Archive Ensembl HomeArchive Ensembl Home
Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor Class Reference
Inheritance diagram for Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor:

List of all members.


Class Summary

Synopsis

  my $registry = "Bio::EnsEMBL::Registry";

  my $archiveStableIdAdaptor =
    $registry-\>get_adaptor( 'Human', 'Core', 'ArchiveStableId' );

  my $stable_id = 'ENSG00000068990';

  my $arch_id = $archiveStableIdAdaptor-\>fetch_by_stable_id($stable_id);

  print("Latest incarnation of this stable ID:\n");
  printf( "  Stable ID: %s.%d\n",
    $arch_id-\>stable_id(), $arch_id-\>version() );
  print("  Release: "
      . $arch_id-\>release() . " ("
      . $arch_id-\>assembly() . ", "
      . $arch_id-\>db_name()
      . ")\n" );

  print "\nStable ID history:\n\n";

  my $history =
    $archiveStableIdAdaptor-\>fetch_history_tree_by_stable_id(
    $stable_id);

  foreach my $a ( @{ $history-\>get_all_ArchiveStableIds } ) {
    printf( "  Stable ID: %s.%d\n", $a-\>stable_id(), $a-\>version() );
    print("  Release: "
        . $a-\>release() . " ("
        . $a-\>assembly() . ", "
        . $a-\>db_name()
        . ")\n\n" );
  }

Description

ArchiveStableIdAdaptor does all SQL to create ArchiveStableIds and works
of
  stable_id_event
  mapping_session
  peptite_archive
  gene_archive
tables inside the core database.
This whole module has a status of At Risk as it is under development.
 

Definition at line 63 of file ArchiveStableIdAdaptor.pm.

Available Methods

protected _columns ()
protected _dbname_index ()
protected _default_where_clause ()
protected _fetch_archive_id ()
protected _final_clause ()
protected _left_join ()
protected _list_dbIDs ()
protected _objs_from_sth ()
protected _resolve_type ()
protected _straight_join ()
protected _tables ()
public void add_all_current_to_history ()
public Listref bind_param_generic_fetch ()
public
Bio::EnsEMBL::DBSQL::DBAdaptor 
db ()
public
Bio::EnsEMBL::DBSQL::DBConnection 
dbc ()
public dump_data ()
public fetch_all ()
public Listref fetch_all_by_archive_id ()
public Listref fetch_all_by_dbID_list ()
public Listref fetch_associated_archived ()
public Bio::EnsEMBL::Feature fetch_by_dbID ()
public
Bio::EnsEMBL::ArchiveStableId 
fetch_by_stable_id ()
public
Bio::EnsEMBL::ArchiveStableId 
fetch_by_stable_id_dbname ()
public
Bio::EnsEMBL::ArchiveStableId 
fetch_by_stable_id_version ()
public
Bio::EnsEMBL::StableIdHistoryTree 
fetch_history_tree_by_stable_id ()
public Listref fetch_predecessor_history ()
public Listref fetch_predecessors_by_archive_id ()
public Listref fetch_successor_history ()
public Listref fetch_successors_by_archive_id ()
public Listref generic_fetch ()
public String get_current_assembly ()
public Int get_current_release ()
public get_dumped_data ()
public String get_peptide ()
public Boolean is_multispecies ()
public Scalar last_insert_id ()
public Listref list_dbnames ()
public Boolean lookup_current ()
public
Bio::EnsEMBL::DBSQL::BaseAdaptor 
new ()
public String next_dbname ()
public DBI::StatementHandle prepare ()
public String previous_dbname ()
public Int species_id ()

Method Documentation

protected Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor::_dbname_index ( )

Undocumented method

Code:
click to view
protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_default_where_clause ( ) [inherited]
protected Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor::_fetch_archive_id ( )

Undocumented method

Code:
click to view
protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_final_clause ( ) [inherited]

Undocumented method

Code:
click to view

Reimplemented in Bio::EnsEMBL::DBSQL::ExonAdaptor, Bio::EnsEMBL::DBSQL::MiscFeatureAdaptor, and Bio::EnsEMBL::DBSQL::PredictionExonAdaptor.

protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_list_dbIDs ( ) [inherited]

Undocumented method

Code:
click to view
protected Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor::_resolve_type ( )

Undocumented method

Code:
click to view
protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_straight_join ( ) [inherited]

Undocumented method

Code:
click to view
public void Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor::add_all_current_to_history ( )
  Arg[1]      : Bio::EnsEMBL::StableIdHistoryTree $history -
                the StableIdHistoryTree object to add the current IDs to
  Description : This method adds the current versions of all stable IDs found
                in a StableIdHistoryTree object to the tree, by creating
                appropriate Events for the stable IDs found in the *_stable_id
                tables. This is a helper method for
                fetch_history_tree_by_stable_id(), see there for more
                documentation.
  Return type : none (passed-in object is manipulated)
  Exceptions  : thrown on missing or wrong argument
  Caller      : internal
  Status      : At Risk
              : under development
 
Code:
click to view
public Listref Bio::EnsEMBL::DBSQL::BaseAdaptor::bind_param_generic_fetch ( ) [inherited]
 Arg [1]   : (optional)  scalar $param
              This is the parameter to bind
 Arg [2]   : (optional) int $sql_type
              Type of the parameter (from DBI (:sql_types))
 Example   :  $adaptor->bind_param_generic_fetch($stable_id,SQL_VARCHAR);
              $adaptor->generic_fetch();
 Description:  When using parameters for the query, will call the bind_param to avoid
               some security issues. If there are no arguments, will return the bind_parameters
 ReturnType : listref
 Exceptions:  if called with one argument
 
Code:
click to view
public Bio::EnsEMBL::DBSQL::DBAdaptor Bio::EnsEMBL::DBSQL::BaseAdaptor::db ( ) [inherited]
  Arg [1]    : (optional) Bio::EnsEMBL::DBSQL::DBAdaptor $obj 
               the database this adaptor is using.
  Example    : $db = $adaptor->db();
  Description: Getter/Setter for the DatabaseConnection that this adaptor is 
               using.
  Returntype : Bio::EnsEMBL::DBSQL::DBAdaptor
  Exceptions : none
  Caller     : Adaptors inherited from BaseAdaptor
  Status     : Stable
 
Code:
click to view
public Bio::EnsEMBL::DBSQL::DBConnection Bio::EnsEMBL::DBSQL::BaseAdaptor::dbc ( ) [inherited]
  Arg [1]    : (optional) Bio::EnsEMBL::DBSQL::DBConnection $obj 
               the database this adaptor is using.
  Example    : $db = $adaptor->db();
  Description: Getter/Setter for the DatabaseConnection that this adaptor is 
               using.
  Returntype : Bio::EnsEMBL::DBSQL::DBConnection
  Exceptions : none
  Caller     : Adaptors inherited from BaseAdaptor
  Status     : Stable
 
Code:
click to view
public Bio::EnsEMBL::DBSQL::BaseAdaptor::dump_data ( ) [inherited]

Undocumented method

Code:
click to view
public Listref Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor::fetch_all_by_archive_id ( )
  Arg [1]     : Bio::EnsEMBL::ArchiveStableId $archive_id
  Arg [2]     : String $return_type - type of ArchiveStableId to fetch
  Example     : my $arch_id = $arch_adaptor->fetch_by_stable_id('ENSG0001');
                my @archived_transcripts =
                 $arch_adaptor->fetch_all_by_archive_id($arch_id, 'Transcript');
  Description : Given a ArchiveStableId it retrieves associated ArchiveStableIds
                of specified type (e.g. retrieve transcripts for genes or vice
                versa).
                See also fetch_associated_archived() for a different approach to
                retrieve this data.
  Returntype  : listref Bio::EnsEMBL::ArchiveStableId
  Exceptions  : none
  Caller      : Bio::EnsEMBL::ArchiveStableId->get_all_gene_archive_ids,
                get_all_transcript_archive_ids, get_all_translation_archive_ids
  Status      : At Risk
              : under development
 
Code:
click to view
public Listref Bio::EnsEMBL::DBSQL::BaseAdaptor::fetch_all_by_dbID_list ( ) [inherited]
  Arg [1]    : listref of integers $id_list
               The unique database identifiers for the features to
               be obtained.
  Arg [2]    : optional - Bio::EnsEMBL::Slice to map features onto.
  Example    : @feats = @{$adaptor->fetch_all_by_dbID_list([1234, 2131, 982]))};
  Description: Returns the features created from the database
               defined by the the IDs in contained in the provided
               ID list $id_list.  The features will be returned
               in their native coordinate system.  That is, the
               coordinate system in which they are stored in the
               database.  In order to convert the features to a
               particular coordinate system use the transfer() or
               transform() method.  If none of the features are
               found in the database a reference to an empty list is
               returned.
  Returntype : listref of Bio::EnsEMBL::Features
  Exceptions : thrown if $id arg is not provided
               does not exist
  Caller     : general
  Status     : Stable
 
Code:
click to view

Reimplemented in Bio::EnsEMBL::DBSQL::OntologyTermAdaptor.

public Listref Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor::fetch_associated_archived ( )
  Arg[1]      : Bio::EnsEMBL::ArchiveStableId $arch_id -
                the ArchiveStableId to fetch associated archived IDs for
  Example     : my ($arch_gene, $arch_tr, $arch_tl, $pep_seq) =
                  @{ $archive_adaptor->fetch_associated_archived($arch_id) };
  Description : Fetches associated archived stable IDs from the db for a given
                ArchiveStableId (version is taken into account).
  Return type : Listref of
                  ArchiveStableId archived gene
                  ArchiveStableId archived transcript
                  (optional) ArchiveStableId archived translation
                  (optional) peptide sequence
  Exceptions  : thrown on missing or wrong argument
                thrown if ArchiveStableID has no type
  Caller      : Bio::EnsEMBL::ArchiveStableId->get_all_associated_archived()
  Status      : At Risk
              : under development
 
Code:
click to view
public Bio::EnsEMBL::Feature Bio::EnsEMBL::DBSQL::BaseAdaptor::fetch_by_dbID ( ) [inherited]
  Arg [1]    : int $id
               The unique database identifier for the feature to be obtained
  Example    : $feat = $adaptor->fetch_by_dbID(1234));
               $feat = $feat->transform('contig');
  Description: Returns the feature created from the database defined by the
               the id $id.  The feature will be returned in its native
               coordinate system.  That is, the coordinate system in which it
               is stored in the database.  In order to convert it to a
               particular coordinate system use the transfer() or transform()
               method.  If the feature is not found in the database then
               undef is returned instead
  Returntype : Bio::EnsEMBL::Feature or undef
  Exceptions : thrown if $id arg is not provided
               does not exist
  Caller     : general
  Status     : Stable
 
Code:
click to view

Reimplemented in Bio::EnsEMBL::DBSQL::AnalysisAdaptor, Bio::EnsEMBL::DBSQL::AssemblyExceptionFeatureAdaptor, Bio::EnsEMBL::DBSQL::CoordSystemAdaptor, Bio::EnsEMBL::DBSQL::DBEntryAdaptor, Bio::EnsEMBL::DBSQL::DensityTypeAdaptor, Bio::EnsEMBL::DBSQL::MiscSetAdaptor, Bio::EnsEMBL::DBSQL::OntologyTermAdaptor, Bio::EnsEMBL::DBSQL::ProteinFeatureAdaptor, Bio::EnsEMBL::DBSQL::RepeatConsensusAdaptor, Bio::EnsEMBL::DBSQL::TranslationAdaptor, Bio::EnsEMBL::Map::DBSQL::DitagAdaptor, Bio::EnsEMBL::Map::DBSQL::DitagFeatureAdaptor, Bio::EnsEMBL::Map::DBSQL::MarkerAdaptor, and Bio::EnsEMBL::Map::DBSQL::QtlAdaptor.

public Bio::EnsEMBL::ArchiveStableId Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor::fetch_by_stable_id ( )
  Arg [1]     : string $stable_id
  Arg [2]     : (optional) string $type
  Example     : none
  Description : Retrives an ArchiveStableId that is the latest incarnation of
                given stable_id.
  Returntype  : Bio::EnsEMBL::ArchiveStableId or undef if not in database
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
 
Code:
click to view
public Bio::EnsEMBL::ArchiveStableId Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor::fetch_by_stable_id_dbname ( )
  Arg [1]     : string $stable_id
  Arg [2]     : string $db_name
  Example     : none
  Description : Create an ArchiveStableId from given arguments.
  Returntype  : Bio::EnsEMBL::ArchiveStableId or undef if not in database
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
 
Code:
click to view
public Bio::EnsEMBL::ArchiveStableId Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor::fetch_by_stable_id_version ( )
  Arg [1]     : string $stable_id
  Arg [2]     : int $version
  Example     : none
  Description : Retrieve an ArchiveStableId with given version and stable ID.
  Returntype  : Bio::EnsEMBL::ArchiveStableId 
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
 
Code:
click to view
public Bio::EnsEMBL::StableIdHistoryTree Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor::fetch_history_tree_by_stable_id ( )
  Arg[1]      : String $stable_id - the stable ID to fetch the history tree for
  Arg[2]      : (optional) Int $num_high_scorers
                number of mappings per stable ID allowed when filtering
  Arg[3]      : (optional) Int $max_rows
                maximum number of stable IDs in history tree (used for
                filtering)
  Example     : my $history = $archive_adaptor->fetch_history_tree_by_stable_id(
                  'ENSG00023747897');
  Description : Returns the history tree for a given stable ID. This will
                include a network of all stable IDs it is related to. The
                method will try to return a minimal (sparse) set of nodes
                (ArchiveStableIds) and links (StableIdEvents) by removing any
                redundant entries and consolidating mapping events so that only
                changes are recorded.
  Return type : Bio::EnsEMBL::StableIdHistoryTree
  Exceptions  : thrown on missing argument
  Caller      : Bio::EnsEMBL::ArchiveStableId::get_history_tree, general
  Status      : At Risk
              : under development
 
Code:
click to view
public Listref Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor::fetch_predecessor_history ( )
  Arg [1]     : Bio::EnsEMBL::ArchiveStableId $arch_id
  Example     : none
  Description : Gives back a list of archive stable ids which are predecessors
                in the stable_id_event tree of the given stable_id. Might well
                be empty.
                This method isn't deprecated, but in most cases you will rather
                want to use fetch_history_tree_by_stable_id().
  Returntype  : listref Bio::EnsEMBL::ArchiveStableId
                Since every ArchiveStableId knows about it's successors, this is
                a linked tree.
  Exceptions  : none
  Caller      : webcode for archive
  Status      : At Risk
              : under development
 
Code:
click to view
public Listref Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor::fetch_predecessors_by_archive_id ( )
  Arg [1]     : Bio::EnsEMBL::ArchiveStableId
  Example     : none
  Description : Retrieve a list of ArchiveStableIds that were mapped to the 
                given one. This method goes back only one level, to retrieve
                a full predecessor history use fetch_predecessor_history, or 
                ideally fetch_history_tree_by_stable_id for the complete
                history network.
  Returntype  : listref Bio::EnsEMBL::ArchiveStableId
  Exceptions  : none
  Caller      : Bio::EnsEMBL::ArchiveStableId->get_all_predecessors
  Status      : At Risk
              : under development
 
Code:
click to view
public Listref Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor::fetch_successor_history ( )
  Arg [1]     : Bio::EnsEMBL::ArchiveStableId $arch_id
  Example     : none
  Description : Gives back a list of archive stable ids which are successors in
                the stable_id_event tree of the given stable_id. Might well be
                empty.
                This method isn't deprecated, but in most cases you will rather
                want to use fetch_history_tree_by_stable_id().
  Returntype  : listref Bio::EnsEMBL::ArchiveStableId
                Since every ArchiveStableId knows about it's successors, this is
                a linked tree.
  Exceptions  : none
  Caller      : webcode for archive
  Status      : At Risk
              : under development
 
Code:
click to view
public Listref Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor::fetch_successors_by_archive_id ( )
  Arg [1]     : Bio::EnsEMBL::ArchiveStableId
  Example     : none
  Description : Retrieve a list of ArchiveStableIds that the given one was 
                mapped to. This method goes forward only one level, to retrieve
                a full successor history use fetch_successor_history, or 
                ideally fetch_history_tree_by_stable_id for the complete
                history network.
  Returntype  : listref Bio::EnsEMBL::ArchiveStableId
  Exceptions  : none
  Caller      : Bio::EnsEMBL::ArchiveStableId->get_all_successors
  Status      : At Risk
              : under development
 
Code:
click to view
public Listref Bio::EnsEMBL::DBSQL::BaseAdaptor::generic_fetch ( ) [inherited]
  Arg [1]    : (optional) string $constraint
               An SQL query constraint (i.e. part of the WHERE clause)
  Arg [2]    : (optional) Bio::EnsEMBL::AssemblyMapper $mapper
               A mapper object used to remap features
               as they are retrieved from the database
  Arg [3]    : (optional) Bio::EnsEMBL::Slice $slice
               A slice that features should be remapped to
  Example    : $fts = $a->generic_fetch('contig_id in (1234, 1235)', 'Swall');
  Description: Performs a database fetch and returns feature objects in
               contig coordinates.
  Returntype : listref of Bio::EnsEMBL::SeqFeature in contig coordinates
  Exceptions : none
  Caller     : BaseFeatureAdaptor, ProxyDnaAlignFeatureAdaptor::generic_fetch
  Status     : Stable
 
Code:
click to view

Reimplemented in Bio::EnsEMBL::DBSQL::DataFileAdaptor.

public String Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor::get_current_assembly ( )
  Example     : my $current_assembly = $archive_adaptor->get_current_assembly;
  Description : Returns the current assembly version (as found in the meta
                table).
  Return type : String
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
 
Code:
click to view
public Int Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor::get_current_release ( )
  Example     : my $current_release = $archive_adaptor->get_current_release;
  Description : Returns the current release number (as found in the meta table).
  Return type : Int
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
 
Code:
click to view
public Bio::EnsEMBL::DBSQL::BaseAdaptor::get_dumped_data ( ) [inherited]

Undocumented method

Code:
click to view
public String Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor::get_peptide ( )
  Arg [1]     : Bio::EnsEMBL::ArchiveStableId $arch_id
  Example     : none
  Description : Retrieves the peptide string for given ArchiveStableId. If its
                not a peptide or not in the database returns undef.
  Returntype  : string or undef
  Exceptions  : none
  Caller      : Bio::EnsEMBL::ArchiveStableId->get_peptide, general
  Status      : At Risk
              : under development
 
Code:
click to view
public Boolean Bio::EnsEMBL::DBSQL::BaseAdaptor::is_multispecies ( ) [inherited]
  Arg [1]    : (optional) boolean $arg
  Example    : if ($adaptor->is_multispecies()) { }
  Description: Getter/Setter for the is_multispecies boolean of
               to use for this adaptor.
  Returntype : boolean
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
click to view
public Scalar Bio::EnsEMBL::DBSQL::BaseAdaptor::last_insert_id ( ) [inherited]
  Arg [1]     : (optional) $field the name of the field the inserted ID was pushed 
                into
  Arg [2]     : (optional) HashRef used to pass extra attributes through to the 
                DBD driver
  Description : Delegating method which uses DBI to extract the last inserted 
                identifier. If using MySQL we just call the DBI method 
                DBI::last_insert_id() since MySQL ignores any extra
                arguments. See DBI for more information about this 
                delegated method. 
  Example     : my $id = $self->last_insert_id('my_id'); my $other_id = $self->last_insert_id();
  Returntype  : Scalar or undef
 
Code:
click to view
public Listref Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor::list_dbnames ( )
  Args        : none
  Example     : none
  Description : A list of available database names from the latest (current) to
                the oldest (ordered).
  Returntype  : listref of strings
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
 
Code:
click to view
public Boolean Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor::lookup_current ( )
  Arg[1]      : Bio::EnsEMBL::ArchiveStableId $arch_id -
                the stalbe ID to find the current version for
  Example     : if ($self->lookup_version($arch_id) {
                  $arch_id->version($arch_id->current_version);
                  $arch_id->db_name($self->dbc->dbname);
  Description : Look in [gene|transcript|translation]_stable_id if you can find
                a current version for this stable ID. Set
                ArchiveStableId->current_version if found.
  Return type : Boolean (TRUE if current version found, else FALSE)
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
 
Code:
click to view
public Bio::EnsEMBL::DBSQL::BaseAdaptor Bio::EnsEMBL::DBSQL::BaseAdaptor::new ( ) [inherited]
  Arg [1]    : Bio::EnsEMBL::DBSQL::DBConnection $dbobj
  Example    : $adaptor = new AdaptorInheritedFromBaseAdaptor($dbobj);
  Description: Creates a new BaseAdaptor object.  The intent is that this
               constructor would be called by an inherited superclass either
               automatically or through $self->SUPER::new in an overridden 
               new method.
  Returntype : Bio::EnsEMBL::DBSQL::BaseAdaptor
  Exceptions : none
  Caller     : Bio::EnsEMBL::DBSQL::DBConnection
  Status     : Stable
 
Code:
click to view

Reimplemented in Bio::EnsEMBL::DBSQL::AnalysisAdaptor, Bio::EnsEMBL::DBSQL::AssemblyExceptionFeatureAdaptor, Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor, Bio::EnsEMBL::DBSQL::AssemblySliceAdaptor, Bio::EnsEMBL::DBSQL::AttributeAdaptor, Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor, Bio::EnsEMBL::DBSQL::CoordSystemAdaptor, Bio::EnsEMBL::DBSQL::DensityFeatureAdaptor, Bio::EnsEMBL::DBSQL::DensityTypeAdaptor, Bio::EnsEMBL::DBSQL::GOTermAdaptor, Bio::EnsEMBL::DBSQL::MetaCoordContainer, Bio::EnsEMBL::DBSQL::MiscSetAdaptor, Bio::EnsEMBL::DBSQL::SequenceAdaptor, Bio::EnsEMBL::DBSQL::SliceAdaptor, Bio::EnsEMBL::DBSQL::SOTermAdaptor, Bio::EnsEMBL::DBSQL::StrainSliceAdaptor, Bio::EnsEMBL::DBSQL::UnmappedObjectAdaptor, and Bio::EnsEMBL::External::BlastAdaptor.

public String Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor::next_dbname ( )
  Arg[1]      : String $dbname - focus db name
  Example     : my $prev_db = $self->next_dbname($curr_db);
  Description : Returns the name of the next newest database which has mapping
                session information.
  Return type : String (or undef if not available)
  Exceptions  : none
  Caller      : general
  Status      : At Risk
 
Code:
click to view
public DBI::StatementHandle Bio::EnsEMBL::DBSQL::BaseAdaptor::prepare ( ) [inherited]
  Arg [1]    : string $string
               a SQL query to be prepared by this adaptors database
  Example    : $sth = $adaptor->prepare("select yadda from blabla")
  Description: provides a DBI statement handle from the adaptor. A convenience
               function so you dont have to write $adaptor->db->prepare all the
               time
  Returntype : DBI::StatementHandle
  Exceptions : none
  Caller     : Adaptors inherited from BaseAdaptor
  Status     : Stable
 
Code:
click to view

Reimplemented in Bio::EnsEMBL::DBSQL::SliceAdaptor, and Bio::EnsEMBL::External::BlastAdaptor.

public String Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor::previous_dbname ( )
  Arg[1]      : String $dbname - focus db name
  Example     : my $prev_db = $self->previous_dbname($curr_db);
  Description : Returns the name of the next oldest database which has mapping
                session information.
  Return type : String (or undef if not available)
  Exceptions  : none
  Caller      : general
  Status      : At Risk
 
Code:
click to view
public Int Bio::EnsEMBL::DBSQL::BaseAdaptor::species_id ( ) [inherited]
  Arg [1]    : (optional) int $species_id
               The internal ID of the species in a multi-species database.
  Example    : $db = $adaptor->db();
  Description: Getter/Setter for the internal ID of the species in a
               multi-species database.  The default species ID is 1.
  Returntype : Integer
  Exceptions : none
  Caller     : Adaptors inherited from BaseAdaptor
  Status     : Stable
 
Code:
click to view

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