I'm not clear on how you'd like this pipeline to work, e.g. what are the inputs & outputs to this annotator?
A) Are you feeding it a stream of CASes created from the pairs of XMI files to be compared? e.g. X1 Y1 X2 Y2 X3 Y3 ... where X1 & Y1 are to be compared, then X2 Y2 etc. If so then your annotator could extract the information from the 1st and save it locally to compare with the information in the 2nd member of the pair when it arrives. B} Or does the input CAS merely contain the names of the two XMI files to be compared, in which case you should follow Eddie's suggestion and implement it as a CAS Multiplier so that it can create a couple of empty CASes to deserialize into. Since the deserialize calls reconstruct a complete CAS they can only be applied to empty CASes so are usually made in Collection Readers or CAS Multipliers. ~Burn
