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

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CONTACT

  Please email comments or questions to the public Ensembl
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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