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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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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