[emboss-dev] Mapping EMBOSS to Ruby, Perl and Python

Pjotr Prins pjotr.public78 at thebird.nl
Tue Dec 1 12:35:10 UTC 2009

On Tue, Dec 01, 2009 at 12:02:21PM +0000, Peter wrote:
> On Mon, Nov 30, 2009 at 11:57 AM, Pjotr Prins <pjotr.public78 at thebird.nl> wrote:
> >
> > The file emboss/function/emboss_transeq.c may get some extra
> > interfaces - the idea is that is contains nicely named and direct
> > methods (unlike the internal 'ajCamelCase' naming conventions).
> >
> Naming conventions and what is "nice" is a personal judgement.


> Why change things? For anyone used to the EMBOSS code base,
> it is very advantageous to preserve the old names in any interface.

The standard naming is available - and not going to disappear. I
don't expect anyone to change his/her ways.

> I would also say it makes sense to keep the "aj" prefix - it acts
> as a namespace, avoiding name collisions with internal names.

It is poor-mans namespacing. And it is fine for the backend. There is
no reason not to provide something better for users. Especially if
the front-end is C with extensions. With Biolib I can even introduce
C++, if needed.

Anyway, if EMBOSS does not like it - it does not have to go into the
main code base. I would prefer to export, at least, transeq and
transeq_acd to the external world. That would align with EMBOSS'
documentation of the binaries. It would make sense (to me) to have
that in the main code base.

The only thing I am really asking is to split code out of the main()


More information about the emboss-dev mailing list