EI/VirtualLeaf Changeset - 137d9d3a313a · Centrum Wiskunde & Informatica (CWI)

Changeset - 137d9d3a313a

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0 19 0

Michael Guravage - 15 years ago 2010-06-15 13:44:36
michael.guravage@cwi.nl

Removed most compilation warnings; see ChangeLogs for details.

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

changed .hgignore
changed src/ChangeLog
changed src/VirtualLeaf.cpp
changed src/apoplastitem.cpp
changed src/build_models/ChangeLog
changed src/build_models/auxingrowthplugin.cpp
changed src/build_models/meinhardtplugin.cpp
changed src/build_models/testplugin.cpp
changed src/canvas.cpp
changed src/cell.cpp
changed src/cellbase.h
changed src/forwardeuler.cpp
changed src/mainbase.h
changed src/mesh.cpp
changed src/nodeitem.cpp
changed src/output.cpp
changed src/qcanvasarrow.h
changed src/simitembase.cpp
changed src/xmlwrite.cpp

19 files changed with 101 insertions and 33 deletions:

.hgignore

src/ChangeLog

src/VirtualLeaf.cpp

src/apoplastitem.cpp

src/build_models/ChangeLog

src/build_models/auxingrowthplugin.cpp

src/build_models/meinhardtplugin.cpp

src/build_models/testplugin.cpp

src/canvas.cpp

src/cell.cpp

src/cellbase.h

src/forwardeuler.cpp

src/mainbase.h

src/mesh.cpp

src/nodeitem.cpp

src/output.cpp

src/qcanvasarrow.h

src/simitembase.cpp

src/xmlwrite.cpp

0 comments (0 inline, 0 general)

.hgignore

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Show inline comments

 # use glob syntax.
 syntax: glob
 *~
 *.a
 *.exe
 *.cache
 *.Debug
 *.o
 *.orig
 *.out
 *.Release
 *.so
 *.vars
 *Makefile.*
 *make.out
 *moc_*.cpp
 src/default.par
 bin*
 TAGS
 BROWSE
 # switch to regexp syntax.
 syntax: regexp
 # finis

src/ChangeLog

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Show inline comments

 -06-15    <guravage@caterpie.sen.cwi.nl>
 	* mesh.cpp (findNextBoundaryNode): Initialize Node *next_boundary_node = NULL;
 	* xmlwrite.cpp (XMLReadSimtime): Removed unused variable cur
 	(XMLReadWalls): viz_flux need not be declared twice; default value of 0.0.
 	(XMLReadCells): Removed unused count variable.
 	(XMLReadSimtime): Removed unused cur variable.
 	(XMLRead): Removed unused v_str variable.
 	* simitembase.cpp (userMove): Use assignment merely to obviate compilation warning.
 	(SimItemBase) Ditto.
 	* qcanvasarrow.h (QGraphicsLineItem): Use assignment merely to obviate compilation warning.
 	* output.cpp (OpenWriteFile): Removed unused par variable.
 	* nodeitem.cpp (paint): Use assignment merely to obviate compilation warning.
 	* forwardeuler.cpp (odeint): Use assignment merely to obviate compilation warning.
 	* cell.cpp (DivideOverGivenLine): Use assignment merely to obviate compilation warning.
 	* canvas.cpp (FigureEditor): Use assignments merely to obviate compilation errors.
 	(mousePressEvent): Removed unused item variable.
 	* apoplastitem.cpp
 	(ApoplastItem): Removed unused par variable.
 	(OnClick): Use NULL assignment merely to obviate compilation warning.
 	* mainbase.h (MainBase): Use assignment merely to obviate compilation warning.
 	* cellbase.h (CellsStaticDatamembers): Use assignment merely to obviate compilation warning.
 	* cell.cpp: Wrapped diagnostic output in QDEBUG blocks.
 	* VirtualLeaf.cpp ditto.
 	* canvas.cpp ditto.
 	* cell.cpp ditto.
 	* cellbase.h
 	* data_plot.cpp ditto.
 	* forwardeuler.cpp ditto.
 	* mesh.cpp ditto.
 	* mesh.h
 	* random.cpp ditto.
 	* wall.cpp ditto.
 	* wallbase.cpp ditto.
 	* wallitem.cpp ditto.
 -06-07    <guravage@caterpie.sen.cwi.nl>
 	* VirtualLeaf.pro: Removed explicit perl invocation to regerenerate parameter files.
 	* libplugin.pro: ditto.
 -06-03    <guravage@caterpie.sen.cwi.nl>
 	* pardialog.h: Added default versions of this automatically generated file.
 	* pardialog.cpp: ditto.
 	* parameter.h: ditto.
 	* parameter.cpp: ditto.
 	* VirtualLeaf.pro: delete/generate  parameter.{h,cpp}and pardialog.{h,cpp} only if perl is installed.
  	* libplugin.pro: dito.

src/VirtualLeaf.cpp

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@@ @@ -101,63 +101,66 @@ public: @@
 class CellInfo {
 public:
   void operator() (Cell &c,std::ostream &os) const {
     os << "Cell " << c.index << " says: " << endl;
     os << "c.nodes.size() = " << c.nodes.size() << endl;
     for (list<Node *>::iterator i=c.nodes.begin();
 	 i!=c.nodes.end();
 	 i++) {
       cerr << (*i)->Index() << " ";
+    }
     cerr << endl;
+  }
 };
 double PINSum(Cell &c) {
   return c.Chemical(1) + c.SumTransporters(1);// + c.ReduceCellAndWalls<double>( complex_PijAj );
+}
 class DrawCell {
 public:
   void operator() (Cell &c,QGraphicsScene &canvas, MainBase &m) const {
     if (m.ShowBorderCellsP() || c.Boundary()==Cell::None) {
-      if (!m.ShowBoundaryOnlyP() && !m.HideCellsP())
+      if (!m.ShowBoundaryOnlyP() && !m.HideCellsP()) {
 	if (m.ShowToolTipsP()) {
 	  QString info_string=QString("Cell %1, chemicals: ( %2, %3, %4, %5, %6)\n %7 of PIN1 at walls.\n Area is %8\n PIN sum is %9\n Circumference is %10\n Boundary type is %11").arg(c.Index()).arg(c.Chemical(0)).arg(c.Chemical(1)).arg(c.Chemical(2)).arg(c.Chemical(3)).arg(c.Chemical(4)).arg(c.SumTransporters(1)).arg(c.Area()).arg(PINSum(c)).arg(c.Circumference()).arg(c.BoundaryStr());
 	  info_string += "\n" + c.printednodelist();
 	  c.Draw(&canvas, info_string);
 	} else {
 	  c.Draw(&canvas);
+	}
       if (m.ShowCentersP())
+      }
       if (m.ShowCentersP()){
 	c.DrawCenter(&canvas);
       if (m.ShowFluxesP())
+      }
       if (m.ShowFluxesP()){
 	c.DrawFluxes(&canvas, par.arrowsize);
+    }
+  }
+  }
 };
 Mesh mesh;
 bool batch=false;
 void MainBase::Plot(int resize_stride) {
   clear();
   static int count=0;
   if (resize_stride) {
     if ( !((++count)%resize_stride) ) {
       FitLeafToCanvas();
+    }
+  }
   mesh.LoopCells(DrawCell(),canvas,*this);
   if (ShowNodeNumbersP())
     mesh.LoopNodes( bind2nd (mem_fun_ref ( &Node::DrawIndex), &canvas ) ) ;
   if (ShowCellNumbersP())
     mesh.LoopCells( bind2nd (mem_fun_ref ( &Cell::DrawIndex), &canvas ) ) ;
   if (ShowCellAxesP())
     mesh.LoopCells( bind2nd (mem_fun_ref ( &Cell::DrawAxis), &canvas ) );
@@ @@ -298,48 +301,51 @@ TIMESTEP { @@
+    }
   } else {
     /*  TransportFunction *transport_f = new CelltoCellTransport();
 	CellReaction *cellreaction_f = new CellDynamics();
 	WallReaction *wall_f = new WallDynamics();
 	mesh.ReactDiffuse_New(transport_f, cellreaction_f, wall_f, par.rd_dt);*/
     mesh.ReactDiffuse(par.rd_dt);
     Plot(par.resize_stride);
+  }
   i++;
   return mesh.getTime();
+}
 /* Called if a cell is clicked */
 void Cell::OnClick(QMouseEvent *e) {
   e = NULL; // use assignment merely to obviate compilation warning
   /* #ifdef HAVE_QWT
   // Launch DataPlot window
   QStringList curvenames;
   for (int i=0;i<NChem();i++) {
   curvenames += QString("Chem #%1").arg(i);
+  }
   PlotDialog *plot = new PlotDialog((Main *)main_window, QString("Monitor for Cell %1").arg(Index()), curvenames);
   QObject::connect(this, SIGNAL(ChemMonValue(double, double *)),
   plot, SLOT(AddValue(double,double *)));
   #endif
   */
   //getMesh().plugin->OnClick(*this);
+}
 /* Custom message handler - Default appends a newline character to the end of each line. */
 void vlMessageOutput(QtMsgType type, const char *msg)
+{
   switch (type) {
   case QtDebugMsg:
     //fprintf(stderr, "Debug: %s\n", msg);
     cerr << msg << flush;
     break;
   case QtWarningMsg:

src/apoplastitem.cpp

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@@ @@ -13,66 +13,63 @@ @@
  *  but WITHOUT ANY WARRANTY; without even the implied warranty of
  *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  *  GNU General Public License for more details.
+ *
  *  You should have received a copy of the GNU General Public License
  *  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.
+ *
  *  Copyright 2010 Roeland Merks.
+ *
  */
 #include <string>
 #include <QGraphicsScene>
 #include "canvas.h"
 #include "parameter.h"
 #include "node.h"
 #include "apoplastitem.h"
 static const std::string _module_id("$Id$");
 ApoplastItem::ApoplastItem( Wall *w, QGraphicsScene *canvas )
 : QGraphicsLineItem( 0, canvas ), SimItemBase( w, canvas){
 	extern Parameter par;
 	setColor();
 	// line with "PIN1"is a bit inside the cell wall
 	Vector edgevec = (*(w->N2())) - (*(w->N1()));
 	Vector perp = edgevec.Normalised().Perp2D();
 	Vector offs = Cell::Offset();
 	double factor = Cell::Factor();
 	Vector from = ( offs + *(w->N1()) ) * factor;// + (wn==1?-1:1) * par.outlinewidth;// * 0.2 * factor * perp;
 	Vector to = ( offs + *(w->N2()) ) *factor;// + (wn==1?-1:1) * par.outlinewidth;// * 0.2 * factor * perp;
 	setLine(( from.x ),
 			( from.y ),
 			( to.x ),
 			( to.y ) );
 	setZValue(12);
+}
 void ApoplastItem::setColor(void) {
 	QColor diffcolor;
 	static const QColor purple("Purple");
 	static const QColor blue("blue");
 	Wall *w=&getWall();
 	double val = w->getApoplast(2);
 	diffcolor.setRgb( 0,0,(int)( ( val / (1 + val) )*255.));
 	setPen (QPen(diffcolor, 20) );
+}
 void ApoplastItem::OnClick(QMouseEvent *e) {
   e = NULL; // merely to obviate compile time warning
+}

src/build_models/ChangeLog

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Show inline comments

 -06-15    <guravage@caterpie.sen.cwi.nl>
 	* testplugin.cpp (CelltoCellTransport) Use NULL assignment merely to obviate compilation warnings.
 	(WallDynamics): Ditto.
 	(CellDynamics): Ditto.
 	(OnDivide): Ditto.
 	* meinhardtplugin.cpp (OnDivide): Use NULL assignment merely to obviate compilation warnings.
 	* (WallDynamics): Ditto.
 	* auxingrowthplugin.cpp (OnDivide): Use NULL assignment merely to obviate compilation warnings.
 -06-03    <guravage@caterpie.sen.cwi.nl>
 	* Makefile: Added top-level Makefile.
 -05-10    <guravage@caterpie.sen.cwi.nl>
 	* plugin_test.pro: Added -fPIC option to QMAKE_CXXFLAGS.
 	* plugin_meinhardt.pro: ditto
 	* plugin_auxingrowth.pro: ditto

src/build_models/auxingrowthplugin.cpp

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@@ @@ -17,48 +17,50 @@ @@
+ *
  *  Copyright 2010 Roeland Merks.
+ *
  */
 #include <QObject>
 #include <QtGui>
 #include "../simplugin.h"
 #include "parameter.h"
 #include "wallbase.h"
 #include "cellbase.h"
 #include "auxingrowthplugin.h"
 #include "far_mem_5.h"
 static const std::string _module_id("$Id$");
 bool batch = false;
 // To be executed after cell division
 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
 	double area1 = daughter1->Area(), area2 = daughter2->Area();
 	double tot_area = area1 + area2;
 	daughter1->SetChemical(0,daughter1->Chemical(0)*(area1/tot_area));
 	daughter2->SetChemical(0,daughter2->Chemical(0)*(area2/tot_area));
 	// After divisions, parent and daughter cells get a standard stock of PINs.
 	daughter1->SetChemical(1, par->initval[1]);
 	daughter2->SetChemical(1, par->initval[1]);
 	// Reset transporter values of parent and daughter
 	QList<WallBase *> walls;
 	foreach(WallBase *w, walls) {
 		w->setTransporter(daughter1, 1, 0.);
+	}
 	//daughter1.LoopWalls(Wall::setTransporter(&daughter1, 1, 0.));
 	/* for (list<Wall *>::const_iterator w=daughter2.walls.begin();
 		 w!=daughter2.walls.end();
 		 w++) {

src/build_models/meinhardtplugin.cpp

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@@ @@ -14,49 +14,50 @@ @@
+ *
  *  You should have received a copy of the GNU General Public License
  *  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.
+ *
  *  Copyright 2010 Roeland Merks.
+ *
  */
 #include <QObject>
 #include <QtGui>
 #include "../simplugin.h"
 #include "parameter.h"
 #include "warning.h"
 #include "wallbase.h"
 #include "cellbase.h"
 #include "meinhardtplugin.h"
 static const std::string _module_id("$Id$");
 bool batch = false;
 // To be executed after cell division
 void MeinhardtPlugin::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) {
   parent_info = NULL;
   daughter1 = daughter2 = NULL;
+}
 void MeinhardtPlugin::SetCellColor(CellBase *c, QColor *color) {
 	if (fpclassify(c->Chemical(0))==FP_NAN) {
 		// somehow the function isnan doesn't work properly on my system... SuSE Linux
 		// 10.0 64-bits (isnan seems not be implemented using fpclassify).
 		MyWarning::warning("Whoops! Numerical instability!!");
 		color->setNamedColor("red");
 	} else {
 		double range_min = 0.;//, range_max = 1.;
 		if (c->Chemical(0)<range_min) {
 			MyWarning::warning("Whoops! Numerical instability!!");
 			color->setNamedColor("blue");
 		} 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.) );
+		}
+	}
+}
 void MeinhardtPlugin::CellHouseKeeping(CellBase *c) {
@@ @@ -83,48 +84,49 @@ void MeinhardtPlugin::CelltoCellTranspor @@
 	// No flux boundaries for all chemicals, except activator: boundary is sink
   if (w->C1()->BoundaryPolP() || w->C2()->BoundaryPolP()) {
 		if (w->C1()->BoundaryPolP()) {
 			dchem_c2[1] -=  w->Length() * ( par->D[1] ) * ( w->C2()->Chemical(1) );
 			} else {
 			dchem_c1[1] -=  w->Length() * ( par->D[1] ) * ( w->C1()->Chemical(1) );
+			}
 		return;
+		}
     // Passive fluxes (Fick's law)
     for (int c=0;c<NChem();c++) {
 		double phi = w->Length() * ( par->D[c] ) * ( w->C2()->Chemical(c) - w->C1()->Chemical(c) );
 		dchem_c1[c] += phi;
 		dchem_c2[c] -= phi;
+	}
+}
 void MeinhardtPlugin::WallDynamics(Wall *w, double *dw1, double *dw2) {
   w = NULL;
 	for (int c = 0;c<NChem();c++) {
 		dw1[c] = 0.; dw2[c] = 0.;
+    }
+}
 void MeinhardtPlugin::CellDynamics(CellBase *c, double *dchem) {
 	double Y = c->Chemical(0);
 	double A = c->Chemical(1);
 	double H = c->Chemical(2);
 	double S = c->Chemical(3);
 	//double expansin = c->Chemical(4);
     dchem[0] = ( par->d * A - par->e * Y + Y*Y/(1 + par->f * Y*Y ) );
 	dchem[1] = ( par->c * A*A*S/H - par->mu * A + par->rho0*Y );
 	dchem[2] = ( par->c * A*A*S - par->nu*H + par->rho1*Y );
 	dchem[3] = ( par->c0 - par->gamma*S - par->eps * Y * S );
 	//dchem[4] = ( -par->expansindecay * expansin );
 	//for (int i=0;i<4;i++) { cerr << "[ " << dchem[i] << " ]"; } cerr << endl;
 //	cerr << "Chemicals: "; for (int i=0;i<NChem();i++) { cerr << c->Chemical(i) << " "; } cerr << endl;
 // test:	dchem[0] = 0.01 * c->Chemical(0) * ( 1. - c->Chemical(0));

src/build_models/testplugin.cpp

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@@ @@ -15,52 +15,63 @@ @@
  *  You should have received a copy of the GNU General Public License
  *  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.
+ *
  *  Copyright 2010 Roeland Merks.
+ *
  */
 #include <QObject>
 #include <QtGui>
 #include "simplugin.h"
 #include "parameter.h"
 #include "wallbase.h"
 #include "cellbase.h"
 #include "testplugin.h"
 static const std::string _module_id("$Id$");
 bool batch = false;
 // To be executed after cell division
 void TestPlugin::OnDivide(ParentInfo *parent_info, CellBase *daughter1, CellBase *daughter2) {
   parent_info = NULL;
   daughter1 = daughter2 = NULL;
+}
 void TestPlugin::SetCellColor(CellBase *c, QColor *color) {
 	static QStringList colors;
 	if (colors.size()==0) {
 		colors << "red" << "green" << "blue";
+	}
 	color->setNamedColor(colors[c->Index()%colors.size()]);
+}
 void TestPlugin::CellHouseKeeping(CellBase *c) {
 	c->EnlargeTargetArea(par->cell_expansion_rate);
 	if (c->Area() > par->rel_cell_div_threshold * c->BaseArea() ) {
 		c->Divide();
+	}
+}
 void TestPlugin::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) {}
 void TestPlugin::WallDynamics(Wall *w, double *dw1, double *dw2) {}
 void TestPlugin::CellDynamics(CellBase *c, double *dchem) { }
 void TestPlugin::CelltoCellTransport(Wall *w, double *dchem_c1, double *dchem_c2) {
   w = NULL;
   dchem_c1 = dchem_c2 = NULL;
+}
 void TestPlugin::WallDynamics(Wall *w, double *dw1, double *dw2) {
   w = NULL;
   dw1 = dw2 = NULL;
+}
 void TestPlugin::CellDynamics(CellBase *c, double *dchem) {
   c = NULL;
   dchem=NULL;
+}
 Q_EXPORT_PLUGIN2(testplugin, TestPlugin)

src/canvas.cpp

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@@ @@ -80,48 +80,51 @@ @@
 #include "psb.xpm"
 #include "cwi.xpm"
 static const std::string _module_id("$Id$");
 // We use a global variable to save memory - all the brushes and pens in
 // the mesh are shared.
 #define QUOTE_ME(s) QUOTE_ME_2NDLEV(s)
 #define QUOTE_ME_2NDLEV(s) #s
 static QColor dark_red("darkRed");
 static const int imageRTTI = 984376;
 extern Parameter par;
 const QString Main::caption("Virtual leaf");
 const QString Main::caption_with_file("Virtual leaf: %1");
 FigureEditor::FigureEditor(
 			   QGraphicsScene& c, Mesh &m, QWidget* parent,
 			   const char* name, Qt::WindowFlags f) :
   QGraphicsView(&c,parent), mesh(m)
+{
   name = NULL; // use these two assignments merely to obviate compile time warnings
   f = Qt::Widget;
   intersection_line = 0;
   //angle_line = 0;
   setInteractive(true);
   moving = 0;
   rotation_mode = false;
+}
 void FigureEditor::clear()
+{
   QList<QGraphicsItem *> list = scene()->items();
   QList<QGraphicsItem *>::Iterator it = list.begin();
   for (; it != list.end(); ++it) {
     delete *it;
+  }
+}
  void FigureEditor::wheelEvent(QWheelEvent *event)
+ {
    scaleView(pow((double)2, -event->delta() / 240.0));
+ }
 void FigureEditor::scaleView (qreal scaleFactor)
@@ @@ -132,50 +135,48 @@ void FigureEditor::scaleView (qreal scal @@
+}
 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());
     QPainter *painter=new QPainter(image);
     render(painter);
     image->save(QString(fname),format);
     delete painter;
     delete image;
+}
 //void FigureEditor::contentsMousePressEvent(QMouseEvent* e)
 void FigureEditor::mousePressEvent(QMouseEvent* e)
+{
   static QList<Node*> selected;
   emit MousePressed();
   //QPointF p = matrix().inverted().map(e->pos());
   QPointF p = mapToScene(e->pos());
   NodeItem *item;
 #ifdef QDEBUG
   qDebug() << endl << "MousePressEvent location: (" << p.x() << "," << p.y() << ")." << endl;
   qDebug() << "Magnification:  " << Cell::Magnification() << endl;
   qDebug() << "Offsets:  " << Cell::Offset() << endl;
 #endif
   /*  if (dynamic_cast<Main *>(parent())->RotationModeP()) {
   // if in rotation mode, exit it upon a mouse click
   dynamic_cast<Main *>(parent())->ExitRotationMode();
   }*/
   QList<QGraphicsItem *> l=scene()->items(p);
 #ifdef QDEBUG
   qDebug() << "MousePressEvents, items: " << l.size() << endl;
   qDebug() << "Mouse button modifier: " << e->modifiers() << endl;
 #endif
     /*  if (rotation_mid_point) {
     // calculate rotation angle alpha
     QPointF q_v1 = intersection_line->line().p2();
@@ @@ -210,49 +211,49 @@ void FigureEditor::mousePressEvent(QMous @@
     return;
     }*/
     if (e->button()==Qt::RightButton || l.size()==0) {
       //cerr << "Drawing an intersection line from " << p.x() << ", " << p.y() << endl;
       intersection_line = new QGraphicsLineItem( 0, scene() );
       intersection_line->setPen( QPen( QColor("red"), 3, Qt::DashLine ) );
       intersection_line->setLine( QLineF(p,p) );
       intersection_line->setZValue( 100 );
       intersection_line->show();
+    }
     for (QList<QGraphicsItem *>::Iterator it=l.begin(); it!=l.end(); ++it) {
       /*if ( (*it)->rtti() == imageRTTI ) {
 	ImageItem *item= (ImageItem*)(*it);
 	if ( !item->hit( p ) )
 	continue;
 	}*/
       #ifdef QDEBUG
       qDebug() << typeid(**it).name() << endl;
-      #endif QDEBUG
       #endif
       if ( !strcmp(typeid(**it).name(),"8NodeItem")) {
 	//moving = dynamic_cast<NodeItem*>(*it);
 	//moving = *it;
 	//moving_start = p;
 	stringstream data_strstream;
 	data_strstream << (dynamic_cast<NodeItem*>(*it))->getNode();
 	dynamic_cast<Main *>(parent())->UserMessage(QString(data_strstream.str().c_str()));
 	(dynamic_cast<NodeItem*>(*it))->OnClick(e->button());
+      }
       else
 	if ( !strcmp(typeid(**it).name(),"8CellItem") ) {
 	  Cell &c=((dynamic_cast<CellItem *>(*it))->getCell());
 	  //static int old_stride=100;
 	  //if (!c.Source()) {
 	  /* if (!c.Source()) {
 	     c.SetChemical(0,par.cellsource);
 	     //flag=true;
 	     //c.SetSource(0,par.cellsource);
 	     //c.Fix();
 	     //cerr << "Setting source\n";

src/cell.cpp

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Show inline comments

@@ @@ -1792,49 +1792,49 @@ void Cell::DrawAxis(QGraphicsScene *c) c @@
 	//cerr << "Length is "  << length << endl;
 	long_axis.Normalise();
 	Vector short_axis=long_axis.Perp2D();
 	Vector centroid = Centroid();
 	Vector from = centroid - 0.5 * width * short_axis;
 	Vector to = centroid + 0.5 * width *short_axis;
 	QGraphicsLineItem *line = new QGraphicsLineItem(0, c);
 	line->setPen( QPen(QColor(par.arrowcolor),2) );
 	line->setZValue(2);
 	line->setLine( ( (offset[0]+from.x)*factor ),
 				  ( (offset[1]+from.y)*factor ),
 				  ( (offset[0]+to.x)*factor ),
 				  ( (offset[1]+to.y)*factor ) );
 	line->setZValue(10);
 	line->show();
+}
 void Cell::DrawStrain(QGraphicsScene *c) const {
-	></i>
+  c = NULL; // assignment merely to obviate compilation warning
 	MyWarning::warning("Sorry, Cell::DrawStrain temporarily not implemented.");
 	/* Vector long_axis;
 	double width;
 	Length(&long_axis, &width);
 	//cerr << "Length is "  << length << endl;
 	long_axis.Normalise();
 	Vector short_axis=long_axis.Perp2D();
 	//  To test method "Strain" temporarily substitute "short_axis" for "strain"
 	Vector strain = Strain();
 	//strain.Normalise();
 	//static ofstream strainf("strain.dat");
 	//strainf << strain.Norm() << endl;
 	Vector centroid = Centroid();
 	// Vector from = centroid - 0.5 * width * short_axis;
     // Vector to = centroid + 0.5 * width *short_axis;
 	Vector from = centroid - 0.5 * strain;
 	Vector to = centroid + 0.5 * strain;
 	QGraphicsArrowItem *arrow = new QGraphicsArrowItem(0, c);
 	arrow->setPen( QPen(QColor(par.arrowcolor),100) );
 	arrow->setLine( ( (offset[0]+from.x)*factor ),

src/cellbase.h

➞

Show inline comments

@@ @@ -469,34 +469,35 @@ protected: @@
     // for length constraint
     mutable double intgrl_xx, intgrl_xy, intgrl_yy, intgrl_x, intgrl_y;
     bool source;
     Vector cellvec;
 	// STATIC DATAMEMBERS MOVED TO CLASS
 	static CellsStaticDatamembers *static_data_members;
 	double source_conc;
     int source_chem;
     // PRIVATE MEMBER FUNCTIONS
     inline static void ClearNCells(void) {
       NCells()=0;
+    }
     bool marked;
     int div_counter;
 };
 ostream &operator<<(ostream &os, const CellBase &v);
 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

src/forwardeuler.cpp

➞

Show inline comments

@@ @@ -46,48 +46,52 @@ const double ForwardEuler::Safety = 0.9 @@
 const double ForwardEuler::PGrow = -0.2;
 const double ForwardEuler::Pshrnk = -0.25;
 const double ForwardEuler::Errcon = 1.89e-4;
 const double ForwardEuler::Maxstp = 10000000;
 const double ForwardEuler::Tiny = 1.0e-30;
 /* User storage for intermediate results. Preset kmax and dxsav in the calling program. If kmax =
 results are stored at approximate intervals dxsav in the arrays xp[1..kount], yp[1..nvar]
    [1..kount], where kount is output by odeint. Defining declarations for these variables, with
    memoryallo cations xp[1..kmax] and yp[1..nvar][1..kmax] for the arrays, should be in
    the calling program.*/
 void ForwardEuler::odeint(double *ystart, int nvar, double x1, double x2, double eps, double h1, double hmin, int *nok, int *nbad)
 /* Runge-Kutta driver with adaptive stepsize control. Integrate starting values ystart[1..nvar]
   from x1 to x2 with accuracy eps, storing intermediate results in global variables. h1 should
   be set as a guessed first stepsize, hmin as the minimum allowed stepsize (can be zero). On
   output nok and nbad are the number of good and bad (but retried and fixed) steps taken, and
   ystart is replaced byv alues at the end of the integration interval. derivs is the user-supplied
   routine for calculating the right-hand side derivative, while rkqs is the name of the stepper
   routine to be used. */
+{
   static bool warning_issued = false;
   eps = hmin = 0.0; // use assignment merely to obviate compilation warning
   nbad = nok = NULL;
   if (!warning_issued) {
     cerr << "Using inaccurate method ForwardEuler\n";
     warning_issued=true;
     //MyWarning::warning("Using inaccurate method ForwardEuler");
+  }
   // N.B. Not for serious use and not fully usage compatible with RungeKutta
   // simply for testing API of integrator.
   double *y,*dydx;
   y=new double[nvar];
   dydx=new double[nvar];
   double x=x1;
   for (int i=0;i<nvar;i++) y[i]=ystart[i];
   //if (kmax > 0) xsav=x-dxsav*2.0; //Assures storage of first step.
   dydx=new double[nvar];
   for (int nstp=0;nstp<Maxstp;nstp++) {
     derivs(x,y,dydx);
     if (kmax > 0 && kount < kmax-1) {

src/mainbase.h

➞

Show inline comments

@@ @@ -99,48 +99,49 @@ class MainBase { @@
     //cerr << "Initializing Pixmap\n";
     cerr << "Saving to file " << fname << endl;
     QPixmap *image=new QPixmap(width, (int) (((double)canvas.height()/
     (double)canvas.width())*((double)width)));
     //QPicture *image = new QPicture();
     //cerr << "Done initializing QPixmap image(640, " << (((double)canvas.height()/(double)canvas.width())*640.) << ")\n";
     QPainter im(image);
     //cerr << "Done initializing image\n";
     im.scale((double)width/canvas.width(),(double)width/canvas.width());
     canvas.render(&im, QRectF(0,0,canvas.width(),canvas.height()) );
     //im.end();
     image->save(QString(fname), format);
     }*/
     void Save(const char *fname, const char *format, int sizex=640, int sizey=480);
     void CutSAM(void);
     void Plot(int resize_stride=10);
     virtual void UserMessage(QString message, int timeout = 0) {
       timeout = 0; // merely to obviate 'warning unused parameter' message
       cerr << message.toAscii().constData() << endl;
+    }
     Mesh &mesh;
  protected:
     QGraphicsScene &canvas;
     virtual xmlNode *XMLSettingsTree(void) const;
  protected:
     bool showcentersp;
     bool showmeshp;
     bool showbordercellp;
     bool shownodenumbersp;
     bool showcellnumbersp;
     bool showcellsaxesp;
     bool showcellstrainp;
     bool movieframesp;
     bool showboundaryonlyp;
     bool showwallsp;
 	bool showapoplastsp;
     bool showfluxesp;
     bool dynamicscellsp;
     bool showtooltipsp;
 	bool hidecellsp;

src/mesh.cpp

➞

Show inline comments

@@ @@ -1637,49 +1637,49 @@ void Mesh::RepairBoundaryPolygon(void) { @@
   foreach(Node* node, nodes) {
     qDebug() << *node;
+  }
   qDebug() << endl;
   qDebug() << "WALLS:" << endl;
   foreach(Wall* wall, walls) {
     qDebug() << *wall;
+  }
   qDebug() << endl;
   qDebug() << "CELLS:" << endl;
   foreach(Cell* cell, cells) {
     qDebug() << *cell;
+  }
   qDebug() << endl;
   #endif
 #endif
+}
 Node* Mesh::findNextBoundaryNode(Node* boundary_node) {
   bool found_next_boundary_node = false;
   Node *next_boundary_node;
+  Node *next_boundary_node = NULL;
   set<int> boundary_node_owners; // This is a list of the current boundary node's owners' Ids
   vector<int> neighborIds; // A list of the current boundary node's owners' 2nd neighbor Ids
   vector<set<int> *>  nodeOwners; // A vector of set pointers where each set contains the owner Ids of the nodes in the neighborIds list.
   vector<int> intersection; // set intersection result
   // The next boundary node is that which has only one owner in common with the current boundary node
   for (list<Neighbor>::iterator it=boundary_node->owners.begin(); it!=boundary_node->owners.end(); ++it) {
     if (it->cell->Index() != -1) boundary_node_owners.insert(it->cell->Index()); // Save each of the current boundary node's owners' Ids - except the boundary polygon
     set<int> *owners = new set<int>; // create a set to hold a 2nd neighbor's owners' Ids
     nodeOwners.push_back(owners);
     neighborIds.push_back(it->nb2->Index());
     foreach(Neighbor neighbor, it->nb2->owners){
       if (neighbor.cell->Index() != -1) owners->insert(neighbor.cell->Index()); // Save second neighbors' owners' Ids - except the boundary polygon
+    }
+  }
   vector<int>::iterator itt = neighborIds.begin();
   vector<set<int> *>::iterator it = nodeOwners.begin();
   #ifdef QDEBUG
   qDebug() << "Boundary node: " <<  boundary_node->Index() << " is owned by the following cells: ";
   foreach (int i, boundary_node_owners){
     qDebug() << i << "  ";
+  }
   qDebug() << endl;

src/nodeitem.cpp

➞

Show inline comments

@@ @@ -51,48 +51,49 @@ void NodeItem::userMove(double dx, doubl @@
 void NodeItem::paint(QPainter *painter, const QStyleOptionGraphicsItem *option, QWidget *)
+{
   // from Qt4.2 example: "elastic nodes"
   //painter->setPen(Qt::NoPen);
   //painter->setBrush(Qt::darkGray);
   //painter->drawEllipse(-70, -70, 200, 200);
   /* QRadialGradient gradient(-30, -30, 100);
   if (option->state & QStyle::State_Sunken) {
   gradient.setCenter(30, 30);
   gradient.setFocalPoint(30, 30);
   gradient.setColorAt(1, QColor(Qt::yellow).light(120));
   gradient.setColorAt(0, QColor(Qt::darkYellow).light(120));
   } else {
   gradient.setColorAt(0, Qt::yellow);
   gradient.setColorAt(1, Qt::darkYellow);
+  }
   painter->setBrush(gradient); */
   option = NULL; // use assignment merely to obviate compilation warning
   painter->setBrush(brush);
   painter->setPen(Qt::NoPen);
   // const static double mag=20.;
   painter->drawEllipse(ellipsesize);
+}
 QPainterPath NodeItem::shape() const
+{
     QPainterPath path;
     path.addEllipse(ellipsesize);
     return path;
+}
 QRectF NodeItem::boundingRect() const
+{
   qreal penwidth = 0;// painter->pen()->widthF();
   return QRectF(ellipsesize.x()-penwidth/2.,ellipsesize.y()-penwidth/2.,
 		ellipsesize.width()+penwidth, ellipsesize.height()+penwidth);
+}
 // polymorphic OnClick functions
 void NodeItem::OnClick(void) {

src/output.cpp

➞

Show inline comments

@@ @@ -96,49 +96,48 @@ int YesNoP(const char *message) { @@
 // 			  ,filename);
 // 	  exit(0);
 // 	}
 //   }
 //   if (fp!=NULL) // file existed, but user wants to overwrite
 // 	fclose(fp);
 //   if ((fp=fopen(filename,"w"))==NULL) {
 // 	fprintf(stderr," Could not open file %s for writing, exiting... \n"
 // 			,filename);
 // 	exit(0);
 //   }
 //   return fp;
 // }
 */
 FILE *OpenWriteFile(const char *filename)
+{
   char fname[FNAMESIZE];
   FILE *fp;
   extern Parameter par;
   fprintf(stderr,"Opening %s for writing\n",filename);
   if(FileExistsP(filename)==TRUE) {
     if (false/*par.interactive*/) {
       char *message=(char *)malloc(2000*sizeof(char));
       if (!YesNoP("File exists, overwrite?")) {
 	sprintf(message," Could not open file %s for writing, exiting... \n"
 		,filename);
 	//exit(0);
 	throw(message);
+      }
     } else {
       /* Rename old file */
       sprintf(fname, "%s~",filename);
       rename(filename, fname);
+    }
+  }
   strncpy(fname, filename, FNAMESIZE-1);
   if ((fp=fopen(fname,"w"))==NULL) {
@@ @@ -189,52 +188,50 @@ FILE *OpenWriteFile(const char *filename @@
   //  strncpy(fname, gzname, FNAMESIZE-1);
   char *command=new char[20+sizeof(gzname)];
   sprintf(command, "gzip -c > %s", gzname);
   if ((fp=popen(command,"w"))==NULL) {
     fprintf(stderr," Could not open file %s for writing: "
 	    ,fname);
     perror("");
     exit(-1);
+  }
   delete[] command;
   return fp;
+}
 */
 FILE *OpenReadFile(const char *filename)
+{
   FILE *fp;
   fprintf(stderr,"Opening %s for reading\n",filename);
   if((OpenFileAndCheckExistance(&fp,filename,"r"))==FALSE) {
     char *message=(char *)malloc(2000*sizeof(char));
     sprintf(message," File %s not found or empty, exiting... \n"
 			,filename);
     sprintf(message," File %s not found or empty, exiting... \n" ,filename);
     throw(message);
+  }
   return fp;
+}
 char *ReadLine(FILE *fp)
+{
   /* does almost the same as fgetln(), but DEC Unix doesn't understand
 	 fgetln(). Also I want my function to return a real C string,
 	 terminated by a \0. */
   /* The function reads a line from file *fp, and returns a pointer to the
 	 line read, which can be freed with a normal free(). The length of the
 	 string is written in *len */
 #define INITIAL_BUFSIZE 100
   char *tmpstring;
   int character;
   long bufsize;
   char *line;
   int pos;
   CheckFile(fp);

src/qcanvasarrow.h

➞

Show inline comments

@@ @@ -15,48 +15,51 @@ @@
  *  GNU General Public License for more details.
+ *
  *  You should have received a copy of the GNU General Public License
  *  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.
+ *
  *  Copyright 2010 Roeland Merks.
+ *
  */
 #ifndef _QCANVASARROW_H_
 #define _QCANVASARROW_H_
 #include <QGraphicsScene>
 class QGraphicsArrowItem : public QGraphicsLineItem {
  public:
   QGraphicsArrowItem(QGraphicsItem *parent, QGraphicsScene *c) : QGraphicsLineItem(parent, c) {
   };
     void paint ( QPainter *p, const QStyleOptionGraphicsItem *option,
 		 QWidget *widget ) {
       widget = NULL; //use assignment merely to obviate compilation warning
       option = NULL;
       // construct arrow head
       QPointF start=line().p1();
       QPointF end=line().p2();
       QPointF mid=start + (3./4.)*(end-start);
       double vx=end.x()-start.x();
       double vy=end.y()-start.y();
       double length = sqrt(vx*vx+vy*vy);
       if (length==0) return;
       // perpendicular vector
       double px=-vy/length;
       double py=vx/length;
       // Arrow head lines go from end point
       // to points about 3/4 of the total arrow, extending sideways about 1/4
       // of the arrow length.
       QPointF arwp1 = mid + QPointF( (int)( (length/4.)*px ),
 				   (int)( (length/4.)*py ) );
       QPointF arwp2 = mid - QPointF( (int)( (length/4.)*px ),
 				   (int)( (length/4.)*py ) );

src/simitembase.cpp

➞

Show inline comments

@@ @@ -5,33 +5,34 @@ @@
  *  The Virtual Leaf is free software: you can redistribute it and/or modify
  *  it under the terms of the GNU General Public License as published by
  *  the Free Software Foundation, either version 3 of the License, or
  *  (at your option) any later version.
+ *
  *  The Virtual Leaf is distributed in the hope that it will be useful,
  *  but WITHOUT ANY WARRANTY; without even the implied warranty of
  *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  *  GNU General Public License for more details.
+ *
  *  You should have received a copy of the GNU General Public License
  *  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.
+ *
  *  Copyright 2010 Roeland Merks.
+ *
  */
 #include <string>
 #include <QBrush>
 #include "simitembase.h"
 static const std::string _module_id("$Id$");
 SimItemBase::SimItemBase( void *v, QGraphicsScene *canvas ) {
   canvas = NULL; // use assignment merely to obviate compilation warning
     obj=v;
 };
 SimItemBase::~SimItemBase(void) {};
 void SimItemBase::userMove(double dx, double dy) {
+  dx = dy = 0.0; // use assignment merely to obviate compilation warning
 };

src/xmlwrite.cpp

➞

Show inline comments

@@ @@ -330,49 +330,49 @@ int Cell::XMLRead(xmlNode *cur) { @@
       xmlChar *nc = xmlGetProp(n, BAD_CAST "n");
       if (nc==0) {
 	unique_warning("Token \"n\" not found in xmlwrite.cpp at or around line no. 966");
+      }
       tmp_nodes.push_back(atoi( (char *)nc));
       xmlFree(nc);
+    }
     n = n->next;
+  }
   int nnodes = tmp_nodes.size();
   for (int i=0;i<nnodes;i++) {
     m->AddNodeToCell( this,
 		      m->nodes[tmp_nodes[i]],
 		      m->nodes[tmp_nodes[(nnodes+i-1)%nnodes]],
 		      m->nodes[tmp_nodes[(i+1)%nnodes]] );
+  }
   n = cur->xmlChildrenNode;
   while(n!=NULL) {
 	  if ((!xmlStrcmp(n->name, (const xmlChar *)"chem"))) {
-	    xmlChar *v_str = xmlGetProp(n, BAD_CAST "n");
 	    xmlNode *v_node = n->xmlChildrenNode;
 	    int nv=0;
 	    while (v_node!=NULL) {
 	      if ((!xmlStrcmp(v_node->name, (const xmlChar *)"val"))) {
 		if (nv>=Cell::NChem()) {
+		  {
 		    stringstream text;
 		    text << "Exception in Mesh::XMLRead: Too many chemical values given for cell(s). Ignoring remaining values.";
 		    //ThrowStringStream(text);
 		    unique_warning(text.str().c_str());
 		    break;
+		  }
+		}
 		xmlChar *nc = xmlGetProp(v_node, (const xmlChar *) "v");
 		if (nc==0) {
 		  unique_warning("Token \"v\" not found in xmlwrite.cpp at or around line no. 1002");
+		}
 		//double v = strtod( (char *)nc, 0 );
 		double v=standardlocale.toDouble((char *)nc, &ok);
 		if (!ok) MyWarning::error("Could not convert \"%s\" to double in XMLRead.",(char *)nc);
@@ @@ -886,49 +886,48 @@ void Mesh::XMLSave(const char *docname, @@
 	xmlSetDocCompressMode(doc,9);
 	xmlSaveFormatFileEnc(docname, doc, "UTF-8", 1);
 	/*free the document */
 	xmlFreeDoc(doc);
 	/*
 	 *Free the global variables that may
 	 *have been allocated by the parser.
 	 */
 	xmlCleanupParser();
 	/*
 	 * this is to debug memory for regression tests
 	 */
 	//xmlMemoryDump();
+}
 void Mesh::XMLReadSimtime(const xmlNode *a_node) {
   xmlNode *root_node;
   root_node = (xmlNode *)a_node;
   xmlNode *cur;
   xmlChar *strsimtime = xmlGetProp(root_node, BAD_CAST "simtime");
   if (strsimtime) {
     //double simtime = strtod((const char *)strsimtime, 0);
     QLocale standardlocale(QLocale::C);
     bool ok;
     double simtime=standardlocale.toDouble((char *)strsimtime, &ok);
     if (!ok) MyWarning::error("Could not convert \"%s\" to double in XMLRead.",(char *)strsimtime);
       time = simtime;
 		cerr << "Simtime = " << strsimtime << endl;
 	} else {
 		cerr << "No simtime found in file \n";
 		time =0;
+	}
+}
 void Mesh::XMLReadPars(const xmlNode * a_node) {
 	xmlNode *root_node;
 	root_node = (xmlNode *)a_node;
 	par.XMLRead(root_node);
 	Seed(par.rseed);
 	MakeDir(par.datadir);
@@ @@ -1202,58 +1201,53 @@ void Mesh::XMLReadWalls(xmlNode *root, v @@
 	xmlFree(nc);
 	nc = xmlGetProp(cur, BAD_CAST "n2");
 	if (	nc==0) {
 	  unique_warning("Token \"n2\" not found in xmlwrite.cpp at or around line no. 801");
+	}
 	int n2 = atoi( (char *)nc);
 	xmlFree(nc);
 	nc = xmlGetProp(cur, BAD_CAST "length");
 	if (	nc==0) {
 	  unique_warning("Token \"length\" not found in xmlwrite.cpp at or around line no. 809");
+	}
 	//double length = strtod( (char *)nc, 0);
 	double length = standardlocale.toDouble((const char *)nc, &ok);
 	if (!ok) MyWarning::error("Could not convert \"%s\" to double in XMLRead.",(const char *)nc);
 	xmlFree(nc);
 	nc = xmlGetProp(cur, BAD_CAST "viz_flux");
 	double viz_flux;
+	double viz_flux = 0.0;
 	if (nc!=0) {
 	  //viz_flux = strtod( (char *)nc, 0);
-	  double viz_flux = standardlocale.toDouble((const char *)nc, &ok);
 	  viz_flux = standardlocale.toDouble((const char *)nc, &ok);
 	  if (!ok) MyWarning::error("Could not convert \"%s\" to double in XMLRead.",(const char *)nc);
 	} else {
 	  // if the info is not there, we really don't care.
 	  // It is just for visualization anyhow.
 	  viz_flux = 0.;
+	}
 	xmlFree(nc);
 	Wall::WallType wall_type;
+	{
 	  xmlChar *v_str = xmlGetProp(cur, BAD_CAST "wall_type");
 	  if (v_str != 0) {
 	    if (!xmlStrcmp(v_str, (const xmlChar *)"aux_source")) {
 	      wall_type = Wall::AuxSource;
 	    } else {
 	      if (!xmlStrcmp(v_str, (const xmlChar *)"aux_sink")) {
 		wall_type = Wall::AuxSink;
 	      } else {
 		wall_type = Wall::Normal;
+	      }
+	    }
 	    xmlFree(v_str);
 	  } else {
 	    wall_type = Wall::Normal;
+	  }
+	}
@@ @@ -1523,49 +1517,49 @@ void Mesh::XMLReadNodeSets(xmlNode *root @@
 		cur=cur->next;
+	}
+}
 void Mesh::XMLReadCells(xmlNode *root) {
 	for (vector<Cell *>::iterator i=cells.begin();
 		 i!=cells.end();
 		 i++) {
 		delete *i;
+	}
 	cells.clear();
 	Cell::NCells() = 0;
 	delete boundary_polygon;
 	xmlNode *cur = root->xmlChildrenNode;
 	while (cur!=NULL) {
 		Cell *new_cell=0;
-		static int count=0;
 		if ((!xmlStrcmp(cur->name, (const xmlChar *)"cell"))){
 			new_cell = new Cell(0,0);
 			new_cell->m = this;
 			cells.push_back(new_cell);
 		} else {
 			if ((!xmlStrcmp(cur->name, (const xmlChar *)"boundary_polygon"))) {
 				new_cell = boundary_polygon = new BoundaryPolygon(0,0);
 				boundary_polygon->m = this;
+			}
+		}
 		if (new_cell == 0) {
 			cur = cur->next;
 			continue;
+		}
 		new_cell->XMLRead(cur);
 		cur=cur->next;
+	}
+}
 void Mesh::XMLRead(const char *docname, xmlNode **settings, bool geometry, bool pars, bool simtime) {

0 comments (0 inline, 0 general)