public PurchaseOrderDocument createDocument(PurchaseOrderDocument poDoc,
    String file) 
{
        // Get object reference of root element.
        PurchaseOrderDocument.PurchaseOrder purchaseOrderElement = poDoc.getPurchaseOrder();
        InvoiceHeaderDocument.InvoiceHeader invHeaders = purchaseOrderElement.addNewInvoiceHeader();
        // Assign values to the newly created invoice-header element.
        NameAddress shipto = invHeaders.addNewShipTo();
        shipto.setName("New Company");
        shipto.setAddress("NewTown, NewCity");
        NameAddress billto = invHeaders.addNewBillTo();
        billto.setName("New Company");
        billto.setAddress("NewTown, NewCity");
        // Create a new Book and add it to the invoice.
        BookType book = BookType.Factory.newInstance();
        book.setId(1000);
        book.setTitle("Where the Red Fern Grows");
        invHeaders.setProduct(book);
        XmlCursor cursor = invHeaders.getProduct().newCursor();
        cursor.setName(new QName("http://xmlbeans.apache.org/samples/substitutiongroup/easypo", "book"));
        cursor.dispose();
        // Creating a new comment - with substitution group member bill-comment element.
        invHeaders.setComment("This is a new bill-comment");
        cursor = invHeaders.xgetComment().newCursor();
        cursor.setName(new QName("http://xmlbeans.apache.org/samples/substitutiongroup/easypo", "bill-comment"));
        cursor.dispose();
        // Add another invoice-header.
        invHeaders = purchaseOrderElement.addNewInvoiceHeader();
        // Assign values to the newly created invoice-header element.
        shipto = invHeaders.addNewShipTo();
        shipto.setName("Other Company");
        shipto.setAddress("OtherTown, OtherCity");
        billto = invHeaders.addNewBillTo();
        billto.setName("Other Company");
        billto.setAddress("OtherTown, OtherCity");
        // Create a new Clothing and add it to the invoice.
        ClothingType clothing = ClothingType.Factory.newInstance();
        clothing.setId(2000);
        clothing.setColor(ClothingType.Color.BLUE);
        invHeaders.setProduct(clothing);
        cursor = invHeaders.getProduct().newCursor();
        cursor.setName(new QName("http://xmlbeans.apache.org/samples/substitutiongroup/easypo", "clothing"));
        cursor.dispose();
        // Creating a new comment - with substitution group member bill-comment element.
        invHeaders.setComment("This is a new bill-comment");
        cursor = invHeaders.xgetComment().newCursor();
        cursor.setName(new QName("http://xmlbeans.apache.org/samples/substitutiongroup/easypo", "ship-comment"));
        cursor.dispose();
        // Validate it.
        validateXml(poDoc);
        XmlOptions xmlOptions = new XmlOptions();
        xmlOptions.setSavePrettyPrint();
        File f = new File(file);
        try
        {
            //Writing the XML Instance to a file.
            poDoc.save(f,xmlOptions);
        }
        catch(IOException e)
        {
            e.printStackTrace();
        }
        System.out.println("\n\n\nXML Instance Document saved at : " + f.getPath());
        return poDoc;
}

This method creates an new invoice-header element and attaches to the existing XML Instance, and saves the new Instance to a file(args[1]).

 public static  void main(String[] args) 
{
        // Create an instance of this class to work with.
        SubstitutionGroup subGrp = new SubstitutionGroup();
        // Create an instance of a type based on the received XML's schema
        PurchaseOrderDocument poDoc = subGrp.parseXml(args[0]);
        // Validate it
        validateXml(poDoc);
        // Prints the comments from the XML, also the name of the substitute tokens.
        subGrp.printComments(poDoc);
        // Creates a new XML and saves the file
        subGrp.createDocument(poDoc,args[1]);
}

Receives an XML Instance and prints the substitution group element names and values, Also creates a new XML Instance.

 public PurchaseOrderDocument parseXml(String file) 
{
        File xmlfile = new File(file);
        PurchaseOrderDocument poDoc = null;
        try 
        {
            poDoc = PurchaseOrderDocument.Factory.parse(xmlfile);
        }
        catch(XmlException e){
            e.printStackTrace();
        }
        catch(IOException e){
            e.printStackTrace();
        }
        return poDoc;
}

 public  void printComments(PurchaseOrderDocument poDoc) 
{
        // Get object reference of root element.
        PurchaseOrderDocument.PurchaseOrder purchaseOrderElement = poDoc.getPurchaseOrder();
        // Get all the invoice-header elements for purchase-order.
        InvoiceHeaderDocument.InvoiceHeader[] invHeaders = purchaseOrderElement.getInvoiceHeaderArray();
        System.out.println("\n\n=========Contents==========\n");
        // Iterate through each invoice-header elements printing only the element name and value for substitution group
        // comment as defined in Easypo.xsd.
        for (int i=0;i< invHeaders.length;i++){
            System.out.println("\nInvoiceHeader["+i+"]");
            XmlCursor cursor = invHeaders[i].xgetComment().newCursor();
            System.out.println("Element Name (Local Part): " + cursor.getName().getLocalPart());
            System.out.println("Element Value: " + invHeaders[i].getComment().trim());
            cursor.dispose();
        }
}

This method prints the substitution group element names(local part) and values for each Invoice-header element in the XML Instance. (The rest of elements are ignored for the sake of simplicity)

 public static boolean validateXml(XmlObject xml) 
{
        boolean isXmlValid = false;
        // A collection instance to hold validation error messages.
        ArrayList validationMessages = new ArrayList();
        // Validate the XML, collecting messages.
        isXmlValid = xml.validate(
                new XmlOptions().setErrorListener(validationMessages));
        // If the XML isn't valid, print the messages.
        if (!isXmlValid)
        {
            System.out.println("\nInvalid XML: ");
            for (int i = 0; i <  validationMessages.size(); i++)
            {
                XmlError error = (XmlError) validationMessages.get(i);
                System.out.println(error.getMessage());
                System.out.println(error.getObjectLocation());
            }
        }
        return isXmlValid;
}

Validates the XML, printing error messages when the XML is invalid. Note that this method will properly validate any instance of a compiled schema type because all of these types extend XmlObject.

Note that in actual practice, you'll probably want to use an assertion when validating if you want to ensure that your code doesn't pass along invalid XML. This sample prints the generated XML whether or not it's valid so that you can see the result in both cases.