Transformer transformer = TransformerFactory.newInstance().newTransformer();
transformer.setOutputProperty(OutputKeys.INDENT, "yes");
transformer.setOutputProperty("{http://xml.apache.org/xslt}indent-amount", "2");
// initialize StreamResult with File object to save to file
StreamResult result = new StreamResult(new StringWriter());
DOMSource source = new DOMSource(doc);
transformer.transform(source, result);
String xmlString = result.getWriter().toString();
System.out.println(xmlString);

Note: Results may vary depending on the Java version. Search for workarounds specific to your platform.

In reply to Espinosa's comment, here is a solution when "the original xml is not already (partially) indented or contain new lines".

Background

Excerpt from the article (see References below) inspiring this solution:

Based on the DOM specification, whitespaces outside the tags are perfectly valid and they are properly preserved. To remove them, we can use XPath’s normalize-space to locate all the whitespace nodes and remove them first.

Java Code

public static String toPrettyString(String xml, int indent) {
    try {
        // Turn xml string into a document
        Document document = DocumentBuilderFactory.newInstance()
                .newDocumentBuilder()
                .parse(new InputSource(new ByteArrayInputStream(xml.getBytes("utf-8"))));

        // Remove whitespaces outside tags
        document.normalize();
        XPath xPath = XPathFactory.newInstance().newXPath();
        NodeList nodeList = (NodeList) xPath.evaluate("//text()[normalize-space()='']",
                                                      document,
                                                      XPathConstants.NODESET);

        for (int i = 0; i < nodeList.getLength(); ++i) {
            Node node = nodeList.item(i);
            node.getParentNode().removeChild(node);
        }

        // Setup pretty print options
        TransformerFactory transformerFactory = TransformerFactory.newInstance();
        transformerFactory.setAttribute("indent-number", indent);
        Transformer transformer = transformerFactory.newTransformer();
        transformer.setOutputProperty(OutputKeys.ENCODING, "UTF-8");
        transformer.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
        transformer.setOutputProperty(OutputKeys.INDENT, "yes");

        // Return pretty print xml string
        StringWriter stringWriter = new StringWriter();
        transformer.transform(new DOMSource(document), new StreamResult(stringWriter));
        return stringWriter.toString();
    } catch (Exception e) {
        throw new RuntimeException(e);
    }
}

Sample usage

String xml = "<root>" + //
             "\n   "  + //
             "\n<name>Coco Puff</name>" + //
             "\n        <total>10</total>    </root>";

System.out.println(toPrettyString(xml, 4));

Output

<root>
    <name>Coco Puff</name>
    <total>10</total>
</root>

References

• Java: Properly Indenting XML String published on MyShittyCode
• Save new XML node to file