Raw content of Bio::EnsEMBL::Analysis::Tools::Otter::DBSQL::DBAdaptor
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=head1 NAME - Bio::EnsEMBL::Analysis::Tools::Otter::DBSQL::DBAdaptor
Inherits from the standard Ensembl Bio::EnsEMBL::DBSQL::DBAdaptor
However - the get_available_adaptors method is overridden here
so that we can read in the Otter DnaAlignFeature and
DnaAlignFeatureHistory adaptors.
=cut
package Bio::EnsEMBL::Analysis::Tools::Otter::DBSQL::DBAdaptor;
use Bio::EnsEMBL::Utils::Exception;
use Bio::EnsEMBL::DBSQL::DBAdaptor;
use vars qw(@ISA);
use strict;
@ISA = qw( Bio::EnsEMBL::DBSQL::DBAdaptor);
=head2 get_available_adaptors
Example : my %pairs = %{$dba->get_available_adaptors()};
Description: gets a hash of the available adaptors
ReturnType : reference to a hash
Exceptions : none
Caller : Bio::EnsEMBL::Utils::ConfigRegistry
Status : Stable
=cut
sub get_available_adaptors {
my %pairs = (
# Firstly those that just have an adaptor named after there object
# in the main DBSQL directory.
map( { $_ => "Bio::EnsEMBL::DBSQL::${_}Adaptor" } qw(
AffyFeature AffyArray AffyProbe
Analysis ArchiveStableId Attribute
AssemblyExceptionFeature AssemblyMapper CoordSystem
CompressedSequence DBEntry
DensityFeature DensityType Exon
Gene KaryotypeBand MiscSet
MiscFeature OligoArray OligoFeature
OligoProbe PredictionTranscript PredictionExon
ProteinFeature ProteinAlignFeature RepeatConsensus
RepeatFeature Sequence SimpleFeature
Slice SupportingFeature Transcript
TranscriptSupportingFeature Translation UnmappedObject
UnconventionalTranscriptAssociation
AssemblySlice
) ),
# Those whose adaptors are in Map::DBSQL
map( { $_ => "Bio::EnsEMBL::Map::DBSQL::${_}Adaptor" } qw(
Marker MarkerFeature QtlFeature Qtl Ditag DitagFeature
) ),
# otter ones
map( { $_ => "Bio::EnsEMBL::Analysis::Tools::Otter::DBSQL::${_}Adaptor" } qw(
DnaAlignFeature DnaAlignFeatureHistory
) ),
# Finally the exceptions... those that have non-standard mapping
# between object / adaptor ....
# 'Blast' => 'Bio::EnsEMBL::External::BlastAdaptor',
'MetaCoordContainer' => 'Bio::EnsEMBL::DBSQL::MetaCoordContainer',
'MetaContainer' => 'Bio::EnsEMBL::DBSQL::MetaContainer',
'SNP' => 'Bio::EnsEMBL::DBSQL::ProxySNPAdaptor',
# Feature Collections:
'GeneCollection' => 'Bio::EnsEMBL::Collection::Gene',
'TranscriptCollection' => 'Bio::EnsEMBL::Collection::Transcript',
'ExonCollection' => 'Bio::EnsEMBL::Collection::Exon',
'RepeatFeatureCollection' =>
'Bio::EnsEMBL::Collection::RepeatFeature' );
return ( \%pairs );
} ## end sub get_available_adaptors
1;
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