Commit 8293b664 authored by Marek Szuba's avatar Marek Szuba
Browse files

Remove deprecated GOTermAdaptor and SOTermAdaptor modules

Deprecated since 2011, non-functional since March 2018. See ENSCORESW-2871.

Note that there is still a reference to GOTermAdaptor in the xref parser
GOSlimParser. However, the parser in question seems to be no longer used
and in any case has not been updated, other than changing the copyright
notices, for years.
parent 5b3acb25
=head1 LICENSE
Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Copyright [2016-2019] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
=cut
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.
Questions may also be sent to the Ensembl help desk at
<http://www.ensembl.org/Help/Contact>.
=cut
=head1 NAME
Bio::EnsEMBL::DBSQL::GOTermAdaptor
=head1 DESCRIPTION
A specialization of Bio::EnsEMBL::DBSQL::OntologyTermAdaptor,
specifically for Gene Ontology (GO) terms. See the documentation of
Bio::EnsEMBL::DBSQL::OntologyTermAdaptor for further information.
=head1 METHODS
=cut
package Bio::EnsEMBL::DBSQL::GOTermAdaptor;
use strict;
use warnings;
use base qw( Bio::EnsEMBL::DBSQL::OntologyTermAdaptor );
=head2 new
Arg [1] : Bio::EnsEMBL::DBSQL::DBAdaptor
Argument required for parent class
Bio::EnsEMBL::DBSQL::BaseAdaptor.
Description : Creates an ontology term adaptor for GO terms.
Example :
my $go_adaptor = Bio::EnsEMBL::DBSQL::GOTermAdaptor->new( $dba );
Return type : Bio::EnsEMBL::DBSQL::GOTermAdaptor
=cut
sub new {
my ( $proto, $dba ) = @_;
my $this = $proto->SUPER::new( $dba, 'GO' );
return $this;
}
1;
=head1 LICENSE
Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Copyright [2016-2019] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
=cut
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.
Questions may also be sent to the Ensembl help desk at
<http://www.ensembl.org/Help/Contact>.
=cut
=head1 NAME
Bio::EnsEMBL::DBSQL::SOTermAdaptor
=head1 DESCRIPTION
A specialization of Bio::EnsEMBL::DBSQL::OntologyTermAdaptor,
specifically for Sequence ontology (SO) terms. See the
documentation of Bio::EnsEMBL::DBSQL::OntologyTermAdaptor for
further information.
=head1 METHODS
=cut
package Bio::EnsEMBL::DBSQL::SOTermAdaptor;
use strict;
use warnings;
use base qw( Bio::EnsEMBL::DBSQL::OntologyTermAdaptor );
=head2 new
Arg [1] : Bio::EnsEMBL::DBSQL::DBAdaptor
Argument required for parent class
Bio::EnsEMBL::DBSQL::BaseAdaptor.
Description : Creates an ontology term adaptor for SO terms.
Example :
my $go_adaptor = Bio::EnsEMBL::DBSQL::SOTermAdaptor->new( $dba );
Return type : Bio::EnsEMBL::DBSQL::SOTermAdaptor
=cut
sub new {
my ( $proto, $dba ) = @_;
my $this = $proto->SUPER::new( $dba, 'SO' );
return $this;
}
1;
...@@ -34,10 +34,8 @@ Bio::EnsEMBL::OntologyTerm ...@@ -34,10 +34,8 @@ Bio::EnsEMBL::OntologyTerm
=head1 DESCRIPTION =head1 DESCRIPTION
An ontology term object, (most often) created by An ontology term object, used in querying for transcripts, genes,
Bio::EnsEMBL::DBSQL::GOTermAdaptor and used in querying for and translations using the relevant adaptors and methods.
transcripts, genes, and translations using the relevant adaptors and
methods.
=head1 METHODS =head1 METHODS
......
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