UDPATE calculate(): default behavior is to NOT subtract the minimum value from the trace. I think this should be explicit since doing this is not the right thing to do unless both acceptor and donor are known to hit background level in this trace. In practice, this happens for our hairpins, but is not necessarily true for other measurements. Less magic is better. Think about these analysis details more and how to include them in an easy to use way, for example, with a sort of OPTIONS class that encapsulates the possible methods.