[Genquire-dev] important update

[Mark Wilkinson]

Hi all,

There has been a reasonably important update to QueryScreen just now.
QueryScreen, and in turn SeqCanvas, now inherit their list of feature types
from Context.pm's  %type_hash value.  The mapping is done 1:1 with the
exception of Gene objects, which by necessity must exist in SeqCanvas as
BioPerl GeneStructure objects for a part of their lives, so a small
translation is made in lines 626, 627 to accomodate this.  If any of you
want to play "let's be Lincoln" and find a prettier one-line way to do that
translation please go ahead... I'm not smart enough   8-)

I also updated the documentation in various places to describe the
relationship between this %type_hash and the FeatureTypes table in the
database - for the case of the default Genquire database they should be
mirrors of each other.

A note for DB administrators:  unless directly specified, $feature->type is
taken from $feature->primary_tag (including in the bulk_parse_contigs.pl
script !!!), so be careful when creating database features via Genquire's
feature hierarchy.  Either specify the type directly during Feature object
creation as the database **index** of the FeatureType entry you wish, or
make the spelling and case of $feature->primary_tag exactly match the
desired entry in FeatureTypes table, and it will be assigned that type
automatically.  If you are loading the features using SQL, then you don't
care about this warning.

Is that clear??  Clear as a Saskatoon snowstorm.... but at least people
shouldn't fall into the same hole as we let Danny fall into.  Sorry about
that Danny!

Dave, I think we actually only need to put Gene and Transcript into the
schema, because by default they are the only two container objects.  If
anyone is going to write the code to accomodate additional container
objects they will already know enough to modify the database by hand.  The
rest of the feature types will write themselves into the table as they are
used, and will default to GQ::Server::Feature as they should.   Are you
going to do this?

NOTE TO USERS:  if you are experiencing strange behavior in Genquire,
please check the FeatureTypes table and see if the types in it match the
types listed as the keys of %type_hash in Context.pm  (line 10-20).

I think we are nearing the end of the changes before we have a final stable
release.  Just one more at my end as far as I can tell.  Dave...??

Everyone please report bugs ASAP if you are noticing them so that we can
have them fixed before the release.

Cheers!

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