public class XML {

private int rowNum = 0;
private int columnNum = 0;

public XMLStreamReader xmlInput() {

    XMLStreamReader reader = null;

    try {

        XMLInputFactory inputFactory = XMLInputFactory.newInstance();
        InputStream file = new FileInputStream(
                "Users/kevlar/Dropbox/PhD/Java/Metabolites/src/HMDB/HMDB00316.xml");
        reader = inputFactory.createXMLStreamReader(file);

    } catch (XMLStreamException e) {
        System.err.println("XMLStreamException : " + e.getMessage());

    } catch (FactoryConfigurationError e) {
        System.err.println("FactoryConfigurationError : " + e.getMessage());

    } catch (FileNotFoundException e) {
        System.err.println("FileNotFoundException : " + e.getMessage());

    }
    return reader;
}

private void findElements(String input) throws XMLStreamException {

    TreeNode[] children;
    Workbook wb = new HSSFWorkbook();
    Sheet sheet1 = wb.createSheet("Metabolites");
    String[] elementsSplit = input.split("\s*,\s*");
    xmlInput();
    XMLStreamReader reader = xmlInput();
    reader.nextTag();

    do {
        if (reader.getEventType() == XMLStreamConstants.START_ELEMENT
                && reader.getLocalName() == "metabolite") {
            children = mainElements(reader).children();

            printValues(children, elementsSplit, sheet1);
            children = null;
        } else {
            reader.next();
        }
    } while (reader.hasNext());

    reader.close();

    try {
        FileOutputStream output = new FileOutputStream("HMDB.xls");
        wb.write(output);
        output.close();
    } catch (Exception e) {
        e.printStackTrace();
    }

}

private void printValues(TreeNode[] children, String[] elementsSplit,
        Sheet sheet1) {

    rowNum++;
    Row row = sheet1.createRow(rowNum);
    Cell cell = row.createCell(columnNum);

    for (int i = 0; i < children.length; i++) {
        TreeNode element = children[i];
        String elementName = element.getElementName();

        for (int j = 0; j < elementsSplit.length; j++) {
            String searchName = elementsSplit[j];

            if (searchName.equals(elementName)) {

                if (element.hasChildren()) {
                    recurse(element.children(), cell);
                } else {
                    columnNum++;
                    cell.setCellValue(element.getElementValue());
                    System.out.println("Element:- "
                            + element.getElementName() + " | Value:- "
                            + element.getElementValue());
                }
            }
        }
    }

    cell = null;
}

private void recurse(TreeNode[] children, Cell cell) {

    for (int i = 0; i < children.length; i++) {
        TreeNode node = children[i];
        if (node.hasChildren()) {
            System.out.println("Element:- " + node.getElementName()
                    + " and it's subelements:- ");
            recurse(node.children(), cell);
        }

        else if (!node.hasChildren()) {
            columnNum++;
            cell.setCellValue(node.getElementValue());
            System.out.println("Element:- " + node.getElementName()
                    + " | Value:- " + node.getElementValue());
        }
    }
}

private TreeNode mainElements(XMLStreamReader reader)
        throws XMLStreamException {

    Element rootElement = new Element();
    rootElement.setName(reader.getLocalName());
    TreeNode root = new TreeNode(rootElement);

    int level = 1;

    do {
        int event = reader.next();

        if (event == XMLStreamConstants.START_ELEMENT) {

            Element element = new Element();
            element.setName(reader.getLocalName());
            TreeNode node = new TreeNode(element);
            level++;

            if (level == 2) {
                root.add(subElements(reader, node));
                level--;

            }

        } else if (event == XMLStreamConstants.END_ELEMENT) {
            level--;
        }

    } while (level > 0);

    return root;
}

private TreeNode subElements(XMLStreamReader reader, TreeNode node)
        throws XMLStreamException {

    int level = 1;

    TreeNode newNode = new TreeNode();
    newNode = node;

    do {
        int event = reader.next();

        if (event == XMLStreamConstants.START_ELEMENT) {

            Element subElement = new Element();
            subElement.setName(reader.getLocalName());
            TreeNode subNode = new TreeNode(subElement);
            level++;

            if (level == 2) {
                newNode.add(subElements(reader, subNode));
                level--;
            }

        } else if (event == XMLStreamConstants.CHARACTERS
                && !reader.isWhiteSpace()) {

            newNode.getElement().setValue(reader.getText());

        } else if (event == XMLStreamConstants.END_ELEMENT) {
            level--;
        }

    } while (level > 0);

    return newNode;
}

public static void main(String[] args) throws XMLStreamException {

    XML test = new XML();
    test.findElements("accession, inchikey");

}

}