[Bioperl-l] Re: fuzzy locations in bioperl-db

[Hilmar Lapp]

This was easy to fix as I realized: I just removed type checking entirely 
from the respective store() method since _store_component() handles types.

This revealed the next bug:

------------- EXCEPTION Bio::Root::NotImplemented -------------
MSG: Abstract method "Bio::LocationI::each_Location" is not implemented by 
package Bio::Location::Fuzzy.
This is not your fault - author of Bio::Location::Fuzzy should be blamed!

It'd be great if someone does this little fix (should just return itself 
as far as I remember) while I get some sleep ...

There are two test scripts remaining in bioperl-db before I'm through 1st
pass. I removed seqlocation.t (I rewrote and kept remove.t) as locations
are tested anyway all over the place. There were also tests which tested
nothing, and some which worked only due to chance (e.g., one worked
consistently 3 times out of 4 when repeated, funny isn't it), fixed all of
that.

	-hilmar
-- 
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Hilmar Lapp                            email: lapp@gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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On Tue, 9 Jul 2002, Hilmar Lapp wrote:

> Two tests in bioperl-db fail (fuzzy2.t being one of them) because Bio::Location::Fuzzy is not handled by the SeqFeatureLocation adaptor (instead it throws an exception).
> 
> Were there any plans laid out on how to support (i.e., store) fuzzy locations in biosql?
> 
> 	-hilmar
>