How to format the text in an XML file

Question

This should be a fairly easy one. A fairly easy one that seems to be hard to actually find.
When I write out the XML file, it's all on a single line. Not a huge problem all things considered (it works), but an annoying one.
Here's the a snippet, to show what I'm doing. There's not enough information for this to actually compile, if one is so inclined, just comment out a bunch of things and have it write out aribitary data.
Is this a case where I just need to manually write the formating myself?
public void saveXML(File file){
        try{
            Document doc = DocumentBuilderFactory.newInstance().
                newDocumentBuilder().newDocument();
            //give that document a root
            Element root = doc.createElement("root");
            doc.appendChild(root);
            Command[] command=getCommands();
            for (int index=0; index < command.length; index++){
                Element element = doc.createElement("Command");
                root.appendChild(element);
                //get the name of the parser class this command should use
                String pName=command[index].getParser().getClass().getName();
                //remove everything but the last word
                pName=pName.substring(JavaMUServer.PARSER_PATH.length());
                //set the information.
                element.setAttribute("name",
                    command[index].getName());               
                element.setAttribute("parser",pName);               
                element.setAttribute("method",
                    command[index].getMethod().getName());
            TransformerFactory tFactory =TransformerFactory.newInstance();
            Transformer transformer = tFactory.newTransformer();
            DOMSource source = new DOMSource(doc);
            StreamResult result = new StreamResult(
                new FileWriter(file));
            transformer.transform(source, result);
        }catch (Exception e){
            e.printStackTrace();
    }

Answer 1

Well, that helped quite a bit. Seems however when I set the indent property, rather then indenting it just makes new lines. Rather counter intuitive.
Here's the slightly modified code (changed one line really. Tried setting a few different properties.)
public void saveXML(File file){
        try{
            Document doc = DocumentBuilderFactory.newInstance().
                newDocumentBuilder().newDocument();
            //give that document a root
            Element root = doc.createElement("root");
            doc.appendChild(root);
            Command[] command=getCommands();
            for (int index=0; index < command.length; index++){
                Element element = doc.createElement("Command");
                root.appendChild(element);
                element.appendChild(doc.createElement("sample"));
                //get the name of the parser class this command should use
                String pName=command[index].getParser().getClass().getName();
                //remove everything but the last word
                pName=pName.substring(JavaMUServer.PARSER_PATH.length());
                //set the information.
                element.setAttribute("name",
                    command[index].getName());               
                element.setAttribute("parser",pName);               
                element.setAttribute("method",
                    command[index].getMethod().getName());
            TransformerFactory tFactory =TransformerFactory.newInstance();
            Transformer transformer = tFactory.newTransformer();
            transformer.setOutputProperty("indent", "yes");
            //transformer.setOutputProperty("method", "xml");
            DOMSource source = new DOMSource(doc);
            StreamResult result = new StreamResult(
                new FileWriter(file));
            transformer.transform(source, result);
        }catch (Exception e){
            e.printStackTrace();