Pretty-printing XML using Java

There are a dozen threads regarding that topic, but all of them contain answers that do not work for me in a satisfactory manner. It seems one needs to use a specific DOM implementation. However, I cannot get it to read the xml input:

@Test
public void testPrettyPrintConvertDomLevel3() {
    String unformattedXml
            = "<?xml version=\"1.0\" encoding=\"UTF-16\"?><QueryMessage\n"
            + "        xmlns=\"http://ift.tt/1m0rTGL\"\n"
            + "        xmlns:query=\"http://ift.tt/WTKLe8\">\n"
            + "    <Query>\n"
            + "        <query:CategorySchemeWhere>\n"
            + "   \t\t\t\t\t         <query:AgencyID>ECB\n\n\n\n</query:AgencyID>\n"
            + "        </query:CategorySchemeWhere>\n"
            + "    </Query>\n\n\n\n\n"
            + "</QueryMessage>";

    System.out.println(prettyPrintWithXercesDomLevel3(unformattedXml));
}

Here is the method:

public static String prettyPrintWithXercesDomLevel3(String xml) {
    try {
        DOMImplementationRegistry registry = DOMImplementationRegistry.newInstance();
        DOMImplementationLS impl = (DOMImplementationLS) registry.getDOMImplementation("XML 3.0 LS 3.0");
        if (impl == null) {
            throw new RuntimeException("No DOMImplementation found !");
        }

        log.info(String.format("DOMImplementationLS: %s", impl.getClass().getName()));

        LSParser parser = impl.createLSParser(
                DOMImplementationLS.MODE_SYNCHRONOUS,
                "http://ift.tt/1Haow7f");
        // http://ift.tt/tphNwY
        log.info(String.format("LSParser: %s", parser.getClass().getName()));
        LSInput lsi = impl.createLSInput();
        lsi.setByteStream(new ByteArrayInputStream(xml.getBytes()));
        Document doc = parser.parse(lsi);

        LSSerializer serializer = impl.createLSSerializer();
        LSOutput output = impl.createLSOutput();
        output.setEncoding("UTF-8");
        ByteArrayOutputStream baos = new ByteArrayOutputStream();
        output.setByteStream(baos);
        serializer.write(doc, output);
        return baos.toString();
    } catch (Exception e) {
        throw new RuntimeException(e);
    }
}

And this is what I get:

java.lang.RuntimeException: org.w3c.dom.ls.LSException: Content is not allowed in prolog.
at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
at org.apache.xerces.impl.XMLScanner.reportFatalError(Unknown Source)
at org.apache.xerces.impl.XMLDocumentScannerImpl$PrologDispatcher.dispatch(Unknown Source)
at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
at org.apache.xerces.parsers.DTDConfiguration.parse(Unknown Source)
at org.apache.xerces.parsers.DTDConfiguration.parse(Unknown Source)
at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
at org.apache.xerces.parsers.DOMParserImpl.parse(Unknown Source)
at tests.javax.xml.XMLWriterTest.prettyPrintWithXercesDomLevel3(XMLWriterTest.java:176)
at tests.javax.xml.XMLWriterTest.testPrettyPrintConvertDomLevel3(XMLWriterTest.java:219)