diff --git a/src/mainbase.cpp b/src/mainbase.cpp
new file mode 100644
--- /dev/null
+++ b/src/mainbase.cpp
@@ -0,0 +1,260 @@
+/*
+ *
+ *  This file is part of the Virtual Leaf.
+ *
+ *  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 <libxml/xpath.h>
+#include <libxml/xmlreader.h>
+
+#include "mainbase.h"
+#include "xmlwrite.h"
+
+#include <sstream>
+#include <string>
+
+static const std::string _module_id("$Id$");
+
+xmlNode *MainBase::XMLSettingsTree(void) const {
+	
+	xmlNode *xmlsettings = xmlNewNode(NULL, BAD_CAST "settings");
+	{
+		xmlNode *xmloption = xmlNewChild(xmlsettings, NULL, BAD_CAST "setting", NULL);
+		xmlNewProp(xmloption, BAD_CAST "name", BAD_CAST "show_cell_centers");
+		ostringstream text;
+		text << bool_name(showcentersp);
+		xmlNewProp(xmloption, BAD_CAST "val", BAD_CAST text.str().c_str());
+	}
+	{
+		xmlNode *xmloption = xmlNewChild(xmlsettings, NULL, BAD_CAST "setting", NULL);
+		xmlNewProp(xmloption, BAD_CAST "name", BAD_CAST "show_nodes");
+		ostringstream text;
+		text << bool_name(showmeshp);
+		xmlNewProp(xmloption, BAD_CAST "val", BAD_CAST text.str().c_str());
+	}
+	{
+		xmlNode *xmloption = xmlNewChild(xmlsettings, NULL, BAD_CAST "setting", NULL);
+		xmlNewProp(xmloption, BAD_CAST "name", BAD_CAST "show_node_numbers");
+		ostringstream text;
+		text << bool_name(shownodenumbersp);
+		xmlNewProp(xmloption, BAD_CAST "val", BAD_CAST text.str().c_str());
+	}
+	{
+		xmlNode *xmloption = xmlNewChild(xmlsettings, NULL, BAD_CAST "setting", NULL);
+		xmlNewProp(xmloption, BAD_CAST "name", BAD_CAST "show_cell_numbers");
+		ostringstream text;
+		text << bool_name(showcellnumbersp);
+		xmlNewProp(xmloption, BAD_CAST "val", BAD_CAST text.str().c_str());
+	}
+	{
+		xmlNode *xmloption = xmlNewChild(xmlsettings, NULL, BAD_CAST "setting", NULL);
+		xmlNewProp(xmloption, BAD_CAST "name", BAD_CAST "show_border_cells");
+		ostringstream text;
+		text << bool_name(showbordercellp);
+		xmlNewProp(xmloption, BAD_CAST "val", BAD_CAST text.str().c_str());
+	}
+	{
+		xmlNode *xmloption = xmlNewChild(xmlsettings, NULL, BAD_CAST "setting", NULL);
+		xmlNewProp(xmloption, BAD_CAST "name", BAD_CAST "show_cell_axes");
+		ostringstream text;
+		text << bool_name(showcellsaxesp);
+		xmlNewProp(xmloption, BAD_CAST "val", BAD_CAST text.str().c_str());
+	}
+	{
+		xmlNode *xmloption = xmlNewChild(xmlsettings, NULL, BAD_CAST "setting", NULL);
+		xmlNewProp(xmloption, BAD_CAST "name", BAD_CAST "show_cell_strain");
+		ostringstream text;
+		text << bool_name(showcellstrainp);
+		xmlNewProp(xmloption, BAD_CAST "val", BAD_CAST text.str().c_str());
+	}
+	{
+		xmlNode *xmloption = xmlNewChild(xmlsettings, NULL, BAD_CAST "setting", NULL);
+		xmlNewProp(xmloption, BAD_CAST "name", BAD_CAST "show_fluxes");
+		ostringstream text;
+		text << bool_name(showfluxesp);
+		xmlNewProp(xmloption, BAD_CAST "val", BAD_CAST text.str().c_str());
+	}
+	{
+		xmlNode *xmloption = xmlNewChild(xmlsettings, NULL, BAD_CAST "setting", NULL);
+		xmlNewProp(xmloption, BAD_CAST "name", BAD_CAST "show_walls");
+		ostringstream text;
+		text << bool_name(showwallsp);
+		xmlNewProp(xmloption, BAD_CAST "val", BAD_CAST text.str().c_str());
+	}
+	{
+		xmlNode *xmloption = xmlNewChild(xmlsettings, NULL, BAD_CAST "setting", NULL);
+		xmlNewProp(xmloption, BAD_CAST "name", BAD_CAST "show_apoplasts");
+		ostringstream text;
+		text << bool_name(showapoplastsp);
+		xmlNewProp(xmloption, BAD_CAST "val", BAD_CAST text.str().c_str());
+	}
+	{
+		xmlNode *xmloption = xmlNewChild(xmlsettings, NULL, BAD_CAST "setting", NULL);
+		xmlNewProp(xmloption, BAD_CAST "name", BAD_CAST "save_movie_frames");
+		ostringstream text;
+		text << bool_name(movieframesp);
+		xmlNewProp(xmloption, BAD_CAST "val", BAD_CAST text.str().c_str());
+	}
+	{
+		xmlNode *xmloption = xmlNewChild(xmlsettings, NULL, BAD_CAST "setting", NULL);
+		xmlNewProp(xmloption, BAD_CAST "name", BAD_CAST "show_only_leaf_boundary");
+		ostringstream text;
+		text << bool_name(showboundaryonlyp);
+		xmlNewProp(xmloption, BAD_CAST "val", BAD_CAST text.str().c_str());
+	}
+	{
+		xmlNode *xmloption = xmlNewChild(xmlsettings, NULL, BAD_CAST "setting", NULL);
+		xmlNewProp(xmloption, BAD_CAST "name", BAD_CAST "cell_growth");
+		ostringstream text;
+		text << bool_name(dynamicscellsp);
+		xmlNewProp(xmloption, BAD_CAST "val", BAD_CAST text.str().c_str());
+	}
+	{
+		xmlNode *xmloption = xmlNewChild(xmlsettings, NULL, BAD_CAST "setting", NULL);
+		xmlNewProp(xmloption, BAD_CAST "name", BAD_CAST "hide_cells");
+		ostringstream text;
+		text << bool_name(hidecellsp);
+		xmlNewProp(xmloption, BAD_CAST "val", BAD_CAST text.str().c_str());
+	}
+	
+	return xmlsettings;
+}
+
+void MainBase::XMLReadSettings(xmlNode *settings) {
+	
+	// Many files have no settings section, so don't complain about it.
+	// Defaults will be used instead.
+	if (settings == 0) {
+		return;
+	}
+	
+	xmlNode *cur = settings->xmlChildrenNode;
+	
+	while (cur!=NULL) {
+		
+		if ((!xmlStrcmp(cur->name, (const xmlChar *)"setting"))){
+			
+			xmlChar *name = xmlGetProp(cur, BAD_CAST "name");
+			xmlChar *val = xmlGetProp(cur, BAD_CAST "val");
+			if (!xmlStrcmp(name, (const xmlChar *)"show_cell_centers")) {
+				showcentersp = strtobool( (const char *)val );
+			}
+			if (!xmlStrcmp(name, (const xmlChar *)"show_nodes")) {
+				showmeshp = strtobool( (const char *)val );
+			}
+			if (!xmlStrcmp(name, (const xmlChar *)"show_node_numbers")) {
+				shownodenumbersp = strtobool( (const char *)val );
+			}
+			if (!xmlStrcmp(name, (const xmlChar *)"show_cell_numbers")) {
+				showcellnumbersp = strtobool( (const char *)val );
+			}
+			if (!xmlStrcmp(name, (const xmlChar *)"show_border_cells")) {
+				showbordercellp = strtobool( (const char *)val );
+			}
+			if (!xmlStrcmp(name, (const xmlChar *)"show_cell_axes")) {
+				showcellsaxesp = strtobool( (const char *)val );
+			}
+			if (!xmlStrcmp(name, (const xmlChar *)"show_cell_strain")) {
+				showcellstrainp = strtobool( (const char *)val );
+			}
+			if (!xmlStrcmp(name, (const xmlChar *)"show_fluxes")) {
+				showfluxesp = strtobool( (const char *)val );
+			}
+			if (!xmlStrcmp(name, (const xmlChar *)"show_walls")) {
+				showwallsp = strtobool( (const char *)val );
+			}
+			if (!xmlStrcmp(name, (const xmlChar *)"show_apoplasts")) {
+				showapoplastsp = strtobool( (const char *)val );
+			}
+			if (!xmlStrcmp(name, (const xmlChar *)"save_movie_frames")) {
+				movieframesp = strtobool( (const char *)val );
+			}
+			if (!xmlStrcmp(name, (const xmlChar *)"show_only_leaf_boundary")) {
+				showboundaryonlyp = strtobool( (const char *)val );
+			}
+			if (!xmlStrcmp(name, (const xmlChar *)"cell_growth")) {
+				dynamicscellsp = strtobool( (const char *)val );
+			}
+			if (!xmlStrcmp(name,(const xmlChar *)"hide_cells")) {
+				hidecellsp = strtobool( (const char *)val ); 
+			}
+			
+			xmlFree(name);
+			xmlFree(val);
+			
+			
+		}
+		cur=cur->next;
+	}
+	
+}
+
+void MainBase::Save(const char *fname, const char *format, int sizex, int sizey) {
+	
+	Vector ll,ur;
+	mesh.BoundingBox(ll, ur);
+	
+	if (QString(fname).isEmpty()) {
+		MyWarning::warning("No output filename given. Saving nothing.\n");
+		return;
+	}
+	
+	
+	ll*=Cell::Magnification(); ur*=Cell::Magnification();
+	
+	// give the leaf some space
+	Vector border = ((ur-ll)/5.);
+	
+	//QRectF bb( ll.x - border.x, ll.y - border.y, ur.x-ll.x + 2*border.x, ur.y-ll.y + 2*border.y );
+	
+	if (!QString(format).contains("pdf", Qt::CaseInsensitive)) {
+	
+		QImage *image = new QImage(QSize(sizex, sizey), QImage::Format_RGB32);
+		image->fill(QColor(Qt::white).rgb());
+		QPainter *painter=new QPainter(image);
+		//canvas.render(painter,QRectF(),QRectF(-5000,-5000, 10000, 10000));
+		canvas.render(painter);
+		if (!image->save(QString(fname))) {
+			MyWarning::warning("Image not saved successfully. Is the disk full or the extension not recognized?");
+		};
+		delete painter;
+		delete image;
+	} else {
+		QPrinter pdf(QPrinter::HighResolution);
+		pdf.setOutputFileName(fname);
+		pdf.setOutputFormat(QPrinter::PdfFormat);
+		//pdf.setPageSize(QPrinter::Custom);
+		QPainter painter(&pdf);
+		//	cerr << "Cell::Magnification() = " << Cell::Magnification() << endl;
+		//if (sizex==0 || sizey==0) {
+			// always fit to page
+		//	canvas.render(&painter);
+		//} else {
+		//	canvas.render(&painter,QRectF(),QRectF(-5000,-5000, 10000, 10000));
+		//}
+		canvas.render(&painter, QRectF(), QRectF(-5000,-5000, 10000, 10000));
+		
+		cerr << "Rendering to printer\n";
+	}
+}
+
+void MainBase::CutSAM() {
+	
+	mesh.CutAwaySAM();
+	
+}