virtleaf;
 };
 #endif
@@ \ No newline at end of file @@

src/mainbase.cpp

➞

Show inline comments

@@ @@ -211,50 +211,39 @@ void MainBase::Save(const char *fname, c @@
 	if (QString(fname).isEmpty()) {
 		MyWarning::warning("No output filename given. Saving nothing.\n");
 		return;
+	}
 	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 );
 	if (!QString(format).contains("pdf", Qt::CaseInsensitive)) {
 		QImage *image = new QImage(QSize(sizex, sizey), QImage::Format_RGB32);
 		image->fill(QColor(Qt::white).rgb());
 		QPainter *painter=new QPainter(image);
 		//canvas.render(painter,QRectF(),QRectF(-5000,-5000, 10000, 10000));
 		canvas.render(painter);
 		if (!image->save(QString(fname))) {
 			MyWarning::warning("Image not saved successfully. Is the disk full or the extension not recognized?");
 		};
 		delete painter;
 		delete image;
 	} else {
 		QPrinter pdf(QPrinter::HighResolution);
 		pdf.setOutputFileName(fname);
 		pdf.setOutputFormat(QPrinter::PdfFormat);
 		//pdf.setPageSize(QPrinter::Custom);
 		QPainter painter(&pdf);
 		//	cerr << "Cell::Magnification() = " << Cell::Magnification() << endl;
 		//if (sizex==0 || sizey==0) {
 			// always fit to page
 		//	canvas.render(&painter);
 		//} else {
 		//	canvas.render(&painter,QRectF(),QRectF(-5000,-5000, 10000, 10000));
 		//}
 		canvas.render(&painter, QRectF(), QRectF(-5000,-5000, 10000, 10000));
 		cerr << "Rendering to printer\n";
+	}
+}
 void MainBase::CutSAM() {
 	mesh.CutAwaySAM();
+}

src/mainbase.h

➞

Show inline comments

@@ @@ -49,80 +49,60 @@ class MainBase { @@
     showmeshp =  false;
     showbordercellp =  false;
     shownodenumbersp =  false;
     showcellnumbersp =  false;
     showcellsaxesp = false;
     showcellstrainp =  false;
     movieframesp = true;
     showboundaryonlyp =  false;
     showwallsp =  false;
     showfluxesp = false;
     dynamicscellsp = true;
     showtooltipsp = false;
-	hidecellsp = 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 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 double getFluxArrowsize(void) { return 10.;}
     /* void Save(const char *fname, const char *format, int width=640) {
     //cerr << "Initializing Pixmap\n";
     cerr << "Saving to file " << fname << endl;
     QPixmap *image=new QPixmap(width, (int) (((double)canvas.height()/
     (double)canvas.width())*((double)width)));
     //QPicture *image = new QPicture();
     //cerr << "Done initializing QPixmap image(640, " << (((double)canvas.height()/(double)canvas.width())*640.) << ")\n";
     QPainter im(image);
     //cerr << "Done initializing image\n";
     im.scale((double)width/canvas.width(),(double)width/canvas.width());
     canvas.render(&im, QRectF(0,0,canvas.width(),canvas.height()) );
     //im.end();
     image->save(QString(fname), format);
     }*/
     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) {
       timeout = 0; // merely to obviate 'warning unused parameter' message
       cerr << message.toAscii().constData() << endl;
+    }
     Mesh &mesh;
  protected:
@@ @@ -131,24 +111,24 @@ class MainBase { @@
  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;
+    bool hidecellsp;
 };
 //#include <qapplication.h>
 #define TIMESTEP double MainBase::TimeStep(void)
 #define INIT void MainBase::Init(char *leaffile)
 #endif

src/matrix.cpp

➞

Show inline comments

@@ @@ -33,38 +33,34 @@ Matrix::Matrix(const Vector &c1, const V @@
   Alloc();
   mat[0][0]=c1.x; mat[0][1]=c2.x; mat[0][2]=c3.x;
   mat[1][0]=c1.y; mat[1][1]=c2.y; mat[1][2]=c3.y;
   mat[2][0]=c1.z; mat[2][1]=c2.z; mat[2][2]=c3.z;
+}
 void Matrix::Alloc(void) {
   // constructor
 //  mat=(double **)malloc(3*sizeof(double *));
 //  mat[0]=(double *)malloc(9*sizeof(double));
   mat = new double*[3];
   mat[0] = new double[9];
   for (int i=1;i<3;i++)
     mat[i]=mat[i-1]+3;
+}
 Matrix::~Matrix() {
   // destructor
   //free(mat[0]);
   //free(mat);
   delete[] mat[0];
   delete[] mat;
+}
 Matrix::Matrix(void) {
   // constructor
   Alloc();
   // clear matrix
   for (int i=0;i<9;i++) {
     mat[0][i]=0.;

src/mesh.h

➞

Show inline comments

@@ @@ -50,148 +50,110 @@ public: @@
 	typedef typename C::value_type value_type;
 	// reimplements push: reject element if it exists already
 	void push(const value_type &x) {
 		if (find (queue<T,C>::c.begin(),queue<T,C>::c.end(),x)==queue<T,C>::c.end()) {
 			queue<T,C>::c.push_back(x);
+		}
+	}
 	void clear(void) {
 		queue<T,C>::c.clear();
+	}
 };
 //template<class P> P& deref_ptr<P>( P *obj) { return *obj; }
 template<class P> P& deref_ptr ( P *obj) { return *obj; }
 class Mesh {
 	friend class Cell;
 	friend class Node;
 	friend class FigureEditor;
 public:
 	Mesh(void) {
 		// Make sure the reserved value is large enough if a cell is added
 		// in "Divide" when the capacity is insufficient, "cells" might be
 		// relocated including the current Cell (i.e. the value of *this)
 		// calling "Mesh::IncreaseCapacityIfNecessary" (from another
 		// object than Cell, e.g. Mesh) before entering Divide will solve
 		// this issue (solved now).
 		cells.reserve(2);
 		nodes.reserve(500);
 		//boundary_polygon = new BoundaryPolygon();
 		time = 0.;
 		plugin = 0;
 	};
 	~Mesh(void) {
 		delete boundary_polygon;
 		/* if (plugin)
 			delete plugin;*/
 	};
 	void Clean(void);
 	//void Plane(int xwidth, int ywidth, int nx, int ny, bool randomP=false);
 	Cell &EllipticCell(double xc, double yc, double ra, double rb, int nnodes=10, double rotation=0);
 	Cell &CircularCell(double xc, double yc, double r, int nnodes=10) {
 		return EllipticCell(xc, yc, r, r, nnodes, 0);
+	}
 	Cell &LeafPrimordium(int n, double pet_length);
 	Cell &LeafPrimordium2(int n);
 	Cell *RectangularCell(const Vector ll, const Vector ur, double rotation = 0);
 	void CellFiles(const Vector ll, const Vector ur);
 	/*  void GMVoutput(ostream &os,
 	 const char *codename=0, const char *codever=0,
 	 const char *comments=0);*/
 	//void RandPoints(int npoints);
 	inline Cell &getCell(int i) {
 		if ((unsigned)i<cells.size())
 			return *cells[i];
 		else {
                         #ifdef QDEBUG
                         qDebug() << i << endl;
                         qDebug() << "size is " << cells.size() << endl;
                         #endif
 			abort();
 			//	throw("Index out of range in Mesh::getCell");
+		}
+	}
 	inline Node &getNode(int i) {
 		//if (i >= nodes.size() || i < 0) {
 		//  cerr << "Mesh::getNode: Warning. Index " << i << " out of range.\n";
 		// }
 		return *nodes[i];
+	}
 	//double Diffusion(void);
 	inline int size(void) {
 		return cells.size();
+	}
 	inline int nnodes(void) {
 		return nodes.size();
+	}
 	//void SortNBLists(void);
 	/*template<class Op> void LoopCells(Op f) {
 	 for (vector<Cell>::iterator i=cells.begin();
 	 i!=cells.end();
 	 i++) {
 	 f(*i);
+	 }
 	 }*/
 	/*! \brief Calls function f for all Cells f.
 	 Using this template requires some fiddling with function adaptors bind2nd and mem_fun_ref.
 	 Example usage for calling a member function on each cell:
 	 mesh.LoopCells( bind2nd (mem_fun_ref( &Cell::DrawDiffEdges), &canvas ) );
 	 This calls Cell's member function DrawDiffEdges, taking one
 	 argument canvas, on all Cell objects in the current Mesh.
 	 */
 	template<class Op> void LoopCells(Op f) {
 		for (vector <Cell *>::iterator i=cells.begin();
 			 i!=cells.end();
 			 i++) {
 			f(**i);
+		}
 		//for_each(cells.begin(),cells.end(),f);
+	}
 	template<class Op> void LoopWalls(Op f) {
 		for (list <Wall *>::iterator i=walls.begin();
 			 i!=walls.end();
 			 i++) {
 			f(**i);
+		}
+	}
 	// if the amount of cells might increase, during looping, use this template
 	template<class Op> void LoopCurrentCells(Op f) {
 		vector<Cell *> current_cells = cells;
 		for (vector <Cell *>::iterator i=current_cells.begin();
 			 i!=current_cells.end();
 			 i++) {
 			f(**i);
+		}
 		//for_each(cells.begin(),cells.end(),f);
+	}
 	template<class Op> void LoopNodes(Op f) {
 		for (vector<Node *>::iterator i=nodes.begin();
 			 i!=nodes.end();
 			 i++) {
 			f(**i);
+		}
+	}
 	template<class Op> void RandomlyLoopNodes(Op f) {
@@ @@ -247,31 +209,24 @@ public: @@
 			if ((*i)->flag_for_divide) {
 				if ((*i)->division_axis) {
 					(*i)->DivideOverAxis(*(*i)->division_axis);
 					delete (*i)->division_axis;
 					(*i)->division_axis = 0;
 				} else {
 					(*i)->Divide();
+				}
 				(*i)->flag_for_divide=false;
+			}
+		}
+	}
 /*	template<class Op1, class Cont> void ExtractFromCells(Op1 f, Cont res) {
 		for (vector<Cell>::iterator i=cells.begin();
 			 i!=cells.end();
 			 i++) {
 			*(res++) = ( f(*i) );
+		}
 	}*/
 	// Apply "f" to cell i
 	// i.e. this is an adapter which allows you to call a function
 	// operating on Cell on its numeric index index
 	template<class Op> void cell_index_adapter(Op f,int i) {
 		f(cells[i]);
+	}
 	double DisplaceNodes(void);
 	void BoundingBox(Vector &LowerLeft, Vector &UpperRight);
 	int NEqs(void) {     int nwalls = walls.size();
@@ @@ -326,43 +281,40 @@ public: @@
 	void SetBaseArea(void);
 	int NCells(void) const {
 		return cells.size();
+	}
 	inline int NNodes(void) const {
 		return nodes.size();
+	}
 	void PrintQueue(ostream &os) {
 		while (!node_insertion_queue.empty()) {
 			os << node_insertion_queue.front() << endl;
 			node_insertion_queue.pop();
+		}
 		//copy (node_insertion_queue.begin(),node_insertion_queue.end(),ostream_iterator<Edge>(cerr, " "));
+	}
 	void InsertNodes(void) {
 		// insert the nodes in the insertion queue
 		while (!node_insertion_queue.empty()) {
 			//cerr << node_insertion_queue.front() << endl;
 			InsertNode(node_insertion_queue.front());
 			node_insertion_queue.pop();
+		}
+	}
 	void Clear();
 	//  template<class ReactFunction> ReactDiffuse(const double D, ReactFunction& react) {
 	void ReactDiffuse( double delta_t = 1 );
 	//void Diffuse(const double D);
 	double SumChemical(int ch);
 	void SetChemical(int ch, double value) {
 		for (vector<Cell *>::iterator c=cells.begin();
 			 c!=cells.end();
 			 c++) {
 			(*c)->chem[ch]=value;
+		}
+	}
 	// used for interacing with ODE-solvers (e.g. NRCRungeKutta)
 	void setValues(double x, double *y);
 	double *getValues(int *neqs);
@@ @@ -418,26 +370,24 @@ public: @@
 	void CleanChemicals(const vector<double> &clean_chem);
 	void CleanTransporters(const vector<double> &clean_transporters);
 	void RandomizeChemicals(const vector<double> &max_chem, const vector<double> &max_transporters);
 	inline double getTime(void) const { return time; }
 	string getTimeHours(void) const;
 	inline void setTime(double t) { time = t; }
 	double CalcProtCellsWalls(int ch) const;
 	void SettoInitVals(void);
 	QVector<qreal> VertexAngles(void);
 	QVector< QPair<qreal,int> > VertexAnglesValues(void);
 	void SetSimPlugin(SimPluginInterface *new_plugin) {
 		/* if (plugin)
 			delete plugin;*/
 		plugin=new_plugin;
+	}
 	QString ModelID(void) { return plugin?plugin->ModelID():QString("undefined"); }
 	void StandardInit(void);
 	Node* findNextBoundaryNode(Node*);
 private:
 	// Data members
 	vector<Cell *> cells;
 	vector<Node *> nodes;
@@ @@ -464,21 +414,16 @@ private: @@
+	}
 	inline Cell *AddCell(Cell *c) {
 		cells.push_back(c);
 		shuffled_cells.push_back(c);
 		//cerr << "Shuffled cell indices:  ";
 		/*copy(shuffled_cells.begin(),shuffled_cells.end(),ostream_iterator<int>(cerr," "));
 		 cerr << endl;*/
 		c->m=this;
 		return c;
+	}
 	//int Delaunay(void);
 	void CircumCircle(double x1,double y1,double x2,double y2,double x3,double y3,
 					  double *xc,double *yc,double *r);
 	// void RenumberCells(void);
 };
 #endif

src/modelcatalogue.cpp

➞

Show inline comments

@@ @@ -95,27 +95,24 @@ void ModelCatalogue::LoadPlugin(const ch @@
     pluginDir.cdUp();
     pluginDir.cdUp();
+  }
   //plugin_filters << "*.dylib";
 #endif
   plugin_filters << model;
   pluginDir.setNameFilters(plugin_filters);
   if (!pluginDir.cd("models")) {
     MyWarning::error("Directory 'models' not found!");
+  }
   //QVector<SimPluginInterface *> plugins;
   QStringList modelnames=pluginDir.entryList(QDir::Files);
   if (modelnames.empty()) {
     MyWarning::error("Model %s not found - hint: do not include path in filename.",model);
+  }
   foreach (QString fileName, modelnames){
     QPluginLoader loader(pluginDir.absoluteFilePath(fileName));
     if (SimPluginInterface *plugin =
 	qobject_cast<SimPluginInterface *>(loader.instance())) {
       models.append(plugin);
       //MyWarning::warning("Successfully loaded model %s",fileName.toStdString().c_str());
     } else {
@@ @@ -151,15 +148,13 @@ void ModelCatalogue::InstallModel(SimPlu @@
   // make sure both main and plugin use the same static datamembers (ncells, nchems...)
   plugin->SetCellsStaticDatamembers(CellBase::GetStaticDataMemberPointer());
   mesh->SetSimPlugin(plugin);
   Cell::SetNChem(plugin->NChem());
   plugin->SetParameters(&par);
   if (mainwin) {
     mainwin->RefreshInfoBar();
     mainwin->Init(0);
+  }
   //	mesh->StandardInit();
+}

src/node.cpp

➞

Show inline comments

@@ @@ -176,26 +176,24 @@ void Node::DrawOwners(QGraphicsScene *c) @@
 QVector<qreal> Node::NeighbourAngles(void) {
 	QVector<qreal> angles;
 	for (list<Neighbor>::iterator i=owners.begin();
 		 i!=owners.end();
 		 i++) {
 		Vector v1 = (*this - *i->nb1).Normalised();
 		Vector v2 = (*this - *i->nb2).Normalised();
 		//angles.push_back(atan2(v2.y,v2.x)-atan2(v1.y,v1.x));
 		//angles.push_back(atan2(v2.y,v2.x)-atan2(v1.y,v1.x));
 		double angle = v1.SignedAngle(v2);
 		if (angle<0) {
 			//cerr << "Changing sign of angle " << angle << endl;
 			angle = angle + 2*Pi;
+		}
 		angles.push_back(angle);
 		//cerr << "Cell " << i->cell->Index() << ": " <<  v1 << " and " << v2 << ": angle = " << angles.back() << ", " << v1.Angle(v2) << endl;
+	}
 	double sum=0.;

src/node.h

➞

Show inline comments

@@ @@ -116,29 +116,27 @@ public: @@
   inline bool BoundaryP(void) const { return boundary; }
   inline void SetBoundary(void) { boundary = true; }
   inline void UnsetBoundary(void) { boundary = false; }
   inline void SetSAM(void) { sam = true; }
   inline void toggleBoundary(void) {
     boundary = !boundary;
+  }
   //void Displace(void);
   Cell &getCell(const Neighbor &i);
   //Node &getNode(int i);
   ostream &print(ostream &os) const;
   void XMLAdd(xmlNodePtr nodes_node) const;
 #ifdef QTGRAPHICS
   void Draw(QGraphicsScene &c, QColor color=QColor("black"), int size = 10) const;
   void DrawIndex(QGraphicsScene *c) const;
   void DrawOwners(QGraphicsScene *c) const;
 #endif
   // temporary function for easier debugging
   inline int CellsSize(void) const {
     return owners.size();
@@ @@ -155,59 +153,40 @@ public: @@
     return fixed;
+  }
   inline void Unfix(void) {
     fixed=false;
+  }
   inline void MarkDead(void) {
     dead=true;
+  }
   inline bool DeadP(void) {
     return dead;
+  }
   /*void UpdateAfterNodeRemoved(int n) {
     for (list<Neighbor>::iterator i=owners.begin();
     i!=owners.end();
     i++) {
     if (i->nb1>=n) i->nb1--;
     if (i->nb2>=n) i->nb2--;
+    }
+    }
     void UpdateAfterCellRemoved(int n) {
     for (list<Neighbor>::iterator i=owners.begin();
     i!=owners.end();
     i++) {
     if (i->cell>=n) i->cell--;
+    }
+    }
   */
   inline void Mark(void) {
     marked=true;
+  }
   inline void Unmark(void) {
     marked=false;
+  }
   inline bool Marked(void) const {
     return marked;
+  }
   inline void setPos( Vector p ) {
     x = p.x;
     y = p.y;
     z = p.z;
+  }
   inline bool SamP(void) const { return sam; }
   //enum boundary_type {NoBoundary, Noflux, SourceSink, SAM};
   //!\brief Calculate angles with neighboring vertices
   //! Sum of angles should be 2*Pi
   QVector<qreal> NeighbourAngles(void);
 private:
   // "owners" lists the cells to which this cell belong
   // and the two neighboring nodes relative to each cell
   list< Neighbor > owners;
   Mesh *m;
   int index;

src/nodeitem.cpp

➞

Show inline comments

@@ @@ -45,47 +45,28 @@ NodeItem::NodeItem( Node *n, QGraphicsSc @@
 void NodeItem::userMove(double dx, double dy) {
   QGraphicsItem::moveBy( dx, dy );
   class_cast<Node *>(obj)->x += (dx/Cell::Magnification());
   class_cast<Node *>(obj)->y += (dy/Cell::Magnification());
+}
 void NodeItem::paint(QPainter *painter, const QStyleOptionGraphicsItem *option, QWidget *)
+{
   // from Qt4.2 example: "elastic nodes"
   //painter->setPen(Qt::NoPen);
   //painter->setBrush(Qt::darkGray);
   //painter->drawEllipse(-70, -70, 200, 200);
   /* QRadialGradient gradient(-30, -30, 100);
   if (option->state & QStyle::State_Sunken) {
   gradient.setCenter(30, 30);
   gradient.setFocalPoint(30, 30);
   gradient.setColorAt(1, QColor(Qt::yellow).light(120));
   gradient.setColorAt(0, QColor(Qt::darkYellow).light(120));
   } else {
   gradient.setColorAt(0, Qt::yellow);
   gradient.setColorAt(1, Qt::darkYellow);
+  }
   painter->setBrush(gradient); */
   option = NULL; // use assignment merely to obviate compilation warning
   painter->setBrush(brush);
   painter->setPen(Qt::NoPen);
   // const static double mag=20.;
   painter->drawEllipse(ellipsesize);
+}
 QPainterPath NodeItem::shape() const
+{
     QPainterPath path;
     path.addEllipse(ellipsesize);
     return path;
+}
 QRectF NodeItem::boundingRect() const

src/nodeset.h

➞

Show inline comments

@@ @@ -22,45 +22,39 @@ @@
  */
 #ifndef _NODESET_H_
 #define _NODESET_H_
 #include <algorithm>
 #include <numeric>
 #include <list>
 #include <iterator>
 #include "node.h"
 //class xmlNode;
 class NodeSet : public list<Node *> {
  public:
   NodeSet(void) {
     done = false;
+  }
   inline bool DoneP(void) { return done; }
   inline void ResetDone(void) { done = false; }
   void AddNode(Node * n) {
     push_back(n);
     n->node_set = this;
+  }
   //  list <Node *? getNodes(void) {
   //  return set;
   //}
   list <Cell *> getCells(void) {
     list<Cell *> cellset;
     for (list<Node *>::const_iterator i=begin();
 	 i!=end();
 	 i++) {
       transform ( (*i)->owners.begin(), (*i)->owners.end(), back_inserter( cellset ) , mem_fun_ref ( &Neighbor::getCell ));
+    }
     cellset.sort();
@@ @@ -147,28 +141,26 @@ class NodeSet : public list<Node *> { @@
     } else {
       // REJECT
       // Move the set's nodes back to their original position
       for ( list<Node *>::iterator n = begin();
 	    n!= end();
 	    ++n ) {
 	(*n)->x-=rx;
 	(*n)->y-=ry;
 	// (*n)->z -= rz;
+	  }
+    }
+  }
   void XMLAdd(xmlNode *root) const;
   void XMLRead(xmlNode *root, Mesh *m);
  private:
   // list<Node *> set;
   bool done;
 };
 ostream &operator<<(ostream &os, const NodeSet &ns);
 #endif

src/output.cpp

➞

Show inline comments

@@ @@ -15,25 +15,24 @@ @@
  *  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 <unistd.h>
 #include <sys/types.h>
 #include <sys/stat.h>
 #include "warning.h"
 #include "parameter.h"
 #include "output.h"
 #include <QDir>
 #include <QFileInfo>
 static const std::string _module_id("$Id$");
@@ @@ -76,49 +75,24 @@ int YesNoP(const char *message) { @@
   while (strcmp(answer,"y") && strcmp(answer,"n")) {
     fprintf(stderr,"\n\bPlease answer 'y' or 'n'. ");
     fflush(stderr);
     scanf("%s",answer);
+  }
   if (!strcmp(answer,"y")) return TRUE;
   return FALSE;
+}
 /* //FILE *OpenWriteFile(char *filename)
 // {
 //   FILE *fp;
 //   fprintf(stderr,"Opening %s for writing\n",filename);
 //   if((OpenFileAndCheckExistance(&fp,filename,"r"))==TRUE) {
 // 	if (!YesNoP("File exists, overwrite?")) {
 // 	  fprintf(stderr," Could not open file %s for writing, exiting... \n"
 // 			  ,filename);
 // 	  exit(0);
 // 	}
 //   }
 //   if (fp!=NULL) // file existed, but user wants to overwrite
 // 	fclose(fp);
 //   if ((fp=fopen(filename,"w"))==NULL) {
 // 	fprintf(stderr," Could not open file %s for writing, exiting... \n"
 // 			,filename);
 // 	exit(0);
 //   }
 //   return fp;
 // }
 */
 FILE *OpenWriteFile(const char *filename)
+{
   char fname[FNAMESIZE];
   FILE *fp;
   fprintf(stderr,"Opening %s for writing\n",filename);
   if(FileExistsP(filename)==TRUE) {
@@ @@ -142,73 +116,24 @@ FILE *OpenWriteFile(const char *filename @@
   if ((fp=fopen(fname,"w"))==NULL) {
     char *message=(char *)malloc(2000*sizeof(char));
     sprintf(message," Could not open file %s for writing: "
 	    ,fname);
     perror("");
     throw(message);
+  }
   return fp;
+}
 /*FILE *OpenGZippedWriteFile(const char *filename)
+{
   // Open file that is zipped while it is written
   // uses a pipe
   char fname[FNAMESIZE];
   char gzname[FNAMESIZE];
   FILE *fp;
   extern Parameter par;
   // step 1, add ".gz" to the filename
   sprintf(gzname, "%s.gz", filename);
   // and check whether it already exists
   fprintf(stderr,"Opening %s for writing\n",gzname);
   if(FileExistsP(gzname)==TRUE) {
     if (par.interactive) {
       if (!YesNoP("File exists, overwrite?")) {
 	fprintf(stderr," Could not open file %s for writing, exiting... \n"
 		,gzname);
 	exit(0);
+      }
     } else {
       // Rename old file
       snprintf(fname, FNAMESIZE-1, "%s~",gzname);
       rename(gzname, fname);
+    }
+  }
   //  strncpy(fname, gzname, FNAMESIZE-1);
   char *command=new char[20+sizeof(gzname)];
   sprintf(command, "gzip -c > %s", gzname);
   if ((fp=popen(command,"w"))==NULL) {
     fprintf(stderr," Could not open file %s for writing: "
 	    ,fname);
     perror("");
     exit(-1);
+  }
   delete[] command;
   return fp;
+}
 */
 FILE *OpenReadFile(const char *filename)
+{
   FILE *fp;
   fprintf(stderr,"Opening %s for reading\n",filename);
   if((OpenFileAndCheckExistance(&fp,filename,"r"))==FALSE) {
     char *message=(char *)malloc(2000*sizeof(char));
     sprintf(message," File %s not found or empty, exiting... \n" ,filename);
     throw(message);
+  }
@@ @@ -322,35 +247,34 @@ char *Chext(char *filename) { @@
   } else {
     /* . found */
     result=(char *)malloc((i+1)*sizeof(char));
     strncpy(result, filename, i);
+  }
   return result;
+}
 void MakeDir(const char *dirname) {
   cerr << "Entering MakeDir for name " << dirname << "\n";
 #ifdef QTGRAPHICS
   QFileInfo file_info(dirname);
   //check for existance
   if (file_info.exists()) {
     if (file_info.isDir()) {
       // OK
-      cerr << "Using existing directory " << dirname << " for data storage.\n";
+      cerr << "Using existing directory " << dirname << " for data storage." << endl;
       return;
     } else {
       char *message = new char[MESS_BUF_SIZE+1];
       snprintf(message, MESS_BUF_SIZE, "%s is not a directory", dirname);
       cerr << message << endl;
       throw(message);
+    }
+  }
   // make directory
   QDir dir;
@@ @@ -406,58 +330,12 @@ void MakeDir(const char *dirname) { @@
       perror(message);
       exit(1);
+    }
+  }
 #endif
+}
 /*bool CanWeWriteP(char *filename) {
   // check for the existance of file "filename"
    // if it exists, ask the user whether we may overwrite it
    //false: do not overwrite. true: do overwrite
   char message[MESS_BUF_SIZE];
   char fname[FNAMESIZE];
   extern const Parameter par;
   int status;
   status=access(filename, F_OK);
   if (status < 0) {// file does not exist, or something else is wrong
     // check error code
     if (errno!=ENOENT) {
       // another error occured
       snprintf(message, MESS_BUF_SIZE, "Error checking for existance of %s",filename);
       perror(message);
       exit(1);
+    }
   } else {
     // file exists, ask for permission to overwrite if interactive
     if (par.interactive) {
       snprintf(message, MESS_BUF_SIZE, "File %s exists. Overwrite? ",filename);
       if (!YesNoP(message))
 	return false;
       else
 	return true;
     } else {
       // Rename old file
       snprintf(fname, FNAMESIZE-1, "%s~",filename);
       rename(filename, fname);
+    }
     return true;
+  }
   // file does not exist, or user permits overwriting
   return true;
 }*/

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
  *  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.
+ *
  */
 #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);
 char *ReadLine(FILE *fp);
 void CheckFile(FILE *fp);
 int FileExistsP(const char *fname);
 char *Chext(char *filename);
 void MakeDir(const char *dirname);
 bool CanWeWriteP(char *filename);
 #ifdef __cplusplus
+}
 #endif
 #define MESS_BUF_SIZE 160
 #ifndef FALSE
 #define FALSE 0
 #define TRUE 1
 #endif
 #endif
 /*
+ *
  *  $Id$
+ *
  *  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.
+ *
  */
 #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);
 char *ReadLine(FILE *fp);
 void CheckFile(FILE *fp);
 int FileExistsP(const char *fname);
 char *Chext(char *filename);
 void MakeDir(const char *dirname);
 bool CanWeWriteP(char *filename);
 #ifdef __cplusplus
+}
 #endif
 #define MESS_BUF_SIZE 160
 #ifndef FALSE
 #define FALSE 0
 #define TRUE 1
 #endif
 #endif

src/parse.cpp

➞

Show inline comments

@@ @@ -62,26 +62,25 @@ char *ParsePar(FILE *fp, char *parameter @@
   value=strdup(token);
   free(line);
   return value;
+}
 int igetpar(FILE *fp,char *parameter, bool wrapflag) {
   // overloaded compatibility function. Doesn't need default parameter
   // default = 0
   return igetpar(fp, parameter, 0, wrapflag);
+}
 int igetpar(FILE *fp,char *parameter, int default_val, bool wrapflag)
+{
   char *token;
   int value;
   /* Get token representing the value */
   token=ParsePar(fp,parameter, wrapflag);
   if (token==0) {
@@ @@ -93,28 +92,25 @@ int igetpar(FILE *fp,char *parameter, in @@
   sscanf(token,"%d",&value);
   fprintf(stderr, "%d]\n",value);
   free(token);
   return value;
+}
 float fgetpar(FILE *fp,char *parameter, bool wrapflag) {
   // overloaded compatibility function. Doesn't need default parameter
   // default = 0
   return fgetpar(fp, parameter, 0., wrapflag);
+}
 float fgetpar(FILE *fp, char *parameter, double default_val, bool wrapflag)
+{
   char *token;
   float value;
   /* Get token representing the value */
   token=ParsePar(fp,parameter, wrapflag);
   if (token==0) {
     /* default value */
@@ @@ -287,26 +283,24 @@ bool bgetpar(FILE *fp, char *parameter, @@
 char *SearchToken(FILE *fp, char *token,bool wrapflag)
+{
   /* This function returns the next line of FILE *fp that contains
      the string stored in the null terminated string token */
   /* remember to free the memory allocated for line */
   unsigned int len;
   char *line;
   int wrapped=false;
   long initial_position;
   /*  rewind(fp); */
   char *tokenplusspace = (char *)malloc( (strlen(token)+3)*sizeof(char));
   strcpy(tokenplusspace, token);
   strcat(tokenplusspace," ");
   initial_position=ftell(fp);
   if (ferror(fp)) /* error occured */
+    {
       error("%s",strerror(errno));
+    }
   if (feof(fp)) {

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
  *  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.
+ *
  */
 #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);
 char *sgetpar(FILE *fp,char *parameter,const char *default_val, bool wrapflag);
 bool bgetpar(FILE *fp, char *parameter, bool wrapflag);
 bool bgetpar(FILE *fp, char *parameter, int default_val, bool wrapflag);
 char *SearchToken(FILE *fp, char *token, bool wrapflag);
 int TokenInLineP(char *line,char *token);
 void SkipToken(FILE *fp,char *token, bool wrapflag);
 void SkipLine(FILE *fp);
 char *bool_str(bool bool_var);
 #endif
 /*
+ *
  *  $Id$
+ *
  *  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.
+ *
  */
 #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);
 char *sgetpar(FILE *fp,char *parameter,const char *default_val, bool wrapflag);
 bool bgetpar(FILE *fp, char *parameter, bool wrapflag);
 bool bgetpar(FILE *fp, char *parameter, int default_val, bool wrapflag);
 char *SearchToken(FILE *fp, char *token, bool wrapflag);
 int TokenInLineP(char *line,char *token);
 void SkipToken(FILE *fp,char *token, bool wrapflag);
 void SkipLine(FILE *fp);
 char *bool_str(bool bool_var);
 #endif

src/random.cpp

➞

Show inline comments

@@ @@ -132,33 +132,18 @@ int RandomCounter(void) { @@
 **/
 int Randomize(void) {
   // Set the seed according to the local time
   struct timeb t;
   int seed;
   ftime(&t);
   seed=abs((int)((t.time*t.millitm)%655337));
   Seed(seed);
   fprintf(stderr,"Random seed is %d\n",seed);
 #ifdef QDEBUG
   qdebug() << "Random seed is " << seed << endl;
 #endif
   return seed;
+}
 /** TESTING random generator
 #include <vector>
 #include <fstream>
 int main(void) {
   MyUrand r(-1);
   vector<int> bucket(100);
   for (int i = 0; i<1000000 ; i++) {
     bucket[r(100)]++;
+  }
   ofstream out("randomtest.dat");
   for (int i = 0; i<=100; i++) {
     out << i << " " << bucket[i] << endl;
+  }
+}
 ***/

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
  *  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.
+ *
  */
 #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();
 int Randomize(void);
 int RandomCounter(void);
 // Class MyUrand, so we can pass the random generator to STL's random_shuffle,
 // and get identical simulations for a given random seed.
 class MyUrand {
   long n;
  public:
   MyUrand(long nn) {
     n=nn;
+  }
   MyUrand(void){};
   void seed(long s) {
     Seed(s);
+  }
   long operator()(long nn) { return RandomNumber(nn)-1; }
   long operator()(void) { return RandomNumber(n); }
 };
 #endif
 /*
+ *
  *  $Id$
+ *
  *  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.
+ *
  */
 #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();
 int Randomize(void);
 int RandomCounter(void);
 // Class MyUrand, so we can pass the random generator to STL's random_shuffle,
 // and get identical simulations for a given random seed.
 class MyUrand {
   long n;
  public:
   MyUrand(long nn) {
     n=nn;
+  }
   MyUrand(void){};
   void seed(long s) {
     Seed(s);
+  }
   long operator()(long nn) { return RandomNumber(nn)-1; }
   long operator()(void) { return RandomNumber(n); }
 };
 #endif

src/sqr.h

➞

Show inline comments

@@ @@ -17,31 +17,24 @@ @@
  *  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_
 /* static float sqrarg;
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 : sqrarg*sqrarg)
 static double dsqrarg;
 #define DSQR(a) ((dsqrarg=(a)) == 0.0 ? 0.0 : dsqrarg*dsqrarg)
 */
 // 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 ) {
   if (a == 0.0) {
     return 0.0;
   } else {

src/vector.h

➞

Show inline comments

@@ @@ -109,25 +109,24 @@ public: @@
     return *this;
+  }
   Vector operator/(const double divisor) const; // division by a double
   Vector operator*(const double multiplier) const; // multiply by a scalar (double)
   Vector &operator/=(const double divisor);
   Vector &operator*=(const double multiplier);
   Vector operator*(const Vector &v) const; // cross product
   bool operator==(const Vector &v) const; // comparison
   bool operator< (const Vector &v) const; // order x,y,z
   //double Norm(void) const; // gives the "norm" (| v |) of v
   inline double Norm(void) const {
     return sqrt(DSQR(x)+DSQR(y)+DSQR(z));
+  }
   // Quick and dirty Norm (i.e. Manhattan distance)
   // (e.g. useful if we want to see if the vec is (0,0,0);
   inline double ManhattanNorm(void) const {
     return x+y+z;
+  }

src/vleafmodel.h

➞

Show inline comments

 /*
  *  vleafmodel.h
  *  mymodel
+ *
  *  $Id$
+ *
  *  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.
+ *
  *  Created by Roeland Merks on 08-06-10.
  *  Copyright 2010 __MyCompanyName__. All rights reserved.
  *  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.
+ *
  */
 #ifndef _VLEAFMODEL_H_
 #define _VLEAFMODEL_H_
 #include <QObject>
 #include <QtGui>
 #include <fstream>
 #include "simplugin.h"
 #include "parameter.h"
 #include "wallbase.h"
 #include "cellbase.h"
 #include "mymodel.h"
 #include "flux_function.h"
 #endif

src/wall.cpp

➞

Show inline comments

@@ @@ -40,31 +40,24 @@ 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
 	/* cerr << "Wall belongs to Cells: ";
      transform(wall_owners.begin(), wall_owners.end(), ostream_iterator<int>(cerr, ", "), mem_fun(&Cell::Index));
 	 cerr << endl;
 	 */
 	//list<Cell *>::iterator f = adjacent_find (++e,owners.end());
 	// For the first division, wall finds three "owners", including the boundary_polygon.
 	// Remove that one from the list.
 	//cerr << "wall_owners.size() = " << wall_owners.size() << endl;
 	if (wall_owners.size() == 3 && nwalls==1 /* bug-fix 22/10/2007; confine this condition to first division only */) {
 	        #ifdef QDEBUG
 	        qDebug() << "nwalls = " << nwalls << endl;
 		#endif
 		// special case for first cleavage
 		// find boundary polygon in the wall owners list
 		list<CellBase *>::iterator bpit = find_if (
@@ @@ -205,27 +198,24 @@ void Wall::ShowStructure(QGraphicsScene @@
 	QGraphicsSimpleTextItem *text1 = new QGraphicsSimpleTextItem( QString("%1").arg(c2->Index()),0,c);
 	QGraphicsSimpleTextItem *text2 = new QGraphicsSimpleTextItem( QString("%1").arg(c1->Index()),0,c);
 	text1 -> setPos( textpos1.x, textpos1.y );
 	text2 -> setPos( textpos2.x, textpos2.y );
 	text1->setZValue(20); text2->setZValue(20);
 	text1->setFont( QFont( "Helvetica", par.nodenumsize, QFont::Bold) );
 	text2->setFont( QFont( "Helvetica", par.nodenumsize, QFont::Bold) );
 	text1->setPen ( QColor(par.textcolor) );
 	text2->setPen ( text1->pen() );
 	//text1->setTextFlags(Qt::AlignCenter);
 	//text2->setTextFlags(Qt::AlignCenter);
 	text1->show(); text2->show();
+}
 string Wall::WallTypetoStr(const WallType &wt) const {
 	if (wt == Normal) {
 		return string("normal");
+	}
 	if (wt == AuxSource) {
 		return string("aux_source");
+	}

src/wallbase.cpp

➞

Show inline comments

@@ @@ -69,25 +69,24 @@ WallBase::WallBase(Node *sn1, Node *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.
 	//length = 0;
 	SetLength();
 	// to visualize flux through WallBase
 	viz_flux=0;
 	dead = false;
 	wall_type = Normal;
 	wall_index = nwalls++;
+}
 void WallBase::CopyWallContents(const WallBase &src) {
@@ @@ -161,28 +160,24 @@ void WallBase::SwapWallContents(WallBase @@
 	wall_type = tmp_wall_type;
+}
 bool WallBase::SAM_P(void) {
 	return N1()->sam || N2()->sam;
+}
 #include <fstream>
 /* double WallBase::Length(void){
  return (*n2 - *n1).Norm();
  }*/
 void WallBase::SetLength(void) {
 	//static bool show_nodes = true;
 	//double old_length = length;
 	// Step 1: find the path of nodes leading along the WallBase.
 	// A WallBase often represents a curved cell wall: we want the total
 	// length _along_ the wall here...
 	// Locate first and second nodes of the edge in Cell's list of nodes
 	list<Node *>::const_iterator first_node_edge = find(c1->nodes.begin(), c1->nodes.end(), n1);
 	list<Node *>::const_iterator second_node_edge_plus_1 = ++find(c1->nodes.begin(), c1->nodes.end(), n2);
@@ @@ -194,87 +189,58 @@ void WallBase::SetLength(void) { @@
 	length = 0.;
 	// Now, walk to the second node of the edge in the list of nodes
 	stringstream deb_str;
 	for (list<Node *>::const_iterator n=
 		 (++first_node_edge==c1->nodes.end()?c1->nodes.begin():first_node_edge);
 		 n!=second_node_edge_plus_1;
 		 (++n == c1->nodes.end()) ? (n=c1->nodes.begin()):n  ) {
 		/* if (n==c1->nodes.end()) {
 		 n=c1->nodes.begin(); // wrap around
 		 }*/
 		list<Node *>::const_iterator prev_n = n;
 		if (prev_n==c1->nodes.begin()) prev_n=c1->nodes.end();
 		--prev_n;
 		//cerr << "Node: " << (Vector)(**n) << endl;
 		// Note that Node derives from a Vector, so we can do vector calculus as defined in vector.h
 		deb_str << "[ " << (*prev_n)->index << " to " << (*n)->index << "]";
 		length += (*(*prev_n) - *(*n)).Norm();
+	}
 	/*  if (length > 100) {
 	 ostringstream warn;
 	 warn << "Strange, length is " << length << "...: " << deb_str.str() << endl;
 	 warn << "Strangeness in WallBase: " << *this << endl << endl << deb_str.str() << endl;
 	 MyWarning::warning (warn.str().c_str());
 	 }*/
 	//cerr << deb_str .str() << ", length is " << length << endl;
 	//of << length << " " << ((*n2)-(*n1)).Norm() << endl;
+}
 void WallBase::CorrectTransporters(double orig_length) {
 	double length_factor = length / orig_length;
 	// cerr << "[ lf = " << length_factor << "]";
 	//cerr << "Correcting amount of transporters on WallBase "  << *this << ", length factor is "  << orig_length << " / " << length << endl;
 	for (int ch=0;ch<CellBase::NChem();ch++) {
 		transporters1[ch] *= length_factor;
 		transporters2[ch] *= length_factor;
 		new_transporters1[ch] *= length_factor;
 		new_transporters2[ch] *= length_factor;
+	}
+}
 Vector WallBase::VizFlux(void) {
 	return viz_flux * ( (*n2) - (*n1) ).Normalised().Perp2D();
 	//return transporters1[1] * ( (*n2) - (*n1) ).Normalised().Perp2D();
+}
 /* TransportFunction::TransportFunction( void ) {
 	//chem_change_c1 = new double[Cell::NChem()];
 	//chem_change_c2 = new double[Cell::NChem()];
 	//for (int i=0;i<Cell::NChem();i++) {
 	// chem_change_c1[i] = chem_change_c2[i] = 0.;
 	//}
 }*/
 void WallBase::SetTransToNewTrans( void ){
 	for (int i=0;i<CellBase::NChem();i++) {
 		transporters1[i] = new_transporters1[i];
 		transporters2[i] = new_transporters2[i];
+	}
+}
 Vector WallBase::getWallVector(CellBase *c) {
 	if ( c == c1 ) {
 		return ( Vector(*n2) - Vector(*n1) );
@@ @@ -292,22 +258,19 @@ Vector WallBase::getInfluxVector(CellBas @@
+}
 //! \brief Test if this wall intersects with division plane p1 -> p2
 bool WallBase::IntersectsWithDivisionPlaneP(const Vector &p1, const Vector &p2) {
 	// Algorithm of http://local.wasp.uwa.edu.au/~pbourke/geometry/lineline2d/
 	double x1 = n1->x, y1 = n1->y;
 	double x2 = n2->x, y2 = n2->y;
 	double x3 = p1.x, y3 = p1.y;
 	double x4 = p2.x, y4 = p2.y;
 	double ua = ( (x4 - x3) * (y1-y3) - (y4 - y3)*(x1-x3) ) / ( (y4 -y3) * (x2 -x1) - (x4-x3)*(y2-y1));
 	//	double ub = ( (x2 - x1) * (y1 - y3)  - (y2 - y1) * (x1 -x3) ) / ( ( y4-y3) * (x2-x1) - (x4-x3)*(y2-y1)) ;
 	// If ua is between 0 and 1, line p1 intersects the line segment
 	if ( ua >=0. && ua <=1.) return true;
 	else return false;
+}

src/wallbase.h

➞

Show inline comments

@@ @@ -182,66 +182,20 @@ public: @@
 	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);
 	/*! Function to be defined in leaf.cpp */
 	//void OnWallInsert(void);
 	void SetTransToNewTrans( void );
 	// implemented in xmlwrite.cpp
 	//void XMLAdd(xmlNode *parent) const;
 private:
 };
 /* class TransportFunction {
 	friend class Mesh;
 public:
 	TransportFunction( void );
 	virtual ~TransportFunction() {
 		//delete[] chem_change_c1;
 		//delete[] chem_change_c2;
+	}
 	virtual void operator()(WallBase *w, double *dchem_c1, double *dchem_c2) = 0;// { cerr << "This is base class TransportFunction.\n"; }
 	//virtual void operator()(WallBase *w, double *dchem_c1, double *dchem_c2, double *dapo) =0;
 protected:
 	int wall_index; //double *chem_change_c1;
 	//double *chem_change_c2;
 };
 class CellReaction {
 public:
 	CellReaction(void) {};
 	virtual ~CellReaction() {};
 	//! Implements the actual, intracellular chemical reactions.
 	virtual void operator()(CellBase * c, double *dchem ) = 0;
 };
 class WallReaction {
 public:
 	WallReaction(void) {};
 	virtual ~WallReaction() {};
 	//! Implements the actual, biochemical reactions occuring at the wall.
 	virtual void operator()(WallBase *, double *dw1, double *dw2) = 0;
 };*/
 ostream &operator<<(ostream &os, const WallBase &w);
 #endif

src/wallitem.cpp

➞

Show inline comments

@@ @@ -28,149 +28,103 @@ @@
 #include "parameter.h"
 #include "node.h"
 #include "transporterdialog.h"
 static const std::string _module_id("$Id$");
 WallItem::WallItem( Wall *w, int wallnumber, QGraphicsScene *canvas )
   : QGraphicsLineItem( 0, canvas ), SimItemBase( w, canvas){
   wn = wallnumber;
   extern Parameter par;
   //Wall *w=&getWall();
   // Draw amount of "PIN1"
   //double val = wn==1?(w->Transporters1(1)/par.Pi_tot)*255.:(w->Transporters2(1)/par.Pi_tot)*255.;
   /* if (val > 255 || val < 0 ) {
      std::cerr << "val = " << val << endl;
      if (wn == 1) {
      std::cerr << "Transporters1(1) = " << w->Transporters1(1) << endl;
      } else {
      std::cerr << "Transporters2(1) = " << w->Transporters2(1) << endl;
+     }
      }*/
 	  setColor();
 	  // line with "PIN1"is a bit inside the cell wall
 	  Vector edgevec = (*(w->N2())) - (*(w->N1()));
 	  Vector perp = edgevec.Normalised().Perp2D();
 	  Vector offs = Cell::Offset();
 	  double factor = Cell::Factor();
 	  Vector from = ( offs + *(w->N1()) ) * factor + (wn==1?-1:1) * par.outlinewidth * 0.5 * factor * perp;
 	  Vector to = ( offs + *(w->N2()) ) *factor + (wn==1?-1:1) * par.outlinewidth * 0.5 * factor * perp;
 	  Vector tmp_centroid = ( *(w->N2()) + *(w->N1()) )/2.;
 	  Vector centroid = ( offs + tmp_centroid ) * factor;
 	  QString text=QString("%1").arg(w->Index());
 	  /*  if (0) {
 		  QGraphicsSimpleTextItem *ctext = new QGraphicsSimpleTextItem ( text, 0, canvas );
 		  ctext->setPen( QPen(QColor("orange")) );
 		  ctext->setZValue(20);
 		  ctext->setFont( QFont( "Helvetica", par.nodenumsize, QFont::Bold) );
 		  //ctext->setTextFlags(Qt::AlignCenter);
 		  ctext->show();
 		  ctext ->setPos(centroid.x,
 						 centroid.y );
 	  }*/
 	  setLine(( from.x ),
 			  ( from.y ),
 			  ( to.x ),
 			  ( to.y ) );
 	  setZValue(12);
+  }
 void WallItem::setColor(void) {
   QColor diffcolor;
   static const QColor purple("Purple");
   static const QColor blue("blue");
   Wall *w=&getWall();
   double tr = wn==1?w->Transporters1(1):w->Transporters2(1);
   CellBase *c = wn==1?w->C1():w->C2();
   diffcolor.setRgb( (int)( ( tr / (1 + tr) )*255.), 0, 0);
   //diffcolor.setRgb( (int)( ((wn==1?w->Transporters1(1):w->Transporters2(1)))*255.), 0, 0);
   /* if (wn==1) {
      cerr << "Transporter: " << w->Transporters1(1) << endl;
      } else {
      cerr << "Transporter: " << w->Transporters2(1) << endl;
      }*/
   if (w->AuxinSource() && c->BoundaryPolP()) {
     setPen( QPen(purple , par.outlinewidth) );
   } else {
     if (w->AuxinSink() && c->BoundaryPolP()) {
       setPen( QPen(blue, par.outlinewidth));
     } else {
       setPen (QPen(diffcolor, par.outlinewidth) );
+    }
+  }
 //   if (c->BoundaryPolP()) {
 //     setPen(QPen(QColor("red"), 20));
 //   }
+}
 void WallItem::OnClick(QMouseEvent *e) {
 	Wall *w=&getWall();
 	#ifdef QDEBUG
 	qDebug() << "Wall ID = " << w->Index() << ", this = " << w << endl;
 	qDebug() << "Wall item = " << this << endl;
 	qDebug() << "C1 = " << w->C1()->Index() << ", C2 = " << w->C2()->Index() << endl;
 	qDebug() << "N1 = " << w->N1()->Index() << ", N2 = " << w->N2()->Index() << endl;
 	#endif
 	//double tr = wn==1?w->Transporters1(1):w->Transporters2(1);
 	CellBase *c = wn==1?w->C1():w->C2();
 	TransporterDialog dialog(w, c, wn);
 	dialog.exec();
 	if (e->button() == Qt::RightButton) {
 		QString message;
 		if (wn==1) {
 			message=QString("Transporter 1 = %1, color = %2, length = %3\n").arg(w->Transporters1(1)).arg(pen().color().red()).arg(getWall().Length());
 		} else {
 			message=QString("Transporter 2 = %1, color = %2, length = %3\n").arg(w->Transporters2(1)).arg(pen().color().red()).arg(getWall().Length());
+		}
 		//extern MainBase *main_window;
 		//((Main *)main_window)->UserMessage(message);
 	} else {
 		if (e->button() == Qt::LeftButton) {
 			if (c->BoundaryPolP()) {
 				w->cycleWallType();
 			} else {
 				if (e->modifiers() == Qt::ShiftModifier) {
 					wn==1?w->setTransporters1(1,0):w->setTransporters2(1,0);
 				} else {
 					// set high amount of PIN1
 					//cerr << "Setting PIN1\n";
 					wn==1?w->setTransporters1(1,10):w->setTransporters2(1,10);
+				}
+			}
 			setColor();
 			update(boundingRect());
+		}
 		/* else {
 			if (e->button() == Qt::MidButton && (e->modifiers == Qt::ShiftModifier & Qt::ControlModifier)) {
 				// hidden feature for correcting
 			}*/
+	}
+}

src/wallitem.h

➞

Show inline comments

@@ @@ -33,20 +33,18 @@ @@
 #include "simitembase.h"
 #include "wall.h"
 //! Shows transporter concentrations at one side of the wall
 class WallItem : public QGraphicsLineItem, public SimItemBase
+{
 public:
   WallItem( Wall *n, int wallnumber, QGraphicsScene *canvas );
   virtual ~WallItem() {}
   Wall &getWall(void) const { return *class_cast<Wall*>(obj); }
   void OnClick(QMouseEvent *e);
   //virtual void userMove(double dx, double dy);
   //virtual void paint( QPainter * painter, const QStyleOptionGraphicsItem * option, QWidget * widget = 0);
   void setColor(void);
  private:
   int wn;
 };
 #endif

src/warning.cpp

➞

Show inline comments

@@ @@ -57,26 +57,24 @@ void MyWarning::error(char * fmt, ...) @@
 void MyWarning::error(const char *fmt, ...)
+{
   va_list ap;
   if (Quiet) return;
   char *message = new char[1000];
   va_start(ap, fmt);
   vsnprintf(message, 999, fmt, ap);		/* invoke interface to printf       */
   va_end(ap);
   QString qmess(message);
   //  bool batch = false;
   if (qApp->type()==QApplication::Tty) {
     // batch mode: print the message to stderr
     fprintf(stderr, "Fatal error: %s\n",qmess.toStdString().c_str());
     exit(1);
   } else { // issue a dialog box
     /* Solve this with signal and slot...! */
 	  //extern MainBase *main_window;
     //((Main *)main_window)->stopSimulation();
 	QMessageBox::critical( 0 , "Fatal error", qmess, QMessageBox::Abort, QMessageBox::NoButton, QMessageBox::NoButton );
     fprintf(stderr, "Error: %s\n",qmess.toStdString().c_str());
     QCoreApplication::exit(1);

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
  *  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.
+ *
  */
 #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
 //static int last_value=UNIDENTIFIED;
 /*#define WATCH(x) if (last_value==UNIDENTIFIED) {   last_value=x;
 } else { if (x!=last_value) { fprintf(stderr,"WATCH value changed. Suspending execution. \n Interrupt within debugger to examine position in program.\n");
 				 last_value=x;
 				 while(1);
 	   } else {
 		      last_value=x;
+	   }
 	   }*/
 /* These functions were a gift from Josh Barnes */
 /* I changed the name "eprintf" to "warning" */
 #ifdef __cplusplus
 extern "C" {
 #endif
   // namespace MyWarning needed because libxml2 also defines a warning token.
   namespace MyWarning {
     void error(const char *, ...);
     void warning(const char *, ...);
     void unique_warning(const char *, ...);
+  }
 #ifdef __cplusplus
+}
 #endif
 #endif
 /*
+ *
  *  $Id$
+ *
  *  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.
+ *
  */
 #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.
   namespace MyWarning {
     void error(const char *, ...);
     void warning(const char *, ...);
     void unique_warning(const char *, ...);
+  }
 #ifdef __cplusplus
+}
 #endif
 #endif

src/xmlwrite.cpp

➞

Show inline comments

@@ @@ -178,25 +178,24 @@ void Cell::XMLAddCore(xmlNodePtr xmlcell @@
+    {
       ostringstream text;
       xmlNodePtr node_xml = xmlNewChild(xmlcell, NULL, BAD_CAST "node", NULL);
       text << (*i)->Index();
       xmlNewProp(node_xml, BAD_CAST "n", BAD_CAST text.str().c_str());
+    }
+  }
   for (list<Wall *>::const_iterator i=walls.begin();i!=walls.end();i++) {
+    {
       ostringstream text;
       xmlNodePtr wall_xml = xmlNewChild(xmlcell, NULL, BAD_CAST "wall", NULL);
       //text <<wall_list_index( *i );
       text << XMLIO::list_index( m->walls.begin(), m->walls.end(), *i );
       xmlNewProp(wall_xml, BAD_CAST "w", BAD_CAST text.str().c_str());
+    }
+  }
   xmlNodePtr chem_xml = xmlNewChild(xmlcell, NULL, BAD_CAST "chem", NULL);
+  {
     ostringstream text;
     text << NChem();
@@ @@ -353,113 +352,106 @@ int Cell::XMLRead(xmlNode *cur) { @@
 	  if ((!xmlStrcmp(n->name, (const xmlChar *)"chem"))) {
 	    xmlNode *v_node = n->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 chemical values given for cell(s). Ignoring remaining values.";
 		    //ThrowStringStream(text);
 		    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. 1002");
+		}
 		//double v = strtod( (char *)nc, 0 );
 		double v=standardlocale.toDouble((char *)nc, &ok);
 		if (!ok) MyWarning::error("Could not convert \"%s\" to double in XMLRead.",(char *)nc);
 		chem[nv++]=v;
 		xmlFree(nc);
+	      }
 	      v_node = v_node->next;
+	    }
+	  }
 	  n = n->next;
+  }
 	// read cell properties
+	{
 		xmlChar *v_str = xmlGetProp(cur, BAD_CAST "area");
 		if (v_str==0) {
 			unique_warning("Token \"area\" not found in xmlwrite.cpp at or around line no. 1018");
+		}
 		if (v_str != NULL) {
 		  //area = strtod( (char *)v_str, 0);
 			area=standardlocale.toDouble((char *)v_str, &ok);
 			if (!ok) MyWarning::error("Could not convert \"%s\" to double in XMLRead.",(char *)v_str);
 			xmlFree(v_str);
+		}
+	}
+	{
 		xmlChar *v_str = xmlGetProp(cur, BAD_CAST "target_area");
 		if (v_str==0) {
 			unique_warning("Token \"target_area\" not found in xmlwrite.cpp at or around line no. 1029");
+		}
     if (v_str != NULL) {
       //target_area = strtod( (char *)v_str, 0);
       	target_area=standardlocale.toDouble((char *)v_str, &ok);
 	if (!ok) MyWarning::error("Could not convert \"%s\" to double in XMLRead.",(char *)v_str);
       xmlFree(v_str);
+    }
+  }
+  {
     xmlChar *v_str = xmlGetProp(cur, BAD_CAST "target_length");
     if (v_str==0) {
       unique_warning("Token \"target_length\" not found in xmlwrite.cpp at or around line no. 1041");
+    }
     if (v_str != NULL) {
       //target_length = strtod( (char *)v_str, 0);
       target_length=standardlocale.toDouble((char *)v_str, &ok);
       if (!ok) MyWarning::error("Could not convert \"%s\" to double in XMLRead.",(char *)v_str);
       xmlFree(v_str);
+    }
+  }
+  {
     xmlChar *v_str = xmlGetProp(cur, BAD_CAST "lambda_celllength");
     if (v_str==0) {
       unique_warning("Token \"lambda_celllength\" not found in xmlwrite.cpp at or around line no. 1052");
+    }
     if (v_str != NULL) {
       //lambda_celllength = strtod( (char *)v_str, 0);
       lambda_celllength=standardlocale.toDouble((char *)v_str, &ok);
       if (!ok) MyWarning::error("Could not convert \"%s\" to double in XMLRead.",(char *)v_str);
       xmlFree(v_str);
+    }
+  }
+  {
     xmlChar *v_str = xmlGetProp(cur, BAD_CAST "stiffness");
     if (v_str==0) {
       unique_warning("Token \"stiffness\" not found in xmlwrite.cpp at or around line no. 1063");
+    }
     if (v_str != NULL) {
       //stiffness = strtod( (char *)v_str, 0);
       stiffness=standardlocale.toDouble((char *)v_str, &ok);
       if (!ok) MyWarning::error("Could not convert \"%s\" to double in XMLRead.",(char *)v_str);
       xmlFree(v_str);
+    }
+  }
+  {
     xmlChar *v_str = xmlGetProp(cur, BAD_CAST "fixed");
     if (v_str==0) {
       unique_warning("Token \"fixed\" not found in xmlwrite.cpp at or around line no. 1075");
@@ @@ -589,30 +581,24 @@ void NodeSet::XMLRead(xmlNode *root, Mes @@
+  }
+}
 void Wall::XMLAdd(xmlNode *parent) const {
   // Save the node to a stream so we can reconstruct its state later
   xmlNodePtr xmlwall = xmlNewChild(parent, NULL, BAD_CAST "wall",NULL);
   /* {
      ostringstream text;
      text << index;
      xmlNewProp(xmlnode, BAD_CAST "index", BAD_CAST text.str().c_str());
      }*/
+  {
     ostringstream text;
     text << Index();
     xmlNewProp(xmlwall, BAD_CAST "index" , BAD_CAST text.str().c_str() );
+  }
+  {
     ostringstream text;
     text << c1->Index();
     xmlNewProp(xmlwall, BAD_CAST "c1", BAD_CAST text.str().c_str());
+  }
@@ @@ -648,30 +634,24 @@ void Wall::XMLAdd(xmlNode *parent) const @@
     text << viz_flux;
     xmlNewProp(xmlwall, BAD_CAST "viz_flux", BAD_CAST text.str().c_str());
+  }
+  {
     ostringstream text;
     text << WallTypetoStr(wall_type);
     xmlNewProp(xmlwall, BAD_CAST "wall_type", BAD_CAST text.str().c_str());
+  }
   xmlNodePtr tr1_xml = xmlNewChild(xmlwall, NULL, BAD_CAST "transporters1", NULL);
   //   {
   //     ostringstream text;
   //     text << Cell::nchem;
   //     xmlNewProp(tr1_xml, BAD_CAST "n", BAD_CAST text.str().c_str());
   //   }
   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) {
@@ @@ -744,41 +724,41 @@ void Mesh::XMLSave(const char *docname, @@
 	doc = xmlNewDoc(BAD_CAST "1.0");
 	root_node = xmlNewNode(NULL, BAD_CAST "leaf");
 	xmlDocSetRootElement(doc, root_node);
 	/*
 	 * xmlNewProp() creates attributes, which is "attached" to an node.
 	 * It returns xmlAttrPtr, which isn't used here.
 	 */
 	xmlNewProp(root_node, BAD_CAST "name", BAD_CAST docname);
 	time_t t;
 	std::time(&t);
-	// asctime_r(localtime(&t),tstring); //Doesn't work for MinGW
 	char *tstring = strdup(asctime(localtime(&t))); // but this does
 	// replace "end of line character by '\0'
 	char *eol=strchr(tstring,'\n');
 	if (eol!=NULL)
 		*eol='\0';
 	xmlNewProp(root_node, BAD_CAST "date", BAD_CAST tstring);
 	free(tstring);
 	QString simtime = QString("%1").arg(time);
 	xmlNewProp(root_node, BAD_CAST "simtime", BAD_CAST simtime.toStdString().c_str());
 	/*
 	 * Creates a DTD declaration. Isn't mandatory.
 	 */
-	//dtd = xmlCreateIntSubset(doc, BAD_CAST "root", NULL, BAD_CAST "tree2.dtd");
 	par.XMLAdd(root_node);
 	xmlNodePtr xmlnodes = xmlNewChild(root_node, NULL, BAD_CAST "nodes",NULL);
 	{ ostringstream text;
 		text << NNodes();
 		xmlNewProp(xmlnodes, BAD_CAST "n", BAD_CAST text.str().c_str());
+	}
 	{ ostringstream text;
 		text << Node::target_length;
 		xmlNewProp(xmlnodes, BAD_CAST "target_length", BAD_CAST text.str().c_str());
+	}
@@ @@ -887,47 +867,50 @@ void Mesh::XMLSave(const char *docname, @@
 	/*free the document */
 	xmlFreeDoc(doc);
 	/*
 	 *Free the global variables that may
 	 *have been allocated by the parser.
 	 */
 	xmlCleanupParser();
 	/*
 	 * this is to debug memory for regression tests
 	 */
 	//xmlMemoryDump();
+}
 void Mesh::XMLReadSimtime(const xmlNode *a_node) {
   xmlNode *root_node;
   root_node = (xmlNode *)a_node;
   xmlChar *strsimtime = xmlGetProp(root_node, BAD_CAST "simtime");
   if (strsimtime) {
-    //double simtime = strtod((const char *)strsimtime, 0);
     QLocale standardlocale(QLocale::C);
     bool ok;
     double simtime=standardlocale.toDouble((char *)strsimtime, &ok);
     if (!ok) MyWarning::error("Could not convert \"%s\" to double in XMLRead.",(char *)strsimtime);
       time = simtime;
 		cerr << "Simtime = " << strsimtime << endl;
 #ifdef QDEBUG
                 qDebug() << "Simtime = " << strsimtime << endl;
 #endif
 	} else {
 		cerr << "No simtime found in file \n";
 #ifdef QDEBUG
     qDebug() << "No simtime found in file." << endl;
 #endif
 		time =0;
+	}
+}
 void Mesh::XMLReadPars(const xmlNode * a_node) {
 	xmlNode *root_node;
 	root_node = (xmlNode *)a_node;
 	par.XMLRead(root_node);
 	Seed(par.rseed);
 	MakeDir(par.datadir);
+}
@@ @@ -955,53 +938,52 @@ void Mesh::XMLReadGeometry(const xmlNode @@
+		}
 		cur=cur->next;
+	}
 	cur=root_node->xmlChildrenNode;
 	while (cur!=NULL) {
 		if ((!xmlStrcmp(cur->name, (const xmlChar *)"nodes"))) {
 			XMLReadNodeSetsToNodes(cur);
+		}
 		cur = cur->next;
+	}
 	//cur = root_node;
 	// allocate Cells
 	cur = root_node;
 	// allocate Cells
 	cur = cur->xmlChildrenNode;
 	while (cur!=NULL) {
 		if ((!xmlStrcmp(cur->name, (const xmlChar *)"cells"))){
 			xmlChar *offsetxc = xmlGetProp(cur, BAD_CAST "offsetx");
 			xmlChar *offsetyc = xmlGetProp(cur, BAD_CAST "offsety");
-			//double ox = strtod((const char*)offsetxc, 0);
 			double ox=standardlocale.toDouble((const char *)offsetxc, &ok);
 			if (!ok) MyWarning::error("Could not convert \"%s\" to double in XMLRead.",(const char *)offsetxc);
-			//double oy = strtod((const char*)offsetyc, 0);
 			double oy=standardlocale.toDouble((const char *)offsetyc, &ok);
 			if (!ok) MyWarning::error("Could not convert \"%s\" to double in XMLRead.",(const char *)offsetyc);
 			Cell::setOffset(ox, oy);
 			xmlFree(offsetxc);
 			xmlFree(offsetyc);
 			xmlChar *magnificationc = xmlGetProp(cur, BAD_CAST "magnification");
-			//Cell::SetMagnification(strtod((const char*)magnificationc, 0 ));
 			Cell::SetMagnification(standardlocale.toDouble((const char *)magnificationc, &ok));
 			if (!ok) MyWarning::error("Could not convert \"%s\" to double in XMLRead.",(const char *)magnificationc);
 			xmlFree(magnificationc);
 			xmlChar *baseareac = xmlGetProp(cur, BAD_CAST "base_area");
-			//Cell::BaseArea()= strtod((const char *)baseareac, 0 );
 			Cell::BaseArea() = standardlocale.toDouble((const char *)baseareac, &ok);
 			if (!ok) MyWarning::error("Could not convert \"%s\" to double in XMLRead.",(const char *)baseareac);
 			xmlFree(baseareac);
 			XMLReadCells(cur);
+		}
 		cur=cur->next;
+	}
 	// allocate Walls (we need to have read the cells before constructing walls)
 	vector <Wall *> tmp_walls;
@@ @@ -1062,25 +1044,25 @@ void Mesh::XMLReadNodes(xmlNode *root) { @@
   for (vector<Node *>::iterator i=nodes.begin();
        i!=nodes.end();
        i++) {
     delete *i;
+  }
   nodes.clear();
   Node::nnodes=0;
   xmlChar *tlc = xmlGetProp(root, BAD_CAST "target_length");
   if (tlc != 0) {
-    //Node::target_length = strtod( (const char *)tlc, 0 );
     Node::target_length = standardlocale.toDouble((const char *)tlc, &ok);
     if (!ok) MyWarning::error("Could not convert \"%s\" to double in XMLRead.",(const char *)tlc);
     xmlFree(tlc);
   } else {
     // note that libxml2 also defines a token "warning"
     MyWarning::unique_warning("Warning: value found in XML file for Node::target_length.");
+  }
   while (cur!=NULL) {
     if ((!xmlStrcmp(cur->name, (const xmlChar *)"node"))){
@@ @@ -1103,29 +1085,28 @@ void Mesh::XMLReadNodes(xmlNode *root) { @@
+      }
       xmlChar *boundaryc = xmlGetProp(cur, BAD_CAST "boundary");
       if (boundaryc==0) {
 	unique_warning("Token \"boundary\" not found in xmlwrite.cpp at or around line.");
+      }
       xmlChar *samc = xmlGetProp(cur, BAD_CAST "sam");
       if (samc==0) {
 	unique_warning("Token \"sam\" not found in xmlwrite.cpp at or around line.");
+      }
-      //double x = strtod( (char *)xc , 0);
       double x = standardlocale.toDouble((const char *)xc, &ok);
       if (!ok) MyWarning::error("Could not convert \"%s\" to double in XMLRead.",(const char *)xc);
       //double y = strtod( (char *)yc , 0 );
       double y = standardlocale.toDouble((const char *)yc, &ok);
       if (!ok) MyWarning::error("Could not convert \"%s\" to double in XMLRead.",(const char *)yc);
       Node *new_node = new Node(x,y);
       nodes.push_back(new_node);
       new_node->m = this;
       new_node->fixed = strtobool( (char *)fixedc);
       new_node->boundary = strtobool( (char *)boundaryc );
       new_node->sam = strtobool ( (char *)samc);
       new_node->node_set = 0;
@@ @@ -1153,26 +1134,24 @@ void Mesh::XMLReadWalls(xmlNode *root, v @@
   xmlNode *cur = root;
   cur = cur->xmlChildrenNode;
   for (list<Wall *>::iterator i=walls.begin();
        i!=walls.end();
        i++) {
     delete *i;
+  }
   walls.clear();
   Wall::nwalls = 0;
   tmp_walls->clear();
   //Node::nnodes=0;
   QLocale standardlocale(QLocale::C);
   bool ok;
   while (cur!=NULL) {
     vector<int> tmp_nodes;
     while(cur!=NULL) {
       if ((!xmlStrcmp(cur->name, (const xmlChar *)"wall"))) {
 	xmlChar *nc = xmlGetProp(cur, BAD_CAST "c1");
@@ @@ -1202,36 +1181,36 @@ void Mesh::XMLReadWalls(xmlNode *root, v @@
 	if (	nc==0) {
 	  unique_warning("Token \"n2\" not found in xmlwrite.cpp at or around line no. 801");
+	}
 	int n2 = atoi( (char *)nc);
 	xmlFree(nc);
 	nc = xmlGetProp(cur, BAD_CAST "length");
 	if (	nc==0) {
 	  unique_warning("Token \"length\" not found in xmlwrite.cpp at or around line no. 809");
+	}
-	//double length = strtod( (char *)nc, 0);
 	double length = standardlocale.toDouble((const char *)nc, &ok);
 	if (!ok) MyWarning::error("Could not convert \"%s\" to double in XMLRead.",(const char *)nc);
 	xmlFree(nc);
 	nc = xmlGetProp(cur, BAD_CAST "viz_flux");
 	double viz_flux = 0.0;
 	if (nc!=0) {
-	  //viz_flux = strtod( (char *)nc, 0);
 	  viz_flux = standardlocale.toDouble((const char *)nc, &ok);
 	  if (!ok) MyWarning::error("Could not convert \"%s\" to double in XMLRead.",(const char *)nc);
+	}
 	xmlFree(nc);
 	Wall::WallType wall_type;
+	{
 	  xmlChar *v_str = xmlGetProp(cur, BAD_CAST "wall_type");
 	  if (v_str != 0) {
 	    if (!xmlStrcmp(v_str, (const xmlChar *)"aux_source")) {
@@ @@ -1279,35 +1258,35 @@ void Mesh::XMLReadWalls(xmlNode *root, v @@
 	while (w_node!=NULL) {
 	  if ((!xmlStrcmp(w_node->name, (const xmlChar *)"transporters1"))) {
 	    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.";
-		    //ThrowStringStream(text);
 		    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. 835");
+		}
-		//double v = strtod( (char *)nc, 0 );
 		double v = standardlocale.toDouble((const char *)nc, &ok);
 		if (!ok) MyWarning::error("Could not convert \"%s\" to double in XMLRead.",(const char *)nc);
 		w->transporters1[nv++]=v;
 		xmlFree(nc);
+	      }
 	      v_node = v_node->next;
+	    }
+	  }
@@ @@ -1315,104 +1294,98 @@ void Mesh::XMLReadWalls(xmlNode *root, v @@
 	  if ((!xmlStrcmp(w_node->name, (const xmlChar *)"transporters2"))) {
 	    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;
-		    // ThrowStringStream(text);
+		  }
+		}
 		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 = strtod( (char *)nc, 0 );
 		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"))) {
 	    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.";
-		    //ThrowStringStream(text);
 		    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 = strtod( (char *)nc, 0 );
 		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;
+    }
+  }
   //  CleanUpWalls();
+}
 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) {
 		//Cell *new_cell=0;
 		if ((!xmlStrcmp(cur->name, (const xmlChar *)"cell")) ||
 			(!xmlStrcmp(cur->name, (const xmlChar *)"boundary_polygon" ))) {
 			vector<int> tmp_walls_ind;
 			xmlNode *n = cur->xmlChildrenNode;
 			while(n!=NULL) {
 				if ((!xmlStrcmp(n->name, (const xmlChar *)"wall"))) {
 					xmlChar *nc = xmlGetProp(n, BAD_CAST "w");
 					if (nc==0) {
@@ @@ -1575,30 +1548,28 @@ void Mesh::XMLRead(const char *docname, @@
 		xmlFreeDoc(doc);
 		return;
+	}
 	if (xmlStrcmp(cur->name, (const xmlChar *) "leaf")) {
 		throw("XML file of the wrong type, it is not a leaf.");
 		xmlFreeDoc(doc);
 		return;
+	}
 	/*Get the root element node */
 	xmlNode *root_element = xmlDocGetRootElement(doc);
 	//XMLParseTree(root_element);
 	if (geometry) XMLReadGeometry(root_element);
 	if (pars) XMLReadPars(root_element);
 	if (simtime) XMLReadSimtime(root_element);
 	//print_element_names(root_element);
 	// If pointer settings defined, return a copy of the settings tree
 	if (settings) {
 		xmlNode *cur = root_element->xmlChildrenNode;
 		// if settings field is not found, *settings will be returned 0.
 		*settings = 0;
 		while (cur!=NULL) {
 			if ((!xmlStrcmp(cur->name, (const xmlChar *)"settings"))){
 				*settings = xmlCopyNode(cur,1);
+			}
 			cur=cur->next;
+		}
@@ @@ -1608,29 +1579,24 @@ void Mesh::XMLRead(const char *docname, @@
 	/*
 	 *Free the global variables that may
 	 *have been allocated by the parser.
 	 */
 	xmlCleanupParser();
 	// We're doing this so we can manually delete walls with by adding the 'delete="true"' property
 	CleanUpCellNodeLists();
+}
 /*  int Mesh::XMLReadWall(xmlNode *cur)  {
     return w;
     }*/
 void Parameter::XMLRead(xmlNode *root) {
 	xmlNode *cur = root->xmlChildrenNode;
 	while (cur!=NULL) {
 		if ((!xmlStrcmp(cur->name, (const xmlChar *)"parameter"))){
 			xmlNode *par_node = cur->xmlChildrenNode;
 			while (par_node!=NULL) {
+				{
 					if (!xmlStrcmp(par_node->name, (const xmlChar *)"par")) {
 						xmlChar *namec = xmlGetProp(par_node, BAD_CAST "name");
 						xmlChar *valc = xmlGetProp(par_node, BAD_CAST "val");
 						if (valc) {

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