EI/VirtualLeaf Changeset - 782330072e62 · Centrum Wiskunde & Informatica (CWI)

Changeset - 782330072e62

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! ! !

Michael Guravage - 15 years ago 2010-06-17 18:13:46
michael.guravage@cwi.nl

Reformatted the source files and generally straighten up the code.

--
user: Michael Guravage <michael.guravage@cwi.nl>
branch 'default'

changed src/Neighbor.cpp
changed src/Neighbor.h
changed src/OptionFileDialog.cpp
changed src/OptionFileDialog.h
changed src/UniqueMessage.cpp
changed src/UniqueMessage.h
changed src/VirtualLeaf.cpp
changed src/apoplastitem.cpp
changed src/apoplastitem.h
changed src/build_models/auxingrowthplugin.cpp
changed src/build_models/auxingrowthplugin.h
changed src/build_models/meinhardtplugin.cpp
changed src/build_models/meinhardtplugin.h
changed src/build_models/testplugin.cpp
changed src/build_models/testplugin.h
changed src/build_models/translate_plugin.pl
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/cellitem.cpp
changed src/cellitem.h
changed src/curvecolors.h
changed src/data_plot.cpp
changed src/data_plot.h
changed src/far_mem_5.h
changed src/flux_function.h
changed src/forwardeuler.cpp
changed src/forwardeuler.h
changed src/infobar.h
changed src/mainbase.cpp
changed src/mainbase.h
changed src/matrix.cpp
changed src/matrix.h
changed src/maxmin.h
changed src/mesh.cpp
changed src/mesh.h
changed src/miscq.cpp
changed src/miscq.h
changed src/modelcatalogue.cpp
changed src/modelcatalogue.h
changed src/modelelement.h
changed src/node.cpp
changed src/node.h
changed src/nodeitem.cpp
changed src/nodeitem.h
changed src/nodeset.cpp
changed src/nodeset.h
changed src/output.cpp
changed src/output.h
changed src/parameter.cpp
changed src/parameter.h
changed src/pardialog.cpp
changed src/pardialog.h
changed src/parse.cpp
changed src/parse.h
changed src/perl/deployapp.pl
changed src/perl/histogram.pl
changed src/perl/make_parameter_source.pl
changed src/perl/make_pardialog_source.pl
changed src/perl/make_xmlwritecode.pl
changed src/pi.h
changed src/qcanvasarrow.h
changed src/random.cpp
changed src/random.h
changed src/rseed.cpp
changed src/rungekutta.cpp
changed src/rungekutta.h
changed src/simitembase.cpp
changed src/simitembase.h
changed src/simplugin.cpp
changed src/simplugin.h
changed src/sqr.h
changed src/tiny.h
changed src/transporterdialog.cpp
changed src/transporterdialog.h
changed src/vector.cpp
changed src/vector.h
changed src/vleafmodel.h
changed src/wall.cpp
changed src/wall.h
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
changed src/xmlwrite.h

87 files changed with 601 insertions and 792 deletions:

src/Neighbor.cpp

src/Neighbor.h

src/OptionFileDialog.cpp

src/OptionFileDialog.h

src/UniqueMessage.cpp

src/UniqueMessage.h

src/VirtualLeaf.cpp

src/apoplastitem.cpp

src/apoplastitem.h

src/build_models/auxingrowthplugin.cpp

src/build_models/auxingrowthplugin.h

src/build_models/meinhardtplugin.cpp

src/build_models/meinhardtplugin.h

src/build_models/testplugin.cpp

src/build_models/testplugin.h

src/build_models/translate_plugin.pl

src/canvas.cpp

src/canvas.h

src/cell.cpp

118

src/cell.h

src/cellbase.cpp

src/cellbase.h

src/cellitem.cpp

src/cellitem.h

src/curvecolors.h

src/data_plot.cpp

src/data_plot.h

src/far_mem_5.h

src/flux_function.h

src/forwardeuler.cpp

src/forwardeuler.h

src/infobar.h

src/mainbase.cpp

src/mainbase.h

src/matrix.cpp

src/matrix.h

src/maxmin.h

src/mesh.cpp

src/mesh.h

src/miscq.cpp

src/miscq.h

src/modelcatalogue.h

src/node.cpp

src/node.h

src/nodeitem.cpp

src/nodeitem.h

src/nodeset.cpp

src/nodeset.h

src/output.cpp

src/output.h

src/parameter.cpp

src/pardialog.cpp

src/parse.cpp

src/parse.h

src/perl/deployapp.pl

src/perl/histogram.pl

src/perl/make_parameter_source.pl

src/perl/make_pardialog_source.pl

src/perl/make_xmlwritecode.pl

src/pi.h

src/qcanvasarrow.h

src/random.cpp

src/random.h

src/rseed.cpp

src/rungekutta.cpp

src/rungekutta.h

src/simitembase.cpp

src/simitembase.h

src/simplugin.cpp

src/simplugin.h

src/sqr.h

src/tiny.h

src/transporterdialog.cpp

src/transporterdialog.h

src/vector.cpp

src/vector.h

src/vleafmodel.h

src/wall.cpp

src/wall.h

src/wallbase.cpp

src/wallbase.h

src/wallitem.cpp

src/wallitem.h

src/warning.cpp

src/warning.h

src/xmlwrite.cpp

src/xmlwrite.h

0 comments (0 inline, 0 general)

src/Neighbor.cpp

➞

Show inline comments

@@ @@ -43,4 +43,5 @@ bool neighbor_cell_eq(const Neighbor &n1 @@
   return (n1.getCell())->Index() == (n2.getCell())->Index(); // Compare cell indices not pointers.
+}
 // finis
 /* finis */

src/Neighbor.h

➞

Show inline comments

@@ @@ -68,4 +68,5 @@ bool neighbor_cell_eq(const Neighbor &n1 @@
 #endif
 // finis
 /* finis */

src/OptionFileDialog.cpp

➞

Show inline comments

@@ @@ -27,8 +27,8 @@ using namespace std; @@
 static const std::string _module_id("$Id$");
 OptionFileDialog::OptionFileDialog(QWidget *parent, const char *name, bool modal) : Q3FileDialog(parent, name, modal) {
 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);
@@ @@ -38,12 +38,13 @@ OptionFileDialog::OptionFileDialog(QWidg @@
 	addToolButton(geometrycheck);
 	addToolButton(parcheck);
 };
 OptionFileDialog::OptionFileDialog ( const QString & dirName, const QString & filter , QWidget * parent, const char * name , bool modal  ) :
 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";
 };
-	};
+/* finis */

src/OptionFileDialog.h

➞

Show inline comments

@@ @@ -30,7 +30,8 @@ class OptionFileDialog : public Q3FileDi @@
 	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 );
   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; }
@@ @@ -41,3 +42,5 @@ private: @@
 };
 #endif
 /* finis */

src/UniqueMessage.cpp

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Show inline comments

@@ @@ -68,7 +68,6 @@ UniqueMessageBox::~UniqueMessageBox(void @@
 	if (show_again->checkState() == Qt::Checked ) {
 		cerr << "Message won't be shown again\n";
 		issued_messages << boxtext;
+	}
+}
 int UniqueMessageBox::exec(void)  {
@@ @@ -78,8 +77,8 @@ int UniqueMessageBox::exec(void) { @@
 	else {
 		return 1;
+	}
+}
 QStringList UniqueMessageBox::issued_messages;
 /* finis */

src/UniqueMessage.h

➞

Show inline comments

@@ @@ -52,3 +52,5 @@ private: @@
 };
 #endif
 /* finis */

src/VirtualLeaf.cpp

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Show inline comments

@@ @@ -138,7 +138,8 @@ public: @@
 Mesh mesh;
 bool batch=false;
 void MainBase::Plot(int resize_stride) {
 void MainBase::Plot(int resize_stride)
+{
   clear();
@@ @@ -261,30 +262,22 @@ TIMESTEP { @@
       // Reaction diffusion
       mesh.ReactDiffuse(par.rd_dt);
       t++;
       Plot(par.resize_stride);
+    }
   } else {
     mesh.ReactDiffuse(par.rd_dt);
     Plot(par.resize_stride);
+  }
   i++;
   return mesh.getTime();
+}
 /* Called if a cell is clicked */
 void Cell::OnClick(QMouseEvent *e) {
 void Cell::OnClick(QMouseEvent *e)
+{
   e = NULL; // use assignment merely to obviate compilation warning
+}
@@ @@ -318,11 +311,7 @@ Parameter par; @@
 int main(int argc,char **argv) {
   try {
     int c;
     char *leaffile=0;
     char *modelfile=0;
@@ @@ -417,11 +406,8 @@ 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()) );
@@ @@ -433,7 +419,6 @@ int main(int argc,char **argv) { @@
       model_catalogue.PopulateModelMenu();
     model_catalogue.InstallFirstModel();
     if (leaffile)
       main_window->Init(leaffile);
@@ @@ -449,11 +434,9 @@ int main(int argc,char **argv) { @@
       do {
 	t = main_window->TimeStep();
       } while (t < par.maxt);
     } else
       return app.exec();
   } catch (const char *message) {
     if (batch) {
       cerr << "Exception caught:" << endl;
@@ @@ -477,3 +460,5 @@ int main(int argc,char **argv) { @@
+    }
+  }
+}
 /* finis */

src/apoplastitem.cpp

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Show inline comments

@@ @@ -66,10 +66,10 @@ void ApoplastItem::setColor(void) { @@
 	diffcolor.setRgb( 0,0,(int)( ( val / (1 + val) )*255.));
 	setPen (QPen(diffcolor, 20) );
+}
 void ApoplastItem::OnClick(QMouseEvent *e) {
   e = NULL; // merely to obviate compilation warnings
+}
 /* finis*/

src/apoplastitem.h

➞

Show inline comments

@@ @@ -23,6 +23,7 @@ @@
 #ifndef _APOPLASTITEM_H_
 #define _APOPLASTITEM_H_
 #include <QGraphicsScene>
 #include <QGraphicsLineItem>
 #include <QPainter>
@@ @@ -46,3 +47,5 @@ private: @@
 };
 #endif
 /* finis*/

src/build_models/auxingrowthplugin.cpp

➞

Show inline comments

@@ @@ -37,7 +37,8 @@ bool batch = false; @@
 // To be executed after cell division
 void AuxinGrowthPlugin::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) {
 void AuxinGrowthPlugin::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2)
+{
   parent_info = NULL; // merely to obviate compile time error
 	// Auxin distributes between parent and daughter according to area
@@ @@ -57,22 +58,23 @@ void AuxinGrowthPlugin::OnDivide(ParentI @@
 	foreach(WallBase *w, walls) {
 		w->setTransporter(daughter1, 1, 0.);
+	}
+}
 void AuxinGrowthPlugin::SetCellColor(CellBase *c, QColor *color) {
 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);
   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.), 0);
+}
 void AuxinGrowthPlugin::CellHouseKeeping(CellBase *c) {
 void AuxinGrowthPlugin::CellHouseKeeping(CellBase *c)
+{
 	if (c->Boundary()==CellBase::None) {
 		if (c->Area() > par->rel_cell_div_threshold * c->BaseArea() ) {
 			c->SetChemical(0,0);
@@ @@ -84,11 +86,10 @@ void AuxinGrowthPlugin::CellHouseKeeping @@
 		// expand according to auxin concentration
    		c->EnlargeTargetArea(par->auxin_dependent_growth?(c->Chemical(0)/(1.+c->Chemical(0)))*par->cell_expansion_rate:par->cell_expansion_rate);
+	}
+}
 void AuxinGrowthPlugin::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) {
 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)
@@ @@ -102,7 +103,6 @@ void AuxinGrowthPlugin::CelltoCellTransp @@
+		}
+	}
 	if (w->C1()->BoundaryPolP()) {
 		if (w->AuxinSource()) {
@@ @@ -146,10 +146,8 @@ void AuxinGrowthPlugin::CelltoCellTransp @@
+}
 void AuxinGrowthPlugin::WallDynamics(Wall *w, double *dw1, double *dw2) {
 void AuxinGrowthPlugin::WallDynamics(Wall *w, double *dw1, double *dw2)
+{
     // Cells polarize available PIN1 to Shoot Apical Meristem
     if (w->C2()->BoundaryPolP()) {
 		if (w->AuxinSink()) {
@@ @@ -227,8 +225,9 @@ void AuxinGrowthPlugin::WallDynamics(Wal @@
     dw2[1] = dPijdt2;
+}
 double AuxinGrowthPlugin::complex_PijAj(CellBase *here, CellBase *nb, Wall *w) {
 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));
@@ @@ -239,7 +238,9 @@ double AuxinGrowthPlugin::complex_PijAj( @@
+}
 void AuxinGrowthPlugin::CellDynamics(CellBase *c, double *dchem) {
 void AuxinGrowthPlugin::CellDynamics(CellBase *c, double *dchem)
+{
 	// Note: Pi and Pij measured in numbers of molecules, not concentrations
 		double dPidt = 0.;
@@ @@ -260,15 +261,11 @@ void AuxinGrowthPlugin::CellDynamics(Cel @@
 		dchem[1] = dPidt;
 		// source of auxin
 		dchem[0] = par->aux_cons - par->aux_breakdown * c->Chemical(0);
+		>
+  }
+	}
+Q_EXPORT_PLUGIN2(auxingrowthplugin, AuxinGrowthPlugin)
+}
 Q_EXPORT_PLUGIN2(auxingrowthplugin, AuxinGrowthPlugin)
 /* finis */

src/build_models/auxingrowthplugin.h

➞

Show inline comments

@@ @@ -61,3 +61,5 @@ private: @@
 };
 #endif
 /* finis */

src/build_models/meinhardtplugin.cpp

➞

Show inline comments

@@ @@ -54,7 +54,6 @@ void MeinhardtPlugin::SetCellColor(CellB @@
 		} else {
 			color->setRgb(c->Chemical(1)/(1+c->Chemical(1)) * 255.,(c->Chemical(0)/(1+c->Chemical(0)) * 255.),(c->Chemical(3)/(1+c->Chemical(3)) *255.) );
+		}
+	}
+}
@@ @@ -77,7 +76,6 @@ void MeinhardtPlugin::CellHouseKeeping(C @@
 			c->EnlargeTargetArea(par->vessel_expansion_rate);
+		}
+	}
+}
 void MeinhardtPlugin::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) {
@@ @@ -100,8 +98,6 @@ void MeinhardtPlugin::CelltoCellTranspor @@
 		dchem_c1[c] += phi;
 		dchem_c2[c] -= phi;
+	}
+}
 void MeinhardtPlugin::WallDynamics(Wall *w, double *dw1, double *dw2) {
@@ @@ -118,8 +114,6 @@ void MeinhardtPlugin::CellDynamics(CellB @@
 	double H = c->Chemical(2);
 	double S = c->Chemical(3);
     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 );
@@ @@ -128,3 +122,5 @@ void MeinhardtPlugin::CellDynamics(CellB @@
 Q_EXPORT_PLUGIN2(meinhardtplugin, MeinhardtPlugin)
 /* finis */

src/build_models/meinhardtplugin.h

➞

Show inline comments

@@ @@ -58,3 +58,5 @@ public: @@
 };
 #endif
 /* finis */

src/build_models/testplugin.cpp

➞

Show inline comments

@@ @@ -75,3 +75,5 @@ void TestPlugin::CellDynamics(CellBase * @@
+}
 Q_EXPORT_PLUGIN2(testplugin, TestPlugin)
 /* finis */

src/build_models/testplugin.h

➞

Show inline comments

@@ @@ -58,3 +58,5 @@ public: @@
 };
 #endif
 /* finis */

src/build_models/translate_plugin.pl

➞

Show inline comments

@@ @@ -75,4 +75,6 @@ while (<pfile>) { @@
 	print opfile;
+}
@@ \ No newline at end of file @@
+}
 #finis

src/canvas.cpp

➞

Show inline comments

@@ @@ -19,8 +19,6 @@ @@
+ *
  */
 #include <QDebug>
 #include <string>
 #include <QGraphicsScene>
 #include <QGraphicsView>
@@ @@ -134,7 +132,8 @@ void FigureEditor::scaleView (qreal scal @@
   scale (scaleFactor, scaleFactor);
+}
 void FigureEditor::Save(const char *fname, const char *format, int sizex, int sizey) {
 void FigureEditor::Save(const char *fname, const char *format, int sizex, int sizey)
+{
     QImage *image = new QImage(sizex, sizey, QImage::Format_RGB32);
     image->fill(QColor(Qt::white).rgb());
@@ @@ -147,7 +146,6 @@ void FigureEditor::Save(const char *fnam @@
     delete image;
+}
 //void FigureEditor::contentsMousePressEvent(QMouseEvent* e)
 void FigureEditor::mousePressEvent(QMouseEvent* e)
+{
   static QList<Node*> selected;
@@ @@ -210,7 +208,6 @@ void FigureEditor::mousePressEvent(QMous @@
   moving = 0;
+}
 //void FigureEditor::contentsMouseMoveEvent(QMouseEvent* e)
 void FigureEditor::mouseMoveEvent(QMouseEvent* e)
+{
@@ @@ -392,8 +389,8 @@ void FigureEditor::mouseReleaseEvent(QMo @@
 // returns a vector of pointer to cells colliding with intersection line
 vector <CellItem *> FigureEditor::getIntersectedCells(void) {
 vector <CellItem *> FigureEditor::getIntersectedCells(void)
+{
   vector <CellItem *> colliding_cells;
   QList<QGraphicsItem *> l = intersection_line->collidingItems( );
@@ @@ -416,10 +413,10 @@ vector <CellItem *> FigureEditor::getInt @@
   delete intersection_line;
   intersection_line = 0;
   return colliding_cells;
+}
 void FigureEditor::FullRedraw(void) {
 void FigureEditor::FullRedraw(void)
+{
 	QList<QRectF> rl;
 	rl << sceneRect();
 	updateScene(rl);
@@ @@ -585,18 +582,17 @@ Main::Main(QGraphicsScene& c, Mesh &m, Q @@
 	infobar = new InfoBar();
 	addDockWindow(infobar);
+}
 void Main::RefreshInfoBar(void) {
 void Main::RefreshInfoBar(void)
+{
 	infobar->SetText(mesh.ModelID());
+}
 void Main::UserMessage(QString message, int timeout) {
 void Main::UserMessage(QString message, int timeout)
+{
   statusBar()->showMessage(message, timeout);
+}
@@ @@ -608,8 +604,6 @@ void Main::init() @@
   srand(++r);
   mainCount++;
+}
 Main::~Main()
@@ @@ -630,7 +624,8 @@ void Main::newView() @@
+}
 void Main::EditParameters() {
 void Main::EditParameters()
+{
   ParameterDialog *pardial = new ParameterDialog(this, "stridediag");
@@ @@ -638,10 +633,10 @@ void Main::EditParameters() { @@
   // 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() {
 void Main::savePars()
+{
   stopSimulation();
@@ @@ -657,10 +652,10 @@ void Main::savePars() { @@
+  }
   startSimulation();
+}
 void Main::readPars() {
 void Main::readPars()
+{
   stopSimulation();
@@ @@ -677,11 +672,11 @@ void Main::readPars() { @@
   emit ParsChanged();
   /* if (timer_active)
      timer->start( 0 );*/
+}
 void Main::saveStateXML() {
 void Main::saveStateXML()
+{
   stopSimulation();
   Q3FileDialog *fd = new Q3FileDialog( this, "file dialog", TRUE );
@@ @@ -708,12 +703,12 @@ void Main::saveStateXML() { @@
+    }
+  }
+}
 void Main::snapshot() {
 void Main::snapshot()
+{
   stopSimulation();
@@ @@ -744,12 +739,12 @@ void Main::snapshot() { @@
 		Save((const char *)fileName, extension, 1024, 768);
+    }
+  }
+}
 void Main::readPrevStateXML() {
 void Main::readPrevStateXML()
+{
   // if we have already read a file, read the next file
   if (!currentFile.isEmpty() && working_dir) {
@@ @@ -783,7 +778,8 @@ void Main::readPrevStateXML() { @@
+  }
+}
 int Main::readStateXML(const char *filename, bool geometry, bool pars, bool simtime) {
 int Main::readStateXML(const char *filename, bool geometry, bool pars, bool simtime)
+{
   try {
     xmlNode *settings;
@@ @@ -820,11 +816,11 @@ int Main::readStateXML(const char *filen @@
     mb.exec();
     return 1;
+  }
+}
 void Main::readNextStateXML() {
 void Main::readNextStateXML()
+{
   // if we have already read a file, read the next file
   if (!currentFile.isEmpty() && working_dir) {
@@ @@ -857,11 +853,10 @@ void Main::readNextStateXML() { @@
     readStateXML((const char*)next_file);
+  }
+}
 void Main::readLastStateXML() {
 void Main::readLastStateXML()
+{
   // if we have already read a file, read the next file
   if (!currentFile.isEmpty() && working_dir) {
@@ @@ -878,12 +873,11 @@ void Main::readLastStateXML() { @@
     readStateXML((const char*)next_file);
+  }
+}
 void Main::readFirstStateXML() {
 void Main::readFirstStateXML()
+{
   // if we have already read a file, read the next file
   if (!currentFile.isEmpty() && working_dir) {
@@ @@ -900,11 +894,10 @@ void Main::readFirstStateXML() { @@
     readStateXML((const char*)next_file);
+  }
+}
 void Main::readStateXML() {
 void Main::readStateXML()
+{
   //  extern Mesh mesh;
@@ @@ -956,8 +949,7 @@ void Main::help() @@
   about->show();
+}
   void Main::aboutQt()
+  {
 void Main::aboutQt(){
     QMessageBox::aboutQt( this, "Virtual Leaf" );
+  }
@@ @@ -970,56 +962,68 @@ void Main::help() @@
+  {
     Plot();
+  }
 void Main::toggleShowApoplasts()
+{
     Plot();
+}
   void Main::toggleShowNodes()
+  {
     Plot();
+  }
   void Main::toggleNodeNumbers(void) {
 void Main::toggleNodeNumbers(void)
+{
     Plot();
+  }
   void Main::toggleCellNumbers(void) {
 void Main::toggleCellNumbers(void)
+{
     Plot();
+  }
   void Main::toggleCellAxes(void) {
 void Main::toggleCellAxes(void)
+{
     Plot();
+  }
   void Main::toggleCellStrain(void) {
 void Main::toggleCellStrain(void)
+{
     Plot();
+  }
   void Main::toggleShowFluxes(void) {
 void Main::toggleShowFluxes(void)
+{
     Plot();
+  }
   void Main::toggleShowBorderCells(){
 void Main::toggleShowBorderCells()
+{
     Plot();
+  }
 void Main::toggleHideCells(void) {
 void Main::toggleHideCells(void)
+{
 	Plot();
 	editor->FullRedraw();
+}
   void Main::toggleMovieFrames(){}
   void Main::toggleLeafBoundary(){}
   void Main::toggleDynCells() {}
   void Main::startSimulation(void) {
 void Main::startSimulation(void)
+{
     timer->start( 0 );
     statusBar()->message("Simulation started");
     running = true;
+  }
   void Main::stopSimulation(void) {
 void Main::stopSimulation(void)
+{
     timer->stop();
     cerr << "Stopping simulation" << endl;
     statusBar()->message("Simulation paused");
@@ @@ -1038,8 +1042,8 @@ void Main::toggleHideCells(void) { @@
+    }
+  }
   void Main::setFluxArrowSize(int size) {
 void Main::setFluxArrowSize(int size)
+{
     flux_arrow_size = size/100.;
+  }
@@ @@ -1055,7 +1059,8 @@ void Main::toggleHideCells(void) { @@
+  }
   void Main::scale(double factor) {
 void Main::scale(double factor)
+{
     QMatrix m = editor->matrix();
     m.scale(factor, factor);
     editor->setMatrix( m );
@@ @@ -1110,8 +1115,8 @@ void Main::toggleHideCells(void) { @@
+  }
   void Main::TimeStepWrap(void) {
 void Main::TimeStepWrap(void)
+{
     static int t=0;
     TimeStep();
     t++;
@@ @@ -1122,7 +1127,8 @@ void Main::toggleHideCells(void) { @@
+  }
   void Main::RestartSim(void) {
 void Main::RestartSim(void)
+{
     stopSimulation();
     if ( QMessageBox::question(
@@ @@ -1143,7 +1149,8 @@ void Main::toggleHideCells(void) { @@
+  }
 void Main::FitCanvasToWindow(void) {
 void Main::FitCanvasToWindow(void)
+{
   double scale_factor_x = (double)editor->width()/(double)canvas.width();
   double scale_factor_y = (double)editor->height()/(double)canvas.height();
@@ @@ -1163,19 +1170,22 @@ void Main::FitCanvasToWindow(void) { @@
   editor->show();
+}
   void Main::PauseIfRunning(void) {
 void Main::PauseIfRunning(void)
+{
     if (running) {
       timer->stop();
+    }
+  }
   void Main::ContIfRunning(void) {
 void Main::ContIfRunning(void)
+{
     if (running) {
       timer->start( 0 );
+    }
+  }
 void Main::FitLeafToCanvas(void) {
 void Main::FitLeafToCanvas(void)
+{
   Vector ll,ur;
   mesh.BoundingBox(ll, ur);
@@ @@ -1192,7 +1202,8 @@ void Main::FitLeafToCanvas(void) { @@
   editor->fitInView(bb, Qt::KeepAspectRatio);
+}
 void Main::CleanMesh(void) {
 void Main::CleanMesh(void)
+{
 	vector<double> clean_chem(Cell::NChem());
 	vector<double> clean_transporters(Cell::NChem());
@@ @@ -1210,7 +1221,8 @@ void Main::CleanMesh(void) { @@
 	editor->FullRedraw();
+}
 void Main::CleanMeshChemicals(void) {
 void Main::CleanMeshChemicals(void)
+{
 	vector<double> clean_chem(Cell::NChem());
@@ @@ -1225,7 +1237,8 @@ void Main::CleanMeshChemicals(void) { @@
 	editor->FullRedraw();
+}
 void Main::CleanMeshTransporters(void) {
 void Main::CleanMeshTransporters(void)
+{
 	vector<double> clean_transporters(Cell::NChem());
 	for (int i=0;i<Cell::NChem();i++) {
 		clean_transporters[i]=0.;
@@ @@ -1239,7 +1252,8 @@ void Main::CleanMeshTransporters(void) { @@
 	editor->FullRedraw();
+}
 void Main::RandomizeMesh(void) {
 void Main::RandomizeMesh(void)
+{
   vector<double> max_chem(Cell::NChem());
   vector<double> max_transporters(Cell::NChem());
@@ @@ -1257,7 +1271,8 @@ void Main::RandomizeMesh(void) { @@
   Plot();
+}
 void Main::XMLReadSettings(xmlNode *settings) {
 void Main::XMLReadSettings(xmlNode *settings)
+{
   MainBase::XMLReadSettings(settings);
@@ @@ -1277,7 +1292,8 @@ void Main::XMLReadSettings(xmlNode *sett @@
 	view->setItemChecked( apoplasts_id, showapoplastsp);
+}
 xmlNode *Main::XMLSettingsTree(void) {
 xmlNode *Main::XMLSettingsTree(void)
+{
   showcentersp = view->isItemChecked(com_id);
   showmeshp = view->isItemChecked(mesh_id);
@@ @@ -1298,4 +1314,3 @@ xmlNode *Main::XMLSettingsTree(void) { @@
+}
 /* finis */

src/canvas.h

➞

Show inline comments

@@ @@ -128,7 +128,8 @@ class Main : public Q3MainWindow, public @@
   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) {
   virtual double getFluxArrowsize(void)
+  {
     return flux_arrow_size;
+  }
@@ @@ -162,7 +163,8 @@ class Main : public Q3MainWindow, public @@
   void stopSimulation(void);
   void RefreshInfoBar(void);
   void EnterRotationMode(void) {
   void EnterRotationMode(void)
+  {
     UserMessage("Rotation mode. Click mouse to exit.");
     if (editor) {
@@ @@ -173,7 +175,8 @@ class Main : public Q3MainWindow, public @@
+    }
+  }
   void ExitRotationMode(void) {
   void ExitRotationMode(void)
+  {
     UserMessage("Exited rotation mode.",2000);
     options->setItemChecked(rotation_mode_id, false);
@@ @@ -263,9 +266,8 @@ class Main : public Q3MainWindow, public @@
   static const QString caption;
   static const QString caption_with_file;
 	InfoBar *infobar;
 };
+#endif
-#endif
+/* finis*/

src/cell.cpp

➞

Show inline comments

@@ @@ -40,35 +40,34 @@ extern Parameter par; @@
 double Cell::factor=1.;
 double Cell::offset[3]={0,0,0};
 Cell::Cell(void) : CellBase() {
 Cell::Cell(void) : CellBase()
+{
 	m=0;
+}
 Cell::Cell(double x, double y, double z) : CellBase(x,y,z) {
 Cell::Cell(double x, double y, double z) : CellBase(x,y,z)
+{
 	m=0;
+}
 Cell::Cell(const Cell &src) :  CellBase(src) {
 Cell::Cell(const Cell &src) :  CellBase(src)
+{
 	m=src.m;
+}
 bool Cell::Cmp(Cell *c) const { return this->Index() < c->Index(); }
 bool Cell::Eq(Cell *c) const { return this->Index() == c->Index(); }
 Cell Cell::operator=(const Cell &src) {
 Cell Cell::operator=(const Cell &src)
+{
 	CellBase::operator=(src);
 	m=src.m;
 	return *this;
+}
 //Cell(void) : CellBase() {}
 void Cell::DivideOverAxis(Vector axis) {
 void Cell::DivideOverAxis(Vector axis)
+{
 	// Build a wall
 	// ->  find the position of the wall
@@ @@ -99,15 +98,16 @@ void Cell::DivideOverAxis(Vector axis) { @@
+	}
 	DivideWalls(new_node_locations, centroid, centroid+axis);
+}
+}
 double Cell::MeanArea(void) {
 double Cell::MeanArea(void)
+{
 	return m->MeanArea();
+}
 void Cell::Apoptose(void) {
 void Cell::Apoptose(void)
+{
 	// First kill walls
         #ifdef QDEBUG
         qDebug() << "This is cell " << Index() << endl;
@@ @@ -168,7 +168,6 @@ void Cell::Apoptose(void) { @@
 				 << (*w)->c1->Index() << ", c2 = " << (*w)->c2->Index() << endl;
                         #endif
+		}
+	}
 	walls.remove(0);
@@ @@ -215,14 +214,12 @@ void Cell::Apoptose(void) { @@
+		}
+	}
 	// mark cell as dead
 	MarkDead();
+}
 void Cell::ConstructConnections(void) {
 void Cell::ConstructConnections(void)
+{
     // Tie up the nodes of this cell, assuming they are correctly ordered
     //cerr << "Constructing connections of cell " << index << endl;
@@ @@ -261,34 +258,14 @@ void Cell::ConstructConnections(void) { @@
 		} else {
 			next=*next_iterator;
+		}
 		//cerr << "[" << *i << "]";
 		//if (*i==10 || *i==11) {
 		//cerr << "previous = " << previous << ", next = " << next << endl;
 		//}
 		//if (*i!=10 && *i!=11)
 		//cerr << "Node " << *i << endl << " = " << *(*i) << endl;
 		(*i)->owners.push_back( Neighbor( this, previous, next ) );
 		// if (*i==50 || *i==51) {
 		//cerr << "Node " << *i << ".size() = " << (*i)->owners.size() << endl;
 		// }
+    }
+}
 /*! \brief Divide the cell over the line v1-v2.
  \param v1: First vertex of line.
  \param v2: Second vertex of line.
  \param fixed_wall: If true: wall will be set to "fixed" (i.e. not motile)
  \return: true if the cell divided, false if not (i.e. no intersection between v1 and v2, and the cell)
  */
 bool Cell::DivideOverGivenLine(const Vector v1, const Vector v2, bool fix_cellwall, NodeSet *node_set ) {
 bool Cell::DivideOverGivenLine(const Vector v1, const Vector v2, bool fix_cellwall, NodeSet *node_set )
+{
 	if (dead) return false;
 	// check each edge for intersection with the line
 	ItList new_node_locations;
@@ @@ -353,11 +330,11 @@ bool Cell::DivideOverGivenLine(const Vec @@
 	DivideWalls(new_node_locations, v1, v2, fix_cellwall, node_set);
 	return true;
+}
 // Core division procedure
 void Cell::DivideWalls(ItList new_node_locations, const Vector from, const Vector to, bool fix_cellwall, NodeSet *node_set) {
 void Cell::DivideWalls(ItList new_node_locations, const Vector from, const Vector to, bool fix_cellwall, NodeSet *node_set)
+{
 	if (dead) return;
@@ @@ -387,7 +364,6 @@ void Cell::DivideWalls(ItList new_node_l @@
 		daughter->new_chem[i]=new_chem[i];
+	}
 	daughter->boundary=boundary;
 	daughter->m=m;
@@ @@ -396,7 +372,6 @@ void Cell::DivideWalls(ItList new_node_l @@
 	target_area/=2;
 	daughter->cellvec=cellvec;
 	// 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) {
@@ @@ -426,7 +401,6 @@ void Cell::DivideWalls(ItList new_node_l @@
 		return;
+	}
 	// We can be sure we only need two positions here because divisions
 	// of non-convex cells are rejected above.
 	Vector new_node[2];
@@ @@ -629,7 +603,9 @@ void Cell::DivideWalls(ItList new_node_l @@
 			list<Neighbor> unique_owners;
 			copy(owners.begin(), owners.end(), back_inserter(unique_owners));
 			unique_owners.unique( mem_fun_ref( &Neighbor::Eq ) );
 			qDebug() << "The dividing edge nodes: " << div_edges[i].first->Index() << " and " << div_edges[i].second->Index() << " are owned by cells: ";
       qDebug() << "The dividing edge nodes: " << div_edges[i].first->Index()
 	       << " and " << div_edges[i].second->Index() << " are owned by cells: ";
 			// spit out each owners' cell index
 			foreach(Neighbor neighbor, unique_owners){
 			  qDebug() << neighbor.cell->Index() << "  ";
@@ @@ -657,7 +633,8 @@ void Cell::DivideWalls(ItList new_node_l @@
 			if (edge_owners.size() > 1){
 			  // Remove the boundary polygon - if its there
 			  list<Neighbor>::iterator it;
 			  if ((it = find_if (edge_owners.begin(), edge_owners.end(), bind2nd(mem_fun_ref(&Neighbor::CellEquals), -1))) != edge_owners.end()) {
 	if ((it = find_if (edge_owners.begin(), edge_owners.end(), bind2nd(mem_fun_ref(&Neighbor::CellEquals), -1)))
 	    != edge_owners.end()) {
                             #ifdef QDEBUG
 			    qDebug() << "deleating: " << it->cell->Index() << " from the list of edge owners." << endl;
                             #endif
@@ @@ -845,6 +822,7 @@ void Cell::DivideWalls(ItList new_node_l @@
 					(*i)->owners.end(),
 				bind2nd(mem_fun_ref( &Neighbor::CellEquals ),this->Index() )  );
 			if (neighb_with_this_cell==(*i)->owners.end()) {
 			        #ifdef QDEBUG
 			  qDebug() << "not found" << endl;
                                 #endif
@@ @@ -981,8 +959,6 @@ void Cell::DivideWalls(ItList new_node_l @@
 	// its daughter
 	broken_neighbors.push_back(daughter);
 	// Recalculate area of parent and daughter
 	area = CalcArea();
 	daughter->area = daughter->CalcArea();
@@ @@ -990,8 +966,6 @@ void Cell::DivideWalls(ItList new_node_l @@
 	SetIntegrals();
 	daughter->SetIntegrals();
 	// Add a "Cell Wall" for diffusion algorithms
 	Wall *wall = new Wall( new_node_ind[0], new_node_ind[1], this, daughter );
@@ @@ -1016,8 +990,6 @@ void Cell::DivideWalls(ItList new_node_l @@
+	}
 	// Correct tranporterconcentrations of divided walls
 	for (int i=0;i<4;i++) {
 		if (div_wall[i]) {
@@ @@ -1035,15 +1007,12 @@ void Cell::DivideWalls(ItList new_node_l @@
 		((Cell *)(*i))->ConstructNeighborList();
+	}
 	ConstructNeighborList();
 	daughter->ConstructNeighborList();
 	m->plugin->OnDivide(&parent_info, daughter, this);
 	daughter->div_counter=(++div_counter);
+}
 // Move the whole cell
@@ @@ -1056,7 +1025,8 @@ void Cell::Move(const Vector T) { @@
+    }
+}
 double Cell::Displace(double dx, double dy, double dh) {
 double Cell::Displace(double dx, double dy, double dh)
+{
 	// Displace whole cell, add resulting energy to dh,
 	// and accept displacement if energetically favorable
@@ @@ -1158,13 +1128,14 @@ double Cell::Displace(double dx, double @@
+}
 void Cell::Displace (void) {
 void Cell::Displace (void)
+{
 	Displace(par.mc_cell_stepsize*(RANDOM()-0.5),par.mc_cell_stepsize*(RANDOM()-0.5),0);
+}
 // Get energy level of whole cell (excluding length constraint?)
 double Cell::Energy(void) const {
 double Cell::Energy(void) const
+{
 	double energy = 0.;
 	double length_contribution = 0.;
@@ @@ -1193,11 +1164,8 @@ double Cell::Energy(void) const { @@
 	energy += DSQR(CalcArea() - target_area);
 	// cell length constraint
 	energy += lambda_celllength * DSQR(Length() - target_length);
 	return energy;
+}
@@ @@ -1205,8 +1173,8 @@ double Cell::Energy(void) const { @@
 bool Cell::SelfIntersect(void) {
 bool Cell::SelfIntersect(void)
+{
     // The (obvious) O(N*N) algorithm
     // Compare each edge against each other edge
@@ @@ -1265,7 +1233,8 @@ bool Cell::SelfIntersect(void) { @@
+}
 bool Cell::MoveSelfIntersectsP(Node *moving_node_ind, Vector new_pos) {
 bool Cell::MoveSelfIntersectsP(Node *moving_node_ind, Vector new_pos)
+{
 	// Check whether the polygon will self-intersect if moving_node_ind
 	// were displaced to new_pos
@@ @@ -1332,27 +1301,19 @@ bool Cell::MoveSelfIntersectsP(Node *mov @@
+			}
+		}
+	}
 	return false;
+}
 /*! \brief Test if this cell intersects with the given line.
  */
 bool Cell::IntersectsWithLineP(const Vector v1, const Vector v2) {
 bool Cell::IntersectsWithLineP(const Vector v1, const Vector v2)
+{
 	// Compare the line against each edge
 	// method used: http://astronomy.swin.edu.au/~pbourke/geometry/lineline2d/
 	for (list<Node *>::const_iterator i=nodes.begin();
 		 i!=nodes.end();
 		 i++)
   for (list<Node *>::const_iterator i=nodes.begin(); i!=nodes.end(); i++)
+    {
 		Vector v3 = *(*i);
 		list<Node *>::const_iterator nb=i;
 		nb++;
@@ @@ -1373,10 +1334,7 @@ bool Cell::IntersectsWithLineP(const Vec @@
 			return true;
+		}
+    }
 	return false;
+}
 /*! \brief Constructs Walls, but only one per cell boundary.
@@ @@ -1386,8 +1344,8 @@ bool Cell::IntersectsWithLineP(const Vec @@
  We can remove this? Well, let's leave it in the code in case we need it for something else. E.g. for importing leaf architectures in different formats than our own... :-)
  */
 void Cell::ConstructWalls(void) {
 void Cell::ConstructWalls(void)
+{
 	return;
 	if (dead) return;
@@ @@ -1406,7 +1364,6 @@ void Cell::ConstructWalls(void) { @@
 			// push onto list
 			corner_points.push_back(*i);
+		}
+	}
 	// Construct Walls between corner points
@@ @@ -1459,7 +1416,6 @@ void Cell::ConstructWalls(void) { @@
 			else {
 				return;
+			}
+		}
@@ @@ -1478,15 +1434,14 @@ void Cell::ConstructWalls(void) { @@
+			}
+		}
+	}
+}
 void BoundaryPolygon::Draw(QGraphicsScene *c, QString tooltip) {
 void BoundaryPolygon::Draw(QGraphicsScene *c, QString tooltip)
+{
 	// Draw the BoundaryPolygon on a QCanvas object
 	CellItem* p = new CellItem(this, c);
 	QPolygonF pa(nodes.size());
@@ @@ -1501,7 +1456,6 @@ void BoundaryPolygon::Draw(QGraphicsScen @@
 						  (int)((Offset().y+i->y)*Factor()) );
+	}
 	p->setPolygon(pa);
 	p->setPen(par.outlinewidth>=0?QPen( QColor(par.cell_outline_color),par.outlinewidth):QPen(Qt::NoPen));
 	p->setBrush( Qt::NoBrush );
@@ @@ -1511,12 +1465,10 @@ void BoundaryPolygon::Draw(QGraphicsScen @@
 		p->setToolTip(tooltip);
 	p->show();
+}
 void Cell::Flux(double *flux, double *D)  {
 void Cell::Flux(double *flux, double *D)
+{
 	// loop over cell edges
 	for (int c=0;c<NChem();c++) flux[c]=0.;
@@ @@ -1543,7 +1495,6 @@ void Cell::Flux(double *flux, double *D) @@
 			flux[c] += phi;
+		}
+	}
+}
@@ @@ -1552,7 +1503,8 @@ void Cell::Flux(double *flux, double *D) @@
 #include "canvas.h"
 void Cell::Draw(QGraphicsScene *c, QString tooltip) {
 void Cell::Draw(QGraphicsScene *c, QString tooltip)
+{
 	// Draw the cell on a QCanvas object
@@ @@ -1591,7 +1543,6 @@ void Cell::Draw(QGraphicsScene *c, QStri @@
 		p->setToolTip(tooltip);
 	p->show();
+}
@@ @@ -1624,7 +1575,6 @@ void Cell::DrawNodes(QGraphicsScene *c) @@
 		item ->setPos(((offset[0]+i->x)*factor),
 					  ((offset[1]+i->y)*factor) );
+	}
+}
 void Cell::DrawIndex(QGraphicsScene *c) const {
@@ @@ -1643,7 +1593,6 @@ void Cell::DrawText(QGraphicsScene *c, c @@
 	ctext->show();
 	ctext ->setPos(((offset[0]+centroid.x)*factor),
 				   ((offset[1]+centroid.y)*factor) );
+}
@@ @@ -1673,7 +1622,6 @@ void Cell::DrawAxis(QGraphicsScene *c) c @@
 				  ( (offset[1]+to.y)*factor ) );
 	line->setZValue(10);
 	line->show();
+}
 void Cell::DrawStrain(QGraphicsScene *c) const {
@@ @@ -1682,7 +1630,8 @@ void Cell::DrawStrain(QGraphicsScene *c) @@
+}
 void Cell::DrawFluxes(QGraphicsScene *c, double arrowsize)  {
 void Cell::DrawFluxes(QGraphicsScene *c, double arrowsize)
+{
 	// get the mean flux through this cell
 	Vector vec_flux = ReduceCellAndWalls<Vector>( PINdir );
@@ @@ -1707,7 +1656,6 @@ void Cell::DrawFluxes(QGraphicsScene *c, @@
 				   ( (offset[1]+to.y)*factor ) );
 	arrow->setZValue(10);
 	arrow->show();
+}
@@ @@ -1723,17 +1671,17 @@ void Cell::DrawWalls(QGraphicsScene *c) @@
 void Cell::DrawValence(QGraphicsScene *c) const {
 	DrawText(c, QString("%1").arg(walls.size()) );
+}
 #endif
+#endif // QTGRAPHICS !
 /*! \brief Recalculate the lengths of the cell's Walls.
  Call this function after the Monte Carlo updates, and before doing the reaction-diffusion iterations.
  */
 void Cell::SetWallLengths(void) {
 void Cell::SetWallLengths(void)
+{
 	for (list<Wall *>::iterator de=walls.begin();
 		 de!=walls.end();
@@ @@ -1779,7 +1727,8 @@ void Cell::SetWallLengths(void) { @@
 //! Add Wall w to the list of Walls
 void Cell::AddWall( Wall *w ) {
 void Cell::AddWall( Wall *w )
+{
 	// if necessary, we could try later inserting it at the correct position
         #ifdef QDEBUG
@@ @@ -1799,11 +1748,11 @@ void Cell::AddWall( Wall *w ) { @@
 		== m->walls.end() ) {
 		m->walls.push_back(w);
+	}
+}
 //! Remove Wall w from the list of Walls
 list<Wall *>::iterator Cell::RemoveWall( Wall *w ) {
 list<Wall *>::iterator Cell::RemoveWall( Wall *w )
+{
 	// remove wall from Mesh's list
 	m->walls.erase(
@@ @@ -1813,20 +1762,15 @@ list<Wall *>::iterator Cell::RemoveWall( @@
 				   );
 	// remove wall from Cell's list
 	return
 	walls.erase (
 				 find(
 					  walls.begin(), walls.end(),
 					  w )
 				 );
   return walls.erase (find( walls.begin(), walls.end(), w ));
+}
 void Cell::EmitValues(double t) {
 void Cell::EmitValues(double t)
+{
 	//  cerr << "Attempting to emit " << t << ", " << chem[0] << ", " << chem[1] << endl;
 	emit ChemMonValue(t, chem);
+}
+}
+/* finis */

src/cell.h

➞

Show inline comments

@@ @@ -92,14 +92,15 @@ public: @@
+    }
     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)
   // divide over the line (if line and cell intersect)
   bool DivideOverGivenLine(const Vector v1, const Vector v2, bool wall_fixed = false, NodeSet *node_set = 0);
     void Divide(void) { // Divide cell over short axis
 		Vector long_axis;
 		Length(&long_axis);
 		DivideOverAxis(long_axis.Perp2D());
+    }
 	//void CheckForGFDrivenDivision(void);
@@ @@ -122,11 +123,6 @@ public: @@
 	void ConstructWalls(void);
 	void Flux(double *flux, double *D);
 	/*! \brief Method called if a cell is clicked.
 	 Define this in the end-user code (e.g. meinhardt.cpp).
 	 */
     void OnClick(QMouseEvent *e);
     inline Mesh& getMesh(void) const { return *m; }
 	double MeanArea(void);
@@ @@ -153,7 +149,6 @@ public: @@
 signals:
     void ChemMonValue(double t, double *x);
 protected:
 	void XMLAddCore(xmlNodePtr xmlcell) const;
     int XMLRead(xmlNode *cur);
@@ @@ -167,7 +162,6 @@ private: @@
 	Mesh *m;
 	void ConstructConnections(void);
 	void SetWallLengths(void);
 };
@@ @@ -196,10 +190,8 @@ public: @@
 	virtual void XMLAdd(xmlNodePtr parent_node) const;
 	virtual bool BoundaryPolP(void) const { return true; }
 };
+#endif
-#endif
+/* finis */

src/cellbase.cpp

➞

Show inline comments

@@ @@ -134,7 +134,6 @@ CellBase::CellBase(double x,double y,dou @@
 	cell_type = 0;
 	flag_for_divide = false;
 	division_axis = 0;
+}
 CellBase::CellBase(const CellBase &src) :  Vector(src), QObject()
@@ @@ -178,7 +177,8 @@ CellBase::CellBase(const CellBase &src) @@
+}
 CellBase CellBase::operator=(const CellBase &src) {
 CellBase CellBase::operator=(const CellBase &src)
+{
 	Vector::operator=(src);
 	for (int i=0;i<NChem();i++) {
@@ @@ -217,7 +217,8 @@ CellBase CellBase::operator=(const CellB @@
 	return *this;
+}
 void CellBase::SetChemical(int c, double conc) {
 void CellBase::SetChemical(int c, double conc)
+{
 	if (c>=NChem()) {
 		stringstream error;
 		error << "SetChemical: value c = " << c << " is out of range\n";
@@ @@ -226,7 +227,8 @@ void CellBase::SetChemical(int c, double @@
 	chem[c]=conc;
+}
 void CellBase::SetTransporters(int ch, double conc) {
 void CellBase::SetTransporters(int ch, double conc)
+{
 	if (ch>=NChem()) {
 		stringstream error;
 		error << "SetChemical: value ch = " << ch << " is out of range\n";
@@ @@ -239,7 +241,8 @@ void CellBase::SetTransporters(int ch, d @@
+	}
+}
 ostream &CellBase::print(ostream &os) const {
 ostream &CellBase::print(ostream &os) const
+{
 	os << "[ index = " << index << " {" << x << ", " << y << ", " << z << "}: {";
@@ @@ -276,16 +279,17 @@ ostream &CellBase::print(ostream &os) co @@
 	os << "cell_type = " << cell_type << endl;
 	os << endl;
 	return os;
+}
 ostream &operator<<(ostream &os, const CellBase &c) {
 ostream &operator<<(ostream &os, const CellBase &c)
+{
 	c.print(os);
 	return os;
+}
 double CellBase::CalcArea(void) const {
 double CellBase::CalcArea(void) const
+{
 	double loc_area=0.;
@@ @@ -302,11 +306,11 @@ double CellBase::CalcArea(void) const { @@
+	}
 	// http://technology.niagarac.on.ca/courses/ctec1335/docs/arrays2.pdf
 	//return loc_area/2.0;
 	return fabs(loc_area)/2.0;
+}
 Vector CellBase::Centroid(void) const {
 Vector CellBase::Centroid(void) const
+{
 	double area=0.;
 	double integral_x_dxdy=0.,integral_y_dxdy=0.;
@@ @@ -332,7 +336,6 @@ Vector CellBase::Centroid(void) const { @@
 			 (*i_plus_1)->x*(*i)->y);
+	}
 	//area/=2.0;
 	area = fabs(area)/2.0;
 	integral_x_dxdy/=6.;
@@ @@ -345,7 +348,8 @@ Vector CellBase::Centroid(void) const { @@
 void CellBase::SetIntegrals(void) const {
 void CellBase::SetIntegrals(void) const
+{
 	// Set the initial values for the integrals over x^2,
 	// xy, yy, x, and y
@@ @@ -392,13 +396,11 @@ void CellBase::SetIntegrals(void) const @@
 			((*i)->x*(*nb)->y-
 			 (*nb)->x*(*i)->y);
+	}
 	area = fabs(area)/2.0;
+}
 double CellBase::Length(Vector *long_axis, double *width)  const {
 double CellBase::Length(Vector *long_axis, double *width)  const
+{
 	// Calculate length and axes of CellBase
@@ @@ -434,12 +436,10 @@ double CellBase::Length(Vector *long_axi @@
+	}
 	return 4*sqrt(lambda_b/area);
+}
 double CellBase::CalcLength(Vector *long_axis, double *width)  const {
 double CellBase::CalcLength(Vector *long_axis, double *width)  const
+{
 	// Calculate length and axes of CellBase, without touching cells raw moments
@@ @@ -515,14 +515,11 @@ double CellBase::CalcLength(Vector *long @@
+	}
 	return 4*sqrt(lambda_b/my_area);
+}
 void CellBase::ConstructNeighborList(void) {
 void CellBase::ConstructNeighborList(void)
+{
 	neighbors.clear();
 	for (//list<Wall *>::const_reverse_iterator wit=walls.rbegin();
@@ @@ -561,11 +558,11 @@ void CellBase::ConstructNeighborList(voi @@
 			break;
+		}
   } while(1);
+}
 	// Save the cell to a stream so we can reconstruct its state later
 	void CellBase::Dump(ostream &os) const {
 void CellBase::Dump(ostream &os) const
+{
 		os << index << " " << nodes.size() << endl;
@@ @@ -583,16 +580,10 @@ void CellBase::ConstructNeighborList(voi @@
 		for (list<CellBase *>::const_iterator i=neighbors.begin();i!=neighbors.end();i++) {
 			os << *i << " ";
+		}
 		os << endl;
 		os << walls.size() << endl;
 		/*for (list<Wall *>::const_iterator i=walls.begin();i!=walls.end(); i++) {
 			(*i)->Dump(os);
 		}*/
   os << endl << walls.size() << endl << endl;
   os << NChem() << " ";
 		os << endl;
 		os << NChem() << " ";
 		for (int i=0;i<NChem();i++) {
 			os << chem[i] << " ";
+		}
@@ @@ -604,7 +595,9 @@ void CellBase::ConstructNeighborList(voi @@
+		}
 		os << endl;
 		os << boundary << " " << area << " " << target_area << " " << target_length << " " << fixed << " " << intgrl_xx << " " << intgrl_xy << " " << intgrl_yy << " " << intgrl_x << " " << intgrl_y << " " << source << " ";
   os << boundary << " " << area << " " << target_area << " " << target_length
      << " " << fixed << " " << intgrl_xx << " " << intgrl_xy << " " << intgrl_yy
      << " " << intgrl_x << " " << intgrl_y << " " << source << " ";
 		cellvec.Dump(os);
@@ @@ -614,8 +607,8 @@ void CellBase::ConstructNeighborList(voi @@
+	}
 	void CellBase::UnfixNodes(void) {
 void CellBase::UnfixNodes(void)
+{
 		for (list<Node *>::const_iterator i=nodes.begin();
 			 i!=nodes.end();
@@ @@ -625,7 +618,9 @@ void CellBase::ConstructNeighborList(voi @@
+	}
 	void CellBase::FixNodes(void) {
 void CellBase::FixNodes(void)
+{
 		for (list<Node *>::const_iterator i=nodes.begin();
 			 i!=nodes.end();
@@ @@ -636,18 +631,14 @@ void CellBase::ConstructNeighborList(voi @@
+	}
 	// returns true if cell is at border
 	bool CellBase::AtBoundaryP(void) const {
 bool CellBase::AtBoundaryP(void) const
+{
 		return at_boundary;
+	}
 QString CellBase::printednodelist(void) {
 QString CellBase::printednodelist(void)
+{
 	QString info_string = "Nodelist = { ";
 	for (list<Node *>::const_iterator i =  nodes.begin(); i!=nodes.end(); i++) {
 		info_string += QString("%1 ").arg((*i)->Index());
@@ @@ -656,3 +647,4 @@ QString CellBase::printednodelist(void) @@
 	return info_string;
+}
 /* finis*/

src/cellbase.h

➞

Show inline comments

@@ @@ -51,7 +51,6 @@ struct ParentInfo { @@
 	Vector polarization;
 	double PINmembrane;
 	double PINendosome;
 };
 // We need a little trick here, to make sure the plugin and the main application will see the same static datamembers
@@ @@ -77,8 +76,6 @@ public: @@
 	int ncells;
 	int nchem;
 	double base_area;
 };
 class CellBase :  public QObject, public Vector
@@ @@ -86,7 +83,6 @@ class CellBase : public QObject, public @@
 	Q_OBJECT
 	friend class Mesh;
 	friend class CellInfo;
 	friend class Node;
@@ @@ -112,14 +108,18 @@ class CellBase : public QObject, public @@
     CellBase operator=(const Vector &src);
     void SetChemical(int chem, double conc);
     inline void SetNewChem(int chem, double conc) {
   inline void SetNewChem(int chem, double conc)
+  {
       new_chem[chem] = conc;
+    }
     void SetSource(int chem, double conc) {
   void SetSource(int chem, double conc)
+  {
       source=true;
       source_chem = chem;
       source_conc = conc;
+	}
 	// set chem 1 to conc in all membranes of this cell
     void SetTransporters(int chem, double conc);
     void UnfixNodes(void);
@@ @@ -154,26 +154,22 @@ class CellBase : public QObject, public @@
     //void print_nblist(void) const;
     boundary_type SetBoundary(boundary_type bound) {
   boundary_type SetBoundary(boundary_type bound)
+  {
       if (bound!=None) {
+      }
       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;
+    }
   boundary_type ResetBoundary(void) { return boundary=None; }
   boundary_type Boundary(void) const { return boundary; }
   static int &NChem(void) { return static_data_members->nchem; }
     double CalcArea(void) const;
     double RecalcArea(void) {
       return area = CalcArea();
+    }
   double RecalcArea(void) { return area = CalcArea(); }
     Vector Centroid(void) const;
@@ @@ -183,49 +179,33 @@ class CellBase : public QObject, public @@
     double CalcLength(Vector *long_axis = 0, double *width = 0) const;
     inline int Index(void) const {
       return index;
+    }
   inline int Index(void) const { return index; }
     void SetTargetArea(double tar_ar) {
       target_area=tar_ar;
+    }
     inline void SetTargetLength(double tar_l) {
       target_length=tar_l;
+    }
     inline void SetLambdaLength(double lambda_length) {
       lambda_celllength = lambda_length;
+    }
     inline double TargetArea(void) {
       return target_area;
+    }
   void SetTargetArea(double tar_ar) { target_area=tar_ar; }
   inline void SetTargetLength(double tar_l) { target_length=tar_l; }
     inline void SetStiffness(double stiff) {
       stiffness = stiff;
+    }
   inline void SetLambdaLength(double lambda_length) { lambda_celllength = lambda_length; }
   inline double TargetArea(void) { return target_area; }
   inline void SetStiffness(double stiff) { stiffness = stiff; }
     inline double Stiffness(void) {
       return stiffness;
+    }
     inline double EnlargeTargetArea(double da) {
       return target_area+=da;
+    }
   inline double Stiffness(void) { return stiffness; }
   inline double EnlargeTargetArea(double da) { return target_area+=da; }
     inline double Area(void) const {
       return area;
+    }
   inline double Area(void) const { return area; }
 	inline void Divide(void) {
 		flag_for_divide = true;
+	}
   inline void Divide(void) { flag_for_divide = true; }
 	inline void DivideOverAxis(const Vector &v) {
   inline void DivideOverAxis(const Vector &v)
+  {
 		division_axis = new Vector(v);
 		flag_for_divide = true;
+	}
     inline double Circumference(void) const {
       double sum=0.;
       for (list<Wall *>::const_iterator w=walls.begin();
@@ @@ -251,18 +231,16 @@ class CellBase : public QObject, public @@
 	QString printednodelist(void);
     inline bool DeadP(void) { return dead; }
     inline void MarkDead(void) { dead  = true; }
 	static double &BaseArea(void) {
   static double &BaseArea(void)
+  {
 		return static_data_members->base_area;
+	}
     void CheckForDivision(void);
     // write flux from neighboring cells into "flux"
     void Flux(double *flux, double *D);
     inline bool FixedP(void) { return fixed; }
@@ @@ -272,24 +250,28 @@ class CellBase : public QObject, public @@
 	bool AtBoundaryP(void) const;
     static inline int &NCells(void) {
   static inline int &NCells(void)
+  {
       return static_data_members->ncells;
+    }
     inline void Mark(void) {
   inline void Mark(void)
+  {
       marked=true;
+    }
     inline void Unmark(void) {
   inline void Unmark(void)
+  {
       marked=false;
+    }
     inline bool Marked(void) const {
       return marked;
+    }
 	//! Returns the sum of chemical "chem" of this CellBase's neighbors
     double SumChemicalsOfNeighbors(int chem) {
   double SumChemicalsOfNeighbors(int chem)
+  {
       double sum=0.;
       for (list<Wall *>::const_iterator w=walls.begin();
 	   w!=walls.end();
@@ @@ -320,11 +302,9 @@ class CellBase : public QObject, public @@
       return sum;
+    }
     //! The same, but now for the walls AND neighbors
     template<class P, class Op> P ReduceCellAndWalls(Op f) {
   template<class P, class Op> P ReduceCellAndWalls(Op f)
+  {
       P sum = 0;
       for (list<Wall *>::const_iterator w=walls.begin();
 	   w!=walls.end();
@@ @@ -338,7 +318,8 @@ class CellBase : public QObject, public @@
     //! Sum transporters at this CellBase's side of the walls
     double SumTransporters(int ch) {
   double SumTransporters(int ch)
+  {
       double sum=0.;
       for (list<Wall *>::const_iterator w=walls.begin();
 	   w!=walls.end();
@@ @@ -346,14 +327,14 @@ class CellBase : public QObject, public @@
 	sum += (*w)->getTransporter(this, ch);
+      }
       return sum;
+    }
     inline int NumberOfDivisions(void) { return div_counter; }
     //! Sum transporters at this CellBase's side of the walls
     double SumLengthTransporters(int ch) {
   double SumLengthTransporters(int ch)
+  {
       double sum=0.;
       for (list<Wall *>::const_iterator w=walls.begin();
 	   w!=walls.end();
@@ @@ -361,13 +342,13 @@ class CellBase : public QObject, public @@
 	sum += (*w)->getTransporter(this, ch) * (*w)->Length();
+      }
       return sum;
+    }
     double SumLengthTransportersChemical(int trch, int ch) {
   double SumLengthTransportersChemical(int trch, int ch)
+  {
       double sum=0.;
       for (list<Wall *>::const_iterator w=walls.begin();
 	   w!=walls.end();
@@ @@ -375,14 +356,14 @@ class CellBase : public QObject, public @@
 	sum += (*w)->getTransporter(this, trch) * ( (*w)->c1!=this ? (*w)->c1->Chemical(ch) : (*w)->c2->Chemical(ch) );
+      }
       return sum;
+    }
 	inline int CellType(void) const { return cell_type; }
 	inline void SetCellType(int ct) { cell_type = ct; }
 	static void SetNChem(int new_nchem) {
   static void SetNChem(int new_nchem)
+  {
 		if (NCells()) {
 			MyWarning::error("CellBase::SetNChem says: not permitted, call SetNChem after deleting all cells.");
 		} else {
@@ @@ -400,12 +381,14 @@ protected: @@
     int index;
 	inline void SetChemToNewchem(void) {
   inline void SetChemToNewchem(void)
+  {
 		for (int c=0;c<CellBase::NChem();c++) {
 			chem[c]=new_chem[c];
+		}
+    }
     inline void SetNewChemToChem(void) {
   inline void SetNewChemToChem(void)
+  {
 		for (int c=0;c<CellBase::NChem();c++) {
 			new_chem[c]=chem[c];
+		}
@@ @@ -446,10 +429,8 @@ protected: @@
 	bool flag_for_divide;
 	Vector *division_axis;
 	int cell_type;
     // for length constraint
     mutable double intgrl_xx, intgrl_xy, intgrl_yy, intgrl_x, intgrl_y;
@@ @@ -462,7 +443,8 @@ protected: @@
     int source_chem;
     // PRIVATE MEMBER FUNCTIONS
     inline static void ClearNCells(void) {
   inline static void ClearNCells(void)
+  {
       NCells()=0;
+    }
@@ @@ -472,15 +454,12 @@ protected: @@
 ostream &operator<<(ostream &os, const CellBase &v);
 inline Vector PINdir(CellBase *here, CellBase *nb, Wall *w) {
 inline Vector PINdir(CellBase *here, CellBase *nb, Wall *w)
+{
 	  nb = NULL; // assignment merely to obviate compilation warning
 	  return w->getTransporter( here, 1)  *  w->getInfluxVector(here);
+}
 #endif
 /* finis*/

src/cellitem.cpp

➞

Show inline comments

@@ @@ -29,7 +29,8 @@ CellItem::CellItem( Cell *c, QGraphicsSc @@
   : QGraphicsPolygonItem( 0, canvas ), SimItemBase( c, canvas){
+}
 void CellItem::userMove(double dx, double dy) {
 void CellItem::userMove(double dx, double dy)
+{
   QGraphicsPolygonItem::moveBy( dx, dy );
   // also move the cell itself
@@ @@ -39,7 +40,8 @@ void CellItem::userMove(double dx, doubl @@
   class_cast<Cell*>(obj)->Move( (dx/Cell::Magnification()), (dy/Cell::Magnification()) );
+}
 QPainterPath CellItem::shape() const { return QGraphicsPolygonItem::shape(); }
 QRectF CellItem::boundingRect() const { return QGraphicsPolygonItem::boundingRect(); }
 /* finis */

src/cellitem.h

➞

Show inline comments

@@ @@ -43,7 +43,8 @@ public: @@
   QRectF boundingRect() const;
  private:
 };
 #endif
 /* finis */

src/curvecolors.h

➞

Show inline comments

@@ @@ -175,3 +175,5 @@ class CurveColors { @@
   QStringList colors;
 };
 #endif
 /* finis */

src/data_plot.cpp

➞

Show inline comments

@@ @@ -66,8 +66,6 @@ DataPlot::DataPlot(QWidget *parent, cons @@
   alignScales();
   //  Initialize data
   for (int i = 0; i< PLOT_SIZE; i++) {
     d_t[i] = 0.;     // time axis
+  }
@@ @@ -98,20 +96,19 @@ DataPlot::DataPlot(QWidget *parent, cons @@
   // Axis
   setAxisTitle(QwtPlot::xBottom, "Time");
   setAxisTitle(QwtPlot::yLeft, "Level");
   setAxisScale(QwtPlot::yLeft, 0, 10);
   data_pos = 0;
+}
 DataPlot::~DataPlot(void) {
 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
 //
@@ @@ -136,7 +133,6 @@ void DataPlot::alignScales() @@
+    }
+}
 //  Generate new values
 void DataPlot::AddValue(double t,double *x)
+{
@@ @@ -154,7 +150,6 @@ void DataPlot::AddValue(double t,double @@
 	d_x[i][j] = d_x[i][j+1];
+    }
     data_pos = PLOT_SIZE - 1;
+  }
   d_t[data_pos] = t;
@@ @@ -165,29 +160,24 @@ void DataPlot::AddValue(double t,double @@
+  }
   setAxisScale(QwtPlot::xBottom, d_t[0], t);
   data_pos++;
   data_pos++;
   // update the display
   replot();
+}
 PlotDialog::PlotDialog(QWidget *parent, const QString title, const QStringList curvenames):
   QDialog(parent)
+{
   plot = new DataPlot(this,title,curvenames);
   plot->resize(400,300);
   show();
+}
 PlotDialog::~PlotDialog(void) {
 PlotDialog::~PlotDialog(void)
+{
   delete plot;
+}
 /* finis */

src/data_plot.h

➞

Show inline comments

@@ @@ -63,7 +63,6 @@ private: @@
     // to write contents of DataPlot to a file
     QFile *datfile;
     QTextStream datstream;
 };
 class PlotDialog : public QDialog {
@@ @@ -82,3 +81,5 @@ Q_OBJECT @@
 };
 #endif
 /* finis */

src/far_mem_5.h

➞

Show inline comments

@@ @@ -21,7 +21,6 @@ @@
+ *
  */
 #ifndef _FAR_MEM_5_h_
 #define _FAR_MEM_5_h_
@@ @@ -45,9 +44,12 @@ Type *m_ptyp; @@
 Result (Type::*m_pmf)(Param1);
 };
 template <class Result, class Type, class Param1>far_1_arg_mem_fun_t<Result,Type,Param1> far_1_arg_mem_fun(Type &ir_typ, Result (Type::*i_pmf)(Param1) ) {
 template <class Result, class Type,
   class Param1>far_1_arg_mem_fun_t<Result,Type,Param1> far_1_arg_mem_fun(Type &ir_typ, Result (Type::*i_pmf)(Param1) )
+{
 	return far_1_arg_mem_fun_t<Result,Type,Param1>(ir_typ,i_pmf);
+ }
 template <class _Arg1, class _Arg2,  class _Result>
 	struct my_2_function
+	{
@@ @@ -55,6 +57,7 @@ typedef _Arg1 argument_type1; @@
 typedef _Arg2 argument_type2;
 typedef _Result result_type;  ///<  result_type is the return type
 };
 template <class Result, class Type,  class Param1, class Param2>
 class far_2_arg_mem_fun_t : public my_2_function<Param1, Param2, Result> {
 public:
@@ @@ -69,9 +72,11 @@ Type *m_ptyp; @@
 Result (Type::*m_pmf)(Param1, Param2);
 };
 template <class Result, class Type, class Param1, class Param2>far_2_arg_mem_fun_t<Result,Type,Param1, Param2> far_2_arg_mem_fun(Type &ir_typ, Result (Type::*i_pmf)(Param1, Param2) ) {
 template <class Result, class Type, class Param1,
   class Param2>far_2_arg_mem_fun_t<Result,Type,Param1, Param2> far_2_arg_mem_fun(Type &ir_typ, Result (Type::*i_pmf)(Param1, Param2) ) {
 	return far_2_arg_mem_fun_t<Result,Type,Param1, Param2>(ir_typ,i_pmf);
+ }
 template <class _Arg1, class _Arg2, class _Arg3,  class _Result>
 	struct my_3_function
+	{
@@ @@ -80,6 +85,7 @@ typedef _Arg2 argument_type2; @@
 typedef _Arg3 argument_type3;
 typedef _Result result_type;  ///<  result_type is the return type
 };
 template <class Result, class Type,  class Param1, class Param2, class Param3>
 class far_3_arg_mem_fun_t : public my_3_function<Param1, Param2, Param3, Result> {
 public:
@@ @@ -94,9 +100,11 @@ Type *m_ptyp; @@
 Result (Type::*m_pmf)(Param1, Param2, Param3);
 };
 template <class Result, class Type, class Param1, class Param2, class Param3>far_3_arg_mem_fun_t<Result,Type,Param1, Param2, Param3> far_3_arg_mem_fun(Type &ir_typ, Result (Type::*i_pmf)(Param1, Param2, Param3) ) {
 template <class Result, class Type, class Param1, class Param2,
 class Param3>far_3_arg_mem_fun_t<Result,Type,Param1, Param2, Param3> far_3_arg_mem_fun(Type &ir_typ, Result (Type::*i_pmf)(Param1, Param2, Param3) ) {
 	return far_3_arg_mem_fun_t<Result,Type,Param1, Param2, Param3>(ir_typ,i_pmf);
+ }
 template <class _Arg1, class _Arg2, class _Arg3, class _Arg4,  class _Result>
 	struct my_4_function
+	{
@@ @@ -106,6 +114,7 @@ typedef _Arg3 argument_type3; @@
 typedef _Arg4 argument_type4;
 typedef _Result result_type;  ///<  result_type is the return type
 };
 template <class Result, class Type,  class Param1, class Param2, class Param3, class Param4>
 class far_4_arg_mem_fun_t : public my_4_function<Param1, Param2, Param3, Param4, Result> {
 public:
@@ @@ -123,6 +132,7 @@ Result (Type::*m_pmf)(Param1, Param2, Pa @@
 template <class Result, class Type, class Param1, class Param2, class Param3, class Param4>far_4_arg_mem_fun_t<Result,Type,Param1, Param2, Param3, Param4> far_4_arg_mem_fun(Type &ir_typ, Result (Type::*i_pmf)(Param1, Param2, Param3, Param4) ) {
 	return far_4_arg_mem_fun_t<Result,Type,Param1, Param2, Param3, Param4>(ir_typ,i_pmf);
+ }
 template <class _Arg1, class _Arg2, class _Arg3, class _Arg4, class _Arg5,  class _Result>
 	struct my_5_function
+	{
@@ @@ -133,6 +143,7 @@ typedef _Arg4 argument_type4; @@
 typedef _Arg5 argument_type5;
 typedef _Result result_type;  ///<  result_type is the return type
 };
 template <class Result, class Type,  class Param1, class Param2, class Param3, class Param4, class Param5>
 class far_5_arg_mem_fun_t : public my_5_function<Param1, Param2, Param3, Param4, Param5, Result> {
 public:
@@ @@ -152,3 +163,5 @@ template <class Result, class Type, clas @@
+ }
 #endif
 /* finis */

src/flux_function.h

➞

Show inline comments

@@ @@ -39,3 +39,5 @@ @@
 (( _vleafcellp_->ReduceCellAndWalls<double>( far_3_arg_mem_fun( *this, &_flux_function_ ) ) ))
 #endif
 /* finis */

src/forwardeuler.cpp

➞

Show inline comments

@@ @@ -91,7 +91,6 @@ void ForwardEuler::odeint(double *ystart @@
       //xsav=x;
+    }
     for (int i=0;i<nvar;i++) {
       y[i]=y[i] + h1 * dydx[i];
+    }
@@ @@ -101,8 +100,6 @@ void ForwardEuler::odeint(double *ystart @@
     if ((x-x2)*(x2-x1) >= 0.0) { //Are we done?
       goto done;
+    }
+  }
  done:
@@ @@ -116,5 +113,6 @@ void ForwardEuler::odeint(double *ystart @@
   delete[] dydx;
   delete[] y;
   return; //Normal exit.
+}
+}
+/* finis */

src/forwardeuler.h

➞

Show inline comments

@@ @@ -22,7 +22,6 @@ @@
+ *
  */
 #ifndef _FORWARDEULER_H_
 #define _FORWARDEULER_H_
@@ @@ -55,7 +54,7 @@ class ForwardEuler { @@
   static const double Errcon;
   static const double Maxstp;
   static const double Tiny;
 };
 #endif
 /* finis */

src/infobar.h

➞

Show inline comments

@@ @@ -54,4 +54,6 @@ private: @@
 	QLabel *virtleaf;
 };
 #endif
@@ \ No newline at end of file @@
 #endif
 /* finis */

src/mainbase.cpp

➞

Show inline comments

@@ @@ -131,11 +131,11 @@ xmlNode *MainBase::XMLSettingsTree(void) @@
 		text << bool_name(hidecellsp);
 		xmlNewProp(xmloption, BAD_CAST "val", BAD_CAST text.str().c_str());
+	}
 	return xmlsettings;
+}
 void MainBase::XMLReadSettings(xmlNode *settings) {
 void MainBase::XMLReadSettings(xmlNode *settings)
+{
 	// Many files have no settings section, so don't complain about it.
 	// Defaults will be used instead.
@@ @@ -196,15 +196,13 @@ void MainBase::XMLReadSettings(xmlNode * @@
 			xmlFree(name);
 			xmlFree(val);
+		}
 		cur=cur->next;
+	}
+}
 void MainBase::Save(const char *fname, const char *format, int sizex, int sizey) {
 void MainBase::Save(const char *fname, const char *format, int sizex, int sizey)
+{
 	Vector ll,ur;
 	mesh.BoundingBox(ll, ur);
@@ @@ -214,7 +212,6 @@ void MainBase::Save(const char *fname, c @@
 		return;
+	}
 	ll*=Cell::Magnification(); ur*=Cell::Magnification();
 	// give the leaf some space
@@ @@ -242,8 +239,9 @@ void MainBase::Save(const char *fname, c @@
+	}
+}
 void MainBase::CutSAM() {
 void MainBase::CutSAM()
+{
 	mesh.CutAwaySAM();
+}
+}
+/* finis */

src/mainbase.h

➞

Show inline comments

@@ @@ -132,3 +132,5 @@ class MainBase { @@
 #define INIT void MainBase::Init(char *leaffile)
 #endif
 /* finis */

src/matrix.cpp

➞

Show inline comments

@@ @@ -35,29 +35,26 @@ Matrix::Matrix(const Vector &c1, const V @@
   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) {
 void Matrix::Alloc(void)
+{
   // constructor
   mat = new double*[3];
   mat[0] = new double[9];
   for (int i=1;i<3;i++)
     mat[i]=mat[i-1]+3;
+}
 Matrix::~Matrix() {
 Matrix::~Matrix()
+{
   // destructor
   delete[] mat[0];
   delete[] mat;
+}
 Matrix::Matrix(void) {
 Matrix::Matrix(void)
+{
   // constructor
   Alloc();
@@ @@ -65,23 +62,21 @@ Matrix::Matrix(void) { @@
   for (int i=0;i<9;i++) {
     mat[0][i]=0.;
+  }
+}
 Matrix::Matrix(const Matrix &source) {
 Matrix::Matrix(const Matrix &source)
+{
   // copy constructor
   Alloc();
   for (int i=0;i<9;i++) {
     mat[0][i]=source.mat[0][i];
+  }
+}
 void Matrix::operator=(const Matrix &source) {
 void Matrix::operator=(const Matrix &source)
+{
   // assignment
   // don't assign to self
@@ @@ -90,14 +85,14 @@ void Matrix::operator=(const Matrix &sou @@
   // copy
   for (int i=0;i<9;i++)
     mat[0][i]=source.mat[0][i];
+}
 void Matrix::print(ostream *os) {
   *os << "{ { " << mat[0][0] << "," << mat[0][1] << "," << mat[0][2] << "},{" << mat[1][0] << "," << mat[1][1] << "," << mat[1][2] << "},{" << mat[2][0] << "," << mat[2][1] << "," << mat[2][2] << "} }";
 void Matrix::print(ostream *os)
+{
   *os << "{ { " << mat[0][0] << "," << mat[0][1] << "," << mat[0][2]
       << "},{" << mat[1][0] << "," << mat[1][1] << "," << mat[1][2]
       << "},{" << mat[2][0] << "," << mat[2][1] << "," << mat[2][2] << "} }";
+}
 ostream &operator<<(ostream &os, Matrix &v) {
@@ @@ -106,8 +101,8 @@ ostream &operator<<(ostream &os, Matrix @@
+}
 Vector Matrix::operator*(const Vector &v) const {
 Vector Matrix::operator*(const Vector &v) const
+{
   // matrix * vector
   Vector result;
@@ @@ -116,23 +111,20 @@ Vector Matrix::operator*(const Vector &v @@
   result.z = mat[2][0]*v.x+mat[2][1]*v.y+mat[2][2]*v.z;
   return result;
+}
 bool Matrix::operator==(Matrix &m) const {
 bool Matrix::operator==(Matrix &m) const
+{
   for (int i=0;i<9;i++) {
     if ((mat[0][i]-m.mat[0][i])>TINY)
       return false;
+  }
   return true;
+}
 double Matrix::Det(void) const {
 double Matrix::Det(void) const
+{
   return
     - mat[0][2]*mat[0][4]*mat[0][6]
     + mat[0][1]*mat[0][5]*mat[0][6]
@@ @@ -140,10 +132,10 @@ double Matrix::Det(void) const { @@
     - mat[0][0]*mat[0][5]*mat[0][7]
     - mat[0][1]*mat[0][3]*mat[0][8]
     + mat[0][0]*mat[0][4]*mat[0][8];
+}
 Matrix Matrix::Inverse(void) const {
 Matrix Matrix::Inverse(void) const
+{
   // return the Inverse of this matrix
   double rd=1./Det(); // Reciproce Det;
@@ @@ -158,17 +150,17 @@ Matrix Matrix::Inverse(void) const { @@
   inverse.mat[0][7]=rd*( mat[0][1]*mat[0][6]-mat[0][0]*mat[0][7]);
   inverse.mat[0][8]=rd*(-mat[0][1]*mat[0][3]+mat[0][0]*mat[0][4]);
   return inverse;
+}
 void Matrix::Rot2D(double theta) {
 void Matrix::Rot2D(double theta)
+{
   // make this matrix a rotation matrix over theta
   // see http://mathworld.wolfram.com/RotationMatrix.html
   mat[0][0] = cos(theta); mat[0][1]=sin(theta);
   mat[1][0] = -sin(theta); mat[1][1]=cos(theta);
   mat[0][2] = mat[1][2] = mat[2][0] = mat[2][1] = mat[2][2] = 0.;
+}
+}
+/* finis */

src/matrix.h

➞

Show inline comments

@@ @@ -55,3 +55,5 @@ private: @@
 ostream &operator<<(ostream &os, Matrix &v);
 #endif
 /* finis */

src/maxmin.h

➞

Show inline comments

		@@ -33,3 +33,4 @@ inline double SIGN(double a, double b) {

		#endif

		/* finis */

src/mesh.cpp

➞

Show inline comments

@@ @@ -61,7 +61,6 @@ void Mesh::AddNodeToCell(Cell *c, Node * @@
   c->nodes.push_back( n );
   n->owners.push_back( Neighbor(c, nb1, nb2 ) );
+}
 void Mesh::PerturbChem(int chemnum, double range) {
@@ @@ -72,7 +71,6 @@ void Mesh::PerturbChem(int chemnum, doub @@
     (*i)->chem[chemnum] += range*(RANDOM()-0.5);
     if ((*i)->chem[chemnum]<0.) (*i)->chem[chemnum]=0.;
+  }
+}
 void Mesh::CellFiles(const Vector ll, const Vector ur) {
@@ @@ -132,7 +130,6 @@ void Mesh::CellFiles(const Vector ll, co @@
   Node::target_length/=4.;
   SetBaseArea();
+}
 Cell *Mesh::RectangularCell(const Vector ll, const Vector ur, double rotation) {
@@ @@ -281,8 +278,6 @@ Cell &Mesh::EllipticCell(double xc, doub @@
   c->at_boundary=true;
   return *c;
+}
 Cell &Mesh::LeafPrimordium(int nnodes, double pet_length) {
@@ @@ -451,9 +446,6 @@ Cell &Mesh::LeafPrimordium(int nnodes, d @@
+}
 /*Cell &Mesh::Box() {
 }*/
@@ @@ -478,7 +470,6 @@ void Mesh::BoundingBox(Vector &LowerLeft @@
     if ((*c)->z > UpperRight.z)
       UpperRight.z = (*c)->z;
+  }
+}
@@ @@ -1029,7 +1020,6 @@ double Mesh::DisplaceNodes(void) { @@
+    }
     return sum_dh;
+}
@@ @@ -1188,7 +1178,6 @@ void Mesh::InsertNode(Edge &e) { @@
     c++;
+  }
   //  debug_stream.flush();
+}
@@ @@ -1238,7 +1227,6 @@ void Mesh::CircumCircle(double x1,double @@
   return;
   // Suggested
   // return((drsqr <= rsqr + EPSILON) ? TRUE : FALSE);
+}
 //
@@ @@ -1254,7 +1242,6 @@ double Mesh::SumChemical(int ch) { @@
     sum+=(*i)->chem[ch];
+  }
   return sum;
+}
@@ @@ -1439,7 +1426,6 @@ void Mesh::CleanUpCellNodeLists(void) { @@
   shuffled_cells.clear();
   shuffled_cells = cells;
+}
 void Mesh::CutAwayBelowLine( Vector startpoint, Vector endpoint) {
@@ @@ -1472,7 +1458,6 @@ void Mesh::CutAwayBelowLine( Vector star @@
   TestIllegalWalls();
   CleanUpCellNodeLists();
+}
 void Mesh::CutAwaySAM(void) {
@@ @@ -1490,8 +1475,6 @@ void Mesh::CutAwaySAM(void) { @@
   TestIllegalWalls();
   CleanUpCellNodeLists();
+}
 void Mesh::TestIllegalWalls(void) {
@@ @@ -1504,7 +1487,6 @@ void Mesh::TestIllegalWalls(void) { @@
       #endif
+    }
+  }
+}
@@ @@ -1521,7 +1503,6 @@ public: @@
     else
       return false;
+  }
 };
@@ @@ -1652,7 +1633,6 @@ void Mesh::RepairBoundaryPolygon(void) { @@
   qDebug() << endl;
   #endif
 #endif
+}
@@ @@ -1755,7 +1735,6 @@ void Mesh::Rotate(double angle, Vector c @@
 void Mesh::PrintWallList( void ) {
    transform ( walls.begin(), walls.end(), ostream_iterator<Wall>(cerr, "\n"), deref_ptr<Wall> );
+}
 #include <QString>
@@ @@ -1828,7 +1807,6 @@ void Mesh::ReactDiffuse(double delta_t) @@
   setTime(getTime()+delta_t);
   setValues(getTime(),ystart);
+}
@@ @@ -1874,7 +1852,6 @@ void Mesh::DeleteLooseWalls(void) { @@
+    }
+  }
+}
 /*void Mesh::FitLeafToCanvas(double width, double height) {
@@ @@ -1913,8 +1890,6 @@ void Mesh::CleanChemicals(const vector<d @@
 		(*c)->SetNewChemToChem();
+	}
+}
@@ @@ -1935,7 +1910,6 @@ void Mesh::CleanTransporters(const vecto @@
 			(*w)->setTransporters2(i,clean_transporters[i]); (*w)->setNewTransporters2(i,clean_transporters[i]);
+		}
+	}
+}
@@ @@ -1966,7 +1940,6 @@ void Mesh::RandomizeChemicals(const vect @@
       (*w)->setTransporters2(i,max_transporters[i] * RANDOM()); (*w)->setNewTransporters2(i, (*w)->Transporters1(i) );
+    }
+  }
+}
 //!\brief Calculates a vector with derivatives of all variables, which
@@ @@ -2024,8 +1997,6 @@ void Mesh::Derivatives(double *derivs) { @@
       //&(derivs[(*w)->c2->Index() * nchems] ) );
     i+=2*nchems;
+  }
+}
 void Mesh::setValues(double x, double *y) {
@@ @@ -2138,7 +2109,6 @@ void Mesh::DrawNodes(QGraphicsScene *c) @@
     item ->setPos(((Cell::offset[0]+i->x)*Cell::factor),
 		  ((Cell::offset[1]+i->y)*Cell::factor) );
+  }
+}
 /*! Returns the sum of protein "ch" of a cycling protein in cells and walls */
@@ @@ -2164,7 +2134,6 @@ double Mesh::CalcProtCellsWalls(int ch) @@
+  }
   return sum_prot;
+}
 void Mesh::SettoInitVals(void) {
@@ @@ -2182,7 +2151,6 @@ void Mesh::SettoInitVals(void) { @@
 	CleanChemicals(clean_chem);
 	CleanTransporters(clean_transporters);
+}
 string Mesh::getTimeHours(void) const {

src/mesh.h

➞

Show inline comments

@@ @@ -165,7 +165,6 @@ public: @@
 			 i++) {
 			f(*shuffled_nodes[*i]);
+		}
+	}
 	template<class Op> void RandomlyLoopCells(Op f) {
@@ @@ -178,8 +177,6 @@ public: @@
 			 i++) {
 			f(*shuffled_cells[*i]);
+		}
+	}
 	template<class Op1, class Op2> void LoopCells(Op1 f, Op2 &g) {
@@ @@ -427,3 +424,5 @@ private: @@
 					  double *xc,double *yc,double *r);
 };
 #endif
 /* finis */

src/miscq.cpp

➞

Show inline comments

@@ @@ -26,12 +26,13 @@ @@
 static const std::string _module_id("$Id$");
 // Returns the extension of a filename
 QString getExtension(const QString fn) {
 QString getExtension(const QString fn)
+{
   // split on dots
   QStringList parts = fn.split(".");
   // return last part, this should be the extension
   return QString(parts.last());
+}
+}
+/* finis */

src/miscq.h

➞

Show inline comments

		@@ -33,3 +33,4 @@ QString getExtension(const QString fn);

		#endif

		/* finis */

src/modelcatalogue.h

➞

Show inline comments

@@ @@ -55,6 +55,5 @@ private: @@
 	QVector<SimPluginInterface *> models;
 	Mesh *mesh;
 	Main *mainwin;
 };
 #endif

src/node.cpp

➞

Show inline comments

@@ @@ -49,7 +49,6 @@ ostream &Neighbor::print(ostream &os) co @@
   os << " {" << cell->Index() << " " << nb1->Index() << " " << nb2->Index() << "}";
   return os;
+}
 ostream &operator<<(ostream &os, const Neighbor &n) {
@@ @@ -58,8 +57,8 @@ ostream &operator<<(ostream &os, const N @@
+}
 Node::Node(void) : Vector() {
 Node::Node(void) : Vector()
+{
   index=(nnodes++);
   node_set =0;
   fixed=false;
@@ @@ -68,7 +67,8 @@ Node::Node(void) : Vector() { @@
   dead=false;
+}
 Node::Node(int ind) : Vector() {
 Node::Node(int ind) : Vector()
+{
   node_set =0;
   index=ind;
   fixed=false;
@@ @@ -77,8 +77,8 @@ Node::Node(int ind) : Vector() { @@
   dead=false;
+}
 Node::Node(const Vector &src) : Vector(src) {
 Node::Node(const Vector &src) : Vector(src)
+{
   node_set = 0;
   index=(nnodes++);
   fixed=false;
@@ @@ -87,8 +87,8 @@ Node::Node(const Vector &src) : Vector(s @@
   dead = false;
+}
 Node::Node(double x,double y, double z) : Vector (x,y,z) {
 Node::Node(double x,double y, double z) : Vector (x,y,z)
+{
   node_set = 0;
   index=(nnodes++);
   fixed=false;
@@ @@ -97,8 +97,8 @@ Node::Node(double x,double y, double z) @@
   dead = false;
+}
 Node::Node(const Node &src) : Vector(src) {
 Node::Node(const Node &src) : Vector(src)
+{
   node_set=0;
   owners=src.owners;
   m=src.m;
@@ @@ -110,7 +110,8 @@ Node::Node(const Node &src) : Vector(src @@
+}
 Cell &Node::getCell(const Neighbor &i) {
 Cell &Node::getCell(const Neighbor &i)
+{
   return *i.getCell(); // use accessor!
+}
@@ @@ -132,7 +133,6 @@ ostream &Node::print(ostream &os) const @@
   os << " } " << endl;
   return os;
+}
@@ @@ -156,12 +156,8 @@ void Node::DrawIndex(QGraphicsScene *c) @@
 void Node::DrawOwners(QGraphicsScene *c) const {
   stringstream text;
   text << owners.size();
   QGraphicsSimpleTextItem *number = new QGraphicsSimpleTextItem ( QString (text.str().c_str()), 0, c );
   number->setFont( QFont( "Helvetica", par.nodenumsize, QFont::Bold) );
   number->setPen( QPen(par.textcolor) );
@@ @@ -174,9 +170,8 @@ void Node::DrawOwners(QGraphicsScene *c) @@
+}
 QVector<qreal> Node::NeighbourAngles(void) {
 QVector<qreal> Node::NeighbourAngles(void)
+{
 	QVector<qreal> angles;
 	for (list<Neighbor>::iterator i=owners.begin();
 		 i!=owners.end();
@@ @@ -192,7 +187,8 @@ QVector<qreal> Node::NeighbourAngles(voi @@
+		}
 		angles.push_back(angle);
 		//cerr << "Cell " << i->cell->Index() << ": " <<  v1 << " and " << v2 << ": angle = " << angles.back() << ", " << v1.Angle(v2) << endl;
     //cerr << "Cell " << i->cell->Index() << ": " <<  v1 << " and " << v2
     //     << ": angle = " << angles.back() << ", " << v1.Angle(v2) << endl;
+	}
@@ @@ -212,12 +208,11 @@ QVector<qreal> Node::NeighbourAngles(voi @@
+}
 #endif
 ostream &operator<<(ostream &os, const Node &n) {
   n.print(os);
   return os;
+}
 /* finis */

src/node.h

➞

Show inline comments

@@ @@ -78,7 +78,6 @@ public: @@
   // Output the Edge
   ostream &print(ostream &os) const;
   Node *first, *second;
 };
@@ @@ -138,45 +137,32 @@ public: @@
 #endif
   // temporary function for easier debugging
   inline int CellsSize(void) const {
     return owners.size();
+  }
   inline int CellsSize(void) const { return owners.size(); }
   inline int Value(void) const { return owners.size(); }
   inline int Value(void) const {
     return owners.size();
+  }
   void Fix(void) { fixed=true; }
   inline bool Fixed(void) const { return fixed; }
   inline void Unfix(void) { fixed=false; }
   void Fix(void) {
     fixed=true;
+  }
   inline bool Fixed(void) const {
     return fixed;
+  }
   inline void Unfix(void) {
     fixed=false;
+  }
   inline void MarkDead(void) {
     dead=true;
+  }
   inline bool DeadP(void) {
     return dead;
+  }
   inline void MarkDead(void) { dead=true; }
   inline bool DeadP(void) { return dead; }
   inline void Mark(void) {
     marked=true;
+  }
   inline void Unmark(void) {
     marked=false;
+  }
   inline bool Marked(void) const {
     return marked;
+  }
   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; }
   //!\brief Calculate angles with neighboring vertices
@@ @@ -210,5 +196,6 @@ inline ostream &operator<<(ostream &os, @@
   return os;
+}
 #endif
-#endif
+/* finis */

src/nodeitem.cpp

➞

Show inline comments

@@ @@ -39,10 +39,10 @@ NodeItem::NodeItem( Node *n, QGraphicsSc @@
   const double mag = par.node_mag;
   ellipsesize=QRectF(-1*mag, -1*mag, 2*mag, 2*mag);
+}
 void NodeItem::userMove(double dx, double dy) {
 void NodeItem::userMove(double dx, double dy)
+{
   QGraphicsItem::moveBy( dx, dy );
   class_cast<Node *>(obj)->x += (dx/Cell::Magnification());
@@ @@ -53,7 +53,6 @@ void NodeItem::userMove(double dx, doubl @@
 void NodeItem::paint(QPainter *painter, const QStyleOptionGraphicsItem *option, QWidget *)
+{
   option = NULL; // use assignment merely to obviate compilation warning
   painter->setBrush(brush);
@@ @@ -77,25 +76,26 @@ QRectF NodeItem::boundingRect() const @@
+}
 // polymorphic OnClick functions
 void NodeItem::OnClick(void) {
 void NodeItem::OnClick(void)
+{
   Node *n = &getNode();
   n->toggleBoundary();
   setColor();
   update();
+}
 void NodeItem::OnClick(const Qt::MouseButton &mb) {
 void NodeItem::OnClick(const Qt::MouseButton &mb)
+{
   if (mb == Qt::LeftButton) {
     Node *n = &getNode();
     n->toggleBoundary();
     setColor();
     update();
+  }
+}
 void NodeItem::setColor(void) {
 void NodeItem::setColor(void)
+{
   static QColor indian_red("IndianRed");
   static QColor deep_sky_blue("DeepSkyBlue");
   static QColor purple("Purple");
@@ @@ -113,3 +113,5 @@ void NodeItem::setColor(void) { @@
+    }
+  }
+}
 /* finis */

src/nodeitem.h

➞

Show inline comments

@@ @@ -56,3 +56,5 @@ private: @@
 };
 #endif
 /* finis */

src/nodeset.cpp

➞

Show inline comments

@@ @@ -29,3 +29,5 @@ ostream &operator<<(ostream &os, const N @@
   ns.print(os);
   return os;
+}
 /* finis */

src/nodeset.h

➞

Show inline comments

@@ @@ -61,8 +61,7 @@ class NodeSet : public list<Node *> { @@
     // remove all non-unique elements
     // (unique moves all unique elements to the front and returns an iterator to the end of the unique elements;
     // so we simply erase all remaining elements.
     cellset.erase(::unique(cellset.begin(), cellset.end() ),
 		  cellset.end() );
     cellset.erase(::unique(cellset.begin(), cellset.end() ), cellset.end() );
     // remove boundary_polygon
     cellset.erase( find_if ( cellset.begin(), cellset.end(), mem_fun( &Cell::BoundaryPolP  ) ) );
@@ @@ -111,7 +110,6 @@ class NodeSet : public list<Node *> { @@
       (*n)->x+=rx;
       (*n)->y+=ry;
       // (*n)->z += rz;
+    }
     // 4. Recalculate the energy
@@ @@ -151,8 +149,6 @@ class NodeSet : public list<Node *> { @@
 	(*n)->x-=rx;
 	(*n)->y-=ry;
+	  }
+    }
+  }
@@ @@ -164,3 +160,5 @@ class NodeSet : public list<Node *> { @@
 ostream &operator<<(ostream &os, const NodeSet &ns);
 #endif
 /* finis */

src/output.cpp

➞

Show inline comments

@@ @@ -61,7 +61,6 @@ int FileExistsP(const char *fname) { @@
   fclose(fp);
   return TRUE;
+}
 int YesNoP(const char *message) {
@@ @@ -81,13 +80,11 @@ int YesNoP(const char *message) { @@
   if (!strcmp(answer,"y")) return TRUE;
   return FALSE;
+}
 FILE *OpenWriteFile(const char *filename)
+{
   char fname[FNAMESIZE];
   FILE *fp;
@@ @@ -108,7 +105,6 @@ FILE *OpenWriteFile(const char *filename @@
       /* Rename old file */
       sprintf(fname, "%s~",filename);
       rename(filename, fname);
+    }
+  }
@@ @@ -121,7 +117,6 @@ FILE *OpenWriteFile(const char *filename @@
     perror("");
     throw(message);
+  }
   return fp;
+}
@@ @@ -170,7 +165,6 @@ char *ReadLine(FILE *fp) @@
   while ((character=getc(fp))!=EOF && /* read a character and check */
 		 character!='\n') {
 	tmpstring[pos]=(char)character;
 	(pos)++;
@@ @@ -178,25 +172,19 @@ char *ReadLine(FILE *fp) @@
 	  /* line is longer than initial_bufsize, reallocate space */
 	  bufsize+=INITIAL_BUFSIZE;
 	  MEMORYCHECK(tmpstring=(char *)realloc(tmpstring,bufsize*sizeof(char)));
+	}
+  }
   if (character==EOF) {
 	if (pos==0) {
 	  /* EOF was reached, while no characters were read */
 	  free(tmpstring);
 	  return NULL;
+	}
 	if (ferror(fp)) {
 	  error("I/O error in ReadLine(%ld): %s\n",fp, strerror(errno));
+	}
+  }
   /* Allocate enough memory for the line */
@@ @@ -207,7 +195,6 @@ char *ReadLine(FILE *fp) @@
   line[pos-1]='\0';
   return line;
+}
@@ @@ -237,7 +224,6 @@ char *Chext(char *filename) { @@
   for (i=strlen(filename)-1;i>=0;i--) {
     if (filename[i]=='.')
       break;
+  }
   /* No . found */
@@ @@ -251,8 +237,6 @@ char *Chext(char *filename) { @@
     strncpy(result, filename, i);
+  }
   return result;
+}
 void MakeDir(const char *dirname) {
@@ @@ -273,7 +257,6 @@ void MakeDir(const char *dirname) { @@
       cerr << message << endl;
       throw(message);
+    }
+  }
   // make directory
@@ @@ -329,13 +312,11 @@ void MakeDir(const char *dirname) { @@
       snprintf(message,MESS_BUF_SIZE,"Error in making directory %s",dirname);
       perror(message);
       exit(1);
+    }
+  }
 #endif
+}
 /* finis */

src/output.h

➞

Show inline comments

@@ @@ -53,3 +53,5 @@ bool CanWeWriteP(char *filename); @@
 #endif
 #endif
 /* finis */

src/parameter.cpp

➞

Show inline comments

@@ @@ -189,7 +189,6 @@ Parameter::~Parameter() { @@
   // free string parameter
   CleanUp();
+}
 void Parameter::CleanUp(void) {
@@ @@ -217,7 +216,6 @@ void Parameter::CleanUp(void) { @@
      free(dir1);
   if (dir2)
      free(dir2);
+}
 void Parameter::Read(const char *filename) {
@@ @@ -339,7 +337,6 @@ void Parameter::Read(const char *filenam @@
   dir2 = sgetpar(fp, "dir2", ".", true);
   if (strcmp(dir2, "."))
     MakeDir(dir2);
+}
 const char *sbool(const bool &p) {
@@ @@ -1876,7 +1873,6 @@ if (!strcmp(namec, "k")) { @@
+    }
     cur=cur->next;
+  }
 }*/
 ostream &operator<<(ostream &os, Parameter &p) {

src/pardialog.cpp

➞

Show inline comments

@@ @@ -694,7 +694,6 @@ void ParameterDialog::write(void) { @@
   par.dir1 = strdup((const char *)dir1_edit->text());
   par.dir2 = strdup((const char *)dir2_edit->text());
   Reset();
+}
 void ParameterDialog::Reset(void) {
   extern Parameter par;

src/parse.cpp

➞

Show inline comments

@@ @@ -64,7 +64,6 @@ char *ParsePar(FILE *fp, char *parameter @@
   free(line);
   return value;
+}
@@ @@ -95,7 +94,6 @@ int igetpar(FILE *fp,char *parameter, in @@
   free(token);
   return value;
+}
 float fgetpar(FILE *fp,char *parameter, bool wrapflag) {
@@ @@ -120,13 +118,9 @@ float fgetpar(FILE *fp, char *parameter, @@
   /* read it */
   sscanf(token,"%e",&value);
   fprintf(stderr,"%e]\n",value);
   free(token);
   return value;
+}
@@ @@ -180,7 +174,6 @@ double *dgetparlist(FILE *fp,char *param @@
+  }
   return value;
+}
 char *sgetpar(FILE *fp,char *parameter, bool wrapflag)
@@ @@ -213,7 +206,6 @@ char *sgetpar(FILE *fp, char *parameter, @@
   fprintf(stderr,"%s]\n",value);
   return value;
+}
 char *bool_str(bool bool_var) {
@@ @@ -229,7 +221,6 @@ char *bool_str(bool bool_var) { @@
   } else {
     return f;
+  }
+}
 bool bgetpar(FILE *fp, char *parameter,  bool wrapflag) {
@@ @@ -238,7 +229,6 @@ bool bgetpar(FILE *fp, char *parameter, @@
   // default = false
   return bgetpar(fp, parameter, 0, wrapflag);
+}
 bool bgetpar(FILE *fp, char *parameter, int default_val, bool wrapflag) {
@@ @@ -276,7 +266,6 @@ bool bgetpar(FILE *fp, char *parameter, @@
   fprintf(stderr, "%s]\n",bool_str(value));
   return value;
+}
@@ @@ -344,9 +333,7 @@ char *SearchToken(FILE *fp, char *token, @@
+	}
+    }
     free(line);
+  }
   free(tokenplusspace);
   return NULL; /* Token Not Found in the file */
@@ @@ -367,7 +354,6 @@ void SkipLine(FILE *fp) { @@
   char *tmpstring;
   tmpstring=ReadLine(fp);
   free(tmpstring);
+}
 void SkipToken(FILE *fp,char *token, bool wrapflag)
@@ @@ -386,6 +372,6 @@ void SkipToken(FILE *fp,char *token, boo @@
+  }
   free(tmppointer);
+}
 /* finis */

src/parse.h

➞

Show inline comments

@@ @@ -44,3 +44,5 @@ void SkipLine(FILE *fp); @@
 char *bool_str(bool bool_var);
 #endif
 /* finis */

src/perl/deployapp.pl

➞

Show inline comments

@@ @@ -112,3 +112,5 @@ for $lib (@additionallibs) { @@
     system "install_name_tool -change $fwfw/Versions/4/$liblib \@executable_path/../Frameworks/$fwfw/Versions/4.0/$liblib  $appdir/Contents/Frameworks/$lib";
+  }
+}
 # finis

src/perl/histogram.pl

➞

Show inline comments

@@ @@ -45,3 +45,6 @@ for ($bin=0;$bin<=$#bins;$bin++) { @@
    $halfwaybin = $bin * $binsize + $binsize/2.;
    print $halfwaybin." ".$bins[$bin]."\n";
+}
 # finis

src/perl/make_parameter_source.pl

➞

Show inline comments

@@ @@ -440,3 +440,5 @@ for ($i=0;$i<$lines;$i++) { @@
     print parfile "  $param[$i] = $value[$i]\n";
+  }
+}
 # finis

src/perl/make_pardialog_source.pl

➞

Show inline comments

@@ @@ -301,3 +301,4 @@ print hfile <<END_TRAILER2; @@
 #endif
 END_TRAILER2
 # finis

src/perl/make_xmlwritecode.pl

➞

Show inline comments

		@@ -221,3 +221,4 @@ print xmlsrc "xmlChar *sourcecode = (xml

		END_MARKER3

		# finis

src/pi.h

➞

Show inline comments

@@ @@ -28,3 +28,5 @@ @@
 const double Pi=3.1415926535897932384626433832795028841971693993751058209749445923078164062862089986280348253421170676;
 #endif
 /* finis */

src/qcanvasarrow.h

➞

Show inline comments

@@ @@ -30,8 +30,7 @@ @@
 class QGraphicsArrowItem : public QGraphicsLineItem {
  public:
   QGraphicsArrowItem(QGraphicsItem *parent, QGraphicsScene *c) : QGraphicsLineItem(parent, c) {
   };
  QGraphicsArrowItem(QGraphicsItem *parent, QGraphicsScene *c) : QGraphicsLineItem(parent, c) {};
     void paint ( QPainter *p, const QStyleOptionGraphicsItem *option,
 		 QWidget *widget ) {
@@ @@ -74,3 +73,5 @@ class QGraphicsArrowItem : public QGraph @@
 };
 #endif
 /* finis */

src/random.cpp

➞

Show inline comments

@@ @@ -147,3 +147,4 @@ int Randomize(void) { @@
   return seed;
+}
 /* finis */

src/random.h

➞

Show inline comments

@@ @@ -58,9 +58,6 @@ class MyUrand { @@
   long operator()(void) { return RandomNumber(n); }
 };
 #endif
 #endif
 /* finis */

src/rseed.cpp

➞

Show inline comments

@@ @@ -28,6 +28,7 @@ static const std::string _module_id("$Id @@
 int main() {
    long rseed=Randomize();
    std::cout << rseed << "\n";
   std::cerr << rseed << std::endl;
+}
+}
+/* finis */

src/rungekutta.cpp

➞

Show inline comments

@@ @@ -85,7 +85,6 @@ void RungeKutta::rkqs(double *y, double @@
   for (i=0;i<n;i++) y[i]=ytemp[i];
   delete[] ytemp;
   delete[] yerr;
+}
@@ @@ -203,3 +202,5 @@ void RungeKutta::odeint(double *ystart, @@
+  }
   MyWarning::error("Too many steps in routine odeint");
+}
 /* finis */

src/rungekutta.h

➞

Show inline comments

@@ @@ -59,7 +59,7 @@ class RungeKutta { @@
   static const double Errcon;
   static const double Maxstp;
   static const double Tiny;
 };
 #endif
 /* finis */

src/simitembase.cpp

➞

Show inline comments

@@ @@ -25,7 +25,8 @@ @@
 static const std::string _module_id("$Id$");
 SimItemBase::SimItemBase( void *v, QGraphicsScene *canvas ) {
 SimItemBase::SimItemBase( void *v, QGraphicsScene *canvas )
+{
   canvas = NULL; // use assignment merely to obviate compilation warning
     obj=v;
 };
@@ @@ -33,6 +34,9 @@ SimItemBase::SimItemBase( void *v, QGrap @@
 SimItemBase::~SimItemBase(void) {};
 void SimItemBase::userMove(double dx, double dy) {
 void SimItemBase::userMove(double dx, double dy)
+{
   dx = dy = 0.0; // use assignment merely to obviate compilation warning
 };
 /* finis */

src/simitembase.h

➞

Show inline comments

@@ @@ -65,3 +65,5 @@ public: @@
   };
 #endif
 /* finis */

src/simplugin.cpp

➞

Show inline comments

@@ @@ -24,7 +24,8 @@ @@
 static const std::string _module_id("$Id$");
 void SimPluginInterface::SetParameters(Parameter *pass_pars) {
 void SimPluginInterface::SetParameters(Parameter *pass_pars)
+{
 	par = pass_pars;
+}
@@ @@ -33,3 +34,4 @@ void SimPluginInterface::SetCellsStaticD @@
 	CellBase::static_data_members = cells_static_data_members_of_main;
+}
 /* finis */

src/simplugin.h

➞

Show inline comments

@@ @@ -71,12 +71,11 @@ public: @@
 protected:
 	class Parameter *par;
 };
 Q_DECLARE_INTERFACE(SimPluginInterface,
                     "nl.cwi.VirtualLeaf.SimPluginInterface/1.2")
 Q_DECLARE_INTERFACE(SimPluginInterface, "nl.cwi.VirtualLeaf.SimPluginInterface/1.2")
 Q_DECLARE_METATYPE(SimPluginInterface *)
 #endif
 #endif
@@ \ No newline at end of file @@
 /* finis */

src/sqr.h

➞

Show inline comments

@@ @@ -40,7 +40,6 @@ inline double DSQR( double a ) { @@
   } else {
     return a*a;
+  }
+}
 inline float SQR( float a ) {
@@ @@ -50,4 +49,7 @@ inline float SQR( float a ) { @@
     return a*a;
+  }
+}
 #endif
 /* finis */

src/tiny.h

➞

Show inline comments

@@ @@ -28,3 +28,5 @@ @@
 #define TINY 1e-5
 #endif
 /* finis */

src/transporterdialog.cpp

➞

Show inline comments

@@ @@ -41,7 +41,8 @@ TransporterDialog::TransporterDialog(Wal @@
   // compose a label for the dialog box
   std::stringstream label_text;
   label_text << "C("<< wall->C1()->Index() << "," << wall->C2()->Index() << "), N(" << wall->N1()->Index() << "," << wall->N2()->Index() << ")";
   label_text << "C("<< wall->C1()->Index() << "," << wall->C2()->Index() << "), N("
 	     << wall->N1()->Index() << "," << wall->N2()->Index() << ")";
   // retrieve the current transporters
   QVector <double> transporters;  // transporter vector
@@ @@ -86,8 +87,8 @@ TransporterDialog::TransporterDialog(Wal @@
   setWindowTitle(tr(label_text.str().c_str()));
+}
 void TransporterDialog::setTransporterValues(){
 void TransporterDialog::setTransporterValues()
+{
   // iterate over the editor widgets soliciting their values and setting the wall's transporters accordingly.
   for (int i=0; i<ntransporters; ++i){
     #ifdef QDEBUG
@@ @@ -102,5 +103,6 @@ void TransporterDialog::setTransporterVa @@
   close();
+}
-// finis
+/* finis */

src/transporterdialog.h

➞

Show inline comments

@@ @@ -55,3 +55,5 @@ class TransporterDialog : public QDialog @@
 };
 #endif
 /* finis */

src/vector.cpp

➞

Show inline comments

@@ @@ -43,18 +43,15 @@ void Vector::operator=(const Vector &sou @@
   x=source.x;
   y=source.y;
   z=source.z;
+}
 ostream &Vector::print(ostream &os) const {
   os << "(" << x << ", " << y << ", " << z << ")";
   return os;
+}
 ostream &operator<<(ostream &os, const Vector &v) {
   v.print(os);
   return os;
@@ @@ -69,7 +66,6 @@ Vector Vector::operator+(const Vector &v @@
   result.z=z+v.z;
   return result;
+}
@@ @@ -80,7 +76,6 @@ Vector& Vector::operator-=(const Vector @@
   z-=v.z;
   return *this;
+}
 Vector Vector::operator/(const double divisor) const {
@@ @@ -93,8 +88,6 @@ Vector Vector::operator/(const double di @@
   result.z=z/divisor;
   return result;
+}
@@ @@ -107,8 +100,6 @@ Vector Vector::operator*(const double mu @@
   result.z=z*multiplier;
   return result;
+}
@@ @@ -121,7 +112,6 @@ Vector operator*(const double multiplier @@
   result.z=v.z*multiplier;
   return result;
+}
 Vector &Vector::operator/=(const double divisor) {
@@ @@ -130,7 +120,6 @@ Vector &Vector::operator/=(const double @@
   z/=divisor;
   return *this;
+}
 Vector &Vector::operator*=(const double multiplier) {
@@ @@ -140,7 +129,6 @@ Vector &Vector::operator*=(const double @@
   z*=multiplier;
   return *this;
+}
 Vector Vector::operator*(const Vector &v) const {
@@ @@ -153,8 +141,6 @@ Vector Vector::operator*(const Vector &v @@
   result.z=x*v.y-y*v.x;
   return result;
+}
@@ @@ -164,7 +150,6 @@ double InnerProduct(const Vector &v1, co @@
   double result;
   result=v1.x*v2.x+v1.y*v2.y+v1.z*v2.z;
   return result;
+}
 double Vector::Angle(const Vector &v) const {
@@ @@ -187,7 +172,6 @@ double Vector::Angle(const Vector &v) co @@
   double angle=acos(cos_angle);
   return angle;
+}
 double Vector::SignedAngle(const Vector &v) const {
@@ @@ -211,7 +195,6 @@ double Vector::SignedAngle(const Vector @@
   double sign = (InnerProduct ( Perp2D(), v ) )>0.?1.:-1.;
   return angle * sign;
+}
@@ @@ -222,7 +205,6 @@ bool Vector::operator==(const Vector &v) @@
     return true;
   else
     return false;
+}
 bool Vector::operator< (const Vector &v) const {
@@ @@ -232,7 +214,6 @@ bool Vector::operator< (const Vector &v) @@
     return true;
   else
     return false;
+}
@@ @@ -242,7 +223,6 @@ double Vector::SqrNorm(void) const { @@
   // added this function to avoid taking the square root and
   // the square again if this value is needed
   return DSQR(x)+DSQR(y)+DSQR(z);
+}
 void Vector::Normalise(void) {
@@ @@ -255,7 +235,6 @@ void Vector::Normalise(void) { @@
     (*this)/=norm;
+  }
+}
 Vector Vector::Normalised(void) const {
@@ @@ -269,7 +248,6 @@ Vector Vector::Normalised(void) const { @@
   } else {
     return *this;
+  }
+}
 bool Vector::SameDirP(const Vector &v) {
@@ @@ -282,7 +260,6 @@ bool Vector::SameDirP(const Vector &v) { @@
     return true;
   else
     return false;
+}
 double Vector::Max(void) {
@@ @@ -334,8 +311,8 @@ void main() { @@
   d.Normalise();
 //  cerr << d << "  " << d.Norm() << "\n";
+}
 #endif
 /* finis */

src/vector.h

➞

Show inline comments

@@ @@ -97,7 +97,6 @@ public: @@
     result.z=z-v.z;
     return result;
+  }
   Vector &operator-=(const Vector &v);
@@ @@ -108,7 +107,6 @@ public: @@
     z+=v.z;
     return *this;
+  }
   Vector operator/(const double divisor) const; // division by a double
@@ @@ -121,7 +119,6 @@ public: @@
   inline double Norm(void) const {
     return sqrt(DSQR(x)+DSQR(y)+DSQR(z));
+  }
   // Quick and dirty Norm (i.e. Manhattan distance)
@@ @@ -141,6 +138,7 @@ public: @@
   Vector Perp2D(void) const {
     return Vector(y,-x,0);
+  }
   // data members
   double x,y,z;
@@ @@ -151,7 +149,6 @@ public: @@
     is >> x >> y >> z;
+  }
 private:
 };
 ostream &operator<<(ostream &os, const Vector &v);
@@ @@ -159,3 +156,5 @@ Vector operator*(const double multiplier @@
 double InnerProduct(const Vector &v1, const Vector &v2);
 #endif
 /* finis */

src/vleafmodel.h

➞

Show inline comments

@@ @@ -37,3 +37,5 @@ @@
 #include "flux_function.h"
 #endif
 /* finis */

src/wall.cpp

➞

Show inline comments

@@ @@ -64,7 +64,6 @@ bool Wall::CorrectWall( void ) { @@
 												   wall_owners.begin(), wall_owners.end(),
 												   mem_fun( &CellBase::BoundaryPolP )
 												   );
 		if (bpit!=wall_owners.end()) {
 			// add a Wall with the boundary_polygon to each cell
@@ @@ -89,9 +88,11 @@ bool Wall::CorrectWall( void ) { @@
 		  transform(wall_owners.begin(), wall_owners.end(), ostream_iterator<int>(qDebug(), "  "), mem_fun (&CellBase::Index) );
 		  qDebug() << endl;
 		  qDebug() << "Owners node " << n1->Index() << ": ";
 		  for (list<Neighbor>::iterator i = n1->owners.begin(); i!=n1->owners.end(); i++) {
 		    qDebug() << i->getCell()->Index() << " ";
+		  }
 		  qDebug() << endl;
 		  qDebug() << "Owners node " << n2->Index() << ": ";
@@ @@ -102,7 +103,6 @@ bool Wall::CorrectWall( void ) { @@
                   #endif
 		  std::exit(1);
+		}
+	}
 	#ifdef QDEBUG
@@ @@ -151,12 +151,7 @@ bool Wall::CorrectWall( void ) { @@
+			}
+		}
+	}
 	return true;
+}
 void Wall::Draw(QGraphicsScene *c) {
@@ @@ -165,13 +160,11 @@ void Wall::Draw(QGraphicsScene *c) { @@
 	WallItem *wi2 = new WallItem(this, 2, c);
 	wi1->show();
 	wi2->show();
+}
 void Wall::DrawApoplast(QGraphicsScene *c) {
 	ApoplastItem *apo = new ApoplastItem(this, c);
 	apo->show();
+}
 void Wall::ShowStructure(QGraphicsScene *c) {
@@ @@ -208,7 +201,6 @@ void Wall::ShowStructure(QGraphicsScene @@
 	text1->setPen ( QColor(par.textcolor) );
 	text2->setPen ( text1->pen() );
 	text1->show(); text2->show();
+}
 string Wall::WallTypetoStr(const WallType &wt) const {
@@ @@ -227,5 +219,4 @@ string Wall::WallTypetoStr(const WallTyp @@
 	return string("");
+}
 /* finis */

src/wall.h

➞

Show inline comments

@@ @@ -54,10 +54,8 @@ public: @@
 private:
 	string WallTypetoStr(const WallType &wt) const;
 };
 #endif
 /* finis */

src/wallbase.cpp

➞

Show inline comments

@@ @@ -53,7 +53,8 @@ ostream &operator<<(ostream &os, const W @@
+}
 WallBase::WallBase(Node *sn1, Node *sn2, CellBase *sc1, CellBase *sc2) {
 WallBase::WallBase(Node *sn1, Node *sn2, CellBase *sc1, CellBase *sc2)
+{
         #ifdef QDEBUG
 	if (sc1==sc2) {
@@ @@ -85,10 +86,10 @@ WallBase::WallBase(Node *sn1, Node *sn2, @@
 	dead = false;
 	wall_type = Normal;
 	wall_index = nwalls++;
+}
 void WallBase::CopyWallContents(const WallBase &src) {
 void WallBase::CopyWallContents(const WallBase &src)
+{
 	for (int i=0; i<CellBase::NChem(); i++) {
 		if (transporters1) {
@@ @@ -112,7 +113,8 @@ void WallBase::CopyWallContents(const Wa @@
 	wall_type = src.wall_type;
+}
 void WallBase::SwapWallContents(WallBase *src) {
 void WallBase::SwapWallContents(WallBase *src)
+{
 	for (int i=0; i<CellBase::NChem(); i++) {
 		if (transporters1) {
@@ @@ -158,22 +160,18 @@ void WallBase::SwapWallContents(WallBase @@
 	tmp_wall_type = src->wall_type;
 	src->wall_type = wall_type;
 	wall_type = tmp_wall_type;
+}
 bool WallBase::SAM_P(void) {
 bool WallBase::SAM_P(void)
+{
 	return N1()->sam || N2()->sam;
+}
 #include <fstream>
 void WallBase::SetLength(void) {
 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...
@@ @@ -206,15 +204,13 @@ void WallBase::SetLength(void) { @@
 		// 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();
+	}
+}
 void WallBase::CorrectTransporters(double orig_length) {
 void WallBase::CorrectTransporters(double orig_length)
+{
 	double length_factor = length / orig_length;
@@ @@ -224,11 +220,11 @@ void WallBase::CorrectTransporters(doubl @@
 		new_transporters1[ch] *= length_factor;
 		new_transporters2[ch] *= length_factor;
+	}
+}
 Vector WallBase::VizFlux(void) {
 Vector WallBase::VizFlux(void)
+{
 	return viz_flux * ( (*n2) - (*n1) ).Normalised().Perp2D();
+}
@@ @@ -241,15 +237,16 @@ void WallBase::SetTransToNewTrans( void @@
+}
 Vector WallBase::getWallVector(CellBase *c) {
 Vector WallBase::getWallVector(CellBase *c)
+{
 	if ( c == c1 ) {
 		return ( Vector(*n2) - Vector(*n1) );
 	} else {
 		return ( Vector(*n1) - Vector(*n2) );
+	}
+}
 Vector WallBase::getInfluxVector(CellBase *c) {
 Vector WallBase::getInfluxVector(CellBase *c)
+{
 	if ( c == c1 ) {
 		return ( Vector(*n2) - Vector(*n1) ).Normalised().Perp2D();
 	} else {
@@ @@ -258,7 +255,8 @@ Vector WallBase::getInfluxVector(CellBas @@
+}
 //! \brief Test if this wall intersects with division plane p1 -> p2
 bool WallBase::IntersectsWithDivisionPlaneP(const Vector &p1, const Vector &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;
@@ @@ -271,6 +269,6 @@ bool WallBase::IntersectsWithDivisionPla @@
 	// If ua is between 0 and 1, line p1 intersects the line segment
 	if ( ua >=0. && ua <=1.) return true;
 	else return false;
+}
 /* finis */

src/wallbase.h

➞

Show inline comments

@@ @@ -28,12 +28,8 @@ @@
 #include <list>
 #include <iostream>
 #include "vector.h"
 class Node;
 class CellBase;
@@ @@ -156,7 +152,10 @@ public: @@
+				}
+	}
 	// checked version. Use during debugging stage.
 	inline double getTransporter(CellBase *c, int ch) const { return c1 == c ? transporters1[ch] : ( c2 == c ? transporters2[ch] : throw "WallBase::getTransporter called with wrong cell") ; }
   inline double getTransporter(CellBase *c, int ch) const
+  {
     return c1 == c ? transporters1[ch] : ( c2 == c ? transporters2[ch] : throw "WallBase::getTransporter called with wrong cell") ; }
 	inline void setTransporter(CellBase *c, int ch, double val) {
 		if ( c1 == c ) {
 			transporters1[ch]=val;
@@ @@ -194,8 +193,9 @@ public: @@
 	void SetTransToNewTrans( void );
 private:
 };
 ostream &operator<<(ostream &os, const WallBase &w);
 #endif
 /* finis */

src/wallitem.cpp

➞

Show inline comments

@@ @@ -128,3 +128,5 @@ void WallItem::OnClick(QMouseEvent *e) { @@
+		}
+	}
+}
 /* finis */

src/wallitem.h

➞

Show inline comments

@@ @@ -48,3 +48,5 @@ public: @@
 };
 #endif
 /* finis */

src/warning.cpp

➞

Show inline comments

@@ @@ -81,7 +81,6 @@ void MyWarning::error(const char *fmt, . @@
     std::exit(1);
+  }
   delete[] message;
+}
 #endif
@@ @@ -131,7 +130,6 @@ void MyWarning::warning(const char *fmt, @@
 	  msgBox.exec();
+  }
   delete[] message;
+}
 #endif
@@ @@ -177,3 +175,5 @@ main(int argc, char * argv[]) @@
+}
 #endif
 /* finis */

src/warning.h

➞

Show inline comments

@@ @@ -45,3 +45,5 @@ extern "C" { @@
 #endif
 #endif
 /* finis */

src/xmlwrite.cpp

➞

Show inline comments

@@ @@ -56,14 +56,12 @@ void Cell::XMLAdd(xmlNodePtr cells_node) @@
   // Save the cell to a stream so we can reconstruct its state later
   xmlNodePtr xmlcell = xmlNewChild(cells_node, NULL, BAD_CAST "cell",NULL);
   XMLAddCore(xmlcell);
+}
 void BoundaryPolygon::XMLAdd(xmlNodePtr parent_node) const {
   xmlNodePtr xmlcell = xmlNewChild(parent_node, NULL, BAD_CAST "boundary_polygon",NULL);
   XMLAddCore(xmlcell);
+}
 void NodeSet::XMLAdd(xmlNode *root) const {
@@ @@ -78,7 +76,6 @@ void NodeSet::XMLAdd(xmlNode *root) cons @@
       xmlNewProp(node_xml, BAD_CAST "n", BAD_CAST text.str().c_str());
+    }
+  }
+}
@@ @@ -208,12 +205,8 @@ void Cell::XMLAddCore(xmlNodePtr xmlcell @@
       ostringstream text;
       text << chem[i];
       xmlNewProp(chem_val_xml, BAD_CAST "v", BAD_CAST text.str().c_str());
+    }
+  }
+}
@@ @@ -223,8 +216,6 @@ void Node::XMLAdd(xmlNodePtr nodes_node) @@
   // Save the node to a stream so we can reconstruct its state later
   xmlNodePtr xmlnode = xmlNewChild(nodes_node, NULL, BAD_CAST "node",NULL);
+  {
     ostringstream text;
     text << x;
@@ @@ -260,8 +251,6 @@ void Node::XMLAdd(xmlNodePtr nodes_node) @@
     text << XMLIO::list_index(m->node_sets.begin(),m->node_sets.end(),node_set);
     xmlNewProp(xmlnode, BAD_CAST "nodeset", BAD_CAST text.str().c_str());
+  }
+}
 void Neighbor::XMLAdd(xmlNodePtr neighbors_node) const {
@@ @@ -284,7 +273,6 @@ void Neighbor::XMLAdd(xmlNodePtr neighbo @@
     text << nb2->Index();
     xmlNewProp(xmlnode, BAD_CAST "nb2", BAD_CAST text.str().c_str());
+  }
+}
@@ @@ -316,7 +304,8 @@ getnodeset (xmlDocPtr doc, xmlChar *xpat @@
 int Cell::XMLRead(xmlNode *cur)  {
 int Cell::XMLRead(xmlNode *cur)
+{
   xmlNode *n = cur->xmlChildrenNode;
   QLocale standardlocale(QLocale::C);
@@ @@ -554,10 +543,10 @@ int Cell::XMLRead(xmlNode *cur) { @@
   // Recalculate moments and area
   SetIntegrals();
   return 0;
+}
 void NodeSet::XMLRead(xmlNode *root, Mesh *m) {
 void NodeSet::XMLRead(xmlNode *root, Mesh *m)
+{
   xmlNode *n = root->xmlChildrenNode;
@@ @@ -579,7 +568,6 @@ void NodeSet::XMLRead(xmlNode *root, Mes @@
   for (int i=0;i<nnodes;i++) {
     AddNode( &(m->getNode(tmp_nodes[i])) );
+  }
+}
@@ @@ -663,7 +651,6 @@ void Wall::XMLAdd(xmlNode *parent) const @@
 	ostringstream text;
 	text << transporters2[i];
 	xmlNewProp(tr2_val_xml, BAD_CAST "v", BAD_CAST text.str().c_str());
+      }
+    }
+  }
@@ @@ -677,14 +664,14 @@ void Wall::XMLAdd(xmlNode *parent) const @@
 	ostringstream text;
 	text << transporters2[i];
 	xmlNewProp(apo_val_xml, BAD_CAST "v", BAD_CAST text.str().c_str());
+      }
+    }
+  }
+}
 vector<double> XMLIO::XMLReadValArray(xmlNode *cur) {
 vector<double> XMLIO::XMLReadValArray(xmlNode *cur)
+{
   vector<double> result;
   QLocale standardlocale(QLocale::C);
@@ @@ -763,8 +750,6 @@ void Mesh::XMLSave(const char *docname, @@
 		xmlNewProp(xmlnodes, BAD_CAST "target_length", BAD_CAST text.str().c_str());
+	}
 	for (vector<Node *>::const_iterator i=nodes.begin();
 		 i!=nodes.end();
 		 i++) {
@@ @@ -842,13 +827,7 @@ void Mesh::XMLSave(const char *docname, @@
 		xmlNewProp(xmlnodesets, BAD_CAST "n", BAD_CAST text.str().c_str());
+	}
 	for_each( node_sets.begin(), node_sets.end(),
 			 bind2nd (
 					  mem_fun( &NodeSet::XMLAdd ),
 					  xmlnodesets
 					  ) );
   for_each( node_sets.begin(), node_sets.end(), bind2nd ( mem_fun( &NodeSet::XMLAdd ), xmlnodesets ) );
 	// Add option tree for interactive application
 	if (options) {
@@ @@ -856,8 +835,6 @@ void Mesh::XMLSave(const char *docname, @@
+	}
 	/*
 	 * Dumping document to stdio or file
 	 */
@@ @@ -880,7 +857,8 @@ void Mesh::XMLSave(const char *docname, @@
 void Mesh::XMLReadSimtime(const xmlNode *a_node) {
 void Mesh::XMLReadSimtime(const xmlNode *a_node)
+{
   xmlNode *root_node;
   root_node = (xmlNode *)a_node;
@@ @@ -906,7 +884,8 @@ void Mesh::XMLReadSimtime(const xmlNode @@
+	}
+}
 void Mesh::XMLReadPars(const xmlNode * a_node) {
 void Mesh::XMLReadPars(const xmlNode * a_node)
+{
 	xmlNode *root_node;
 	root_node = (xmlNode *)a_node;
 	par.XMLRead(root_node);
@@ @@ -979,7 +958,6 @@ void Mesh::XMLReadGeometry(const xmlNode @@
 			if (!ok) MyWarning::error("Could not convert \"%s\" to double in XMLRead.",(const char *)baseareac);
 			xmlFree(baseareac);
 			XMLReadCells(cur);
+		}
 		cur=cur->next;
@@ @@ -1021,19 +999,18 @@ void Mesh::XMLReadGeometry(const xmlNode @@
 	MyUrand r(shuffled_cells.size());
 	random_shuffle(shuffled_cells.begin(),shuffled_cells.end(),r);
+}
 void Mesh::XMLParseTree(const xmlNode *root_node) {
 void Mesh::XMLParseTree(const xmlNode *root_node)
+{
 	XMLReadSimtime(root_node);
 	XMLReadPars(root_node);
 	XMLReadGeometry(root_node);
+}
 void Mesh::XMLReadNodes(xmlNode *root) {
 void Mesh::XMLReadNodes(xmlNode *root)
+{
   QLocale standardlocale(QLocale::C);
   bool ok;
@@ @@ -1054,7 +1031,6 @@ void Mesh::XMLReadNodes(xmlNode *root) { @@
   if (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);
@@ @@ -1115,8 +1091,6 @@ void Mesh::XMLReadNodes(xmlNode *root) { @@
       xmlFree(boundaryc);
       xmlFree(fixedc);
       xmlFree(samc);
+    }
     cur=cur->next;
+  }
@@ @@ -1126,10 +1100,10 @@ void Mesh::XMLReadNodes(xmlNode *root) { @@
   MyUrand r(shuffled_nodes.size());
   random_shuffle(shuffled_nodes.begin(),shuffled_nodes.end(),r);
+}
 void Mesh::XMLReadWalls(xmlNode *root, vector<Wall *> *tmp_walls) {
 void Mesh::XMLReadWalls(xmlNode *root, vector<Wall *> *tmp_walls)
+{
   xmlNode *cur = root;
   cur = cur->xmlChildrenNode;
@@ @@ -1240,7 +1214,6 @@ void Mesh::XMLReadWalls(xmlNode *root, v @@
 	    dead = strtobool( (char *)v_str);
 	    xmlFree(v_str);
+	  }
+	}
 	Cell *cc1 = c1 != -1 ? cells[c1] : boundary_polygon;
@@ @@ -1287,10 +1260,8 @@ void Mesh::XMLReadWalls(xmlNode *root, v @@
+	      }
 	      v_node = v_node->next;
+	    }
+	  }
 	  if ((!xmlStrcmp(w_node->name, (const xmlChar *)"transporters2"))) {
 	    xmlNode *v_node = w_node->xmlChildrenNode;
@@ @@ -1303,7 +1274,6 @@ void Mesh::XMLReadWalls(xmlNode *root, v @@
 		    text << "Exception in Mesh::XMLRead: Too many transporter values given for wall(s). Ignoring remaining values.";
 		    unique_warning(text.str().c_str());
 		    break;
+		  }
+		}
@@ @@ -1321,7 +1291,6 @@ void Mesh::XMLReadWalls(xmlNode *root, v @@
+	      }
 	      v_node = v_node->next;
+	    }
+	  }
 	  if ((!xmlStrcmp(w_node->name, (const xmlChar *)"apoplast"))) {
@@ @@ -1364,7 +1333,8 @@ void Mesh::XMLReadWalls(xmlNode *root, v @@
+}
 void Mesh::XMLReadWallsToCells(xmlNode *root, vector<Wall *> *tmp_walls) {
 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
@@ @@ -1409,19 +1379,16 @@ void Mesh::XMLReadWallsToCells(xmlNode * @@
 				for (int i=0;i<nwalls;i++) {
 					cells[ci]->walls.push_back((*tmp_walls)[tmp_walls_ind[i]]);
+				}
 				ci++;
+			}
+		}
 		cur=cur->next;
+	}
+}
 void Mesh::XMLReadNodeSetsToNodes(xmlNode *root) {
 void Mesh::XMLReadNodeSetsToNodes(xmlNode *root)
+{
 	xmlNode *cur = root->xmlChildrenNode;
 	int ci=0; // cell index
@@ @@ -1448,18 +1415,15 @@ void Mesh::XMLReadNodeSetsToNodes(xmlNod @@
 				n = n->next;
+			}
 			ci++;
+		}
 		cur=cur->next;
+	}
+}
 void Mesh::XMLReadNodeSets(xmlNode *root) {
 void Mesh::XMLReadNodeSets(xmlNode *root)
+{
 	for (vector<NodeSet *>::iterator i=node_sets.begin();
 		 i!=node_sets.end();
@@ @@ -1487,10 +1451,10 @@ void Mesh::XMLReadNodeSets(xmlNode *root @@
 		new_nodeset->XMLRead(cur, this);
 		cur=cur->next;
+	}
+}
 void Mesh::XMLReadCells(xmlNode *root) {
 void Mesh::XMLReadCells(xmlNode *root)
+{
 	for (vector<Cell *>::iterator i=cells.begin();
 		 i!=cells.end();
@@ @@ -1530,10 +1494,10 @@ void Mesh::XMLReadCells(xmlNode *root) { @@
 		new_cell->XMLRead(cur);
 		cur=cur->next;
+	}
+}
 void Mesh::XMLRead(const char *docname, xmlNode **settings, bool geometry, bool pars, bool simtime) {
 void Mesh::XMLRead(const char *docname, xmlNode **settings, bool geometry, bool pars, bool simtime)
+{
 	xmlDocPtr doc = xmlParseFile(docname);
 	if (doc == NULL ) {
@@ @@ -1584,11 +1548,11 @@ void Mesh::XMLRead(const char *docname, @@
 	// We're doing this so we can manually delete walls with by adding the 'delete="true"' property
 	CleanUpCellNodeLists();
+}
 void Parameter::XMLRead(xmlNode *root) {
 void Parameter::XMLRead(xmlNode *root)
+{
 	xmlNode *cur = root->xmlChildrenNode;
 	while (cur!=NULL) {
@@ @@ -1617,10 +1581,9 @@ void Parameter::XMLRead(xmlNode *root) { @@
+				}
 				par_node = par_node->next;
+			}
+		}
 		cur=cur->next;
+	}
+}
 /* finis */

src/xmlwrite.h

➞

Show inline comments

@@ @@ -45,7 +45,6 @@ namespace XMLIO { @@
+    }
     return -1;
+  }
+}
@@ @@ -66,3 +65,5 @@ inline bool strtobool(const char *str) { @@
+}
 #endif
 /* finis */

0 comments (0 inline, 0 general)