* Ketil Malde <ke...@malde.org> [10.12.2012 12:56]:
> Christian Höner zu Siederdissen <choe...@tbi.univie.ac.at> writes:
>
> > do you want to have certain laws? Like header = id + (" " +)
> > description? In general, seqid + seqheader seems the most useful
> > combination in terms of fasta http://en.wikipedia.org/wiki/FASTA_format
> > assuming that the full line is a header (id + desc). Of course, that
> > would be a "3." -- and I am ignoring all other formats out there that
> > could be BioSeq's.
>
> Yes, it strikes me as perhaps the best option: add seqid and seqheader,
> remove seqlabel from the class, but make it a separate alias with a
> deprecation warning.
>
> Anyone opposed?If seqid returns an (unspecified) substring of seqheader , it sounds ok. Unspecified as it may not always be something like the 1st word. > > Also, I think one should be able to work with sequences as far as > possible without resorting to Bytestring operations (exposing the > internals). What about a Functor instance working on the payload? Assuming that one "copy"s the seqheader? In general I am not a fan of hiding implementation details, I tend to find odd uses. > > Is it okay to use Monoid for appending and (m)empty? And have separate > 'slice' and 'copy' (or perhaps 'defragment')? Any implementor of the > classes would have to bear the burden of implementing this as well, of > course. > > -k Though generalization sounds good. Gruss, Christian
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