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Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute

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     http://www.apache.org/licenses/LICENSE-2.0

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NAME

Bio::EnsEMBL::DBSQL::AltAlleleGroupAdaptor - Adaptor for the manipulation of Alternative allele groupings

SYNOPSIS

  use Bio::EnsEMBL::AltAlleleGroup;
  use Bio::EnsEMBL::DBSQL::AltAlleleGroupAdaptor;
  
  my $aag_adaptor = Bio::EnsEMBL::Registry->get_DBAdaptor("Human","core","AltAlleleGroup");
  
  # For a known Gene, find the reference alternative allele
  my $aag = $aag_adaptor->fetch_by_gene_id($gene->dbID);
  my $reference_gene = $aag->get_ref_Gene;
  
  # Get a list of AltAlleleGroups
  my $list = $aag_adaptor->fetch_all_('IS_REPRESENTATIVE');
  $list = $aag_adaptor->fetch_all();
  
  my $dbID = $aag_adaptor->store($aag);
  
  $aag = $aag_adaptor->fetch_by_dbID($dbID);
  $aag_adaptor->remove($aag);

DESCRIPTION

  The AltAlleleGroupAdaptor provides CRUD for AltAlleleGroup objects. It allows
  groups of alleles to be retrieved by group and gene ids.

fetch_all

  Arg[1]      : (optional) String - type of group
                Restrict group fetches to just one type. Technically it selects 
                out mixed-annotation groups where a single member contains that type.
  Description : Fetches all the alt-allele groups, creates objects to represent
                them and returns them in a list. Specifying a group type 
                identifies all groups containing a member of this type. It 
                does not filter out the other members
                
                Multispecies support is triggered by the is_multispecies flag
                and species_id of the DBAdaptor.
  Returntype  : ArrayRef of Bio::EnsEMBL::AltAlleleGroup

fetch_by_dbID

  Arg[1]      : AltAlleleGroup dbID.
  Description : Creates and returns an AltAlleleGroup for the given group id
                
  Returntype  : Bio::EnsEMBL::AltAlleleGroup

fetch_by_gene_id

  Arg[1]      : Integer Gene ID of the member to query by
  Description : Returns an AltAlleleGroup which contains
                the specified gene member                
  Returntype  : Bio::EnsEMBL::AltAlleleGroup

fetch_all_by_gene_id

  Arg[1]      : Integer Gene ID of the member to query by
  Description : Returns an array of one or more AltAlleleGroups,
                which each contain the specified gene member                
  Returntype  : Array of Bio::EnsEMBL::AltAlleleGroup objects

store

  Arg[1]     : Bio::EnsEMBL::AltAlleleGroup
  Description: Used for persisting new groups to the database.
               It updates the dbID of the object handed to it to match the
               database.
  Returntype : Integer Alt Allele Group id

update

  Arg [1]    : AltAlleleGroup 
  Description: Removes the existing DB record of an AltAlleleGroup and stores 
               the altered version.
  Returntype : Integer - the return value of the store method, viz. whether the
               insert was successful.

remove

  Arg [1]    : The AltAlleleGroup to remove.
  Arg [2]    : Boolean indicates if the entry in alt_allele_group should be retained or remove. Defaults to removing the entry
  Example    : $aaga->remove($alt_allele_group);
  Description: This removes an AltAlleleGroup from all tables of the database. 
  Exceptions : None