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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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<http://www.ensembl.org/Help/Contact>.NAME
Bio::EnsEMBL::DBSQL::DBAdaptor
SYNOPSIS
$db = Bio::EnsEMBL::DBSQL::DBAdaptor->new(
-user => 'root',
-dbname => 'pog',
-host => 'caldy',
-driver => 'mysql'
);
$gene_adaptor = $db->get_GeneAdaptor();
$gene = $gene_adaptor->fetch_by_stable_id($stable_id);
$slice =
$db->get_SliceAdaptor()->fetch_by_chr_start_end( 'X', 1, 10000 );DESCRIPTION
Formerly this class provided database connectivity and a means to retrieve object adaptors. This class is now provided for convenience and backwards compatibility, and delegates its connection responsibilities to the DBConnection class (no longer inherited from) and its object adaptor retrieval to the static Bio::EnsEMBL::Registry.
Please use Bio::EnsEMBL::Registry to retrieve object adaptors.
METHODS
new
Arg [-DNADB]: (optional) Bio::EnsEMBL::DBSQL::DBAdaptor DNADB
All sequence, assembly, contig information etc, will
be retrieved from this database instead.
Arg [-NO_CACHE]: (optional) int 1
This option will turn off caching for slice features,
so, every time a set of features is retrieved,
they will come from the database instead of the
cache. This option is only recommended for advanced
users, specially if you need to store and retrieve
features. It might reduce performance when querying
the database if not used properly. If in doubt, do
not use it or ask in the developer mailing list.
Arg [-ADD_ALIASES]: (optional) boolean
Used to automatically load aliases for this
species into the Registry upon loading.
Arg [-ADD_SPECIES_ID]: (optional) boolean
Used to automatically load the species id
based on the species if none is defined.
Arg [..] : Other args are passed to superclass
Bio::EnsEMBL::DBSQL::DBConnection
Example : $db = new Bio::EnsEMBL::DBSQL::DBAdaptor(
-user => 'root',
-dbname => 'pog',
-host => 'caldy',
-driver => 'mysql'
);
$db = new Bio::EnsEMBL::DBSQL::DBAdaptor(
-species => 'Homo_sapiens',
-group => 'core',
-user => 'root',
-dbname => 'pog',
-host => 'caldy',
-driver => 'mysql'
);
$db = new Bio::EnsEMBL::DBSQL::DBAdaptor(
-species => 'staphylococcus_aureus',
-group => 'core',
-user => 'root',
-dbname => 'staphylococcus_collection_1_52_1a',
-multispecies_db => 1,
-host => 'caldy',
-driver => 'mysql'
);
Description: Constructor for DBAdaptor.
Returntype : Bio::EnsEMBL::DBSQL::DBAdaptor
Exceptions : none
Caller : general
Status : Stableclear_caches
Example : $dba->clear_caches();
Description : Loops through all linked adaptors and clears their
caches if C<clear_cache()> is implemented. Not all caches
are cleared & the DBAdaptor instance should be removed from
the registry to clear these remaining essential caches.
Returntype : None
Exceptions : Nonefind_and_add_aliases
Example : $dba->find_and_add_aliases();
Description : When executed we delegate to the find_and_add_aliases
method in Bio::EnsEMBL::Registry which scans the
database's MetaContainer for species.alias entries
indicating alternative names for this species. This
is best executed on a core DBAdaptor instance.
Returntype : None
Exceptions : Nonefind_and_add_species_id
Description :
Returntype : None
Exceptions : Nonedbc
Arg[1] : (optional) Bio::EnsEMBL::DBSQL::DBConnection
Example : $dbc = $dba->dbc();
Description: Getter/Setter for DBConnection.
Returntype : Bio::EnsEMBL::DBSQL::DBConnection
Exceptions : throws if argument not a Bio::EnsEMBL::DBSQL::DBConnection
Caller : general
Status : Stableadd_db_adaptor
Arg [1] : string $name
the name of the database to attach to this database
Arg [2] : Bio::EnsEMBL::DBSQL::DBConnection
the db adaptor to attach to this database
Example : $db->add_db_adaptor('lite', $lite_db_adaptor);
Description: Attaches another database instance to this database so
that it can be used in instances where it is required.
Returntype : none
Exceptions : none
Caller : EnsWeb
Status : At Riskremove_db_adaptor
Arg [1] : string $name
the name of the database to detach from this database.
Example : $lite_db = $db->remove_db_adaptor('lite');
Description: Detaches a database instance from this database and returns
it.
Returntype : none
Exceptions : none
Caller : ?
Status : At Riskget_all_db_adaptors
Arg [1] : none
Example : @attached_dbs = values %{$db->get_all_db_adaptors()};
Description: returns all of the attached databases as
a hash reference of key/value pairs where the keys are
database names and the values are the attached databases
Returntype : hash reference with Bio::EnsEMBL::DBSQL::DBConnection values
Exceptions : none
Caller : Bio::EnsEMBL::DBSQL::ProxyAdaptor
Status : At Risk
: please use Bio::EnsEMBL::Registry->get_all_db_adaptorsget_db_adaptor
Arg [1] : string $name
the name of the attached database to retrieve
Example : $lite_db = $db->get_db_adaptor('lite');
Description: returns an attached db adaptor of name $name or undef if
no such attached database exists
Returntype : Bio::EnsEMBL::DBSQL::DBConnection
Exceptions : none
Caller : ?
Status : At Risk
: please use Bio::EnsEMBL::Registry->get_db_adaptorsget_available_adaptors
Example : my %pairs = %{$dba->get_available_adaptors()};
Description: gets a hash of the available adaptors
ReturnType : reference to a hash
Exceptions : none
Caller : Bio::EnsEMBL::Utils::ConfigRegistry
Status : Stableadd_DASFeatureFactory
Arg [1] : Bio::EnsEMBL::ExternalFeatureFactory $value
Example : none
Description: Attaches a DAS Feature Factory to this method.
ExternalFeatureFactory objects are not really used right now.
They may be reintroduced or taken out completely. The fate
of this function is unknown (although it is presently needed).
Returntype : none
Exceptions : none
Caller : EnsWeb
Status : At Risk
: with the new web code this may not be needed/supported_each_DASFeatureFactory
Args : none
Example : none
Description: Not sure if this is used, or if it should be removed. It
does not seem to be used at the moment
Returntype : Bio::EnsEMBL::ExternalFeatureFactory
Exceptions : none
Caller : ??
Status : At Risk
: with the new web code this may not be needed/supportedadd_ExternalFeatureAdaptor
Arg [1] : Bio::EnsEMBL::External::ExternalFeatureAdaptor
Example : $db_adaptor->add_ExternalFeatureAdaptor($xfa);
Description: Adds an external feature adaptor to this database adaptor.
Adding the external adaptor in this way allows external
features to be obtained from Slices and from RawContigs.
The external feature adaptor which is passed to this method
will have its db attribute set to this DBAdaptor object via
the db accessor method.
ExternalFeatureAdaptors passed to this method are stored
internally in a hash keyed on the string returned by the
ExternalFeatureAdaptors track_name method.
If the track name method is not implemented then the
a default key named 'External features' is assigned. In the
event of duplicate key names, a number is appended to the
key name, and incremented for each subsequent adaptor with the
same track name. For example, if no track_names are specified
then the the external feature adaptors will be stored under the
keys 'External features', 'External features2'
'External features3' etc.
Returntype : none
Exceptions : none
Caller : general
get_ExternalFeatureAdaptors
Arg [1] : none
Example : @xfas = values %{$db_adaptor->get_ExternalFeatureAdaptors};
Description: Retrieves all of the ExternalFeatureAdaptors which have been
added to this DBAdaptor. The ExternalFeatureAdaptors are
returned in a reference to a hash keyed on the track names
of the external adaptors
Returntype : Reference to a hash of ExternalFeatureAdaptors keyed on
their track names.
Exceptions : none
Caller : generaladd_ExternalFeatureFactory
Arg [1] : Bio::EnsEMBL::DB::ExternalFeatureFactoryI $value
Example : $db_adaptor->add_ExternalFeatureFactory
Description: It is recommended that add_ExternalFeatureAdaptor be used
instead. See documentation for
Bio::EnsEMBL::External::ExternalFeatureAdaptor
Adds an external feature factory to the core database
so that features from external sources can be displayed in
ensembl. This method is still available mainly for legacy
support for external EnsEMBL installations.
Returntype : none
Exceptions : none
Caller : externalget_adaptor
Arg [1] : Canonical data type for which an adaptor is required.
Example : $db_adaptor->get_adaptor("Protein")
Description: Gets an adaptor object for a standard data type.
Returntype : Adaptor Object of arbitrary type or undef
Exceptions : none
Caller : external
Status : Medium Risk
: please use the Registry method, as at some time this
: may no longer be supported.
set_adaptor
Arg [1] : Canonical data type for new adaptor.
Arg [2] : Object defining the adaptor for arg1.
Example : $aa = Bio::EnsEMBL::DBSQL::GeneAdaptor->new($db_adaptor);
: $db_adaptor->set_adaptor("Gene", $ga)
Description: Stores the object which represents the adaptor for the
arg1 data type.
Returntype : none
Exceptions : none
Caller : external
Status : Medium Risk
: please use the Registry method, as at some time this
: may no longer be supported.
get_GenericFeatureAdaptors
Arg [1] : List of names of feature adaptors to get. If no
adaptor names are given, all the defined adaptors are returned.
Example : $db->get_GenericFeature("SomeFeature", "SomeOtherFeature")
Description: Returns a hash containing the named feature adaptors (or
all feature adaptors).
Returntype : reference to a Hash containing the named
feature adaptors (or all feature adaptors).
Exceptions : If any of the the named generic feature adaptors do not exist.
Caller : externaladd_GenericFeatureAdaptor
Arg [1] : The name of the feature.
Arg [2] : Adaptor object for a generic feature.
Example : $db->add_GenericFeatureAdaptor("SomeFeature",
"Bio::EnsEMBL::DBSQL::SomeFeatureAdaptor")
Description: Stores the object which represents the adaptor for the
named feature type.
Returntype : none
Exceptions :
Caller : externalspecies
Arg [1] : (optional) string $arg
The new value of the species used by this DBAdaptor.
Example : $species = $dba->species()
Description: Getter/Setter for the species of to use for
this connection. There is currently no point in setting
this value after the connection has already been established
by the constructor.
Returntype : string
Exceptions : none
Caller : new
Status : Stableall_species
Args : NONE
Example : @all_species = @{$dba->all_species()};
Description: Returns the names of all species contained in the
database to which this DBAdaptor is connected.
Returntype : array reference
Exceptions : none
Caller : general
Status : Stableis_multispecies
Arg [1] : (optional) boolean $arg
Example : if ($dba->is_multispecies()) { }
Description: Getter/Setter for the is_multispecies boolean of
to use for this connection. There is currently no
point in setting this value after the connection has
already been established by the constructor.
Returntype : boolean
Exceptions : none
Caller : new
Status : Stablespecies_id
Arg [1] : (optional) string $arg
The new value of the species_id used by this DBAdaptor
when dealing with multi-species databases.
Example : $species_id = $dba->species_id()
Description: Getter/Setter for the species_id of to use for this
connection. There is currently no point in setting
this value after the connection has already been
established by the constructor.
Returntype : string
Exceptions : none
Caller : new
Status : Stableno_cache
Arg [1] : (optional) int $arg
The new value of the no cache attribute used by this DBAdaptor.
Example : $no_cache = $dba->no_cache();
Description: Getter/Setter for the no_cache to use for
this connection. There is currently no point in setting
this value after the connection has already been established
by the constructor.
Returntype : int
Exceptions : none
Caller : new
Status : Stablegroup
Arg [1] : (optional) string $arg
The new value of the group used by this DBAdaptor.
Example : $group = $dba->group()
Description: Getter/Setter for the group of to use for
this connection. There is currently no point in setting
this value after the connection has already been established
by the constructor.
Returntype : string
Exceptions : none
Caller : new
Status : Stableget_SeqRegionCache
Arg [1] : none
Example : my $srcache = $dba->get_SeqRegionCache();
Description: Retrieves a seq_region cache for this database
Returntype : Bio::EnsEMBL::Utils::SeqRegionCache
Exceptions : none
Caller : SliceAdaptor, AssemblyMapperAdaptor
Status : Stablednadb
Title : dnadb
Usage : my $dnadb = $db->dnadb();
Function: returns the database adaptor where the dna lives
Useful if you only want to keep one copy of the dna
on disk but have other databases with genes and features in
Returns : dna database adaptor
Args : Bio::EnsEMBL::DBSQL::BaseAdaptor
Status : Medium Risk.
: Use the Registry method add_DNAAdaptor/get_DNAAdaptor insteadto_hash
Example : my $hash = $dba->to_hash();
my $new_dba = $dba->new(%{$hash});
Description: Provides a hash which is compatible with the
parameters for DBAdaptor's new() method. This can be
useful during serialisation but be aware that Registry
Returntype : Hash
Exceptions : none
Caller : general
Status : New switch_adaptor
Arg [1] : String name of the adaptor type to switch out
Arg [2] : Reference The switchable adaptor implementation
Arg [3] : (optional) CodeRef Provide a subroutine reference as a callback. The
adaptor will be switched before your codeblock is executed and
the adaptor switched back to the original once your code has finished running
Arg [4] : (optional) Boolean override any existing switchable adaptor
Example : $dba->switch_adaptor("sequence", $my_replacement_sequence_adaptor);
$dba->switch_adaptor("sequence", $my_other_replacement_sequence_adaptor, 1);
$dba->switch_adaptor("sequence", $my_replacement_sequence_adaptor, sub {
#Make calls as normal without having to do manual cleanup
});
Returntype : None
Description : Provides a wrapper around the Registry add_switchable_adaptor() method
defaulting both species and group to the current DBAdaptor. Callbacks are
also available providing automatic resource cleanup.
The method also remembers the last switch you did. It will not remember
multiple switches though.
Exceptions : Thrown if no switchable adaptor instance was givenhas_switched_adaptor
Arg [1] : String name of the adaptor type to switch back in
Example : $dba->has_switchable_adaptor("sequence"); #explicit switching back
Returntype : Boolean indicating if the given adaptor is being actively switched
Description : Provides a wrapper around the Registry has_switchable_adaptor() method
defaulting both species and group to the current DBAdaptor. This will
inform if the specified adaptor is being switched out
Exceptions : Nonerevert_adaptor
Arg [1] : (optional) String name of the adaptor type to switch back in
Example : $dba->revert_adaptor(); #implicit switching back whatever was the last switch_adaptor() call
$dba->revert_adaptor("sequence"); #explicit switching back
Returntype : The removed adaptor
Description : Provides a wrapper around the Registry remove_switchable_adaptor() method
defaulting both species and group to the current DBAdaptor. This will remove
a switchable adaptor. You can also remove the last adaptor you switched
in without having to specify any parameter.
Exceptions : Thrown if no switchable adaptor name was given or could be found in the internal
last adaptor variable