[Bioperl-l] GFF mysql adapter schema problem

[Lincoln Stein]

I put in the constraint thinking that if you have multiple features 
that occupy the same locations and are of the same method and source, 
then this is probably a bug due to loading the same feature file 
twice.

Shouldn't you be giving these redundant features different sources or 
methods?

Lincoln

On Friday 28 May 2004 04:32 pm, Dmitri Bichko wrote:
> Hello all,
>
> What is the reason for the (fref,fbin,fstart,fstop,ftypeid,gid)
> index on fdata being unique?
>
> I need to display groups with many features with identical
> locations (but different labels).  To get this to work I took off
> the unique constraint and fixed the resulting problem with getting
> the last fid for the attribute inserts.  The changes are below.
>
> Am I likely to run into other problems because of this change? 
> Does anyone know the original reason for this constraint?
>
> Thanks,
> Dmitri
>
> Changes to Bio::DB::GFF::Adaptor::dbi::mysql
>
> 473c473
> <     unique index(fref,fbin,fstart,fstop,ftypeid,gid),
> ---
>
> >     index(fref,fbin,fstart,fstop,ftypeid,gid),
>
> 623a624
>
> >   my $last_insert_id = $dbh->prepare_delayed('SELECT
>
> LAST_INSERT_ID()');
> 641a643
>
> >   $self->{load_stuff}{sth}{last_insert_id} = $last_insert_id;
>
> 695,698c697,700
> <
> <   my $fid = $dbh->{mysql_insertid}
> <     ||
> $self->get_feature_id($gff->{ref},$gff->{start},$gff->{stop},$typei
>d,$gr oupid);
> <
> ---
>
> >   $s->{sth}{last_insert_id}->execute
> >     or warn $s->{sth}{last_insert_id}->errstr;
> >   my ($fid) = $s->{sth}{last_insert_id}->fetchrow_array;
>
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-- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724