Bio::EnsEMBL::Analysis::Tools::Otter::DBSQL DBAdaptor
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Included modules
Bio::EnsEMBL::DBSQL::DBAdaptor
Bio::EnsEMBL::Utils::Exception
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Bio::EnsEMBL::DBSQL::DBAdaptor
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Methods
get_available_adaptorsDescriptionCode
Methods description
get_available_adaptorscode    nextTop
  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
Methods code
get_available_adaptorsdescriptionprevnextTop
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;
}
General documentation
NAME - Bio::EnsEMBL::Analysis::Tools::Otter::DBSQL::DBAdaptor Top
  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.