Bio-Das-ProServer
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lib/Bio/Das/ProServer/SourceAdaptor/Transport/ensembl.pm view on Meta::CPAN
database group (optional, default configured in INI or 'core')
Returns:
listref of L<Bio::EnsEMBL::Gene|Bio::EnsEMBL::Gene> objects
=head2 version - Gets the Ensembl API's release number.
$sVersion = $oTransport->version();
=head2 last_modified - Gets a last modified date from the database.
$sVersion = $oTransport->version();
=head2 disconnect - ProServer hook to disconnect all connected databases.
$oTransport->disconnect();
=head1 CONFIGURATION AND ENVIRONMENT
Configured as part of each source's ProServer 2 INI file.
The transport will automatically load database connection settings from
the Ensembl Registry at ensembldb.ensembl.org. To skip this, set the
'skip_registry' INI property.
A specific database may also be overridden using these INI properties:
dbname
host (defaults to localhost)
port (defaults to 3306)
username (defaults to ensro)
password
The 'default database' used in the transport's data access methods may be
configured using these INI properties:
species (defaults to human)
group (defaults to core)
=head1 DIAGNOSTICS
=head1 CONFIGURATION AND ENVIRONMENT
=head1 DEPENDENCIES
=over
=item L<Carp|Carp>
=item L<English|English>
=item L<Bio::Das::ProServer::SourceAdaptor::Transport::generic|Bio::Das::ProServer::SourceAdaptor::Transport::generic>
=item Ensembl core API
=item Additional Ensembl APIs if used
=back
=head1 INCOMPATIBILITIES
None reported
=head1 BUGS AND LIMITATIONS
None reported
=head1 REFERENCES
=over
=item L<http://www.ensembl.org/info/software/Pdoc/ensembl/|http://www.ensembl.org/info/software/Pdoc/ensembl/> Ensembl API
=back
=head1 AUTHOR
Andy Jenkinson <andy.jenkinson@ebi.ac.uk>
=head1 LICENSE AND COPYRIGHT
Copyright (c) 2007 EMBL-EBI
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