Unused module.

modules/Bio/EnsEMBL/Utils/User_defined_load.pm

-=head1 LICENSE
-
-  Copyright (c) 1999-2011 The European Bioinformatics Institute and
-  Genome Research Limited.  All rights reserved.
-
-  This software is distributed under a modified Apache license.
-  For license details, please see
-
-    http://www.ensembl.org/info/about/code_licence.html
-
-=head1 CONTACT
-
-  Please email comments or questions to the public Ensembl
-  developers list at <dev@ensembl.org>.
-
-  Questions may also be sent to the Ensembl help desk at
-  <helpdesk@ensembl.org>.
-
-=cut
-
-use strict;
-use warnings;
-
-use Bio::EnsEMBL::Registry;
-use Bio::EnsEMBL::Utils::Argument qw(rearrange);
-use Bio::EnsEMBL::DBSQL::DBConnection;
-use Bio::EnsEMBL::DBSQL::DBAdaptor;
-use Bio::EnsEMBL::Utils::Exception qw(warning throw);
-
-
-=head2 Example of user defined loading
-
-Add new databases by creating the load method and use it by setting
-ENSEMBL_REGISTRY to your configuration file.
-
-sub load_dupgene {
-  my ( $class, @args ) = @_;
-
-  my ($species) = rearrange( [qw(SPECIES)], @args );
-  my $group = 'dupgene';
-
-  push( @args, '-group' );
-  push( @args, $group );
-
-  my ( $spec, $gro ) =
-    Bio::EnsEMBL::Registry->check_if_already_there(@args);
-  if ($spec) {
-    print STDERR "already defined returning\n";
-    return;
-  }
-
-  my $dbc = new Bio::EnsEMBL::DBSQL::DBConnection(@args);
-
-  my $dba = new_fast Bio::EnsEMBL::DBSQL::DBAdaptor( '-con' => $dbc );
-
-  Bio::EnsEMBL::Registry->add_DBAdaptor( $species, $group, $dba );
-
-  my %pairs = (
-    'Analysis'        => 'Bio::EnsEMBL::DBSQL::AnalysisAdaptor',
-    'ArchiveStableId' => 'Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor',
-    'Attribute'       => 'Bio::EnsEMBL::DBSQL::AttributeAdaptor',
-    'AssemblyExceptionFeature' =>
-      'Bio::EnsEMBL::DBSQL::AssemblyExceptionFeatureAdaptor',
-    'AssemblyMapper' => 'Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor',
-    'Blast'          => 'Bio::EnsEMBL::External::BlastAdaptor',
-    'MetaContainer'  => 'Bio::EnsEMBL::DBSQL::MetaContainer',
-    'CoordSystem'    => 'Bio::EnsEMBL::DBSQL::CoordSystemAdaptor',
-    'CompressedSequence' =>
-      'Bio::EnsEMBL::DBSQL::CompressedSequenceAdaptor',
-    'DBEntry'         => 'Bio::EnsEMBL::DBSQL::DBEntryAdaptor',
-    'DnaAlignFeature' => 'Bio::EnsEMBL::DBSQL::DnaAlignFeatureAdaptor',
-    'DensityFeature'  => 'Bio::EnsEMBL::DBSQL::DensityFeatureAdaptor',
-    'DensityType'     => 'Bio::EnsEMBL::DBSQL::DensityTypeAdaptor',
-    'Exon'            => 'Bio::EnsEMBL::DBSQL::ExonAdaptor',
-    'Gene'            => 'Bio::EnsEMBL::DBSQL::GeneAdaptor',
-    'KaryotypeBand'   => 'Bio::EnsEMBL::DBSQL::KaryotypeBandAdaptor',
-    'Marker'          => 'Bio::EnsEMBL::Map::DBSQL::MarkerAdaptor',
-    'MarkerFeature' => 'Bio::EnsEMBL::Map::DBSQL::MarkerFeatureAdaptor',
-    'MetaCoordContainer' => 'Bio::EnsEMBL::DBSQL::MetaCoordContainer',
-    'MiscSet'            => 'Bio::EnsEMBL::DBSQL::MiscSetAdaptor',
-    'MiscFeature'        => 'Bio::EnsEMBL::DBSQL::MiscFeatureAdaptor',
-    'PredictionTranscript' =>
-      'Bio::EnsEMBL::DBSQL::PredictionTranscriptAdaptor',
-    'PredictionExon' => 'Bio::EnsEMBL::DBSQL::PredictionExonAdaptor',
-    'ProteinFeature' => 'Bio::EnsEMBL::DBSQL::ProteinFeatureAdaptor',
-    'ProteinAlignFeature' =>
-      'Bio::EnsEMBL::DBSQL::ProteinAlignFeatureAdaptor',
-    'ProxySNP'        => 'Bio::EnsEMBL::DBSQL::ProxySNPAdaptor',
-    'QtlFeature'      => 'Bio::EnsEMBL::Map::DBSQL::QtlFeatureAdaptor',
-    'Qtl'             => 'Bio::EnsEMBL::Map::DBSQL::QtlAdaptor',
-    'RepeatConsensus' => 'Bio::EnsEMBL::DBSQL::RepeatConsensusAdaptor',
-    'RepeatFeature'   => 'Bio::EnsEMBL::DBSQL::RepeatFeatureAdaptor',
-    'Sequence'        => 'Bio::EnsEMBL::DBSQL::SequenceAdaptor',
-    'SimpleFeature'   => 'Bio::EnsEMBL::DBSQL::SimpleFeatureAdaptor',
-    'Slice'           => 'Bio::EnsEMBL::DBSQL::SliceAdaptor',
-    'SupportingFeature' =>
-      'Bio::EnsEMBL::DBSQL::SupportingFeatureAdaptor',
-    'Transcript'  => 'Bio::EnsEMBL::DBSQL::TranscriptAdaptor',
-    'Translation' => 'Bio::EnsEMBL::DBSQL::TranslationAdaptor'
-  );
-
-  foreach my $key ( keys %pairs ) {
-    Bio::EnsEMBL::Registry->add_adaptor( $species, $group, $key,
-      $pairs{$key} );
-  }
-
-  #if dnadb has been set then for the follwing use it.
-  foreach my $type (
-    qw(Sequence AssemblyMapper KaryotypeBand RepeatFeature CoordSystem AssemblyExceptionFeature)
-    )
-  {
-    Bio::EnsEMBL::Registry->set_get_via_dnadb_if_set( $species, $type );
-  }
-} ## end sub load_dupgene
-
-=cut
-
-1;