[Biocorba-l] idl 0.2 discussion

[ableasby@hgmp.mrc.ac.uk]

Jason writes:

>(I'm not leaving EMBOSS out in the cold here intentionally, I just don't
>know how/where they fit in right now.)

First, just committed some EMBOSS (ajax) code to the repository on
bio.perl.org along with an application "corbatest" to retrieve
sequence and feature data using IDL 0.2 (not pretty but enough
for what's described below)..

Secondly, I'm not sure either without knowing what the other projects
are doing with corba. From the EMBOSS point of view (the word
philosophy is overused) we want to be able to provide seamless access
to data from any source. So, you can get EMBL entries from emblcd
indexed flatfiles, GCG databases (God help us), BLAST databases, SRS
servers or by firing up external applications. The sequences are easy.
When the database provision method gives feature table information it
can be used. Currently the feature tables must be as supplied by EMBL
or GenBank so (e.g) srs is OK, blast isn't. Applications allow you,
for example, to construct CDS sequences however they're joined,
complemented or spread across entries.

At the moment we're reorganising the internal representation of features
to what I've christened the EMBOSS Flexible Open Feature Format (EFOFF)
although the following points apply to the current format also.

Given the IDL we can get the sequence quite quickly. To get the full
feature information takes lots of iterations and this can take quite a
while to load up an object.
We'll then have to write another routine to convert this info to EFOFF.
(that's why I've committed the code; so another developer who's doing
EFOFF can have a look to see if the information from IDL 0.2 can mesh).

What would be ideal from our point of view would be if the original-format
feature text could be retrieved in one (or a few) slurps. We could then
use the existing parsers to get the information into EFOFF quickly.

Other applications of CORBA for us will be (e.g.) remote execution of
EMBOSS (or bio*) applications.

Hope that explains things a bit.

(the other)
Alan