diff --git a/build.gradle b/build.gradle
index ee49e0e..92593cf 100644
--- a/build.gradle
+++ b/build.gradle
@@ -10,7 +10,7 @@ description = "juppaal"
 sourceCompatibility = 1.7
 targetCompatibility = 1.7
 
-task wrapper(type: Wrapper) {
+wrapper {
 	 gradleVersion = '2.10' 
 }
 
diff --git a/src/main/java/uppaal/NTA.java b/src/main/java/uppaal/NTA.java
index dcfb20d..89716d5 100644
--- a/src/main/java/uppaal/NTA.java
+++ b/src/main/java/uppaal/NTA.java
@@ -1,475 +1,484 @@
-package uppaal;
-
-
-import java.io.IOException;
-import java.io.PrintStream;
-import java.util.ArrayList;
-import java.util.Iterator;
-import java.util.LinkedList;
-import java.util.List;
-
-import org.jdom.DocType;
-import org.jdom.Document;
-import org.jdom.Element;
-import org.jdom.JDOMException;
-import org.jdom.input.JDOMParseException;
-import org.jdom.input.SAXBuilder;
-import org.jdom.output.Format;
-import org.jdom.output.XMLOutputter;
-
-
-public class NTA extends UppaalElement{
-	private Declaration declarations = new Declaration();
-	private SystemDeclaration systemDeclaration = new SystemDeclaration();
-	
-	public SystemDeclaration getSystemDeclaration() {
-		return systemDeclaration;
-	}
-
-	public void setSystemDeclaration(SystemDeclaration systemDeclaration) {
-		this.systemDeclaration = systemDeclaration;
-	}
-
-	private List<Automaton> automata = new LinkedList<Automaton>();
-	private String systemName;
-
-	public NTA() {
-	}
-	
-	public void setAutoPositioned(boolean autoPositioned) {
-		for(Automaton a: automata)
-			a.setAutoPositioned(autoPositioned);
-	}
-
-	
-//	public void normalize(){
-//		for (Automaton automaton : automata){
-//			
-//		}
-//	}
-	
-	public NTA(String uppaalFile){
-		SAXBuilder builder = new SAXBuilder();
-		try {
-			Document uppaalDoc = builder.build(uppaalFile);
-			@SuppressWarnings("unchecked")
-			Iterator<Element> i = uppaalDoc.getRootElement().getChildren().iterator();
-			while (i.hasNext()) {
-				Element child = i.next();
-				if (child.getName().equals("declaration")) {
-					assert child.getContent().size() == 1 : "Declaration elements should not have children";
-					declarations = new Declaration(child);
-				} else if (child.getName().equals("template")) {
-					Automaton automaton = new Automaton(child);
-					automata.add(automaton);
-				} else if (child.getName().equals("system")) {
-					systemDeclaration = new SystemDeclaration(child);
-				} else {
-					System.err.println("unhandled element: "+child.getName());
-				}
-			}
-		} catch (JDOMException e) {
-			// TODO Auto-generated catch block
-			e.printStackTrace();
-		} catch (IOException e) {
-			// TODO Auto-generated catch block
-			e.printStackTrace();
-		}
-	}
-
-	public Declaration getDeclarations() {
-		return declarations;
-	}
-
-	public void setDeclarations(Declaration declarations) {
-		this.declarations = declarations;
-	}
-
-	public List<Automaton> getAutomata() {
-		return automata;
-	}
-
-	public void setTemplates(ArrayList<Automaton> automata) {
-		this.automata = automata;
-	}
-
-	public String getSystemName() {
-		return systemName;
-	}
-
-	public void setSystemName(String systemName) {
-		this.systemName = systemName;
-	}
-	
-	public void addAutomaton(Automaton automaton) {
-		automata.add(automaton);
-	}
-	public void addAutomata(List<Automaton> automataList) {
-		automata.addAll(automataList);
-	}
-	public boolean removeAutomaton(Automaton automaton) {
-		return automata.remove(automaton);
-	}
-	public boolean removeAutomaton(String automatonName) {
-		for(Automaton aut : this.automata) {
-			if(aut.getName().getName().equals(automatonName)) {
-				return this.automata.remove(aut);
-			}
-		}
-		return false;
-	}
-	@Deprecated
-	private void updateLabelPositions() {
-		int spaceBetweenLabels = 15; //The size between lines in UPPAAL
-		int locationDistance = 30;
-
-		for (Automaton template : automata) {
-			for (Location location : template.getLocations()) {
-				int x = location.getPosX();
-				int y = location.getPosY();
-				int offset = locationDistance;
-				if (location.getName()!= null) {
-					location.getName().setPosX(x - spaceBetweenLabels);
-					location.getName().setPosY(y - offset);
-					offset += spaceBetweenLabels;
-				}
-				if (location.getInvariant()!=null) {
-					location.getInvariant().setPosX(x - spaceBetweenLabels);
-					location.getInvariant().setPosY(y - offset);
-				}
-			}
-			for (Transition transition : template.getTransitions()) {
-				Location source = transition.getSource();
-				Location target = transition.getTarget();
-				int sourceX = 0;
-				int sourceY = 0;
-				int targetX = 0;
-				int targetY = 0;
-
-				List<Nail> nails = transition.getNails();
-				int nrNails = nails.size();
-				if (nrNails == 0) {
-					for (Location location : template.getLocations()) {
-						if (location.equals(source)) {
-							sourceX = location.getPosX();
-							sourceY = location.getPosY();
-						}
-						if (location.equals(target)) {
-							targetX = location.getPosX();
-							targetY = location.getPosY();
-						}
-					}
-				} else if (nrNails == 1) {
-					for (Location location : template.getLocations()) {
-						if (location.equals(source)) {
-							sourceX = location.getPosX();
-							sourceY = location.getPosY();
-							break;
-						}
-					}
-					targetX = nails.get(0).getPosX();
-					targetY = nails.get(0).getPosY();
-				} else {
-					sourceX = nails.get((nrNails / 2) - 1).getPosX();
-					sourceY = nails.get((nrNails / 2) - 1).getPosY();
-					targetX = nails.get(nrNails / 2).getPosX();
-					targetY = nails.get(nrNails / 2).getPosY();
-				}
-
-				int x = sourceX + (targetX - sourceX) / 2;
-				int y = sourceY + (targetY - sourceY) / 2;
-
-				// TODO test if it works
-				int offset = -locationDistance;
-				if (transition.getSelect()!=null) {
-					transition.getSelect().setPosX(x - locationDistance);
-					transition.getSelect().setPosY(y + offset);
-					//offset must be added with spaceBetweenLabels as many times there are newlines
-					offset += spaceBetweenLabels * transition.getSelect().toString().split("\n").length;
-				}
-				if (transition.getGuard()!=null) {
-					transition.getGuard().setPosX(x - locationDistance);
-					transition.getGuard().setPosY(y + offset);
-					//offset must be added with spaceBetweenLabels as many times there are newlines
-					offset += spaceBetweenLabels * transition.getGuard().toString().split("\n").length;
-				}
-				if (transition.getSync()!=null) {
-					transition.getSync().setPosX(x - locationDistance);
-					transition.getSync().setPosY(y + offset);
-				}
-				if (transition.getUpdate()!=null) {
-					transition.getUpdate().setPosX(x - locationDistance);
-					transition.getUpdate().setPosY(y + offset);
-					//offset must be added with spaceBetweenLabels as many times there are newlines
-					offset += spaceBetweenLabels * transition.getUpdate().toString().split("\n").length;
-				}
-			}
-		}
-	}
-
-	final int xInterval = 200;
-	final int yInterval = 125;
-	final int nailX1 = 25;
-	final int nailY1 = 25;
-	final int nailX2 = 25;
-	final int nailY2 = -25;
-
-	@Deprecated
-	public void userFriendlyOutput() {
-		for (Automaton automaton : automata) {
-			if (automaton.getInit() == null) {
-				int initId = Integer.MAX_VALUE;
-				Location initLoc = null;
-				for (Location location : automaton.getLocations()) {
-					// if no init is set, the location with the lowest ID is
-					// chosen
-					if (location.getId() < initId) {
-						initId = location.getId();
-						initLoc = location;
-					}
-					// reset all positions
-					location.setPosX(-1);
-					location.setPosY(-1);
-				}
-				initLoc.setPosX(0);
-				initLoc.setPosY(0);
-				automaton.setInit(initLoc);
-			} else {
-				for (Location location : automaton.getLocations()) {
-					// if no init is set, the location with the lowest ID is
-					// chosen
-					location.setPosX(-1);
-					location.setPosY(-1);
-				}
-				automaton.getInit().setPosX(0);
-				automaton.getInit().setPosY(0);
-			}
-
-			updateLocations(automaton, automaton.getInit());
-			
-			//Add nails to loops
-			for (Transition transition : automaton.getTransitions()) {
-				if (transition.getSource() == transition.getTarget()) {
-					for (Location location : automaton.getLocations()) {
-						if (location.equals(transition.getSource())){
-							transition.addNail(new Nail(location.getPosX() + nailX1,
-									location.getPosY() + nailY1));
-							transition.addNail(new Nail(location.getPosX() + nailX2,
-									location.getPosY() + nailY2));
-						}
-					}
-				}
-			}
-		}
-		
-		
-		// Updates the position of the labels after the locations and
-		// transitions has been moved
-		updateLabelPositions();
-	}
-
-	@Deprecated
-	private void updateLocations(Automaton automaton,
-			Location currentLocation) {
-		ArrayList<Location> succ = new ArrayList<Location>();
-		int locationOffset = 0;
-		for (Transition transition : automaton.getTransitions()) {
-			// Only change location if it is not a loop
-			if (transition.getSource() != transition.getTarget()) {
-				if (transition.getSource().equals(currentLocation)) {
-					// Find the opposite location
-					for (Location location : automaton.getLocations()) {
-						if (location.equals(transition.getTarget())) {
-							// only update the position if it has not already
-							// been updated
-							if (location.getPosX() == -1) {
-								location.setPosX(currentLocation.getPosX()
-										+ xInterval * locationOffset);
-								location.setPosY(currentLocation.getPosY()
-										+ yInterval);
-								succ.add(location);
-								locationOffset++;
-								// Check if it is a A -> B -> A set of
-								// transitions
-								for (Transition trans2 : automaton
-										.getTransitions()) {
-									if (trans2.getSource() == transition
-											.getTarget()
-											&& trans2.getTarget() == transition
-													.getSource()) {
-										if (trans2.getNails().size() == 0
-												&& transition.getNails().size() == 0) {
-											// if it is a A -> B -> A then we
-											// want B to be to the right of A,
-											// but it must not interfere with
-											// other locations so subtract 50
-											// from the X position
-											location.setPosX(currentLocation
-													.getPosX()
-													+ xInterval
-													* (locationOffset) - 50);
-											location.setPosY(currentLocation
-													.getPosY());
-											trans2.addNail(new Nail(
-													currentLocation.getPosX()
-															+ nailX1,
-													currentLocation.getPosY()
-															+ nailY1));
-											transition.addNail(new Nail(
-													currentLocation.getPosX()
-															+ nailX2,
-													currentLocation.getPosY()
-															+ nailY2));
-											break;
-										}
-									}
-								}
-								break;
-							} else {
-								// Check if the location is above the current
-								// location and at the same X coordinate
-								if (currentLocation.getPosX() == location
-										.getPosX()
-										&& currentLocation.getPosY() > location
-												.getPosY()) {
-									currentLocation.setPosX(currentLocation
-											.getPosX()
-											+ xInterval - 50);
-								}
-							}
-						}
-					}
-				}
-			}
-		}
-		for (Location location : succ) {
-			updateLocations(automaton, location);
-		}
-	}
-	
-	public void writeXML(PrintStream printStream){
-//		updateLabelPositions();
-		writeDocument(generateXMLDocument(), printStream);
-	}
-	
-	public void writeXMLWithPrettyLayout(PrintStream printStream) {
-		try {
-			Document uDoc = UPPAALPrettyfy.getPrettyLayoutXml(generateXMLDocument());
-			writeDocument(uDoc, printStream);
-		} catch (IOException e) {
-			e.printStackTrace();
-		} catch (InterruptedException e) {
-			e.printStackTrace();
-		} catch (JDOMException e) {
-			e.printStackTrace();
-		}
-	}
-	
-	private void writeDocument(Document uppaalXMLDoc, PrintStream pStream) {
-		Format format = Format.getPrettyFormat();
-		XMLOutputter output = new XMLOutputter(format);
-		try {
-			
-			output.output(uppaalXMLDoc, pStream);
-		} catch (IOException e) {
-			e.printStackTrace();
-		}
-	}
-	
-	@Override
-	protected Element generateXMLElement() {
-		Element result=super.generateXMLElement(); 
-		
-		result.addContent(declarations.generateXMLElement());
-		for(Automaton automaton : automata){
-			result.addContent(automaton.generateXMLElement());
-		}
-		result.addContent(systemDeclaration.generateXMLElement());
-		return result;
-	}
-	
-	/**
-	 * Creates a valid UPPAAL XML document, containing the entire model
-	 * 
-	 * @return The UPPAAL model as an XML document
-	 */
-	private Document generateXMLDocument() {
-		return new Document(this.generateXMLElement(),new DocType("nta",
-				"-//Uppaal Team//DTD Flat System 1.1//EN",
-		"flat-1_1.dtd"));
-	}
-	
-	/**
-	 * Writes the entire XML document of the model to a file
-	 * 
-	 * @param outputFile
-	 *            The target file
-	 */
-	public void writeModelToFile(String outputFile) {
-		try {
-			java.io.PrintStream printStream = new PrintStream(outputFile);
-			this.writeXML(printStream);
-			printStream.close();
-		} catch (IOException e) {
-			e.printStackTrace();
-		}
-	}
-	
-	public void writePrettyLayoutModelToFile(String outputFile) {
-		try {
-			java.io.PrintStream printStream = new PrintStream(outputFile);
-			this.writeXMLWithPrettyLayout(printStream);
-			printStream.close();
-		} catch (IOException e) {
-			e.printStackTrace();
-		}
-	}
-	
-	public static Boolean correctXML(String inputFile) {
-		// Check whether the output is valid UPPAAL XML
-		System.out.println("Validating XML file...");
-		try {
-			SAXBuilder b = new SAXBuilder();
-			b.setValidation(true);
-			String msg = "Correct XML!";
-			try {
-				b.build(inputFile);
-			} catch (JDOMParseException e) {
-				msg = e.getMessage();
-			}
-			System.out.println(msg);
-		} catch (Exception e) {
-			e.printStackTrace();
-			return false;
-		}
-		System.out.println("XML validation complete.");
-		return true;
-	}
-	
-	//TODO Reconsider this! -- replace by getChannelIdentifier
-	static int ID = 0;
-	
-	@Override
-	public String getXMLElementName() {
-		return "nta";
-	}
-
-	public Automaton getAutomaton(String string) {
-		List<Automaton> automata = getAutomata();
-		for(Automaton automaton : automata){
-			if(automaton.getName().toString().equals(string)){
-				return automaton;
-			}
-		}
-		System.err.println("Automaton ["+string +"] not found in "+this.getSystemName());
-		return null;
-	}
-
-	public int removeStumpAngles(double angleThreshold, double lengthThreshold) {
-		int count = 0;
-		for(Automaton a: automata){
-			count += a.removeStumpAngles(angleThreshold, lengthThreshold);
-		}
-		return count;
-	}
-}
+package uppaal;
+
+
+import java.io.*;
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.LinkedList;
+import java.util.List;
+
+import org.jdom.DocType;
+import org.jdom.Document;
+import org.jdom.Element;
+import org.jdom.JDOMException;
+import org.jdom.input.JDOMParseException;
+import org.jdom.input.SAXBuilder;
+import org.jdom.output.Format;
+import org.jdom.output.XMLOutputter;
+
+
+public class NTA extends UppaalElement{
+	private Declaration declarations = new Declaration();
+	private SystemDeclaration systemDeclaration = new SystemDeclaration();
+	
+	public SystemDeclaration getSystemDeclaration() {
+		return systemDeclaration;
+	}
+
+	public void setSystemDeclaration(SystemDeclaration systemDeclaration) {
+		this.systemDeclaration = systemDeclaration;
+	}
+
+	private List<Automaton> automata = new LinkedList<Automaton>();
+	private String systemName;
+
+	public NTA() {
+	}
+	
+	public void setAutoPositioned(boolean autoPositioned) {
+		for(Automaton a: automata)
+			a.setAutoPositioned(autoPositioned);
+	}
+
+	
+//	public void normalize(){
+//		for (Automaton automaton : automata){
+//			
+//		}
+//	}
+
+	public NTA(String uppaalFile) {
+		SAXBuilder builder = new SAXBuilder();
+		try {
+			Document uppaalDoc = builder.build(uppaalFile);
+			buildNTA(uppaalDoc);
+		} catch (IOException | JDOMException e) {
+			e.printStackTrace();
+		}
+	}
+
+	public NTA(InputStream uppaalFile) {
+		SAXBuilder builder = new SAXBuilder();
+		try {
+			Document uppaalDoc = builder.build(uppaalFile);
+			buildNTA(uppaalDoc);
+		} catch (IOException | JDOMException e) {
+			e.printStackTrace();
+		}
+	}
+
+	private void buildNTA(Document uppaalDoc){
+		@SuppressWarnings("unchecked")
+		Iterator<Element> i = uppaalDoc.getRootElement().getChildren().iterator();
+		while (i.hasNext()) {
+			Element child = i.next();
+			if (child.getName().equals("declaration")) {
+				assert child.getContent().size() == 1 : "Declaration elements should not have children";
+				declarations = new Declaration(child);
+			} else if (child.getName().equals("template")) {
+				Automaton automaton = new Automaton(child);
+				automata.add(automaton);
+			} else if (child.getName().equals("system")) {
+				systemDeclaration = new SystemDeclaration(child);
+			} else {
+				System.err.println("unhandled element: "+child.getName());
+			}
+		}
+	}
+
+	public Declaration getDeclarations() {
+		return declarations;
+	}
+
+	public void setDeclarations(Declaration declarations) {
+		this.declarations = declarations;
+	}
+
+	public List<Automaton> getAutomata() {
+		return automata;
+	}
+
+	public void setTemplates(ArrayList<Automaton> automata) {
+		this.automata = automata;
+	}
+
+	public String getSystemName() {
+		return systemName;
+	}
+
+	public void setSystemName(String systemName) {
+		this.systemName = systemName;
+	}
+	
+	public void addAutomaton(Automaton automaton) {
+		automata.add(automaton);
+	}
+	public void addAutomata(List<Automaton> automataList) {
+		automata.addAll(automataList);
+	}
+	public boolean removeAutomaton(Automaton automaton) {
+		return automata.remove(automaton);
+	}
+	public boolean removeAutomaton(String automatonName) {
+		for(Automaton aut : this.automata) {
+			if(aut.getName().getName().equals(automatonName)) {
+				return this.automata.remove(aut);
+			}
+		}
+		return false;
+	}
+	@Deprecated
+	private void updateLabelPositions() {
+		int spaceBetweenLabels = 15; //The size between lines in UPPAAL
+		int locationDistance = 30;
+
+		for (Automaton template : automata) {
+			for (Location location : template.getLocations()) {
+				int x = location.getPosX();
+				int y = location.getPosY();
+				int offset = locationDistance;
+				if (location.getName()!= null) {
+					location.getName().setPosX(x - spaceBetweenLabels);
+					location.getName().setPosY(y - offset);
+					offset += spaceBetweenLabels;
+				}
+				if (location.getInvariant()!=null) {
+					location.getInvariant().setPosX(x - spaceBetweenLabels);
+					location.getInvariant().setPosY(y - offset);
+				}
+			}
+			for (Transition transition : template.getTransitions()) {
+				Location source = transition.getSource();
+				Location target = transition.getTarget();
+				int sourceX = 0;
+				int sourceY = 0;
+				int targetX = 0;
+				int targetY = 0;
+
+				List<Nail> nails = transition.getNails();
+				int nrNails = nails.size();
+				if (nrNails == 0) {
+					for (Location location : template.getLocations()) {
+						if (location.equals(source)) {
+							sourceX = location.getPosX();
+							sourceY = location.getPosY();
+						}
+						if (location.equals(target)) {
+							targetX = location.getPosX();
+							targetY = location.getPosY();
+						}
+					}
+				} else if (nrNails == 1) {
+					for (Location location : template.getLocations()) {
+						if (location.equals(source)) {
+							sourceX = location.getPosX();
+							sourceY = location.getPosY();
+							break;
+						}
+					}
+					targetX = nails.get(0).getPosX();
+					targetY = nails.get(0).getPosY();
+				} else {
+					sourceX = nails.get((nrNails / 2) - 1).getPosX();
+					sourceY = nails.get((nrNails / 2) - 1).getPosY();
+					targetX = nails.get(nrNails / 2).getPosX();
+					targetY = nails.get(nrNails / 2).getPosY();
+				}
+
+				int x = sourceX + (targetX - sourceX) / 2;
+				int y = sourceY + (targetY - sourceY) / 2;
+
+				// TODO test if it works
+				int offset = -locationDistance;
+				if (transition.getSelect()!=null) {
+					transition.getSelect().setPosX(x - locationDistance);
+					transition.getSelect().setPosY(y + offset);
+					//offset must be added with spaceBetweenLabels as many times there are newlines
+					offset += spaceBetweenLabels * transition.getSelect().toString().split("\n").length;
+				}
+				if (transition.getGuard()!=null) {
+					transition.getGuard().setPosX(x - locationDistance);
+					transition.getGuard().setPosY(y + offset);
+					//offset must be added with spaceBetweenLabels as many times there are newlines
+					offset += spaceBetweenLabels * transition.getGuard().toString().split("\n").length;
+				}
+				if (transition.getSync()!=null) {
+					transition.getSync().setPosX(x - locationDistance);
+					transition.getSync().setPosY(y + offset);
+				}
+				if (transition.getUpdate()!=null) {
+					transition.getUpdate().setPosX(x - locationDistance);
+					transition.getUpdate().setPosY(y + offset);
+					//offset must be added with spaceBetweenLabels as many times there are newlines
+					offset += spaceBetweenLabels * transition.getUpdate().toString().split("\n").length;
+				}
+			}
+		}
+	}
+
+	final int xInterval = 200;
+	final int yInterval = 125;
+	final int nailX1 = 25;
+	final int nailY1 = 25;
+	final int nailX2 = 25;
+	final int nailY2 = -25;
+
+	@Deprecated
+	public void userFriendlyOutput() {
+		for (Automaton automaton : automata) {
+			if (automaton.getInit() == null) {
+				int initId = Integer.MAX_VALUE;
+				Location initLoc = null;
+				for (Location location : automaton.getLocations()) {
+					// if no init is set, the location with the lowest ID is
+					// chosen
+					if (location.getId() < initId) {
+						initId = location.getId();
+						initLoc = location;
+					}
+					// reset all positions
+					location.setPosX(-1);
+					location.setPosY(-1);
+				}
+				initLoc.setPosX(0);
+				initLoc.setPosY(0);
+				automaton.setInit(initLoc);
+			} else {
+				for (Location location : automaton.getLocations()) {
+					// if no init is set, the location with the lowest ID is
+					// chosen
+					location.setPosX(-1);
+					location.setPosY(-1);
+				}
+				automaton.getInit().setPosX(0);
+				automaton.getInit().setPosY(0);
+			}
+
+			updateLocations(automaton, automaton.getInit());
+			
+			//Add nails to loops
+			for (Transition transition : automaton.getTransitions()) {
+				if (transition.getSource() == transition.getTarget()) {
+					for (Location location : automaton.getLocations()) {
+						if (location.equals(transition.getSource())){
+							transition.addNail(new Nail(location.getPosX() + nailX1,
+									location.getPosY() + nailY1));
+							transition.addNail(new Nail(location.getPosX() + nailX2,
+									location.getPosY() + nailY2));
+						}
+					}
+				}
+			}
+		}
+		
+		
+		// Updates the position of the labels after the locations and
+		// transitions has been moved
+		updateLabelPositions();
+	}
+
+	@Deprecated
+	private void updateLocations(Automaton automaton,
+			Location currentLocation) {
+		ArrayList<Location> succ = new ArrayList<Location>();
+		int locationOffset = 0;
+		for (Transition transition : automaton.getTransitions()) {
+			// Only change location if it is not a loop
+			if (transition.getSource() != transition.getTarget()) {
+				if (transition.getSource().equals(currentLocation)) {
+					// Find the opposite location
+					for (Location location : automaton.getLocations()) {
+						if (location.equals(transition.getTarget())) {
+							// only update the position if it has not already
+							// been updated
+							if (location.getPosX() == -1) {
+								location.setPosX(currentLocation.getPosX()
+										+ xInterval * locationOffset);
+								location.setPosY(currentLocation.getPosY()
+										+ yInterval);
+								succ.add(location);
+								locationOffset++;
+								// Check if it is a A -> B -> A set of
+								// transitions
+								for (Transition trans2 : automaton
+										.getTransitions()) {
+									if (trans2.getSource() == transition
+											.getTarget()
+											&& trans2.getTarget() == transition
+													.getSource()) {
+										if (trans2.getNails().size() == 0
+												&& transition.getNails().size() == 0) {
+											// if it is a A -> B -> A then we
+											// want B to be to the right of A,
+											// but it must not interfere with
+											// other locations so subtract 50
+											// from the X position
+											location.setPosX(currentLocation
+													.getPosX()
+													+ xInterval
+													* (locationOffset) - 50);
+											location.setPosY(currentLocation
+													.getPosY());
+											trans2.addNail(new Nail(
+													currentLocation.getPosX()
+															+ nailX1,
+													currentLocation.getPosY()
+															+ nailY1));
+											transition.addNail(new Nail(
+													currentLocation.getPosX()
+															+ nailX2,
+													currentLocation.getPosY()
+															+ nailY2));
+											break;
+										}
+									}
+								}
+								break;
+							} else {
+								// Check if the location is above the current
+								// location and at the same X coordinate
+								if (currentLocation.getPosX() == location
+										.getPosX()
+										&& currentLocation.getPosY() > location
+												.getPosY()) {
+									currentLocation.setPosX(currentLocation
+											.getPosX()
+											+ xInterval - 50);
+								}
+							}
+						}
+					}
+				}
+			}
+		}
+		for (Location location : succ) {
+			updateLocations(automaton, location);
+		}
+	}
+	
+	public void writeXML(PrintStream printStream){
+//		updateLabelPositions();
+		writeDocument(generateXMLDocument(), printStream);
+	}
+	
+	public void writeXMLWithPrettyLayout(PrintStream printStream) {
+		try {
+			Document uDoc = UPPAALPrettyfy.getPrettyLayoutXml(generateXMLDocument());
+			writeDocument(uDoc, printStream);
+		} catch (IOException e) {
+			e.printStackTrace();
+		} catch (InterruptedException e) {
+			e.printStackTrace();
+		} catch (JDOMException e) {
+			e.printStackTrace();
+		}
+	}
+	
+	private void writeDocument(Document uppaalXMLDoc, PrintStream pStream) {
+		Format format = Format.getPrettyFormat();
+		XMLOutputter output = new XMLOutputter(format);
+		try {
+			
+			output.output(uppaalXMLDoc, pStream);
+		} catch (IOException e) {
+			e.printStackTrace();
+		}
+	}
+	
+	@Override
+	protected Element generateXMLElement() {
+		Element result=super.generateXMLElement(); 
+		
+		result.addContent(declarations.generateXMLElement());
+		for(Automaton automaton : automata){
+			result.addContent(automaton.generateXMLElement());
+		}
+		result.addContent(systemDeclaration.generateXMLElement());
+		return result;
+	}
+	
+	/**
+	 * Creates a valid UPPAAL XML document, containing the entire model
+	 * 
+	 * @return The UPPAAL model as an XML document
+	 */
+	private Document generateXMLDocument() {
+		return new Document(this.generateXMLElement(),new DocType("nta",
+				"-//Uppaal Team//DTD Flat System 1.1//EN",
+		"flat-1_1.dtd"));
+	}
+	
+	/**
+	 * Writes the entire XML document of the model to a file
+	 * 
+	 * @param outputFile
+	 *            The target file
+	 */
+	public void writeModelToFile(String outputFile) {
+		try {
+			java.io.PrintStream printStream = new PrintStream(outputFile);
+			this.writeXML(printStream);
+			printStream.close();
+		} catch (IOException e) {
+			e.printStackTrace();
+		}
+	}
+	
+	public void writePrettyLayoutModelToFile(String outputFile) {
+		try {
+			java.io.PrintStream printStream = new PrintStream(outputFile);
+			this.writeXMLWithPrettyLayout(printStream);
+			printStream.close();
+		} catch (IOException e) {
+			e.printStackTrace();
+		}
+	}
+	
+	public static Boolean correctXML(String inputFile) {
+		// Check whether the output is valid UPPAAL XML
+		System.out.println("Validating XML file...");
+		try {
+			SAXBuilder b = new SAXBuilder();
+			b.setValidation(true);
+			String msg = "Correct XML!";
+			try {
+				b.build(inputFile);
+			} catch (JDOMParseException e) {
+				msg = e.getMessage();
+			}
+			System.out.println(msg);
+		} catch (Exception e) {
+			e.printStackTrace();
+			return false;
+		}
+		System.out.println("XML validation complete.");
+		return true;
+	}
+	
+	//TODO Reconsider this! -- replace by getChannelIdentifier
+	static int ID = 0;
+	
+	@Override
+	public String getXMLElementName() {
+		return "nta";
+	}
+
+	public Automaton getAutomaton(String string) {
+		List<Automaton> automata = getAutomata();
+		for(Automaton automaton : automata){
+			if(automaton.getName().toString().equals(string)){
+				return automaton;
+			}
+		}
+		System.err.println("Automaton ["+string +"] not found in "+this.getSystemName());
+		return null;
+	}
+
+	public int removeStumpAngles(double angleThreshold, double lengthThreshold) {
+		int count = 0;
+		for(Automaton a: automata){
+			count += a.removeStumpAngles(angleThreshold, lengthThreshold);
+		}
+		return count;
+	}
+}