E-Invoice is an XML document having a special format. The signing of E-Invoices is very similar to enveloped signatures explained in Signature Structures. The signature must be placed in the particular field defined in E-Invoice standard.

// get the element that signature will be added
Element exts = (Element)faturaDoc.getDocumentElement().getElementsByTagName("ext:UBLExtensions").item(0);
Element ext = (Element)exts.getElementsByTagName("ext:UBLExtension").item(0);
Element extContent = (Element)exts.getElementsByTagName("ext:ExtensionContent").item(0);

// generate signature
Context context = createContext();
context.setDocument(faturaDoc);
XMLSignature signature = new XMLSignature(context, false);
// attach signature to envelope structure
extContent.appendChild(signature.getElement());

Then, the method transform ,in which the whole document is included and only the signature is omitted, is added.

// use enveloped signature transform
Transforms transforms = new Transforms(context);
transforms.addTransform(new Transform(context, TransformType.ENVELOPED.getUrl()));

// add whole document(="") with envelope transform, with SHA256
// and don't include it into signature(false)
signature.addDocument("", "text/xml", transforms, DigestMethod.SHA_256, false);

Finally, the signer role ,verification public key and signing time attributes are added as stated in E-Invoice standard.

// add signer role information
SignerRole rol = new SignerRole(context, new ClaimedRole[]{new ClaimedRole(context, "Supplier")});
signature.getQualifyingProperties().getSignedSignatureProperties().setSignerRole(rol);

// e-fatura standard wants public key info in the signature
PublicKey pk = KeyUtil.decodePublicKey(new ECertificate(cert.getEncoded()).getSubjectPublicKeyInfo());
signature.getKeyInfo().add(new KeyValue(context, pk));

// add signing time
signature.getQualifyingProperties().getSignedSignatureProperties().setSigningTime(getTime());

The code is in tr.gov.tubitak.uekae.esya.api.xades.example.efatura.EFatura.