Commit ff7450de authored by Leo Gordon's avatar Leo Gordon
Browse files

removed Extensions.pm and all internal references to it

parent 7f232810
......@@ -46,7 +46,6 @@ use strict;
use Bio::EnsEMBL::Utils::Exception ('throw');
use Bio::EnsEMBL::Hive::URLFactory;
use Bio::EnsEMBL::Hive::Extensions;
use base ( 'Bio::EnsEMBL::Hive::Storable' );
......
......@@ -43,7 +43,6 @@ package Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor;
use strict;
use Bio::EnsEMBL::Utils::Argument;
use Bio::EnsEMBL::Utils::Exception ('throw');
use Bio::EnsEMBL::Hive::AnalysisStats;
......
=pod
=head1 NAME
Bio::EnsEMBL::Hive::Extensions
=head1 DESCRIPTION
Performs method injection into (mainly) ensembl-core classes
=head1 LICENSE
Copyright [1999-2014] Wellcome Trust Sanger Institute and the 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.
=head1 CONTACT
Please subscribe to the Hive mailing list: http://listserver.ebi.ac.uk/mailman/listinfo/ehive-users to discuss Hive-related questions or to be notified of our updates
=cut
use strict;
#######################################
# extensions to
# Bio::EnsEMBL::Pipeline::RunnableDB
#######################################
sub Bio::EnsEMBL::Pipeline::RunnableDB::debug {
my $self = shift;
$self->{'_debug'} = shift if(@_);
$self->{'_debug'}=0 unless(defined($self->{'_debug'}));
return $self->{'_debug'};
}
#######################################
# extensions to
# Bio::EnsEMBL::Analysis::RunnableDB
#######################################
sub Bio::EnsEMBL::Analysis::RunnableDB::debug {
my $self = shift;
$self->{'_debug'} = shift if(@_);
$self->{'_debug'}=0 unless(defined($self->{'_debug'}));
return $self->{'_debug'};
}
1;
......@@ -69,7 +69,6 @@ use Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor;
use Bio::EnsEMBL::Hive::Analysis;
use Bio::EnsEMBL::Hive::AnalysisStats;
use Bio::EnsEMBL::Hive::AnalysisJob;
use Bio::EnsEMBL::Hive::Extensions;
use Bio::EnsEMBL::Hive::Valley;
use base ('Bio::EnsEMBL::Hive::DependentOptions');
......
......@@ -45,12 +45,10 @@ my $_URLFactory_global_instance;
package Bio::EnsEMBL::Hive::URLFactory;
use strict;
use Bio::EnsEMBL::Utils::Argument;
use Bio::EnsEMBL::Utils::Exception;
use Bio::EnsEMBL::Hive::Utils::URL;
use Bio::EnsEMBL::Hive::DBSQL::DBAdaptor;
use Bio::EnsEMBL::Hive::Extensions;
use Bio::EnsEMBL::Hive::Accumulator;
use Bio::EnsEMBL::Hive::NakedTable;
......
......@@ -76,7 +76,6 @@ use POSIX;
use Bio::EnsEMBL::Hive::Analysis;
use Bio::EnsEMBL::Hive::AnalysisStats;
use Bio::EnsEMBL::Hive::Extensions;
use Bio::EnsEMBL::Hive::Limiter;
use Bio::EnsEMBL::Hive::Process;
use Bio::EnsEMBL::Hive::DBSQL::AccumulatorAdaptor;
......
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