LICENSE
Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] 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-2.0Unless 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.
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>.NAME
Bio::EnsEMBL::DB::ExternalFeatureFactoryI - Legacy Abstract interface for External Feature Factories. Bio::EnsEMBL::External::ExternalFeatureAdaptor should be used instead if possible.
SYNOPSIS
$external_ff = new ImplementingExternalFeatureFactoryClass;
$database_adaptor = new Bio::EnsEMBL::DBSQL::DBAdaptor(
-host => 'blah',
-dbname => 'other',
-pass => 'pass'
);
# alternatively, you can add external databases to an obj once made
$database_adaptor->add_ExternalFeatureFactory($external_ff);
# now the ExternalFeatureFactory has been added, Ensembl RawContigs
# and Slices will now have ExternalFeatures on them
$contig =
$db_adaptor->get_RawContigAdaptor->fetch_by_name('AC00056.00001');
@external = @{ $contig->get_all_ExternalFeatures() };
# this works on Slices as well
$slice =
$db_adaptor->get_SliceAdaptor->fetch_by_chr_start_end( '12', 10000,
30000 );
@external = @{ $slice->get_all_ExternalFeatures() };DESCRIPTION
This is a legacy class. It is included only for backwards compatibility with ExternalFeatureFactories which are presumably still used to place data into ensembl. It is recommended that if you wish to create EnsEMBL features externally that you use the Bio::EnsEMBL::External::ExternalFeatureAdaptor instead.
This object defines the abstract interface for External Database access inside Ensembl. The aim is that one can attach an External Database which will generate Sequence Features and these Sequence Features will be accessible along side all the internal Ensembl sequence features, for drawing, EMBL dumping etc. In particular, the external database does not have to worry about the transformation of the Sequence Feature objects into VirtualContigs.
Sequence Features have to be defined in one of two coordinate systems: Original EMBL/GenBank coordinates of a particular sequnence version or the Ensembl contig coordinates. This means you have to calculate your sequence features in one these two coordinate systems
The methods that have to be implemented are:
get_External_SeqFeatures_contig( $ensembl_contig_identifier,
$sequence_version, $start, $end );
get_External_SeqFeatures_clone( $embl_accession_number,
$sequence_version, $start, $end );The semantics of this method is as follows:
$ensembl_contig_identifier - the ensembl contig id (external id).
$sequence_version - embl/genbank sequence version
$embl_accession_number - the embl/genbank accession numberThe $start/$end can be ignored, but methods can take advantage of it. This is so that ensembl can ask for features only on a region of DNA, and if desired, the external database can respond with features only in this region, rather than the entire sequence.
The hope is that the second method could potentially have a very complex set of mappings of other embl_accession numbers to one embl_accession number and provide the complex mapping.
The methods should return Sequence Features with the following spec:
a) must implement the Bio::SeqFeatureI interface.
b) must accept "set" calls on
start,end,strand
to provide coordinate transformation of the feature.
c) must be unique in-memory objects, ie, the implementation is not
allowed to cache the sequence feature in its entirity. Two separate
calls to get_External_SeqFeatures_contig must be able to separately
set start,end,strand information without clobbering each other. The
other information, if so wished, can be cached by each SeqFeature
holding onto another object, but this is left to the implementor to
decide on the correct strategy.
d) must return an unique identifier when called with method id.You must implement both functions. In most cases, one function will always return an empty list, whereas the other function will actually query the external database.
The second way of accessing the External Database from Ensembl is using unique internal identifiers in that database. The method is:
get_SeqFeature_by_id($id);It should return exactly one Sequence Feature object of the same type as above.
METHODS
coordinate_systems
Arg [1] : none
Example : none
Description: This method is present to make the ExternalFeatureFactory
interface behave as an ExternalFeatureAdaptor. It is for
backwards compatibility.
Returntype : none
Exceptions : none
Caller : internalfetch_all_by_contig_name
Arg [1] : none
Example : none
Description: This method is present to make the ExternalFeatureFactory
interface behave as an ExternalFeatureAdaptor. It is for
backwards compatibility.
Returntype : none
Exceptions : none
Caller : internalget_Ensembl_SeqFeatures_contig
Title : get_Ensembl_SeqFeatures_contig (Abstract)
Usage :
Function:
Example :
Returns :
Args :get_Ensembl_SeqFeatures_clone
Title : get_Ensembl_SeqFeatures_clone (Abstract)
Usage :
Function:
Example :
Returns :
Args :get_Ensembl_Genes_clone
Title : get_Ensembl_Genes_clone
Function: returns Gene objects in clone coordinates from a gene id
Returns : An array of Gene objects
Args : clone idget_SeqFeature_by_id
Title : get_SeqFeature_by_id (Abstract)
Usage :
Function: Return SeqFeature object for any valid unique id
Example :
Returns :
Args : id as determined by the External Database