Merge lp:~sgaflv/workcraft/trunk-hierarchical into lp:workcraft

[Stan]

- adding pages, hierarchical names and namespaces
- adaptation to all model types, also simulation, verification, and traces

[Danil Sokolov (danilovesky)]

review: Approve

=== modified file '.bzrignore'
--- .bzrignore	2010-10-07 15:30:31 +0000
+++ .bzrignore	2014-07-11 09:42:10 +0000
@@ -10,4 +10,8 @@
 generated
 /.metadata
 *.jar
-
+*.orig
+*.moved
+*.BASE
+*.OTHER
+*.THIS
\ No newline at end of file

=== modified file 'CircuitPlugin/src/org/workcraft/plugins/circuit/Circuit.java'
--- CircuitPlugin/src/org/workcraft/plugins/circuit/Circuit.java	2010-10-08 15:48:47 +0000
+++ CircuitPlugin/src/org/workcraft/plugins/circuit/Circuit.java	2014-07-11 09:42:10 +0000
@@ -21,24 +21,79 @@
 
 package org.workcraft.plugins.circuit;
 
+import org.workcraft.dom.Connection;
+import org.workcraft.dom.Container;
 import org.workcraft.dom.Node;
+import org.workcraft.dom.hierarchy.NamespaceProvider;
 import org.workcraft.dom.math.AbstractMathModel;
+import org.workcraft.dom.math.CommentNode;
 import org.workcraft.dom.math.MathConnection;
 import org.workcraft.dom.math.MathGroup;
 import org.workcraft.dom.math.MathNode;
+import org.workcraft.dom.math.PageNode;
+import org.workcraft.dom.references.HierarchicalUniqueNameReferenceManager;
 import org.workcraft.exceptions.InvalidConnectionException;
 import org.workcraft.exceptions.ModelValidationException;
+import org.workcraft.gui.propertyeditor.DefaultNamePropertyDescriptor;
+import org.workcraft.gui.propertyeditor.Properties;
+import org.workcraft.plugins.circuit.Contact.IOType;
+import org.workcraft.plugins.circuit.references.CircuitReferenceManager;
+import org.workcraft.serialisation.References;
+import org.workcraft.util.Func;
 import org.workcraft.util.Hierarchy;
+import org.workcraft.util.Identifier;
+
 
 public class Circuit extends AbstractMathModel {
 
+	
 	public Circuit() {
-		this(null);
+		this(new MathGroup());
 	}
 	
 	public Circuit(MathGroup root) {
-		super(root);
-	}
+		this(root, null);
+	}
+	
+	
+	public Circuit(Container root, References refs) {
+		
+		super(root, 
+				new CircuitReferenceManager((NamespaceProvider)root, refs, new Func<Node, String>() {
+					@Override
+					public String eval(Node arg) {
+						if (arg instanceof CircuitComponent) return "cc";
+						if (arg instanceof Contact) {
+							Contact cont = (Contact)arg;
+							
+							if (cont.getParent() instanceof CircuitComponent)
+								return "x";
+							
+							if (cont.getIOType()==IOType.INPUT) 
+								return "in";
+							else
+								return "out";
+							
+						}
+						
+						if (arg instanceof Connection) return "con";
+						if (arg instanceof PageNode) return "pg";
+						if (arg instanceof CommentNode) return "comment";
+						
+						if (arg instanceof Container) return "gr";
+						
+						return "v";					
+					}
+				}
+				
+			));
+		
+		if (root==null) {
+			Container r  = getRoot();
+			getReferenceManager().attach(r);
+		}
+	}
+	
 
 	public void validate() throws ModelValidationException {
 	}
@@ -51,5 +106,18 @@
 		
 		return con;
 	}
+	
+	
+	@Override
+	public Properties getProperties(Node node) {
+		if (node != null) {
+			if (node instanceof CircuitComponent)
+				return Properties.Mix.from(new DefaultNamePropertyDescriptor(this, node));
+			if (node instanceof Contact)
+				return Properties.Mix.from(new DefaultNamePropertyDescriptor(this, node));
+		}
+		return super.getProperties(node);
+	}
+	
 
 }

=== modified file 'CircuitPlugin/src/org/workcraft/plugins/circuit/CircuitComponent.java'
--- CircuitPlugin/src/org/workcraft/plugins/circuit/CircuitComponent.java	2013-08-22 18:27:32 +0000
+++ CircuitPlugin/src/org/workcraft/plugins/circuit/CircuitComponent.java	2014-07-11 09:42:10 +0000
@@ -29,6 +29,7 @@
 import org.workcraft.dom.Container;
 import org.workcraft.dom.DefaultGroupImpl;
 import org.workcraft.dom.Node;
+import org.workcraft.dom.math.MathGroup;
 import org.workcraft.dom.math.MathNode;
 import org.workcraft.observation.HierarchyObserver;
 import org.workcraft.observation.ObservableHierarchy;
@@ -39,10 +40,11 @@
 @DisplayName("Component")
 @VisualClass(org.workcraft.plugins.circuit.VisualCircuitComponent.class)
 
-public class CircuitComponent extends MathNode implements Container, ObservableHierarchy {
+public class CircuitComponent extends MathGroup implements Container, ObservableHierarchy {
 	
 	DefaultGroupImpl groupImpl = new DefaultGroupImpl(this);
 	private String name = "";
+	
 	private boolean isEnvironment;
 
 	public boolean getIsEnvironment() {
@@ -59,7 +61,7 @@
 
 	public void setParent(Node parent) {
 		groupImpl.setParent(parent);
-		checkName(parent);
+		//checkName(parent);
 	}
 	
 	public void addObserver(HierarchyObserver obs) {
@@ -98,7 +100,7 @@
 	@Override
 	public void reparent(Collection<Node> nodes, Container newParent) {
 		groupImpl.reparent(nodes, newParent);
-		checkName(newParent);
+		//checkName(newParent);
 	}
 
 	@Override
@@ -118,35 +120,35 @@
 		return result;
 	}
 
-	public String getNewName(Node n, String start) {
-		// iterate through all contacts, check that the name doesn't exist
-		int num=0;
-		boolean found = true;
-		
-		while (found) {
-			num++;
-			found=false;
-			
-			for (Node vn : n.getChildren()) {
-				if (vn instanceof CircuitComponent && vn!=this) {
-					if (((CircuitComponent)vn).getName().equals(start+num)) {
-						found=true;
-						break;
-					}
-				}
-			}
-		}
-		return start+num;
-	}
+//	public String getNewName(Node n, String start) {
+//		// iterate through all contacts, check that the name doesn't exist
+//		int num=0;
+//		boolean found = true;
+//		
+//		while (found) {
+//			num++;
+//			found=false;
+//			
+//			for (Node vn : n.getChildren()) {
+//				if (vn instanceof CircuitComponent && vn!=this) {
+//					if (((CircuitComponent)vn).getName().equals(start+num)) {
+//						found=true;
+//						break;
+//					}
+//				}
+//			}
+//		}
+//		return start+num;
+//	}
 	
-	public void checkName(Node parent) {
-		if (parent==null) return;
-		String start=getName();
-		if (start==null||start=="") {
-			start="c";
-			setName(getNewName(parent, start));
-		}
-	}
+//	public void checkName(Node parent) {
+//		if (parent==null) return;
+//		String start=getName();
+//		if (start==null||start=="") {
+//			start="c";
+//			setName(getNewName(parent, start));
+//		}
+//	}
 
 	public void setName(String name) {
 		this.name = name;

=== modified file 'CircuitPlugin/src/org/workcraft/plugins/circuit/CircuitModelDescriptor.java'
--- CircuitPlugin/src/org/workcraft/plugins/circuit/CircuitModelDescriptor.java	2010-11-30 01:14:08 +0000
+++ CircuitPlugin/src/org/workcraft/plugins/circuit/CircuitModelDescriptor.java	2014-07-11 09:42:10 +0000
@@ -2,6 +2,7 @@
 
 import org.workcraft.dom.ModelDescriptor;
 import org.workcraft.dom.VisualModelDescriptor;
+import org.workcraft.dom.math.MathGroup;
 import org.workcraft.dom.math.MathModel;
 import org.workcraft.dom.visual.VisualModel;
 import org.workcraft.exceptions.VisualModelInstantiationException;

=== modified file 'CircuitPlugin/src/org/workcraft/plugins/circuit/Contact.java'
--- CircuitPlugin/src/org/workcraft/plugins/circuit/Contact.java	2014-06-27 14:48:42 +0000
+++ CircuitPlugin/src/org/workcraft/plugins/circuit/Contact.java	2014-07-11 09:42:10 +0000
@@ -19,8 +19,8 @@
 *
 */
 
-package org.workcraft.plugins.circuit;
-
+package org.workcraft.plugins.circuit;
+
 import java.util.LinkedHashMap;
 import java.util.Map;
 
@@ -32,10 +32,10 @@
 import org.workcraft.plugins.cpog.optimisation.BooleanVariable;
 import org.workcraft.plugins.cpog.optimisation.expressions.BooleanVisitor;
 
-@DisplayName("Contact")
-@VisualClass(org.workcraft.plugins.circuit.VisualContact.class)
-
-public class Contact extends MathNode implements BooleanVariable {
+@DisplayName("Contact")
+@VisualClass(org.workcraft.plugins.circuit.VisualContact.class)
+
+public class Contact extends MathNode implements BooleanVariable {
 
 	public enum IOType {
 		INPUT("Input"),
@@ -70,82 +70,29 @@
 		sendNotification(new PropertyChangedEvent(this, "initOne"));
 	}
 
-	public Contact() {
+	public Contact() {
 	}
-	
+	
 	public Contact(IOType iot) {
 		super();
 		setIOType(iot);
 	}
 	
-	static public String getNewName(Node paren, String prefix, Node node, boolean allowShort) {
-		// iterate through all contacts, check that the name doesn't exist
-		int index=0;
-		boolean found = false;
-		if (allowShort) {
-			for (Node n : paren.getChildren()) {
-				if (n instanceof Contact && n != node) {
-					if (((Contact)n).getName().equals(prefix)) {
-						found = true;
-						break;
-					}
-				}
-			}
-			if (!found) return prefix;
-		}
-		do {
-			found = false;
-			index++;
-			for (Node n : paren.getChildren()) {
-				if (n instanceof Contact && n != node) {
-					if (((Contact)n).getName().equals(prefix + index)) {
-						found = true;
-						break;
-					}
-				}
-			}
-		} while (found);
-		return (prefix + index);
-	}
-	
-	public void checkName(Node parent) {
-		if (parent == null) return;
-		String prefix = getName();
-		if (prefix == null || prefix == "") {
-			if (getIOType()==IOType.INPUT) {
-				prefix="input";
-			} else {
-				prefix="output";
-			}
-			setName(getNewName(parent, prefix, this, false));
-		}
-	}
-	
-	@Override
-	public void setParent(Node parent) {
-		super.setParent(parent);
-		checkName(parent);
-	}
-
-	public void setIOType(IOType t) {
+	public void setIOType(IOType t) {
 		this.ioType = t;
-		if (getName().startsWith("input") && getIOType()==IOType.OUTPUT) {
-			setName(getNewName(getParent(), "output", this, false));
-		} else if (getName().startsWith("output") && getIOType()==IOType.INPUT) {
-			setName(getNewName(getParent(), "input", this, false));
-		}
-		sendNotification(new PropertyChangedEvent(this, "ioType"));
-	}
-	
-	public IOType getIOType() {
-		return ioType;
-	}
-	
+		sendNotification(new PropertyChangedEvent(this, "ioType"));
+	}
+	
+	public IOType getIOType() {
+		return ioType;
+	}
+	
+	// this is only for information, use Circuit to set component's names
 	public void setName(String name) {
 		this.name = name;
 		sendNotification(new PropertyChangedEvent(this, "name"));
 	}
-
+	
 	public String getName() {
 		return name;
 	}
@@ -160,4 +107,4 @@
 		return getName();
 	}
 
-}
+}

=== modified file 'CircuitPlugin/src/org/workcraft/plugins/circuit/VisualCircuit.java'
--- CircuitPlugin/src/org/workcraft/plugins/circuit/VisualCircuit.java	2014-06-27 14:48:42 +0000
+++ CircuitPlugin/src/org/workcraft/plugins/circuit/VisualCircuit.java	2014-07-11 09:42:10 +0000
@@ -28,16 +28,22 @@
 import org.workcraft.annotations.CustomTools;
 import org.workcraft.annotations.DisplayName;
 import org.workcraft.dom.Connection;
+import org.workcraft.dom.Container;
 import org.workcraft.dom.Node;
+import org.workcraft.dom.hierarchy.NamespaceProvider;
 import org.workcraft.dom.math.MathConnection;
+import org.workcraft.dom.references.HierarchicalUniqueNameReferenceManager;
+import org.workcraft.dom.references.ReferenceManager;
 import org.workcraft.dom.visual.AbstractVisualModel;
 import org.workcraft.dom.visual.VisualComponent;
 import org.workcraft.dom.visual.VisualGroup;
+import org.workcraft.dom.visual.VisualNode;
 import org.workcraft.exceptions.InvalidConnectionException;
 import org.workcraft.exceptions.NodeCreationException;
 import org.workcraft.exceptions.VisualModelInstantiationException;
 import org.workcraft.gui.propertyeditor.Properties;
 import org.workcraft.plugins.circuit.Contact.IOType;
+import org.workcraft.plugins.cpog.optimisation.expressions.One;
 import org.workcraft.serialisation.xml.NoAutoSerialisation;
 import org.workcraft.util.Hierarchy;
 
@@ -117,15 +123,93 @@
 	}
 
 	public VisualFunctionContact getOrCreateOutput(String name, double x, double y) {
-		for(VisualFunctionContact c : getVisualFunctionContacts()) {
-			if(c.getName().equals(name)) return c;
-		}
-		VisualFunctionContact vc = new VisualFunctionContact(new FunctionContact(IOType.OUTPUT));
+		
+		VisualFunctionContact vc = getOrCreateContact(getCurrentLevel(), name, IOType.OUTPUT, x, y);
+        
+		return vc;
+		
+	}
+	
+	public VisualFunctionContact  getOrCreateComponentOutput(VisualFunctionComponent component,  String name, double x, double y) {
+		
+		VisualFunctionContact vc = getOrCreateContact(component, name, IOType.OUTPUT, x, y);
         vc.setPosition(new Point2D.Double(x, y));
-        addFunctionContact(vc);
-        vc.setName(name);
-		return vc;
-	}
+		
+		return vc;
+	}
+	
+	public VisualFunctionContact getOrCreateContact(Container container, String name, IOType ioType, double x, double y) {
+		// here "parent" is a container of a visual model
+		
+		if (name!=null) {
+			
+			for (Node n: container.getChildren()) {
+				if (n instanceof VisualFunctionContact) {
+					if (getMathModel().getName(((VisualFunctionContact)n).getReferencedContact()).equals(name))
+						return (VisualFunctionContact)n;
+				} // TODO: if found something else with that name, return null?
+			}
+			
+		}
+		
+		// the name is available 
+		// create a new contact if it was not found
+		VisualContact.Direction dir=null;
+		if (ioType==null) ioType = IOType.OUTPUT;
+		dir=VisualContact.Direction.WEST;
+		if (ioType==IOType.OUTPUT)
+			dir=VisualContact.Direction.EAST;
+		
+		
+		
+		
+		VisualFunctionContact vc = new VisualFunctionContact(new FunctionContact(ioType));
+		vc.setDirection(dir);
+		vc.setPosition(new Point2D.Double(x, y));
+		
+		if (container instanceof VisualFunctionComponent) {
+			VisualFunctionComponent component = (VisualFunctionComponent)container;
+			
+			component.addContact(this, vc);
+			
+			if (name!=null)
+				circuit.setName(vc.getReferencedComponent(), name);
+	        
+			
+			vc.setSetFunction(One.instance());
+			vc.setResetFunction(One.instance());
+		} else {
+			
+	        AbstractVisualModel.getMathContainer(this, getRoot()).add(vc.getReferencedComponent());
+			add(vc);
+			
+			if (name!=null)
+				circuit.setName(vc.getReferencedComponent(), name);
+			
+		}
+        
+		return vc;
+	}
+	
+//	public VisualFunctionContact addFunction(VisualCircuitComponent component, IOType ioType) {
+//		VisualContact.Direction dir=null;
+//		if (ioType==null) ioType = IOType.OUTPUT;
+//		dir=VisualContact.Direction.WEST;
+//		
+//		if (ioType==IOType.OUTPUT) {
+//			dir=VisualContact.Direction.EAST;
+//		}
+//		
+//		FunctionContact c = new FunctionContact(ioType);
+//		VisualFunctionContact vc = new VisualFunctionContact(c);
+//		vc.setDirection(dir);
+//		
+//		//circuit.setName(component.getReferencedComponent(), Contact.getNewName(component.getReferencedComponent(), prefix, null, allowShort));
+//		
+//		component.addContact(vc);
+//		return vc;
+//	}
+	
 	
 	public void addFunctionComponent(VisualFunctionComponent component) {
 		for (Node node : component.getMathReferences()) {
@@ -141,10 +225,10 @@
 		 super.add(joint);
 	 }
 	 
-	 public void addFunctionContact(VisualFunctionContact contact) {
-		 circuit.add(contact.getReferencedFunctionContact());
-		 super.add(contact);
-	 }
+//	 public void addFunctionContact(VisualFunctionComponent component, VisualFunctionContact contact) {
+//		 component.add(contact);
+//		 component.getReferencedCircuitComponent().add(contact.getReferencedContact());
+//	 }
 
 	 @NoAutoSerialisation
 	public File getEnvironmentFile() {
@@ -170,14 +254,18 @@
 		Properties properties = super.getProperties(node);
 		if (node == null) {
 			properties = Properties.Merge.add(properties, new EnvironmentFilePropertyDescriptor(this));
-		} else if(node instanceof VisualFunctionContact) {
+		} 
+		
+		if (node instanceof VisualFunctionContact) {
 			VisualFunctionContact contact = (VisualFunctionContact)node;
 			VisualContactFormulaProperties props = new VisualContactFormulaProperties(this);
+			
 			properties = Properties.Merge.add(properties,
 					props.getSetProperty(contact),
 					props.getResetProperty(contact));
 		}
 		return properties;
 	}
+
 	
 }

=== modified file 'CircuitPlugin/src/org/workcraft/plugins/circuit/VisualCircuitComponent.java'
--- CircuitPlugin/src/org/workcraft/plugins/circuit/VisualCircuitComponent.java	2014-06-27 14:48:42 +0000
+++ CircuitPlugin/src/org/workcraft/plugins/circuit/VisualCircuitComponent.java	2014-07-11 09:42:10 +0000
@@ -39,6 +39,7 @@
 import org.workcraft.dom.Container;
 import org.workcraft.dom.DefaultGroupImpl;
 import org.workcraft.dom.Node;
+import org.workcraft.dom.visual.AbstractVisualModel;
 import org.workcraft.dom.visual.BoundingBoxHelper;
 import org.workcraft.dom.visual.CustomTouchable;
 import org.workcraft.dom.visual.DrawRequest;
@@ -86,15 +87,16 @@
 	}
 
 	private void addPropertyDeclarations() {
-		addPropertyDeclaration(new PropertyDeclaration<VisualCircuitComponent, String>(
-				this, "Name", String.class) {
-			protected void setter(VisualCircuitComponent object, String value) {
-				object.getReferencedCircuitComponent().setName(value);
-			}
-			protected String getter(VisualCircuitComponent object) {
-				return object.getReferencedCircuitComponent().getName();
-			}
-		});
+//		addPropertyDeclaration(new PropertyDeclaration<VisualCircuitComponent, String>(
+//				this, "Name", String.class) {
+//			protected void setter(VisualCircuitComponent object, String value) {
+//				get
+//				object.getReferencedCircuitComponent().setName(value);
+//			}
+//			protected String getter(VisualCircuitComponent object) {
+//				return object.getReferencedCircuitComponent().getName();
+//			}
+//		});
 		
 		addPropertyDeclaration(new PropertyDeclaration<VisualCircuitComponent, Boolean>(
 				this, "Treat as environment", Boolean.class) {
@@ -142,13 +144,13 @@
 		return (CircuitComponent)this.getReferencedComponent();
 	}
 	
-	public String getName() {
-		return getReferencedCircuitComponent().getName();
-	}
-	
-	public void setName(String value) {
-		getReferencedCircuitComponent().setName(value);
-	}
+//	public String getName() {
+//		return getReferencedCircuitComponent().getName();
+//	}
+//	
+//	public void setName(String value) {
+//		getReferencedCircuitComponent().setName(value);
+//	}
 	
 	public boolean getIsEnvironment() {
 		if (getReferencedCircuitComponent() != null) {
@@ -241,17 +243,20 @@
 		}
 	}
 
-	public void updateDirection(VisualContact vc, VisualContact.Direction dir) {
+	public void updateDirection(VisualCircuit vcircuit, VisualContact vc, VisualContact.Direction dir) {
 		vc.setDirection(dir);
 		contactLabelBB = null;
 		updateSidePosition(vc);
 		updateStepPositions();
 	}
 
-	public void addContact(VisualContact vc) {
+	public void addContact(VisualCircuit vcircuit, VisualContact vc) {
 		if (!getChildren().contains(vc)) {
-			this.getReferencedCircuitComponent().add(vc.getReferencedComponent());
+			
+	        Container container = AbstractVisualModel.getMathContainer(vcircuit, this);
+			container.add(vc.getReferencedComponent());
 			add(vc);
+			
 			contactLabelBB = null;
 			updateSidePosition(vc);
 			updateStepPositions();
@@ -259,7 +264,9 @@
 	}
 	
 	protected void updateTotalBB() {
+		
 		totalBB = BoundingBoxHelper.mergeBoundingBoxes(Hierarchy.getChildrenOfType(this, Touchable.class));
+		
 		if (contactLabelBB != null && totalBB != null) {
 			Rectangle2D.union(totalBB, contactLabelBB, totalBB);
 		}
@@ -273,7 +280,7 @@
 		return result;
 	}
 
-	public void updateContactLabelBB(Graphics2D g) {
+	public void updateContactLabelBB(Circuit circuit, Graphics2D g) {
 		int north=0;
 		int south=0;
 		int east=0;
@@ -295,7 +302,7 @@
 		for (Node vn: getChildren()) {
 			if (!(vn instanceof VisualContact)) continue;
 			VisualContact vc = (VisualContact)vn;
-			GlyphVector gv = vc.getNameGlyphs(g);
+			GlyphVector gv = vc.getNameGlyphs(circuit, g);
 			Rectangle2D cur = gv.getVisualBounds();
 			double xx = (double)(Math.round(cur.getWidth() * 4))/4;
 
@@ -358,13 +365,15 @@
 	protected void drawContacts(DrawRequest r) {
 		Graphics2D g = r.getGraphics();
 		Color colorisation = r.getDecoration().getColorisation();
+		Circuit circuit = (Circuit)r.getModel().getMathModel();
+		
 		Rectangle2D bb = getBestBB();
 		double step_pos;
 		for (Node n: getChildren()) {
 			if (n instanceof VisualContact) {
 				VisualContact c = (VisualContact)n;
 				if (!c.getDirection().equals(Direction.WEST)) continue;
-				GlyphVector gv = c.getNameGlyphs(g);
+				GlyphVector gv = c.getNameGlyphs(circuit, g);
 				Rectangle2D cur = gv.getVisualBounds();
 				g.setColor(Coloriser.colorise((c.getIOType()==IOType.INPUT) ? inputColor : outputColor, colorisation));
 				step_pos = c.getY();
@@ -376,7 +385,7 @@
 			if (n instanceof VisualContact) {
 				VisualContact c = (VisualContact)n;
 				if (!c.getDirection().equals(Direction.EAST)) continue;
-				GlyphVector gv = c.getNameGlyphs(g);
+				GlyphVector gv = c.getNameGlyphs(circuit, g);
 				Rectangle2D cur = gv.getVisualBounds();
 				g.setColor(Coloriser.colorise((c.getIOType()==IOType.INPUT) ? inputColor : outputColor, colorisation));
 				step_pos = c.getY();
@@ -392,7 +401,7 @@
 			if (n instanceof VisualContact) {
 				VisualContact c = (VisualContact)n;
 				if (!c.getDirection().equals(Direction.NORTH)) continue;
-				GlyphVector gv = c.getNameGlyphs(g);
+				GlyphVector gv = c.getNameGlyphs(circuit, g);
 				Rectangle2D cur = gv.getVisualBounds();
 				g.setColor(Coloriser.colorise((c.getIOType()==IOType.INPUT) ? inputColor : outputColor, colorisation));
 				step_pos = c.getX();
@@ -404,7 +413,7 @@
 			if (n instanceof VisualContact) {
 				VisualContact c = (VisualContact)n;
 				if (!c.getDirection().equals(Direction.SOUTH)) continue;
-				GlyphVector gv = c.getNameGlyphs(g);
+				GlyphVector gv = c.getNameGlyphs(circuit, g);
 				Rectangle2D cur = gv.getVisualBounds();
 				g.setColor(Coloriser.colorise((c.getIOType()==IOType.INPUT) ? inputColor : outputColor, colorisation));
 				step_pos = c.getX();
@@ -413,20 +422,28 @@
 		}
 	}
 	
+	
 	@Override
 	public Rectangle2D getInternalBoundingBoxInLocalSpace() {
 		if (groupImpl == null) {
 			return super.getInternalBoundingBoxInLocalSpace();
 		}
-		return BoundingBoxHelper.union(totalBB, BoundingBoxHelper.mergeBoundingBoxes(Hierarchy.getChildrenOfType(this, Touchable.class)));
+		Rectangle2D rect = BoundingBoxHelper.union(totalBB, BoundingBoxHelper.mergeBoundingBoxes(Hierarchy.getChildrenOfType(this, Touchable.class)));
+		
+		if (rect==null)
+			return super.getInternalBoundingBoxInLocalSpace();
+		
+		return rect;
 	}	
 	
+	
 	@Override
 	public void draw(DrawRequest r) {
 		Graphics2D g = r.getGraphics();
-
+		Circuit circuit = (Circuit)r.getModel().getMathModel();
+		
 		cacheRenderedText(r); // needed to better estimate the bounding box
-		updateContactLabelBB(g);
+		updateContactLabelBB(circuit, g);
 		drawContactConnections(r);
 		
 		Rectangle2D shape = getBestBB();
@@ -580,27 +597,30 @@
 		}
 	}
 
-	public VisualContact addInput(String name, VisualContact.Direction dir) {
-		VisualContact vc = new VisualContact(new Contact(IOType.INPUT));
-		if (dir==null) {
-			dir=VisualContact.Direction.WEST;
-		}
-		vc.setDirection(dir);
-		vc.setName(name);
-		addContact(vc);
-		return vc;
-	}
-	
-	public VisualContact addOutput(String name, VisualContact.Direction dir) {
-		VisualContact vc = new VisualContact(new Contact(IOType.OUTPUT));
-		if (dir==null) {
-			dir=VisualContact.Direction.EAST;
-		}
-		vc.setDirection(dir);
-		vc.setName(name);
-		addContact(vc);
-		return vc;
-	}
+//	public VisualContact addInput(Circuit circuit, String name, VisualContact.Direction dir) {
+//		VisualContact vc = new VisualContact(new Contact(IOType.INPUT));
+//		if (dir==null) {
+//			dir=VisualContact.Direction.WEST;
+//		}
+//		vc.setDirection(dir);
+//		
+//		circuit.setName(vc.getReferencedComponent(), name);
+//		
+//		addContact(vc);
+//		return vc;
+//	}
+//	
+//	public VisualContact addOutput(VisualCircuit vcircuit, String name, VisualContact.Direction dir) {
+//		VisualContact vc = new VisualContact(new Contact(IOType.OUTPUT));
+//		if (dir==null) {
+//			dir=VisualContact.Direction.EAST;
+//		}
+//		vc.setDirection(dir);
+//		
+//		circuit.setName(vc.getReferencedComponent(), name);
+//		addContact(vc);
+//		return vc;
+//	}
 
 	@Override
 	public void addObserver(HierarchyObserver obs) {

=== modified file 'CircuitPlugin/src/org/workcraft/plugins/circuit/VisualContact.java'
--- CircuitPlugin/src/org/workcraft/plugins/circuit/VisualContact.java	2014-07-07 13:20:59 +0000
+++ CircuitPlugin/src/org/workcraft/plugins/circuit/VisualContact.java	2014-07-11 09:42:10 +0000
@@ -167,15 +167,15 @@
 			}
 		});
 
-		addPropertyDeclaration(new PropertyDeclaration<VisualContact, String>(
-				this, "Name", String.class) {
-			protected void setter(VisualContact object, String value) {
-				object.setName(value);
-			}
-			protected String getter(VisualContact object) {
-				return object.getName();
-			}
-		});
+//		addPropertyDeclaration(new PropertyDeclaration<VisualContact, String>(
+//				this, "Name", String.class) {
+//			protected void setter(VisualContact object, String value) {
+//				object.setName(value);
+//			}
+//			protected String getter(VisualContact object) {
+//				return object.getName();
+//			}
+//		});
 
 
 		addPropertyDeclaration(new PropertyDeclaration<VisualContact, Boolean>(
@@ -203,6 +203,8 @@
 	public void draw(DrawRequest r) {
 		Graphics2D g = r.getGraphics();
 		Decoration d = r.getDecoration();
+		Circuit circuit = (Circuit)r.getModel().getMathModel();
+		
 		boolean inSimulationMode = ((d.getColorisation() != null) || (d.getBackground() != null)); 
 		Color colorisation = d.getColorisation();
 		Color fillColor = d.getBackground();
@@ -237,7 +239,7 @@
 			}
 			g.transform(at);
 			
-			GlyphVector gv = getNameGlyphs(g);
+			GlyphVector gv = getNameGlyphs(circuit, g);
 			Rectangle2D cur = gv.getVisualBounds();
 			g.setColor(Coloriser.colorise((getIOType()==IOType.INPUT)?inputColor:outputColor, colorisation));
 			
@@ -293,19 +295,19 @@
 		}
 	}	
 	
-	public GlyphVector getNameGlyphs(Graphics2D g) {
+	public GlyphVector getNameGlyphs(Circuit circuit, Graphics2D g) {
 		if (nameGlyph == null) {
 			if (getDirection() == VisualContact.Direction.NORTH || getDirection() == VisualContact.Direction.SOUTH) {
 				AffineTransform at = new AffineTransform();
 				at.quadrantRotate(1);
 			}
-			nameGlyph = nameFont.createGlyphVector(g.getFontRenderContext(), getName());
+			nameGlyph = nameFont.createGlyphVector(g.getFontRenderContext(), circuit.getName(this.getReferencedContact()));
 		}
 		return nameGlyph;
 	}
 	
-	public Rectangle2D getNameBB(Graphics2D g) {
-		return getNameGlyphs(g).getVisualBounds();
+	public Rectangle2D getNameBB(Circuit circuit, Graphics2D g) {
+		return getNameGlyphs(circuit, g).getVisualBounds();
 	}
 	
 	public void setDirection(VisualContact.Direction dir) {
@@ -336,20 +338,34 @@
 	public String getName() {
 		return getReferencedContact().getName();
 	}
-
+	
 	@NoAutoSerialisation
 	public void setName(String name) {
 		getReferencedContact().setName(name);
 	}
+	
+	
+////
+//	public void updateLocalName(String name) {
+//		resetNameGlyph();
+//		getReferencedContact().setName(name);
+//		sendNotification(new PropertyChangedEvent(this, "name"));
+//	}
 
 	public Contact getReferencedContact() {
 		return (Contact)getReferencedComponent();
 	}
 
+	
+	/*
+	 * returns true if 
+	 */
 	public static boolean isDriver(Node node) {
 		if (node instanceof VisualContact) {
 			VisualContact contact = (VisualContact)node;
-			return (contact.getIOType() == IOType.OUTPUT) || !(contact.getParent() instanceof VisualComponent);
+			boolean ret =	(contact.getIOType() == IOType.OUTPUT) || 
+							!(contact.getParent() instanceof VisualCircuitComponent); 
+			return ret;
 		}
 		return false;
 	}

=== modified file 'CircuitPlugin/src/org/workcraft/plugins/circuit/VisualContactFormulaProperties.java'
--- CircuitPlugin/src/org/workcraft/plugins/circuit/VisualContactFormulaProperties.java	2014-06-27 14:48:42 +0000
+++ CircuitPlugin/src/org/workcraft/plugins/circuit/VisualContactFormulaProperties.java	2014-07-11 09:42:10 +0000
@@ -3,7 +3,9 @@
 import java.lang.reflect.InvocationTargetException;
 import java.util.Map;
 
+import org.workcraft.dom.Container;
 import org.workcraft.gui.propertyeditor.PropertyDescriptor;
+import org.workcraft.plugins.circuit.Contact.IOType;
 import org.workcraft.plugins.cpog.optimisation.BooleanFormula;
 import org.workcraft.plugins.cpog.optimisation.booleanvisitors.FormulaToString;
 import org.workcraft.plugins.cpog.optimisation.javacc.BooleanParser;
@@ -11,10 +13,10 @@
 import org.workcraft.util.Func;
 
 public class VisualContactFormulaProperties {
-	VisualCircuit circuit;
+	VisualCircuit vcircuit;
 	
 	public VisualContactFormulaProperties(VisualCircuit circuit) {
-		this.circuit = circuit;
+		this.vcircuit = circuit;
 	}
 	
 	private BooleanFormula parseFormula(final VisualFunctionContact contact, String resetFunction) {
@@ -23,13 +25,19 @@
 					new Func<String, BooleanFormula>() {
 						@Override
 						public BooleanFormula eval(String name) {
+							
+							
 							if (contact.getParent() instanceof VisualFunctionComponent) {
-								return ((VisualFunctionComponent)contact.getParent()).getOrCreateInput(name)
-								.getReferencedContact();
-							}
-							
-							else
-								return circuit.getOrCreateOutput(name, contact.getX()+1, contact.getY()+1).getReferencedContact();
+								return 
+									(BooleanFormula)
+									vcircuit.getOrCreateContact(
+											(Container)contact.getParent(),
+											name, 
+											IOType.INPUT, 0, 0
+										).getReferencedContact();
+							} else
+								return (BooleanFormula)
+										vcircuit.getOrCreateOutput(name, contact.getX()+1, contact.getY()+1).getReferencedContact();
 						}
 					});
 		} catch (ParseException e) {

=== modified file 'CircuitPlugin/src/org/workcraft/plugins/circuit/VisualFunctionComponent.java'
--- CircuitPlugin/src/org/workcraft/plugins/circuit/VisualFunctionComponent.java	2014-06-27 14:48:42 +0000
+++ CircuitPlugin/src/org/workcraft/plugins/circuit/VisualFunctionComponent.java	2014-07-11 09:42:10 +0000
@@ -39,9 +39,9 @@
 	
 	public VisualFunctionComponent(CircuitComponent component) {
 		super(component);
-		if (component.getChildren().isEmpty()) {
-			this.addFunction("x", null, false);
-		}
+//		if (component.getChildren().isEmpty()) {
+//			this.addFunction("x", null, false);
+//		}
 	}
 
 	ComponentRenderingResult renderingResult = null;
@@ -100,32 +100,6 @@
 			return super.hitTestInLocalSpace(pointInLocalSpace);
 		}
 	}
-	
-	public VisualFunctionContact addFunction(String prefix, IOType ioType, boolean allowShort) {
-		VisualContact.Direction dir=null;
-		if (ioType==null) ioType = IOType.OUTPUT;
-		
-		dir=VisualContact.Direction.WEST;
-		if (ioType==IOType.OUTPUT) {
-			dir=VisualContact.Direction.EAST;
-		}
-		FunctionContact c = new FunctionContact(ioType);
-		VisualFunctionContact vc = new VisualFunctionContact(c);
-		vc.setDirection(dir);
-		vc.setName(Contact.getNewName(this.getReferencedComponent(), prefix, null, allowShort));
-		addContact(vc);
-		return vc;
-	}
-	
-	public VisualFunctionContact getOrCreateInput(String arg) {
-		for (VisualFunctionContact c : Hierarchy.filterNodesByType(getChildren(), VisualFunctionContact.class)) {
-			if(c.getName().equals(arg)) return c;
-		}
-		VisualFunctionContact vc = addFunction(arg, IOType.INPUT, true);
-		vc.setSetFunction(One.instance());
-		vc.setResetFunction(One.instance());
-		return vc;
-	}
 
 	@Override
 	public void setRenderType(RenderType renderType) {
@@ -185,8 +159,11 @@
 						vc.setTransform(ct, !firstUpdate); // suppress notifications at first recalculation of contact coordinates
 						continue;
 					}
+					
 					if (vc.getIOType() != IOType.INPUT) continue;
-					Point2D position = res.contactPositions().get(vc.getName());
+					
+					String vcName = vc.getName();
+					Point2D position = res.contactPositions().get(vcName);
 					if (position != null) {
 						bt.translate(snapP5(res.boundingBox().getMinX() - GateRenderer.contactMargin), position.getY());
 						
@@ -221,6 +198,9 @@
 		GateRenderer.foreground = Coloriser.colorise(getForegroundColor(), r.getDecoration().getColorisation());
 		GateRenderer.background  = Coloriser.colorise(getFillColor(), r.getDecoration().getBackground());
 		ComponentRenderingResult res = getRenderingResult();
+		VisualCircuit vcircuit = (VisualCircuit)r.getModel();
+		
+		
 		if (res == null) {
 			super.draw(r);
 		} else {
@@ -290,7 +270,8 @@
 					
 					if (vc.getIOType() != IOType.INPUT) continue;
 					
-					Point2D position = res.contactPositions().get(vc.getName());
+					String cname = vc.getReferencedContact().getName();
+					Point2D position = res.contactPositions().get(cname);
 					if (position != null) {
 						line = new Line2D.Double(snapP5(res.boundingBox().getMinX() - GateRenderer.contactMargin),
 							position.getY(), position.getX(), position.getY());

=== modified file 'CircuitPlugin/src/org/workcraft/plugins/circuit/VisualFunctionContact.java'
--- CircuitPlugin/src/org/workcraft/plugins/circuit/VisualFunctionContact.java	2014-06-27 14:48:42 +0000
+++ CircuitPlugin/src/org/workcraft/plugins/circuit/VisualFunctionContact.java	2014-07-11 09:42:10 +0000
@@ -19,7 +19,7 @@
 *
 */
 
-package org.workcraft.plugins.circuit;
+package org.workcraft.plugins.circuit;
 
 import java.awt.BasicStroke;
 import java.awt.Color;
@@ -87,7 +87,7 @@
 	public BooleanFormula getSetFunction() {
 		return getReferencedFunctionContact().getSetFunction();
 	}
-
+	
 	@NoAutoSerialisation
 	public void setSetFunction(BooleanFormula setFunction) {
 		if (getParent() instanceof VisualFunctionComponent) {
@@ -126,7 +126,7 @@
 		}
 		return renderedSetFormula;
 	}
-	
+
 	FormulaRenderingResult getRenderedResetFormula(FontRenderContext fcon) {
 		if (((FunctionContact)getReferencedContact()).getResetFunction() == null) {
 			return null;
@@ -255,5 +255,5 @@
 		}
 		super.notify(e);
 	}
-	
-}
+	
+}

=== added directory 'CircuitPlugin/src/org/workcraft/plugins/circuit/references'
=== added file 'CircuitPlugin/src/org/workcraft/plugins/circuit/references/CircuitReferenceManager.java'
--- CircuitPlugin/src/org/workcraft/plugins/circuit/references/CircuitReferenceManager.java	1970-01-01 00:00:00 +0000
+++ CircuitPlugin/src/org/workcraft/plugins/circuit/references/CircuitReferenceManager.java	2014-07-11 09:42:10 +0000
@@ -0,0 +1,72 @@
+package org.workcraft.plugins.circuit.references;
+
+import org.workcraft.dom.Node;
+import org.workcraft.dom.hierarchy.NamespaceHelper;
+import org.workcraft.dom.hierarchy.NamespaceProvider;
+import org.workcraft.dom.references.HierarchicalUniqueNameReferenceManager;
+import org.workcraft.dom.references.NameManager;
+import org.workcraft.plugins.circuit.CircuitComponent;
+import org.workcraft.plugins.circuit.Contact;
+import org.workcraft.plugins.circuit.FunctionComponent;
+import org.workcraft.serialisation.References;
+import org.workcraft.util.Func;
+import org.workcraft.util.Identifier;
+
+
+public class CircuitReferenceManager extends HierarchicalUniqueNameReferenceManager {
+
+	public CircuitReferenceManager(NamespaceProvider provider,
+			References existing, Func<Node, String> defaultName) {
+		super(existing, defaultName);
+	}
+	
+	@Override
+	public String getName(Node node) {
+		
+		NameManager<Node> man = getNameManager(getNamespaceProvider(node));
+		
+		if (node instanceof Contact && !man.isNamed(node)) {
+			return ((Contact)node).getName();
+		}
+		
+		if (node instanceof FunctionComponent && (!man.isNamed(node))) {
+			return ((FunctionComponent)node).getName();
+		}
+		
+		if (!man.isNamed(node)) return null;
+		
+		return super.getName(node);
+	}
+	
+	@Override
+	public void setName(Node node, String name) {
+		
+		// support for the older models
+		if (Identifier.isNumber(name) && node instanceof Contact) {
+			
+			String n = ((Contact)node).getName();
+			
+			if (n!=null&&!n.equals("")) name=n;
+		} else if (Identifier.isNumber(name) && node instanceof CircuitComponent) {
+				
+			String n = ((CircuitComponent)node).getName();
+			if (n!=null&&!n.equals("")) name=n;
+			
+		} else if (Identifier.isNumber(name)) {
+			// name="_"+name;
+			name=defaultName.eval(node)+name;
+		}
+		
+		if (node instanceof Contact) {
+			// propagate info to the node itself
+			((Contact)node).setName(name);
+		}
+		if (node instanceof CircuitComponent) {
+			// propagate info to the node itself
+			((CircuitComponent)node).setName(name);
+		}
+		
+		super.setName(node, name);
+	}	
+
+}

=== modified file 'CircuitPlugin/src/org/workcraft/plugins/circuit/tools/CircuitSelectionTool.java'
--- CircuitPlugin/src/org/workcraft/plugins/circuit/tools/CircuitSelectionTool.java	2013-07-25 12:29:40 +0000
+++ CircuitPlugin/src/org/workcraft/plugins/circuit/tools/CircuitSelectionTool.java	2014-07-11 09:42:10 +0000
@@ -15,8 +15,13 @@
 import org.workcraft.gui.events.GraphEditorMouseEvent;
 import org.workcraft.gui.graph.tools.GraphEditor;
 import org.workcraft.gui.graph.tools.SelectionTool;
+import org.workcraft.plugins.circuit.Circuit;
+import org.workcraft.plugins.circuit.FunctionContact;
+import org.workcraft.plugins.circuit.VisualCircuit;
 import org.workcraft.plugins.circuit.VisualCircuitComponent;
 import org.workcraft.plugins.circuit.VisualFunctionComponent;
+import org.workcraft.plugins.circuit.VisualFunctionContact;
+import org.workcraft.plugins.circuit.Contact.IOType;
 
 public class CircuitSelectionTool extends SelectionTool {
 
@@ -52,11 +57,15 @@
 			popup.addSeparator();
 			
 			JMenuItem addFunction = new JMenuItem("Add function");
+			
 			addFunction.addActionListener(new ActionListener() {
 				@Override
 				public void actionPerformed(ActionEvent e) {
 					editor.getWorkspaceEntry().saveMemento();
-					comp.addFunction("x", null, false);
+					VisualCircuit vcircuit = (VisualCircuit)editor.getModel();
+					
+					vcircuit.getOrCreateContact(comp, null, IOType.OUTPUT, 0, 0);
+//					comp.addFunction("x", null, false);
 				}
 			});
 			
@@ -76,7 +85,10 @@
 				@Override
 				public void actionPerformed(ActionEvent e) {
 					editor.getWorkspaceEntry().saveMemento();
-					comp.addInput("", null);
+					VisualCircuit vcircuit = (VisualCircuit)editor.getModel();
+					
+					vcircuit.getOrCreateContact(comp, null, IOType.INPUT, 0, 0);
+//					comp.addInput((Circuit)vcircuit.getMathModel(), "", null);
 				}
 			});
 			
@@ -85,7 +97,10 @@
 				@Override
 				public void actionPerformed(ActionEvent e) {
 					editor.getWorkspaceEntry().saveMemento();
-					comp.addOutput("", null);
+					VisualCircuit vcircuit = (VisualCircuit)editor.getModel();
+					
+					vcircuit.getOrCreateContact(comp, null, IOType.OUTPUT, 0, 0);
+//					comp.addOutput((Circuit)vcircuit.getMathModel(), "", null);
 				}
 			});
 			

=== modified file 'CircuitPlugin/src/org/workcraft/plugins/circuit/tools/STGGenerator.java'
--- CircuitPlugin/src/org/workcraft/plugins/circuit/tools/STGGenerator.java	2014-07-07 13:20:59 +0000
+++ CircuitPlugin/src/org/workcraft/plugins/circuit/tools/STGGenerator.java	2014-07-11 09:42:10 +0000
@@ -15,7 +15,9 @@
 import java.util.TreeSet;
 
 import org.workcraft.dom.Connection;
+import org.workcraft.dom.Container;
 import org.workcraft.dom.Node;
+import org.workcraft.dom.hierarchy.NamespaceHelper;
 import org.workcraft.dom.visual.Movable;
 import org.workcraft.dom.visual.TransformHelper;
 import org.workcraft.dom.visual.VisualComponent;
@@ -31,7 +33,6 @@
 import org.workcraft.plugins.circuit.VisualFunctionContact;
 import org.workcraft.plugins.circuit.VisualJoint;
 import org.workcraft.plugins.cpog.optimisation.BooleanFormula;
-import org.workcraft.plugins.cpog.optimisation.BooleanVariable;
 import org.workcraft.plugins.cpog.optimisation.Literal;
 import org.workcraft.plugins.cpog.optimisation.booleanvisitors.FormulaToString;
 import org.workcraft.plugins.cpog.optimisation.dnf.Dnf;
@@ -87,14 +88,23 @@
 	
 	private static ContactSTG generatePlaces(VisualCircuit circuit, VisualSTG stg, VisualContact contact) {
 		String contactName = getContactName(circuit, contact);
-		VisualPlace zeroPlace = stg.createPlace(contactName+"_0");
+		
+		String path = NamespaceHelper.getParentReference(circuit.getMathModel().getNodeReference(contact.getReferencedComponent()));
+		Container curContainer = (Container)createdContainers.get(path);
+		while (curContainer==null) {
+			path = NamespaceHelper.getParentReference(path);
+			curContainer = (Container)createdContainers.get(path);
+		}
+
+		
+		VisualPlace zeroPlace = stg.createPlace(contactName+"_0", curContainer);
 		zeroPlace.setLabel(contactName+"=0");
 		
 		if (!contact.getInitOne()) {
 			zeroPlace.getReferencedPlace().setTokens(1);
 		}
 		
-		VisualPlace onePlace = stg.createPlace(contactName+"_1");
+		VisualPlace onePlace = stg.createPlace(contactName+"_1", curContainer);
 		onePlace.setLabel(contactName+"=1");
 		if (contact.getInitOne()) {
 			onePlace.getReferencedPlace().setTokens(1);
@@ -131,15 +141,23 @@
 		}
 	}
 	
-	public static VisualSTG generate(VisualCircuit circuit) {
+	
+	
+	// store created containers in a separate map
+	private static HashMap<String, Node> createdContainers = null;
+	
+	public synchronized static VisualSTG generate(VisualCircuit circuit) {
 		try {
 			VisualSTG stg = new VisualSTG(new STG());
 			
+			// first, create the same page structure
+			createdContainers = NamespaceHelper.copyPageStructure(stg, stg.getRoot(), circuit, circuit.getRoot(), null);
+			
 			Map<Contact, VisualContact> targetDrivers = new HashMap<Contact, VisualContact>();
 			Map<VisualContact, ContactSTG> drivers = new HashMap<VisualContact, ContactSTG>(); 
 			
 			// generate all possible drivers and fill out the targets
-			for(VisualContact contact : Hierarchy.getDescendantsOfType(circuit.getRoot(), VisualContact.class)) {
+			for (VisualContact contact : Hierarchy.getDescendantsOfType(circuit.getRoot(), VisualContact.class)) {
 				ContactSTG cstg;
 				
 				if(VisualContact.isDriver(contact)) {
@@ -171,10 +189,10 @@
 				BooleanFormula resetFunc = null;
 				Type signalType = Type.INPUT;
 				if (driver instanceof VisualFunctionContact) {
+					// Determine signal type
 					VisualFunctionContact contact = (VisualFunctionContact)driver;
-					if ((contact.getIOType() == IOType.OUTPUT) && !isFromEnvironment(contact)) {
-						signalType = Type.OUTPUT;
-					}
+					signalType = getSignalType(contact);
+					
 					if ((contact.getIOType() == IOType.OUTPUT) && !(contact.getParent() instanceof VisualCircuitComponent)) {
 						// Driver of the primary output port
 						VisualContact outputDriver = findDriver(circuit, contact);
@@ -203,11 +221,19 @@
 		}
 	}
 
-	private static boolean isFromEnvironment(VisualContact contact) {
-		if (contact.getParent() instanceof VisualCircuitComponent) {
-			return ((VisualCircuitComponent)contact.getParent()).getIsEnvironment();
-		}
-		return false;
+	private static Type getSignalType(VisualFunctionContact contact) {
+		Type result = Type.INPUT;
+		if (contact.getIOType() == IOType.OUTPUT) {
+			if (contact.getParent() instanceof VisualCircuitComponent) {
+				VisualCircuitComponent component = (VisualCircuitComponent)contact.getParent();
+				if (!component.getIsEnvironment()) {
+					result = Type.INTERNAL;
+				}
+			} else {
+				result = Type.OUTPUT;
+			   }
+		  }
+		  return result;
 	}
 	
 	private static void implementDriver(VisualCircuit circuit, VisualSTG stg,
@@ -284,8 +310,22 @@
 				reset, subtract(add(center, direction), pOffset),  minusDirection, 
 				signalName, ttype, SignalTransition.Direction.MINUS, p.p1, p.p0));
 		
+		Container currentLevel = null;
+		Container oldLevel = stg.getCurrentLevel();
+				
+		for (Node node:nodes) {
+			if (currentLevel==null) 
+				currentLevel = (Container)node.getParent();
+			
+			if (currentLevel!=node.getParent())
+				throw new RuntimeException("Current level is not the same among the processed nodes");
+		}
+		
+		
+		stg.setCurrentLevel(currentLevel);
 		stg.select(nodes);
 		stg.groupSelection();
+		stg.setCurrentLevel(oldLevel);
 	}
 
 	private static LinkedList<VisualNode> buildTransitions(VisualContact parentContact,
@@ -296,6 +336,15 @@
 		
 		LinkedList<VisualNode> nodes = new LinkedList<VisualNode>();
 		
+		
+		String path = NamespaceHelper.getParentReference(circuit.getMathModel().getNodeReference(parentContact.getReferencedComponent()));
+		Container curContainer = (Container)createdContainers.get(path);
+		while (curContainer==null) {
+			path = NamespaceHelper.getParentReference(path);
+			curContainer = (Container)createdContainers.get(path);
+		}
+		
+		
 		TreeSet<DnfClause> clauses = new TreeSet<DnfClause>(
 				new Comparator<DnfClause>() {
 					@Override
@@ -311,7 +360,7 @@
 		
 		for(DnfClause clause : clauses)
 		{	
-			VisualSignalTransition transition = stg.createSignalTransition(signalName, type, transitionDirection);
+			VisualSignalTransition transition = stg.createSignalTransition(signalName, type, transitionDirection, curContainer);
 			nodes.add(transition);
 			parentContact.getReferencedTransitions().add(transition.getReferencedTransition());
 			
@@ -333,7 +382,7 @@
 				ContactSTG source = drivers.get(driverContact);
 				
 				if(source == null)
-					throw new RuntimeException("No source for " + targetContact.getName() + " while generating " + signalName);
+					throw new RuntimeException("No source for " + circuit.getMathModel().getName(targetContact) + " while generating " + signalName);
 				
 				VisualPlace p = literal.getNegation() ? source.p0 : source.p1;
 				
@@ -365,12 +414,19 @@
 				}
 			}
 			
-			result = ((VisualFunctionComponent)parent).getName();
+			result = NamespaceHelper.getFlatName(
+						circuit.getMathModel().getName(vc.getReferencedComponent())
+					);
+			
+//			result = HierarchicalNames.getFlatName(
+//					circuit.getMathModel().getNodeReference(vc.getReferencedComponent())
+//					);
+			
 			if (contact.getIOType() == IOType.INPUT || output_cnt > 1) {
-				result += "_" + contact.getName();
+				result += "_" + circuit.getMathModel().getName(contact.getReferencedContact());
 			}
 		} else {
-			result = contact.getName();
+			result = circuit.getMathModel().getName(contact.getReferencedContact());
 		}
 		return result;
 	}

=== modified file 'CpogsPlugin/.classpath'
--- CpogsPlugin/.classpath	2014-01-29 19:00:22 +0000
+++ CpogsPlugin/.classpath	2014-07-11 09:42:10 +0000
@@ -5,5 +5,6 @@
 	<classpathentry combineaccessrules="false" kind="src" path="/WorkcraftCore"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.junit.JUNIT_CONTAINER/4"/>
 	<classpathentry combineaccessrules="false" kind="src" path="/STGPlugin"/>
+	<classpathentry kind="lib" path="/ThirdParty/TableLayout-bin-jdk1.5-2009-08-26.jar"/>
 	<classpathentry kind="output" path="bin"/>
 </classpath>

=== modified file 'CpogsPlugin/src/org/workcraft/plugins/cpog/CPOG.java'
--- CpogsPlugin/src/org/workcraft/plugins/cpog/CPOG.java	2014-04-07 16:35:42 +0000
+++ CpogsPlugin/src/org/workcraft/plugins/cpog/CPOG.java	2014-07-11 09:42:10 +0000
@@ -27,7 +27,10 @@
 import org.workcraft.dom.Connection;
 import org.workcraft.dom.Container;
 import org.workcraft.dom.Node;
+import org.workcraft.dom.hierarchy.NamespaceProvider;
 import org.workcraft.dom.math.AbstractMathModel;
+import org.workcraft.dom.math.MathGroup;
+import org.workcraft.dom.references.HierarchicalUniqueNameReferenceManager;
 import org.workcraft.dom.references.UniqueNameReferenceManager;
 import org.workcraft.exceptions.InvalidConnectionException;
 import org.workcraft.observation.HierarchyEvent;
@@ -42,11 +45,11 @@
 public class CPOG extends AbstractMathModel {
 
 	public CPOG() {
-		this(null, null);
+		this(new MathGroup(), null);
 	}
 
 	public CPOG(Container root, References refs) {
-		super(root, new UniqueNameReferenceManager(refs, new Func<Node, String>() {
+		super(root, new HierarchicalUniqueNameReferenceManager(refs, new Func<Node, String>() {
 			@Override
 			public String eval(Node arg) {
 				if (arg instanceof Vertex)

=== modified file 'CpogsPlugin/src/org/workcraft/plugins/cpog/ConsistencyEnforcer.java'
--- CpogsPlugin/src/org/workcraft/plugins/cpog/ConsistencyEnforcer.java	2010-05-01 15:12:53 +0000
+++ CpogsPlugin/src/org/workcraft/plugins/cpog/ConsistencyEnforcer.java	2014-07-11 09:42:10 +0000
@@ -5,6 +5,7 @@
 import org.workcraft.observation.HierarchySupervisor;
 import org.workcraft.observation.NodesAddedEvent;
 import org.workcraft.observation.NodesDeletedEvent;
+import org.workcraft.observation.NodesReparentedEvent;
 
 public class ConsistencyEnforcer extends HierarchySupervisor {
 
@@ -20,7 +21,7 @@
 	@Override
 	public void handleEvent(HierarchyEvent e)
 	{
-		if (e instanceof NodesAddedEvent)
+		if (e instanceof NodesAddedEvent  || e instanceof NodesReparentedEvent)
 		{
 			updateEncoding();
 			createDefaultLabels(e);

=== removed file 'CpogsPlugin/src/org/workcraft/plugins/cpog/CpogEncoder.java'
--- CpogsPlugin/src/org/workcraft/plugins/cpog/CpogEncoder.java	2013-10-21 17:36:57 +0000
+++ CpogsPlugin/src/org/workcraft/plugins/cpog/CpogEncoder.java	1970-01-01 00:00:00 +0000
@@ -1,311 +0,0 @@
-package org.workcraft.plugins.cpog;
-
-import java.awt.geom.Point2D;
-import java.util.ArrayList;
-import java.util.HashMap;
-import javax.swing.JOptionPane;
-
-import org.workcraft.Tool;
-import org.workcraft.dom.visual.VisualComponent;
-import org.workcraft.dom.visual.connections.VisualConnection;
-import org.workcraft.plugins.cpog.optimisation.BooleanFormula;
-import org.workcraft.plugins.cpog.optimisation.CleverCnfGenerator;
-import org.workcraft.plugins.cpog.optimisation.CpogEncoding;
-import org.workcraft.plugins.cpog.optimisation.DefaultCpogSolver;
-import org.workcraft.plugins.cpog.optimisation.OneHotIntBooleanFormula;
-import org.workcraft.plugins.cpog.optimisation.OneHotNumberProvider;
-import org.workcraft.plugins.cpog.optimisation.Optimiser;
-import org.workcraft.plugins.cpog.optimisation.expressions.One;
-import org.workcraft.util.Geometry;
-import org.workcraft.workspace.WorkspaceEntry;
-
-public class CpogEncoder implements Tool {
-
-	@Override
-	public String getDisplayName() {
-		return "CPOG Encoding";
-	}
-
-	@Override
-	public String getSection() {
-		return "Encoding";
-	}
-
-	@Override
-	public boolean isApplicableTo(WorkspaceEntry we)
-	{		
-		if (we.getModelEntry() == null) return false;		
-		if (we.getModelEntry().getVisualModel() instanceof VisualCPOG) return true;		
-		return false;
-	}
-
-	
-	private String generateConstraint(char [][][] constraints, int numScenarios, int event1, int event2)
-	{
-		StringBuilder s = new StringBuilder();
-		for(int k = 0; k < numScenarios; k++) s.append(constraints[k][event1][event2]);
-		return s.toString();
-	}
-	
-	private char trivialEncoding(char [][][] constraints, int numScenarios, int event1, int event2)
-	{
-		char trivial = '-';
-		
-		for(int k = 0; k < numScenarios; k++)
-		{
-			if (constraints[k][event1][event2] == '0')
-			{
-				if (trivial == '1') return '?';
-				trivial = '0';
-			}
-
-			if (constraints[k][event1][event2] == '1')
-			{
-				if (trivial == '0') return '?';
-				trivial = '1';
-			}
-		}
-		
-		return trivial;
-	}	 
-	
-	@Override
-	public void run(WorkspaceEntry we)
-	{
-		VisualCPOG cpog = (VisualCPOG)(we.getModelEntry().getVisualModel());
-		
-		we.captureMemento();
-		
-		HashMap<String, Integer> events = new HashMap<String, Integer>();
-		int n = 0;
-		ArrayList<Point2D> positions = new ArrayList<Point2D>();
-		ArrayList<Integer> count = new ArrayList<Integer>();		
-
-		// TODO: remove deprecated method
-		ArrayList<VisualScenario> scenarios = new ArrayList<VisualScenario>(cpog.getGroups());
-		
-		int m = scenarios.size();
-		
-		if (m < 2)
-		{
-			JOptionPane.showMessageDialog(null,
-					"At least two scenarios are expected.",
-					"Not enough scenarios",
-					JOptionPane.ERROR_MESSAGE);
-			we.cancelMemento();
-			return;
-		}
-		
-		// find all events
-		for(int k = 0; k < m; k++)
-		{
-			for(VisualComponent component : scenarios.get(k).getComponents())
-			if (component instanceof VisualVertex)
-			{
-				VisualVertex vertex = (VisualVertex)component;
-				
-				if (!events.containsKey(vertex.getLabel()))
-				{
-					events.put(vertex.getLabel(), n);
-					count.add(1);
-					Point2D p = vertex.getCenter();
-					p.setLocation(p.getX() - scenarios.get(k).getBoundingBox().getMinX(), p.getY() - scenarios.get(k).getBoundingBox().getMinY());
-					positions.add(p);
-					n++;
-				}
-				else
-				{
-					int id = events.get(vertex.getLabel());
-					count.set(id, count.get(id) + 1);
-					Point2D p = vertex.getCenter();
-					p.setLocation(p.getX() - scenarios.get(k).getBoundingBox().getMinX(), p.getY() - scenarios.get(k).getBoundingBox().getMinY());
-					positions.set(id, Geometry.add(positions.get(id), p));							
-				}
-			}
-		}
-		
-		// construct constraints
-		
-		char [][][] constraints = new char[m][n][n];
-		int [][] graph = new int[n][n];
-		
-		for(int k = 0; k < m; k++)
-		{
-			for(int i = 0; i < n; i++) for(int j = 0; j < n; j++) constraints[k][i][j] = '0';
-			
-			for(VisualComponent component : scenarios.get(k).getComponents())
-			if (component instanceof VisualVertex)
-			{
-				VisualVertex vertex = (VisualVertex)component;
-				int id = events.get(vertex.getLabel());
-				constraints[k][id][id] = '1';
-			}
-
-			for(int i = 0; i < n; i++) for(int j = 0; j < n; j++) graph[i][j] = 0;
-			
-			for(VisualConnection c : scenarios.get(k).getConnections())
-			if (c instanceof VisualArc)
-			{
-				VisualArc arc = (VisualArc)c;
-				VisualComponent c1 = arc.getFirst(), c2 = arc.getSecond();
-				if (c1 instanceof VisualVertex && c2 instanceof VisualVertex)
-				{
-					int id1 = events.get(((VisualVertex)c1).getLabel());
-					int id2 = events.get(((VisualVertex)c2).getLabel());
-					graph[id1][id2] = 1;
-				}
-			}
-			
-			// compute transitive closure
-			
-			for(int t = 0; t < n; t++)
-				for(int i = 0; i < n; i++)
-				if (graph[i][t] > 0)
-					for(int j = 0; j < n; j++)
-					if (graph[t][j] > 0) graph[i][j] = 1;
-			
-			// detect transitive arcs
-			
-			for(int t = 0; t < n; t++)
-				for(int i = 0; i < n; i++)
-				if (graph[i][t] > 0)
-					for(int j = 0; j < n; j++)
-					if (graph[t][j] > 0) graph[i][j] = 2;
-			
-			// report cyclic scenario
-			
-			for(int i = 0; i < n; i++)
-				if (graph[i][i] > 0)
-				{
-					JOptionPane.showMessageDialog(null,
-												"Scenario '" + scenarios.get(k).getLabel() + "' is cyclic.",
-												"Invalid scenario",
-												JOptionPane.ERROR_MESSAGE);
-					we.cancelMemento();
-					return;
-				}
-			
-			for(int i = 0; i < n; i++)
-				for(int j = 0; j < n; j++)
-				if (i != j)
-				{
-					char ch = '0';
-					
-					if (graph[i][j] > 0) ch = '1';
-					if (graph[i][j] > 1) ch = '-';
-					if (constraints[k][i][i] == '0' || constraints[k][j][j] == '0') ch = '-';
-					
-					constraints[k][i][j] = ch;
-				}					
-		}
-		
-		// group similar constraints
-		
-		HashMap<String, Integer> task = new HashMap<String, Integer>();
-		
-		for(int i = 0; i < n; i++)
-			for(int j = 0; j < n; j++)
-				if (trivialEncoding(constraints, m, i, j) == '?')
-				{
-					String constraint = generateConstraint(constraints, m, i, j); 
-					if (!task.containsKey(constraint)) task.put(constraint, task.size());
-				}
-		
-		// call CPOG encoder
-		
-		char [][] matrix = new char[m][task.size()];
-		
-		String [] instance = new String[m];
-		for(String s : task.keySet())
-			for(int i = 0; i < m; i++) matrix[i][task.get(s)] = s.charAt(i);	
-
-		for(int i = 0; i < m; i++) instance[i] = new String(matrix[i]);
-		
-		int freeVariables = CpogSettings.getEncodingWidth();
-		int derivedVariables = CpogSettings.getCircuitSize();
-		
-		Optimiser<OneHotIntBooleanFormula> oneHot = new Optimiser<OneHotIntBooleanFormula>(new OneHotNumberProvider());
-		
-		DefaultCpogSolver<BooleanFormula> solverCnf = new DefaultCpogSolver<BooleanFormula>(oneHot, new CleverCnfGenerator());
-
-		Variable [] vars = new Variable[freeVariables];
-		for(int i = 0; i < freeVariables; i++) vars[i] = cpog.createVisualVariable().getMathVariable();
-		
-		CpogEncoding solution = null;
-		try
-		{
-			solution = solverCnf.solve(instance, vars, derivedVariables);
-			if (solution == null)
-			{
-				we.cancelMemento();
-				JOptionPane.showMessageDialog(null, "No solution.", "Encoding result", JOptionPane.INFORMATION_MESSAGE);
-			}
-
-		}
-		catch(Exception e)
-		{
-			we.cancelMemento();
-			JOptionPane.showMessageDialog(null, e.getMessage(), "Encoding result", JOptionPane.ERROR_MESSAGE);
-		}
-		
-		if(solution == null) return;
-		
-		// create result
-		
-		boolean[][] encoding = solution.getEncoding();
-		
-		for(int k = 0; k < m; k++)
-		{
-			for(int i = 0; i < freeVariables; i++)
-				scenarios.get(k).getEncoding().setState(vars[i], VariableState.fromBoolean(encoding[k][i]));
-		}
-		
-		VisualScenario result = cpog.createVisualScenario();
-		result.setLabel("Composition");
-		VisualVertex [] vertices = new VisualVertex[n];
-		for(String eventName : events.keySet())
-		{
-			int id = events.get(eventName);
-			vertices[id] = cpog.createVisualVertex(result);
-			vertices[id].setLabel(eventName);			
-			vertices[id].setPosition(Geometry.multiply(positions.get(id), 1.0/count.get(id)));
-		}
-		
-		BooleanFormula[] functions = solution.getFunctions();
-		for(int i = 0; i < n; i++)
-			for(int j = 0; j < n; j++)
-			{
-				BooleanFormula condition;
-				
-				char trivial = trivialEncoding(constraints, m, i, j);
-				if (trivial != '?')
-				{
-					if (trivial == '1')
-					{
-						condition = One.instance();
-					}
-					else
-					{
-						continue;
-					}
-				}
-				else
-				{
-					String constraint = generateConstraint(constraints, m, i, j);
-					condition = functions[task.get(constraint)];
-				}
-				
-				if (i == j)
-				{
-					vertices[i].setCondition(condition);
-				}
-				else
-				{
-					VisualArc arc = cpog.connect(vertices[i], vertices[j]);
-					arc.setCondition(condition);
-				}
-			}
-		we.saveMemento();
-	}
-	
-}

=== modified file 'CpogsPlugin/src/org/workcraft/plugins/cpog/CpogModule.java'
--- CpogsPlugin/src/org/workcraft/plugins/cpog/CpogModule.java	2013-12-27 19:04:57 +0000
+++ CpogsPlugin/src/org/workcraft/plugins/cpog/CpogModule.java	2014-07-11 09:42:10 +0000
@@ -16,6 +16,7 @@
 import org.workcraft.plugins.cpog.serialisation.VertexSerialiser;
 import org.workcraft.plugins.cpog.serialisation.VisualCPOGGroupDeserialiser;
 import org.workcraft.plugins.cpog.serialisation.VisualCPOGGroupSerialiser;
+import org.workcraft.plugins.cpog.tools.EncoderPreferencesTool;
 import org.workcraft.plugins.cpog.tools.GraphStatisticsTool;
 import org.workcraft.serialisation.xml.XMLDeserialiser;
 import org.workcraft.serialisation.xml.XMLSerialiser;
@@ -40,7 +41,9 @@
 		p.registerClass(XMLDeserialiser.class, ArcDeserialiser.class);
 		p.registerClass(SettingsPage.class, CpogSettings.class);
 		
-		p.registerClass(Tool.class, CpogEncoder.class);
+		//p.registerClass(Tool.class, CpogEncoder.class);
+		
+		p.registerClass(Tool.class, EncoderPreferencesTool.class, framework);
 
 		p.registerClass(Tool.class, new Initialiser<Tool>() {
 			@Override

=== added file 'CpogsPlugin/src/org/workcraft/plugins/cpog/CpogProgrammer.java'
--- CpogsPlugin/src/org/workcraft/plugins/cpog/CpogProgrammer.java	1970-01-01 00:00:00 +0000
+++ CpogsPlugin/src/org/workcraft/plugins/cpog/CpogProgrammer.java	2014-07-11 09:42:10 +0000
@@ -0,0 +1,1023 @@
+package org.workcraft.plugins.cpog;
+
+import java.awt.geom.Point2D;
+import java.io.BufferedReader;
+import java.io.DataInputStream;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.PrintStream;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.StringTokenizer;
+
+import javax.swing.JOptionPane;
+
+import org.workcraft.dom.visual.RemovedNodeDeselector;
+import org.workcraft.dom.visual.VisualComponent;
+import org.workcraft.dom.visual.connections.VisualConnection;
+import org.workcraft.plugins.cpog.EncoderSettings.generationMode;
+import org.workcraft.plugins.cpog.optimisation.BooleanFormula;
+import org.workcraft.plugins.cpog.optimisation.CleverCnfGenerator;
+import org.workcraft.plugins.cpog.optimisation.CpogEncoding;
+import org.workcraft.plugins.cpog.optimisation.CpogOptimisationTask;
+import org.workcraft.plugins.cpog.optimisation.DefaultCpogSolver;
+import org.workcraft.plugins.cpog.optimisation.OneHotIntBooleanFormula;
+import org.workcraft.plugins.cpog.optimisation.OneHotNumberProvider;
+import org.workcraft.plugins.cpog.optimisation.Optimiser;
+import org.workcraft.plugins.cpog.optimisation.booleanvisitors.FormulaToString;
+import org.workcraft.plugins.cpog.optimisation.expressions.One;
+import org.workcraft.plugins.cpog.optimisation.expressions.Zero;
+import org.workcraft.plugins.cpog.optimisation.javacc.BooleanParser;
+import org.workcraft.util.Func;
+import org.workcraft.util.Geometry;
+import org.workcraft.workspace.WorkspaceEntry;
+
+import com.sun.org.apache.regexp.internal.RE;
+
+public class CpogProgrammer {
+	
+	private EncoderSettings settings;
+	private File scenarioFile, encodingFile ;
+	private String toolPath = "../tools/";
+	private int bits = 1;
+	private Double minArea;
+	
+	// SETTING PARAMETERS FOR CALLING PROGRAMMER.X
+	private String espressoCommand, abcFolder , gatesLibrary ,
+			verbose = "", genMode= "", numSol= "", customFlag= "", customPath= "", effort= "", espressoFlag= "", abcFlag= "", gateLibFlag= "", cpogSize= "", disableFunction= "",
+			oldSynt= "";
+	// Allocation data structures
+	private Process process;
+	private String[] opt_enc, opt_formulaeVertices,truthTableVertices, opt_vertices, opt_sources, opt_dests,
+			opt_formulaeArcs, truthTableArcs, arcNames;
+	private int v,a,n;
+	
+	public CpogProgrammer(EncoderSettings settings){
+		this.setSettings(settings);
+	}
+	
+	private String binaryToInt(String string) {
+		int value = 0, wg = 1;
+		if(string != null){
+			for(int i = string.length()-1; i>=0; i--){
+				if(string.charAt(i) == '1'){
+					value += wg;
+				}
+				wg *= 2;
+			}
+			
+			return String.valueOf(value);
+		}
+		return "0";
+	}
+	
+	private static boolean deleteDir(File dir) {
+	    if (dir.isDirectory()) {
+	        String[] children = dir.list();
+	        for (int i = 0; i < children.length; i++) {
+	            boolean success = deleteDir(new File(dir, children[i]));
+	            if (!success) {
+	                return false;
+	            }
+	        }
+	    }
+
+	    return dir.delete(); // The directory is empty now and can be deleted.
+	}
+	
+	private String generateConstraint(char [][][] constraints, int numScenarios, int event1, int event2)
+	{
+		StringBuilder s = new StringBuilder();
+		for(int k = 0; k < numScenarios; k++) s.append(constraints[k][event1][event2]);
+		return s.toString();
+	}
+	
+	private char trivialEncoding(char [][][] constraints, int numScenarios, int event1, int event2)
+	{
+		char trivial = '-';
+		
+		for(int k = 0; k < numScenarios; k++)
+		{
+			if (constraints[k][event1][event2] == '0')
+			{
+				if (trivial == '1') return '?';
+				trivial = '0';
+			}
+
+			if (constraints[k][event1][event2] == '1')
+			{
+				if (trivial == '0') return '?';
+				trivial = '1';
+			}
+		}
+		
+		return trivial;
+	}
+	
+	private int WriteCpogIntoFile(int m, ArrayList<VisualScenario> scenarios)
+	{
+		try{
+			scenarioFile = File.createTempFile("scenarios", "cpog");			
+
+		     PrintStream Output = new PrintStream(scenarioFile);
+			
+			
+			for(int k = 0; k < m; k++)
+			{
+				Map<String, Integer> nodes = new HashMap<String, Integer>();
+				// Print arcs
+				Output.println(".scenario CPOG_" + k);
+				for(VisualConnection c : scenarios.get(k).getConnections()){
+					if (c instanceof VisualArc)
+					{
+						VisualArc arc = (VisualArc)c;
+						VisualComponent c1 = arc.getFirst(), c2 = arc.getSecond();
+						if (c1 instanceof VisualVertex && c2 instanceof VisualVertex)
+						{
+							nodes.put(c1.getLabel(), 0);
+							nodes.put(c2.getLabel(), 0);
+							Output.println(c1.getLabel() + " " + c2.getLabel());
+						}
+					}
+				}
+				
+				// Print conditions on vertices
+				for(VisualComponent component : scenarios.get(k).getComponents()){
+					if(component instanceof VisualVertex){
+						VisualVertex vertex = (VisualVertex)component;
+						BooleanFormula condition = vertex.getCondition();
+						if (condition != One.instance() && condition != Zero.instance()){
+							
+							// Format output by substituting ' with !
+							String cond = FormulaToString.toString(condition).replaceAll("'", "!");
+							String result = "";
+							String tmp = "";
+							for(int i=0; i<cond.length(); i++){
+								if(cond.charAt(i) != '(' && cond.charAt(i) != ')' && cond.charAt(i) != '+' &&
+										cond.charAt(i) != '*' && cond.charAt(i) != '!' && cond.charAt(i) != ' '){
+									tmp = "";
+									while(i < cond.length() && cond.charAt(i) != '(' && cond.charAt(i) != ')' && cond.charAt(i) != '+' && 
+											cond.charAt(i) != '*' && cond.charAt(i) != '!' && cond.charAt(i) != ' '){
+										tmp += cond.charAt(i);
+										i++;
+									}
+									//System.out.println("TMP: " + tmp);
+									for(int j= tmp.length()-1; j >= 0; j--){
+										//System.out.println(j + ") " +  tmp.charAt(j));
+										result += tmp.charAt(j);
+									}
+									if(i < cond.length()){
+										result += cond.charAt(i);
+									}
+								}
+								else{
+									result += cond.charAt(i);;
+								}
+							}
+							
+							String end = "";
+							for(int i = 0; i<result.length(); i++){
+								if(result.charAt(i) == '(') end += ')';
+								else if (result.charAt(i) == ')') end += '(';
+								else end += result.charAt(i);
+							}
+							
+							// Print conditions on each vertices
+							Output.print(":");
+							for(int i=end.length()-1; i>=0; i--){
+								Output.print(end.charAt(i));
+							}
+							Output.println(" " + vertex.getLabel());
+						}
+						
+						//VisualVertex vertex = (VisualVertex)component;
+						if(!nodes.containsKey(vertex.getLabel())){
+							Output.println(vertex.getLabel());
+						}
+					}
+					
+				}
+				Output.println(".end");
+				if(k != m-1){
+					Output.println();
+				}
+			}
+			Output.close();
+		
+			// WRITING CUSTOM ENCODING FILE
+			if(settings.getGenMode() != generationMode.SCENCO){
+				encodingFile = File.createTempFile("custom", "enc");
+				if(settings.isCustomEncMode()){
+					    PrintStream Output1 = new PrintStream(encodingFile);
+						
+						String [] enc = settings.getCustomEnc();
+						for(int k = 0; k < m; k++)
+						{
+							if(enc[k].contains("2") || enc[k].contains("3") || enc[k].contains("4") ||
+									enc[k].contains("5") || enc[k].contains("6") || enc[k].contains("7") ||
+									enc[k].contains("8") || enc[k].contains("9")){
+								JOptionPane.showMessageDialog(null,
+										"Op-code " + enc[k] + " not allowed.",
+										"Custom encoding error",
+										JOptionPane.ERROR_MESSAGE);
+								return -1;
+								
+							}
+							String empty = "";
+							for(int i=0; i<settings.getBits(); i++) empty += 'X';
+							if(enc[k].equals("") || enc[k].equals(empty)){
+								Output1.println("/");
+							}
+							else{
+								Output1.println(enc[k]);
+							}
+						}
+						Output1.println(settings.getBits());
+						Output1.close();
+				}
+			}
+		}catch (IOException e) {
+			System.out.println("Error: " + e);
+		}
+		
+		return 0;
+	}
+	
+	private void printController(int m){
+		System.out.println();
+		String fileName = toolPath + "results/generated_encoding/";
+		for(int i=0; i<m; i++) fileName = fileName.concat(binaryToInt(opt_enc[i]) + "_");
+		fileName = fileName.concat(".prg");
+		File f = new File(fileName);
+		if(f.exists() && !f.isDirectory()){
+			System.out.println("Boolean controller:");
+			try{
+				  FileInputStream fstream = new FileInputStream(fileName);
+				  DataInputStream in = new DataInputStream(fstream);
+				  BufferedReader bre = new BufferedReader(new InputStreamReader(in));
+				  String strLine;
+				  bre.readLine();
+				  bre.readLine();
+				  while ((strLine = bre.readLine()) != null)   {
+					  System.out.println (strLine);
+				  }
+				  in.close();
+			}catch (Exception e){ //Catch exception if any
+				System.err.println("Error: " + e.getMessage());
+			}
+			System.out.println();
+		}
+		return;
+	}
+	
+	private void deleteTempFiles(){
+		if(scenarioFile.exists()) scenarioFile.delete();
+		if(encodingFile.exists()) encodingFile.delete();
+		return;
+	}
+
+	private int callingProgrammer(Double currArea, WorkspaceEntry we, int it, boolean continuous) throws IOException{
+		//Debug Printing: launching executable
+		/*System.out.println(toolPath + "programmer.x" + " " + scenarioFile.getAbsolutePath() + " " +
+				"-m" + " " + effort + " " + genMode + " " + numSol + " " + customFlag + " " + customPath + " " + 
+				verbose + " " + cpogSize + " " + disableFunction + " " + oldSynt + " " + 
+				espressoFlag + " " + espressoCommand + " " + abcFlag + " " + abcFolder + " " + gateLibFlag + " " +
+				gatesLibrary);*/
+		process = new ProcessBuilder(toolPath + "programmer.x", scenarioFile.getAbsolutePath(),
+				"-m",effort,genMode, numSol,customFlag,customPath,verbose,cpogSize,disableFunction,oldSynt,
+				espressoFlag,espressoCommand, abcFlag, abcFolder, gateLibFlag, gatesLibrary).start();
+		InputStream is = process.getInputStream();
+		InputStreamReader isr = new InputStreamReader(is);
+		BufferedReader br = new BufferedReader(isr);
+		String line;
+		boolean finish = false;
+		if(continuous){
+			while ( (line = br.readLine()) != null && finish == false) {
+				// Read Area
+				if(line.contains(".area")){
+					line = br.readLine();
+					currArea = Double.valueOf(line);
+					line = br.readLine();
+					if(currArea < minArea){
+						v = 0; a = 0;
+						minArea = currArea;
+						System.out.println(it + ") " + "Area of current circuit: " + minArea);
+						while((line = br.readLine()) != null){
+							// Read Optimal Encoding
+							if(line.contains("MIN: ")){
+								StringTokenizer st2 = new StringTokenizer(line, " ");
+								int j = 0;
+								st2.nextElement();
+								while (st2.hasMoreElements()) {
+									opt_enc[j++] = (String) st2.nextElement(); 
+								}
+							}
+							
+							// Read Optimal Formulae
+							if(line.contains(".start_formulae")){
+								line = br.readLine();
+								while(line.contains(".end_formulae") == false){
+									StringTokenizer st2 = new StringTokenizer(line, ",");
+									String el = (String)st2.nextElement();
+									if(el.equals("V")){ //formula of a vertex
+										opt_vertices[v] = (String) st2.nextElement();
+										truthTableVertices[v] = (String) st2.nextElement();
+										opt_formulaeVertices[v++] = (String) st2.nextElement();
+									}else{
+										opt_sources[a] = (String) st2.nextElement();
+										opt_dests[a] = (String) st2.nextElement();
+										arcNames[a] = opt_sources[a] + "->" + opt_dests[a];
+										truthTableArcs[a] = (String) st2.nextElement();
+										opt_formulaeArcs[a++] = (String) st2.nextElement();
+									}
+									line = br.readLine();
+								}
+								
+							}
+							
+							// Read statistics
+							if(line.contains(".statistics")){
+								line = br.readLine();
+								while(line.contains(".end_statistics") == false){
+									line = br.readLine();
+								}	
+							}
+							
+							// Read errors
+							if(line.contains(".error")){
+								line = br.readLine();
+								while(line.contains(".end_error") == false){
+									JOptionPane.showMessageDialog(null,
+											line,
+											"Programmer.x error",
+											JOptionPane.ERROR_MESSAGE);
+									line = br.readLine();
+								}
+								return -1;
+								
+							}
+						}
+					}else{
+						finish = true;
+					}
+				}
+				
+			}
+		}else{
+			while ( (line = br.readLine()) != null){
+				if(settings.isVerboseMode())
+					System.out.println(line);
+				
+				// Read Optimal Encoding
+				if(line.contains("MIN: ")){
+					StringTokenizer st2 = new StringTokenizer(line, " ");
+					int j = 0;
+					st2.nextElement();
+					while (st2.hasMoreElements()) {
+						opt_enc[j++] = (String) st2.nextElement(); 
+					}
+				}
+				
+				// Read Optimal Formulae
+				if(line.contains(".start_formulae")){
+					line = br.readLine();
+					while(line.contains(".end_formulae") == false){
+						if(settings.isVerboseMode())
+							System.out.println(line);
+						StringTokenizer st2 = new StringTokenizer(line, ",");
+						String el = (String)st2.nextElement();
+						if(el.equals("V")){ //formula of a vertex
+							opt_vertices[v] = (String) st2.nextElement();
+							truthTableVertices[v] = (String) st2.nextElement();
+							opt_formulaeVertices[v++] = (String) st2.nextElement();
+						}else{
+							opt_sources[a] = (String) st2.nextElement();
+							opt_dests[a] = (String) st2.nextElement();
+							arcNames[a] = opt_sources[a] + "->" + opt_dests[a];
+							truthTableArcs[a] = (String) st2.nextElement();
+							opt_formulaeArcs[a++] = (String) st2.nextElement();
+						}
+						line = br.readLine();
+					}
+					
+				}
+				
+				// Read statistics
+				if(line.contains(".statistics")){
+					line = br.readLine();
+					while(line.contains(".end_statistics") == false){
+						System.out.println(line);
+						line = br.readLine();
+					}	
+				}
+				
+				// Read errors
+				if(line.contains(".error")){
+					line = br.readLine();
+					while(line.contains(".end_error") == false){
+						JOptionPane.showMessageDialog(null,
+								line,
+								"Programmer.x error",
+								JOptionPane.ERROR_MESSAGE);
+						line = br.readLine();
+					}
+					return -1;
+					
+				}
+			}
+		}
+		
+		process.destroy();
+		is.close();
+		isr.close();
+		br.close();
+		return 0;
+	}
+	
+	private void reset_vars(){
+		verbose = ""; genMode= ""; numSol= ""; customFlag= ""; customPath= ""; effort= ""; espressoFlag= "";
+		abcFlag= ""; gateLibFlag= ""; cpogSize= ""; disableFunction= ""; oldSynt= "";
+		
+		return;
+	}
+	
+	public void run(WorkspaceEntry we)
+	{
+		VisualCPOG cpog = (VisualCPOG)(we.getModelEntry().getVisualModel());
+
+		we.captureMemento();
+		
+		reset_vars();
+		
+		HashMap<String, Integer> events = new HashMap<String, Integer>();
+		n = 0;
+		ArrayList<Point2D> positions = new ArrayList<Point2D>();
+		ArrayList<Integer> count = new ArrayList<Integer>();
+
+		// TODO: remove deprecated method
+		ArrayList<VisualScenario> scenarios = new ArrayList<VisualScenario>(cpog.getGroups());
+		
+		// Scenario contains single graphs compose CPOG 
+		int m = scenarios.size();
+		
+		// If less than two, do not encode scenarios
+		if (m < 2)
+		{
+			JOptionPane.showMessageDialog(null,
+					"At least two scenarios are expected.",
+					"Not enough scenarios",
+					JOptionPane.ERROR_MESSAGE);
+			we.cancelMemento();
+			deleteTempFiles();
+			return;
+		}
+		
+		// Scan every scenarios
+		for(int k = 0; k < m; k++)
+		{
+			// Scan every elements of each scenario
+			for(VisualComponent component : scenarios.get(k).getComponents())
+			if (component instanceof VisualVertex)	// If element is a vertex
+			{
+				VisualVertex vertex = (VisualVertex)component;
+				
+				if (!events.containsKey(vertex.getLabel())) // Check if a condition is present on vertex
+				{
+					events.put(vertex.getLabel(), n);
+					count.add(1);
+					Point2D p = vertex.getCenter();
+					p.setLocation(p.getX() - scenarios.get(k).getBoundingBox().getMinX(), p.getY() - scenarios.get(k).getBoundingBox().getMinY());
+					positions.add(p);
+					n++;
+				}
+				else
+				{
+					int id = events.get(vertex.getLabel());
+					count.set(id, count.get(id) + 1);
+					Point2D p = vertex.getCenter();
+					p.setLocation(p.getX() - scenarios.get(k).getBoundingBox().getMinX(), p.getY() - scenarios.get(k).getBoundingBox().getMinY());
+					positions.set(id, Geometry.add(positions.get(id), p));							
+				}
+			}
+		}
+		
+		// construct constraints
+		
+		char [][][] constraints = new char[m][n][n];
+		int [][] graph = new int[n][n];
+		
+		for(int k = 0; k < m; k++)
+		{
+			for(int i = 0; i < n; i++) for(int j = 0; j < n; j++) {
+				constraints[k][i][j] = '0';
+			}
+
+			for(VisualComponent component : scenarios.get(k).getComponents())
+			if (component instanceof VisualVertex)
+			{
+				VisualVertex vertex = (VisualVertex)component;
+				int id = events.get(vertex.getLabel());
+				constraints[k][id][id] = '1';
+			}
+
+			for(int i = 0; i < n; i++) for(int j = 0; j < n; j++) graph[i][j] = 0;
+			
+			for(VisualConnection c : scenarios.get(k).getConnections())
+			if (c instanceof VisualArc)
+			{
+				VisualArc arc = (VisualArc)c;
+				VisualComponent c1 = arc.getFirst(), c2 = arc.getSecond();
+				if (c1 instanceof VisualVertex && c2 instanceof VisualVertex)
+				{
+					int id1 = events.get(((VisualVertex)c1).getLabel());
+					int id2 = events.get(((VisualVertex)c2).getLabel());
+					graph[id1][id2] = 1;
+				}
+			}
+			
+			// compute transitive closure
+			
+			for(int t = 0; t < n; t++)
+				for(int i = 0; i < n; i++)
+					if (graph[i][t] > 0)
+						for(int j = 0; j < n; j++)
+							if (graph[t][j] > 0) graph[i][j] = 1;
+			
+			// detect transitive arcs
+			
+			for(int t = 0; t < n; t++)
+				for(int i = 0; i < n; i++)
+					if (graph[i][t] > 0)
+						for(int j = 0; j < n; j++)
+							if (graph[t][j] > 0) graph[i][j] = 2;
+			
+			// report cyclic scenario
+			
+			for(int i = 0; i < n; i++)
+				if (graph[i][i] > 0)
+				{
+					deleteTempFiles();
+					JOptionPane.showMessageDialog(null,
+												"Scenario '" + scenarios.get(k).getLabel() + "' is cyclic.",
+												"Invalid scenario",
+												JOptionPane.ERROR_MESSAGE);
+					we.cancelMemento();
+					return;
+				}
+			
+			for(int i = 0; i < n; i++)
+				for(int j = 0; j < n; j++)
+				if (i != j)
+				{
+					char ch = '0';
+					
+					if (graph[i][j] > 0) ch = '1';
+					if (graph[i][j] > 1) ch = '-';
+					if ( constraints[k][i][i] == '0' || constraints[k][j][j] == '0' ) ch = '-';
+					
+					constraints[k][i][j] = ch;
+				}
+		}
+		
+		// Write scenarios into file.
+		int res;
+		if((res = WriteCpogIntoFile(m, scenarios)) != 0){
+			deleteTempFiles();
+			if(res != -1){
+				JOptionPane.showMessageDialog(null,
+						"Error on writing scenario file.",
+						"Workcraft error",
+						JOptionPane.ERROR_MESSAGE);
+			}
+			we.cancelMemento();
+			return;
+		}
+		
+		espressoCommand = CpogSettings.getEspressoCommand();
+		abcFolder = CpogSettings.getAbcFolder(); 
+		gatesLibrary = CpogSettings.getGatesLibrary();
+		opt_enc = new String[m];
+		opt_formulaeVertices = new String[n*n];
+		truthTableVertices =  new String[n*n];
+		opt_vertices = new String[n];
+		opt_sources = new String[n*n];
+		opt_dests = new String[n*n];
+		opt_formulaeArcs = new String[n*n];
+		truthTableArcs =  new String[n*n];
+		arcNames = new String[n*n];
+		espressoCommand = CpogSettings.getEspressoCommand();
+		abcFolder = CpogSettings.getAbcFolder();
+		gatesLibrary = CpogSettings.getGatesLibrary();
+		espressoFlag = "-e";
+		v=0; 
+		a=0; 
+		
+		// CALLING PROGRAMMER.X
+		boolean SCENCO = false;
+		try {
+			File f;
+			f = new File(espressoCommand);
+			if(!f.exists() || f.isDirectory()){
+				deleteTempFiles();
+				JOptionPane.showMessageDialog(null,
+						"Espresso tool is needed to programmer to work properly",
+						"Espresso tool not present",
+						JOptionPane.ERROR_MESSAGE);
+				we.cancelMemento();
+				return;
+			}
+			
+			espressoCommand = espressoCommand.replace(" ", "\\ ");
+
+			f = new File(abcFolder);
+			if(!f.exists() || !f.isDirectory()){
+				JOptionPane.showMessageDialog(null,
+						"You can download it at http://www.eecs.berkeley.edu/~alanmi/abc/",
+						"Abc tool not present",
+						JOptionPane.ERROR_MESSAGE);
+			}
+			else{
+				abcFlag = "-a";
+				gateLibFlag = "-lib";
+				f = new File(abcFolder + gatesLibrary);
+				if(!f.exists() || f.isDirectory()){
+					deleteTempFiles();
+					JOptionPane.showMessageDialog(null,
+							"It is needed to compute area of circuit properly",
+							"Gate library not present",
+							JOptionPane.ERROR_MESSAGE);
+					we.cancelMemento();
+					return;
+				}
+			}
+			
+			if(settings.isCpogSize()) cpogSize = "-cs";
+			if(settings.isCostFunc()) disableFunction = "-d";
+			if(settings.isVerboseMode()) verbose = "-v";
+			if(settings.isEffort()) effort = "all";
+			else effort = "min";
+			if(settings.isCustomEncMode()){
+				customFlag = "-set";
+				customPath = encodingFile.getAbsolutePath();
+			}
+			switch(settings.getGenMode()){
+				case OPTIMAL_ENCODING:
+					genMode = "-top";
+					numSol = String.valueOf(settings.getSolutionNumber());
+					break;
+				case RECURSIVE:
+					if(settings.isCustomEncMode()){
+						deleteTempFiles();
+						JOptionPane.showMessageDialog(null,
+								"Recursive encodings generation combined with custom op-codes is not supported.",
+								"Encodings generation error",
+								JOptionPane.ERROR_MESSAGE);
+						we.cancelMemento();
+						return;
+					}
+					break;
+				case RANDOM:
+					genMode = "-r";
+					if(settings.isCustomEncMode()){
+						deleteTempFiles();
+						JOptionPane.showMessageDialog(null,
+								"Random encodings generation combined with custom op-codes is not supported.",
+								"Encodings generation error",
+								JOptionPane.ERROR_MESSAGE);
+						we.cancelMemento();
+						return;
+					}
+					numSol = String.valueOf(settings.getSolutionNumber());
+					break;
+				case SCENCO:
+					SCENCO = true;
+					customFlag = "-set";
+					genMode = "-top";
+					numSol = "1";
+					break;
+				case OLD_SYNT:
+					customFlag = "-set";
+					customPath = encodingFile.getAbsolutePath();
+					oldSynt = "-old";
+					genMode = "-top";
+					numSol = "1";
+					break;
+				default:
+					System.out.println("Error");
+			}
+			
+			deleteDir(new File(toolPath + "results/"));
+			File d = new File("../tools/results/generated_encoding/");
+			d.mkdirs();
+			
+		if(!SCENCO){	
+			// CALLING PROGRAMMER.X
+			boolean out = false;
+			boolean continuous = false;
+			int limit, it = 0;
+				if(settings.isContMode()){
+					limit = 100;
+					numSol = "1";
+					continuous = true;
+				}else{
+					limit = 1; 
+				}
+				minArea = Double.MAX_VALUE; 
+				Double currArea = Double.MAX_VALUE;
+				while(!out && it < limit){
+					if(callingProgrammer(currArea, we,it, continuous) != 0){
+						deleteTempFiles();
+						we.cancelMemento();
+						return;
+					}
+					it++;
+				}				
+				// Print controller
+				printController(m);
+				
+			}
+			} catch (IOException e1) {
+				System.out.println("Error.");
+				e1.printStackTrace();
+			}
+		// group similar constraints
+		HashMap<String, BooleanFormula> formulaeName = new HashMap<String, BooleanFormula>();
+		HashMap<String, Integer> task = new HashMap<String, Integer>();
+		for(int i = 0; i < n; i++)
+			for(int j = 0; j < n; j++)
+				if (trivialEncoding(constraints, m, i, j) == '?')
+				{
+					String constraint = generateConstraint(constraints, m, i, j);
+					if (!task.containsKey(constraint)){
+						task.put(constraint, task.size());
+					}
+				}
+		
+		// call CPOG encoder
+		
+		char [][] matrix = new char[m][task.size()];
+		
+		String [] instance = new String[m];
+		for(String s : task.keySet())
+			for(int i = 0; i < m; i++) matrix[i][task.get(s)] = s.charAt(i);	
+
+		for(int i = 0; i < m; i++) instance[i] = new String(matrix[i]);
+		
+		int freeVariables;
+		if(settings.getGenMode() != generationMode.SCENCO)
+			freeVariables = opt_enc[0].length();
+		else
+			freeVariables = settings.getBits();
+		int derivedVariables = CpogSettings.getCircuitSize();
+		
+		Optimiser<OneHotIntBooleanFormula> oneHot = new Optimiser<OneHotIntBooleanFormula>(new OneHotNumberProvider());
+		
+		DefaultCpogSolver<BooleanFormula> solverCnf = new DefaultCpogSolver<BooleanFormula>(oneHot, new CleverCnfGenerator());
+
+		VisualVariable predicatives[] = new VisualVariable[n];
+		int pr = 0;
+		for(int k = 0; k < m; k++)
+		{
+			for(VisualComponent component : scenarios.get(k).getComponents()){
+				if(component instanceof VisualVariable){
+					predicatives[pr++] = (VisualVariable) component;
+				}
+			}
+		}
+		
+		Variable [] vars = new Variable[freeVariables + pr];
+		for(int i = 0; i < freeVariables; i++) vars[i] = cpog.createVisualVariable().getMathVariable();
+		for(int i = 0; i< pr; i++) vars[freeVariables +i] = predicatives[i].getMathVariable();
+		
+		// DEBUG PRINTING: printing variables needed to encode graph.
+		/*System.out.println("PRINTING VARIABLES:");
+		for(int i = 0; i< freeVariables + pr; i++)
+			System.out.println(vars[i].getLabel());*/
+		
+		CpogEncoding solution = null;
+		try
+		{
+			// SCENCO EXECUTION TO FIND VARIABLES AND FUNCTIONS
+			solution = solverCnf.solve(instance, vars, derivedVariables);
+			CpogOptimisationTask opt_task = (CpogOptimisationTask) solverCnf.getTask(instance, vars, derivedVariables);
+			if (solution == null)
+			{
+				if(SCENCO){
+					we.cancelMemento();
+					JOptionPane.showMessageDialog(null, "SCENCO is not able to solve the CPOG, try other options.",
+							"Encoding result", JOptionPane.ERROR_MESSAGE);
+					deleteTempFiles();
+					return;
+				}
+				System.out.println("INFORMATION: Scenco cannot solve the CPOG.");
+				System.out.println();
+			}
+			
+			System.out.println("Op-code selected for graphs:");
+			for(int i=0; i<m; i++){
+				String name;
+				if(scenarios.get(i).getLabel().equals("")){
+					name = "CPOG " + i;
+				}
+				else{
+					name = scenarios.get(i).getLabel();
+				}
+				System.out.println(name + ": " + opt_enc[i]);
+			}
+			solution = new CpogEncoding(null, null);
+			
+			if(!SCENCO){
+				
+				solution = new CpogEncoding(null, null);
+				BooleanFormula[][] encodingVars = opt_task.getEncodingVars();
+				BooleanFormula[] formule = new BooleanFormula[v + a];
+				// Set optimal formulae to graphs
+				final Variable [] variables = vars;
+				for(int i=0; i<v; i++){
+					if(opt_formulaeVertices[i].contains("x")){
+						BooleanFormula formula_opt = null;
+						formula_opt = BooleanParser.parse(opt_formulaeVertices[i], new Func<String, BooleanFormula>() {
+							
+							@Override
+							public BooleanFormula eval(String arg) {
+								arg = arg.substring("x_".length());
+								int id = Integer.parseInt(arg);
+								return variables[id];
+							}
+						});
+
+						formulaeName.put(opt_vertices[i], formula_opt);
+						
+						// OLD formulae array
+						/*if(task.containsKey(truthTableVertices[i])){
+							formule[task.get(truthTableVertices[i])] = formula_opt;
+						}*/
+					}
+				}
+				for(int i=0; i<a; i++){
+					if(opt_formulaeArcs[i].contains("x")){
+						BooleanFormula formula_opt = null;
+						formula_opt = BooleanParser.parse(opt_formulaeArcs[i], new Func<String, BooleanFormula>() {
+							@Override
+							public BooleanFormula eval(String arg) {
+								arg = arg.substring("x_".length());
+								int id = Integer.parseInt(arg);
+								return variables[id];
+							}
+						});
+						
+						formulaeName.put(arcNames[i], formula_opt);
+						
+						/*if(task.containsKey(truthTableArcs[i])){
+							formule[task.get(truthTableArcs[i])] = formula_opt;
+						}*/
+					}
+				}
+				solution.setFormule(formule);
+				//TODO
+				// Set optimal encoding to graphs				
+				boolean[][] opt_encoding = new boolean[m][];
+				for(int i=0;i<m;i++)
+				{
+					opt_encoding[i] = new boolean[freeVariables + pr];
+					for(int j=0;j<freeVariables;j++){
+						if(opt_enc[i].charAt(j) == '0' || opt_enc[i].charAt(j) == '-') opt_encoding[i][j] = false;
+						else	opt_encoding[i][j] = true;
+					}
+					for(int j=freeVariables;j<freeVariables + pr;j++){
+						opt_encoding[i][j] = false;
+					}
+	
+				}
+				solution.setEncoding(opt_encoding);
+			}
+		}
+		catch(Exception e)
+		{
+			we.cancelMemento();
+			JOptionPane.showMessageDialog(null, e.getMessage(), "Encoding result", JOptionPane.ERROR_MESSAGE);
+		}
+		
+		if(solution == null){
+			return;
+		}
+		
+		// create result
+		
+		boolean[][] encoding = solution.getEncoding();
+		
+		if(settings.getGenMode() == generationMode.SCENCO){
+			
+			try{
+				 encodingFile = File.createTempFile("encoding", "cpog");
+			     PrintStream Output = new PrintStream(encodingFile);
+				
+			     for(int i=0; i<m; i++){
+			    	 for(int j=0; j<settings.getBits(); j++){
+			    		 if(encoding[i][j]){
+			    			 Output.print("1");
+			    		 }
+			    		 else{
+			    			 Output.print("0");
+			    		 }
+			    	 }
+			    	 Output.println();
+			     }
+			     Output.close();
+			     
+			     customPath = encodingFile.getAbsolutePath();
+			     if(callingProgrammer(Double.MAX_VALUE, we, 0, false) != 0){
+			    	 deleteTempFiles();
+					we.cancelMemento();
+					return;
+			     }
+			     
+			     // Print controller
+			     printController(m);
+			}catch (IOException e) {
+				System.out.println("Error: " + e);
+			}	
+		}
+
+		//TODO
+		for(int k = 0; k < m; k++)
+		{
+			for(int i = 0; i < freeVariables; i++){
+				scenarios.get(k).getEncoding().setState(vars[i], VariableState.fromBoolean(encoding[k][i]));
+			}
+			for(int i = freeVariables; i < freeVariables + pr; i++){
+				scenarios.get(k).getEncoding().setState(vars[i], VariableState.fromBoolean(encoding[k][i]));
+			}
+		}
+		
+		VisualScenario result = cpog.createVisualScenario();
+		result.setLabel("Composition");
+		VisualVertex [] vertices = new VisualVertex[n];
+		for(String eventName : events.keySet())
+		{
+			int id = events.get(eventName);
+			vertices[id] = cpog.createVisualVertex(result);
+			vertices[id].setLabel(eventName);			
+			vertices[id].setPosition(Geometry.multiply(positions.get(id), 1.0/count.get(id)));
+			if(formulaeName.containsKey(eventName)){
+				vertices[id].setCondition(formulaeName.get(eventName));
+			}else
+				vertices[id].setCondition(One.instance());
+		}
+		
+
+		// SET FORMULAE INTO RESULT GRAPH
+		BooleanFormula[] functions = solution.getFunctions();
+		for(int i = 0; i < n; i++)
+			for(int j = 0; j < n; j++)
+			{
+				BooleanFormula condition;
+				
+				char trivial = trivialEncoding(constraints, m, i, j);
+				if (trivial != '?')
+				{
+					if (trivial == '1')
+					{
+						condition = One.instance();
+					}
+					else
+					{
+						continue;
+					}
+				}
+				/*else
+				{
+					String constraint = generateConstraint(constraints, m, i, j);
+					condition = functions[task.get(constraint)];
+				}*/
+				
+				/*if (i == j)
+				{
+					vertices[i].setCondition(condition);
+				}*/
+				if (i != j)
+				{
+					VisualArc arc = cpog.connect(vertices[i], vertices[j]);
+					String arcName = vertices[i].getLabel() + "->" + vertices[j].getLabel();
+					
+					if(formulaeName.containsKey(arcName)){
+						condition = formulaeName.get(arcName);
+					}else
+						condition = One.instance();
+					
+					arc.setCondition(condition);
+				}
+			}
+		
+		we.saveMemento();
+	}
+	
+	public void setSettings(EncoderSettings settings) {
+		this.settings = settings;
+	}
+}

=== modified file 'CpogsPlugin/src/org/workcraft/plugins/cpog/CpogSettings.java'
--- CpogsPlugin/src/org/workcraft/plugins/cpog/CpogSettings.java	2014-06-04 13:07:53 +0000
+++ CpogsPlugin/src/org/workcraft/plugins/cpog/CpogSettings.java	2014-07-11 09:42:10 +0000
@@ -12,6 +12,8 @@
 
 public class CpogSettings implements SettingsPage {
 
+	private static LinkedList<PropertyDescriptor> properties;
+
 	public enum SatSolver {
 		MINISAT("MiniSat"),
 		CLASP("Clasp");
@@ -30,27 +32,15 @@
 			return choice;
 		}
 	}
-
-	private static LinkedList<PropertyDescriptor> properties;
-
-	private static final String prefix = "CpogSettings";
-	private static final String keySatSolver  = prefix + ".satSolver";
-	private static final String keyEncodingWidth = prefix + ".encodingWidth";
-	private static final String keyCircuitSize = prefix + ".circuitSize";
-	private static final String keyClaspCommand = prefix + ".claspCommand";
-	private static final String keyMinisatCommand = prefix + ".minisatCommand";
-
-	private static final SatSolver defaultSatSolver = SatSolver.CLASP;
-	private static final int defaultEncodingWidth = 2;
-	private static final int defaultCircuitSize = 4;
-	private static final String defaultClaspCommand = "clasp";
-	private static final String defaultMinisatCommand = "minisat";
 	
-	private static SatSolver satSolver = defaultSatSolver;
-	private static int encodingWidth = defaultEncodingWidth;
-	private static int circuitSize = defaultCircuitSize;
-	private static String claspCommand = defaultClaspCommand;
-	private static String minisatCommand = defaultMinisatCommand;
+	private static SatSolver satSolver = SatSolver.CLASP;
+	//private static int encodingWidth = 2;
+	private static int circuitSize = 4;
+	private static String claspCommand = "clasp";
+	private static String minisatCommand = "minisat";
+	private static String espressoCommand = "espresso";
+	private static String abcFolder = "abc/";
+	private static String gatesLibrary = "90nm.genlib";
 	
 	@Override
 	public Collection<PropertyDescriptor> getDescriptors() {
@@ -71,16 +61,6 @@
 		});
 
 		properties.add(new PropertyDeclaration<CpogSettings, Integer>(
-				this, "Encoding bit-width", Integer.class) {
-			protected void setter(CpogSettings object, Integer value) {
-				CpogSettings.setEncodingWidth(value);
-			}
-			protected Integer getter(CpogSettings object) {
-				return CpogSettings.getEncodingWidth();
-			}
-		});
-
-		properties.add(new PropertyDeclaration<CpogSettings, Integer>(
 				this, "Circuit size in 2-input gates", Integer.class) {
 			protected void setter(CpogSettings object, Integer value) {
 				CpogSettings.setCircuitSize(value);
@@ -109,11 +89,41 @@
 				return CpogSettings.getMinisatCommand();
 			}
 		});
+		
+		properties.add(new PropertyDeclaration<CpogSettings, String>(
+				this, "Espresso solver", String.class) {
+			protected void setter(CpogSettings object, String value) {
+				CpogSettings.setEspressoCommand(value);
+			}
+			protected String getter(CpogSettings object) {
+				return CpogSettings.getEspressoCommand();
+			}
+		});
+		
+		properties.add(new PropertyDeclaration<CpogSettings, String>(
+				this, "Abc folder path", String.class) {
+			protected void setter(CpogSettings object, String value) {
+				CpogSettings.setAbcFolder(value);
+			}
+			protected String getter(CpogSettings object) {
+				return CpogSettings.getAbcFolder();
+			}
+		});
+		
+		properties.add(new PropertyDeclaration<CpogSettings, String>(
+				this, "Gate library (genlib format) inside abc folder", String.class) {
+			protected void setter(CpogSettings object, String value) {
+				CpogSettings.setGatesLibrary(value);
+			}
+			protected String getter(CpogSettings object) {
+				return CpogSettings.getGatesLibrary();
+			}
+		});
 	}
 	
 	@Override
 	public String getName() {
-		return "Scenco"; // SCENario ENCOder!
+		return "SCENCO";
 	}
 
 	@Override
@@ -123,59 +133,81 @@
 
 	@Override
 	public void load(Config config) {
-		setSatSolver(config.getEnum(keySatSolver, SatSolver.class, defaultSatSolver));
-		setEncodingWidth(config.getInt(keyEncodingWidth, defaultEncodingWidth));
-		setCircuitSize(config.getInt(keyCircuitSize, defaultCircuitSize));
-		setClaspCommand(config.getString(keyClaspCommand, defaultClaspCommand));
-		setMinisatCommand(config.getString(keyMinisatCommand, defaultMinisatCommand));
+		satSolver = config.getEnum("CpogSettings.satSolver", SatSolver.class, SatSolver.CLASP);
+		circuitSize = config.getInt("CpogSettings.circuitSize", 4);
+		setClaspCommand(config.getString("CpogSettings.claspCommand", "clasp"));
+		setMinisatCommand(config.getString("CpogSettings.minisatCommand", "minisat"));
+		setEspressoCommand(config.getString("CpogSettings.espressoCommand", "espresso"));
+		setAbcFolder(config.getString("CpogSettings.abcFolder", "abc/"));
+		setGatesLibrary(config.getString("CpogSettings.gatesLibrary", "90nm.genlib"));
 	}
 
 	@Override
 	public void save(Config config) {
-		config.setEnum(keySatSolver, SatSolver.class, satSolver);
-		config.setInt(keyEncodingWidth, getEncodingWidth());
-		config.setInt(keyCircuitSize, getCircuitSize());
-		config.set(keyClaspCommand, getClaspCommand());
-		config.set(keyMinisatCommand, getMinisatCommand());
+		config.setEnum("CpogSettings.satSolver", SatSolver.class, satSolver);
+		config.setInt("CpogSettings.circuitSize", circuitSize);
+		config.set("CpogSettings.claspCommand", claspCommand);
+		config.set("CpogSettings.minisatCommand", minisatCommand);
+		config.set("CpogSettings.espressoCommand", espressoCommand);
+		config.set("CpogSettings.abcFolder", abcFolder);
+		config.set("CpogSettings.gatesLibrary", gatesLibrary);
 	}
 
 	public static SatSolver getSatSolver() {
 		return satSolver;
 	}
 
-	public static void setSatSolver(SatSolver value) {
-		satSolver = value;
-	}
-
-	public static int getEncodingWidth() {
-		return encodingWidth;
-	}
-
-	public static void setEncodingWidth(int value) {
-		encodingWidth = value;
+	public static void setSatSolver(SatSolver satSolver) {
+		CpogSettings.satSolver = satSolver;
 	}
 
 	public static int getCircuitSize() {
 		return circuitSize;
 	}
 
-	public static void setCircuitSize(int value) {
-		circuitSize = value;
+	public static void setCircuitSize(int circuitSize) {
+		CpogSettings.circuitSize = circuitSize;
 	}
 
 	public static String getClaspCommand() {
 		return claspCommand;
 	}
 
-	public static void setClaspCommand(String value) {
-		claspCommand = value;
+	public static void setClaspCommand(String claspCommand) {
+		CpogSettings.claspCommand = claspCommand;
 	}
 
 	public static String getMinisatCommand() {
 		return minisatCommand;
 	}
 
-	public static void setMinisatCommand(String value) {
-		minisatCommand = value;
-	}
+	public static void setMinisatCommand(String minisatCommand) {
+		CpogSettings.minisatCommand = minisatCommand;
+	}
+
+	public static String getEspressoCommand() {
+		return espressoCommand;
+	}
+
+	public static void setEspressoCommand(String espressoCommand) {
+		CpogSettings.espressoCommand = espressoCommand;
+	}
+
+	public static String getAbcFolder() {
+		return abcFolder;
+	}
+
+	public static void setAbcFolder(String abcFolder) {
+		CpogSettings.abcFolder = abcFolder;
+	}
+
+	public static String getGatesLibrary() {
+		return gatesLibrary;
+	}
+
+	public static void setGatesLibrary(String gatesLibrary) {
+		CpogSettings.gatesLibrary = gatesLibrary;
+	}
+	
+	
 }

=== added file 'CpogsPlugin/src/org/workcraft/plugins/cpog/EncoderSettings.java'
--- CpogsPlugin/src/org/workcraft/plugins/cpog/EncoderSettings.java	1970-01-01 00:00:00 +0000
+++ CpogsPlugin/src/org/workcraft/plugins/cpog/EncoderSettings.java	2014-07-11 09:42:10 +0000
@@ -0,0 +1,208 @@
+package org.workcraft.plugins.cpog;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.LinkedHashMap;
+import java.util.Map;
+
+import org.workcraft.util.FileUtils;
+
+public class EncoderSettings {
+	
+	public enum generationMode{
+		OPTIMAL_ENCODING("Simulated annealing"),
+		RECURSIVE("Exhaustive search"),
+		RANDOM("Random search"),
+		SCENCO("Old tool SCENCO"),
+		OLD_SYNT("Old synthesise");
+		
+		public final String name;
+		
+		public static final generationMode[] modes = 
+			{
+				OPTIMAL_ENCODING,
+				RECURSIVE,
+				RANDOM,
+				SCENCO,
+				OLD_SYNT
+			};
+		
+		private generationMode(String name){
+			this.name = name;
+		}
+		
+		static public Map<String, generationMode> getChoice() {
+			LinkedHashMap<String, generationMode> choice = new LinkedHashMap<String, generationMode>();
+			for (generationMode item : generationMode.values()) {
+				choice.put(item.name, item);
+			}
+			return choice;
+		}
+	}
+	
+	public EncoderSettings(String espressoPath, String abcPath, String libPath) {
+		this.espressoPath = espressoPath;
+		this.abcPath = abcPath;
+		this.libPath = libPath;
+	}
+
+	private int solutionNumber = 10, numPO,bits;
+	private generationMode genMode = generationMode.OPTIMAL_ENCODING;
+	private boolean verboseMode, customEncMode, effort, contMode, cpogSize, costFunc;
+	private String[] customEnc;
+	private String espressoPath,abcPath,libPath;
+
+	public boolean isCpogSize() {
+		return cpogSize;
+	}
+
+	public void setCpogSize(boolean cpogSize) {
+		this.cpogSize = cpogSize;
+	}
+
+	public boolean isCostFunc() {
+		return costFunc;
+	}
+
+	public void setCostFunc(boolean costFunc) {
+		this.costFunc = costFunc;
+	}
+
+	public boolean isContMode() {
+		return contMode;
+	}
+
+	public void setContMode(boolean contMode) {
+		this.contMode = contMode;
+	}
+	
+	public boolean isEffort() {
+		return effort;
+	}
+
+	public void setEffort(boolean effort) {
+		this.effort = effort;
+	}
+	public int getBits() {
+		return bits;
+	}
+
+	public void setBits(int bits) {
+		this.bits = bits;
+	}
+	
+	public String getEspressoPath() {
+		return espressoPath;
+	}
+
+	public void setEspressoPath(String espressoPath) {
+		this.espressoPath = espressoPath;
+	}
+
+	public String getAbcPath() {
+		return abcPath;
+	}
+
+	public void setAbcPath(String abcPath) {
+		this.abcPath = abcPath;
+	}
+
+	public EncoderSettings(int solutionNumber, generationMode genMode, boolean verboseMode,
+			boolean customEncMode, String[] customEnc, int numPO) {
+		this.solutionNumber = solutionNumber;
+		this.genMode = genMode;
+		this.verboseMode = verboseMode;
+		this.customEncMode = customEncMode;
+		this.numPO = numPO;
+		this.customEnc = customEnc;
+	}
+
+	public EncoderSettings(int solutionNumber, generationMode genMode, boolean verboseMode,
+			boolean customEncMode) {
+		this.solutionNumber = solutionNumber;
+		this.genMode = genMode;
+		this.verboseMode = verboseMode;
+		this.customEncMode = customEncMode;
+	}
+
+	public int getSolutionNumber() {
+		return solutionNumber;
+	}
+	
+	public void setSolutionNumber(int number){
+		solutionNumber = number;
+	}
+	
+	public void setGenerationModeInt(int index){
+		switch(index){
+		case 0:
+			genMode = generationMode.OPTIMAL_ENCODING;
+			break;
+		case 1:
+			genMode = generationMode.RECURSIVE;
+			break;
+		case 2:
+			genMode = generationMode.RANDOM;
+			break;
+		case 3:
+			genMode = generationMode.SCENCO;
+			break;
+		case 4:
+			genMode = generationMode.OLD_SYNT;
+			break;
+		default:
+			System.out.println("Error.");
+		}
+	}
+	
+	public int getNumPO() {
+		return numPO;
+	}
+
+	public void setNumPO(int numPO) {
+		this.numPO = numPO;
+	}
+
+	public generationMode getGenMode() {
+		return genMode;
+	}
+
+	public void setGenMode(generationMode genMode) {
+		this.genMode = genMode;
+	}
+
+	public boolean isVerboseMode() {
+		return verboseMode;
+	}
+
+	public void setVerboseMode(boolean verboseMode) {
+		this.verboseMode = verboseMode;
+	}
+
+	public boolean isCustomEncMode() {
+		return customEncMode;
+	}
+
+	public void setCustomEncMode(boolean customEncMode) {
+		this.customEncMode = customEncMode;
+	}
+
+	public String[] getCustomEnc() {
+		return customEnc;
+	}
+
+	public void setCustomEnc(String[] customEnc) {
+		this.customEnc = customEnc;
+	}
+
+	public String getLibPath() {
+		return libPath;
+	}
+
+	public void setLibPath(String libPath) {
+		this.libPath = libPath;
+	}
+
+	
+}

=== added file 'CpogsPlugin/src/org/workcraft/plugins/cpog/EncoderSettingsSerialiser.java'
--- CpogsPlugin/src/org/workcraft/plugins/cpog/EncoderSettingsSerialiser.java	1970-01-01 00:00:00 +0000
+++ CpogsPlugin/src/org/workcraft/plugins/cpog/EncoderSettingsSerialiser.java	2014-07-11 09:42:10 +0000
@@ -0,0 +1,29 @@
+package org.workcraft.plugins.cpog;
+
+import org.w3c.dom.Element;
+import org.workcraft.plugins.shared.presets.SettingsSerialiser;
+import org.workcraft.util.XmlUtil;
+
+public class EncoderSettingsSerialiser implements SettingsSerialiser<EncoderSettings> {
+
+	@Override
+	public EncoderSettings fromXML(Element e) {
+		String espressoPath = XmlUtil.readStringAttr(e, "Espresso");
+		String abcPath = XmlUtil.readStringAttr(e, "Abc");
+		String libraryPath = XmlUtil.readStringAttr(e, "Library");
+		
+		return new EncoderSettings(espressoPath,abcPath,libraryPath);
+	}
+
+	@Override
+	public void toXML(EncoderSettings settings, Element parent) {
+		Element e = parent.getOwnerDocument().createElement("settings");
+		e.setAttribute("Espresso", settings.getEspressoPath());
+		e.setAttribute("Abc", settings.getAbcPath());
+		e.setAttribute("Library", settings.getLibPath());
+		
+		parent.appendChild(e);
+		
+	}
+
+}

=== added file 'CpogsPlugin/src/org/workcraft/plugins/cpog/ProgrammerChainResultHandler.java'
--- CpogsPlugin/src/org/workcraft/plugins/cpog/ProgrammerChainResultHandler.java	1970-01-01 00:00:00 +0000
+++ CpogsPlugin/src/org/workcraft/plugins/cpog/ProgrammerChainResultHandler.java	2014-07-11 09:42:10 +0000
@@ -0,0 +1,95 @@
+package org.workcraft.plugins.cpog;
+
+import javax.swing.JOptionPane;
+import javax.swing.SwingUtilities;
+
+import org.workcraft.plugins.cpog.EncoderSettings.generationMode;
+import org.workcraft.plugins.cpog.tasks.ProgrammerChainResult;
+import org.workcraft.plugins.cpog.tasks.ProgrammerChainTask;
+import org.workcraft.plugins.shared.tasks.ExternalProcessResult;
+import org.workcraft.tasks.DummyProgressMonitor;
+import org.workcraft.tasks.Result;
+import org.workcraft.tasks.Result.Outcome;
+
+public class ProgrammerChainResultHandler extends DummyProgressMonitor<ProgrammerChainResult> {
+	private String errorMessage;
+	private final ProgrammerChainTask task;
+	
+	public ProgrammerChainResultHandler(ProgrammerChainTask task) {
+		this.task = task;
+	}
+	
+	@Override
+	public void finished(final Result<? extends ProgrammerChainResult> result, String description) {
+		if (result.getOutcome() == Outcome.FINISHED) {
+			final generationMode programmerMode = result.getReturnValue().getProgrammerSettings().getGenMode();
+			switch (programmerMode) {
+			case OPTIMAL_ENCODING:
+			case RECURSIVE:
+				//SwingUtilities.invokeLater(new MpsatStgReachabilityResultHandler(task, result));
+				break;
+			default:
+				SwingUtilities.invokeLater(new Runnable() {
+					@Override
+					public void run() {
+						JOptionPane.showMessageDialog(null, 
+								"Scenco mode \"" + programmerMode + "\" is not (yet) supported." , 
+								"Sorry..", JOptionPane.WARNING_MESSAGE);
+					}
+				});
+				break;
+			}			
+		}
+		else if (result.getOutcome() != Outcome.CANCELLED) {
+			errorMessage = "Scenco tool chain execution failed :-(";
+
+			Throwable cause1 = result.getCause();
+
+			if (cause1 != null) {
+				// Exception was thrown somewhere in the chain task run() method (not in any of the subtasks)
+				errorMessage += "\n\nFailure caused by: " + cause1.toString() + "\nPlease see the \"Problems\" tab for more details.";
+			} else
+			{
+				Result<? extends Object> exportResult = result.getReturnValue().getExportResult();
+				if (exportResult.getOutcome() == Outcome.FAILED) {
+					errorMessage += "\n\nFailed to export the model as a .g file.";
+					Throwable cause = exportResult.getCause();
+					if (cause != null)
+						errorMessage += "\n\nFailure caused by: " + cause.toString() + "\nPlease see the \"Problems\" tab for more details.";
+					else
+						errorMessage += "\n\nThe exporter class did not offer further explanation.";
+				} else {
+					Result<? extends ExternalProcessResult> punfResult = result.getReturnValue().getPunfResult();
+
+					if (punfResult.getOutcome() == Outcome.FAILED) {
+						errorMessage += "\n\nPunf could not build the unfolding prefix.";
+						Throwable cause = punfResult.getCause();
+						if (cause != null)
+							errorMessage += "\n\nFailure caused by: " + cause.toString() + "\nPlease see the \"Problems\" tab for more details.";
+						else
+							errorMessage += "\n\nFailure caused by the following errors:\n" + new String(punfResult.getReturnValue().getErrors()); 
+					} else {
+						Result<? extends ExternalProcessResult> encoderResult = result.getReturnValue().getEncoderResult();
+
+						if (encoderResult.getOutcome() == Outcome.FAILED) {
+							errorMessage += "\n\nEncoder failed to execute as expected.";
+							Throwable cause = encoderResult.getCause();
+							if (cause != null)
+								errorMessage += "\n\nFailure caused by: " + cause.toString() + "\nPlease see the \"Problems\" tab for more details.";
+							else
+								errorMessage += "\n\nFailure caused by the following errors:\n" + new String(encoderResult.getReturnValue().getErrors());
+						}
+						else {
+							errorMessage += "\n\nEncoder chain task returned failure status without further explanation. This should not have happened -_-a.";
+						}
+					}
+				}
+			}
+			SwingUtilities.invokeLater(new Runnable() {
+				@Override
+				public void run() {
+					JOptionPane.showMessageDialog(null, errorMessage, "Oops..", JOptionPane.ERROR_MESSAGE);				}
+			});
+		}
+	}
+}
\ No newline at end of file

=== added file 'CpogsPlugin/src/org/workcraft/plugins/cpog/ProgrammerMode.java'
--- CpogsPlugin/src/org/workcraft/plugins/cpog/ProgrammerMode.java	1970-01-01 00:00:00 +0000
+++ CpogsPlugin/src/org/workcraft/plugins/cpog/ProgrammerMode.java	2014-07-11 09:42:10 +0000
@@ -0,0 +1,41 @@
+package org.workcraft.plugins.cpog;
+
+public enum ProgrammerMode {
+	MICROCONTROLLER("-M", "Microcontroller synthesising", false),
+	CPOG_SIZE("-C", "Element controller synthesising", false);
+	
+	private String argument;
+	private String description;
+	private boolean reach;
+	
+	public static final ProgrammerMode[] modes = 
+	{
+		MICROCONTROLLER,
+		CPOG_SIZE
+	};
+
+	public static ProgrammerMode getMode (String arg) {
+		for (int i=0; i<modes.length; i++)
+			if (modes[i].getArgument().equals(arg))
+				return modes[i];
+		return null;
+	}
+	
+	ProgrammerMode(String argument, String description, boolean reach) {
+		this.argument = argument;
+		this.description = description;
+		this.reach = reach;
+	}
+
+	public String toString() {
+		return description;
+	}
+	
+	public String getArgument() {
+		return argument;
+	}
+
+	public boolean isReach() {
+		return reach;
+	}
+}
\ No newline at end of file

=== added file 'CpogsPlugin/src/org/workcraft/plugins/cpog/ProgrammerUtilitySettings.java'
--- CpogsPlugin/src/org/workcraft/plugins/cpog/ProgrammerUtilitySettings.java	1970-01-01 00:00:00 +0000
+++ CpogsPlugin/src/org/workcraft/plugins/cpog/ProgrammerUtilitySettings.java	2014-07-11 09:42:10 +0000
@@ -0,0 +1,110 @@
+package org.workcraft.plugins.cpog;
+
+import java.util.Collection;
+import java.util.LinkedList;
+import java.util.List;
+
+import org.workcraft.Config;
+import org.workcraft.gui.propertyeditor.PropertyDeclaration;
+import org.workcraft.gui.propertyeditor.PropertyDescriptor;
+import org.workcraft.gui.propertyeditor.SettingsPage;
+import org.workcraft.plugins.cpog.EncoderSettings.generationMode;
+
+public class ProgrammerUtilitySettings implements SettingsPage {
+private static LinkedList<PropertyDescriptor> properties;
+	
+	private static final String commandKey = "Tools.encoder.command";
+	private static final String solutionModeKey = "Tools.encoder.solutionMode";
+	private static final String extraArgsKey = "Tools.encoder.args";
+	
+	private static String command = "scenco";
+	private static generationMode genMode = generationMode.OPTIMAL_ENCODING;
+	private static String extraArgs = "";
+
+	public ProgrammerUtilitySettings() {
+		properties = new LinkedList<PropertyDescriptor>();
+		
+		properties.add(new PropertyDeclaration<ProgrammerUtilitySettings, String>(
+				this, "Scenco command", String.class) {
+			protected void setter(ProgrammerUtilitySettings object, String value) {
+				ProgrammerUtilitySettings.setCommand(value);
+			}
+			protected String getter(ProgrammerUtilitySettings object) {
+				return ProgrammerUtilitySettings.getCommand();
+			}
+		});
+		
+		properties.add(new PropertyDeclaration<ProgrammerUtilitySettings, generationMode>(
+				this, "Check mode", generationMode.class, generationMode.getChoice()) {
+			protected void setter(ProgrammerUtilitySettings object, generationMode value) {
+				ProgrammerUtilitySettings.setGenerationMode(value);
+			}
+			protected generationMode getter(ProgrammerUtilitySettings object) {
+				return ProgrammerUtilitySettings.getGenerationMode();
+			}
+		});
+
+		properties.add(new PropertyDeclaration<ProgrammerUtilitySettings, String>(
+				this, "Scenco additional arguments", String.class) {
+			protected void setter(ProgrammerUtilitySettings object, String value) {
+				ProgrammerUtilitySettings.setExtraArgs(value);
+			}
+			protected String getter(ProgrammerUtilitySettings object) {
+				return ProgrammerUtilitySettings.getExtraArgs();
+			}
+		});
+	}
+	
+	@Override
+	public List<PropertyDescriptor> getDescriptors() {
+		return properties;
+	}
+
+	@Override
+	public void load(Config config) {
+		command = config.getString(commandKey, "scenco");
+		genMode = config.getEnum(solutionModeKey, generationMode.class, generationMode.OPTIMAL_ENCODING);
+		extraArgs = config.getString(extraArgsKey, "");
+	}
+
+	@Override
+	public void save(Config config) {
+		config.set(commandKey, command);
+		config.setEnum(solutionModeKey, generationMode.class, genMode);
+		config.set(extraArgsKey, extraArgs);
+	}
+	
+	@Override
+	public String getSection() {
+		return "External tools";
+	}
+
+	@Override
+	public String getName() {
+		return "Scenco";
+	}
+
+	public static String getCommand() {
+		return command;
+	}
+
+	public static void setCommand(String value) {
+		ProgrammerUtilitySettings.command = value;
+	}
+
+	public static String getExtraArgs() {
+		return extraArgs;
+	}
+
+	public static void setExtraArgs(String value) {
+		ProgrammerUtilitySettings.extraArgs = value;
+	}
+
+	public static void setGenerationMode(generationMode value) {
+		ProgrammerUtilitySettings.genMode = value;
+	}
+
+	public static generationMode getGenerationMode() {
+		return genMode;
+	}
+}

=== modified file 'CpogsPlugin/src/org/workcraft/plugins/cpog/Variable.java'
--- CpogsPlugin/src/org/workcraft/plugins/cpog/Variable.java	2014-04-07 16:35:42 +0000
+++ CpogsPlugin/src/org/workcraft/plugins/cpog/Variable.java	2014-07-11 09:42:10 +0000
@@ -31,7 +31,8 @@
 @DisplayName("Variable")
 @VisualClass(org.workcraft.plugins.cpog.VisualVariable.class)
 public class Variable extends MathNode implements Comparable<Variable>, BooleanVariable
-{
+{
+	
 	private VariableState state = VariableState.UNDEFINED;
 	
 	private String label = "";

=== added directory 'CpogsPlugin/src/org/workcraft/plugins/cpog/gui'
=== added file 'CpogsPlugin/src/org/workcraft/plugins/cpog/gui/EncoderConfigurationDialog.java'
--- CpogsPlugin/src/org/workcraft/plugins/cpog/gui/EncoderConfigurationDialog.java	1970-01-01 00:00:00 +0000
+++ CpogsPlugin/src/org/workcraft/plugins/cpog/gui/EncoderConfigurationDialog.java	2014-07-11 09:42:10 +0000
@@ -0,0 +1,451 @@
+package org.workcraft.plugins.cpog.gui;
+
+import info.clearthought.layout.TableLayout;
+
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.FlowLayout;
+import java.awt.Window;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.KeyEvent;
+import java.util.ArrayList;
+
+import javax.swing.BorderFactory;
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JComboBox;
+import javax.swing.JComponent;
+import javax.swing.JDialog;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTable;
+import javax.swing.JTextField;
+import javax.swing.KeyStroke;
+
+import org.workcraft.gui.SimpleFlowLayout;
+import org.workcraft.plugins.cpog.CpogProgrammer;
+import org.workcraft.plugins.cpog.EncoderSettings;
+import org.workcraft.plugins.cpog.EncoderSettings.generationMode;
+import org.workcraft.plugins.cpog.VisualCPOG;
+import org.workcraft.plugins.cpog.VisualScenario;
+import org.workcraft.plugins.shared.presets.PresetManager;
+import org.workcraft.workspace.WorkspaceEntry;
+
+public class EncoderConfigurationDialog extends JDialog {
+	
+	private JLabel numberOfSolutionsLabel, contLabel,
+					verboseModeLabel,exampleLabel,exampleLabel2,exampleLabel3,exampleLabel4,
+					exampleLabel5,customEncLabel,bitsLabel,effortLabel,genLabel,
+					optimiseLabel, disableLabel;
+	private JCheckBox verboseModeCheck, customEncodings, effortCheck,
+					disableCheck, contCheck;
+	private JComboBox generationModeBox,OptimiseBox;
+	private JPanel generationPanel, buttonsPanel, content;
+	private JButton saveButton, closeButton;
+	private JTextField numberOfSolutionsText, bitsText;
+	private PresetManager<EncoderSettings> presetManager;
+	private JTable encodingTable;
+	JScrollPane scrollPane;
+	private TableLayout layout;
+	private int m,bits;
+	
+	// Core variables
+	private CpogProgrammer encoder;
+	private EncoderSettings settings;
+	private WorkspaceEntry we;
+	private static boolean settingsPresent = false;
+	
+	Dimension dimensionLabel = new Dimension(270, 22);
+	Dimension dimensionBox = new Dimension(270, 22);
+	Dimension dimensionText = new Dimension(585,22);
+	Dimension dimensionTable = new Dimension(942,100);
+	Dimension dimensionWindow = new Dimension(100,400);
+	
+	//generationPanel.getPreferredSize().height
+	
+	public EncoderSettings getSettings() {
+		return settings;
+	}
+	
+	public EncoderConfigurationDialog(Window owner, PresetManager<EncoderSettings> presetManager, EncoderSettings settings,WorkspaceEntry we) {
+		super(owner, "SCENCO configuration", ModalityType.APPLICATION_MODAL);
+		this.presetManager = presetManager;
+		this.settings = settings;
+		this.we = we;
+		
+		createGenerationPanel();
+		createButtonPanel();		
+		
+		/*double size[][] = new double[][] {
+				{TableLayout.FILL},
+				{TableLayout.PREFERRED, TableLayout.PREFERRED, TableLayout.FILL, dimensionWindow.height }
+		};*/
+		double size[][] = new double[][] {
+				{946},
+				{430,100}
+		};
+
+		layout = new TableLayout(size);
+		//layout.setHGap(3);
+		//layout.setVGap(3);
+		
+		content = new JPanel(layout);
+		content.setBorder(BorderFactory.createEmptyBorder(3, 3, 3, 3));
+		
+		content.add(generationPanel, "0 0");
+		content.add(buttonsPanel, "0 1");
+		setContentPane(content);
+		
+		
+		
+		getRootPane().registerKeyboardAction(new ActionListener() {
+	    	@Override
+	    	public void actionPerformed(ActionEvent e) {
+	    		setVisible(false);  
+	    	}
+	    },
+	    KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0),
+	    JComponent.WHEN_IN_FOCUSED_WINDOW);
+		
+	}
+
+	private void createButtonPanel() {
+		buttonsPanel = new JPanel (new FlowLayout(FlowLayout.RIGHT));
+		
+		saveButton = new JButton ("Run");
+		saveButton.addActionListener(new ActionListener() {
+			@Override
+			public void actionPerformed(ActionEvent e) {
+				setVisible(false);
+				
+				
+				// ENCODER EXECUTION
+				
+				// Read parameters
+				if (effortCheck.isSelected())
+					settings.setEffort(false);
+				else
+					settings.setEffort(true);
+				settings.setBits(Integer.valueOf(bitsText.getText()));
+				settings.setCpogSize(OptimiseBox.getSelectedIndex() == 0 ? false : true);
+				settings.setCostFunc(disableCheck.isSelected());
+				settings.setVerboseMode(verboseModeCheck.isSelected());
+				settings.setContMode(contCheck.isSelected());
+				settings.setGenerationModeInt(generationModeBox.getSelectedIndex());
+				settings.setSolutionNumber(Integer.parseInt(numberOfSolutionsText.getText()));
+				settings.setNumPO(m);
+				if(customEncodings.isSelected()){
+					settings.setCustomEncMode(true);
+					String encodings[] = new String[m];
+					for(int i = 0; i<m; i++){
+						encodings[i] = (String) encodingTable.getModel().getValueAt(i, 1);
+					}
+					settings.setCustomEnc(encodings);
+				}else{
+					settings.setBits(bits+1);
+					settings.setCustomEncMode(false);
+				}
+				
+				// Set them on encoder
+				if(settingsPresent == false){
+					settingsPresent = true;
+					encoder = new CpogProgrammer(settings);
+				}else{
+					encoder.setSettings(settings);
+				}
+				
+				// Execute programmer.x
+				encoder.run(we);
+			}
+		});
+		
+		closeButton = new JButton ("Close");
+		closeButton.addActionListener(new ActionListener() {
+			@Override
+			public void actionPerformed(ActionEvent e) {
+				setVisible(false);		
+			}
+		});
+		
+		buttonsPanel.add(saveButton);
+		buttonsPanel.add(closeButton);
+		
+	}
+
+	private void createGenerationPanel() {
+		setMinimumSize(new Dimension(600, 400));
+		generationPanel = new JPanel(new SimpleFlowLayout());
+		JPanel numberOfSolutionsPanel = new JPanel (new FlowLayout(FlowLayout.LEFT, 3, 0));
+		VisualCPOG cpog = (VisualCPOG)(we.getModelEntry().getVisualModel());
+		ArrayList<VisualScenario> scenarios = new ArrayList<VisualScenario>(cpog.getGroups());
+		m = scenarios.size();
+
+		// GENERATION MODE COMBOBOX
+		genLabel = new JLabel("Mode:");
+		genLabel.setPreferredSize(dimensionLabel);
+		generationModeBox = new JComboBox();
+		generationModeBox.setEditable(false);
+		generationModeBox.setPreferredSize(dimensionBox);
+		for (generationMode mode : generationMode.modes) {
+			generationModeBox.addItem(mode.name);
+		}
+		generationModeBox.setSelectedIndex(settings.getGenMode().ordinal());
+		generationModeBox.setBackground(Color.WHITE);
+		generationModeBox.addActionListener(new ActionListener() {
+
+            @Override
+            public void actionPerformed(ActionEvent e) {
+            	switch(generationModeBox.getSelectedIndex()){
+            		// SIMULATED ANNEALING
+            		case 0:
+	            		numberOfSolutionsText.setBackground(Color.WHITE);
+	            		numberOfSolutionsText.setEnabled(true);
+	            		contCheck.setEnabled(true);
+	            		customEncodings.setEnabled(true);
+	            		disableCheck.setSelected(false);
+                		disableCheck.setEnabled(true);
+	            		break;
+	            	// EXHAUSTIVE SEARCH
+            		case 1:
+            			numberOfSolutionsText.setBackground(Color.LIGHT_GRAY);
+                		numberOfSolutionsText.setEnabled(false);
+                		contCheck.setEnabled(false);
+                		contCheck.setSelected(false);
+                		customEncodings.setEnabled(false);
+                		customEncodings.setSelected(false);
+                		encodingTable.setEnabled(false);
+                		encodingTable.setBackground(Color.LIGHT_GRAY);
+                		bitsText.setBackground(Color.LIGHT_GRAY);
+                		bitsText.setEnabled(false);
+                		disableCheck.setSelected(false);
+                		disableCheck.setEnabled(false);
+                		break;
+                	// RANDOM SEARCH
+            		case 2:
+            			numberOfSolutionsText.setBackground(Color.WHITE);
+                		numberOfSolutionsText.setEnabled(true);
+                		contCheck.setEnabled(true);
+                		customEncodings.setEnabled(false);
+                		customEncodings.setSelected(false);
+                		encodingTable.setEnabled(false);
+                		encodingTable.setBackground(Color.LIGHT_GRAY);
+                		bitsText.setBackground(Color.LIGHT_GRAY);
+                		bitsText.setEnabled(false);
+                		disableCheck.setSelected(false);
+                		disableCheck.setEnabled(false);
+                		break;
+                	// OLD SCENCO
+            		case 3:
+            			numberOfSolutionsText.setBackground(Color.LIGHT_GRAY);
+                		numberOfSolutionsText.setEnabled(false);
+                		contCheck.setEnabled(false);
+                		contCheck.setSelected(false);
+                		customEncodings.setSelected(false);
+                		customEncodings.setEnabled(false);
+                		encodingTable.setEnabled(false);
+                		encodingTable.setBackground(Color.LIGHT_GRAY);
+                		bitsText.setBackground(Color.LIGHT_GRAY);
+                		bitsText.setEnabled(false);
+                		disableCheck.setSelected(false);
+                		disableCheck.setEnabled(false);
+                		break;
+                	// OLD SYNTHESISE
+            		case 4:
+            			numberOfSolutionsText.setBackground(Color.LIGHT_GRAY);
+                		numberOfSolutionsText.setEnabled(false);
+                		contCheck.setEnabled(false);
+                		contCheck.setSelected(false);
+                		customEncodings.setSelected(false);
+                		customEncodings.setEnabled(false);
+                		encodingTable.setEnabled(false);
+                		encodingTable.setBackground(Color.LIGHT_GRAY);
+                		bitsText.setBackground(Color.LIGHT_GRAY);
+                		bitsText.setEnabled(false);
+                		disableCheck.setSelected(false);
+                		disableCheck.setEnabled(false);
+                		break;
+                	default:
+            	}
+            }
+        });
+		
+		// OPTIMISE FOR MICROCONTROLLER/CPOG SIZE
+		optimiseLabel = new JLabel("Optimise for:");
+		optimiseLabel.setPreferredSize(dimensionLabel);
+		OptimiseBox = new JComboBox();
+		OptimiseBox.setEditable(false);
+		OptimiseBox.setPreferredSize(dimensionBox);
+		OptimiseBox.addItem("microcontroller");
+		OptimiseBox.addItem("CPOG size");
+		OptimiseBox.setSelectedIndex(settings.isCpogSize() ? 1 : 0);
+		OptimiseBox.setBackground(Color.WHITE);
+		
+		// DISABLE COST FUNCTION
+		disableLabel = new JLabel("Disable cost function approximation: ");
+		disableLabel.setPreferredSize(dimensionLabel);
+		disableCheck = new JCheckBox("",settings.isCostFunc());
+		disableCheck.setToolTipText("Requires a big amount of time");
+		
+		
+		// Speed-up
+		effortLabel = new JLabel("Using heuristic for speed-up:");
+		effortLabel.setPreferredSize(dimensionLabel);
+		effortCheck = new JCheckBox("",settings.isEffort());
+		
+		// NUMBER OF SOLUTIONS TO GENERATE
+		numberOfSolutionsLabel = new JLabel("Number of encodings to generate: ");
+		numberOfSolutionsLabel.setPreferredSize(dimensionLabel);
+		numberOfSolutionsText = new JTextField();
+		numberOfSolutionsText.setText(String.valueOf(settings.getSolutionNumber()));
+		numberOfSolutionsText.setPreferredSize(new Dimension(70, 15));
+		
+		// CONTINUOUS MODE
+		contCheck = new JCheckBox("",settings.isContMode());
+		contLabel = new JLabel("Continuous mode");
+		contLabel.setPreferredSize(new Dimension(150, 15));
+		contCheck.addActionListener(new ActionListener() {
+
+            @Override
+            public void actionPerformed(ActionEvent e) {
+            	if(contCheck.isSelected()){
+            		numberOfSolutionsText.setBackground(Color.LIGHT_GRAY);
+            		numberOfSolutionsText.setEnabled(false);
+            	}else{
+            		numberOfSolutionsText.setBackground(Color.WHITE);
+            		numberOfSolutionsText.setEnabled(true);
+            	}
+            }
+        });
+		
+		// TABLE OF ENCODINGS
+		exampleLabel = new JLabel("Fill in the table below if you want to set a custom op-code to a whichever Partial Order Graph. Below symbols allowed:");
+		exampleLabel2 = new JLabel("- 0 1    assign a specific bit 0 or 1;");
+		exampleLabel3 = new JLabel("-  X      find the best bit assignment;");
+		exampleLabel4 = new JLabel("-  -       a Don't Care bit.");
+		exampleLabel5 = new JLabel("You have to take care of selecting an enough number of bits for encoding all Partial Order.");
+		exampleLabel.setPreferredSize(new Dimension(942,15));
+		exampleLabel2.setPreferredSize(new Dimension(800,15));
+		exampleLabel3.setPreferredSize(new Dimension(800,15));
+		exampleLabel4.setPreferredSize(new Dimension(800,15));
+		exampleLabel5.setPreferredSize(new Dimension(800,15));
+		customEncLabel = new JLabel("Custom encodings: ");
+		customEncLabel.setPreferredSize(dimensionLabel);
+		customEncodings = new JCheckBox("", false);
+		customEncodings.addActionListener(new ActionListener() {
+
+            @Override
+            public void actionPerformed(ActionEvent e) {
+            	if(customEncodings.isSelected()){
+            		encodingTable.setEnabled(true);
+            		encodingTable.setBackground(Color.WHITE);
+            		bitsText.setBackground(Color.WHITE);
+            		bitsText.setEnabled(true);
+            	}
+            	else{
+            		encodingTable.setEnabled(false);
+            		encodingTable.setBackground(Color.LIGHT_GRAY);
+            		bitsText.setBackground(Color.LIGHT_GRAY);
+            		bitsText.setEnabled(false);
+            	}
+            }
+        });
+		
+		bitsLabel = new JLabel("Number of bits to use: ");
+		bitsLabel.setPreferredSize(dimensionLabel);
+		int value = 2;
+		while(value < m){
+			value *=2;
+			bits++;
+		}
+		
+		bitsText = new JTextField();
+		bitsText.setText(String.valueOf(bits + 1));
+		bitsText.setPreferredSize(new Dimension(70, 15));
+		bitsText.setBackground(Color.LIGHT_GRAY);
+		bitsText.setEnabled(false);
+		bitsText.addActionListener(new ActionListener() {
+
+            @Override
+            public void actionPerformed(ActionEvent e) {
+            	if(Integer.parseInt(bitsText.getText()) < bits +1) 
+            		bitsText.setText(String.valueOf(bits + 1));
+            	for(int i=0;i<m;i++){
+            		String data = "";
+            		for(int j=0; j < Integer.valueOf(bitsText.getText()); j++) data = data + "X";
+            		encodingTable.getModel().setValueAt(data, i, 1);
+            	}
+            }
+        });
+		
+		String[] columnNames = {"Partial Order Name","Encoding"};
+		Object[][] data = new Object[m][3];
+		for(int i=0; i<m; i++){
+			String name;
+			if(scenarios.get(i).getLabel().equals("")){
+				name = "CPOG " + i;
+			}
+			else{
+				name = scenarios.get(i).getLabel();
+			}
+			data[i][0] = name;
+			data[i][1] = "";
+			for(int j=0; j < Integer.valueOf(bitsText.getText()); j++) data[i][1] = data[i][1] + "X";
+		}
+		encodingTable = new JTable(data, columnNames);
+		MyTableCellRenderer renderer = new MyTableCellRenderer();
+		encodingTable.setDefaultRenderer(Object.class, renderer);
+		scrollPane = new JScrollPane(encodingTable);
+		scrollPane.setPreferredSize(dimensionTable);
+		encodingTable.setFillsViewportHeight(false);
+		encodingTable.setEnabled(false);
+		encodingTable.setBackground(Color.LIGHT_GRAY);
+		
+		
+		// VERBOSE MODE INSTANTIATION
+		verboseModeLabel = new JLabel("Activate verbose mode:");
+		verboseModeLabel.setPreferredSize(dimensionLabel);
+		verboseModeCheck = new JCheckBox("",false);
+		
+		// INSTANTATING PANEL
+		generationPanel.add(genLabel);
+		generationPanel.add(generationModeBox);
+		generationPanel.add(new SimpleFlowLayout.LineBreak());
+		generationPanel.add(optimiseLabel);
+		generationPanel.add(OptimiseBox);
+		generationPanel.add(new SimpleFlowLayout.LineBreak());
+		generationPanel.add(disableLabel);
+		generationPanel.add(disableCheck);
+		generationPanel.add(new SimpleFlowLayout.LineBreak());
+		generationPanel.add(effortLabel);
+		generationPanel.add(effortCheck);
+		generationPanel.add(new SimpleFlowLayout.LineBreak());
+		generationPanel.add(numberOfSolutionsLabel);
+		generationPanel.add(numberOfSolutionsText);
+		generationPanel.add(contCheck);
+		generationPanel.add(contLabel);
+		generationPanel.add(new SimpleFlowLayout.LineBreak());
+		generationPanel.add(verboseModeLabel);
+		generationPanel.add(verboseModeCheck);
+		generationPanel.add(new SimpleFlowLayout.LineBreak());
+		generationPanel.add(exampleLabel);
+		generationPanel.add(new SimpleFlowLayout.LineBreak());
+		generationPanel.add(exampleLabel2);
+		generationPanel.add(new SimpleFlowLayout.LineBreak());
+		generationPanel.add(exampleLabel3);
+		generationPanel.add(new SimpleFlowLayout.LineBreak());
+		generationPanel.add(exampleLabel4);
+		generationPanel.add(new SimpleFlowLayout.LineBreak());
+		generationPanel.add(exampleLabel5);
+		generationPanel.add(new SimpleFlowLayout.LineBreak());
+		generationPanel.add(customEncLabel);
+		generationPanel.add(customEncodings);
+		generationPanel.add(new SimpleFlowLayout.LineBreak());
+		generationPanel.add(bitsLabel);
+		generationPanel.add(bitsText);
+		generationPanel.add(new SimpleFlowLayout.LineBreak());
+		generationPanel.add(scrollPane);
+		generationPanel.add(new SimpleFlowLayout.LineBreak());
+	}
+}

=== added file 'CpogsPlugin/src/org/workcraft/plugins/cpog/gui/MyTableCellRenderer.java'
--- CpogsPlugin/src/org/workcraft/plugins/cpog/gui/MyTableCellRenderer.java	1970-01-01 00:00:00 +0000
+++ CpogsPlugin/src/org/workcraft/plugins/cpog/gui/MyTableCellRenderer.java	2014-07-11 09:42:10 +0000
@@ -0,0 +1,15 @@
+package org.workcraft.plugins.cpog.gui;
+
+import java.awt.Component;
+
+import javax.swing.JTable;
+import javax.swing.table.DefaultTableCellRenderer;
+
+public class MyTableCellRenderer extends DefaultTableCellRenderer{ 
+	public Component getTableCellRendererComponent(JTable table,Object value,
+			boolean isSelected, boolean hasFocus, int row, int column){ 
+		super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column); 
+		setHorizontalAlignment( CENTER ); 
+		return this; 
+		} 
+	}
\ No newline at end of file

=== modified file 'CpogsPlugin/src/org/workcraft/plugins/cpog/optimisation/CpogEncoding.java'
--- CpogsPlugin/src/org/workcraft/plugins/cpog/optimisation/CpogEncoding.java	2010-04-09 17:40:12 +0000
+++ CpogsPlugin/src/org/workcraft/plugins/cpog/optimisation/CpogEncoding.java	2014-07-11 09:42:10 +0000
@@ -31,6 +31,15 @@
 	public boolean[][] getEncoding() {
 		return encoding;
 	}
-	private final BooleanFormula[] functions;
-	private final boolean[][] encoding;
+	public void setEncoding(boolean[][] encoding){
+		this.encoding = encoding;
+	}
+	public void setFormula(BooleanFormula formula,int index){
+		this.functions[index] = formula;
+	}
+	public void setFormule(BooleanFormula[] formula){
+		this.functions = formula;
+	}
+	private  BooleanFormula[] functions;
+	private boolean[][] encoding;
 }

=== modified file 'CpogsPlugin/src/org/workcraft/plugins/cpog/optimisation/DefaultCpogSolver.java'
--- CpogsPlugin/src/org/workcraft/plugins/cpog/optimisation/DefaultCpogSolver.java	2010-12-03 20:17:13 +0000
+++ CpogsPlugin/src/org/workcraft/plugins/cpog/optimisation/DefaultCpogSolver.java	2014-07-11 09:42:10 +0000
@@ -11,6 +11,12 @@
 				this.cnfConverter = simpleCnfTaskProvider;
 	}
 
+	public CpogOptimisationTask<? extends T> getTask(String[] scenarios, BooleanVariable [] variables, int derivedVars)
+	{
+		CpogOptimisationTask<? extends T> task = problemGenerator.getFormula(scenarios, variables, derivedVars);
+		return task;
+	}
+	
 	public CpogEncoding solve(String[] scenarios, BooleanVariable [] variables, int derivedVars)
 	{
 		CpogOptimisationTask<? extends T> task = problemGenerator.getFormula(scenarios, variables, derivedVars);

=== modified file 'CpogsPlugin/src/org/workcraft/plugins/cpog/optimisation/FreeVariable.java'
--- CpogsPlugin/src/org/workcraft/plugins/cpog/optimisation/FreeVariable.java	2010-04-13 15:52:01 +0000
+++ CpogsPlugin/src/org/workcraft/plugins/cpog/optimisation/FreeVariable.java	2014-07-11 09:42:10 +0000
@@ -3,7 +3,7 @@
 import org.workcraft.plugins.cpog.optimisation.expressions.BooleanVisitor;
 
 public class FreeVariable implements BooleanVariable, Comparable<FreeVariable> {
-
+	
 	private final String label;
 
 	public FreeVariable(String label) {

=== modified file 'CpogsPlugin/src/org/workcraft/plugins/cpog/serialisation/BooleanFormulaSerialiser.java'
--- CpogsPlugin/src/org/workcraft/plugins/cpog/serialisation/BooleanFormulaSerialiser.java	2010-10-22 14:07:56 +0000
+++ CpogsPlugin/src/org/workcraft/plugins/cpog/serialisation/BooleanFormulaSerialiser.java	2014-07-11 09:42:10 +0000
@@ -22,6 +22,8 @@
 package org.workcraft.plugins.cpog.serialisation;
 
 import org.w3c.dom.Element;
+import org.workcraft.dom.hierarchy.NamespaceHelper;
+import org.workcraft.dom.references.HierarchicalUniqueNameReferenceManager;
 import org.workcraft.exceptions.SerialisationException;
 import org.workcraft.plugins.cpog.optimisation.BooleanFormula;
 import org.workcraft.plugins.cpog.optimisation.BooleanVariable;
@@ -31,6 +33,7 @@
 import org.workcraft.serialisation.ReferenceProducer;
 import org.workcraft.serialisation.xml.CustomXMLSerialiser;
 import org.workcraft.serialisation.xml.NodeSerialiser;
+import org.workcraft.util.Identifier;
 
 public abstract class BooleanFormulaSerialiser implements CustomXMLSerialiser
 {
@@ -52,10 +55,21 @@
 		}
 		
 		PrinterSuite printers = new FormulaToString.PrinterSuite();
-		printers.vars = new FormulaToString.VariablePrinter(){
+		printers.vars = new FormulaToString.VariablePrinter() {
 			@Override
 			public Void visit(BooleanVariable node) {
-				append("var_"+internalReferences.getReference(node));
+				
+				String ref = internalReferences.getReference(node);
+				// use full path to a flattened name
+				String flat = NamespaceHelper.getFlatName(ref);
+				
+				// old style naming, if number is used as an ID for a contact
+				if (Identifier.isNumber(ref)) {
+					append("var_"+ref);
+				} else
+					append(flat);
+				
+				
 				return null;
 			}
 		};

=== modified file 'CpogsPlugin/src/org/workcraft/plugins/cpog/serialisation/BooleanFunctionDeserialiser.java'
--- CpogsPlugin/src/org/workcraft/plugins/cpog/serialisation/BooleanFunctionDeserialiser.java	2010-10-22 14:07:56 +0000
+++ CpogsPlugin/src/org/workcraft/plugins/cpog/serialisation/BooleanFunctionDeserialiser.java	2014-07-11 09:42:10 +0000
@@ -22,6 +22,7 @@
 package org.workcraft.plugins.cpog.serialisation;
 
 import org.w3c.dom.Element;
+import org.workcraft.dom.hierarchy.NamespaceHelper;
 import org.workcraft.exceptions.DeserialisationException;
 import org.workcraft.plugins.cpog.optimisation.BooleanFormula;
 import org.workcraft.plugins.cpog.optimisation.BooleanVariable;
@@ -43,7 +44,30 @@
 			this.internalReferenceResolver = internalReferenceResolver;
 		}
 
-		public BooleanVariable eval(String ref){ return (BooleanVariable) internalReferenceResolver.getObject(ref.substring("var_".length())); }
+		public BooleanVariable eval(String ref){
+			
+			if (ref.startsWith("var_")) {
+				ref = ref.substring("var_".length());
+				
+				BooleanVariable bv = (BooleanVariable)internalReferenceResolver.getObject(ref);
+				if (bv!=null) 
+					return bv;
+				
+//				for (Object o: internalReferenceResolver.getObjects()) {
+//					if (o instanceof BooleanVariable) {
+//						bv = (BooleanVariable)o;
+//						if (bv.getLegacyID().equals(Integer.valueOf(ref)))
+//							return bv;
+//						
+//						return null;
+//					}
+//				}
+			}
+			
+			String hier = NamespaceHelper.flatToHierarchicalName(ref);
+			
+			return (BooleanVariable) internalReferenceResolver.getObject(hier); 
+		}
 	}
 
 	@Override

=== added directory 'CpogsPlugin/src/org/workcraft/plugins/cpog/tasks'
=== added file 'CpogsPlugin/src/org/workcraft/plugins/cpog/tasks/ProgrammerChainResult.java'
--- CpogsPlugin/src/org/workcraft/plugins/cpog/tasks/ProgrammerChainResult.java	1970-01-01 00:00:00 +0000
+++ CpogsPlugin/src/org/workcraft/plugins/cpog/tasks/ProgrammerChainResult.java	2014-07-11 09:42:10 +0000
@@ -0,0 +1,56 @@
+package org.workcraft.plugins.cpog.tasks;
+
+import org.workcraft.plugins.cpog.EncoderSettings;
+import org.workcraft.plugins.shared.tasks.ExternalProcessResult;
+import org.workcraft.tasks.Result;
+
+public class ProgrammerChainResult {
+	private Result<? extends ExternalProcessResult> punfResult;
+	private Result<? extends ExternalProcessResult> encoderResult;
+	private Result<? extends Object> exportResult; 
+	private EncoderSettings encoderSettings;
+	private String message;
+		
+	public ProgrammerChainResult(Result<? extends Object> exportResult,
+				Result<? extends ExternalProcessResult> punfResult,
+			Result<? extends ExternalProcessResult> encoderResult,
+			EncoderSettings encoderSettings) {
+		this.punfResult = punfResult;
+		this.encoderResult = encoderResult;
+		this.exportResult = exportResult;
+		this.encoderSettings = encoderSettings;
+	}
+	
+	public ProgrammerChainResult(Result<? extends Object> exportResult,
+			Result<? extends ExternalProcessResult> punfResult,
+		Result<? extends ExternalProcessResult> encoderResult,
+		EncoderSettings encoderSettings, String message) {
+		
+		this.punfResult = punfResult;
+		this.encoderResult = encoderResult;
+		this.exportResult = exportResult;
+		this.encoderSettings = encoderSettings;
+		
+		this.message = message;
+	}
+	
+	public EncoderSettings getProgrammerSettings() {
+		return encoderSettings;
+	}
+
+	public Result<? extends ExternalProcessResult> getPunfResult() {
+		return punfResult;
+	}
+	
+	public Result<? extends ExternalProcessResult> getEncoderResult() {
+		return encoderResult;
+	}
+	
+	public String getMessage() {
+		return message;
+	}
+
+	public Result<? extends Object> getExportResult() {
+		return exportResult;
+	}
+}

=== added file 'CpogsPlugin/src/org/workcraft/plugins/cpog/tasks/ProgrammerChainTask.java'
--- CpogsPlugin/src/org/workcraft/plugins/cpog/tasks/ProgrammerChainTask.java	1970-01-01 00:00:00 +0000
+++ CpogsPlugin/src/org/workcraft/plugins/cpog/tasks/ProgrammerChainTask.java	2014-07-11 09:42:10 +0000
@@ -0,0 +1,103 @@
+package org.workcraft.plugins.cpog.tasks;
+
+import java.io.File;
+
+import org.workcraft.Framework;
+import org.workcraft.dom.visual.VisualModel;
+import org.workcraft.interop.Exporter;
+import org.workcraft.plugins.cpog.EncoderSettings;
+import org.workcraft.plugins.shared.tasks.ExternalProcessResult;
+import org.workcraft.serialisation.Format;
+import org.workcraft.tasks.ProgressMonitor;
+import org.workcraft.tasks.Result;
+import org.workcraft.tasks.SubtaskMonitor;
+import org.workcraft.tasks.Task;
+import org.workcraft.tasks.Result.Outcome;
+import org.workcraft.util.Export;
+import org.workcraft.util.WorkspaceUtils;
+import org.workcraft.util.Export.ExportTask;
+import org.workcraft.workspace.WorkspaceEntry;
+
+public class ProgrammerChainTask implements Task<ProgrammerChainResult> {
+
+	private final WorkspaceEntry we;
+	private final EncoderSettings settings;
+	private final Framework framework;
+	private VisualModel model;
+
+	public ProgrammerChainTask(WorkspaceEntry we, EncoderSettings settings, Framework framework) {
+		this.we = we;
+		this.settings = settings;
+		this.framework = framework;
+		this.model = null;
+	}
+	
+	@Override
+	public Result<? extends ProgrammerChainResult> run(ProgressMonitor<? super ProgrammerChainResult> monitor) {
+		try {
+			if(model == null) {
+				model = WorkspaceUtils.getAs(getWorkspaceEntry(), VisualModel.class);
+			}
+			Exporter exporter = Export.chooseBestExporter(framework.getPluginManager(), model, Format.DOT);
+			if (exporter == null) {
+				throw new RuntimeException ("Exporter not available: model class " + model.getClass().getName() + " to format STG.");
+			}
+			File netFile = File.createTempFile("net", exporter.getExtenstion());
+			ExportTask exportTask;
+			exportTask = new ExportTask(exporter, model, netFile.getCanonicalPath());
+			SubtaskMonitor<Object> mon = new SubtaskMonitor<Object>(monitor);
+			Result<? extends Object> exportResult = framework.getTaskManager().execute(exportTask, "Exporting .g", mon);
+			if (exportResult.getOutcome() != Outcome.FINISHED) {
+				netFile.delete();
+				if (exportResult.getOutcome() == Outcome.CANCELLED)
+					return new Result<ProgrammerChainResult>(Outcome.CANCELLED);
+				return new Result<ProgrammerChainResult>(Outcome.FAILED, new ProgrammerChainResult(exportResult, null, null, settings));
+			}
+			monitor.progressUpdate(0.33);
+			
+//			File mciFile = File.createTempFile("unfolding", ".mci");
+//			PunfTask punfTask = new PunfTask(netFile.getCanonicalPath(), mciFile.getCanonicalPath());
+//			Result<? extends ExternalProcessResult> punfResult = framework.getTaskManager().execute(punfTask, "Unfolding .g", mon);
+//			netFile.delete();
+//			
+//			if (punfResult.getOutcome() != Outcome.FINISHED) {
+//				mciFile.delete();
+//				if (punfResult.getOutcome() == Outcome.CANCELLED)
+//					return new Result<ProgrammerChainResult>(Outcome.CANCELLED);
+//				return new Result<ProgrammerChainResult>(Outcome.FAILED, new ProgrammerChainResult(exportResult, punfResult, null, settings));
+//			}
+//
+//			monitor.progressUpdate(0.66);
+//
+//			ProgrammerTask programmerTask = new ProgrammerTask(null, mciFile.getCanonicalPath());
+//			Result<? extends ExternalProcessResult> encoderResult = framework.getTaskManager().execute(programmerTask, "Running scenco model-checking", mon);
+//			mciFile.delete();
+//			
+//			if (encoderResult.getOutcome() != Outcome.FINISHED) {
+//				if (encoderResult.getOutcome() == Outcome.CANCELLED)
+//					return new Result<ProgrammerChainResult>(Outcome.CANCELLED);
+//				return new Result<ProgrammerChainResult>(Outcome.FAILED, new ProgrammerChainResult(exportResult, punfResult, encoderResult, settings ));
+//			}
+		
+			monitor.progressUpdate(1.0);
+			
+//			return new Result<ProgrammerChainResult>(Outcome.FINISHED, new ProgrammerChainResult(exportResult, punfResult, encoderResult, settings));
+			return new Result<ProgrammerChainResult>(Outcome.FINISHED, null);
+		} catch (Throwable e) {
+			return new Result<ProgrammerChainResult>(e);
+		}
+	}
+	
+	public EncoderSettings getSettings() {
+		return settings;
+	}
+
+	public Framework getFramework() {
+		return framework;
+	}
+
+	public WorkspaceEntry getWorkspaceEntry() {
+		return we;
+	}
+
+}

=== added file 'CpogsPlugin/src/org/workcraft/plugins/cpog/tasks/ProgrammerTask.java'
--- CpogsPlugin/src/org/workcraft/plugins/cpog/tasks/ProgrammerTask.java	1970-01-01 00:00:00 +0000
+++ CpogsPlugin/src/org/workcraft/plugins/cpog/tasks/ProgrammerTask.java	2014-07-11 09:42:10 +0000
@@ -0,0 +1,73 @@
+package org.workcraft.plugins.cpog.tasks;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Map;
+
+import org.workcraft.plugins.cpog.ProgrammerUtilitySettings;
+import org.workcraft.plugins.shared.tasks.ExternalProcessResult;
+import org.workcraft.plugins.shared.tasks.ExternalProcessTask;
+import org.workcraft.tasks.ProgressMonitor;
+import org.workcraft.tasks.Result;
+import org.workcraft.tasks.Task;
+import org.workcraft.tasks.Result.Outcome;
+import org.workcraft.util.FileUtils;
+
+public class ProgrammerTask implements Task<ExternalProcessResult> {
+	private String[] args;
+	private String inputFileName;
+			
+	public ProgrammerTask(String[] args, String inputFileName) {
+		this.args = args;
+		this.inputFileName = inputFileName;
+	}
+	
+	@Override
+	public Result<? extends ExternalProcessResult> run(ProgressMonitor<? super ExternalProcessResult> monitor) {
+		
+		ArrayList<String> command = new ArrayList<String>();
+		command.add(ProgrammerUtilitySettings.getCommand());
+		
+		for (String arg : ProgrammerUtilitySettings.getExtraArgs().split(" "))
+			if (!arg.isEmpty())
+				command.add(arg);
+		
+		for (String arg : args)
+			command.add(arg);
+		
+		command.add(inputFileName);
+
+		File workingDir = FileUtils.createTempDirectory("scenco");
+
+		ExternalProcessTask externalProcessTask = new ExternalProcessTask(command, workingDir);
+		
+		Result<? extends ExternalProcessResult> res = externalProcessTask.run(monitor);
+		
+		if(res.getOutcome() == Outcome.CANCELLED)
+			return res;
+		
+		Map<String, byte[]> outputFiles = new HashMap<String, byte[]>();
+		
+		try {
+			File mci = new File(workingDir, "scenco.mci");
+			if(mci.exists())
+				outputFiles.put("scenco.mci", FileUtils.readAllBytes(mci));
+			
+			File g = new File(workingDir, "scenco.g");
+			if(g.exists())
+				outputFiles.put("scenco.g", FileUtils.readAllBytes(g));
+		} catch (IOException e) {
+			return new Result<ExternalProcessResult>(e);
+		}
+		
+		ExternalProcessResult retVal = res.getReturnValue();
+		ExternalProcessResult result = new ExternalProcessResult(retVal.getReturnCode(), retVal.getOutput(), retVal.getErrors(), outputFiles);
+		
+		if (retVal.getReturnCode() < 2)
+			return Result.finished(result);
+		else
+			return Result.failed(result);
+	}
+}

=== added file 'CpogsPlugin/src/org/workcraft/plugins/cpog/tools/EncoderPreferencesTool.java'
--- CpogsPlugin/src/org/workcraft/plugins/cpog/tools/EncoderPreferencesTool.java	1970-01-01 00:00:00 +0000
+++ CpogsPlugin/src/org/workcraft/plugins/cpog/tools/EncoderPreferencesTool.java	2014-07-11 09:42:10 +0000
@@ -0,0 +1,65 @@
+package org.workcraft.plugins.cpog.tools;
+
+import java.io.File;
+
+import org.workcraft.Framework;
+import org.workcraft.Tool;
+import org.workcraft.plugins.cpog.CpogProgrammer;
+import org.workcraft.plugins.cpog.EncoderSettings;
+import org.workcraft.plugins.cpog.EncoderSettings.generationMode;
+import org.workcraft.plugins.cpog.EncoderSettingsSerialiser;
+import org.workcraft.plugins.cpog.ProgrammerChainResultHandler;
+import org.workcraft.plugins.cpog.VisualCPOG;
+import org.workcraft.plugins.cpog.gui.EncoderConfigurationDialog;
+import org.workcraft.plugins.cpog.tasks.ProgrammerChainTask;
+import org.workcraft.plugins.shared.presets.PresetManager;
+import org.workcraft.util.GUI;
+import org.workcraft.workspace.WorkspaceEntry;
+
+public class EncoderPreferencesTool implements Tool {
+	
+	private final Framework framework;
+	private static boolean settingPresent = false;
+	private EncoderSettings settings;
+	private EncoderConfigurationDialog dialog;
+	PresetManager<EncoderSettings> pmgr;
+
+	public EncoderPreferencesTool(Framework framework) {
+		this.framework = framework;
+	}
+
+	@Override
+	public boolean isApplicableTo(WorkspaceEntry we) {
+		if (we.getModelEntry() == null) return false;		
+		if (we.getModelEntry().getVisualModel() instanceof VisualCPOG) return true;		
+		return false;
+	}
+
+	@Override
+	public String getSection() {
+		return "Encoding";
+	}
+
+	@Override
+	public String getDisplayName() {
+		return "Cpog Programmer";
+	}
+
+	@Override
+	public void run(WorkspaceEntry we) {
+		if(settingPresent == false){
+			settingPresent = true;
+			settings = new EncoderSettings(10,generationMode.OPTIMAL_ENCODING,false, false);
+			pmgr = new PresetManager<EncoderSettings>(new File("config/cpog_presets.xml"), new EncoderSettingsSerialiser());
+			dialog = new EncoderConfigurationDialog(framework.getMainWindow(), pmgr, settings, we);
+		}
+		
+		GUI.centerAndSizeToParent(dialog, framework.getMainWindow());
+		dialog.setVisible(true);
+		// TASK INSERTION
+		/*final ProgrammerChainTask programmerTask = new ProgrammerChainTask(we, dialog.getSettings(), framework);
+		framework.getTaskManager().queue(programmerTask, "Scenco tool chain", 
+				new ProgrammerChainResultHandler(programmerTask));*/
+	}
+
+}

=== modified file 'DfsPlugin/src/org/workcraft/plugins/dfs/Dfs.java'
--- DfsPlugin/src/org/workcraft/plugins/dfs/Dfs.java	2013-11-11 18:10:34 +0000
+++ DfsPlugin/src/org/workcraft/plugins/dfs/Dfs.java	2014-07-11 09:42:10 +0000
@@ -26,10 +26,12 @@
 import org.workcraft.dom.Connection;
 import org.workcraft.dom.Container;
 import org.workcraft.dom.Node;
+import org.workcraft.dom.hierarchy.NamespaceProvider;
 import org.workcraft.dom.math.AbstractMathModel;
 import org.workcraft.dom.math.MathConnection;
+import org.workcraft.dom.math.MathGroup;
 import org.workcraft.dom.math.MathNode;
-import org.workcraft.dom.references.UniqueNameReferenceManager;
+import org.workcraft.dom.references.HierarchicalUniqueNameReferenceManager;
 import org.workcraft.gui.propertyeditor.Properties;
 import org.workcraft.serialisation.References;
 import org.workcraft.util.Func;
@@ -40,11 +42,12 @@
 public class Dfs extends AbstractMathModel {
 
 	public Dfs() {
-		this(null, null);
+		this(new MathGroup(), null);
 	}
 	
 	public Dfs(Container root, References refs) {
-		super(root, new UniqueNameReferenceManager(refs, new Func<Node, String>() {
+		
+		super(root, new HierarchicalUniqueNameReferenceManager(refs, new Func<Node, String>() {
 			@Override
 			public String eval(Node arg) {
 				if ((arg instanceof Logic) || (arg instanceof CounterflowLogic))
@@ -82,11 +85,4 @@
 		return null;
 	}
 
-	public String getName(Node node) {
-		return ((UniqueNameReferenceManager)getReferenceManager()).getName(node);
-	}
-
-	public void setName(Node node, String name) {
-		((UniqueNameReferenceManager)getReferenceManager()).setName(node, name);
-	}
 }

=== modified file 'DfsPlugin/src/org/workcraft/plugins/dfs/stg/StgGenerator.java'
--- DfsPlugin/src/org/workcraft/plugins/dfs/stg/StgGenerator.java	2014-01-29 19:00:22 +0000
+++ DfsPlugin/src/org/workcraft/plugins/dfs/stg/StgGenerator.java	2014-07-11 09:42:10 +0000
@@ -10,6 +10,7 @@
 import java.util.Set;
 
 import org.workcraft.dom.Connection;
+import org.workcraft.dom.Container;
 import org.workcraft.dom.Node;
 import org.workcraft.dom.visual.Movable;
 import org.workcraft.dom.visual.Positioning;
@@ -197,7 +198,10 @@
 		SignalTransition.Type type = SignalTransition.Type.INTERNAL;
 		ColorGenerator tokenColorGenerator = createColorGenerator(dfs.getPreset(l).size() == 0);
 		
-		VisualPlace C0 = stg.createPlace(nameC + name + name0);
+		
+		Container curContainer = null;
+		
+		VisualPlace C0 = stg.createPlace(nameC + name + name0, curContainer);
 		C0.setLabel(labelC + name + label0);
 		C0.setLabelPositioning(Positioning.BOTTOM);
 		if (!l.getReferencedLogic().isComputed()) {
@@ -208,7 +212,7 @@
 		setPosition(C0, x + 2.0, y + 1.0);
 		nodes.add(C0);
 
-		VisualPlace C1 = stg.createPlace(nameC + name + name1);
+		VisualPlace C1 = stg.createPlace(nameC + name + name1, curContainer);
 		C1.setLabel(labelC + name + label1);
 		C1.setLabelPositioning(Positioning.TOP);
 		if (l.getReferencedLogic().isComputed()) {
@@ -235,7 +239,7 @@
 		double dy = 0.0;
 		for (Node n: preset) {
 			if (CR == null || l.getReferencedLogic().isEarlyEvaluation()) { 
-				CR = stg.createSignalTransition(nameC + name, type, SignalTransition.Direction.PLUS);
+				CR = stg.createSignalTransition(nameC + name, type, SignalTransition.Direction.PLUS, curContainer);
 				CR.setTokenColorGenerator(tokenColorGenerator);
 				createConsumingArc(C0, CR, false);
 				createProducingArc(CR, C1, true);
@@ -244,7 +248,7 @@
 			}
 			CRs.put(n, CR);
 			if (CF == null) { 
-				CF = stg.createSignalTransition(nameC + name, type, SignalTransition.Direction.MINUS);
+				CF = stg.createSignalTransition(nameC + name, type, SignalTransition.Direction.MINUS, curContainer);
 				createConsumingArc(C1, CF, false);
 				createProducingArc(CF, C0, false);
 				setPosition(CF, x - 2.0, y - 1.0 - dy);
@@ -305,8 +309,9 @@
 			type = SignalTransition.Type.OUTPUT;
 		}
 		ColorGenerator tokenColorGenerator = createColorGenerator(dfs.getPreset(r).size() == 0);
+		Container curContainer = null;
 
-		VisualPlace M0 = stg.createPlace(nameM + name + name0);
+		VisualPlace M0 = stg.createPlace(nameM + name + name0, curContainer);
 		M0.setLabel(labelM + name + label0);
 		M0.setLabelPositioning(Positioning.BOTTOM);
 		if (!r.getReferencedRegister().isMarked()) {
@@ -317,7 +322,7 @@
 		setPosition(M0, x + 2.0, y + 1.0);
 		nodes.add(M0);
 	
-		VisualPlace M1 = stg.createPlace(nameM + name + name1);
+		VisualPlace M1 = stg.createPlace(nameM + name + name1, curContainer);
 		M1.setLabel(labelM + name + label1);
 		M1.setLabelPositioning(Positioning.TOP);
 		if (r.getReferencedRegister().isMarked()) {
@@ -327,14 +332,14 @@
 		setPosition(M1, x + 2.0, y - 1.0);
 		nodes.add(M1);
 	
-		VisualSignalTransition MR = stg.createSignalTransition(nameM + name, type, SignalTransition.Direction.PLUS);
+		VisualSignalTransition MR = stg.createSignalTransition(nameM + name, type, SignalTransition.Direction.PLUS, curContainer);
 		MR.setTokenColorGenerator(tokenColorGenerator);
 		createConsumingArc(M0, MR, false);
 		createProducingArc(MR, M1, true);
 		setPosition(MR, x - 2.0, y + 1.0);
 		nodes.add(MR);
 	
-		VisualSignalTransition MF = stg.createSignalTransition(nameM + name, type, SignalTransition.Direction.MINUS);
+		VisualSignalTransition MF = stg.createSignalTransition(nameM + name, type, SignalTransition.Direction.MINUS, curContainer);
 		createConsumingArc(M1, MF, false);
 		createProducingArc(MF, M0, false);
 		setPosition(MF, x - 2.0, y - 1.0);
@@ -423,7 +428,9 @@
 		ColorGenerator presetTokenColorGenerator = createColorGenerator(dfs.getPreset(l).size() == 0);
 		ColorGenerator postsetTokenColorGenerator = createColorGenerator(dfs.getPostset(l).size() == 0);
 		
-		VisualPlace fwC0 = stg.createPlace(nameFwC + name + name0);
+		Container curContainer = null;
+		
+		VisualPlace fwC0 = stg.createPlace(nameFwC + name + name0, curContainer);
 		fwC0.setLabel(labelFwC + name + label0);
 		fwC0.setLabelPositioning(Positioning.BOTTOM);
 		if (!l.getReferencedCounterflowLogic().isForwardComputed()) {
@@ -434,7 +441,7 @@
 		setPosition(fwC0, x + 2.0, y - 2.0);
 		nodes.add(fwC0);
 
-		VisualPlace fwC1 = stg.createPlace(nameFwC + name + name1);
+		VisualPlace fwC1 = stg.createPlace(nameFwC + name + name1, curContainer);
 		fwC1.setLabel(labelFwC + name + label1);
 		fwC1.setLabelPositioning(Positioning.TOP);
 		if (l.getReferencedCounterflowLogic().isForwardComputed()) {
@@ -459,7 +466,7 @@
 			double dy = 0.0;
 			for (Node n: preset) {
 				if (fwCR == null || l.getReferencedCounterflowLogic().isForwardEarlyEvaluation()) { 
-					fwCR = stg.createSignalTransition(nameFwC + name, type, SignalTransition.Direction.PLUS);
+					fwCR = stg.createSignalTransition(nameFwC + name, type, SignalTransition.Direction.PLUS, curContainer);
 					fwCR.setTokenColorGenerator(presetTokenColorGenerator);
 					createConsumingArc(fwC0, fwCR, false);
 					createProducingArc(fwCR, fwC1, true);
@@ -468,7 +475,7 @@
 				}
 				fwCRs.put(n, fwCR);
 				if (fwCF == null) { 
-					fwCF = stg.createSignalTransition(nameFwC + name, type, SignalTransition.Direction.MINUS);
+					fwCF = stg.createSignalTransition(nameFwC + name, type, SignalTransition.Direction.MINUS, curContainer);
 					createConsumingArc(fwC1, fwCF, false);
 					createProducingArc(fwCF, fwC0, false);
 					stg.connect(fwC1, fwCF);
@@ -481,7 +488,7 @@
 			}
 		}
 		
-		VisualPlace bwC0 = stg.createPlace(nameBwC + name + name0);
+		VisualPlace bwC0 = stg.createPlace(nameBwC + name + name0, curContainer);
 		bwC0.setLabel(labelBwC + name + label0);
 		bwC0.setLabelPositioning(Positioning.BOTTOM);
 		if (!l.getReferencedCounterflowLogic().isBackwardComputed()) {
@@ -492,7 +499,7 @@
 		setPosition(bwC0, x + 2.0, y + 4.0);
 		nodes.add(bwC0);
 
-		VisualPlace bwC1 = stg.createPlace(nameBwC + name + name1);
+		VisualPlace bwC1 = stg.createPlace(nameBwC + name + name1, curContainer);
 		bwC1.setLabel(labelBwC + name + label1);
 		bwC1.setLabelPositioning(Positioning.TOP);
 		if (l.getReferencedCounterflowLogic().isBackwardComputed()) {
@@ -517,7 +524,7 @@
 			double dy = 0.0;
 			for (Node n: postset) {
 				if (bwCR == null || l.getReferencedCounterflowLogic().isBackwardEarlyEvaluation()) { 
-					bwCR = stg.createSignalTransition(nameBwC + name, type, SignalTransition.Direction.PLUS);
+					bwCR = stg.createSignalTransition(nameBwC + name, type, SignalTransition.Direction.PLUS, curContainer);
 					bwCR.setTokenColorGenerator(postsetTokenColorGenerator);
 					stg.connect(bwC0, bwCR);
 					stg.connect(bwCR, bwC1);
@@ -526,7 +533,7 @@
 				}
 				bwCRs.put(n, bwCR);
 				if (bwCF == null) { 
-					bwCF = stg.createSignalTransition(nameBwC + name, type, SignalTransition.Direction.MINUS);
+					bwCF = stg.createSignalTransition(nameBwC + name, type, SignalTransition.Direction.MINUS, curContainer);
 					stg.connect(bwC1, bwCF);
 					stg.connect(bwCF, bwC0);
 					setPosition(bwCF, x - 2.0, y + 2.0 - dy);
@@ -585,7 +592,9 @@
 		ColorGenerator presetTokenColorGenerator = createColorGenerator(dfs.getPreset(r).size() == 0);
 		ColorGenerator postsetTokenColorGenerator = createColorGenerator(dfs.getPostset(r).size() == 0);
 
-		VisualPlace orM0 = stg.createPlace(nameOrM + name + name0);
+		Container curContainer = null;
+		
+		VisualPlace orM0 = stg.createPlace(nameOrM + name + name0, curContainer);
 		orM0.setLabel(labelOrM + name + label0);
 		orM0.setLabelPositioning(Positioning.BOTTOM);
 		if (!r.getReferencedCounterflowRegister().isOrMarked()) {
@@ -596,7 +605,7 @@
 		setPosition(orM0, x + 2.0, y - 2.0);
 		nodes.add(orM0);
 
-		VisualPlace orM1 = stg.createPlace(nameOrM + name + name1);
+		VisualPlace orM1 = stg.createPlace(nameOrM + name + name1, curContainer);
 		orM1.setLabel(labelOrM + name + label1);
 		orM1.setLabelPositioning(Positioning.TOP);
 		if (r.getReferencedCounterflowRegister().isOrMarked()) {
@@ -607,33 +616,33 @@
 		setPosition(orM1, x + 2.0, y - 4.0);
 		nodes.add(orM1);
 
-		VisualSignalTransition orMRfw = stg.createSignalTransition(nameOrM + name, type, SignalTransition.Direction.PLUS);
+		VisualSignalTransition orMRfw = stg.createSignalTransition(nameOrM + name, type, SignalTransition.Direction.PLUS, curContainer);
 		orMRfw.setTokenColorGenerator(presetTokenColorGenerator);
 		createConsumingArc(orM0, orMRfw, false);
 		createProducingArc(orMRfw, orM1, true);
 		setPosition(orMRfw, x - 2.0, y - 2.5);
 		nodes.add(orMRfw);
 
-		VisualSignalTransition orMRbw = stg.createSignalTransition(nameOrM + name, type, SignalTransition.Direction.PLUS);
+		VisualSignalTransition orMRbw = stg.createSignalTransition(nameOrM + name, type, SignalTransition.Direction.PLUS, curContainer);
 		orMRbw.setTokenColorGenerator(postsetTokenColorGenerator);
 		createConsumingArc(orM0, orMRbw, false);
 		createProducingArc(orMRbw, orM1, true);
 		setPosition(orMRbw, x - 2.0, y - 1.5);
 		nodes.add(orMRbw);
 
-		VisualSignalTransition orMFfw = stg.createSignalTransition(nameOrM + name, type, SignalTransition.Direction.MINUS);
+		VisualSignalTransition orMFfw = stg.createSignalTransition(nameOrM + name, type, SignalTransition.Direction.MINUS, curContainer);
 		createConsumingArc(orM1, orMFfw, false);
 		createProducingArc(orMFfw, orM0, false);
 		setPosition(orMFfw, x - 2.0, y - 4.5);
 		nodes.add(orMFfw);
 
-		VisualSignalTransition orMFbw = stg.createSignalTransition(nameOrM + name, type, SignalTransition.Direction.MINUS);
+		VisualSignalTransition orMFbw = stg.createSignalTransition(nameOrM + name, type, SignalTransition.Direction.MINUS, curContainer);
 		createConsumingArc(orM1, orMFbw, false);
 		createProducingArc(orMFbw, orM0, false);
 		setPosition(orMFbw, x - 2.0, y - 3.5);
 		nodes.add(orMFbw);
 
-		VisualPlace andM0 = stg.createPlace(nameAndM + name + name0);
+		VisualPlace andM0 = stg.createPlace(nameAndM + name + name0, curContainer);
 		andM0.setLabel(labelAndM + name + label0);
 		andM0.setLabelPositioning(Positioning.BOTTOM);
 		if (!r.getReferencedCounterflowRegister().isAndMarked()) {
@@ -644,7 +653,7 @@
 		setPosition(andM0, x + 2.0, y + 4.0);
 		nodes.add(andM0);
 
-		VisualPlace andM1 = stg.createPlace(nameAndM + name + name1);
+		VisualPlace andM1 = stg.createPlace(nameAndM + name + name1, curContainer);
 		andM1.setLabel(labelAndM + name + label1);
 		andM1.setLabelPositioning(Positioning.TOP);
 		if (r.getReferencedCounterflowRegister().isAndMarked()) {
@@ -655,13 +664,13 @@
 		setPosition(andM1, x + 2.0, y + 2.0);
 		nodes.add(andM1);
 
-		VisualSignalTransition andMR = stg.createSignalTransition(nameAndM + name, type, SignalTransition.Direction.PLUS);
+		VisualSignalTransition andMR = stg.createSignalTransition(nameAndM + name, type, SignalTransition.Direction.PLUS, curContainer);
 		createConsumingArc(andM0, andMR, false);
 		createProducingArc(andMR, andM1, false);
 		setPosition(andMR, x - 2.0, y + 4.0);
 		nodes.add(andMR);
 
-		VisualSignalTransition andMF = stg.createSignalTransition(nameAndM + name, type, SignalTransition.Direction.MINUS);
+		VisualSignalTransition andMF = stg.createSignalTransition(nameAndM + name, type, SignalTransition.Direction.MINUS, curContainer);
 		createConsumingArc(andM1, andMF, false);
 		createProducingArc(andMF, andM0, false);
 		setPosition(andMF, x - 2.0, y + 2.0);
@@ -749,8 +758,9 @@
 			type = SignalTransition.Type.OUTPUT;
 		}
 		ColorGenerator tokenColorGenerator = createColorGenerator(dfs.getPreset(r).size() == 0);
+		Container curContainer = null;
 
-		VisualPlace M0 = stg.createPlace(nameM + name + name0);
+		VisualPlace M0 = stg.createPlace(nameM + name + name0, curContainer);
 		M0.setLabel(labelM + name + label0);
 		M0.setLabelPositioning(Positioning.BOTTOM);
 		if (!r.getReferencedBinaryRegister().isTrueMarked() && !r.getReferencedBinaryRegister().isFalseMarked()) {
@@ -761,7 +771,7 @@
 		setPosition(M0, x - 4.0, y + 1.0);
 		nodes.add(M0);
 
-		VisualPlace M1 = stg.createPlace(nameM + name + name1);
+		VisualPlace M1 = stg.createPlace(nameM + name + name1, curContainer);
 		M1.setLabel(labelM + name + label1);
 		M1.setLabelPositioning(Positioning.TOP);
 		if (r.getReferencedBinaryRegister().isTrueMarked() || r.getReferencedBinaryRegister().isFalseMarked()) {
@@ -772,7 +782,7 @@
 		setPosition(M1, x - 4.0, y - 1.0);
 		nodes.add(M1);
 
-		VisualPlace tM0 = stg.createPlace(nameTrueM + name + name0);
+		VisualPlace tM0 = stg.createPlace(nameTrueM + name + name0, curContainer);
 		tM0.setLabel(labelTrueM + name + label0);
 		tM0.setLabelPositioning(Positioning.BOTTOM);
 		if (!r.getReferencedBinaryRegister().isTrueMarked()) {
@@ -783,7 +793,7 @@
 		setPosition(tM0, x + 4.0, y - 2.0);
 		nodes.add(tM0);
 
-		VisualPlace tM1 = stg.createPlace(nameTrueM + name + name1);
+		VisualPlace tM1 = stg.createPlace(nameTrueM + name + name1, curContainer);
 		tM1.setLabel(labelTrueM + name + label1);
 		tM1.setLabelPositioning(Positioning.TOP);
 		if (r.getReferencedBinaryRegister().isTrueMarked()) {
@@ -805,7 +815,7 @@
 		double dy = 0.0;
 		for (Node n: preset) {
 			if (tMR == null || orSync) { 
-				tMR = stg.createSignalTransition(nameTrueM + name, type, SignalTransition.Direction.PLUS);
+				tMR = stg.createSignalTransition(nameTrueM + name, type, SignalTransition.Direction.PLUS, curContainer);
 				tMR.setTokenColorGenerator(tokenColorGenerator);
 				createConsumingArc(tM0, tMR, false);
 				createProducingArc(tMR, tM1, true);
@@ -817,7 +827,7 @@
 			tMRs.put(n, tMR);
 			dy += 1.0;
 		}
-		VisualSignalTransition tMF = stg.createSignalTransition(nameTrueM + name, type, SignalTransition.Direction.MINUS);
+		VisualSignalTransition tMF = stg.createSignalTransition(nameTrueM + name, type, SignalTransition.Direction.MINUS, curContainer);
 		createConsumingArc(tM1, tMF, false);
 		createProducingArc(tMF, tM0, false);
 		createConsumingArc(M1, tMF, false);
@@ -825,7 +835,8 @@
 		setPosition(tMF, x, y - 4.0 - dy);
 		nodes.add(tMF);
 
-		VisualPlace fM0 = stg.createPlace(nameFalseM + name + name0);
+		
+		VisualPlace fM0 = stg.createPlace(nameFalseM + name + name0, curContainer);
 		fM0.setLabel(labelFalseM + name + label0);
 		fM0.setLabelPositioning(Positioning.BOTTOM);
 		if (!r.getReferencedBinaryRegister().isFalseMarked()) {
@@ -836,7 +847,7 @@
 		setPosition(fM0, x + 4.0, y + 4.0);
 		nodes.add(fM0);
 
-		VisualPlace fM1 = stg.createPlace(nameFalseM + name + name1);
+		VisualPlace fM1 = stg.createPlace(nameFalseM + name + name1, curContainer);
 		fM1.setLabel(labelFalseM + name + label1);
 		fM1.setLabelPositioning(Positioning.TOP);
 		if (r.getReferencedBinaryRegister().isFalseMarked()) {
@@ -852,7 +863,7 @@
 		dy = 0.0;
 		for (Node n: preset) {
 			if (fMR == null || andSync) { 
-				fMR = stg.createSignalTransition(nameFalseM + name, type, SignalTransition.Direction.PLUS);
+				fMR = stg.createSignalTransition(nameFalseM + name, type, SignalTransition.Direction.PLUS, curContainer);
 				fMR.setTokenColorGenerator(tokenColorGenerator);
 				createConsumingArc(fM0, fMR, false);
 				createProducingArc(fMR, fM1, true);
@@ -864,7 +875,7 @@
 			fMRs.put(n, fMR);
 			dy += 1.0;
 		}
-		VisualSignalTransition fMF = stg.createSignalTransition(nameFalseM + name, type, SignalTransition.Direction.MINUS);
+		VisualSignalTransition fMF = stg.createSignalTransition(nameFalseM + name, type, SignalTransition.Direction.MINUS, curContainer);
 		createConsumingArc(fM1, fMF, false);
 		createProducingArc(fMF, fM0, false);
 		createConsumingArc(M1, fMF, false);

=== modified file 'GraphPlugin/src/org/workcraft/plugins/graph/ToolsProvider.java'
--- GraphPlugin/src/org/workcraft/plugins/graph/ToolsProvider.java	2013-11-08 13:40:13 +0000
+++ GraphPlugin/src/org/workcraft/plugins/graph/ToolsProvider.java	2014-07-11 09:42:10 +0000
@@ -2,12 +2,14 @@
 
 import java.util.ArrayList;
 
+import org.workcraft.dom.math.PageNode;
 import org.workcraft.gui.graph.tools.CommentGeneratorTool;
 import org.workcraft.gui.graph.tools.ConnectionTool;
 import org.workcraft.gui.graph.tools.CustomToolsProvider;
 import org.workcraft.gui.graph.tools.DefaultNodeGenerator;
 import org.workcraft.gui.graph.tools.GraphEditorTool;
 import org.workcraft.gui.graph.tools.NodeGeneratorTool;
+import org.workcraft.gui.graph.tools.PageGeneratorTool;
 import org.workcraft.gui.graph.tools.SelectionTool;
 
 public class ToolsProvider implements CustomToolsProvider {
@@ -18,6 +20,7 @@
 		
 		result.add(new SelectionTool());
 		result.add(new CommentGeneratorTool());
+		result.add(new PageGeneratorTool(new DefaultNodeGenerator(PageNode.class)));
 		result.add(new ConnectionTool(true, false));
 		result.add(new NodeGeneratorTool(new DefaultNodeGenerator(Vertex.class)));
 		return result;

=== modified file 'GraphPlugin/src/org/workcraft/plugins/graph/VisualGraph.java'
--- GraphPlugin/src/org/workcraft/plugins/graph/VisualGraph.java	2013-11-08 13:40:13 +0000
+++ GraphPlugin/src/org/workcraft/plugins/graph/VisualGraph.java	2014-07-11 09:42:10 +0000
@@ -65,6 +65,7 @@
 	public void connect(Node first, Node second) throws InvalidConnectionException {
 		validateConnection(first, second);
 
+		
 		VisualComponent c1 = (VisualComponent) first;
 		VisualComponent c2 = (VisualComponent) second;
 

=== modified file 'MpsatPlugin/src/org/workcraft/plugins/mpsat/MpsatResultParser.java'
--- MpsatPlugin/src/org/workcraft/plugins/mpsat/MpsatResultParser.java	2010-10-06 15:51:01 +0000
+++ MpsatPlugin/src/org/workcraft/plugins/mpsat/MpsatResultParser.java	2014-07-11 09:42:10 +0000
@@ -8,6 +8,7 @@
 import java.util.regex.Pattern;
 
 import org.workcraft.Trace;
+import org.workcraft.dom.hierarchy.NamespaceHelper;
 import org.workcraft.plugins.shared.tasks.ExternalProcessResult;
 
 public class MpsatResultParser {
@@ -34,6 +35,8 @@
 				String[] ss = mpsatTrace.split(",");
 
 				for (String k: ss) {
+					k=k.replace(NamespaceHelper.flatNameSeparator, NamespaceHelper.hierarchySeparator);
+					
 					if (k.charAt(1) == '.')
 						trace.add(k.substring(2).trim());
 					else

=== modified file 'PetriNetPlugin/src/org/workcraft/plugins/petri/PetriNet.java'
--- PetriNetPlugin/src/org/workcraft/plugins/petri/PetriNet.java	2013-10-07 09:51:12 +0000
+++ PetriNetPlugin/src/org/workcraft/plugins/petri/PetriNet.java	2014-07-11 09:42:10 +0000
@@ -29,10 +29,12 @@
 import org.workcraft.dom.Connection;
 import org.workcraft.dom.Container;
 import org.workcraft.dom.Node;
+import org.workcraft.dom.hierarchy.NamespaceProvider;
 import org.workcraft.dom.math.AbstractMathModel;
 import org.workcraft.dom.math.MathConnection;
+import org.workcraft.dom.math.MathGroup;
 import org.workcraft.dom.math.MathNode;
-import org.workcraft.dom.references.UniqueNameReferenceManager;
+import org.workcraft.dom.references.HierarchicalUniqueNameReferenceManager;
 import org.workcraft.exceptions.InvalidConnectionException;
 import org.workcraft.exceptions.ModelValidationException;
 import org.workcraft.gui.propertyeditor.Properties;
@@ -44,7 +46,7 @@
 public class PetriNet extends AbstractMathModel implements PetriNetModel {
 
 	public PetriNet() {
-		this(null, null);
+		this(new MathGroup(), null);
 	}
 
 	public PetriNet(Container root) {
@@ -61,7 +63,7 @@
 	}
 
 	public PetriNet(Container root, References refs, final Func<Node, String> nodePrefixFunc) {
-		super(root, new UniqueNameReferenceManager(refs, new Func<Node, String>() {
+		super(root, new HierarchicalUniqueNameReferenceManager(refs, new Func<Node, String>() {
 			@Override
 			public String eval(Node arg) {
 				String result = nodePrefixFunc.eval(arg);
@@ -79,15 +81,9 @@
 				return result;
 			}
 		}));
-	}
-
-	public void setName(Node node, String name) {
-		((UniqueNameReferenceManager)getReferenceManager()).setName(node, name);
-	}
-
-	public String getName(Node node) {
-		return ((UniqueNameReferenceManager)getReferenceManager()).getName(node);
-	}
+		
+	}
+
 
 	final public Place createPlace(String name) {
 		Place newPlace = new Place();
@@ -125,7 +121,6 @@
 	final public Collection<Transition> getTransitions() {
 		return Hierarchy.getDescendantsOfType(getRoot(), Transition.class);
 	}
-
 	
 	public boolean isUnfireEnabled(Transition t) {
 		return isUnfireEnabled (this, t);