On Mon, Mar 28, 2011 at 9:26 PM, Nicholas Ingolia <n...@ingolia.org> wrote: > On Mar 28, 2011, at 5:16 PM, Ketil Malde wrote: >> this line of thought is interesting, I think. Perhaps we can supply an >> Offset1 newtype as well for use with 1-based data formats? Probably >> only internally, so that e.g. a SeqLoc will always use zero-based >> offsets. > > I was thinking that there could be an alternate Bio.SeqLoc.Position1Based > module that re-exported Offset as an opaque data type and provided > > mkOffset1 :: Int64 -> Offset > unOffset1 :: Offset -> Int64 > > The internal representation would be unchanged but the client would see the > conversion of offsets to numbers using 1-based indexing (and your call on how > it deals with the -1/+1 jump). > > Handling the Num instance would be tricky, some of the operations would be > wrong (e.g., literal 0 of type (Num a) => a would not be shifted properly) > and others would be confusing (e.g., you don't add two 1-based offsets) but I > don't believe we can control the re-export of the Offset Num instance.
I believe this will be a great source of confusion. I propose that we use only one kind of Offset. The frontend may use +1 or -1 where appropriate. Cheers, -- Felipe. _______________________________________________ Biohaskell mailing list Biohaskell@biohaskell.org http://malde.org/cgi-bin/mailman/listinfo/biohaskell
