Format XML file in java

I already created an xml, and i was obliged to modify it using PrintWriter Class. (copying line by line the xml file and modify what i need) but i lost my indentation.

i tried this :

DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
DocumentBuilder builder = factory.newDocumentBuilder();
Document document = builder.parse(new InputSource(new InputStreamReader(new FileInputStream(
"notes.xml"))));
Transformer xformer = TransformerFactory.newInstance().newTransformer();
xformer.setOutputProperty(OutputKeys.METHOD, "xml");
xformer.setOutputProperty(OutputKeys.INDENT, "yes");
xformer.setOutputProperty("b;http://xml.apache.org/xsltd;indent-amount", "4");
//xformer.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
Source source = new DOMSource(document);
Result result = new StreamResult(new File("notes.xml"));
xformer.transform(source, result);

but this isn't working : having an exception in the third line :

[Fatal Error] :3:6537: XML document structures must start and end within the same entity.
org.xml.sax.SAXParseException; lineNumber: 3; columnNumber: 6537; XML document structures must start and end within the same entity.
at com.sun.org.apache.xerces.internal.parsers.DOMParser.parse(DOMParser.java:257)
at com.sun.org.apache.xerces.internal.jaxp.DocumentBuilderImpl.parse(DocumentBuilderImpl.java:347)

So, Is there a way to format an already created XML file in java ?