[Biojava-dev] Re: biosql

[david de beule]

"My point at the time was that querying
 location_qualifier_value every single time you obtain a location
 regardless of type is going to be a huge waste of time, given that 99%
 of locations are *not* fuzzy."

I may be wrong but I think 'BetweenLocations' are NOT always fuzzy
locations.  There are three types of exact sequence locations
 which in feature table notation are: 23, 34..55 and 46^47.  Respectively
Point, Range and Between locations.  The notation 46^47 (between 46 and 47)
is ESSENTIAL when you have clean insertions between residues and may not be
confused with the FUZZY location:  46^78, meaning: somewhere (not exactly
determined) between 46 and 78.

So I think the bug reported by Frederik Decouttere, that handled about these
EXACT between locations, should be fixed as soon as possible, because it has
nothing to do with 'rarely used' fuzzy locations.

Regards,
David

----- Original Message -----
From: "Hilmar Lapp" <hlapp at gnf.org>
To: "Len Trigg" <len at reeltwo.com>
Cc: "Matthew Pocock" <matthew_pocock at yahoo.co.uk>;
<biojava-dev at biojava.org>; "Thomas Down" <td2 at sanger.ac.uk>;
<biosql-l at open-bio.org>
Sent: Thursday, March 18, 2004 10:22 PM
Subject: Re: [BioSQL-l] Re: [Biojava-dev] Re: biosql


>
> On Wednesday, March 17, 2004, at 12:58  PM, Len Trigg wrote:
>
> > The problem is that when a BetweenLocation (and probably a whole bunch
> > of others) get persisted, they get retrieved as regular
> > RangeLocations. It would be straight forward to store a term
> > corresponding to the location type in the term_id of the location
> > table (currently unused in our binding).
>
> This is what I proposed this foreign key for.
>
> >  It's just a matter of determining what terms to use. Either (easiest
> > to hardest): a) the
> > classname of the location type; b) whatever BioPerl uses (if it is
> > capable of persisting the location type); c) jump through a few hoops
> > and look up an appropriate obda name.
>
> Please don't use classnames, although that would be easiest obviously,
> or otherwise bioperl (or any other language) won't interoperate with
> this properly.
>
> As a matter of fact, bioperl-db doesn't use this currently, and
> therefore doesn't support fuzzy locations (which is what we call them
> in bioperl) to roundtrip to fuzzy locations (they'll become exact
> locations).
>
> Note also that generally speaking the location_qualifier_value table is
> supposed to hold information from which you could infer the type of
> location. My point at the time was that querying
> location_qualifier_value every single time you obtain a location
> regardless of type is going to be a huge waste of time, given that 99%
> of locations are *not* fuzzy.
>
> -hilmar
> --
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp at gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> -------------------------------------------------------------
>
>
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