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Bio-EnsEMBL-112.0.0_58
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/ Bio::EnsEMBL::DBSQL::OperonAdaptor

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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

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NAME

Bio::EnsEMBL::DBSQL::OperonAdaptor - Database adaptor for the retrieval and storage of Operon objects

SYNOPSIS

my $operon_adaptor = Bio::EnsEMBL::DBSQL::OperonAdaptor->new($dba); $operon_adaptor->store($operon); my $operon2 = $operon_adaptor->fetch_by_dbID( $operon->dbID() );

DESCRIPTION

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

METHODS

list_dbIDs

Example    : @operon_ids = @{$operon_adaptor->list_dbIDs()};
Description: Gets an array of internal ids for all operons 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_operon_ids = @{$operon_adaptor->list_stable_ids()};
Description: Gets an listref of stable ids for all operons in the current db
Returntype : reference to a list of strings
Exceptions : none
Caller     : general
Status     : Stable

fetch_by_name

Arg [1]    : String $label - name of operon to fetch
Example    : my $operon = $operonAdaptor->fetch_by_name("accBC");
Description: Returns the operon 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::Operon
Exceptions : none
Caller     : general
Status     : Stable

fetch_by_stable_id

Arg [1]    : String $id 
             The stable ID of the operon to retrieve
Example    : $operon = $operon_adaptor->fetch_by_stable_id('ENSG00000148944');
Description: Retrieves a operon object from the database via its stable id.
             The operon 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 or exon is not found
             undef is returned instead.
Returntype : Bio::EnsEMBL::Operon or undef
Exceptions : if we cant get the operon in given coord system
Caller     : general
Status     : Stable

fetch_all

Example     : $operons = $operon_adaptor->fetch_all();
Description : Similar to fetch_by_stable_id, but retrieves all
              operons stored in the database.
Returntype  : listref of Bio::EnsEMBL::Operon
Caller      : general
Status      : At Risk

fetch_by_stable_id_version

Arg [1]    : String $id 
             The stable ID of the operon to retrieve
Arg [2]    : Integer $version
             The version of the stable_id to retrieve
Example    : $operon = $operon_adaptor->fetch_by_stable_id('16152-16153-4840', 2);
Description: Retrieves an operon object from the database via its stable id and version.
             The operon 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 is not found
             undef is returned instead.
Returntype : Bio::EnsEMBL::Operon or undef
Exceptions : if we cant get the operon in given coord system
Caller     : general
Status     : Stable

fetch_all_versions_by_stable_id

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

fetch_all_by_Slice

Arg [1]    : Bio::EnsEMBL::Slice $slice
             The slice to fetch operons 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 $source
             the source name of the features to obtain.
Arg [5]    : (optional) string biotype
              the biotype of the features to obtain.
Example    : @operons = @{$operon_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 operons whose
             transcripts are going to be used.
Returntype : reference to list of operons 
Exceptions : thrown if exon cannot be placed on transcript slice
Caller     : Slice::get_all_operons
Status     : Stable

fetch_by_transcript_id

Arg [1]    : Int $trans_id
             Unique database identifier for the transcript whose operon should
             be retrieved. The operon is returned in its native coord
             system (i.e. the coord_system it is stored in). If the coord
             system needs to be changed, then tranform or transfer should
             be called on the returned object. undef is returned if the
             operon or transcript is not found in the database.
Example    : $operon = $operon_adaptor->fetch_by_transcript_id(1241);
Description: Retrieves a operon from the database via the database identifier
             of one of its transcripts.
Returntype : Bio::EnsEMBL::Operon
Exceptions : none
Caller     : operonral
Status     : Stable

fetch_by_operon_transcript_stable_id

Arg [1]    : string $trans_stable_id
             transcript stable ID whose operon should be retrieved
Example    : my $operon = $operon_adaptor->fetch_by_operon_transcript_stable_id
               ('ENST0000234');
Description: Retrieves a operon from the database via the stable ID of one of
             its transcripts
Returntype : Bio::EnsEMBL::Operon
Exceptions : none
Caller     : operonral
Status     : Stable

store

Arg [1]    : Bio::EnsEMBL::Operon $operon
             The operon 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    : $operon_adaptor->store($operon);
Description: Stores a operon in the database.
Returntype : the database identifier (dbID) of the newly stored operon
Exceptions : thrown if the $operon is not a Bio::EnsEMBL::Operon or if 
             $operon does not have an analysis object
Caller     : general
Status     : Stable

remove

Arg [1]    : Bio::EnsEMBL::Operon $operon
             the operon to remove from the database
Example    : $operon_adaptor->remove($operon);
Description: Removes a operon completely from the database. All associated
             transcripts, exons, stable_identifiers, descriptions, etc.
             are removed as well. Use with caution!
Returntype : none
Exceptions : throw on incorrect arguments 
             warning if operon is not stored in this database
Caller     : general
Status     : Stable