Commit 282ea98d authored by Andreas Kusalananda Kähäri's avatar Andreas Kusalananda Kähäri
Browse files

Merge from branch-featurecollection-dev:

In get_available_adaptors(), add GeneCollection, TranscriptCollection,
ExonCollection, and RepeatFeatureCollection so that one may say, e.g.

  my $rfc = $registry->get_adaptor( 'Human', 'Core',
                                    'RepeatFeatureCollection' );
parent ab2471da
......@@ -252,40 +252,45 @@ sub get_db_adaptor {
=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 DnaAlignFeature
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
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 DnaAlignFeature
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
) ),
# 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'
);
return (\%pairs);
}
Marker MarkerFeature QtlFeature Qtl Ditag DitagFeature
) ),
# 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
###########################################################
#
......
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