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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::DensityTypeAdaptor

SYNOPSIS

my $density_type_adaptor =
  $registry->get_adaptor( 'Human', 'Core', 'DensityType' );

my @density_types = @{ $density_type_adaptor->fetch_all() };

my $dt = $density_type_adaptor->fetch_by_dbID(12);

DESCRIPTION

DensityTypeAdaptor - Performs database interaction for DensityType objects.

METHODS

new

Arg [1]    : see superclass (Bio::EnsEMBL::DBSQL::BaseAdaptor) arguments
Example    : #use this instead of the constructor directly:
             my $dta = $db_adaptor->get_DensityTypeAdaptor();
Description: Constructor. Creates a new DensityTypeAdaptor
Returntype : Bio::EnsEMBL::DBSQL::DensityTypeAdaptor
Exceptions : none
Caller     : DBAdaptor
Status     : Stable

fetch_all

Arg [1]    : none
Example    : my @density_types = @{$density_type_adaptor->fetch_all};
Description: Retrieves every density type in the database.
             NOTE:  In a multi-species database, this method will
             return all the entries, not just the ones associated with
             the current species.
Returntype : reference to list of Bio::EnsEMBL::DensityType objects
Exceptions : none
Caller     : general, new
Status     : Stable

fetch_by_dbID

Arg [1]    : int $dbID
Example    : my $dt = $density_type_adaptor->fetch_by_dbID($dbID);
Description: Retrieves a density type object via its internal identifier
Returntype : Bio::EnsEMBL::DensityType
Exceptions : throw if dbID argument not defined
Caller     : general
Status     : Stable

fetch_all_by_logic_name

Arg [1]    : string $logic_name
Example    : my @dts = @{$dtype_adaptor->fetch_all('repeat_coverage')};
Description: Retrieves all density types with a given logic name.
             NOTE:  In a multi-species database, this method will
             return all the entries matching the search criteria, not
             just the ones associated with the current species.
Returntype : reference to list of Bio::EnsEMBL::DensityTypes
Exceptions : thrown if logic_name argument is not provided
Caller     : general
Status     : Stable

store

Arg [1]    : list of Bio::EnsEMBL::DensityType @dt
             the density types to store in the database
Example    : $density_type->store(@density_types);
Description: Stores a list of density type objects in the database
Returntype : none
Exceptions : thrown if @dt is not defined
             or if any elements of @dt are not Bio::EnsEMBL::DensityType 
Caller     : general
Status     : Stable