Authenticated encryption requires that we use some accepted standard for encrypting and authenticating a message. So we both encrypt the message and compute a MAC on the messag
When transferring files from one server to another through secure ftp, I use private/public key pairs with the private key residing on the "from" server and the public key residing on the "to" server.
Using private/public key pairs is a secure standard when transferring files.
I believe it would also be a secure means in the context of a Java application.
Check out Generating and Verifying Signatures and Generate Public and Private Keys for more details on using a private/public key pair setup for digital signatures in Java.