/ 
Bio-EnsEMBL-112.0.0_57
River stage zero No dependents
/ Bio::EnsEMBL::DBSQL::OperonTranscriptAdaptor

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::OperonAdaptor - Database adaptor for the retrieval and storage of OperonTranscript objects

SYNOPSIS

my $operon_transcript_adaptor = Bio::EnsEMBL::DBSQL::OperonTranscriptAdaptor->new($dba); $operon_transcript_adaptor->store($operon_transcript); my $operon_transcript2 = $operon_transcript_adaptor->fetch_by_dbID( $operon->dbID() ); my $operon_transcripts = $operon_transcript_adaptor->fetch_all_by_gene( $gene );

DESCRIPTION

This is a database aware adaptor for the retrieval and storage of operon transcript objects.

METHODS

list_dbIDs

Example    : @ot_ids = @{$ot_adaptor->list_dbIDs()};
Description: Gets an array of internal ids for all operon_transcripts in the current db
Arg[1]     : <optional> int. not 0 for the ids to be sorted by the seq_region.
Returntype : Listref of Ints
Exceptions : none
Caller     : general
Status     : Stable

list_stable_ids

Example    : @stable_ot_ids = @{$ot_adaptor->list_stable_ids()};
Description: Gets an listref of stable ids for all operon_transcripts in the current db
Returntype : reference to a list of strings
Exceptions : none
Caller     : general
Status     : Stable

fetch_by_stable_id

Arg [1]    : String $id 
             The stable ID of the operon_transcript to retrieve
Example    : $operon_transcript = $operon_transcript_adaptor->fetch_by_stable_id('T16152-16153-4840');
Description: Retrieves a operon_transcript object from the database via its stable id.
             The operon_transcript 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 operon_transcript is not found
             undef is returned instead.
Returntype : Bio::EnsEMBL::OperonTranscript or undef
Exceptions : if we cant get the operon_transcript in given coord system
Caller     : general
Status     : Stable

fetch_by_stable_id_version

Arg [1]    : String $id 
             The stable ID of the operon_transcript to retrieve
Arg [2]    : Integer $version
             The version of the stable_id to retrieve
Example    : $operon_transcript = $operon_transcript_adaptor->fetch_by_stable_id('T16152-16153-4840', 2);
Description: Retrieves an operon_transcript object from the database via its stable id and version.
             The operon_transcript 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 operon_transcript is not found
             undef is returned instead.
Returntype : Bio::EnsEMBL::OperonTranscript or undef
Exceptions : if we cant get the operon_transcript in given coord system
Caller     : general
Status     : Stable

fetch_by_name

Arg [1]    : String $label - name of operon transcript to fetch
Example    : my $operon_transcript = $operonAdaptor->fetch_by_name("ECK0012121342");
Description: Returns the operon transcript which has the given display label or undef if
             there is none. If there are more than 1, only the first is
             reported.
Returntype : Bio::EnsEMBL::OperonTranscript
Exceptions : none
Caller     : general
Status     : Stable

fetch_all

Example     : $operon_transcripts = $operon_adaptor->fetch_all();
Description : Retrieves all operon transcripts stored in the database.
Returntype  : listref of Bio::EnsEMBL::OperonTranscript
Caller      : general
Status      : At Risk

fetch_all_versions_by_stable_id

Arg [1]     : String $stable_id 
              The stable ID of the operon_transcript to retrieve
Example     : $operon_transcript = $operon_transcript_adaptor->fetch_all_versions_by_stable_id
                ('ENSG00000148944');
Description : Similar to fetch_by_stable_id, but retrieves all versions of a
              operon_transcript stored in the database.
Returntype  : listref of Bio::EnsEMBL::OperonTranscript
Exceptions  : if we cant get the operon_transcript in given coord system
Caller      : general
Status      : At Risk

fetch_all_by_Slice

Arg [1]    : Bio::EnsEMBL::Slice $slice
             The slice to fetch operon_transcripts on.
Arg [2]    : (optional) string $logic_name
             the logic name of the type of features to obtain
Arg [3]    : (optional) boolean $load_transcripts
             if true, transcripts will be loaded immediately rather than
             lazy loaded later.
Arg [4]    : (optional) string $source
             the source name of the features to obtain.
Arg [5]    : (optional) string biotype
              the biotype of the features to obtain.
Example    : @operon_transcripts = @{$operon_transcript_adaptor->fetch_all_by_Slice()};
Description: Overrides superclass method to optionally load transcripts
             immediately rather than lazy-loading them later.  This
             is more efficient when there are a lot of operon_transcripts whose
             transcripts are going to be used.
Returntype : reference to list of operon_transcripts 
Exceptions : thrown if exon cannot be placed on transcript slice
Caller     : Slice::get_all_OperonTranscripts
Status     : Stable

fetch_by_Operon

Arg [1]    : Bio::EnsEMBL::Operon
Example    : $ot = $ot_adaptor->fetch_by_Operon($operon);
Description: Retrieves all operon transcripts belonging to an operon
Returntype : arrayref of Bio::EnsEMBL::OperonTranscript
Exceptions : none
Caller     : general
Status     : Stable

fetch_by_operon_id

Arg [1]    : Int id
Example    : $ot = $ot_adaptor->fetch_by_operon_transcript($operon);
Description: Retrieves all operon transcripts belonging to an operon
Returntype : arrayref of Bio::EnsEMBL::OperonTranscript
Exceptions : none
Caller     : general
Status     : Stable

fetch_genes_by_operon_transcript

Arg [1]    : Bio::EnsEMBL::OperonTranscript
Example    : $ot = $ot_adaptor->fetch_genes_by_operon_transcript($operon_transcript);
Description: Retrieves all genes attached to an operon transcript
Returntype : arrayref of Bio::EnsEMBL::Gene
Exceptions : none
Caller     : general
Status     : Stable

fetch_genes_by_operon_transcript_id

Arg [1]    : Int id
Example    : $ot = $ot_adaptor->fetch_genes_by_operon_transcript($operon_transcript_id);
Description: Retrieves all genes attached to an operon transcript
Returntype : arrayref of Bio::EnsEMBL::Gene
Exceptions : none
Caller     : general
Status     : Stable

fetch_all_by_gene

Arg [1]    : Bio::EnsEMBL::Gene
Example    : $ots = $ot_adaptor->fetch_all_by_gene($gene);
Description: Retrieves all operon transcripts attached to a given gene
Returntype : arrayref of Bio::EnsEMBL::OperonTranscript
Exceptions : none
Caller     : general
Status     : Stable

fetch_all_by_gene_id

Arg [1]    : Int id of Bio::EnsEMBL::Gene
Example    : $ots = $ot_adaptor->fetch_all_by_gene($gene);
Description: Retrieves all operon transcripts attached to a given gene
Returntype : arrayref of Bio::EnsEMBL::OperonTranscript
Exceptions : none
Caller     : general
Status     : Stable

store

Arg [1]    : Bio::EnsEMBL::OperonTranscript $gene
             The gene to store in the database
Arg [2]    : ignore_release in xrefs [default 1] set to 0 to use release info 
             in external database references
Example    : $gene_adaptor->store($gene);
Description: Stores a gene in the database.
Returntype : the database identifier (dbID) of the newly stored gene
Exceptions : thrown if the $gene is not a Bio::EnsEMBL::OperonTranscript or if 
             $gene does not have an analysis object
Caller     : general
Status     : Stable

store_genes_on_OperonTranscript

Arg [1]    : Bio::EnsEMBL::OperonTranscript $ot
             the operon_transcript to store genes on
Arg [2]    : arrayref of Bio::EnsEMBL::Gene $gene
             the genes to store on operon transcript
Example    : $ot_adaptor->store_genes_on_OperonTranscript(\@genes);
Description: Associates genes with operon transcript
Returntype : none
Exceptions : throw on incorrect arguments 
             warning if operon_transcript is not stored in this database
Caller     : general, store
Status     : Stable

remove

Arg [1]    : Bio::EnsEMBL::OperonTranscript $ot
             the operon_transcript to remove from the database
Example    : $ot_adaptor->remove($ot);
Description: Removes a operon transcript completely from the database.
Returntype : none
Exceptions : throw on incorrect arguments 
             warning if operon_transcript is not stored in this database
Caller     : general
Status     : Stable