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Bio-EnsEMBL-112.0_53
River stage zero No dependents
/ Bio::EnsEMBL::DBSQL::OperonAdaptor

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

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  Questions may also be sent to the Ensembl help desk 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