replace copy mechanism

logo now in jar, extracted when needed to temp dir
change version to 3.10

CityDoctorParent/CityDoctorModel/src/main/java/de/hft/stuttgart/citydoctor2/datastructure/BoundarySurface.java

@@ -31,6 +31,8 @@ import de.hft.stuttgart.citydoctor2.check.CheckError;
 import de.hft.stuttgart.citydoctor2.check.CheckId;
 import de.hft.stuttgart.citydoctor2.parser.ParserConfiguration;
 import de.hft.stuttgart.citydoctor2.utils.CityGmlUtils;
+import de.hft.stuttgart.citydoctor2.utils.CopyHandler;
+import de.hft.stuttgart.citydoctor2.utils.Copyable;
 
 /**
  * Representing a boundary surface in CityGML
@@ -45,7 +47,7 @@ public class BoundarySurface extends CityObject {
 	private SurfaceFeatureType featureType;
 	private BoundarySurfaceType type;
 
-	private List<Opening> openings;
+	private List<Opening> openings = new ArrayList<>(2);
 	private CityObject parent;
 
 	private AbstractCityObject gmlObject;
@@ -54,16 +56,10 @@ public class BoundarySurface extends CityObject {
 		this(SurfaceFeatureType.BUILDING, BoundarySurfaceType.UNDEFINED, aco);
 	}
 
-	@Override
-	public CityObject copy() {
-		throw new UnsupportedOperationException("Cannot copy BoundarySurface");
-	}
-
 	public BoundarySurface(SurfaceFeatureType featureType, BoundarySurfaceType type, AbstractCityObject aco) {
 		this.featureType = featureType;
 		this.type = type;
 		gmlObject = aco;
-		openings = new ArrayList<>(2);
 	}
 
 	public void setFeatureType(SurfaceFeatureType featureType) {
@@ -313,4 +309,31 @@ public class BoundarySurface extends CityObject {
 		}
 	}
 
+	@Override
+	public Copyable createCopyInstance() {
+		return new BoundarySurface(gmlObject);
+	}
+	
+	@Override
+	public void collectInstances(CopyHandler handler) {
+		super.collectInstances(handler);
+		for (Opening o : openings) {
+			handler.addInstance(o);
+		}
+		handler.addInstance(parent);
+	}
+	
+	@Override
+	public void fillValues(Copyable original, CopyHandler handler) {
+		super.fillValues(original, handler);
+		BoundarySurface originalBs = (BoundarySurface) original;
+		featureType = originalBs.featureType;
+		type = originalBs.type;
+		for (Opening originalOpening : originalBs.openings) {
+			openings.add(handler.getCopyInstance(originalOpening));
+		}
+		parent = handler.getCopyInstance(originalBs.parent);
+		gmlObject = originalBs.gmlObject;
+	}
+	
 }

CityDoctorParent/CityDoctorModel/src/main/java/de/hft/stuttgart/citydoctor2/datastructure/BridgeObject.java

@@ -18,7 +18,7 @@
  */
 package de.hft.stuttgart.citydoctor2.datastructure;
 
-import java.util.LinkedList;
+import java.util.ArrayList;
 import java.util.List;
 
 import org.citygml4j.factory.GMLGeometryFactory;
@@ -33,6 +33,8 @@ import de.hft.stuttgart.citydoctor2.check.CheckError;
 import de.hft.stuttgart.citydoctor2.check.CheckId;
 import de.hft.stuttgart.citydoctor2.parser.ParserConfiguration;
 import de.hft.stuttgart.citydoctor2.utils.CityGmlUtils;
+import de.hft.stuttgart.citydoctor2.utils.CopyHandler;
+import de.hft.stuttgart.citydoctor2.utils.Copyable;
 
 /**
  * Bridge representation object of CityGML bridge objects
@@ -51,8 +53,8 @@ public class BridgeObject extends CityObject {
 	private AbstractBridge ab;
 	private BridgeType type;
 
-	private List<BoundarySurface> boundarySurfaces = new LinkedList<>();
-
+	private List<BoundarySurface> boundarySurfaces = new ArrayList<>();
+	
 	public BridgeObject(BridgeType type, AbstractBridge ab) {
 		this.ab = ab;
 		this.type = type;
@@ -239,5 +241,27 @@ public class BridgeObject extends CityObject {
 			bs.clearMetaInformation();
 		}
 	}
+	
+	@Override
+	public void collectInstances(CopyHandler handler) {
+		super.collectInstances(handler);
+		for (BoundarySurface bs : boundarySurfaces) {
+			handler.addInstance(bs);
+		}
+	}
+	
+	@Override
+	public void fillValues(Copyable original, CopyHandler handler) {
+		super.fillValues(original, handler);
+		BridgeObject originalBo = (BridgeObject) original;
+		for (BoundarySurface originalBs : originalBo.boundarySurfaces) {
+			boundarySurfaces.add(handler.getCopyInstance(originalBs));
+		}
+	}
+
+	@Override
+	public Copyable createCopyInstance() {
+		return new BridgeObject(type, ab);
+	}
 
 }

CityDoctorParent/CityDoctorModel/src/main/java/de/hft/stuttgart/citydoctor2/datastructure/Building.java

@@ -30,6 +30,8 @@ import de.hft.stuttgart.citydoctor2.check.Check;
 import de.hft.stuttgart.citydoctor2.check.CheckError;
 import de.hft.stuttgart.citydoctor2.check.CheckId;
 import de.hft.stuttgart.citydoctor2.parser.ParserConfiguration;
+import de.hft.stuttgart.citydoctor2.utils.CopyHandler;
+import de.hft.stuttgart.citydoctor2.utils.Copyable;
 
 public class Building extends AbstractBuilding {
 
@@ -41,11 +43,6 @@ public class Building extends AbstractBuilding {
 		return buildingParts;
 	}
 
-	@Override
-	public Building copy() {
-		return (Building) super.copy();
-	}
-	
 	@Override
 	public void reCreateGeometries(GMLGeometryFactory factory, ParserConfiguration config) {
 		super.reCreateGeometries(factory, config);
@@ -150,4 +147,27 @@ public class Building extends AbstractBuilding {
 			part.prepareForChecking();
 		}
 	}
+	
+	@Override
+	public void fillValues(Copyable original, CopyHandler handler) {
+		super.fillValues(original, handler);
+		Building originalBuilding = (Building) original;
+		for (BuildingPart originalBp : originalBuilding.buildingParts) {
+			buildingParts.add(handler.getCopyInstance(originalBp));
+		}
+	}
+	
+	@Override
+	public void collectInstances(CopyHandler handler) {
+		super.collectInstances(handler);
+		for (BuildingPart bp : buildingParts) {
+			handler.addInstance(bp);
+		}
+	}
+
+	@Override
+	public Copyable createCopyInstance() {
+		return new Building();
+	}
+
 }

CityDoctorParent/CityDoctorModel/src/main/java/de/hft/stuttgart/citydoctor2/datastructure/BuildingInstallation.java

@@ -35,6 +35,8 @@ import de.hft.stuttgart.citydoctor2.check.CheckError;
 import de.hft.stuttgart.citydoctor2.check.CheckId;
 import de.hft.stuttgart.citydoctor2.parser.ParserConfiguration;
 import de.hft.stuttgart.citydoctor2.utils.CityGmlUtils;
+import de.hft.stuttgart.citydoctor2.utils.CopyHandler;
+import de.hft.stuttgart.citydoctor2.utils.Copyable;
 
 public class BuildingInstallation extends CityObject {
 
@@ -67,11 +69,6 @@ public class BuildingInstallation extends CityObject {
 		}
 	}	
 	
-	@Override
-	public CityObject copy() {
-		throw new UnsupportedOperationException("Cannot copy BuildingInstallation");
-	}
-	
 	private void setGeometryAccordingToLod(Lod lod, GeometryProperty<?> ms) {
 		switch (lod) {
 		case LOD2:
@@ -219,6 +216,29 @@ public class BuildingInstallation extends CityObject {
 		}
 	}
 	
+	@Override
+	public void fillValues(Copyable original, CopyHandler handler) {
+		super.fillValues(original, handler);
+		BuildingInstallation originalBi = (BuildingInstallation) original;
+		for (BoundarySurface originalBs : originalBi.boundarySurfaces) {
+			boundarySurfaces.add(handler.getCopyInstance(originalBs));
+		}
+		gmlBi = originalBi.gmlBi;
+		parent = handler.getCopyInstance(parent);
+	}
 	
+	@Override
+	public void collectInstances(CopyHandler handler) {
+		super.collectInstances(handler);
+		for (BoundarySurface bs : boundarySurfaces) {
+			handler.addInstance(bs);
+		}
+		handler.addInstance(parent);
+	}
+
+	@Override
+	public Copyable createCopyInstance() {
+		return new BuildingInstallation();
+	}
 
 }

CityDoctorParent/CityDoctorModel/src/main/java/de/hft/stuttgart/citydoctor2/datastructure/BuildingPart.java

@@ -18,22 +18,23 @@
  */
 package de.hft.stuttgart.citydoctor2.datastructure;
 
+import de.hft.stuttgart.citydoctor2.utils.CopyHandler;
+import de.hft.stuttgart.citydoctor2.utils.Copyable;
+
 public class BuildingPart extends AbstractBuilding {
 	
 	private static final long serialVersionUID = 8200322261958679163L;
 	
 	private Building parent;
 	
+	private BuildingPart() {
+	}
+	
 	public BuildingPart(Building parent) {
 		this.parent = parent;
 		parent.addBuildingPart(this);
 	}
 	
-	@Override
-	public CityObject copy() {
-		throw new UnsupportedOperationException("Cannot copy BuildingPart");
-	}
-
 	public Building getParent() {
 		return parent;
 	}
@@ -48,5 +49,22 @@ public class BuildingPart extends AbstractBuilding {
 		return "BuildingPart [id=" + getGmlId() + "]";
 	}
 	
+	@Override
+	public void fillValues(Copyable original, CopyHandler handler) {
+		super.fillValues(original, handler);
+		BuildingPart originalPart = (BuildingPart) original;
+		parent = handler.getCopyInstance(originalPart.parent);
+	}
 	
+	@Override
+	public void collectInstances(CopyHandler handler) {
+		super.collectInstances(handler);
+		handler.addInstance(parent);
+	}
+
+	@Override
+	public Copyable createCopyInstance() {
+		return new BuildingPart();
+	}
+
 }

CityDoctorParent/CityDoctorModel/src/main/java/de/hft/stuttgart/citydoctor2/datastructure/CityDoctorModel.java

@@ -18,15 +18,21 @@
  */
 package de.hft.stuttgart.citydoctor2.datastructure;
 
+import java.io.BufferedWriter;
 import java.io.File;
+import java.io.IOException;
+import java.io.UncheckedIOException;
+import java.nio.file.Files;
 import java.time.ZonedDateTime;
 import java.util.ArrayList;
+import java.util.EnumMap;
 import java.util.HashMap;
 import java.util.HashSet;
+import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
-import java.util.ServiceLoader;
 import java.util.Map.Entry;
+import java.util.ServiceLoader;
 import java.util.Set;
 import java.util.concurrent.atomic.AtomicInteger;
 import java.util.stream.Stream;
@@ -44,6 +50,8 @@ import org.citygml4j.xml.io.CityGMLOutputFactory;
 import org.citygml4j.xml.io.writer.CityGMLWriteException;
 import org.citygml4j.xml.io.writer.CityGMLWriter;
 
+import de.hft.stuttgart.citydoctor2.check.AbstractCheck;
+import de.hft.stuttgart.citydoctor2.check.Check;
 import de.hft.stuttgart.citydoctor2.check.CheckError;
 import de.hft.stuttgart.citydoctor2.check.ErrorId;
 import de.hft.stuttgart.citydoctor2.parser.ParserConfiguration;
@@ -127,6 +135,14 @@ public class CityDoctorModel {
 	}
 
 	public void saveAs(String file) throws CityGMLBuilderException, CityGMLWriteException, ADEException {
+		if (file.endsWith(".off")) {
+			exportAsOff(file);
+		} else {
+			exportAsGML(file);
+		}
+	}
+
+	private void exportAsGML(String file) throws ADEException, CityGMLBuilderException, CityGMLWriteException {
 		CityGMLContext gmlContext = CityGMLContext.getInstance();
 		// setup energy ade stuff, so the parser doesn't crash on encountering this
 		if (!gmlContext.hasADEContexts()) {
@@ -165,6 +181,83 @@ public class CityDoctorModel {
 		}
 	}
 
+	private void exportAsOff(String file) {
+		file = file.substring(0, file.lastIndexOf('.'));
+		File folder = new File(file);
+		folder.mkdirs();
+		createFeatureStream().forEach(co -> {
+			Map<Lod, Set<Polygon>> polygonMap = new EnumMap<>(Lod.class);
+			Check c = new AbstractCheck() {
+				
+				@Override
+				public void check(Geometry geom) {
+					polygonMap.compute(geom.getLod(), (lod, polys) -> {
+						if (polys == null) {
+							polys = new HashSet<>();
+						}
+						for (Polygon poly : geom.getPolygons()) {
+							polys.add(poly.getOriginal());
+						}
+						return polys;
+					});
+				}
+			};
+			co.accept(c);
+			
+			Set<Polygon> highestLod = polygonMap.get(Lod.LOD2);
+			if (highestLod == null) {
+				highestLod = polygonMap.get(Lod.LOD1);
+			}
+			if (highestLod == null) {
+				return;
+			}
+			Map<Vertex, Integer> idMap = new LinkedHashMap<>();
+			int counter = 0;
+			for (Polygon poly : highestLod) {
+				counter = addRing(poly.getExteriorRing(), idMap, counter);
+			}
+			
+			try (BufferedWriter writer = Files.newBufferedWriter(folder.toPath().resolve(co.getGmlId() + ".off"))) {
+				writer.write("OFF\n");
+				writer.write(Integer.toString(idMap.size()));
+				writer.write(' ');
+				writer.write(Integer.toString(highestLod.size()));
+				writer.write(" 0\n");
+				for (Vertex v : idMap.keySet()) {
+					writer.write(Double.toString(v.getX()));
+					writer.write(' ');
+					writer.write(Double.toString(v.getY()));
+					writer.write(' ');
+					writer.write(Double.toString(v.getZ()));
+					writer.write('\n');
+				}
+				for (Polygon poly : highestLod) {
+					writer.write(Integer.toString(poly.getExteriorRing().getVertices().size() - 1));
+					writer.write(' ');
+					for (int i = 0; i < poly.getExteriorRing().getVertices().size() - 1; i++) {
+						Vertex v = poly.getExteriorRing().getVertices().get(i);
+						writer.write(Integer.toString(idMap.get(v)));
+						writer.write(' ');
+					}
+					writer.write('\n');
+				}
+			} catch (IOException e) {
+				throw new UncheckedIOException(e);
+			} 
+			
+		});
+	}
+
+	private int addRing(LinearRing ring, Map<Vertex, Integer> idMap, int counter) {
+		for (Vertex v : ring.getVertices()) {
+			if (!idMap.containsKey(v)) {
+				idMap.put(v, counter);
+				counter++;
+			}
+		}
+		return counter;
+	}
+
 	private void storeCityObjects(List<? extends CityObject> cos, GMLGeometryFactory gmlFactory) {
 		for (CityObject co : cos) {
 			QualityADEUtils.removeValidationResult(co);

CityDoctorParent/CityDoctorModel/src/main/java/de/hft/stuttgart/citydoctor2/datastructure/CityObject.java

@@ -30,6 +30,8 @@ import de.hft.stuttgart.citydoctor2.check.Check;
 import de.hft.stuttgart.citydoctor2.check.CheckError;
 import de.hft.stuttgart.citydoctor2.check.CheckId;
 import de.hft.stuttgart.citydoctor2.parser.ParserConfiguration;
+import de.hft.stuttgart.citydoctor2.utils.CopyHandler;
+import de.hft.stuttgart.citydoctor2.utils.Copyable;
 
 /**
  * Abstract class for general features such as Buildings, Water objects, ...
@@ -69,11 +71,14 @@ public abstract class CityObject extends GmlElement {
 	 * Remove the CityGML4j geometries from the data structure to save memory
 	 */
 	public abstract void unsetGmlGeometries();
-
-	@Override
-	public CityObject copy() {
-		return (CityObject) super.copy();
-	}
+	
+//	void copyAttributesInto(CityObject copy, ReferenceStore store) {
+//		super.copyAttributesInto(copy);
+//		copy.geometryList = new ArrayList<>();
+//		for (Geometry geom : geometryList) {
+//			copy.geometryList.add(geom.copy(store));
+//		}
+//	}
 
 	public void addGeometry(Geometry geom) {
 		Objects.requireNonNull(geom);
@@ -186,4 +191,20 @@ public abstract class CityObject extends GmlElement {
 			geom.clearMetaInformation();
 		}
 	}
+	
+	@Override
+	public void collectInstances(CopyHandler handler) {
+		for (Geometry geom : geometryList) {
+			handler.addInstance(geom);
+		}
+	}
+	
+	@Override
+	public void fillValues(Copyable original, CopyHandler handler) {
+		super.fillValues(original, handler);
+		CityObject originalCo = (CityObject) original;
+		for (Geometry geom : originalCo.geometryList) {
+			geometryList.add(handler.getCopyInstance(geom));
+		}
+	}
 }

CityDoctorParent/CityDoctorModel/src/main/java/de/hft/stuttgart/citydoctor2/datastructure/ConcretePolygon.java

@@ -27,8 +27,10 @@ import de.hft.stuttgart.citydoctor2.check.CheckError;
 import de.hft.stuttgart.citydoctor2.check.CheckId;
 import de.hft.stuttgart.citydoctor2.check.Checkable;
 import de.hft.stuttgart.citydoctor2.math.Vector3d;
-import de.hft.stuttgart.citydoctor2.tesselation.TesselatedPolygon;
 import de.hft.stuttgart.citydoctor2.tesselation.JoglTesselator;
+import de.hft.stuttgart.citydoctor2.tesselation.TesselatedPolygon;
+import de.hft.stuttgart.citydoctor2.utils.CopyHandler;
+import de.hft.stuttgart.citydoctor2.utils.Copyable;
 
 /**
  * A polygon that actually contains the rings and points representing the
@@ -455,4 +457,44 @@ public class ConcretePolygon extends Polygon {
 	public void clearMetaInformation() {
 		parent.clearMetaInformation();
 	}
+
+	@Override
+	public void collectInstances(CopyHandler handler) {
+		handler.addInstance(exterior);
+		if (innerRings != null) {
+			for (LinearRing lr : innerRings) {
+				handler.addInstance(lr);
+			}
+		}
+		handler.addInstance(partOfSurface);
+		handler.addInstance(partfOfInstallation);
+		handler.addInstance(parent);
+		handler.addInstance(linkedFromPolygon);
+	}
+	
+
+	@Override
+	public Copyable createCopyInstance() {
+		return new ConcretePolygon();
+	}
+	
+	@Override
+	public void fillValues(Copyable original, CopyHandler handler) {
+		super.fillValues(original, handler);
+		ConcretePolygon originalPoly = (ConcretePolygon) original;
+		exterior = handler.getCopyInstance(originalPoly.exterior);
+		if (originalPoly.innerRings != null) {
+			innerRings = new ArrayList<>(originalPoly.innerRings.size());
+			for (LinearRing originalRing : originalPoly.innerRings) {
+				innerRings.add(handler.getCopyInstance(originalRing));
+			}
+		}
+		parent = handler.getCopyInstance(originalPoly.parent);
+		partfOfInstallation = handler.getCopyInstance(originalPoly.partfOfInstallation);
+		partOfSurface = handler.getCopyInstance(originalPoly.partOfSurface);
+		linkedFromPolygon = handler.getCopyInstance(originalPoly.linkedFromPolygon);
+	}
+	
+	
+
 }

CityDoctorParent/CityDoctorModel/src/main/java/de/hft/stuttgart/citydoctor2/datastructure/Edge.java

@@ -22,13 +22,16 @@ import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.List;
 
+import de.hft.stuttgart.citydoctor2.utils.CopyHandler;
+import de.hft.stuttgart.citydoctor2.utils.Copyable;
+
 /**
  * Representing an edge between two consecutive points of a linear ring
  * 
  * @author Matthias Betz
  *
  */
-public class Edge implements Serializable {
+public class Edge implements Serializable, Copyable {
 
 	private static final long serialVersionUID = -504694863498128296L;
 
@@ -47,6 +50,9 @@ public class Edge implements Serializable {
 		this.to = to;
 	}
 
+	private Edge() {
+	}
+
 	public Vertex getFrom() {
 		return from;
 	}
@@ -67,7 +73,8 @@ public class Edge implements Serializable {
 			numberOfOppositeHalfEdges++;
 			return;
 		}
-		throw new IllegalStateException("The given vertices do not form this edge\n v0=" + v0 + ", v1=" + v1 + ", edge" + this);
+		throw new IllegalStateException(
+				"The given vertices do not form this edge\n v0=" + v0 + ", v1=" + v1 + ", edge" + this);
 	}
 
 	private boolean isPointOfEdge(Vertex v0, Vertex edgePoint) {
@@ -192,4 +199,32 @@ public class Edge implements Serializable {
 		return null;
 	}
 
+	@Override
+	public void collectInstances(CopyHandler handler) {
+		handler.addInstance(from);
+		handler.addInstance(to);
+		handler.addInstance(adjacentPolygons);
+		handler.addInstance(adjacentRings);
+	}
+
+	@Override
+	public Copyable createCopyInstance() {
+		return new Edge();
+	}
+
+	@Override
+	public void fillValues(Copyable original, CopyHandler handler) {
+		Edge originalEdge = (Edge) original;
+		from = handler.getCopyInstance(originalEdge.from);
+		to = handler.getCopyInstance(originalEdge.to);
+		numberOfHalfEdges = originalEdge.numberOfHalfEdges;
+		numberOfOppositeHalfEdges = originalEdge.numberOfOppositeHalfEdges;
+		for (Polygon originalPoly : originalEdge.adjacentPolygons) {
+			adjacentPolygons.add(handler.getCopyInstance(originalPoly));
+		}
+		for (LinearRing originalRing : originalEdge.adjacentRings) {
+			adjacentRings.add(handler.getCopyInstance(originalRing));
+		}
+	}
+
 }

CityDoctorParent/CityDoctorModel/src/main/java/de/hft/stuttgart/citydoctor2/datastructure/Geometry.java

@@ -23,6 +23,7 @@ import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
+import java.util.Map.Entry;
 import java.util.Random;
 import java.util.Set;
 
@@ -33,6 +34,8 @@ import de.hft.stuttgart.citydoctor2.math.Triangle3d;
 import de.hft.stuttgart.citydoctor2.math.Vector3d;
 import de.hft.stuttgart.citydoctor2.tesselation.TesselatedPolygon;
 import de.hft.stuttgart.citydoctor2.utils.BoundingBoxCalculator;
+import de.hft.stuttgart.citydoctor2.utils.CopyHandler;
+import de.hft.stuttgart.citydoctor2.utils.Copyable;
 import de.hft.stuttgart.citydoctor2.utils.SerializablePair;
 
 /**
@@ -367,16 +370,11 @@ public class Geometry extends GmlElement {
 		return false;
 	}
 
-	@Override
-	public Geometry copy() {
-		return (Geometry) super.copy();
-	}
-	
 	@Override
 	public void prepareForChecking() {
 		updateEdgesAndVertices();
 	}
-	
+
 	@Override
 	public void clearMetaInformation() {
 		if (vertices != null) {
@@ -388,4 +386,58 @@ public class Geometry extends GmlElement {
 		edges = null;
 		edgeMap = null;
 	}
+
+	@Override
+	public void collectInstances(CopyHandler handler) {
+		handler.addInstance(parent);
+		handler.addInstance(polygons);
+		handler.addInstance(edges);
+		handler.addInstance(vertices);
+		if (edgeMap != null) {
+			for (Entry<SerializablePair<Vertex, Vertex>, Edge> e : edgeMap.entrySet()) {
+				handler.addInstance(e.getKey().getValue0());
+				handler.addInstance(e.getKey().getValue1());
+				handler.addInstance(e.getValue());
+			}
+		}
+	}
+
+	@Override
+	public Copyable createCopyInstance() {
+		return new Geometry(type, lod);
+	}
+
+	@Override
+	public void fillValues(Copyable original, CopyHandler handler) {
+		super.fillValues(original, handler);
+		Geometry originalGeometry = (Geometry) original;
+		for (Polygon originalPoly : originalGeometry.polygons) {
+			polygons.add(handler.getCopyInstance(originalPoly));
+		}
+		if (originalGeometry.edges != null) {
+			edges = new ArrayList<>(originalGeometry.edges.size());
+			for (Edge originalEdge : originalGeometry.edges) {
+				edges.add(handler.getCopyInstance(originalEdge));
+			}
+		}
+		if (originalGeometry.edgeMap != null) {
+			edgeMap = new HashMap<>(originalGeometry.edgeMap.size());
+			for (Entry<SerializablePair<Vertex, Vertex>, Edge> originalEntry : originalGeometry.edgeMap.entrySet()) {
+				Vertex copyV0 = handler.getCopyInstance(originalEntry.getKey().getValue0());
+				Vertex copyV1 = handler.getCopyInstance(originalEntry.getKey().getValue1());
+				SerializablePair<Vertex, Vertex> pair = new SerializablePair<>(copyV0, copyV1);
+				Edge copyEdge = handler.getCopyInstance(originalEntry.getValue());
+				edgeMap.put(pair, copyEdge);
+			}
+		}
+		if (originalGeometry.vertices != null) {
+			vertices = new ArrayList<>(originalGeometry.vertices.size());
+			for (Vertex originalVertex : originalGeometry.vertices) {
+				vertices.add(handler.getCopyInstance(originalVertex));
+			}
+		}
+		parent = handler.getCopyInstance(originalGeometry.parent);
+
+	}
+
 }

CityDoctorParent/CityDoctorModel/src/main/java/de/hft/stuttgart/citydoctor2/datastructure/GmlElement.java

@@ -18,14 +18,9 @@
  */
 package de.hft.stuttgart.citydoctor2.datastructure;
 
-import java.io.ByteArrayInputStream;
-import java.io.ByteArrayOutputStream;
-import java.io.IOException;
-import java.io.ObjectInputStream;
-import java.io.ObjectOutputStream;
-import java.io.UncheckedIOException;
-
 import de.hft.stuttgart.citydoctor2.check.Checkable;
+import de.hft.stuttgart.citydoctor2.utils.CopyHandler;
+import de.hft.stuttgart.citydoctor2.utils.Copyable;
 
 /**
  * A general GML element that has a gml id
@@ -33,26 +28,12 @@ import de.hft.stuttgart.citydoctor2.check.Checkable;
  * @author Matthias Betz
  *
  */
-public abstract class GmlElement extends Checkable {
+public abstract class GmlElement extends Checkable implements Copyable {
 
 	private static final long serialVersionUID = -3242505393303017359L;
 
 	private GmlId gmlId;
 
-	public GmlElement copy() {
-		ByteArrayOutputStream arrayOutputStream = new ByteArrayOutputStream();
-		try {
-			ObjectOutputStream oos = new ObjectOutputStream(arrayOutputStream);
-			oos.writeObject(this);
-			ObjectInputStream ooi = new ObjectInputStream(new ByteArrayInputStream(arrayOutputStream.toByteArray()));
-			return (GmlElement) ooi.readObject();
-		} catch (IOException e) {
-			throw new UncheckedIOException(e);
-		} catch (ClassNotFoundException e) {
-			throw new IllegalStateException(e);
-		}
-	}
-
 	public void setGmlId(GmlId id) {
 		gmlId = id;
 	}
@@ -64,4 +45,12 @@ public abstract class GmlElement extends Checkable {
 		}
 		return gmlId;
 	}
+	
+	@Override
+	public void fillValues(Copyable original, CopyHandler handler) {
+		GmlElement originalElement = (GmlElement) original;
+		// generate gml id before copying
+		gmlId = originalElement.getGmlId();
+	}
+	
 }

CityDoctorParent/CityDoctorModel/src/main/java/de/hft/stuttgart/citydoctor2/datastructure/LandObject.java

@@ -27,6 +27,7 @@ import org.citygml4j.model.gml.geometry.aggregates.MultiSurfaceProperty;
 import de.hft.stuttgart.citydoctor2.check.Check;
 import de.hft.stuttgart.citydoctor2.parser.ParserConfiguration;
 import de.hft.stuttgart.citydoctor2.utils.CityGmlUtils;
+import de.hft.stuttgart.citydoctor2.utils.Copyable;
 
 /**
  * Represents a land use CityGML object.
@@ -111,5 +112,10 @@ public class LandObject extends CityObject {
 	public String toString() {
 		return "LandObject [id=" + getGmlId() + "]";
 	}
+	
+	@Override
+	public Copyable createCopyInstance() {
+		return new LandObject(lu);
+	}
 
 }

CityDoctorParent/CityDoctorModel/src/main/java/de/hft/stuttgart/citydoctor2/datastructure/LinearRing.java

@@ -27,6 +27,8 @@ import de.hft.stuttgart.citydoctor2.math.Ring2d;
 import de.hft.stuttgart.citydoctor2.math.UnitVector3d;
 import de.hft.stuttgart.citydoctor2.math.Vector2d;
 import de.hft.stuttgart.citydoctor2.math.Vector3d;
+import de.hft.stuttgart.citydoctor2.utils.CopyHandler;
+import de.hft.stuttgart.citydoctor2.utils.Copyable;
 
 /**
  * Represents a linear ring used in polygons. The ring contains the vertices.
@@ -252,4 +254,28 @@ public class LinearRing extends GmlElement {
 	public void clearMetaInformation() {
 		parent.getParent().clearMetaInformation();
 	}
+	
+	@Override
+	public void fillValues(Copyable original, CopyHandler handler) {
+		super.fillValues(original, handler);
+		LinearRing originalRing = (LinearRing) original;
+		type = originalRing.type;
+		parent = handler.getCopyInstance(originalRing.parent);
+		for (Vertex v : originalRing.vertices) {
+			vertices.add(handler.getCopyInstance(v));
+		}
+	}
+
+	@Override
+	public void collectInstances(CopyHandler handler) {
+		for (Vertex v : vertices) {
+			handler.addInstance(v);
+		}
+		handler.addInstance(parent);
+	}
+
+	@Override
+	public Copyable createCopyInstance() {
+		return new LinearRing(type);
+	}
 }

CityDoctorParent/CityDoctorModel/src/main/java/de/hft/stuttgart/citydoctor2/datastructure/LinkedPolygon.java

@@ -27,6 +27,8 @@ import de.hft.stuttgart.citydoctor2.check.CheckId;
 import de.hft.stuttgart.citydoctor2.check.CheckResult;
 import de.hft.stuttgart.citydoctor2.math.Vector3d;
 import de.hft.stuttgart.citydoctor2.tesselation.TesselatedPolygon;
+import de.hft.stuttgart.citydoctor2.utils.CopyHandler;
+import de.hft.stuttgart.citydoctor2.utils.Copyable;
 
 /**
  * A polygon that does not contain the geometry but is only a link to an actual
@@ -41,7 +43,10 @@ public class LinkedPolygon extends Polygon {
 
 	private Geometry parent;
 	private ConcretePolygon poly;
-
+	
+	private LinkedPolygon() {
+	}
+	
 	/**
 	 * 
 	 * @param poly   polygon this is linked to
@@ -267,4 +272,22 @@ public class LinkedPolygon extends Polygon {
 		return false;
 	}
 
+	@Override
+	public void collectInstances(CopyHandler handler) {
+		handler.addInstance(parent);
+		handler.addInstance(poly);
+	}
+
+	@Override
+	public Copyable createCopyInstance() {
+		return new LinkedPolygon();
+	}
+	
+	@Override
+	public void fillValues(Copyable original, CopyHandler handler) {
+		LinkedPolygon linkedOriginal = (LinkedPolygon) original;
+		parent = handler.getCopyInstance(linkedOriginal.parent);
+		poly = handler.getCopyInstance(linkedOriginal.poly);
+	}
+
 }

CityDoctorParent/CityDoctorModel/src/main/java/de/hft/stuttgart/citydoctor2/datastructure/Opening.java

@@ -26,6 +26,8 @@ import org.citygml4j.model.gml.geometry.aggregates.MultiSurfaceProperty;
 import de.hft.stuttgart.citydoctor2.check.Check;
 import de.hft.stuttgart.citydoctor2.parser.ParserConfiguration;
 import de.hft.stuttgart.citydoctor2.utils.CityGmlUtils;
+import de.hft.stuttgart.citydoctor2.utils.CopyHandler;
+import de.hft.stuttgart.citydoctor2.utils.Copyable;
 
 /**
  * Represents an Opening suchs a window or Door in a surface of a feature.
@@ -44,6 +46,10 @@ public class Opening extends CityObject {
 	private SurfaceFeatureType featureType;
 
 	private AbstractCityObject ao;
+	
+	private Opening(OpeningType type) {
+		this.type = type;
+	}
 
 	public Opening(OpeningType type, SurfaceFeatureType featureType, BoundarySurface partOf, AbstractCityObject ao) {
 		this.featureType = featureType;
@@ -52,11 +58,6 @@ public class Opening extends CityObject {
 		this.ao = ao;
 	}
 
-	@Override
-	public CityObject copy() {
-		throw new UnsupportedOperationException("Cannot copy Opening");
-	}
-
 	public void reCreateGeometries(GMLGeometryFactory factory, ParserConfiguration config) {
 		if (!ao.isSetId()) {
 			ao.setId(getGmlId().getGmlString());
@@ -183,4 +184,25 @@ public class Opening extends CityObject {
 		return FeatureType.OPENING;
 	}
 
+	@Override
+	public Copyable createCopyInstance() {
+		return new Opening(type);
+	}
+	
+	@Override
+	public void collectInstances(CopyHandler handler) {
+		super.collectInstances(handler);
+		handler.addInstance(partOf);
+	}
+	
+	@Override
+	public void fillValues(Copyable original, CopyHandler handler) {
+		super.fillValues(original, handler);
+		Opening originalOpening = (Opening) original;
+		partOf = handler.getCopyInstance(originalOpening.partOf);
+		type = originalOpening.type;
+		featureType = originalOpening.featureType;
+		ao = originalOpening.ao;
+	}
+
 }

CityDoctorParent/CityDoctorModel/src/main/java/de/hft/stuttgart/citydoctor2/datastructure/TransportationObject.java

@@ -35,6 +35,8 @@ import de.hft.stuttgart.citydoctor2.check.CheckError;
 import de.hft.stuttgart.citydoctor2.check.CheckId;
 import de.hft.stuttgart.citydoctor2.parser.ParserConfiguration;
 import de.hft.stuttgart.citydoctor2.utils.CityGmlUtils;
+import de.hft.stuttgart.citydoctor2.utils.CopyHandler;
+import de.hft.stuttgart.citydoctor2.utils.Copyable;
 
 /**
  * Representation of a transportation object.
@@ -272,5 +274,28 @@ public class TransportationObject extends CityObject {
 			child.clearMetaInformation();
 		}
 	}
+	
+	@Override
+	public void collectInstances(CopyHandler handler) {
+		super.collectInstances(handler);
+		for (TransportationObject to : composesOf) {
+			handler.addInstance(to);
+		}
+	}
+	
+	@Override
+	public void fillValues(Copyable original, CopyHandler handler) {
+		super.fillValues(original, handler);
+		TransportationObject originalTo = (TransportationObject) original;
+		for (TransportationObject to : originalTo.composesOf) {
+			composesOf.add(handler.getCopyInstance(to));
+		}
+		ato = originalTo.ato;
+	}
+
+	@Override
+	public Copyable createCopyInstance() {
+		return new TransportationObject(type);
+	}
 
 }

CityDoctorParent/CityDoctorModel/src/main/java/de/hft/stuttgart/citydoctor2/datastructure/Vegetation.java

@@ -33,6 +33,8 @@ import org.citygml4j.model.gml.geometry.primitives.SolidProperty;
 import de.hft.stuttgart.citydoctor2.check.Check;
 import de.hft.stuttgart.citydoctor2.parser.ParserConfiguration;
 import de.hft.stuttgart.citydoctor2.utils.CityGmlUtils;
+import de.hft.stuttgart.citydoctor2.utils.CopyHandler;
+import de.hft.stuttgart.citydoctor2.utils.Copyable;
 
 /**
  * Representation of CityGML vegetation objects
@@ -205,4 +207,15 @@ public class Vegetation extends CityObject {
 		return "Vegetation [id=" + getGmlId() + "]";
 	}
 
+	@Override
+	public Copyable createCopyInstance() {
+		return new Vegetation(type);
+	}
+	
+	@Override
+	public void fillValues(Copyable original, CopyHandler handler) {
+		super.fillValues(original, handler);
+		
+	}
+
 }

CityDoctorParent/CityDoctorModel/src/main/java/de/hft/stuttgart/citydoctor2/datastructure/Vertex.java

@@ -24,6 +24,8 @@ import java.util.List;
 import java.util.Set;
 
 import de.hft.stuttgart.citydoctor2.math.Vector3d;
+import de.hft.stuttgart.citydoctor2.utils.CopyHandler;
+import de.hft.stuttgart.citydoctor2.utils.Copyable;
 import de.hft.stuttgart.citydoctor2.utils.SerializablePair;
 
 /**
@@ -32,7 +34,7 @@ import de.hft.stuttgart.citydoctor2.utils.SerializablePair;
  * @author Matthias Betz
  *
  */
-public class Vertex extends Vector3d {
+public class Vertex extends Vector3d implements Copyable {
 
 	private static final long serialVersionUID = -5525361920397934892L;
 
@@ -134,4 +136,35 @@ public class Vertex extends Vector3d {
 	void clearAdjacentRings() {
 		adjacentRings = new ArrayList<>(2);
 	}
+
+	@Override
+	public void collectInstances(CopyHandler handler) {
+		for (SerializablePair<Geometry, HashSet<LinearRing>> pair : adjacentRings) {
+			handler.addInstance(pair.getValue0());
+			for (LinearRing lr : pair.getValue1()) {
+				handler.addInstance(lr);
+			}
+		}
+	}
+
+	@Override
+	public Copyable createCopyInstance() {
+		return new Vertex(this);
+	}
+
+	@Override
+	public void fillValues(Copyable original, CopyHandler handler) {
+		Vertex originalVertex = (Vertex) original;
+		// vertex point data already filled
+		for (SerializablePair<Geometry, HashSet<LinearRing>> pair : originalVertex.adjacentRings) {
+			Geometry geomCopy = handler.getCopyInstance(pair.getValue0());
+			HashSet<LinearRing> set = new HashSet<>();
+			for (LinearRing originalRing : pair.getValue1()) {
+				set.add(handler.getCopyInstance(originalRing));
+			}
+			SerializablePair<Geometry, HashSet<LinearRing>> copyPair = new SerializablePair<>(geomCopy, set);
+			adjacentRings.add(copyPair);
+		}
+	}
+	
 }

CityDoctorParent/CityDoctorModel/src/main/java/de/hft/stuttgart/citydoctor2/datastructure/WaterObject.java

@@ -27,6 +27,8 @@ import org.citygml4j.model.gml.geometry.aggregates.MultiSurfaceProperty;
 import de.hft.stuttgart.citydoctor2.check.Check;
 import de.hft.stuttgart.citydoctor2.parser.ParserConfiguration;
 import de.hft.stuttgart.citydoctor2.utils.CityGmlUtils;
+import de.hft.stuttgart.citydoctor2.utils.CopyHandler;
+import de.hft.stuttgart.citydoctor2.utils.Copyable;
 
 /**
  * Represents cityGML water body objects.
@@ -96,4 +98,15 @@ public class WaterObject extends CityObject {
 		return "WaterObject [id=" + getGmlId() + "]";
 	}
 
+	@Override
+	public WaterObject createCopyInstance() {
+		return new WaterObject();
+	}
+
+	@Override
+	public void fillValues(Copyable original, CopyHandler handler) {
+		WaterObject wo = (WaterObject) original;
+		gmlWater = wo.gmlWater;
+	}
+
 }

CityDoctorParent/CityDoctorModel/src/main/java/de/hft/stuttgart/citydoctor2/math/UnitVector3d.java

@@ -71,7 +71,7 @@ public class UnitVector3d extends Vector3d {
 	}
 	
 	@Override
-	public UnitVector3d copy() {
+	public UnitVector3d copyVector() {
 		return new UnitVector3d(getX(), getY(), getZ());
 	}