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-2.0

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.

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::DBSQL::ExonAdaptor - An adaptor responsible for the retrieval and storage of exon objects

SYNOPSIS

my $exon_adaptor = $registry->get_adaptor( 'Human', 'Core', 'Exon' );

my $exon = $exon_adaptor->fetch_by_dbID($dbID);

DESCRIPTION

The ExonAdaptor is responsible for retrieving and storing Exon objects from an Ensembl database. Most of the ExonAdaptor functionality is inherited from the Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor class.

METHODS

fetch_by_stable_id

Arg [1]    : string $stable_id
             the stable id of the exon to retrieve
Example    : $exon = $exon_adaptor->fetch_by_stable_id('ENSE0000988221');
Description: Retrieves an Exon from the database via its stable id
Returntype : Bio::EnsEMBL::Exon in native coordinates.
Exceptions : none
Caller     : general
Status     : Stable

fetch_by_stable_id_version

Arg [1]    : String $id 
             The stable ID of the exon to retrieve
Arg [2]    : Integer $version
             The version of the stable_id to retrieve
Example    : $exon = $exon_adaptor->fetch_by_stable_id('ENSE0000988221', 3);
Description: Retrieves an exon object from the database via its stable id and version.
             The exon will be retrieved in its native coordinate system (i.e.
             in the coordinate system it is stored in the database). It may
             be converted to a different coordinate system through a call to
             transform() or transfer(). If the exon is not found
             undef is returned instead.
Returntype : Bio::EnsEMBL::Exon or undef
Exceptions : if we cant get the exon in given coord system
Caller     : general
Status     : Stable

fetch_all_versions_by_stable_id

Arg [1]     : String $stable_id 
              The stable ID of the exon to retrieve
Example     : my $exon = $exon_adaptor->fetch_all_version_by_stable_id
                ('ENSE00000309301');
Description : Similar to fetch_by_stable_id, but retrieves all versions of an
              exon stored in the database.
Returntype  : listref of Bio::EnsEMBL::Exon objects
Exceptions  : if we cant get the gene in given coord system
Caller      : general
Status      : At Risk

fetch_all_by_Transcript

Arg [1]    : Bio::EnsEMBL::Transcript $transcript
Example    : none
Description: Retrieves all Exons for the Transcript in 5-3 order
Returntype : listref Bio::EnsEMBL::Exon on Transcript slice 
Exceptions : throws if transcript has no slice
Caller     : Transcript->get_all_Exons()
Status     : Stable

store

Arg [1]    : Bio::EnsEMBL::Exon $exon
             the exon to store in this database
Example    : $exon_adaptor->store($exon);
Description: Stores an exon in the database
Returntype : none
Exceptions : thrown if exon (or component exons) do not have a contig_id
             or if $exon->start, $exon->end, $exon->strand, or $exon->phase 
             are not defined or if $exon is not a Bio::EnsEMBL::Exon
Caller     : general
Status     : Stable

remove

Arg [1]    : Bio::EnsEMBL::Exon $exon
             the exon to remove from the database
Example    : $exon_adaptor->remove($exon);
Description: Removes an exon from the database.  This method is generally
             called by the TranscriptAdaptor::store method. Database
             integrity will not be maintained if this method is simply
             called on its own without taking into account transcripts which
             may refer to the exon being removed.
Returntype : none
Exceptions : none
Caller     : general
Status     : Stable

list_dbIDs

Arg [1]    : none
Example    : @exon_ids = @{$exon_adaptor->list_dbIDs()};
Description: Gets an array of internal ids for all exons in the current db
Arg[1]     : <optional> int. not 0 for the ids to be sorted by the seq_region.
Returntype : list of ints
Exceptions : none
Caller     : ?
Status     : Stable

list_stable_ids

Arg [1]    : none
Example    : @stable_exon_ids = @{$exon_adaptor->list_stable_dbIDs()};
Description: Gets an array of stable ids for all exons in the current db
Returntype : list of ints
Exceptions : none
Caller     : ?
Status     : Stable