Create method to align single model to a reference.

[TJGorrie]

Ideally we shouldn't have to re-align a full experiment if only 1-2 structures change so a method is needed that takes the name of the reference and is used so that new, incoming data or old, updated data can be processed without affecting the remaining results. For data integrity purposes. As a result we need to be able to store the name of the reference file (OR copy the reference file and call it reference and just ignore it later on...)