EI/VirtualLeaf Changeset - f4023d64bb53 · Centrum Wiskunde & Informatica (CWI)

Changeset - f4023d64bb53

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Roeland Merks - 11 years ago 2014-05-01 16:15:10
merks@cwi.nl

Fixed some minor syntactic errors that popped up after compiling on MacOSX10.8.5

5 files changed with 8 insertions and 8 deletions:

src/VirtualLeaf.cpp

src/canvas.cpp

src/modelcatalogue.cpp

src/parameter.cpp

src/xmlwrite.cpp

0 comments (0 inline, 0 general)

src/VirtualLeaf.cpp

➞

Show inline comments

@@ @@ -411,59 +411,59 @@ int main(int argc,char **argv) { @@
+    }
     canvas.setSceneRect(QRectF());
     if (!batch) {
       QObject::connect( qApp, SIGNAL(lastWindowClosed()), qApp, SLOT(quit()) );
+    }
     //    main_window->Init(leaffile);
     // Install model or read catalogue of models
     ModelCatalogue model_catalogue(&mesh, main_window,modelfile);
     if (useGUI)
       model_catalogue.PopulateModelMenu();
     model_catalogue.InstallFirstModel();
     /*    Cell::SetMagnification(1);
 	  Cell::setOffset(0,0);
 	  main_window->FitLeafToCanvas();
 	  main_window->Plot();
     */
     if (batch) {
       double t=0.;
       do {
 	t = main_window->TimeStep();
       } while (t < par.maxt);
     } else
       return app.exec();
   } catch (const char *message) {
     if (batch) {
       cerr << "Exception caught:" << endl;
       cerr << message << endl;
       abort();
     } else {
       QString qmess=QString("Exception caught: %1").arg(message);
       QMessageBox::critical(0, "Critical Error", qmess);
       abort();
+    }
   } catch (ios_base::failure) {
     stringstream error_message;
     error_message << "I/O failure: " << strerror(errno);
     if (batch) {
       cerr << error_message.str() <<endl;
+      cerr << error_message.str().c_str() <<endl;
       abort();
     } else {
       QString qmess(error_message.str().c_str());
       QMessageBox::critical(0, "I/O Error", qmess );
       abort();
+    }
+  }
+}
 /* finis */

src/canvas.cpp

➞

Show inline comments

@@ @@ -674,224 +674,224 @@ void Main::readPars() @@
     fileName = fd->selectedFile();
     par.Read((const char *)fileName);
+  }
   emit ParsChanged();
+}
 void Main::saveStateXML()
+{
   stopSimulation();
   Q3FileDialog *fd = new Q3FileDialog( this, "file dialog", TRUE );
   fd->setMode( Q3FileDialog::AnyFile );
   fd->setFilter( "LeafML files (*.xml)");
   fd->setDir(par.datadir);
   QString fileName;
   if ( fd->exec() == QDialog::Accepted ) {
     fileName = fd->selectedFile();
     // extract extension from filename
     QFileInfo fi(fileName);
     QString extension = fi.suffix();
     if (extension.isEmpty()) {
       extension = "xml";
       fileName += ".";
       fileName += extension;
+    }
     if ( QFile::exists( fileName ) &&
 	 QMessageBox::question(
 			       this,
 			       tr("Overwrite File? -- Leaf Growth"),
 			       tr("A file called %1 already exists."
 				  " Do you want to overwrite it?")
 			       .arg( fileName ),
 			       tr("&Yes"), tr("&No"),
 			       QString::null, 1, 1 ) ) {
       return saveStateXML();
     } else {
       mesh.XMLSave((const char *)fileName, XMLSettingsTree());
       QString status_message;
       status_message = QString("Wrote LeafML to %1").arg(fileName);
       cerr << status_message.toStdString() << endl;
+      cerr << status_message.toStdString().c_str() << endl;
       statusBar()->showMessage(status_message);
+    }
+  }
+}
 void Main::snapshot()
+{
 #ifdef QDEBUG
   qDebug() << "Supported Image Formats: " << QImageWriter::supportedImageFormats() << endl;
 #endif
   stopSimulation();
   Q3FileDialog *fd = new Q3FileDialog( this, "Save snapshot", TRUE );
   fd->setDir(par.datadir);
   fd->setMode( Q3FileDialog::AnyFile );
   QString supported_file_formats = " *.pdf";
   foreach (QString format, QImageWriter::supportedImageFormats()){
     supported_file_formats += (" *." + format);
+  }
   fd->setFilter("Image files (" + supported_file_formats + " )");
   QString fileName;
   if ( fd->exec() == QDialog::Accepted ) {
     fileName = fd->selectedFile();
     // extract extension from filename
     QFileInfo fi(fileName);
     QString extension = fi.suffix();
     if (extension.isEmpty()) {
       extension = "png";
       fileName += ".";
       fileName += extension;
+    }
     if ( QFile::exists( fileName ) &&
 	 QMessageBox::question(
 			       this,
 			       tr("Overwrite file? -- Cell data export"),
 			       tr("A file called %1 already exists."
 				  " Do you want to overwrite it?").arg( fileName ),
 			       QMessageBox::Yes, QMessageBox::No
 			       ) == QMessageBox::No
 	 ) {
       return snapshot();
     } else {
       // Save bitmaps at 1024x768
       QString status_message;
       if (Save((const char *)fileName, extension, 1024, 768)==0) {
 	status_message = QString("Wrote snapshot to %1").arg(fileName);
       } else {
 	status_message = QString("Error writing snapshot to %1").arg(fileName);
+      }
       cerr << status_message.toStdString() << endl;
+      cerr << status_message.toStdString().c_str() << endl;
       statusBar()->showMessage(status_message);
+    }
+  }
+}
 void Main::readPrevStateXML()
+{
   // if we have already read a file, read the next file
   if (!currentFile.isEmpty() && working_dir) {
     QString next_file;
     QStringList xml_files = working_dir->entryList("*.xml");
     QString currentFile_nopath = currentFile.section( '/', -1 );
     QString currentFile_path = currentFile.section( '/', 0, -2 );
     QList<QString>::iterator f = xml_files.find( currentFile_nopath );
     if (f == xml_files.end()) {
       return;
+    }
     if (f==xml_files.begin()) {
       QMessageBox mb( "Read previous leaf",
 		      "No more files",
 		      QMessageBox::Information,
 		      QMessageBox::Ok | QMessageBox::Default,
 		      QMessageBox::NoButton,
 		      QMessageBox::NoButton);
       mb.exec();
       return;
+    }
     next_file = *(--f);
     next_file = currentFile_path+"/"+next_file;
     readStateXML((const char *)next_file);
+  }
+}
 int Main::readStateXML(const char *filename, bool geometry, bool pars, bool simtime)
+{
   try {
     xmlNode *settings;
     mesh.XMLRead((const char *)filename, &settings, geometry, pars, simtime);
 #ifdef QDEBUG
     qDebug() << "Reading done."<< endl;
 #endif
     XMLReadSettings(settings);
     xmlFree(settings);
     Cell::SetMagnification(1);
     Cell::setOffset(0,0);
     FitLeafToCanvas();
     currentFile =  QString(filename);
     Plot();
     QString status_message = QString("Successfully read leaf from file %1. Time is %2 h.").arg(currentFile).arg(mesh.getTimeHours().c_str());
     cerr << status_message.toStdString() << endl;
+    cerr << status_message.toStdString().c_str() << endl;
     setCaption(caption_with_file.arg(filename));
     statusBar()->message(status_message);
     emit ParsChanged();
 #ifdef QDEBUG
     qDebug() << "Done. Returning 0." << endl;
 #endif
     return 0;
   } catch (const char *error_message) {
     QMessageBox mb( "Read leaf from XML file",
 		    QString(error_message),
 		    QMessageBox::Critical,
 		    QMessageBox::Ok | QMessageBox::Default,
 		    Qt::NoButton,
 		    Qt::NoButton);
     mb.exec();
     return 1;
+  }
+}
 void Main::readNextStateXML()
+{
   // if we have already read a file, read the next file
   if (!currentFile.isEmpty() && working_dir) {
     QString next_file;
     QStringList xml_files = working_dir->entryList("*.xml");
     QString currentFile_nopath = currentFile.section( '/', -1 );
     QString currentFile_path = currentFile.section( '/', 0, -2 );
     QList<QString>::iterator f = xml_files.find( currentFile_nopath );
     if (f == xml_files.end()) {
       return;
+    }
     ++f;
     if (f==xml_files.end()) {
       QMessageBox mb( "Read next leaf",
 		      "No more files",
 		      QMessageBox::Information,
 		      QMessageBox::Ok | QMessageBox::Default,
 		      QMessageBox::NoButton,
 		      QMessageBox::NoButton);
       mb.exec();
       return;

src/modelcatalogue.cpp

➞

Show inline comments

@@ @@ -94,97 +94,97 @@ void ModelCatalogue::LoadPlugin(const ch @@
     pluginDir.cdUp();
     pluginDir.cdUp();
     pluginDir.cdUp();
+  }
   //plugin_filters << "*.dylib";
 #endif
   plugin_filters << model;
   pluginDir.setNameFilters(plugin_filters);
   if (!pluginDir.cd("models")) {
     MyWarning::error("Directory 'models' not found!");
+  }
   QStringList modelnames=pluginDir.entryList(QDir::Files);
   if (modelnames.empty()) {
     MyWarning::error("Model %s not found - hint: do not include path in filename.",model);
+  }
   foreach (QString fileName, modelnames){
     QPluginLoader loader(pluginDir.absoluteFilePath(fileName));
     if (SimPluginInterface *plugin =
 	qobject_cast<SimPluginInterface *>(loader.instance())) {
       models.append(plugin);
       //MyWarning::warning("Successfully loaded model %s",fileName.toStdString().c_str());
     } else {
       MyWarning::warning("Could not load plugin %s",fileName.toStdString().c_str());
+    }
+  }
+}
 void ModelCatalogue::InstallFirstModel() {
   InstallModel(models[0]);
+}
 void ModelCatalogue::PopulateModelMenu() {
   foreach (SimPluginInterface *model, models) {
     QAction *modelaction = new QAction(model->ModelID(), (Main *)mainwin);
     QVariant data;
     data.setValue(model);
     modelaction->setData(data);
     ((Main *)mainwin)->modelmenu->addAction(modelaction);
+  }
   connect(((Main *)mainwin)->modelmenu, SIGNAL(triggered(QAction *)), this, SLOT(InstallModel(QAction *)) );
+}
 void ModelCatalogue::InstallModel(QAction *modelaction) {
   QVariant data = modelaction->data();
   SimPluginInterface *model = data.value<SimPluginInterface *>();
   cerr << "You chose model " << model->ModelID().toStdString() << "!\n";
+  cerr << "You chose model " << model->ModelID().toStdString().c_str() << "!\n";
   mesh->Clean();
   InstallModel(model);
+}
 void ModelCatalogue::InstallModel(SimPluginInterface *plugin) {
   // make sure both main and plugin use the same static datamembers (ncells, nchems...)
   mesh->Clean();
   plugin->SetCellsStaticDatamembers(CellBase::GetStaticDataMemberPointer());
   mesh->SetSimPlugin(plugin);
   Cell::SetNChem(plugin->NChem());
   plugin->SetParameters(&par);
   if (mainwin) {
     if (!qApp->type()==QApplication::Tty)  // only do this if we are running a GUI
       ((Main *)mainwin)->RefreshInfoBar();
     if (plugin->DefaultLeafML().isEmpty()) {
       mainwin->Init(0);
     } else {
       // locate LeafML file
       QDir pluginDir(QApplication::applicationDirPath());
       QStringList plugin_filters; // filter for plugins, i.e "*.dll", "*.dylib"
 #if defined(Q_OS_WIN)
       if (pluginDir.dirName().toLower() =="debug"
 	  ||pluginDir.dirName().toLower() =="release")
 	pluginDir.cdUp();
       //plugin_filters << "*.dll";
 #elif defined(Q_OS_MAC)
       if (pluginDir.dirName() =="MacOS"){
 	pluginDir.cdUp();
 	pluginDir.cdUp();
 	pluginDir.cdUp();
+      }
 #endif
       // for all OS-es. Move from "bin" directory to root application folder.
       if (pluginDir.dirName() == "bin") {
 	pluginDir.cdUp();
+      }
       cerr << "pluginDir: " << pluginDir.dirName().toStdString().c_str() << endl;

src/parameter.cpp

➞

Show inline comments

@@ @@ -343,97 +343,97 @@ void Parameter::Read(const char *filenam @@
   s3 = sgetpar(fp, "s3", "", true);
   b1 = bgetpar(fp, "b1", false, true);
   b2 = bgetpar(fp, "b2", false, true);
   b3 = bgetpar(fp, "b3", false, true);
   b4 = bgetpar(fp, "b4", false, true);
   dir1 = sgetpar(fp, "dir1", ".", true);
   if (strcmp(dir1, "."))
     MakeDir(dir1);
   dir2 = sgetpar(fp, "dir2", ".", true);
   if (strcmp(dir2, "."))
     MakeDir(dir2);
+}
 const char *sbool(const bool &p) {
   const char *true_str="true";
   const char *false_str="false";
   if (p)
     return true_str;
   else
     return false_str;
+}
 void Parameter::Write(ostream &os) const {
   if (arrowcolor)
   os << " arrowcolor = " << arrowcolor << endl;
   os << " arrowsize = " << arrowsize << endl;
   if (textcolor)
   os << " textcolor = " << textcolor << endl;
   os << " cellnumsize = " << cellnumsize << endl;
   os << " nodenumsize = " << nodenumsize << endl;
   os << " node_mag = " << node_mag << endl;
   os << " outlinewidth = " << outlinewidth << endl;
   if (cell_outline_color)
   os << " cell_outline_color = " << cell_outline_color << endl;
   os << " resize_stride = " << resize_stride << endl;
   os << " export_interval = " << export_interval << endl;
   if (export_fn_prefix)
   os << " export_fn_prefix = " << export_fn_prefix << endl;
   os << " storage_stride = " << storage_stride << endl;
   os << " xml_storage_stride = " << xml_storage_stride << endl;
   if (datadir) {
                                      QDir dataDir = QDir::home().relativeFilePath(datadir);
                                      os << " datadir = " << dataDir.dirName().toStdString() << endl;
+                                     os << " datadir = " << dataDir.dirName().toStdString().c_str() << endl;
+                                 }
                                  else {
                                      os << "datadir = ." << endl;
+                                 }
   os << " T = " << T << endl;
   os << " lambda_length = " << lambda_length << endl;
   os << " yielding_threshold = " << yielding_threshold << endl;
   os << " lambda_celllength = " << lambda_celllength << endl;
   os << " target_length = " << target_length << endl;
   os << " cell_expansion_rate = " << cell_expansion_rate << endl;
   os << " cell_div_expansion_rate = " << cell_div_expansion_rate << endl;
   os << " auxin_dependent_growth = " << sbool(auxin_dependent_growth) << endl;
   os << " ode_accuracy = " << ode_accuracy << endl;
   os << " mc_stepsize = " << mc_stepsize << endl;
   os << " mc_cell_stepsize = " << mc_cell_stepsize << endl;
   os << " energy_threshold = " << energy_threshold << endl;
   os << " bend_lambda = " << bend_lambda << endl;
   os << " alignment_lambda = " << alignment_lambda << endl;
   os << " rel_cell_div_threshold = " << rel_cell_div_threshold << endl;
   os << " rel_perimeter_stiffness = " << rel_perimeter_stiffness << endl;
   os << " collapse_node_threshold = " << collapse_node_threshold << endl;
   os << " morphogen_div_threshold = " << morphogen_div_threshold << endl;
   os << " morphogen_expansion_threshold = " << morphogen_expansion_threshold << endl;
   os << " copy_wall = " << sbool(copy_wall) << endl;
   os << " source = " << source << endl;
   os << " D = "<< D[0] << ", " << D[1] << ", " << D[2] << ", " << D[3] << ", " << D[4] << ", " << D[5] << ", " << D[6] << ", " << D[7] << ", " << D[8] << ", " << D[9] << ", " << D[10] << ", " << D[11] << ", " << D[12] << ", " << D[13] << ", " << D[14] << endl;
   os << " initval = "<< initval[0] << ", " << initval[1] << ", " << initval[2] << ", " << initval[3] << ", " << initval[4] << ", " << initval[5] << ", " << initval[6] << ", " << initval[7] << ", " << initval[8] << ", " << initval[9] << ", " << initval[10] << ", " << initval[11] << ", " << initval[12] << ", " << initval[13] << ", " << initval[14] << endl;
   os << " k1 = " << k1 << endl;
   os << " k2 = " << k2 << endl;
   os << " r = " << r << endl;
   os << " kr = " << kr << endl;
   os << " km = " << km << endl;
   os << " Pi_tot = " << Pi_tot << endl;
   os << " transport = " << transport << endl;
   os << " ka = " << ka << endl;
   os << " pin_prod = " << pin_prod << endl;
   os << " pin_prod_in_epidermis = " << pin_prod_in_epidermis << endl;
   os << " pin_breakdown = " << pin_breakdown << endl;
   os << " pin_breakdown_internal = " << pin_breakdown_internal << endl;
   os << " aux1prod = " << aux1prod << endl;
   os << " aux1prodmeso = " << aux1prodmeso << endl;
   os << " aux1decay = " << aux1decay << endl;
   os << " aux1decaymeso = " << aux1decaymeso << endl;
   os << " aux1transport = " << aux1transport << endl;
   os << " aux_cons = " << aux_cons << endl;
   os << " aux_breakdown = " << aux_breakdown << endl;
   os << " kaux1 = " << kaux1 << endl;
   os << " kap = " << kap << endl;
@@ @@ -555,97 +555,97 @@ xmlNewProp(xmlpar, BAD_CAST "val", BAD_C @@
   if (cell_outline_color)
     text << cell_outline_color;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "resize_stride" );
   ostringstream text;
     text << resize_stride;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "export_interval" );
   ostringstream text;
     text << export_interval;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "export_fn_prefix" );
   ostringstream text;
   if (export_fn_prefix)
     text << export_fn_prefix;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "storage_stride" );
   ostringstream text;
     text << storage_stride;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "xml_storage_stride" );
   ostringstream text;
     text << xml_storage_stride;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "datadir" );
   ostringstream text;
   if (datadir) {
                                      QDir dataDir = QDir::home().relativeFilePath(datadir);
                                      text << dataDir.dirName().toStdString();
+                                     text << dataDir.dirName().toStdString().c_str();
+                                   }
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "T" );
   ostringstream text;
     text << T;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "lambda_length" );
   ostringstream text;
     text << lambda_length;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "yielding_threshold" );
   ostringstream text;
     text << yielding_threshold;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "lambda_celllength" );
   ostringstream text;
     text << lambda_celllength;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "target_length" );
   ostringstream text;
     text << target_length;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "cell_expansion_rate" );
   ostringstream text;
     text << cell_expansion_rate;
 xmlNewProp(xmlpar, BAD_CAST "val", BAD_CAST text.str().c_str());
+}
+{
   xmlNode *xmlpar = xmlNewChild(xmlparameter, NULL, BAD_CAST "par", NULL);
   xmlNewProp(xmlpar, BAD_CAST "name", BAD_CAST "cell_div_expansion_rate" );

src/xmlwrite.cpp

➞

Show inline comments

@@ @@ -580,97 +580,97 @@ void Wall::XMLAdd(xmlNode *parent) const @@
+  {
     ostringstream text;
     text << Index();
     xmlNewProp(xmlwall, BAD_CAST "index" , BAD_CAST text.str().c_str() );
+  }
+  {
     ostringstream text;
     text << c1->Index();
     xmlNewProp(xmlwall, BAD_CAST "c1", BAD_CAST text.str().c_str());
+  }
+  {
     ostringstream text;
     text << c2->Index();
     xmlNewProp(xmlwall, BAD_CAST "c2", BAD_CAST text.str().c_str());
+  }
+  {
     ostringstream text;
     text << n1->Index();
     xmlNewProp(xmlwall, BAD_CAST "n1", BAD_CAST text.str().c_str());
+  }
+  {
     ostringstream text;
     text << n2->Index();
     xmlNewProp(xmlwall, BAD_CAST "n2", BAD_CAST text.str().c_str());
+  }
+  {
     ostringstream text;
     text << length;
     xmlNewProp(xmlwall, BAD_CAST "length", BAD_CAST text.str().c_str());
+  }
+  {
     ostringstream text;
     text << viz_flux;
     xmlNewProp(xmlwall, BAD_CAST "viz_flux", BAD_CAST text.str().c_str());
+  }
+  {
     ostringstream text;
     text << WallTypetoStr(wall_type);
+    text << WallTypetoStr(wall_type).c_str();
     xmlNewProp(xmlwall, BAD_CAST "wall_type", BAD_CAST text.str().c_str());
+  }
   xmlNodePtr tr1_xml = xmlNewChild(xmlwall, NULL, BAD_CAST "transporters1", NULL);
   if (transporters1) {
     for (int i=0;i<Cell::NChem();i++) {
       xmlNodePtr tr1_val_xml = xmlNewChild(tr1_xml, NULL, BAD_CAST "val", NULL);
+      {
 	ostringstream text;
 	text << transporters1[i];
 	xmlNewProp(tr1_val_xml, BAD_CAST "v", BAD_CAST text.str().c_str());
+      }
+    }
+  }
   if (transporters2) {
     xmlNodePtr tr2_xml = xmlNewChild(xmlwall, NULL, BAD_CAST "transporters2", NULL);
     for (int i=0;i<Cell::NChem();i++) {
       xmlNodePtr tr2_val_xml = xmlNewChild(tr2_xml, NULL, BAD_CAST "val", NULL);
+      {
 	ostringstream text;
 	text << transporters2[i];
 	xmlNewProp(tr2_val_xml, BAD_CAST "v", BAD_CAST text.str().c_str());
+      }
+    }
+  }
 /*  if (apoplast) {
     xmlNodePtr apo_xml = xmlNewChild(xmlwall, NULL, BAD_CAST "apoplast", NULL);
     for (int i=0;i<Cell::NChem();i++) {
       xmlNodePtr apo_val_xml = xmlNewChild(apo_xml, NULL, BAD_CAST "val", NULL);
+      {
 	ostringstream text;
 	text << transporters2[i];
 	xmlNewProp(apo_val_xml, BAD_CAST "v", BAD_CAST text.str().c_str());
+      }
+    }
   } */
+}
 vector<double> XMLIO::XMLReadValArray(xmlNode *cur)
+{
   vector<double> result;

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