[Genquire-dev] dbObj

[Mark Wilkinson]

Hey Dave!

I have decided (since we are about to publish the Genquire paper and book
chapter) that it is about time we tested this adaptor API to ensure that
a person with half a brain can put together their own adaptor layer...
and I seem like a perfect candidate for THAT  job!!    ;-)

I have imediately hit a point of confusion:

In the gq_local.cfg file the first thing that is created is a DbObj, and
this is sent as an initialization parameter for Context.  Is it necessary
for all Adaptor layers to have a DbObj, or is this required only by our
own Genquire_local adaptor?  If the latter, then I will add a note in the
gq_local.cfg file indicating this, and will also clarify the API docs.
It seems to be that the only thing that calls DbObj is the Context module
itself, so I am guessing that a DbObj is not a 'deep' part of Genquire.

I am also wondering if it might be a good idea to put Context.pm into the
/Adaptor/  folder, since any new adaptor is going to require its own
version of the Context module anyway (according to the API docs).  I am
guessing we can leave ContextI where it is, since it should be common to
all adaptors, but Context.pm itself seems to belong with its
"brothers"....  what say you?

To make my own adaptor layer, I have created a new folder
/GB_FlatAdaptor/ and copied all of the modules from /Adaptor? into that
folder.  I then updated the identities of the package statements, and the
@ISA and use statements.  There isn't anything more to this... right?...
no hidden land mines that I should look out for?  (at least, none that
you know about...)

To be honest, it looks like it is going to be quite straightforward.  My
gb_flat.cfg file is going to create a BioPerl Seq object from the GB flat
file, so I already have almost all of the Genquire functionality right at
hand before I even start coding!!

please get back to me with *quick* answers ASAP so that I can continue.

Actually, this looks like it is going to be a lot of fun!!!  I like being
a guinea pig   8^)

M



--
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"Speed is subsittute fo accurancy."
________________________________

Dr. Mark Wilkinson
Bioinformatics Group
National Research Council of Canada
Plant Biotechnology Institute
110 Gymnasium Place
Saskatoon, SK
Canada