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Bio::EnsEMBL::Storable Class Reference
Inheritance diagram for Bio::EnsEMBL::Storable:

List of all members.

Class Summary


  my $dbID    = $storable_object-\>dbID();
  my $adaptor = $storable_object-\>adaptor();
  if ( $storable_object-\>is_stored($db_adaptor) ) { ... }


This is a storable base class.  All objects which are storable
in the database should inherit from this class.  It provides two
getter/setters: dbID() adaptor().  And a is_stored() method that can be
used to determine if an object is already stored in a database.

Definition at line 23 of file

Available Methods

adaptor ()
public Int dbID ()
public get_all_DAS_Features ()
public Boolean is_stored ()
public Bio::EnsEMBL::Storable new ()

Method Documentation

public Bio::EnsEMBL::DBSQL::BaseAdaptor Bio::EnsEMBL::Storable::adaptor ( )
  Arg [1]    : Bio::EnsEMBL::DBSQL::BaseAdaptor $adaptor
  Example    : none
  Description: get/set for this objects Adaptor
  Returntype : Bio::EnsEMBL::DBSQL::BaseAdaptor
  Exceptions : none
  Caller     : general, set from adaptor on store
  Status     : Stable
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public Int Bio::EnsEMBL::Storable::dbID ( )
  Arg [1]    : int $dbID
  Example    : none
  Description: getter/setter for the database internal id
  Returntype : int
  Exceptions : none
  Caller     : general, set from adaptor on store
  Status     : Stable
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Reimplemented in Bio::EnsEMBL::Map::Ditag, and Bio::EnsEMBL::Map::DitagFeature.

public Bio::EnsEMBL::Storable::get_all_DAS_Features ( )

Undocumented method

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Reimplemented in Bio::EnsEMBL::Gene, Bio::EnsEMBL::Transcript, and Bio::EnsEMBL::Translation.

public Boolean Bio::EnsEMBL::Storable::is_stored ( )
  Arg [1]    : Bio::EnsEMBL::DBSQL::DBConnection 
             : or Bio::EnsEMBL::DBSQL::DBAdaptor
  Example    : do_something if($object->is_stored($db));
  Description: Returns true if this object is stored in the provided database.
               This works under the assumption that if the adaptor and dbID are
               set and the database of the adaptor shares the port, dbname and
               hostname with the provided database, this object is stored in
               that database.
  Returntype : 1 or 0
  Exceptions : throw if dbID is set but adaptor is not
               throw if adaptor is set but dbID is not
               throw if incorrect argument is passed
  Caller     : store methods
  Status     : Stable
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public Bio::EnsEMBL::Storable Bio::EnsEMBL::Storable::new ( )
  Arg [-ADAPTOR] : Bio::EnsEMBL::DBSQL::BaseAdaptor
  Arg [-dbID]    : database internal id
  Example        : none 
  Caller         : internal calls
  Description    : create a new Storable object 
  Returntype     : Bio::EnsEMBL::Storable
  Exceptions     : Adaptor not a Bio::EnsEMBL::DBSQL::BaseAdaptor
  Status         : Stable
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Reimplemented in Bio::EnsEMBL::Analysis, Bio::EnsEMBL::AssemblyExceptionFeature, Bio::EnsEMBL::BaseAlignFeature, Bio::EnsEMBL::CoordSystem, Bio::EnsEMBL::DataFile, Bio::EnsEMBL::DBEntry, Bio::EnsEMBL::DensityFeature, Bio::EnsEMBL::DensityType, Bio::EnsEMBL::DnaDnaAlignFeature, Bio::EnsEMBL::Exon, Bio::EnsEMBL::Feature, Bio::EnsEMBL::FeaturePair, Bio::EnsEMBL::Gene, Bio::EnsEMBL::IdentityXref, Bio::EnsEMBL::Intron, Bio::EnsEMBL::KaryotypeBand, Bio::EnsEMBL::Map::Ditag, Bio::EnsEMBL::Map::DitagFeature, Bio::EnsEMBL::Map::Marker, Bio::EnsEMBL::Map::MarkerFeature, Bio::EnsEMBL::Map::Qtl, Bio::EnsEMBL::Map::QtlFeature, Bio::EnsEMBL::MiscFeature, Bio::EnsEMBL::MiscSet, Bio::EnsEMBL::OntologyTerm, Bio::EnsEMBL::Operon, Bio::EnsEMBL::OperonTranscript, Bio::EnsEMBL::PredictionExon, Bio::EnsEMBL::PredictionTranscript, Bio::EnsEMBL::ProteinFeature, Bio::EnsEMBL::RepeatConsensus, Bio::EnsEMBL::RepeatFeature, Bio::EnsEMBL::SeqRegionSynonym, Bio::EnsEMBL::SimpleFeature, Bio::EnsEMBL::Transcript, Bio::EnsEMBL::Translation, Bio::EnsEMBL::UnmappedObject, and Bio::EnsEMBL::Upstream.

The documentation for this class was generated from the following file: