DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
DocumentBuilder db = dbf.newDocumentBuilder();
// read
Document doc = db.parse(filepath);

// modify
...

// write
TransformerFactory tfactory = TransformerFactory.newInstance();
Transformer xform = tfactory.newTransformer();
Source src = new DOMSource(newDoc);

StringWriter writer = new FileWriter("c:/123.xml");
Result result = new StreamResult(writer);
xform.transform(src, result);