# HG changeset patch
# User Michael Guravage <michael.guravage@cwi.nl>
# Date 2010-06-15 13:44:36
# Node ID 137d9d3a313a299a351f252e67c21e2823127171
# Parent  18e4f7f50259418d7bf744bad8782bfd803328c6

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

diff --git a/.hgignore b/.hgignore
--- a/.hgignore
+++ b/.hgignore
@@ -17,6 +17,8 @@ syntax: glob
 *moc_*.cpp
 src/default.par
 bin*
+TAGS
+BROWSE
 
 # switch to regexp syntax.
 syntax: regexp
diff --git a/src/ChangeLog b/src/ChangeLog
--- a/src/ChangeLog
+++ b/src/ChangeLog
@@ -1,10 +1,42 @@
 2010-06-15    <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.
diff --git a/src/VirtualLeaf.cpp b/src/VirtualLeaf.cpp
--- a/src/VirtualLeaf.cpp
+++ b/src/VirtualLeaf.cpp
@@ -122,7 +122,7 @@ 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());
 					
@@ -131,10 +131,13 @@ public:
 	} else {
 	  c.Draw(&canvas);
 	}
-      if (m.ShowCentersP())
+      }
+      if (m.ShowCentersP()){
 	c.DrawCenter(&canvas);
-      if (m.ShowFluxesP())
+      }
+      if (m.ShowFluxesP()){
 	c.DrawFluxes(&canvas, par.arrowsize);
+      }
     }
   }
 };
@@ -319,6 +322,9 @@ TIMESTEP {
 				
 /* 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;
diff --git a/src/apoplastitem.cpp b/src/apoplastitem.cpp
--- a/src/apoplastitem.cpp
+++ b/src/apoplastitem.cpp
@@ -34,8 +34,6 @@ 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
@@ -72,7 +70,6 @@ void ApoplastItem::setColor(void) {
 }
 
 void ApoplastItem::OnClick(QMouseEvent *e) {
-	
-	
+  e = NULL; // merely to obviate compile time warning
 }
 
diff --git a/src/build_models/ChangeLog b/src/build_models/ChangeLog
--- a/src/build_models/ChangeLog
+++ b/src/build_models/ChangeLog
@@ -1,3 +1,16 @@
+2010-06-15    <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.
+
 2010-06-03    <guravage@caterpie.sen.cwi.nl>
 
 	* Makefile: Added top-level Makefile.
diff --git a/src/build_models/auxingrowthplugin.cpp b/src/build_models/auxingrowthplugin.cpp
--- a/src/build_models/auxingrowthplugin.cpp
+++ b/src/build_models/auxingrowthplugin.cpp
@@ -38,6 +38,8 @@ 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;
diff --git a/src/build_models/meinhardtplugin.cpp b/src/build_models/meinhardtplugin.cpp
--- a/src/build_models/meinhardtplugin.cpp
+++ b/src/build_models/meinhardtplugin.cpp
@@ -35,7 +35,8 @@ 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) { 
@@ -104,6 +105,7 @@ void MeinhardtPlugin::CelltoCellTranspor
 }
 
 void MeinhardtPlugin::WallDynamics(Wall *w, double *dw1, double *dw2) {
+  w = NULL;
 	for (int c = 0;c<NChem();c++) {
 		dw1[c] = 0.; dw2[c] = 0.;
     }
diff --git a/src/build_models/testplugin.cpp b/src/build_models/testplugin.cpp
--- a/src/build_models/testplugin.cpp
+++ b/src/build_models/testplugin.cpp
@@ -36,7 +36,8 @@ 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) { 
@@ -58,9 +59,19 @@ void TestPlugin::CellHouseKeeping(CellBa
 	}
 }
 
-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)
diff --git a/src/canvas.cpp b/src/canvas.cpp
--- a/src/canvas.cpp
+++ b/src/canvas.cpp
@@ -101,6 +101,9 @@ FigureEditor::FigureEditor(
 			   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);
@@ -153,8 +156,6 @@ void FigureEditor::mousePressEvent(QMous
   //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;
@@ -231,7 +232,7 @@ void FigureEditor::mousePressEvent(QMous
 	}*/
       #ifdef QDEBUG
       qDebug() << typeid(**it).name() << endl;
-      #endif QDEBUG
+      #endif
 
       if ( !strcmp(typeid(**it).name(),"8NodeItem")) {
 	//moving = dynamic_cast<NodeItem*>(*it);
diff --git a/src/cell.cpp b/src/cell.cpp
--- a/src/cell.cpp
+++ b/src/cell.cpp
@@ -1813,7 +1813,7 @@ void Cell::DrawAxis(QGraphicsScene *c) c
 }
 
 void Cell::DrawStrain(QGraphicsScene *c) const {
-	
+  c = NULL; // assignment merely to obviate compilation warning
 	MyWarning::warning("Sorry, Cell::DrawStrain temporarily not implemented.");
 	/* Vector long_axis;
 	double width;
diff --git a/src/cellbase.h b/src/cellbase.h
--- a/src/cellbase.h
+++ b/src/cellbase.h
@@ -490,7 +490,8 @@ protected:
 ostream &operator<<(ostream &os, const CellBase &v);
 
 inline Vector PINdir(CellBase *here, CellBase *nb, Wall *w) {
-	return w->getTransporter( here, 1)  *  w->getInfluxVector(here);
+	  nb = NULL; // assignment merely to obviate compilation warning
+	  return w->getTransporter( here, 1)  *  w->getInfluxVector(here);
 }
 
 
diff --git a/src/forwardeuler.cpp b/src/forwardeuler.cpp
--- a/src/forwardeuler.cpp
+++ b/src/forwardeuler.cpp
@@ -67,6 +67,10 @@ void ForwardEuler::odeint(double *ystart
   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;
diff --git a/src/mainbase.h b/src/mainbase.h
--- a/src/mainbase.h
+++ b/src/mainbase.h
@@ -120,6 +120,7 @@ class MainBase  {
     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;
diff --git a/src/mesh.cpp b/src/mesh.cpp
--- a/src/mesh.cpp
+++ b/src/mesh.cpp
@@ -1658,7 +1658,7 @@ void Mesh::RepairBoundaryPolygon(void) {
 
 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.
diff --git a/src/nodeitem.cpp b/src/nodeitem.cpp
--- a/src/nodeitem.cpp
+++ b/src/nodeitem.cpp
@@ -72,6 +72,7 @@ void NodeItem::paint(QPainter *painter, 
   }
   
   painter->setBrush(gradient); */
+  option = NULL; // use assignment merely to obviate compilation warning
   
   painter->setBrush(brush);
   painter->setPen(Qt::NoPen);
diff --git a/src/output.cpp b/src/output.cpp
--- a/src/output.cpp
+++ b/src/output.cpp
@@ -117,7 +117,6 @@ FILE *OpenWriteFile(const char *filename
   char fname[FNAMESIZE];
 
   FILE *fp;
-  extern Parameter par;
 
   fprintf(stderr,"Opening %s for writing\n",filename);
 	
@@ -210,10 +209,8 @@ FILE *OpenReadFile(const char *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;
 }
diff --git a/src/qcanvasarrow.h b/src/qcanvasarrow.h
--- a/src/qcanvasarrow.h
+++ b/src/qcanvasarrow.h
@@ -35,7 +35,10 @@ class QGraphicsArrowItem : public QGraph
     
     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();
diff --git a/src/simitembase.cpp b/src/simitembase.cpp
--- a/src/simitembase.cpp
+++ b/src/simitembase.cpp
@@ -26,6 +26,7 @@
 static const std::string _module_id("$Id$");
 
 SimItemBase::SimItemBase( void *v, QGraphicsScene *canvas ) {
+  canvas = NULL; // use assignment merely to obviate compilation warning
     obj=v;
 };
 
@@ -33,5 +34,5 @@ SimItemBase::~SimItemBase(void) {};
 
 
 void SimItemBase::userMove(double dx, double dy) {
-
+  dx = dy = 0.0; // use assignment merely to obviate compilation warning
 };
diff --git a/src/xmlwrite.cpp b/src/xmlwrite.cpp
--- a/src/xmlwrite.cpp
+++ b/src/xmlwrite.cpp
@@ -351,7 +351,7 @@ int Cell::XMLRead(xmlNode *cur)  {
   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) {
@@ -907,7 +907,6 @@ void Mesh::XMLReadSimtime(const xmlNode 
 	
   xmlNode *root_node;
   root_node = (xmlNode *)a_node;
-  xmlNode *cur;
   xmlChar *strsimtime = xmlGetProp(root_node, BAD_CAST "simtime");
   
   
@@ -1223,16 +1222,11 @@ void Mesh::XMLReadWalls(xmlNode *root, v
 				
 	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);
 				
@@ -1544,7 +1538,7 @@ void Mesh::XMLReadCells(xmlNode *root) {
 	while (cur!=NULL) {
 		
 		Cell *new_cell=0;
-		static int count=0;
+
 		if ((!xmlStrcmp(cur->name, (const xmlChar *)"cell"))){
 			
 			new_cell = new Cell(0,0);