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

[Pjotr Prins]

For your inspection, I have committed a patch for splitting out the
logic of ./emboss/transeq.c. The patch is here:

  http://github.com/pjotrp/EMBOSS/commit/713800c4aa08ddf70b87f245a524c1a0b30c0942

The simplified transeq.c is here:

  http://github.com/pjotrp/EMBOSS/blob/biolib/emboss/transeq.c

The new interfaces are here:

  http://github.com/pjotrp/EMBOSS/blob/biolib/emboss/function/emboss_transeq.c

Basically I have split out the ACD logic and programming logic and
given them new names:

  int transeq_acd(int argc, char **argv)

  AjPSeqout transeq( AjPSeqall seqall, AjPStr *framelist, AjPStr tablename, AjPRange regions, AjBool trim, AjBool clean, AjBool alternate)

so you can call either from an external program. The advantage being
the call interface is exactly the same, whether from the command
line, the web interface, or directly through a shared linked library.

What do you think? I propose to (slowly) accept splitting out the
other routines in this fashion. As it does not interfere with EMBOSS
it can be done in small steps.

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). A
useful one would be a simple one reading frame translation with
pre-selected translation table (for speed). But more on that later -
I can also weight-lift that in biolib itself.

The reason I want to do this here is to prevent duplication of
functionality at different levels. 

Pj.