diff --git a/src/VirtualLeaf.cpp b/src/VirtualLeaf.cpp
--- a/src/VirtualLeaf.cpp
+++ b/src/VirtualLeaf.cpp
@@ -97,9 +97,7 @@ 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++) {
+    for (list<Node *>::iterator i=c.nodes.begin(); i!=c.nodes.end(); i++) {
       cerr << (*i)->Index() << " ";
     }
     cerr << endl;
diff --git a/src/canvas.cpp b/src/canvas.cpp
--- a/src/canvas.cpp
+++ b/src/canvas.cpp
@@ -295,12 +295,9 @@ void FigureEditor::mouseReleaseEvent(QMo
 
       NodeSet *node_set = new NodeSet;
 
-      for (vector<CellItem *>::iterator it = intersected_cells.begin();
-	   it != intersected_cells.end();
-	   it++) {
-
+      for (vector<CellItem *>::iterator it = intersected_cells.begin(); it != intersected_cells.end(); it++) {
 	(*it)->setBrush(QBrush("purple"));
-
+	
 	Cell &c=(*it)->getCell();
 
 	// sometimes the cell hasn't properly divided yet before the
@@ -330,10 +327,7 @@ void FigureEditor::mouseReleaseEvent(QMo
 	mesh.CutAwayBelowLine( startpoint, endpoint ); 
 
 	// Correct flags of nodeset
-	for (
-	     NodeSet::iterator i = node_set->begin(); 
-	     i != node_set->end();
-	     i++) {
+	for (NodeSet::iterator i = node_set->begin(); i != node_set->end(); i++) {
 	  (*i)->SetSAM();
 	  (*i)->SetBoundary();
 	}
@@ -344,9 +338,7 @@ void FigureEditor::mouseReleaseEvent(QMo
 	//   we must insert a new node into the node set.
 	// For now, we add a layer of "virtual cells" inbetween. 
 	list<Cell *> cells_attached_to_nodeset = node_set->getCells();
-	for ( list<Cell *>::iterator c = cells_attached_to_nodeset.begin();
-	      c != cells_attached_to_nodeset.end(); 
-	      c++) {
+	for ( list<Cell *>::iterator c = cells_attached_to_nodeset.begin(); c != cells_attached_to_nodeset.end(); c++) {
 	  (*c)->SetBoundary(Cell::SAM);
 	}
 
diff --git a/src/cell.cpp b/src/cell.cpp
--- a/src/cell.cpp
+++ b/src/cell.cpp
@@ -82,9 +82,7 @@ void Cell::DivideOverAxis(Vector axis)
 
   ItList new_node_locations;
 
-  for (list<Node *>::iterator i=nodes.begin();
-       i!=nodes.end();
-       i++) {
+  for (list<Node *>::iterator i=nodes.begin(); i!=nodes.end(); i++) {
 
     // cross product to detect position of division
     Vector cross = axis * (centroid - *(*i));
@@ -119,9 +117,7 @@ void Cell::Apoptose(void)
 	     << (*w)->c1->Index() << ", c2 = " << (*w)->c2->Index() << endl;
 #endif
   }
-  for (list<Wall *>::iterator w=walls.begin();
-       w!=walls.end();
-       w++) {
+  for (list<Wall *>::iterator w=walls.begin(); w!=walls.end(); w++) {
 
     bool illegal_flag = false;
     if ((*w)->c1 == (*w)->c2 ) 
@@ -173,17 +169,13 @@ void Cell::Apoptose(void)
 
   // Unregister me from my nodes, and delete the node if it no longer belongs to any cells
   list<Node *> superfluous_nodes;
-  for (list<Node *>::iterator n=nodes.begin();
-       n!=nodes.end();
-       n++) {
+  for (list<Node *>::iterator n=nodes.begin(); n!=nodes.end(); n++) {
 
     Node &no(*(*n));
     // locate myself in the node's owner list
     list<Neighbor>::iterator cellpos;
     bool cell_found=false;
-    for (list<Neighbor>::iterator nb=no.owners.begin();
-	 nb!=no.owners.end();
-	 nb++) {
+    for (list<Neighbor>::iterator nb=no.owners.begin(); nb!=no.owners.end(); nb++) {
       if (nb->cell == this) {
 	cellpos = nb;
 	cell_found = true;
@@ -224,9 +216,7 @@ void Cell::ConstructConnections(void)
 
   //cerr << "Constructing connections of cell " << index << endl;
 
-  for (list<Node *>::iterator i=nodes.begin();
-       i!=nodes.end();
-       i++) {
+  for (list<Node *>::iterator i=nodes.begin(); i!=nodes.end(); i++) {
 
     //cerr << "Connecting node " << *i << endl;
     //cerr << "Node " << *i << endl << " = " << *(*i) << endl;
@@ -272,9 +262,7 @@ bool Cell::DivideOverGivenLine(const Vec
 #ifdef QDEBUG
   qDebug() << "Cell " << Index() << " is doing DivideOverGivenLine" << endl;
 #endif
-  for (list<Node *>::iterator i=nodes.begin();
-       i!=nodes.end();
-       i++) {
+  for (list<Node *>::iterator i=nodes.begin(); i!=nodes.end(); i++) {
 
     Vector v3 = *(*i);
     list<Node *>::iterator nb=i;
@@ -300,7 +288,7 @@ bool Cell::DivideOverGivenLine(const Vec
       new_node_locations.push_back(nb);
 
     } 
-}
+  }
 
 #ifdef QDEBUG
   if (new_node_locations.size()<2) { 
@@ -309,27 +297,27 @@ bool Cell::DivideOverGivenLine(const Vec
     return false;
   }
 
-ItList::iterator i = new_node_locations.begin();
-list< Node *>::iterator j;
-qDebug() << "-------------------------------" << endl;
-qDebug() << "Location of new nodes: " << (**i)->Index() << " and ";
+  ItList::iterator i = new_node_locations.begin();
+  list< Node *>::iterator j;
+  qDebug() << "-------------------------------" << endl;
+  qDebug() << "Location of new nodes: " << (**i)->Index() << " and ";
 
-++i;
-j = *i; 
-if (j==nodes.begin()) j=nodes.end(); j--;
+  ++i;
+  j = *i; 
+  if (j==nodes.begin()) j=nodes.end(); j--;
 
-qDebug() << (*j)->Index() << endl;
-qDebug() << "-------------------------------" << endl;
+  qDebug() << (*j)->Index() << endl;
+  qDebug() << "-------------------------------" << endl;
 
-if ( **new_node_locations.begin() == *j ) {
-  qDebug() << "Rejecting proposed division (cutting off zero area)." << endl;
-  return false;
- }
+  if ( **new_node_locations.begin() == *j ) {
+    qDebug() << "Rejecting proposed division (cutting off zero area)." << endl;
+    return false;
+  }
 #endif
 
-DivideWalls(new_node_locations, v1, v2, fix_cellwall, node_set);
+  DivideWalls(new_node_locations, v1, v2, fix_cellwall, node_set);
 
-return true;
+  return true;
 }
 
 // Core division procedure
@@ -417,9 +405,7 @@ void Cell::DivideWalls(ItList new_node_l
 
   // construct new Nodes at the intersection points
   // unless they coincide with existing points
-  for ( ItList::const_iterator i=new_node_locations.begin();
-	i!=new_node_locations.end();
-	i++) {
+  for ( ItList::const_iterator i=new_node_locations.begin(); i!=new_node_locations.end(); i++) {
 
     // intersection between division axis
     // and line from this node to its predecessor
@@ -694,9 +680,7 @@ void Cell::DivideWalls(ItList new_node_l
       owners.sort( mem_fun_ref( &Neighbor::Cmp ) );
 
       list<Neighbor>::iterator c;
-      for (c=owners.begin();
-	   c!=owners.end();
-	   c++) {
+      for (c=owners.begin(); c!=owners.end(); c++) {
 	c=adjacent_find(c,owners.end(),neighbor_cell_eq);
 	if (c->cell->Index() != this->Index() || c==owners.end()) break;
       }
@@ -977,9 +961,7 @@ void Cell::DivideWalls(ItList new_node_l
 
   // Move Walls to daughter cell
   list <Wall *> copy_walls = walls;
-  for (list<Wall *>::iterator w = copy_walls.begin();
-       w!=copy_walls.end();
-       w++) {
+  for (list<Wall *>::iterator w = copy_walls.begin(); w!=copy_walls.end(); w++) {
 
     //cerr << "Doing wall, before:  " << **w << endl;
 
@@ -1002,8 +984,7 @@ void Cell::DivideWalls(ItList new_node_l
 
   // now reconstruct neighbor list for all "broken" neighbors
 
-  for (list<CellBase *>::iterator i=broken_neighbors.begin();
-       i!=broken_neighbors.end();i++) {
+  for (list<CellBase *>::iterator i=broken_neighbors.begin(); i!=broken_neighbors.end(); i++) {
     ((Cell *)(*i))->ConstructNeighborList();
   }
 
@@ -1018,9 +999,7 @@ void Cell::DivideWalls(ItList new_node_l
 // Move the whole cell
 void Cell::Move(const Vector T) {
 
-  for (list<Node *>::const_iterator i=nodes.begin();
-       i!=nodes.end();
-       i++) {
+  for (list<Node *>::const_iterator i=nodes.begin(); i!=nodes.end(); i++) {
     *(*i)+=T;
   }
 }
@@ -1052,15 +1031,8 @@ double Cell::Displace(double dx, double 
   // the length of these edges will change
 
   double old_length=0.;
-  for (list<Node *>::const_iterator i=nodes.begin();
-       i!=nodes.end();
-       i++) {
-
-
-    for (list<Neighbor>::const_iterator n=(*i)->owners.begin();
-	 n!=(*i)->owners.end();
-	 n++) {
-
+  for (list<Node *>::const_iterator i=nodes.begin(); i!=nodes.end(); i++) {
+    for (list<Neighbor>::const_iterator n=(*i)->owners.begin(); n!=(*i)->owners.end(); n++) {
       if (n->getCell()!=this) {
 	length_edges.push_back( pair <Node *,Node *> (*i, n->nb1) );
 	length_edges.push_back( pair <Node *,Node *> (*i, n->nb2) );
@@ -1074,9 +1046,7 @@ double Cell::Displace(double dx, double 
   // calculate area energy difference of neighboring cells
   // (this cells' shape remains unchanged)
   double old_area_energy=0., old_length_energy=0.;
-  for (list<CellBase *>::const_iterator i=neighbors.begin();
-       i!=neighbors.end();
-       i++) {
+  for (list<CellBase *>::const_iterator i=neighbors.begin(); i!=neighbors.end(); i++) {
     old_area_energy += DSQR((*i)->Area()-(*i)->TargetArea());
     old_length_energy += DSQR((*i)->Length()-(*i)->TargetLength());
   }
@@ -1084,20 +1054,15 @@ double Cell::Displace(double dx, double 
   Move(movement);
 
   double new_area_energy=0., new_length_energy=0.;
-  for (list<CellBase *>::const_iterator i=neighbors.begin();
-       i!=neighbors.end();
-       i++) {
+  for (list<CellBase *>::const_iterator i=neighbors.begin(); i!=neighbors.end(); i++) {
     cellareas.push_back((*i)->CalcArea());
     new_area_energy += DSQR(cellareas.back()-(*i)->TargetArea());
     new_length_energy += DSQR((*i)->CalcLength()-(*i)->TargetLength());
   }
 
   double new_length=0;
-  for ( vector< pair< Node *, Node * > >::const_iterator e = length_edges.begin();
-	e != length_edges.end();
-	e++) {
-    new_length +=  DSQR(Node::target_length-
-			(*(e->first)-*(e->second)).Norm());
+  for ( vector< pair< Node *, Node * > >::const_iterator e = length_edges.begin(); e != length_edges.end(); e++) {
+    new_length +=  DSQR(Node::target_length - (*(e->first) - *(e->second)).Norm());
   }
 
 
@@ -1109,9 +1074,7 @@ double Cell::Displace(double dx, double 
     // update areas of cells
     //cerr << "neighbors: ";
     list<CellBase *>::const_iterator nb_it = neighbors.begin();
-    for (vector<double>::const_iterator ar_it = cellareas.begin();
-	 ar_it!=cellareas.end();
-	 ( ar_it++, nb_it++) ) {
+    for (vector<double>::const_iterator ar_it = cellareas.begin(); ar_it!=cellareas.end(); ( ar_it++, nb_it++) ) {
       ((Cell *)(*nb_it))->area = *ar_it;
       (*nb_it)->SetIntegrals(); 
     }
@@ -1139,20 +1102,12 @@ double Cell::Energy(void) const
   double energy = 0.;
   double length_contribution = 0.;
 
-  for (list<Node *>::const_iterator i=nodes.begin();
-       i!=nodes.end();
-       i++) {
-
-    for (list<Neighbor>::const_iterator n=(*i)->owners.begin();
-	 n!=(*i)->owners.end();
-	 n++) {
-
+  for (list<Node *>::const_iterator i=nodes.begin(); i!=nodes.end(); i++) {
+    for (list<Neighbor>::const_iterator n=(*i)->owners.begin(); n!=(*i)->owners.end(); n++) {
       if (n->getCell()==this) {
-
 	length_contribution += 
-	  DSQR(Node::target_length-(*(*i)-*(n->nb1)).Norm())+
+	  DSQR(Node::target_length-(*(*i)-*(n->nb1)).Norm()) +
 	  DSQR(Node::target_length-(*(*i)-*(n->nb2)).Norm());
-
       }
     }
   }
@@ -1187,15 +1142,11 @@ bool Cell::SelfIntersect(void)
 
   // 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++) {
 
     list<Node *>::const_iterator j=i; 
     ++j;
-    for (;
-	 j!=nodes.end();
-	 j++) 
+    for (; j!=nodes.end(); j++) 
       {
 	
 	Vector v1 = *(*i);
@@ -1269,10 +1220,7 @@ bool Cell::MoveSelfIntersectsP(Node *mov
   neighbor_of_moving_node[1]=*( *nb ); 
 
 
-  for (list<Node *>::const_iterator i=nodes.begin();
-       i!=nodes.end();
-       i++) {
-
+  for (list<Node *>::const_iterator i=nodes.begin(); i!=nodes.end(); i++) {
     for (int j=0;j<2;j++) { // loop over the two neighbors of moving node
       list<Node *>::const_iterator nb=i;
       nb++;
@@ -1355,8 +1303,7 @@ void Cell::ConstructWalls(void)
   // Get "corner points; i.e. nodes where more than 2 cells are connected
   list<Node *> corner_points;
 
-  for (list<Node *>::const_iterator i=nodes.begin();
-       i!=nodes.end();i++) {
+  for (list<Node *>::const_iterator i=nodes.begin(); i!=nodes.end();i++) {
 
     // look for nodes belonging to >2 cells
     if ((*i)->owners.size()>2) {
@@ -1372,24 +1319,19 @@ void Cell::ConstructWalls(void)
   list<Node *>::const_iterator nb = (--corner_points.end());
 
   // loop over list, 
-  for (list<Node *>::const_iterator i=corner_points.begin();
-       i!=corner_points.end(); ( i++, nb++) ) {
+  for (list<Node *>::const_iterator i=corner_points.begin(); i!=corner_points.end(); ( i++, nb++) ) {
 
     if (nb==corner_points.end()) nb=corner_points.begin();
     // add owning cells to a list
     list<Cell *> owning_cells;
     Node &n(*(*i));
 
-    for (list<Neighbor>::const_iterator j=n.owners.begin();
-	 j!=n.owners.end();
-	 j++) {
+    for (list<Neighbor>::const_iterator j=n.owners.begin(); j!=n.owners.end(); j++) {
       owning_cells.push_back(j->cell);
     }
 
     Node &n2(*(*nb));
-    for (list<Neighbor>::const_iterator j=n2.owners.begin();
-	 j!=n2.owners.end();
-	 j++) {
+    for (list<Neighbor>::const_iterator j=n2.owners.begin(); j!=n2.owners.end(); j++) {
       owning_cells.push_back(j->cell);
     }
 
@@ -1399,16 +1341,13 @@ void Cell::ConstructWalls(void)
     // find duplicates
     vector<Cell *> duplicates;
     list<Cell *>::const_iterator prevj = (--owning_cells.end());
-    for (list<Cell *>::const_iterator j=owning_cells.begin();
-	 j!=owning_cells.end();
-	 ( j++, prevj++) ) {
-
-      if (prevj==owning_cells.end()) prevj=owning_cells.begin();
-      if (*j==*prevj) duplicates.push_back(*j);
-
+    for (list<Cell *>::const_iterator j=owning_cells.begin(); j!=owning_cells.end(); ( j++, prevj++) ) {
+      if (prevj==owning_cells.end())
+	prevj=owning_cells.begin();
+      if (*j==*prevj) 
+	duplicates.push_back(*j);
     }
 
-
     if (duplicates.size()==3) { // ignore cell boundary (this occurs only after the first division, I think)
       vector<Cell *>::iterator dup_it = find_if(duplicates.begin(),duplicates.end(),mem_fun(&Cell::BoundaryPolP) );
       if (dup_it!=duplicates.end()) 
@@ -1447,13 +1386,9 @@ void BoundaryPolygon::Draw(QGraphicsScen
   QPolygonF pa(nodes.size());
   int cc=0;
 
-  for (list<Node *>::const_iterator n=nodes.begin();
-       n!=nodes.end();
-       n++) {
+  for (list<Node *>::const_iterator n=nodes.begin(); n!=nodes.end(); n++) {
     Node *i=*n;
-
-    pa[cc++] = QPoint((int)((Offset().x+i->x)*Factor()),
-		      (int)((Offset().y+i->y)*Factor()) );
+    pa[cc++] = QPoint((int)((Offset().x+i->x)*Factor()), (int)((Offset().y+i->y)*Factor()) );
   }
 
   p->setPolygon(pa);
@@ -1471,12 +1406,10 @@ void Cell::Flux(double *flux, double *D)
 {
   // loop over cell edges
 
-  for (int c=0;c<NChem();c++) flux[c]=0.;
+  for (int c=0;c<NChem();c++)
+    flux[c]=0.;
 
-  for (list<Wall *>::iterator i=walls.begin();
-       i!=walls.end();
-       i++) {
-
+  for (list<Wall *>::iterator i=walls.begin(); i!=walls.end(); i++) {
 
     // leaf cannot take up chemicals from environment ("no flux boundary")
     if ((*i)->c2->BoundaryPolP()) continue;
@@ -1520,9 +1453,7 @@ void Cell::Draw(QGraphicsScene *c, QStri
   QPolygonF pa(nodes.size());
   int cc=0;
 
-  for (list<Node *>::const_iterator n=nodes.begin();
-       n!=nodes.end();
-       n++) {
+  for (list<Node *>::const_iterator n=nodes.begin(); n!=nodes.end(); n++) {
     Node *i=*n;
 
     pa[cc++] = QPoint((int)((offset[0]+i->x)*factor),
@@ -1562,18 +1493,14 @@ void Cell::DrawCenter(QGraphicsScene *c)
 
 void Cell::DrawNodes(QGraphicsScene *c) const {
 
-  for (list<Node *>::const_iterator n=nodes.begin();
-       n!=nodes.end();
-       n++) {
+  for (list<Node *>::const_iterator n=nodes.begin(); n!=nodes.end(); n++) {
     Node *i=*n;
 
-
     NodeItem *item = new NodeItem ( &(*i), c );
     item->setColor();
     item->setZValue(5);
     item->show();
-    item ->setPos(((offset[0]+i->x)*factor),
-		  ((offset[1]+i->y)*factor) );
+    item ->setPos(((offset[0]+i->x)*factor), ((offset[1]+i->y)*factor) );
   }
 }
 
@@ -1683,9 +1610,7 @@ void Cell::DrawValence(QGraphicsScene *c
 void Cell::SetWallLengths(void)
 {
 
-  for (list<Wall *>::iterator de=walls.begin();
-       de!=walls.end();
-       de++) {
+  for (list<Wall *>::iterator de=walls.begin(); de!=walls.end(); de++) {
 
     // Step 1: find the path of nodes leading along the Wall.
     // A Wall often represents a curved cell wall: we want the total
@@ -1699,18 +1624,14 @@ void Cell::SetWallLengths(void)
     double sum_length = 0.;
 
     // Now, walk to the second node of the edge in the list of nodes
-    for (list<Node *>::const_iterator n=++first_node_edge;
-	 n!=second_node_edge_plus_1;
-	 ++n ) {
-
-      if (n==nodes.end()) n=nodes.begin(); /* wrap around */ 
-
-
+    for (list<Node *>::const_iterator n=++first_node_edge; n!=second_node_edge_plus_1; ++n ) {
+      if (n==nodes.end())
+	n=nodes.begin(); /* wrap around */ 
       list<Node *>::const_iterator prev_n = n; 
-      if (prev_n==nodes.begin()) prev_n=nodes.end();
+      if (prev_n==nodes.begin())
+	prev_n=nodes.end();
       --prev_n;
 
-
       // Note that Node derives from a Vector, so we can do vector calculus as defined in vector.h 
       sum_length += (*(*prev_n) - *(*n)).Norm(); 
 
@@ -1741,12 +1662,7 @@ void Cell::AddWall( Wall *w )
   walls.push_back( w );
 
   // Add wall to Mesh's list if it isn't there yet
-
-  if (find (
-	    m->walls.begin(), m->walls.end(),
-	    w )
-      == m->walls.end() ) {
-    m->walls.push_back(w);
+  if (find ( m->walls.begin(), m->walls.end(), w ) == m->walls.end() ) { m->walls.push_back(w);
   }
 }
 
@@ -1755,11 +1671,7 @@ list<Wall *>::iterator Cell::RemoveWall(
 {
 
   // remove wall from Mesh's list
-  m->walls.erase(
-		 find(
-		      m->walls.begin(), m->walls.end(),
-		      w )
-		 );
+  m->walls.erase( find( m->walls.begin(), m->walls.end(), w ) );
 
   // remove wall from Cell's list
   return walls.erase (find( walls.begin(), walls.end(), w ));
@@ -1768,7 +1680,6 @@ list<Wall *>::iterator Cell::RemoveWall(
 
 void Cell::EmitValues(double t)
 {
-
   //  cerr << "Attempting to emit " << t << ", " << chem[0] << ", " << chem[1] << endl;
   emit ChemMonValue(t, chem);
 }
diff --git a/src/cellbase.cpp b/src/cellbase.cpp
--- a/src/cellbase.cpp
+++ b/src/cellbase.cpp
@@ -234,9 +234,7 @@ void CellBase::SetTransporters(int ch, d
     error << "SetChemical: value ch = " << ch << " is out of range\n";
     throw error.str().c_str();
   }
-  for (list<Wall *>::iterator w=walls.begin();
-       w!=walls.end();
-       w++) {
+  for (list<Wall *>::iterator w=walls.begin(); w!=walls.end(); w++) {
     (*w)->setTransporter(this, ch, conc);
   }
 }
@@ -269,9 +267,7 @@ ostream &CellBase::print(ostream &os) co
   os << " [ area = " << area << " ]";
   os << " [ walls = ";
 
-  for (list<Wall *>::const_iterator i= walls.begin();
-       i!=walls.end();
-       i++) {
+  for (list<Wall *>::const_iterator i= walls.begin(); i!=walls.end(); i++) {
     os << (*i)->n1->Index() << " -> " << (*i)->n2->Index() << ", " <<  (*i)->c1->Index() << " | " << (*i)->c2->Index() << ", ";
   }
   os << " ] ";
@@ -293,9 +289,7 @@ double CellBase::CalcArea(void) const
 
   double loc_area=0.;
 
-  for (list<Node *>::const_iterator i=nodes.begin();
-       i!=(nodes.end());
-       i++) {
+  for (list<Node *>::const_iterator i=nodes.begin(); i!=(nodes.end()); i++) {
 
     list<Node *>::const_iterator i_plus_1=i; i_plus_1++;
     if (i_plus_1==nodes.end())
@@ -315,9 +309,7 @@ Vector CellBase::Centroid(void) const
   double area=0.;
   double integral_x_dxdy=0.,integral_y_dxdy=0.;
 
-  for (list<Node *>::const_iterator i=nodes.begin();
-       i!=(nodes.end());
-       i++) {
+  for (list<Node *>::const_iterator i=nodes.begin(); i!=(nodes.end()); i++) {
 
     list<Node *>::const_iterator i_plus_1=i; i_plus_1++;
     if (i_plus_1==nodes.end())
@@ -362,9 +354,7 @@ void CellBase::SetIntegrals(void) const
   list<Node *>::const_iterator nb;
   list<Node *>::const_iterator i=nodes.begin();
 
-  for (;
-       i!=(nodes.end());
-       i++) {
+  for (; i!=(nodes.end()); i++) {
 
     nb = i; nb++; if (nb==nodes.end()) nb=nodes.begin();
 
@@ -452,9 +442,7 @@ double CellBase::CalcLength(Vector *long
   list<Node *>::const_iterator nb;
   list<Node *>::const_iterator i=nodes.begin();
 
-  for (;
-       i!=(nodes.end());
-       i++) {
+  for (; i!=(nodes.end()); i++) {
 
     nb = i; nb++; if (nb==nodes.end()) nb=nodes.begin();
 
@@ -603,31 +591,22 @@ void CellBase::Dump(ostream &os) const
 
   os << " " << source_conc << " " << source_chem;
   os << endl;
-
 }
 
 
 void CellBase::UnfixNodes(void)
 {
-
-  for (list<Node *>::const_iterator i=nodes.begin();
-       i!=nodes.end();
-       i++) {
+  for (list<Node *>::const_iterator i=nodes.begin(); i!=nodes.end(); i++) {
     (*i)->Unfix();
   }
-
 }
 
 
 void CellBase::FixNodes(void)
 {
-
-  for (list<Node *>::const_iterator i=nodes.begin();
-       i!=nodes.end();
-       i++) {
+  for (list<Node *>::const_iterator i=nodes.begin(); i!=nodes.end(); i++) { 
     (*i)->Fix();
   }
-
 }
 
 // returns true if cell is at border
diff --git a/src/mesh.cpp b/src/mesh.cpp
--- a/src/mesh.cpp
+++ b/src/mesh.cpp
@@ -65,9 +65,7 @@ void Mesh::AddNodeToCell(Cell *c, Node *
 
 void Mesh::PerturbChem(int chemnum, double range) {
 
-  for (vector<Cell *>::iterator i=cells.begin();
-       i!=cells.end();
-       i++) {
+  for (vector<Cell *>::iterator i=cells.begin(); i!=cells.end(); i++) {
     (*i)->chem[chemnum] += range*(RANDOM()-0.5);
     if ((*i)->chem[chemnum]<0.) (*i)->chem[chemnum]=0.;
   }
@@ -90,8 +88,7 @@ void Mesh::CellFiles(const Vector ll, co
     IncreaseCellCapacityIfNecessary();
 
     vector <Cell *> current_cells = cells;
-    for (vector<Cell *>::iterator j=current_cells.begin();
-	 j!=current_cells.end();j++) {
+    for (vector<Cell *>::iterator j=current_cells.begin(); j!=current_cells.end();j++) {
       (*j)->DivideOverAxis(axis);
     }
     axis=axis.Perp2D();
@@ -103,16 +100,13 @@ void Mesh::CellFiles(const Vector ll, co
   axis=axis.Perp2D();
 
   vector <Cell *> current_cells = cells;
-  for (vector<Cell *>::iterator j=current_cells.begin();
-       j!=current_cells.end();j++) {
+  for (vector<Cell *>::iterator j=current_cells.begin(); j!=current_cells.end();j++) {
     (*j)->DivideOverAxis(axis);
   }
 
 
   double sum_l=0; int n_l=0;
-  for (list<Node *>::const_iterator i=cell->nodes.begin();
-       i!=cell->nodes.end();
-       i++) {
+  for (list<Node *>::const_iterator i=cell->nodes.begin(); i!=cell->nodes.end(); i++) {
     list<Node *>::const_iterator nb=i; nb++; 
     if (nb==cell->nodes.end()) 
       nb=cell->nodes.begin();
@@ -244,37 +238,7 @@ Cell &Mesh::EllipticCell(double xc, doub
   // a bit more tension
   Node::target_length/=2;
 
-  //boundary_polygon = c;
-  /*  list<int>::iterator nb;
-      for (list<int>::iterator i=c->nodes.begin();
-      i!=c->nodes.end();
-      i++) {
-
-      nb = i; nb++;
-      if (nb==c->nodes.end()) {
-      nb=c->nodes.begin();
-      }
-      int next = *nb;
-
-      nb = i; 
-      if (nb==c->nodes.begin()) {
-      nb=c->nodes.end();
-      } 
-      nb--;
-      int previous = *nb;
-
-
-      getNode(*i).cells.push_back( Neighbor(boundary_polygon->index, next, previous) );
-      }*/
-
   c->SetIntegrals(); 
-  //c->ConstructNeighborList();
-
-  //c->ConstructWalls();
-
-  // initial cell has one wall with the outside world
-  //c->walls.push_back( new Wall ( nodes.front(), nodes.front(), c, boundary_polygon )); 
-
   c->at_boundary=true;
 
   return *c;
@@ -331,13 +295,11 @@ Cell &Mesh::LeafPrimordium(int nnodes, d
   // get position of the (n/4)'th and (3*(n/4))'th node.
 
   list<Node *>::reverse_iterator it_n1=circle->nodes.rbegin();
-  for (int i=0;i<nnodes/2;i++)
+  for (int i=0; i<nnodes/2; i++) 
     it_n1++;
   it_n1--;
 
   list<Node *>::reverse_iterator it_n2=--circle->nodes.rend();
-  /* for (int i=0;i<n/2;i++)
-     it_n2++;*/
 
   Cell *petiole=AddCell(new Cell());
 
@@ -358,35 +320,18 @@ Cell &Mesh::LeafPrimordium(int nnodes, d
 
 
   list<Node *>::reverse_iterator i=it_n1; i++;
-  for (;
-       i!=it_n2; 
-       //(++i) == circle->nodes.rend() ? i : i=circle->nodes.rbegin() ) {
-       ++i) {
-    AddNodeToCell(petiole,
-		  *i,
+  for (; i!=it_n2; ++i) {
+    AddNodeToCell(petiole, *i,
 		  nodes[(*it_n2)->Index() + (((*i)->Index()-(*it_n2)->Index()) + 1)%nnodes],
 		  nodes[(*it_n2)->Index() + (((*i)->Index()-(*it_n2)->Index())-1+nnodes)%nnodes]);
-
   }
 
-
-  AddNodeToCell(petiole, *it_n2, 
-		*it_n2 + 1,
-		n3);
-
+  AddNodeToCell(petiole, *it_n2, *it_n2 + 1, n3);
 
   (*it_n2)->boundary=true;
 
-  //petiole.nodes.push_back(n3.Index());
-  //petiole.nodes.push_back(n4.Index());
-  AddNodeToCell(petiole,
-		n3,
-		n2,
-		n4);
-  AddNodeToCell(petiole,
-		n4,
-		n3,
-		n1);
+  AddNodeToCell(petiole, n3, n2, n4);
+  AddNodeToCell(petiole, n4, n3, n1);
 
 
 #ifdef QDEBUG  
@@ -394,9 +339,7 @@ Cell &Mesh::LeafPrimordium(int nnodes, d
   qDebug() << petiole << endl;
 #endif
 
-  AddNodeToCell(boundary_polygon, *it_n1, 
-		n4,
-		*it_n2 + ((*it_n1-*it_n2)+1)%nnodes); // is this gonna work?
+  AddNodeToCell(boundary_polygon, *it_n1, n4, *it_n2 + ((*it_n1-*it_n2)+1)%nnodes); // is this gonna work?
 
   (*it_n1)->boundary=true;
 
@@ -412,23 +355,12 @@ Cell &Mesh::LeafPrimordium(int nnodes, d
     }
   }
 
-  AddNodeToCell(boundary_polygon, *it_n2, 
-		nodes[(nnodes+(*it_n2)->Index() - 1)%nnodes],
-		n3);
-
-  AddNodeToCell(boundary_polygon,
-		n3,
-		n2,
-		n4);
-  AddNodeToCell(boundary_polygon,
-		n4,
-		n3,
-		n1);
+  AddNodeToCell(boundary_polygon, *it_n2, nodes[(nnodes+(*it_n2)->Index() - 1)%nnodes], n3);
+  AddNodeToCell(boundary_polygon, n3, n2, n4);
+  AddNodeToCell(boundary_polygon, n4, n3, n1);
 
   // make petiole solid
-  for (list<Node *>::iterator i=petiole->nodes.begin();
-       i!=petiole->nodes.end();
-       i++) {
+  for (list<Node *>::iterator i=petiole->nodes.begin(); i!=petiole->nodes.end(); i++) {
     (*i)->Fix();
   }
   petiole->Fix();
@@ -454,9 +386,7 @@ void Mesh::BoundingBox(Vector &LowerLeft
 
   LowerLeft = **nodes.begin();
   UpperRight = **nodes.begin();
-  for (vector<Node *>::iterator c=nodes.begin();
-       c!=nodes.end();
-       c++) {
+  for (vector<Node *>::iterator c=nodes.begin(); c!=nodes.end(); c++) {
     if ((*c)->x < LowerLeft.x)
       LowerLeft.x = (*c)->x;
     if ((*c)->y < LowerLeft.y)
@@ -512,9 +442,7 @@ public:
 void Mesh::Clear(void) {
 
   // clear nodes
-  for (vector<Node *>::iterator i=nodes.begin();
-       i!=nodes.end();
-       i++) {
+  for (vector<Node *>::iterator i=nodes.begin(); i!=nodes.end(); i++) {
     delete *i;
   }
 
@@ -523,9 +451,7 @@ void Mesh::Clear(void) {
 
   node_insertion_queue.clear();
   // Clear NodeSets
-  for (vector<NodeSet *>::iterator i=node_sets.begin();
-       i!=node_sets.end();
-       i++) {
+  for (vector<NodeSet *>::iterator i=node_sets.begin(); i!=node_sets.end(); i++) {
     delete *i;
   }
 
@@ -534,9 +460,7 @@ void Mesh::Clear(void) {
 
   // clear cells
 
-  for (vector<Cell *>::iterator i=cells.begin();
-       i!=cells.end();
-       i++) {
+  for (vector<Cell *>::iterator i=cells.begin(); i!=cells.end(); i++) {
     delete *i;
   }
 
@@ -546,9 +470,7 @@ void Mesh::Clear(void) {
   delete boundary_polygon;
 
   // Clear walls
-  for (list<Wall *>::iterator i=walls.begin();
-       i!=walls.end();
-       i++) {
+  for (list<Wall *>::iterator i=walls.begin(); i!=walls.end(); i++) {
     delete *i;
   }
 
@@ -589,9 +511,7 @@ double Mesh::DisplaceNodes(void) {
 
   for_each( node_sets.begin(), node_sets.end(), mem_fun( &NodeSet::ResetDone ) );
 
-  for (vector<Node *>::const_iterator i=shuffled_nodes.begin();
-       i!=shuffled_nodes.end();
-       i++) {
+  for (vector<Node *>::const_iterator i=shuffled_nodes.begin(); i!=shuffled_nodes.end(); i++) {
 
     //int n=shuffled_nodes[*i];
     Node &node(**i);
@@ -642,9 +562,7 @@ double Mesh::DisplaceNodes(void) {
       double sum_stiff=0.;
       double dh=0.;
 
-      for (list<Neighbor>::const_iterator cit=node.owners.begin();
-	   cit!=node.owners.end();
-	   cit++) {
+      for (list<Neighbor>::const_iterator cit=node.owners.begin(); cit!=node.owners.end(); cit++) {
 
 	//Cell &c=m->getCell(cit->cell);
 	//Cell &c=cit->cell->BoundaryPolP()?*boundary_polygon:*(cit->cell);
@@ -960,9 +878,7 @@ double Mesh::DisplaceNodes(void) {
 	// search the fixed cell to which this node belongs
 	// and displace these cells as a whole
 	// WARNING: undefined things will happen for connected fixed cells...
-	for (list<Neighbor>::iterator c=node.owners.begin();
-	     c!=node.owners.end();
-	     c++) {
+	for (list<Neighbor>::iterator c=node.owners.begin(); c!=node.owners.end(); c++) {
 	  if (!c->cell->BoundaryPolP() && c->cell->FixedP()) {
 	    sum_dh+=c->cell->Displace(rx,ry,0);
 	  }
@@ -974,11 +890,7 @@ double Mesh::DisplaceNodes(void) {
 
 	  // update areas of cells
 	  list<DeltaIntgrl>::const_iterator di_it = delta_intgrl_list.begin();
-	  for (list<Neighbor>::iterator cit=node.owners.begin();
-	       cit!=node.owners.end();
-	       ( cit++) ) {
-	    //m->getCell(cit->cell).area -= *da_it;
-	    //if (cit->cell>=0) {
+	  for (list<Neighbor>::iterator cit=node.owners.begin(); cit!=node.owners.end(); ( cit++) ) {
 	    if (!cit->cell->BoundaryPolP()) {
 	      cit->cell->area -= di_it->area;
 	      if (par.lambda_celllength) {
@@ -1235,10 +1147,7 @@ void Mesh::CircumCircle(double x1,double
 double Mesh::SumChemical(int ch) {
 
   double sum=0.;
-  for (vector<Cell *>::iterator i=cells.begin();
-       i!=cells.end();
-       i++) {
-
+  for (vector<Cell *>::iterator i=cells.begin(); i!=cells.end(); i++) {
     sum+=(*i)->chem[ch];
   }
   return sum;
@@ -1256,10 +1165,7 @@ void Mesh::CleanUpCellNodeLists(void) {
   // Start of by removing all stale walls.
   //DeleteLooseWalls();
   // collect all dead cells that need to be removed from the simulation
-  for (vector<Cell *>::iterator i=cells.begin();
-       i!=cells.end();
-       i++) {
-
+  for (vector<Cell *>::iterator i=cells.begin(); i!=cells.end(); i++) {
     if ((*i)->DeadP()) {
       // collect the iterators
       cellstoberemoved.push_back(i);
@@ -1268,9 +1174,7 @@ void Mesh::CleanUpCellNodeLists(void) {
       cellind.push_back((*i)->index);
     } else {
       // Remove pointers to dead Walls
-      for (list<Wall *>::iterator w=(*i)->walls.begin();
-	   w!=(*i)->walls.end();
-	   w++) {
+      for (list<Wall *>::iterator w=(*i)->walls.begin(); w!=(*i)->walls.end(); w++) {
 	if ((*w)->DeadP()) {
 	  (*w)=0;
 	}
@@ -1280,9 +1184,7 @@ void Mesh::CleanUpCellNodeLists(void) {
   }
 
   // Remove pointers to dead Walls from BoundaryPolygon
-  for (list<Wall *>::iterator w=boundary_polygon->walls.begin();
-       w!=boundary_polygon->walls.end();
-       w++) {
+  for (list<Wall *>::iterator w=boundary_polygon->walls.begin(); w!=boundary_polygon->walls.end(); w++) {
     if ((*w)->DeadP()) {
       (*w)=0;
     }
@@ -1295,26 +1197,16 @@ void Mesh::CleanUpCellNodeLists(void) {
 
 
   // Reindexing of Cells
-  for (vector<int>::reverse_iterator j=cellind.rbegin();
-       j!=cellind.rend();
-       j++) {
-
-    for (vector<Cell *>::reverse_iterator i=cells.rbegin();
-	 i!=cells.rend();
-	 i++) {
-
+  for (vector<int>::reverse_iterator j=cellind.rbegin(); j!=cellind.rend(); j++) {
+    for (vector<Cell *>::reverse_iterator i=cells.rbegin(); i!=cells.rend(); i++) {
       if (*j < (*i)->index) (*i)->index--;
-
     }
-
   }
 
 
   // Actual deleting of Cells
   // We must delete in reverse order, otherwise the iterators become redefined
-  for ( CellItVect::reverse_iterator i=cellstoberemoved.rbegin();
-	i!=cellstoberemoved.rend();
-	i++) {
+  for ( CellItVect::reverse_iterator i=cellstoberemoved.rbegin(); i!=cellstoberemoved.rend(); i++) {
     Cell::NCells()--;
     cells.erase(*i);
   }
@@ -1327,14 +1219,10 @@ void Mesh::CleanUpCellNodeLists(void) {
   vector<int> nodeindlist;
 
   // collect iterators and indices of dead nodes
-  for (vector<Node *>::iterator i=nodes.begin();
-       i!=nodes.end();
-       i++) {
-
+  for (vector<Node *>::iterator i=nodes.begin(); i!=nodes.end(); i++) {
     if ((*i)->DeadP()) {
       nodestoberemoved.push_back( i );
       nodeindlist.push_back((*i)->index);
-
     }
   }
 
@@ -1343,38 +1231,24 @@ void Mesh::CleanUpCellNodeLists(void) {
 
 
   // Reindicing of Nodes
-  for (vector<int>::reverse_iterator j=nodeindlist.rbegin();
-       j!=nodeindlist.rend();
-       j++) {
-
-    for (vector<Node *>::reverse_iterator i=nodes.rbegin();
-	 i!=nodes.rend();
-	 i++) {
-
+  for (vector<int>::reverse_iterator j=nodeindlist.rbegin(); j!=nodeindlist.rend(); j++) {
+    for (vector<Node *>::reverse_iterator i=nodes.rbegin(); i!=nodes.rend(); i++) {
       if (*j < (*i)->index) { 
-
 	(*i)->index--;
       } 
-
-
     }
-
   }
 
   // Actual deleting of nodes
   // We must delete in reverse order, otherwise the iterators become redefined
-  for ( NodeItVect::reverse_iterator i=nodestoberemoved.rbegin();
-	i!=nodestoberemoved.rend();
-	i++) {
+  for ( NodeItVect::reverse_iterator i=nodestoberemoved.rbegin(); i!=nodestoberemoved.rend(); i++) {
     Node::nnodes--;
     nodes.erase(*i);
   }
 
 
 
-  for (list<Wall *>::iterator w=walls.begin();
-       w!=walls.end();
-       w++) {
+  for (list<Wall *>::iterator w=walls.begin(); w!=walls.end(); w++) {
     if ((*w)->DeadP()) {
       Wall::nwalls--;
       delete *w;
@@ -1387,39 +1261,16 @@ void Mesh::CleanUpCellNodeLists(void) {
 
 
   // Clean up all intercellular connections and redo everything
-  for (vector<Node *>::iterator i=nodes.begin();
-       i!=nodes.end();
-       i++) {
-
+  for (vector<Node *>::iterator i=nodes.begin(); i!=nodes.end(); i++) {
     (*i)->owners.clear();
   }
 
-  for (vector<Cell *>::iterator i=cells.begin();
-       i!=cells.end();
-       i++) {
-
+  for (vector<Cell *>::iterator i=cells.begin(); i!=cells.end(); i++) {
     (*i)->ConstructConnections();
-
   }
 
   boundary_polygon->ConstructConnections();
 
-  /* for (list<Wall *>::iterator w=walls.begin();
-     w!=walls.end();
-     w++) {
-     delete *w;    
-     }
-
-     walls.clear(); 
-     cerr << "Cleared walls\n"; 
-     for (vector<Cell *>::iterator i=cells.begin();
-     i!=cells.end();
-     i++) {
-
-     (*i)->ConstructWalls();
-     }
-  */
-
   // remake shuffled_nodes and shuffled cells
   shuffled_nodes.clear();
   shuffled_nodes = nodes;
@@ -1439,9 +1290,7 @@ void Mesh::CutAwayBelowLine( Vector star
 #endif
 
   TestIllegalWalls();
-  for (vector<Cell *>::iterator i=cells.begin();
-       i!=cells.end();
-       i++) {
+  for (vector<Cell *>::iterator i=cells.begin(); i!=cells.end(); i++) {
 
     // do some vector geometry to check whether the cell is below the cutting line
     Vector cellvec = ((*i)->Centroid()-startpoint);
@@ -1462,25 +1311,18 @@ void Mesh::CutAwayBelowLine( Vector star
 
 void Mesh::CutAwaySAM(void) {
 
-  for (vector<Cell *>::iterator i=cells.begin();
-       i!=cells.end();
-       i++) {
-
+  for (vector<Cell *>::iterator i=cells.begin(); i!=cells.end(); i++) {
     if( (*i)->Boundary() == Cell::SAM ) {
-
       (*i)->Apoptose();
     }
   }
-
   TestIllegalWalls();
-
   CleanUpCellNodeLists();
 }
+
 void Mesh::TestIllegalWalls(void) {
 
-  for (list<Wall *>::iterator w = walls.begin();
-       w!=walls.end();
-       w++) {
+  for (list<Wall *>::iterator w = walls.begin(); w!=walls.end(); w++) {
     if ((*w)->IllegalP() ) {
 #ifdef QDEBUG
       qDebug() << "Wall " << **w << " is illegal." << endl;
@@ -1596,9 +1438,7 @@ void Mesh::RepairBoundaryPolygon(void) {
   }
 
   boundary_polygon->ConstructConnections();
-  for (list<Wall *>::iterator w=boundary_polygon->walls.begin();
-       w!=boundary_polygon->walls.end();
-       w++) {
+  for (list<Wall *>::iterator w=boundary_polygon->walls.begin(); w!=boundary_polygon->walls.end(); w++) {
     if ((*w)->DeadP()) {
       (*w)=0;
     }
@@ -1702,10 +1542,7 @@ Node* Mesh::findNextBoundaryNode(Node* b
 
 
 void Mesh::CleanUpWalls(void) {
-  for (list<Wall *>::iterator w=walls.begin();
-       w!=walls.end();
-       w++) {
-
+  for (list<Wall *>::iterator w=walls.begin(); w!=walls.end(); w++) {
     if ((*w)->DeadP()) {
       delete *w;
       (*w)=0;      
@@ -1722,12 +1559,8 @@ void Mesh::Rotate(double angle, Vector c
 
   rotmat.Rot2D(angle);
 
-  for (vector<Node *>::iterator n=nodes.begin();
-       n!=nodes.end();
-       n++) {
-
+  for (vector<Node *>::iterator n=nodes.begin(); n!=nodes.end(); n++) {
     (*n)->setPos ( rotmat * ( *(*n) - center ) + center );  
-
   }
 }
 
@@ -1768,17 +1601,6 @@ protected:
     m->setValues(x,y);
     m->Derivatives(dydx);
 
-    /*static int c=0;
-      QString fname("derivs%1.dat");
-
-      ofstream of(fname.arg(++c).ascii());
-
-      for (int i=0;i<m->NEqs();i++) {
-      of << x << " " << dxdy[i] << endl;
-      }
-      of.close();
-    */
-
     //cerr << "Calculated derivatives at " << x << "\n";    
   }
 
@@ -1813,14 +1635,9 @@ void Mesh::ReactDiffuse(double delta_t) 
 Vector Mesh::FirstConcMoment(int chem) {
 
   Vector moment;
-  for (vector<Cell *>::const_iterator c=cells.begin();
-       c!=cells.end();
-       c++) {
-
+  for (vector<Cell *>::const_iterator c=cells.begin(); c!=cells.end(); c++) {
     moment += (*c)->Chemical(chem) * (*c)->Centroid();
-
   }
-
   return moment / (double)cells.size();
 }
 
@@ -1880,15 +1697,11 @@ void Mesh::CleanChemicals(const vector<d
   if (clean_chem.size()!=(unsigned)Cell::NChem()) {
     throw "Run time error in Mesh::CleanChemicals: size of clean_chem should be equal to Cell::NChem()";
   }
-  for (vector<Cell *>::iterator c=cells.begin();
-       c!=cells.end();
-       c++) {
-
+  for (vector<Cell *>::iterator c=cells.begin(); c!=cells.end(); c++) {
     for (int i=0;i<Cell::NChem();i++) {
       (*c)->SetChemical(i,clean_chem[i]);
     }
     (*c)->SetNewChemToChem();
-
   }
 }
 
@@ -1901,10 +1714,7 @@ void Mesh::CleanTransporters(const vecto
 
 
   // clean transporters
-  for (list<Wall *>::iterator w=walls.begin();
-       w!=walls.end();
-       w++) {
-
+  for (list<Wall *>::iterator w=walls.begin(); w!=walls.end(); w++) {
     for (int i=0;i<Cell::NChem();i++) {
       (*w)->setTransporters1(i,clean_transporters[i]); (*w)->setNewTransporters1(i,clean_transporters[i]);
       (*w)->setTransporters2(i,clean_transporters[i]); (*w)->setNewTransporters2(i,clean_transporters[i]);
@@ -1919,22 +1729,15 @@ void Mesh::RandomizeChemicals(const vect
     throw "Run time error in Mesh::CleanChemicals: size of max_chem and max_transporters should be equal to Cell::NChem()";
   }
 
-  for (vector<Cell *>::iterator c=cells.begin();
-       c!=cells.end();
-       c++) {
-
+  for (vector<Cell *>::iterator c=cells.begin(); c!=cells.end(); c++) {
     for (int i=0;i<Cell::NChem();i++) {
       (*c)->SetChemical(i,max_chem[i]*RANDOM());
     }
     (*c)->SetNewChemToChem();
-
   }
 
   // randomize transporters
-  for (list<Wall *>::iterator w=walls.begin();
-       w!=walls.end();
-       w++) {
-
+  for (list<Wall *>::iterator w=walls.begin(); w!=walls.end(); w++) {
     for (int i=0;i<Cell::NChem();i++) {
       (*w)->setTransporters1(i,max_transporters[i] * RANDOM()); (*w)->setNewTransporters1(i, (*w)->Transporters1(i) );
       (*w)->setTransporters2(i,max_transporters[i] * RANDOM()); (*w)->setNewTransporters2(i, (*w)->Transporters1(i) );
@@ -1958,23 +1761,20 @@ void Mesh::Derivatives(double *derivs) {
   //static double *derivs = 0; 
   // derivs is allocated by RungeKutta class.
 
-  for (int i=0;i<neqs;i++) { derivs[i]=0.;}
+  for (int i=0;i<neqs;i++) {
+    derivs[i]=0.;
+  }
 
   // Layout of derivatives: cells [ chem1 ... chem n]  walls [ [ w1(chem 1) ... w1(chem n) ] [ w2(chem 1) ... w2(chem n) ] ]
 
   int i=0;
 
-  for (vector<Cell *>::iterator c=cells.begin();
-       c!=cells.end();
-       c++) {
-    //(*cr)(*c, &(derivs[i]));
+  for (vector<Cell *>::iterator c=cells.begin(); c!=cells.end(); c++) {
     plugin->CellDynamics(*c, &(derivs[i]));
     i+=nchems;
   }
 
-  for (list<Wall *>::iterator w=walls.begin();
-       w!=walls.end();
-       w++) {
+  for (list<Wall *>::iterator w=walls.begin(); w!=walls.end(); w++) {
     // (*wr)(*w, &(derivs[i]), &(derivs[i+nchems]));
     plugin->WallDynamics(*w,  &(derivs[i]), &(derivs[i+nchems]));
     // Transport function adds to derivatives of cell chemicals
@@ -2015,9 +1815,7 @@ void Mesh::setValues(double x, double *y
   int i=0;
   static int emit_count=0;
   const int stride = 100;
-  for (vector<Cell *>::iterator c=cells.begin();
-       c!=cells.end();
-       c++) {
+  for (vector<Cell *>::iterator c=cells.begin(); c!=cells.end(); c++) {
     for (int ch=0;ch<nchems;ch++) {
       (*c)->SetChemical(ch, y[i+ch]);
     }
@@ -2027,10 +1825,7 @@ void Mesh::setValues(double x, double *y
     i+=nchems;
   }
 
-  for (list<Wall *>::iterator w=walls.begin();
-       w!=walls.end();
-       w++) {
-
+  for (list<Wall *>::iterator w=walls.begin(); w!=walls.end(); w++) {
     for (int ch=0;ch<nchems;ch++) {
       (*w)->setTransporters1(ch,y[i+ch]);
     }
@@ -2040,9 +1835,7 @@ void Mesh::setValues(double x, double *y
       (*w)->setTransporters2(ch,y[i+ch]);
     }
     i+=nchems;
-
   }
-
   emit_count++;
 }
 
@@ -2065,19 +1858,14 @@ double *Mesh::getValues(int *neqs) {
   values = new double[*neqs];
 
   int i=0;
-  for (vector<Cell *>::iterator c=cells.begin();
-       c!=cells.end();
-       c++) {
+  for (vector<Cell *>::iterator c=cells.begin(); c!=cells.end(); c++) {
     for (int ch=0;ch<nchems;ch++) {
       values[i+ch]=(*c)->Chemical(ch);
     }
     i+=nchems;
   }
 
-  for (list<Wall *>::iterator w=walls.begin();
-       w!=walls.end();
-       w++) {
-
+  for (list<Wall *>::iterator w=walls.begin(); w!=walls.end(); w++) {
     for (int ch=0;ch<nchems;ch++) {
       values[i+ch]=(*w)->Transporters1(ch);
     }
@@ -2087,18 +1875,13 @@ double *Mesh::getValues(int *neqs) {
       values[i+ch]=(*w)->Transporters2(ch);
     }
     i+=nchems;
-
   }
-
   return values;
 }
 
 void Mesh::DrawNodes(QGraphicsScene *c) const {
 
-  for (vector<Node *>::const_iterator n=nodes.begin();
-       n!=nodes.end();
-       n++) {
-
+  for (vector<Node *>::const_iterator n=nodes.begin(); n!=nodes.end(); n++) {
     Node *i=*n;
 
     NodeItem *item = new NodeItem ( &(*i), c );
@@ -2118,21 +1901,15 @@ double Mesh::CalcProtCellsWalls(int ch) 
   double sum_prot=0.;
 
   // At membranes
-  for (list<Wall *>::const_iterator w=walls.begin();
-       w!=walls.end();
-       w++) {
+  for (list<Wall *>::const_iterator w=walls.begin(); w!=walls.end(); w++) {
     sum_prot += (*w)->Transporters1(ch);
     sum_prot += (*w)->Transporters2(ch);
   }
 
   // At cells
-  for (vector<Cell *>::const_iterator c=cells.begin();
-       c!=cells.end();
-       c++) {
-
+  for (vector<Cell *>::const_iterator c=cells.begin(); c!=cells.end(); c++) {
     sum_prot += (*c)->Chemical(ch);
   }
-
   return sum_prot;
 }
 
@@ -2164,9 +1941,7 @@ string Mesh::getTimeHours(void) const {
 
 QVector<qreal> Mesh::VertexAngles(void) {
   QVector<qreal> angles;
-  for (vector<Node *>::const_iterator n=nodes.begin();
-       n!=nodes.end();
-       n++) {
+  for (vector<Node *>::const_iterator n=nodes.begin(); n!=nodes.end(); n++) {
     if ((*n)->Value()>2 && !(*n)->BoundaryP() ) {
       angles+=(*n)->NeighbourAngles();
     }
@@ -2177,17 +1952,11 @@ QVector<qreal> Mesh::VertexAngles(void) 
 QVector< QPair<qreal,int> > Mesh::VertexAnglesValues(void) {
 
   QVector< QPair<qreal,int> > anglesvalues;
-  for (vector<Node *>::const_iterator n=nodes.begin();
-       n!=nodes.end();
-       n++) {
+  for (vector<Node *>::const_iterator n=nodes.begin(); n!=nodes.end(); n++) {
     if ((*n)->Value()>2 && !(*n)->BoundaryP() ) {
-
       QVector<qreal> angles = (*n)->NeighbourAngles();
       int value_vertex = angles.size();
-      for (QVector<qreal>::ConstIterator i=angles.begin();
-	   i!=angles.end();
-	   i++) {
-
+      for (QVector<qreal>::ConstIterator i=angles.begin(); i!=angles.end(); i++) {
 	anglesvalues += QPair< qreal, int > (*i, value_vertex);
       }
     }
@@ -2199,9 +1968,7 @@ void Mesh::Clean(void) {
 #ifdef QDEBUG
   qDebug() << "Freeing nodes" << endl;
 #endif
-  for (vector<Node *>::iterator i=nodes.begin();
-       i!=nodes.end();
-       i++) {
+  for (vector<Node *>::iterator i=nodes.begin(); i!=nodes.end(); i++) {
     delete *i;
   }
   nodes.clear();
@@ -2210,9 +1977,7 @@ void Mesh::Clean(void) {
 #ifdef QDEBUG
   qDebug() << "Freeing node sets" << endl;
 #endif
-  for (vector<NodeSet *>::iterator i=node_sets.begin();
-       i!=node_sets.end();
-       i++) {
+  for (vector<NodeSet *>::iterator i=node_sets.begin(); i!=node_sets.end(); i++) {
     delete *i;
   }
   node_sets.clear();
@@ -2222,9 +1987,7 @@ void Mesh::Clean(void) {
   qDebug() << "Freeing cells" << endl;
 #endif	
   //CellsStaticDatamembers *old_static_data_mem = Cell::GetStaticDataMemberPointer();
-  for (vector<Cell *>::iterator i=cells.begin();
-       i!=cells.end();
-       i++) {
+  for (vector<Cell *>::iterator i=cells.begin(); i!=cells.end(); i++) {
     delete *i;
   }
   //Cell::static_data_members = old_static_data_mem;
@@ -2237,9 +2000,7 @@ void Mesh::Clean(void) {
 #ifdef QDEBUG
   qDebug() << "Freeing walls" << endl;
 #endif
-  for (list<Wall *>::iterator i=walls.begin();
-       i!=walls.end();
-       i++) {
+  for (list<Wall *>::iterator i=walls.begin(); i!=walls.end(); i++) {
     delete *i;
   }
   walls.clear();
@@ -2266,4 +2027,4 @@ void Mesh::StandardInit(void) {
   }
 }
 
-
+/* finis */
diff --git a/src/modelcatalogue.h b/src/modelcatalogue.h
--- a/src/modelcatalogue.h
+++ b/src/modelcatalogue.h
@@ -56,4 +56,7 @@ class ModelCatalogue : public QObject {
   Mesh *mesh;
   Main *mainwin;
 };
+
 #endif
+
+/* finis */
diff --git a/src/modelelement.h b/src/modelelement.h
--- a/src/modelelement.h
+++ b/src/modelelement.h
@@ -35,4 +35,7 @@ class ModelElement {
   virtual void Displace(void) {};
   virtual ~ModelElement() {};
 };
+
 #endif
+
+/* finis */
diff --git a/src/node.cpp b/src/node.cpp
--- a/src/node.cpp
+++ b/src/node.cpp
@@ -173,10 +173,7 @@ void Node::DrawOwners(QGraphicsScene *c)
 QVector<qreal> Node::NeighbourAngles(void)
 {
   QVector<qreal> angles;
-  for (list<Neighbor>::iterator i=owners.begin();
-       i!=owners.end();
-       i++) {
-
+  for (list<Neighbor>::iterator i=owners.begin(); i!=owners.end(); i++) {
     Vector v1 = (*this - *i->nb1).Normalised();
     Vector v2 = (*this - *i->nb2).Normalised();	
 
@@ -193,9 +190,7 @@ QVector<qreal> Node::NeighbourAngles(voi
   }
 
   double sum=0.;
-  for (QVector<qreal>::iterator i=angles.begin();
-       i!=angles.end();
-       i++) {
+  for (QVector<qreal>::iterator i=angles.begin(); i!=angles.end(); i++) {
     sum+=*i;
   }
   //cerr << "Angle sum = " << sum << endl;
diff --git a/src/parameter.cpp b/src/parameter.cpp
--- a/src/parameter.cpp
+++ b/src/parameter.cpp
@@ -1880,3 +1880,4 @@ ostream &operator<<(ostream &os, Paramet
   return os;
 }
 
+/* finis */
diff --git a/src/parameter.h b/src/parameter.h
--- a/src/parameter.h
+++ b/src/parameter.h
@@ -145,5 +145,6 @@ class Parameter {
 ostream &operator<<(ostream &os, Parameter &p);
 const char *sbool(const bool &p);
 
+#endif
 
-#endif
+/* finis */
diff --git a/src/pardialog.cpp b/src/pardialog.cpp
--- a/src/pardialog.cpp
+++ b/src/pardialog.cpp
@@ -803,3 +803,5 @@ void ParameterDialog::Reset(void) {
   dir2_edit->setText( QString("%1").arg(par.dir2) );
 }
 
+
+/* finis */
diff --git a/src/pardialog.h b/src/pardialog.h
--- a/src/pardialog.h
+++ b/src/pardialog.h
@@ -142,4 +142,7 @@ class ParameterDialog : public QDialog {
   QLineEdit *dir1_edit;
   QLineEdit *dir2_edit;
 };
+
 #endif
+
+/* finis */
diff --git a/src/xmlwrite.cpp b/src/xmlwrite.cpp
--- a/src/xmlwrite.cpp
+++ b/src/xmlwrite.cpp
@@ -750,9 +750,7 @@ 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++) {
+  for (vector<Node *>::const_iterator i=nodes.begin(); i!=nodes.end(); i++) {
     (*i)->XMLAdd(xmlnodes) ;
   }
 
@@ -797,9 +795,7 @@ void Mesh::XMLSave(const char *docname, 
     xmlNewProp(xmlcells, BAD_CAST "nchem", BAD_CAST text.str().c_str());
   }
 
-  for (vector<Cell *>::const_iterator i=cells.begin();
-       i!=cells.end();
-       i++) {
+  for (vector<Cell *>::const_iterator i=cells.begin(); i!=cells.end(); i++) {
     (*i)->XMLAdd(xmlcells) ;
   }
 
@@ -813,9 +809,7 @@ void Mesh::XMLSave(const char *docname, 
   }
 
 
-  for (list<Wall *>::const_iterator i=walls.begin();
-       i!=walls.end();
-       i++) {
+  for (list<Wall *>::const_iterator i=walls.begin(); i!=walls.end(); i++) {
     (*i)->XMLAdd(xmlwalls) ;
   }
 
@@ -985,13 +979,9 @@ void Mesh::XMLReadGeometry(const xmlNode
   boundary_polygon->ConstructNeighborList();
   boundary_polygon->ConstructConnections();
 
-  for (vector<Cell *>::iterator c=cells.begin();
-       c!=cells.end();
-       c++) {
-
+  for (vector<Cell *>::iterator c=cells.begin(); c!=cells.end(); c++) {
     (*c)->ConstructNeighborList();
     (*c)->ConstructConnections();
-
   }
 
   shuffled_cells.clear();
@@ -1018,9 +1008,7 @@ void Mesh::XMLReadNodes(xmlNode *root)
   xmlNode *cur = root;
   cur = cur->xmlChildrenNode;
 
-  for (vector<Node *>::iterator i=nodes.begin();
-       i!=nodes.end();
-       i++) {
+  for (vector<Node *>::iterator i=nodes.begin(); i!=nodes.end(); i++) {
     delete *i;
   }
 
@@ -1108,9 +1096,7 @@ void Mesh::XMLReadWalls(xmlNode *root, v
   xmlNode *cur = root;
   cur = cur->xmlChildrenNode;
 
-  for (list<Wall *>::iterator i=walls.begin();
-       i!=walls.end();
-       i++) {
+  for (list<Wall *>::iterator i=walls.begin(); i!=walls.end(); i++) {
     delete *i;
   }
 
@@ -1425,9 +1411,7 @@ void Mesh::XMLReadNodeSetsToNodes(xmlNod
 void Mesh::XMLReadNodeSets(xmlNode *root)
 {
 
-  for (vector<NodeSet *>::iterator i=node_sets.begin();
-       i!=node_sets.end();
-       i++) {
+  for (vector<NodeSet *>::iterator i=node_sets.begin(); i!=node_sets.end(); i++) {
     delete *i;
   }
 
@@ -1455,10 +1439,7 @@ void Mesh::XMLReadNodeSets(xmlNode *root
 
 void Mesh::XMLReadCells(xmlNode *root)
 {
-
-  for (vector<Cell *>::iterator i=cells.begin();
-       i!=cells.end();
-       i++) {
+  for (vector<Cell *>::iterator i=cells.begin(); i!=cells.end(); i++) {
     delete *i;
   }
 
@@ -1467,7 +1448,6 @@ void Mesh::XMLReadCells(xmlNode *root)
 
   delete boundary_polygon;
 
-
   xmlNode *cur = root->xmlChildrenNode;
 
   while (cur!=NULL) {