Recursive XML-parser

Unless your file is huge, you can use the java DOM parser (the DOM parser keeps the file in memory)

Given a node (starting with the root), you can enumerate its children, and then call the same function on each child recursively.

import java.io.IOException;
import java.util.ArrayList;
import java.util.List;

import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.ParserConfigurationException;

import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
import org.xml.sax.SAXException;

public class RecursiveDOM {
    public static void main(final String[] args) throws SAXException, IOException, ParserConfigurationException {
        new RecursiveDOM("file.xml");
    }

    public RecursiveDOM(final String file) throws SAXException, IOException, ParserConfigurationException {
        final DocumentBuilderFactory dbfac = DocumentBuilderFactory.newInstance();
        final DocumentBuilder docBuilder = dbfac.newDocumentBuilder();
        final Document doc = docBuilder.parse(this.getClass().getResourceAsStream(file));
        final List<String> l = new ArrayList<String>();
        parse(doc, l, doc.getDocumentElement());
        System.out.println(l);
    }

    private void parse(final Document doc, final List<String> list, final Element e) {
        final NodeList children = e.getChildNodes();
        for (int i = 0; i < children.getLength(); i++) {
            final Node n = children.item(i);
            if (n.getNodeType() == Node.ELEMENT_NODE) {
                list.add(n.getNodeName());
                parse(doc, list, (Element) n);
            }
        }
    }

}

Result:

[FUNCTION, NAME, CALLS, FUNCTION, NAME, CALLS, FUNCTION, NAME, FUNCTION, NAME]

Also, you can consider using JAXB (mapping classes to XML), which would result in a tree of java classes, if implemented properly each class can implement a particular type of function so the tree can be recursively "calculated".

This is a basic JAXB implementation, use Config.unmarshal to rebuild it from an InputStream:

import java.io.OutputStream;
import java.io.Reader;

import javax.xml.bind.JAXBContext;
import javax.xml.bind.JAXBException;
import javax.xml.bind.Marshaller;
import javax.xml.bind.Unmarshaller;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlRootElement;

public class TestJAXB {

    public static void main(final String[] args) throws JAXBException {
        final Function e5 = new Function("N5", null);
        final Function e6 = new Function("N6", null);
        final Function e4 = new Function("N4", null);
        final Function e2 = new Function("N2", ((new Call[] { new Call(e4) })));
        final Function e3 = new Function("N3", ((new Call[] { new Call(e5) })));
        final Function e1 = new Function("N1", ((new Call[] { new Call(e2), new Call(e3) })));
        new Config(new Function[] { e1, e6 }).marshall(System.out);
    }

    @XmlRootElement(name = "CONFIG")
    static class Config {
        @XmlElement(name = "FUNCTION")
        private Function[] functions;

        public Config(final Function[] f) {
            this.functions = f;
        }

        protected Config() {
        }

        public void marshall(final OutputStream out) throws JAXBException {
            final JAXBContext jaxbContext = JAXBContext.newInstance(this.getClass());
            final Marshaller marshaller = jaxbContext.createMarshaller();
            marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, Boolean.TRUE);
            marshaller.marshal(this, out);
        }

        public final static Config unmarshall(final Reader r) throws JAXBException {
            final JAXBContext jaxbContext = JAXBContext.newInstance(Config.class);
            final Unmarshaller unmarshaller = jaxbContext.createUnmarshaller();
            return (Config) unmarshaller.unmarshal(r);
        }

    }

    @XmlRootElement(name = "FUNCTION")
    static class Function {
        @XmlElement(name = "NAME")
        String name;

        @XmlElement(name = "CALLS")
        Call[] calls;

        public Function(final String name, final Call[] calls) {
            this.name = name;
            this.calls = calls;
        }

        protected Function() {
        }

    }

    @XmlRootElement(name = "CALL")
    static class Call {
        @XmlElement(name = "FUNCTION")
        Function f;

        protected Call() {
        }

        public Call(final Function f) {
            this.f = f;
        }

    }
}