James, Deserialization can only be done into an empty CAS, and from within an annotator that means one passed by the framework in the getNext method of a Collection Reader or acquired by the GetEmptyCAS() method in a CAS Multiplier.
If for each text file you have two XMI files each containing the text as their Sofas, I'd think the simplest solution would be to implement A) by modifying the XmiCollectionReader in the examples folder to alternatively read the XMI files from the two types of annotators and make your comparison annotator act like a CAS Consumer and save the results from the odd-numbered CASes to compare with the even-numbered ones. ~Burn
