LICENSE

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::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