Load and Store Controller finished

src/TypeAdapter/ColorAdapter.java

@@ -6,6 +6,7 @@ import java.lang.reflect.Type;
 import com.google.gson.JsonDeserializationContext;
 import com.google.gson.JsonDeserializer;
 import com.google.gson.JsonElement;
+import com.google.gson.JsonObject;
 import com.google.gson.JsonParseException;
 import com.google.gson.JsonPrimitive;
 import com.google.gson.JsonSerializationContext;
@@ -16,13 +17,20 @@ public class ColorAdapter implements JsonSerializer<Color>, JsonDeserializer<Col
 	@Override
 	public Color deserialize(JsonElement arg0, Type arg1, JsonDeserializationContext arg2) throws JsonParseException {
 		// TODO Auto-generated method stub
-		return new Color(arg0.getAsInt());
+		JsonObject object = arg0.getAsJsonObject();
+		return new Color(object.get("R").getAsInt(), object.get("G").getAsInt(), object.get("B").getAsInt());
+		
 	}
 
 	@Override
 	public JsonElement serialize(Color arg0, Type arg1, JsonSerializationContext arg2) {
 		// TODO Auto-generated method stub
-		return new JsonPrimitive(Integer.toHexString(arg0.getRGB()));
+		JsonObject object = new JsonObject();
+		object.add("R", new JsonPrimitive(arg0.getRed()));
+		object.add("G", new JsonPrimitive(arg0.getGreen()));
+		object.add("B", new JsonPrimitive(arg0.getBlue()));
+		
+		return object;
 	}
 
 }

src/TypeAdapter/PositionAdapter.java

@@ -26,7 +26,7 @@ public class PositionAdapter implements JsonSerializer<Position>, JsonDeserializ
 			String arg = arg0.getAsString();
 			int mid = arg.indexOf(':');
 			int x = Integer.parseInt(arg.substring(0, mid));
-			int y = Integer.parseInt(arg.substring(mid + 1, arg.length() - 1));
+			int y = Integer.parseInt(arg.substring(mid + 1, arg.length()));
 			return new Position(x, y);
 
 		} catch (Exception e) {

src/classes/HolonElement.java

@@ -45,9 +45,9 @@ public class HolonElement {
 	 * Energy at each point of the graph with 100 predefined points. At the
 	 * beginning, it starts with all values at energy
 	 */
-	private float[] energyAt = new float[100];
+	private float[] energyAt;
 	// Points on the UnitGraph
-	LinkedList<Point> graphPoints = new LinkedList<>();
+	LinkedList<Point> graphPoints;
 
 	/**
 	 * Create a new HolonElement with a user-defined name, amount of the same
@@ -67,6 +67,7 @@ public class HolonElement {
 		setActive(true);
 		setSign(energy);
 		setEnergyAt(energy);
+		setGraphPoints(new LinkedList<>());
 		setId(IdCounterElem.nextId());
 	}
 
@@ -86,6 +87,7 @@ public class HolonElement {
 		for (int i = 0; i < energyAt.length; i++) {
 			energyAt[i] = element.getEnergyAt()[i];
 		}
+		setGraphPoints(new LinkedList<>());
 		for (Point p : element.getGraphPoints()) {
 			this.graphPoints.add(new Point((int) p.getX(), (int) p.getY()));
 		}
@@ -110,6 +112,7 @@ public class HolonElement {
 	 *            the value
 	 */
 	public void setEnergyAt(float energy) {
+		this.energyAt = new float[100];
 		for (int i = 0; i < energyAt.length; i++) {
 			this.energyAt[i] = energy;
 		}

src/classes/HolonSwitch.java

@@ -62,6 +62,7 @@ public class HolonSwitch extends AbstractCpsObject {
 		setAutoState(true);
 		setActiveAt(true);
 		setManualMode(false);
+		setGraphPoints(new LinkedList<>());
 	}
 
 	/**
@@ -75,9 +76,11 @@ public class HolonSwitch extends AbstractCpsObject {
 		super.setName(obj.getName());
 		setManualState(((HolonSwitch)obj).getActiveManual());
 		setAutoState(true);
+		setActiveAt(true);
 		for (int i = 0; i < activeAt.length; i++) {
 			activeAt[i] = ((HolonSwitch)obj).getActiveAt()[i];
 		}
+		setGraphPoints(new LinkedList<>());
 		for (Point p :((HolonSwitch)obj).getGraphPoints()) {
 			this.graphPoints.add(new Point((int)p.getX(), (int)p.getY()));
 		}
@@ -213,6 +216,7 @@ public class HolonSwitch extends AbstractCpsObject {
 	 *            the default value
 	 */
 	public void setActiveAt(boolean active) {
+		activeAt = new boolean[100];
 		for (int i = 0; i < activeAt.length; i++) {
 			this.activeAt[i] = active;
 		}

src/ui/controller/Control.java

@@ -59,12 +59,13 @@ public class Control {
 		this.canvasController = new CanvasController(model, multiPurposeController);
 		this.globalController = new GlobalController(model);
 		this.storeController = new StoreController(model);
-		this.loadController = new LoadController(model, categoryController, canvasController, objectController, multiPurposeController);
+		this.nodeController = new NodeController(model, canvasController, multiPurposeController);
+		this.loadController = new LoadController(model, categoryController, canvasController, objectController, nodeController, multiPurposeController);
 		this.simulationManager = new SimulationManager(model);
 		this.autoSaveController = new AutoSaveController(model);
 		this.consoleController = new ConsoleController(model);
 		this.statsController = new StatsController(model);
-		this.nodeController = new NodeController(model, canvasController, multiPurposeController);
+
 		autoPath = System.getProperty("user.home") + "/HolonGUI/Autosave/";
 		File dest = new File(autoPath);
 		// deleteDirectory(dest);

src/ui/controller/LoadController.java

@@ -8,6 +8,7 @@ import java.util.ArrayList;
 import java.util.Collections;
 import java.util.HashMap;
 import java.util.Iterator;
+import java.util.LinkedList;
 import java.util.List;
 import java.util.stream.Collector;
 import java.util.stream.Collectors;
@@ -28,6 +29,7 @@ import TypeAdapter.PositionAdapter;
 import classes.Category;
 import classes.CpsEdge;
 import classes.CpsNode;
+import classes.CpsUpperNode;
 import classes.AbstractCpsObject;
 import classes.HolonElement;
 import classes.HolonObject;
@@ -50,18 +52,10 @@ public class LoadController {
 		COMPLETE, PARTIAL
 	}
 
-	public enum TYPE {
-		CATEGORY, CANVAS
-	}
-
 	public enum EDGETYPE {
 		CANVAS, CONNECTION, NODE, OLD
 	}
 
-	public enum NUMTYPE {
-		CATEGORY, OBJECT, ELEMENT, EDGE, CONNECTION, NODEEDGE, OLDEDGE, UNITGRAPH
-	}
-
 	public enum GRAPHTYPE {
 		SWITCH, ELEMENT
 	}
@@ -70,10 +64,10 @@ public class LoadController {
 	private CategoryController cgC;
 	private CanvasController cvsC;
 	private ObjectController objC;
+	private NodeController uppC;
 	private MultiPurposeController mpC;
 	private Gson gson;
-	// uninitialized arrays only init when needed
-	ArrayList<String> jCat, jObj, jEle, jEdge, jConn, jNodeEdge, jOldEdge, jUnitGraph;
+	private JsonParser parser;
 
 	/**
 	 * Constructor.
@@ -89,11 +83,13 @@ public class LoadController {
 	 * @param mp
 	 *            MultiPurposeController
 	 */
-	public LoadController(Model model, CategoryController cg, CanvasController cvs, ObjectController obj, MultiPurposeController mp) {
+	public LoadController(Model model, CategoryController cg, CanvasController cvs, ObjectController obj,
+			NodeController uppC, MultiPurposeController mp) {
 		this.model = model;
 		this.cgC = cg;
 		this.cvsC = cvs;
 		this.objC = obj;
+		this.uppC = uppC;
 		this.mpC = mp;
 		initGson();
 	}
@@ -108,281 +104,300 @@ public class LoadController {
 	 */
 	public void readJson(String path) throws IOException {
 
-		JsonParser parser = new JsonParser();
 		JsonObject json = (JsonObject) parser.parse(new FileReader(path));
-
 		// get all keys via stream
-		List<String> keys = json.entrySet().stream().map(i -> i.getKey())
+		List<String> keys = getKeys(json);
+		List<String> edges = keys.stream().filter(key -> key.contains("EDGE"))
 				.collect(Collectors.toCollection(ArrayList::new));
+
+		HashMap<Integer, AbstractCpsObject> objDispatch = new HashMap<>();
+		HashMap<Integer, HolonElement> eleDispatch = new HashMap<>();
+
 		initialize(keys, json);
-		distribute(keys, json, parser);
-
-//		for (Object key : keys) {
-//			if (key.equals("CG"))
-//				readCategory((JSONArray) json.get((String) key));
-//			else if (key.equals("ID"))
-//				IdCounter.setCounter(Integer.parseInt(json.get(key.toString()).toString()));
-//			// else if (key.equals("SIZEX"))
-//			// global.setCanvasX(Integer.parseInt(json.get(key.toString()).toString()));
-//			// else if (key.equals("SIZEY"))
-//			// global.setCanvasY(Integer.parseInt(json.get(key.toString()).toString()));
-//			else if (key.toString().contains("CGO") || key.toString().contains("CVSO"))
-//				obj.add(key.toString());
-//			else if (key.toString().contains("CGE") || key.toString().contains("CVSE"))
-//				ele.add(key.toString());
-//			else if (key.toString().contains("EDGE"))
-//				edge.add(key.toString());
-//			else if (key.toString().contains("CGGP") || key.toString().contains("CVSGP"))
-//				gp.add(key.toString());
-//
-//		}
-//
-//		dispatch(obj, json);
-//		dispatch(ele, json);
-//		dispatch(edge, json);
-//		dispatch(gp, json);
+		distribute(keys, json, objDispatch, eleDispatch);
+		distEdges(edges, json, objDispatch);
+
+	}
+
+	private void distEdges(List<String> edges, JsonObject json, HashMap<Integer, AbstractCpsObject> objDispatch) {
+		// TODO Auto-generated method stub
 
+		for (String edge : edges) {
+			if (edge.contains("CVSEDGE"))
+				loadEdge(EDGETYPE.CANVAS, json.get(edge), objDispatch);
+			if (edge.contains("CONNEDGE"))
+				loadEdge(EDGETYPE.CONNECTION, json.get(edge), objDispatch);
+			if (edge.contains("NODE"))
+				loadEdge(EDGETYPE.NODE, json.get(edge), objDispatch);
+			if (edge.contains("OLD"))
+				loadEdge(EDGETYPE.OLD, json.get(edge), objDispatch);
+		}
 	}
 
-	private void distribute(List<String> keys, JsonObject json, JsonParser parser) {
+	private void distribute(List<String> keys, JsonObject json, HashMap<Integer, AbstractCpsObject> objDispatch,
+			HashMap<Integer, HolonElement> eleDispatch) {
 		// TODO Auto-generated method stub
 		for (String key : keys) {
-			if(key.contains("CATEGORY"))
+			if (key.contains("CATEGORY"))
 				loadCategory(json.get(key));
-			if(key.contains("CGOBJECT"))
-				loadCategoryObject(TYPE.CATEGORY, json.get(key).getAsJsonObject());
+			if (key.contains("CGOBJECT"))
+				loadCategoryObject(json.get(key));
+			if (key.contains("CGELEMENT"))
+				loadCategoryElements(json.get(key));
+			if (key.contains("CVSOBJECT"))
+				loadCanvasObject(json.get(key), objDispatch);
+			if (key.contains("CVSELEMENT"))
+				loadCanvasElements(json.get(key), objDispatch, eleDispatch);
+			if (key.contains("SWUNITGRAPH"))
+				loadUnitGraph(GRAPHTYPE.SWITCH, json.get(key), objDispatch, null);
+			if (key.contains("ELEUNITGRAPH"))
+				loadUnitGraph(GRAPHTYPE.ELEMENT, json.get(key), null, eleDispatch);
 		}
 
-
 	}
 
-	private void loadCategoryObject(TYPE type, JsonObject jsonElement) {
+	private void loadUnitGraph(GRAPHTYPE type, JsonElement jsonElement, HashMap<Integer, AbstractCpsObject> objDispatch,
+			HashMap<Integer, HolonElement> eleDispatch) {
 		// TODO Auto-generated method stub
-		AbstractCpsObject temp = gson.fromJson(jsonElement., AbstractCpsObject.class);
-		cgC.addObject(mpC.searchCat(temp.getSav()), temp);
-	}
 
-	private void loadCategory(JsonElement jsonElement) {
-		// TODO Auto-generated method stub
-		cgC.addCategory(new Category(jsonElement.getAsString()));
-	}
+		JsonObject object = jsonElement.getAsJsonObject();
+		List<String> keys = getKeys(object);
+		String p = null;
+		int mid, x, y = 0;
 
-	private void initialize(List<String> keys, JsonObject json) {
+		LinkedList<Point> graphpoint = new LinkedList<>();
+		int sav = 0;
 
-		switch (MODE.valueOf(json.get("MODE").getAsString())) {
-		case COMPLETE:
-			model.setCgIdx(new HashMap<String, Integer>());
-			model.setCategories(new ArrayList<Category>());
-			model.setCvsObjIdx(new HashMap<Integer, Integer>());
-			model.setObjectsOnCanvas(new ArrayList<AbstractCpsObject>());
-			model.setEdgesOnCanvas(new ArrayList<CpsEdge>());
-			model.setCanvasX(json.get("CANVAS_SIZE_X").getAsInt());
-			model.setCanvasX(json.get("CANVAS_SIZE_Y").getAsInt());
+		for (String k : keys) {
+			if (!k.equals("ID")) {
+				p = object.get(k).getAsString();
+				mid = p.indexOf(':');
+				x = Integer.parseInt(p.substring(0, mid));
+				y = Integer.parseInt(p.substring(mid + 1, p.length()));
+				graphpoint.add(new Point(x, y));
+			} else
+				sav = object.get(k).getAsInt();
+
+		}
+
+		switch (type) {
+		case SWITCH:
+			HolonSwitch sw = (HolonSwitch) objDispatch.get(sav);
+			sw.setGraphPoints(graphpoint);
 			break;
-		case PARTIAL:
-			model.setCvsObjIdx(new HashMap<Integer, Integer>());
-			model.setObjectsOnCanvas(new ArrayList<AbstractCpsObject>());
-			model.setEdgesOnCanvas(new ArrayList<CpsEdge>());
+		case ELEMENT:
+			HolonElement ele = eleDispatch.get(sav);
+			ele.setGraphPoints(graphpoint);
 			break;
-
 		default:
 			break;
 		}
-		IdCounter.setCounter(json.get("IDCOUNTER").getAsInt());
 	}
 
-	/**
-	 * dispatch the Keys into the right processing.
-	 * 
-	 * @param input
-	 *            input
-	 * @param json
-	 *            Json
-	 */
-	public void dispatch(ArrayList<String> input, JSONObject json) {
-
-		for (String str : input) {
-			if (str.contains("CGO")) {
-				readCategoryObject((JSONArray) json.get(str));
-			} else if (str.contains("CVSO")) {
-				readCanvasObject((JSONArray) json.get(str));
-			} else if (str.contains("CGE") || str.contains("CVSE")) {
-				readElement((JSONArray) json.get(str));
-			} else if (str.contains("EDGE")) {
-				readEdge((JSONArray) json.get(str));
-			} else if (str.contains("CGGP") || str.contains("CVSGP")) {
-				readElementGraph((JSONArray) json.get(str));
-			}
+	private void loadEdge(EDGETYPE type, JsonElement jsonElement, HashMap<Integer, AbstractCpsObject> objDispatch) {
+		// TODO Auto-generated method stub
+		JsonObject object = jsonElement.getAsJsonObject();
+		CpsEdge temp = gson.fromJson(object.get("properties"), CpsEdge.class);
+		initCpsEdge(temp);
+		temp.setA(objDispatch.get(object.get("A").getAsInt()));
+		System.out.println(temp.getA());
+		temp.setB(objDispatch.get(object.get("B").getAsInt()));
+
+		int sav = 0;
+
+		switch (type) {
+		case CANVAS:
+			model.getEdgesOnCanvas().add(temp);
+			temp.getA().getConnections().remove(temp);
+			temp.getB().getConnections().remove(temp);
+			break;
+		case CONNECTION:
+			if (!uppC.lookforDuplicates(temp.getA(), temp.getB(), temp.getA().getConnections()))
+				temp.getA().getConnections().add(temp);
+			if (!uppC.lookforDuplicates(temp.getA(), temp.getB(), temp.getB().getConnections()))
+				temp.getB().getConnections().add(temp);
+			break;
+		case NODE:
+			sav = object.get("ID").getAsInt();
+			((CpsUpperNode) objDispatch.get(sav)).getNodeEdges().add(temp);
+			break;
+		case OLD:
+			sav = object.get("ID").getAsInt();
+			((CpsUpperNode) objDispatch.get(sav)).getOldEdges().add(temp);
+			break;
+		default:
+			break;
 		}
 
 	}
 
 	/**
-	 * Read all Categories from the JSON file.
 	 * 
-	 * @param arr
-	 *            JSONArray
+	 * @param jsonElement
+	 * @param objDispatch
+	 * @param eleDispatch
 	 */
-	public void readCategory(JSONArray arr) {
-
-		Iterator<Object> i = arr.iterator();
+	private void loadCanvasElements(JsonElement jsonElement, HashMap<Integer, AbstractCpsObject> objDispatch,
+			HashMap<Integer, HolonElement> eleDispatch) {
+		// TODO Auto-generated method stub
 
-		while (i.hasNext()) {
-			cgC.addNewCategory(next(i));
-		}
-	}
+		JsonObject object = jsonElement.getAsJsonObject();
+		HolonElement temp = gson.fromJson(object.get("properties"), HolonElement.class);
+		initElements(temp);
 
-	/**
-	 * Read all Objects in Category from the JSON File.
-	 * 
-	 * @param arr
-	 *            JSON Array
-	 */
-	public void readCategoryObject(JSONArray arr) {
-		Iterator<Object> i = arr.iterator();
+		int stored = object.get("ID").getAsInt();
 
-		String type = next(i);
-
-		if (type.equals("HolonObject")) {
-			cgC.addNewHolonObject(mpC.searchCat(next(i)), next(i), new ArrayList<HolonElement>(), next(i));
-		} else if (type.equals("HolonTransformer")) {
-			cgC.addNewHolonTransformer(mpC.searchCat(next(i)), next(i), next(i));
-		} else if (type.equals("HolonSwitch")) {
-			cgC.addNewHolonSwitch(mpC.searchCat(next(i)), next(i), next(i));
-		}
+		HolonObject temp2 = (HolonObject) objDispatch.get(stored);
 
+		objC.addElement(temp2, temp);
+		eleDispatch.put(temp.getId(), temp);
 	}
 
 	/**
-	 * Read all Objects in Canvas from JSON File.
 	 * 
-	 * @param arr
-	 *            JSON Array
+	 * @param jsonElement
+	 * @param objDispatch
 	 */
-	public void readCanvasObject(JSONArray arr) {
-		Iterator<Object> i = arr.iterator();
-		AbstractCpsObject cps = null;
-
-		String type = next(i);
-
-		if (type.equals("HolonObject")) {
-			cps = new HolonObject(next(i));
-		} else if (type.equals("HolonTransformer")) {
-			cps = new HolonTransformer(next(i));
-		} else if (type.equals("HolonSwitch")) {
-			cps = new HolonSwitch(next(i));
-		} else if (type.equals("CpsNode")) {
-			cps = new CpsNode(next(i));
+	private void loadCanvasObject(JsonElement jsonElement, HashMap<Integer, AbstractCpsObject> objDispatch) {
+		// TODO Auto-generated method stub
+		AbstractCpsObject temp = gson.fromJson(jsonElement.getAsJsonObject(), AbstractCpsObject.class);
+		initObjects(temp);
+
+		if (temp.getSav().equals("CVS")) {
+			cvsC.addObject(temp);
+		} else {
+			CpsUpperNode temp2 = (CpsUpperNode) objDispatch.get(Integer.parseInt(temp.getSav()));
+			uppC.addObjectInUpperNode(temp, temp2);
 		}
 
-		cps.setName(next(i));
-		cps.setID(Integer.parseInt(next(i)));
-		cps.setImage(next(i));
-		cps.setPosition(Integer.parseInt(next(i)), Integer.parseInt(next(i)));
+		objDispatch.put(temp.getID(), temp);
 
-		cvsC.addNewObject(cps);
 	}
 
 	/**
-	 * Read all Elements in Category and Canvas from JSON File.
 	 * 
-	 * @param arr
-	 *            JSON Array
+	 * @param jsonElement
 	 */
-	public void readElement(JSONArray arr) {
-		Iterator<Object> i = arr.iterator();
-
-		String sav = next(i);
-		String obj = next(i);
-
-		HolonElement ele = new HolonElement(next(i), Integer.parseInt(next(i)), Float.parseFloat(next(i)));
-
-		if (sav.equals("CVS")) {
-			ele.setActive(convert(Integer.parseInt(next(i))));
-			objC.addElementIntoCanvasObject((HolonObject) mpC.searchByID(Integer.parseInt(obj)), ele);
-		} else
-			objC.addElementIntoCategoryObject(sav, obj, ele);
+	private void loadCategoryElements(JsonElement jsonElement) {
+		// TODO Auto-generated method stub
+		HolonElement temp = gson.fromJson(jsonElement.getAsJsonObject().get("properties").getAsJsonObject(),
+				HolonElement.class);
+		initElements(temp);
+		objC.addElementIntoCategoryObject(temp.getSav(), temp.getObj(), temp);
 	}
 
 	/**
-	 * Read.
 	 * 
-	 * @param arr
-	 *            JSON Array
+	 * @param jsonElement
 	 */
-	public void readEdge(JSONArray arr) {
-		Iterator<Object> i = arr.iterator();
+	private void loadCategoryObject(JsonElement jsonElement) {
+		// TODO Auto-generated method stub
+		AbstractCpsObject temp = gson.fromJson(jsonElement.getAsJsonObject(), AbstractCpsObject.class);
+		initObjects(temp);
 
-		CpsEdge edge = new CpsEdge(mpC.searchByID(Integer.parseInt(next(i))),
-				mpC.searchByID(Integer.parseInt(next(i))));
-		edge.setCapacity(Float.parseFloat(next(i)));
-		edge.setFlow(Float.parseFloat(next(i)));
+		cgC.addObject(mpC.searchCat(temp.getSav()), temp);
+	}
 
-		cvsC.addEdgeOnCanvas(edge);
+	private void loadCategory(JsonElement jsonElement) {
+		// TODO Auto-generated method stub
+		cgC.addCategory(new Category(jsonElement.getAsString()));
 	}
 
 	/**
-	 * Read the Element Graph.
 	 * 
-	 * @param arr
-	 *            JSON Array
+	 * @param keys
+	 * @param json
 	 */
-	public void readElementGraph(JSONArray arr) {
-		Iterator<Object> i = arr.iterator();
+	private void initialize(List<String> keys, JsonObject json) {
 
-		String sav = next(i);
-		HolonElement ele;
+		switch (MODE.valueOf(json.get("MODE").getAsString())) {
+		case COMPLETE:
+			model.setCgIdx(new HashMap<String, Integer>());
+			model.setCategories(new ArrayList<Category>());
+			model.setCvsObjIdx(new HashMap<Integer, Integer>());
+			model.setObjectsOnCanvas(new ArrayList<AbstractCpsObject>());
+			model.setEdgesOnCanvas(new ArrayList<CpsEdge>());
+			model.setCanvasX(json.get("CANVAS_SIZE_X").getAsInt());
+			model.setCanvasX(json.get("CANVAS_SIZE_Y").getAsInt());
+			break;
+		case PARTIAL:
+			model.setCvsObjIdx(new HashMap<Integer, Integer>());
+			model.setObjectsOnCanvas(new ArrayList<AbstractCpsObject>());
+			model.setEdgesOnCanvas(new ArrayList<CpsEdge>());
+			break;
 
-		if (sav.equals("CVS")) {
-			ele = mpC.searchEle((HolonObject) mpC.searchByID(Integer.parseInt(next(i))), next(i));
-			while (i.hasNext())
-				ele.getGraphPoints().add(new Point(Integer.parseInt(next(i)), Integer.parseInt(next(i))));
-		} else {
-			ele = mpC.searchEle((HolonObject) mpC.searchCatObj(mpC.searchCat(sav), next(i)), next(i));
-			while (i.hasNext())
-				ele.getGraphPoints().add(new Point(Integer.parseInt(next(i)), Integer.parseInt(next(i))));
+		default:
+			break;
 		}
-
-	}
-
-	/**
-	 * Get the Next Element from an Iterator.
-	 * 
-	 * @param i
-	 *            Iterator
-	 * @return next Element from the Iterator
-	 */
-	public String next(Iterator<Object> i) {
-		return i.next().toString();
+		IdCounter.setCounter(json.get("IDCOUNTER").getAsInt());
 	}
 
-	/**
-	 * converting saved Integers into Booleans.
-	 * 
-	 * @param x
-	 *            integer
-	 * @return boolean
-	 */
-	public boolean convert(int x) {
-		return x == 1 ? true : false;
-	}
-	
 	/**
 	 * Initialize the Gson with wanted parameters
 	 */
 	private void initGson() {
 		// TODO Auto-generated method stub
 		GsonBuilder builder = new GsonBuilder();
-		builder.excludeFieldsWithoutExposeAnnotation().serializeNulls().setPrettyPrinting();
+		builder.serializeNulls();
 		builder.registerTypeAdapter(AbstractCpsObject.class, new AbstractCpsObjectAdapter());
 		builder.registerTypeAdapter(Position.class, new PositionAdapter());
 		builder.registerTypeAdapter(Color.class, new ColorAdapter());
 		// use the builder and make a instance of the Gson
 		this.gson = builder.create();
+		this.parser = new JsonParser();
 	}
-	
-	private void initArrays() {
-		
+
+	/**
+	 * Init new Arrays which havent been serialized along the object
+	 * 
+	 * @param obj
+	 */
+	private void initObjects(AbstractCpsObject obj) {
+
+		obj.setConnections(new ArrayList<>());
+		obj.setTags(new ArrayList<>());
+		obj.setPseudoTags(new ArrayList<>());
+
+		if (obj instanceof HolonObject) {
+			((HolonObject) obj).setElements(new ArrayList<HolonElement>());
+			((HolonObject) obj).setEleIdx(new HashMap<String, Integer>());
+
+			((HolonObject) obj).setTrackingProd(new float[100]);
+			((HolonObject) obj).setTrackingCons(new float[100]);
+		}
+
+		if (obj instanceof HolonSwitch) {
+			((HolonSwitch) obj).setActiveAt(true);
+			((HolonSwitch) obj).setGraphPoints(new LinkedList<>());
+		}
+
+		if (obj instanceof CpsUpperNode) {
+			((CpsUpperNode) obj).setNodes(new ArrayList<AbstractCpsObject>());
+			((CpsUpperNode) obj).setNodeEdges(new ArrayList<CpsEdge>());
+			((CpsUpperNode) obj).setOldEdges(new ArrayList<CpsEdge>());
+			((CpsUpperNode) obj).setNodesIdx(new HashMap<Integer, Integer>());
+		}
+	}
+
+	/**
+	 * 
+	 * @param ele
+	 */
+	private void initElements(HolonElement ele) {
+
+		ele.setEnergyAt(ele.getEnergy());
+		ele.setGraphPoints(new LinkedList<>());
+	}
+
+	private void initCpsEdge(CpsEdge edge) {
+		edge.setTags(new ArrayList<>());
+		edge.setPseudoTag(new ArrayList<>());
+		edge.setA(null);
+		edge.setB(null);
+	}
+
+	private List<String> getKeys(JsonObject json) {
+		return json.entrySet().stream().map(i -> i.getKey()).collect(Collectors.toCollection(ArrayList::new));
 	}
 
 }

src/ui/controller/NodeController.java

@@ -314,7 +314,7 @@ public class NodeController {
 	 * @param list
 	 * @return
 	 */
-	private boolean lookforDuplicates(AbstractCpsObject a, AbstractCpsObject b, ArrayList<CpsEdge> list) {
+	public boolean lookforDuplicates(AbstractCpsObject a, AbstractCpsObject b, ArrayList<CpsEdge> list) {
 		for (CpsEdge cpsEdge : list) {
 			if ((a.equals(cpsEdge.getA()) && b.equals(cpsEdge.getB()))
 					|| (b.equals(cpsEdge.getA()) && a.equals(cpsEdge.getB())))
@@ -476,7 +476,7 @@ public class NodeController {
 	 * @param upperNode
 	 */
 	public void addObjectInUpperNode(AbstractCpsObject object, CpsUpperNode upperNode) {
-		object.setSav("UPPER" + upperNode.getID());
+		object.setSav(""+upperNode.getID());
 		upperNode.getNodesIdx().put(object.getID(), upperNode.getNodes().size());
 		upperNode.getNodes().add(object);
 	}

src/ui/controller/StoreController.java

@@ -165,8 +165,7 @@ public class StoreController {
 			file.add(key, new JsonPrimitive(cat.getName()));
 
 			for (AbstractCpsObject obj : cat.getObjects()) {
-				file.add("CGOBJECT" + getNumerator(NUMTYPE.OBJECT),
-						new JsonPrimitive(gson.toJson(obj, AbstractCpsObject.class)));
+				file.add("CGOBJECT" + getNumerator(NUMTYPE.OBJECT), gson.toJsonTree(obj, AbstractCpsObject.class));
 				if (obj instanceof HolonObject)
 					elementsToJson(TYPE.CATEGORY, gson, file, obj);
 			}
@@ -183,8 +182,6 @@ public class StoreController {
 		Queue<AbstractCpsObject> queue = new Queue<>();
 		AbstractCpsObject u = null;
 
-		edgeToJson(EDGETYPE.CANVAS, gson, file, 0, model.getEdgesOnCanvas());
-
 		for (AbstractCpsObject cps : model.getObjectsOnCanvas()) {
 			queue.enqueue(cps);
 		}
@@ -197,25 +194,24 @@ public class StoreController {
 				e.printStackTrace();
 			}
 			String key = "CVSOBJECT" + getNumerator(NUMTYPE.OBJECT);
-			file.add(key, new JsonPrimitive(gson.toJson(u, AbstractCpsObject.class)));
-			edgeToJson(EDGETYPE.CONNECTION, gson, file, u.getID(), u.getConnections());
+			file.add(key, gson.toJsonTree(u, AbstractCpsObject.class));
+			edgeToJson(EDGETYPE.CONNECTION, file, u.getID(), u.getConnections());
 
 			if (u instanceof HolonObject)
 				elementsToJson(TYPE.CANVAS, gson, file, u);
 			if (u instanceof HolonSwitch)
 				if (((HolonSwitch) u).getGraphPoints().size() != 0)
-					unitgraphToJson(GRAPHTYPE.SWITCH, gson, file, u.getID(), ((HolonSwitch) u).getGraphPoints());
+					unitgraphToJson(GRAPHTYPE.SWITCH, file, u.getID(), ((HolonSwitch) u).getGraphPoints());
 			if (u instanceof CpsUpperNode) {
 				for (AbstractCpsObject adjacent : ((CpsUpperNode) u).getNodes()) {
 					queue.enqueue(adjacent);
 
 				}
-				edgeToJson(EDGETYPE.NODE, gson, file, u.getID(), ((CpsUpperNode) u).getNodeEdges());
-				edgeToJson(EDGETYPE.OLD, gson, file, u.getID(), ((CpsUpperNode) u).getOldEdges());
+				edgeToJson(EDGETYPE.NODE, file, u.getID(), ((CpsUpperNode) u).getNodeEdges());
+				edgeToJson(EDGETYPE.OLD, file, u.getID(), ((CpsUpperNode) u).getOldEdges());
 			}
 		}
-
-		datasetToJson(gson, file);
+		edgeToJson(EDGETYPE.CANVAS, file, 0, model.getEdgesOnCanvas());
 
 	}
 
@@ -232,10 +228,9 @@ public class StoreController {
 		String key = null;
 
 		for (HolonElement ele : ((HolonObject) obj).getElements()) {
-			temp.add("properties", new JsonPrimitive(gson.toJson(ele)));
+			temp.add("properties", gson.toJsonTree(ele));
 			temp.add("ID", new JsonPrimitive(obj.getID()));
-			if (ele.getGraphPoints().size() != 0)
-				unitgraphToJson(GRAPHTYPE.ELEMENT, gson, file, ele.getId(), ele.getGraphPoints());
+
 			switch (type) {
 			case CANVAS:
 				key = "CVSELEMENT" + getNumerator(NUMTYPE.ELEMENT);
@@ -247,6 +242,8 @@ public class StoreController {
 				break;
 			}
 			file.add(key, gson.toJsonTree(temp));
+			if (ele.getGraphPoints().size() != 0)
+				unitgraphToJson(GRAPHTYPE.ELEMENT, file, ele.getId(), ele.getGraphPoints());
 			temp = new JsonObject();
 		}
 
@@ -256,13 +253,13 @@ public class StoreController {
 	 * 
 	 * @param ele
 	 */
-	private void unitgraphToJson(GRAPHTYPE type, Gson gson, JsonObject file, int id, LinkedList<Point> graph) {
+	private void unitgraphToJson(GRAPHTYPE type, JsonObject file, int id, LinkedList<Point> graph) {
 
 		JsonObject temp = new JsonObject();
 		String key = null;
 
 		for (int i = 0; i < graph.size(); i++) {
-			temp.add("" + i, new JsonPrimitive(graph.get(i).getX() + ":" + graph.get(i).getY()));
+			temp.add("" + i, new JsonPrimitive(graph.get(i).x + ":" + graph.get(i).y));
 		}
 
 		switch (type) {
@@ -284,19 +281,18 @@ public class StoreController {
 	/**
 	 * 
 	 * @param type
-	 * @param gson
 	 * @param file
 	 * @param id
 	 * @param arr
 	 */
-	private void edgeToJson(EDGETYPE type, Gson gson, JsonObject file, int id, ArrayList<CpsEdge> arr) {
+	private void edgeToJson(EDGETYPE type, JsonObject file, int id, ArrayList<CpsEdge> arr) {
 		// TODO Auto-generated method stub
 		String k = null;
 		JsonObject temp = new JsonObject();
 
 		for (CpsEdge edge : arr) {
 
-			temp.add("properties", new JsonPrimitive(gson.toJson(edge)));
+			temp.add("properties", gson.toJsonTree(edge));
 			temp.add("A", new JsonPrimitive(edge.getA().getID()));
 			temp.add("B", new JsonPrimitive(edge.getB().getID()));
 
@@ -305,7 +301,7 @@ public class StoreController {
 				k = "CVSEDGE" + getNumerator(NUMTYPE.EDGE);
 				break;
 			case CONNECTION:
-				k = "OBJCONNECTION" + getNumerator(NUMTYPE.CONNECTION);
+				k = "CONNEDGE" + getNumerator(NUMTYPE.CONNECTION);
 				break;
 			case NODE:
 				k = "NODEEDGE" + getNumerator(NUMTYPE.NODEEDGE);
@@ -325,11 +321,6 @@ public class StoreController {
 
 	}
 
-	private void datasetToJson(Gson gson, JsonObject file) {
-		JsonObject temp = new JsonObject();
-
-	}
-
 	/**
 	 * Initialize the Gson with wanted parameters
 	 */