This is an example for Java's XML Signature API. The foundation is a straight copy of [this Oracle tutorial] (http://java.sun.com/developer/technicalArticles/xml/dig_signature_api/). It reads both private key and public key from PKCS12 to sign or validate XML files.
Create PrivateKeyData by handing a path and the passphrase for the key file and the private key inside.
Create either an XmlSigner or an XmlValidator with it.
Call sign with the path to the unsigned XML file you want to sign and another path indicating where to put the result.
Call verify with the path to the signed XML file you want to verify.
Do what you want. Whether it's modify, copy, distribute, use comercially - I don't care. The project comes without any warranty whatsoever.