f@0: /*  
f@0:  CCmI Editor - A Collaborative Cross-Modal Diagram Editing Tool
f@0:   
f@0:  Copyright (C) 2011  Queen Mary University of London (http://ccmi.eecs.qmul.ac.uk/)
f@0: 
f@0:  This program is free software: you can redistribute it and/or modify
f@0:  it under the terms of the GNU General Public License as published by
f@0:  the Free Software Foundation, either version 3 of the License, or
f@0:  (at your option) any later version.
f@0: 
f@0:  This program is distributed in the hope that it will be useful,
f@0:  but WITHOUT ANY WARRANTY; without even the implied warranty of
f@0:  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
f@0:  GNU General Public License for more details.
f@0: 
f@0:  You should have received a copy of the GNU General Public License
f@0:  along with this program.  If not, see <http://www.gnu.org/licenses/>.
f@0: */  
f@0: 
f@0: package uk.ac.qmul.eecs.ccmi.gui.persistence;
f@0: 
f@0: import java.io.BufferedWriter;
f@0: import java.io.File;
f@0: import java.io.FileWriter;
f@0: import java.io.IOException;
f@0: import java.io.InputStream;
f@0: import java.io.OutputStream;
f@0: import java.text.MessageFormat;
f@0: import java.util.ArrayList;
f@0: import java.util.Collection;
f@0: import java.util.Enumeration;
f@0: import java.util.LinkedHashMap;
f@0: import java.util.List;
f@0: import java.util.Map;
f@0: import java.util.ResourceBundle;
f@0: 
f@0: import javax.swing.tree.TreeNode;
f@0: import javax.xml.parsers.DocumentBuilder;
f@0: import javax.xml.parsers.DocumentBuilderFactory;
f@0: import javax.xml.parsers.ParserConfigurationException;
f@0: import javax.xml.transform.OutputKeys;
f@0: import javax.xml.transform.Transformer;
f@0: import javax.xml.transform.TransformerConfigurationException;
f@0: import javax.xml.transform.TransformerException;
f@0: import javax.xml.transform.TransformerFactory;
f@0: import javax.xml.transform.dom.DOMSource;
f@0: import javax.xml.transform.stream.StreamResult;
f@0: 
f@0: import org.w3c.dom.Document;
f@0: import org.w3c.dom.Element;
f@0: import org.w3c.dom.NodeList;
f@0: import org.xml.sax.SAXException;
f@0: 
f@0: import uk.ac.qmul.eecs.ccmi.diagrammodel.CollectionModel;
f@0: import uk.ac.qmul.eecs.ccmi.diagrammodel.DiagramTreeNode;
f@0: import uk.ac.qmul.eecs.ccmi.diagrammodel.TreeModel;
f@0: import uk.ac.qmul.eecs.ccmi.gui.Diagram;
f@0: import uk.ac.qmul.eecs.ccmi.gui.DiagramEventSource;
f@0: import uk.ac.qmul.eecs.ccmi.gui.Edge;
f@0: import uk.ac.qmul.eecs.ccmi.gui.Node;
f@0: import uk.ac.qmul.eecs.ccmi.utils.CharEscaper;
f@0: 
f@0: /**
f@0:  * The PersistanceManager provides methods for saving and retrieving diagrams from an XML
f@0:  * file. Both templates diagrams (prototypes from which actual diagram instances are created
f@0:  * through cloning) and diagram instances can be saved to a file. The tag name used in the XML 
f@0:  * file can be accessed via the static {@code String} variables of this class.  
f@0:  * 
f@0:  */
f@0: public abstract class PersistenceManager {
f@0: 	/**
f@0: 	 * Encodes a diagram template in a file in XML format
f@0: 	 * 
f@0: 	 * @param diagram the diagram to be encoded
f@0: 	 * @param file the file where the diagram is going to be encoded
f@0: 	 * @throws IOException if there are any I/O problems with the file 
f@0: 	 */
f@0: 	public static void encodeDiagramTemplate(Diagram diagram, File file) throws IOException{
f@0: 		ResourceBundle resources = ResourceBundle.getBundle(PersistenceManager.class.getName());
f@0: 		if(file.createNewFile() == false)
f@0: 			throw new IOException(resources.getString("dialog.error.file_exists"));
f@0: 		
f@0: 		DocumentBuilderFactory dbfac = DocumentBuilderFactory.newInstance();
f@0:         DocumentBuilder docBuilder = null;
f@0: 		try {
f@0: 			docBuilder = dbfac.newDocumentBuilder();
f@0: 		} catch (ParserConfigurationException e) {
f@0: 			throw new IOException(resources.getString("dialog.error.problem.save"),e);
f@0: 		}
f@0:         Document doc = docBuilder.newDocument();
f@0:         
f@0:         Element root = doc.createElement(DIAGRAM);
f@0:         doc.appendChild(root);
f@0:         /* diagram name and prototypePersstenceDelegate */
f@0:         root.setAttribute(NAME, diagram.getName());
f@0:         root.setAttribute(PROTOTYPE_PERSISTENCE_DELEGATE, diagram.getPrototypePersistenceDelegate().getClass().getName());
f@0:         
f@0:         writePrototypes(doc, root, diagram);
f@0:         
f@0:         //set up a transformer
f@0:         TransformerFactory transfac = TransformerFactory.newInstance();
f@0:         Transformer trans = null;
f@0: 		try {
f@0: 			trans = transfac.newTransformer();
f@0: 		} catch (TransformerConfigurationException tce) {
f@0: 			throw new IOException(resources.getString("dialog.error.problem.save"),tce);
f@0: 		}
f@0: 		trans.setOutputProperty(OutputKeys.INDENT, "yes");
f@0: 		trans.setOutputProperty("{http://xml.apache.org/xslt}indent-amount", String.valueOf(2));
f@0: 		 
f@0:         StreamResult result = new StreamResult(new BufferedWriter(new FileWriter(file)));
f@0:         DOMSource source = new DOMSource(doc);
f@0:         try {
f@0: 			trans.transform(source, result);
f@0: 		} catch (TransformerException te) {
f@0: 			throw new IOException(resources.getString("dialog.error.problem.save"),te);
f@0: 		}
f@0: 	}
f@0: 	
f@0: 	/**
f@0: 	 * Decodes a diagram template from a file in XML format
f@0: 	 * 
f@0: 	 * @param XMLFile the file to read the diagram from 
f@0: 	 * @throws IOException if there are any I/O problems with the file 
f@0: 	 * 
f@0: 	 * @return the diagram encoded in {@code XMLFile}
f@0: 	 */
f@0: 	public static Diagram decodeDiagramTemplate(File XMLFile) throws IOException{
f@0: 		ResourceBundle resources = ResourceBundle.getBundle(PersistenceManager.class.getName());
f@0: 		DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance();
f@0: 	    DocumentBuilder dBuilder = null;
f@0: 		try {
f@0: 			dBuilder = dbFactory.newDocumentBuilder();
f@0: 		} catch (ParserConfigurationException pce) {
f@0: 			throw new IOException(resources.getString("dialog.error.problem.open"),pce);
f@0: 		}
f@0: 	    Document doc = null;
f@0: 		try {
f@0: 			doc = dBuilder.parse(XMLFile);
f@0: 		} catch (SAXException se) {
f@0: 			throw new IOException(resources.getString("dialog.error.problem.open"),se);
f@0: 		}
f@0: 	    doc.getDocumentElement().normalize();
f@0: 	    
f@0: 	    if(doc.getElementsByTagName(DIAGRAM).item(0) == null)
f@0: 	    	throw new IOException(resources.getString("dialog.error.malformed_file"));
f@0: 	    Element root = (Element)doc.getElementsByTagName(DIAGRAM).item(0);
f@0: 	    String diagramName = root.getAttribute(NAME);
f@0: 	    if(diagramName.isEmpty())
f@0: 	    	throw new IOException(resources.getString("dialog.error.malformed_file"));
f@0: 	    String persistenceDelegateClassName = root.getAttribute(PROTOTYPE_PERSISTENCE_DELEGATE);
f@0: 	    PrototypePersistenceDelegate persistenceDelegate = null;
f@0: 	    try{
f@0: 	    	Class<? extends PrototypePersistenceDelegate> c = Class.forName(persistenceDelegateClassName).asSubclass(PrototypePersistenceDelegate.class);
f@0: 	    	persistenceDelegate = c.newInstance();
f@0: 	    }catch(Exception e){
f@0: 	    	throw new IOException(resources.getString("dialog.error.problem.open"),e);
f@0: 	    }
f@0: 	    
f@0: 	    final List<Node> nList = readNodePrototypes(doc,persistenceDelegate);
f@0: 	    final List<Edge> eList = readEdgePrototypes(doc,persistenceDelegate);
f@0: 	    Node[] nArray = new Node[nList.size()];
f@0: 	    Edge[] eArray = new Edge[eList.size()];
f@0: 	    return  Diagram.newInstance(diagramName,nList.toArray(nArray),eList.toArray(eArray),persistenceDelegate);
f@0: 	}
f@0: 	
f@0: 	/**
f@0: 	 * Encodes a diagram instance into the given output stream. Using output stream
f@0: 	 * instead of {@code Writer} as it's advised by the <i>StreamResult API</i> 
f@0: 	 * @see http://download.oracle.com/javase/6/docs/api/javax/xml/transform/stream/StreamResult.html
f@0: 	 * 
f@0: 	 * @param diagram the diagram to encode
f@0: 	 * @param newName the new name of the diagram to encode. This will also be the name of the file but {@code diagram}
f@0: 	 * will still keep the old name, that is the value returned by {@code getName()} won't be changed to {@code newName}. 
f@0: 	 * If a {@code null} value is passed than the value returned by {@code diagram.getName()} will be used.
f@0: 	 * 
f@0: 	 * @param out where the diagram will be encoded
f@0: 	 * @throws IOException if there are any I/O problems with the file 
f@0: 	 */
f@0: 	public static void encodeDiagramInstance(Diagram diagram, String newName, OutputStream out) throws IOException{
f@0: 		ResourceBundle resources = ResourceBundle.getBundle(PersistenceManager.class.getName());
f@0: 		DocumentBuilderFactory dbfac = DocumentBuilderFactory.newInstance();
f@0:         DocumentBuilder docBuilder = null;
f@0: 		try {
f@0: 			docBuilder = dbfac.newDocumentBuilder();
f@0: 		} catch (ParserConfigurationException pce) {
f@0: 			throw new IOException(resources.getString("dialog.error.problem.save"),pce);
f@0: 		}
f@0:         Document doc = docBuilder.newDocument();
f@0:         
f@0:         Element root = doc.createElement(DIAGRAM);
f@0:         root.setAttribute(NAME, (newName != null) ? newName : diagram.getName());
f@0:         root.setAttribute(PROTOTYPE_PERSISTENCE_DELEGATE, diagram.getPrototypePersistenceDelegate().getClass().getName());
f@0:         doc.appendChild(root);
f@0:         
f@0:         /* store bookmarks */
f@0:         Element bookmarksTag = doc.createElement(BOOKMARKS);
f@0:         TreeModel<Node,Edge> treeModel = diagram.getTreeModel();
f@0:         for(String key : treeModel.getBookmarks()){
f@0:         	Element bookmarkTag = doc.createElement(BOOKMARK);
f@0:         	bookmarkTag.setAttribute(KEY, key);
f@0:         	if(treeModel.getBookmarkedTreeNode(key).isRoot())
f@0:         		bookmarkTag.setTextContent(ROOT_AS_STRING);
f@0:         	else
f@0:         		bookmarkTag.setTextContent(getTreeNodeAsString(treeModel.getBookmarkedTreeNode(key)));
f@0:         	bookmarksTag.appendChild(bookmarkTag);
f@0:         }
f@0:         if(bookmarksTag.hasChildNodes())
f@0:         	root.appendChild(bookmarksTag);
f@0:         
f@0:         /* store notes */
f@0:         Element notesTag = doc.createElement(NOTES);
f@0:         DiagramTreeNode treeRoot = (DiagramTreeNode)diagram.getTreeModel().getRoot();
f@0:         for( @SuppressWarnings("unchecked")
f@0: 		Enumeration<DiagramTreeNode> enumeration = treeRoot.depthFirstEnumeration(); enumeration.hasMoreElements();){
f@0:         	DiagramTreeNode treeNode = enumeration.nextElement();
f@0:         	if(!treeNode.getNotes().isEmpty()){
f@0:         		Element noteTag = doc.createElement(NOTE);
f@0:         		Element treeNodeTag = doc.createElement(TREE_NODE);
f@0:         		if(treeNode.isRoot())
f@0:         			treeNodeTag.setTextContent(ROOT_AS_STRING);
f@0:         		else	
f@0:         			treeNodeTag.setTextContent(getTreeNodeAsString(treeNode));
f@0:         		Element contentTag = doc.createElement(CONTENT);
f@0:         		contentTag.setTextContent(CharEscaper.replaceNewline(treeNode.getNotes()));
f@0:         		noteTag.appendChild(treeNodeTag);
f@0:         		noteTag.appendChild(contentTag);
f@0:         		notesTag.appendChild(noteTag);
f@0:         	}
f@0:         }
f@0:         
f@0:         if(notesTag.hasChildNodes())
f@0:         	root.appendChild(notesTag);
f@0:         
f@0:         writePrototypes(doc,root,diagram);
f@0:         
f@0:         Element components = doc.createElement(COMPONENTS);
f@0:         root.appendChild(components);
f@0:         
f@0:         synchronized(diagram.getCollectionModel().getMonitor()){
f@0: 	        Collection<Node> nodes = diagram.getCollectionModel().getNodes();
f@0: 	        Collection<Edge> edges = diagram.getCollectionModel().getEdges();
f@0: 	        
f@0: 	        /* store nodes */
f@0: 	        Element nodesTag = doc.createElement(NODES);
f@0: 	        components.appendChild(nodesTag);
f@0: 	        List<Node> nList = new ArrayList<Node>(nodes);        
f@0: 	        for(Node n : nList){
f@0: 	        	Element nodeTag = doc.createElement(NODE);
f@0: 	    		nodeTag.setAttribute(ID, String.valueOf(n.getId()));
f@0: 	    		nodeTag.setAttribute(TYPE, n.getType());
f@0: 	    		nodesTag.appendChild(nodeTag);
f@0: 	        	n.encode(doc, nodeTag);
f@0: 	        }
f@0: 	        
f@0: 	        Element edgesTag = doc.createElement(EDGES);
f@0: 	        components.appendChild(edgesTag);
f@0: 	        for(Edge e : edges){
f@0: 	        	Element edgeTag = doc.createElement(EDGE);
f@0: 	        	edgesTag.appendChild(edgeTag);
f@0: 	        	e.encode(doc,edgeTag,nList);
f@0: 	        }
f@0:         }
f@0:         //set up a transformer
f@0:         TransformerFactory transfac = TransformerFactory.newInstance();
f@0:         Transformer trans = null;
f@0: 		try {
f@0: 			trans = transfac.newTransformer();
f@0: 		} catch (TransformerConfigurationException tec) {
f@0: 			throw new IOException(resources.getString("dialog.error.problem.save"));
f@0: 		}
f@0: 		trans.setOutputProperty(OutputKeys.INDENT, "yes");
f@0: 		trans.setOutputProperty("{http://xml.apache.org/xslt}indent-amount", String.valueOf(2));
f@0: 		
f@0:         
f@0:         StreamResult result = new StreamResult(out);
f@0:         DOMSource source = new DOMSource(doc);
f@0:         try {
f@0: 			trans.transform(source, result);
f@0: 		} catch (TransformerException te) {
f@0: 			throw new IOException(resources.getString("dialog.error.problem.save"),te);
f@0: 		}
f@0: 	}
f@0: 	
f@0: 	/**
f@0: 	 * Encodes a diagram instance into the given output stream. Using output stream
f@0: 	 * instead of {@code Writer} as it's advised by the <i>StreamResult API</i> 
f@0: 	 * @see http://download.oracle.com/javase/6/docs/api/javax/xml/transform/stream/StreamResult.html
f@0: 	 * 
f@0: 	 * @param diagram the diagram to encode
f@0: 	 * @param out an output stram to the file where the diagram will be encoded
f@0: 	 * @throws IOException if there are any I/O problems with the file 
f@0: 	 */
f@0: 	public static void encodeDiagramInstance(Diagram diagram, OutputStream out) throws IOException{
f@0: 		encodeDiagramInstance(diagram,null,out);
f@0: 	}
f@0: 	
f@0: 	/**
f@0: 	 * Decodes a diagram instance from the given input stream. Using input stream
f@0: 	 * instead of {@code Reader} as it's advised by the <i>StreamResult API</i> 
f@0: 	 * @see http://download.oracle.com/javase/6/docs/api/javax/xml/transform/stream/StreamResult.html
f@0: 	 * 
f@0: 	 * @param in an input stream to the file the diagram is decoded from 
f@0: 	 * @throws IOException if there are any I/O problems with the file 
f@0: 	 * 
f@0: 	 * @return the diagram encoded in the file 
f@0: 	 */
f@0: 	public static Diagram decodeDiagramInstance(InputStream in) throws IOException {
f@0: 		ResourceBundle resources = ResourceBundle.getBundle(PersistenceManager.class.getName());
f@0: 		DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance();
f@0: 	    DocumentBuilder dBuilder = null;
f@0: 		try {
f@0: 			dBuilder = dbFactory.newDocumentBuilder();
f@0: 		} catch (ParserConfigurationException pce) {
f@0: 			throw new IOException(resources.getString("dialog.error.problem.open"),pce);
f@0: 		}
f@0: 	    Document doc = null;
f@0: 		try {
f@0: 			doc = dBuilder.parse(in);
f@0: 		} catch (SAXException se) {
f@0: 			throw new IOException(resources.getString("dialog.error.problem.open"),se);
f@0: 		}
f@0: 	    doc.getDocumentElement().normalize();
f@0: 	    
f@0: 	    if(doc.getElementsByTagName(DIAGRAM).item(0) == null)
f@0: 	    	throw new IOException(resources.getString("dialog.error.malformed_file"));
f@0: 	    Element root = (Element)doc.getElementsByTagName(DIAGRAM).item(0);
f@0: 	    String diagramName = root.getAttribute(NAME);
f@0: 	    if(diagramName.isEmpty())
f@0: 	    	throw new IOException(resources.getString("dialog.error.malformed_file"));
f@0: 	    String persistenceDelegateClassName = root.getAttribute(PROTOTYPE_PERSISTENCE_DELEGATE);
f@0: 	    PrototypePersistenceDelegate persistenceDelegate = null;
f@0: 	    try{
f@0: 	    	Class<? extends PrototypePersistenceDelegate> c = Class.forName(persistenceDelegateClassName).asSubclass(PrototypePersistenceDelegate.class);
f@0: 	    	persistenceDelegate = c.newInstance();
f@0: 	    }catch(Exception e){
f@0: 	    	throw new IOException(resources.getString("dialog.error.problem.open"),e);
f@0: 	    }
f@0: 	    
f@0: 	    final List<Node> nList = readNodePrototypes(doc,persistenceDelegate);
f@0: 	    final List<Edge> eList = readEdgePrototypes(doc,persistenceDelegate);
f@0: 	    
f@0: 	    final Node[] nodes = nList.toArray(new Node[nList.size()]);
f@0: 	    final Edge[] edges = eList.toArray(new Edge[eList.size()]);
f@0: 	    
f@0: 	    Diagram diagram = Diagram.newInstance(diagramName, nodes,edges,persistenceDelegate);
f@0: 	    CollectionModel<Node,Edge> collectionModel = diagram.getCollectionModel();
f@0: 	    TreeModel<Node,Edge> treeModel = diagram.getTreeModel();
f@0: 	    
f@0: 	    /* a map linking node ids in the XML file to the actual Node object they represent */
f@0: 	    Map<String,Node> nodesId = new LinkedHashMap<String,Node>();
f@0: 	    
f@0: 	    if(doc.getElementsByTagName(COMPONENTS).item(0) == null)
f@0: 	    	throw new IOException(resources.getString("dialog.error.malformed_file"));
f@0: 	    Element componentsTag = (Element)doc.getElementsByTagName(COMPONENTS).item(0);
f@0: 	    NodeList componentsChildren = componentsTag.getChildNodes();
f@0: 	    Element nodesTag = null;
f@0: 	    for(int i=0;i<componentsChildren.getLength();i++){
f@0: 	    	if(NODES.equals(componentsChildren.item(i).getNodeName()))
f@0: 	    		nodesTag = (Element)componentsChildren.item(i);
f@0: 	    }
f@0: 	    
f@0: 	    NodeList elemList = nodesTag.getElementsByTagName(NODE);
f@0: 	    for(int i=0; i<elemList.getLength();i++){
f@0: 	    	Element nodeTag = (Element)elemList.item(i);
f@0: 	    	String idAsString = nodeTag.getAttribute(ID);
f@0: 	    	String type = nodeTag.getAttribute(TYPE);
f@0: 	    	Node prototype = null;	    	
f@0: 	    	for(Node n : nList)
f@0: 	    		if(n.getType().equals(type)){
f@0: 	    			prototype = n;
f@0: 	    			break;
f@0: 	    		}
f@0: 	    	if(prototype == null)
f@0: 	    		throw new IOException(
f@0: 	    				MessageFormat.format(
f@0: 	    						resources.getString("dialog.error.node_type_not_present"),
f@0: 	    						type));
f@0: 	    	Node node = (Node)prototype.clone(); 
f@0: 	    	
f@0: 	    	nodesId.put(idAsString, node);
f@0: 	    	
f@0: 			try {
f@0: 				Long id = Long.valueOf(idAsString);
f@0: 				node.setId(id);
f@0: 			}catch(NumberFormatException nfe){
f@0: 				throw new IOException(resources.getString("dialog.error.malformed_file"),nfe);
f@0: 			}
f@0: 			collectionModel.insert(node,DiagramEventSource.PERS);
f@0: 			try{
f@0: 				node.decode(doc, nodeTag);
f@0: 			}catch(IOException ioe){ // just give a message to the exception 
f@0: 				throw new IOException(resources.getString("dialog.error.malformed_file"),ioe);
f@0: 			}
f@0: 	    }
f@0: 	    
f@0: 	    Element edgesTag = null;
f@0: 	    for(int i=0;i<componentsChildren.getLength();i++)
f@0: 	    	if(EDGES.equals(componentsChildren.item(i).getNodeName()))
f@0: 	    		edgesTag = (Element)componentsChildren.item(i);
f@0: 
f@0: 	    elemList = edgesTag.getElementsByTagName(EDGE);
f@0: 	    for(int i=0; i<elemList.getLength();i++){
f@0: 	    	Element edgeTag = (Element)elemList.item(i);
f@0: 	    	String type = edgeTag.getAttribute(TYPE);
f@0: 	    	
f@0: 	    	Edge prototype = null;
f@0: 	    	for(Edge e : eList)
f@0: 	    		if(e.getType().equals(type)){
f@0: 	    			prototype = e;
f@0: 	    			break;
f@0: 	    		}
f@0: 	    	if(prototype == null)
f@0: 	    		throw new IOException(MessageFormat.format(
f@0: 	    				resources.getString("dialog.error.edge_type_not_present"),
f@0: 	    				type
f@0: 	    				));
f@0: 	    	
f@0: 	    	Edge edge = (Edge)prototype.clone();
f@0: 
f@0: 	    	try{
f@0: 	    		edge.decode(doc, edgeTag, nodesId);
f@0: 	    	}catch(IOException ioe){
f@0: 	    		throw new IOException(resources.getString("dialog.error.malformed_file"),ioe);
f@0: 	    	}
f@0: 	    	collectionModel.insert(edge,DiagramEventSource.PERS);
f@0: 	    }
f@0: 	    
f@0: 	    /* retrieve bookmarks */
f@0: 	    NodeList bookmarkList = root.getElementsByTagName(BOOKMARK);
f@0: 	    for(int i=0;i<bookmarkList.getLength();i++){
f@0: 	    	Element bookmarkTag = (Element)bookmarkList.item(i);
f@0: 	    	String key  = bookmarkTag.getAttribute(KEY);
f@0: 	    	if(key.isEmpty()) 
f@0: 	    		throw new IOException(resources.getString("dialog.error.malformed_file"));
f@0: 	    	String path = bookmarkTag.getTextContent();
f@0: 	    	DiagramTreeNode treeNode = getTreeNodeFromString(treeModel,path);
f@0: 	    	treeModel.putBookmark(key, treeNode,DiagramEventSource.PERS);
f@0: 	    }
f@0: 	    
f@0: 	    /* retrieve notes */
f@0: 	    NodeList noteList = root.getElementsByTagName(NOTE);
f@0: 	    for(int i=0;i<noteList.getLength();i++){
f@0: 	    	Element noteTag = (Element)noteList.item(i);
f@0: 	    	if(noteTag.getElementsByTagName(TREE_NODE).item(0) == null )
f@0: 	    		throw new IOException(resources.getString("dialog.error.malformed_file"));
f@0: 	    	Element pathTag = (Element)noteTag.getElementsByTagName(TREE_NODE).item(0);
f@0: 	    	String path = pathTag.getTextContent();
f@0: 	    	if(noteTag.getElementsByTagName(CONTENT).item(0) == null)
f@0: 	    		throw new IOException(resources.getString("dialog.error.malformed_file"));
f@0: 	    	Element contentTag = (Element)noteTag.getElementsByTagName(CONTENT).item(0);
f@0: 	    	String content = CharEscaper.restoreNewline(contentTag.getTextContent());
f@0: 	    	DiagramTreeNode treeNode = getTreeNodeFromString(treeModel,path);
f@0: 	    	treeModel.setNotes(treeNode,content,DiagramEventSource.PERS);
f@0: 	    }
f@0: 	    
f@0: 	    /* normally nodes and edges should be saved in order, this is to prevent *
f@0: 	     * a manual editing of the xml to affect  the program logic              */
f@0: 	    collectionModel.sort();
f@0: 	    /* we have to do this has the insertion in the model made it modified */
f@0: 	    collectionModel.setUnmodified();
f@0:     	return diagram;	    
f@0: 	}
f@0: 	
f@0: 	private static void writePrototypes(Document doc, Element root, Diagram diagram){
f@0: 		Node[] nodes = diagram.getNodePrototypes();
f@0: 		Edge[] edges = diagram.getEdgePrototypes();
f@0: 		Element components = doc.createElement(PROTOTYPES);
f@0:         root.appendChild(components);
f@0:         
f@0:         PrototypePersistenceDelegate delegate = diagram.getPrototypePersistenceDelegate();
f@0:         for(Node n : nodes){
f@0:         	Element nodeTag = doc.createElement(NODE);
f@0:     		components.appendChild(nodeTag);
f@0:         	delegate.encodeNodePrototype(doc, nodeTag, n);
f@0:         }
f@0:         
f@0:         for(Edge e : edges){
f@0:         	Element edgeTag = doc.createElement(EDGE);
f@0:     		components.appendChild(edgeTag);
f@0:     		delegate.encodeEdgePrototype(doc, edgeTag, e);
f@0:         }
f@0: 	}
f@0: 	
f@0: 	private static List<Node> readNodePrototypes(Document doc, PrototypePersistenceDelegate delegate) throws IOException{
f@0: 		if(doc.getElementsByTagName(PROTOTYPES).item(0) == null)
f@0: 			throw new IOException(ResourceBundle.getBundle(PersistenceManager.class.getName()).getString("dialog.error.malformed_file"));
f@0: 		Element prototypesTag = (Element)doc.getElementsByTagName(PROTOTYPES).item(0);
f@0: 		NodeList elemList = prototypesTag.getElementsByTagName(NODE);
f@0: 		final List<Node> nList = new ArrayList<Node>(elemList.getLength());
f@0: 	    for(int i=0; i<elemList.getLength();i++){
f@0: 	    	Element element = (Element)elemList.item(i);
f@0: 	    	try{
f@0: 	    		Node n = delegate.decodeNodePrototype(element);
f@0: 	    		nList.add(n);
f@0: 	    	}catch(IOException ioe){ // just set the message for the exception
f@0: 	    		throw new IOException(ResourceBundle.getBundle(PersistenceManager.class.getName()).getString("dialog.error.malformed_file"),ioe);
f@0: 	    	}
f@0: 	    }
f@0: 	    return nList;
f@0: 	}
f@0: 	
f@0: 	private static List<Edge> readEdgePrototypes(Document doc, PrototypePersistenceDelegate delegate) throws IOException{
f@0: 		if(doc.getElementsByTagName(PROTOTYPES).item(0) == null)
f@0: 			throw new IOException(ResourceBundle.getBundle(PersistenceManager.class.getName()).getString("dialog.error.malformed_file"));
f@0: 		Element prototypesTag = (Element)doc.getElementsByTagName(PROTOTYPES).item(0);
f@0: 		NodeList elemList = prototypesTag.getElementsByTagName(EDGE);
f@0: 	    final List<Edge> eList = new ArrayList<Edge>(elemList.getLength());
f@0: 	    for(int i=0; i<elemList.getLength();i++){
f@0: 	    	Element element = (Element)elemList.item(i);
f@0: 	    	try{
f@0: 	    		Edge e = delegate.decodeEdgePrototype(element);
f@0: 	    		eList.add(e);
f@0: 	    	}catch(IOException ioe){
f@0: 	    		throw new IOException(ResourceBundle.getBundle(PersistenceManager.class.getName()).getString("dialog.error.malformed_file"),ioe);
f@0: 	    	}
f@0: 	    }
f@0: 	    return eList;
f@0: 	}
f@0: 	
f@0: 	private static String getTreeNodeAsString(DiagramTreeNode treeNode){
f@0: 		TreeNode[] path = treeNode.getPath();
f@0: 		StringBuilder builder = new StringBuilder();
f@0: 		for(int i=0;i<path.length-1; i++)
f@0: 			builder.append(String.valueOf(path[i].getIndex(path[i+1]))).append(' ');
f@0: 		if(builder.toString().endsWith(" "))
f@0: 			builder.deleteCharAt(builder.length()-1);
f@0: 		return builder.toString();
f@0: 		
f@0: 	}
f@0: 	
f@0: 	private static DiagramTreeNode getTreeNodeFromString(TreeModel<Node,Edge> model, String path) throws IOException{
f@0: 		DiagramTreeNode treeNode = (DiagramTreeNode)model.getRoot();
f@0: 		if(ROOT_AS_STRING.equals(path))
f@0: 			return treeNode;
f@0: 		String[] nodesAsString = path.split(" ");
f@0: 		
f@0: 		try {
f@0: 			for(String nodeAsString : nodesAsString)
f@0: 				treeNode = (DiagramTreeNode) treeNode.getChildAt(Integer.parseInt(nodeAsString));
f@0: 		}catch(Exception e){
f@0: 			throw new IOException(e);
f@0: 		}
f@0: 		return treeNode;
f@0: 	}
f@0: 	
f@0: 	public final static String NAME = "Name";
f@0: 	public final static String DIAGRAM = "Diagram";
f@0: 	public final static String PROTOTYPE_PERSISTENCE_DELEGATE = "PrototypeDelegate";
f@0: 	public final static String COMPONENTS = "Components";
f@0: 	public final static String PROTOTYPES = "Prototypes";
f@0: 	public final static String NODE = "Node";
f@0: 	public final static String NODES = "Nodes";
f@0: 	public final static String EDGE = "Edge";
f@0: 	public final static String EDGES = "Edges";
f@0: 	public final static String POSITION = "Position";
f@0: 	public final static String PROPERTIES = "Properties";
f@0: 	public final static String PROPERTY = "Property";
f@0: 	public final static String TYPE = "Type";
f@0: 	public final static String VALUE = "Value";
f@0: 	public final static String ELEMENT = "Element";
f@0: 	public static final String LABEL = "Label";
f@0: 	public final static String POINTS = "Points";
f@0: 	public final static String POINT = "Point";
f@0: 	public final static String ID = "id";
f@0: 	public final static String NEIGHBOURS = "Neighbours";
f@0: 	public static final String MODIFIER = "Modifier";
f@0: 	public static final String MODIFIERS = "Modifiers";
f@0: 	public static final String X = "x";
f@0: 	public static final String Y = "y";
f@0: 	public static final String BOOKMARKS = "Bookmarks";
f@0: 	public static final String BOOKMARK = "Bookmark";
f@0: 	public static final String KEY = "Key";
f@0: 	public static final String NOTES = "Notes";
f@0: 	public static final String NOTE = "Note";
f@0: 	public static final String CONTENT = "Content";
f@0: 	public static final String TREE_NODE = "TreeNode";
f@0: 	private static final String ROOT_AS_STRING = "-1"; 
f@0: }