[Bioperl-l] Bio::DB::Registry get_all_primary_ids

[Daniel Lang]

Hi Marc,

sorry for my late reply!
Thanks, for your answer!

Am Mittwoch, den 04.01.2006, 14:01 +0100 schrieb Marc Logghe:
> As far as I can see, you are using actually only 1 database (no need to
> use Bio::DB::Failover), of type Bio::DB::Flat::BinarySearch.
I'm actually retrieving from more than one database (different formats).
Not to litter this list I just provided one object dump:)
My last remark concerning Failover was, whether it is normal, that I'm
getting a Failover object when asking for a Registry database like:
$db=$registry->get_database('test');

> Using a Bio::DB::Failover object you can attach multiple databases (e.g.
> Bio::DB::SeqI compliant objects). In case it fails to fetch a seq from
> the first database in the list, it will try the second and so on.
> Bio::DB::Failover ISA Bio::DB::RandomAccessI while
> Bio::DB::Flat::BinarySearch ISA Bio::DB::SeqI. In the first case an
> implementation of get_all_primary_ids is not necessary, in contrast to
> the latter case.
> So, you might think of using Bio::DB::Flat::BinarySearch directly if you
> depend on that method and you need only 1 database.
So is there a method to call the Bio::DB::Flat::BinarySearch attached to
the Failover object, which allows me to call all methods suggested by
Bio::DB::SeqI on?
For I want to get rid of the ugly hashref and arrayref invocations:
$db->{_database}->[0]->get_all_primary_ids

Cheers,

Daniel:)