Bio::EnsEMBL::DBSQL
DBAdaptor
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Summary
Bio::EnsEMBL::DBSQL::DBAdaptor
Package variables
Privates (from "my" definitions)
$reg = "Bio::EnsEMBL::Registry"
Included modules
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
Methods description
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/supported |
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 |
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 attribuite 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 |
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 : external |
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 : external |
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', $lite_db_adaptor);
Description: Attaches another database instance to this database so
that it can be used in instances where it is required.
Returntype : none
Exceptions : none
Caller : EnsWeb
Status : At Risk
: may get deprecated, please use add_db from the registry instead |
Args : NONE
Example : @all_species = @{$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 : Stable |
Description: DEPRECATED - Use CoordSystemAdaptor to obtain default coordinate
system instead. |
Arg[1] : (optional) Bio::EnsEMBL::DBSQL::DBConnection
Exmaple : $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 : Stable |
Title : dnadb
Usage : my $dnadb = $db->dnadb();
Function: returns the database adaptor where the dna lives
Useful if you only want to keep one copy of the dna
on disk but have other databases with genes and features in
Returns : dna database adaptor
Args : Bio::EnsEMBL::DBSQL::BaseAdaptor
Status : Medium Risk.
: Use the Registry method add_DNAAdaptor/get_DNAAdaptor instead |
Arg [1] : none
Example : @xfas = values %{$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 : general |
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 : external |
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 : Stable |
Arg [1] : Canonical data type for which an adaptor is required.
Example : $db_adaptor->get_adaptor("Protein")
Description: Gets an adaptor object for a standard data type.
Returntype : Adaptor Object of arbitrary type or undef
Exceptions : none
Caller : external
Status : Medium Risk
: please use the Registry method, as at some time this
: may no longer be supprted. |
Arg [1] : none
Example : @attached_dbs = values %{$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
: may get deprecated soon
: please use Bio::EnsEMBL::Registry->get_all_db_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 : Stable |
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
: may get deprecated soon
: please use Bio::EnsEMBL::Registry->get_db_adaptors |
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 : Stable |
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 : Stable |
Description: DEPRECATED - Use CoordSystemAdaptor to obtain list of top-level
coordinate systems instead |
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 ensembl-dev.
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'
);
Exmaple2 : $db = new Bio::EnsEMBL::DBSQL::DBAdaptor(
-species => 'Homo_sapiens',
-group => 'core' -user => 'root',
-dbname => 'pog',
-host => 'caldy',
-driver => 'mysql'
);
Exmaple3 : $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 : Stable |
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 : Stable |
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 Risk
: mey get deprecated, use remove_db instead from the Registry |
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 supprted. |
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 : Stable |
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 = $dba->species_id()
Description: Getter/Setter for the species_id of to use for this
connection. There is currently no point in setting
this value after the connection has already been
established by the constructor.
Returntype : string
Exceptions : none
Caller : new
Status : Stable |
Methods code
sub AUTOLOAD
{ my ($self,@args) = @_;
my $type;
if($AUTOLOAD =~ /^.*::get_(\w+)Adaptor$/){
$type = $1;
}
elsif($AUTOLOAD =~ /^.*::get_(\w+)$/){
$type = $1;
}
else{
throw("Could not work out type for $AUTOLOAD\n ");
}
my $ret = $reg->get_adaptor($self->species(),$self->group(),$type);
if($ret){
return $ret;
}
else{
throw( "Couldnt get adaptor $type for ".$self->species." ".$self->group."\n");
warning("Could not find $type adaptor in the registry for ".$self->species." ".$self->group."\n");
return $ret;
}
die("No such method: $AUTOLOAD\n");} | sub _each_DASFeatureFactory
{ my ($self) = @_;
return @{$self->{'_das_ff'}||[]}
}
} | sub _get_schema_build
{ my ($self) = @_;
my @dbname = split/_/, $self->dbc->dbname();
my $schema_build = pop @dbname;
$schema_build = pop(@dbname).'_'.$schema_build;
return $schema_build; } | sub add_DASFeatureFactory
{
my ($self,$value) = @_;
push(@{$self->{'_das_ff'}},$value);} | sub add_ExternalFeatureAdaptor
{ my ($self, $adaptor) = @_;
unless($adaptor && ref $adaptor &&
$adaptor->isa('Bio::EnsEMBL::External::ExternalFeatureAdaptor')) {
throw("[$adaptor] is not a " .
"Bio::EnsEMBL::External::ExternalFeatureAdaptor");
}
unless(exists $self->{'_xf_adaptors'}) {
$self->{'_xf_adaptors'} = {};
}
my $track_name = $adaptor->{'_track_name'};
if(!$track_name) {
$track_name = $adaptor->track_name();
}
unless(defined $track_name) {
$track_name = "External features";
}
if(exists $self->{'_xf_adaptors'}->{"$track_name"}) {
my $num = 2;
$num++ while(exists $self->{'_xf_adaptors'}->{"$track_name$num"});
$self->{'_xf_adaptors'}->{"$track_name$num"} = $adaptor;
} else {
$self->{'_xf_adaptors'}->{"$track_name"} = $adaptor;
}
$adaptor->ensembl_db($self);} | sub add_ExternalFeatureFactory
{ my ($self,$value) = @_;
$self->add_ExternalFeatureAdaptor($value);
}
} | sub add_GenericFeatureAdaptor
{ my ($self, $name, $adaptor_obj) = @_;
if (!$adaptor_obj->isa("Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor")) {
throw("$name is a " . ref($adaptor_obj) . "which is not a " .
"subclass of Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor" );
}
$self->{'generic_feature_adaptors'}->{$name} = $adaptor_obj; } | sub add_db_adaptor
{ my ($self, $name, $adaptor) = @_;
unless($name && $adaptor && ref $adaptor) {
throw('adaptor and name arguments are required');
}
Bio::EnsEMBL::Registry->add_db($self, $name, $adaptor);} | sub all_species
{ my ($self) = @_;
if ( !$self->is_multispecies() ) { return [ $self->species() ] }
if ( exists( $self->{'_all_species'} ) ) {
return $self->{'_all_species'};
}
my $statement =
"SELECT meta_value "
. "FROM meta "
. "WHERE meta_key = 'species.db_name'";
my $sth = $self->dbc()->db_handle()->prepare($statement);
$sth->execute();
my $species;
$sth->bind_columns(\$ species );
my @all_species;
while ( $sth->fetch() ) { push( @all_species, $species ) }
$self->{'_all_species'} =\@ all_species;
return $self->{'_all_species'};
}
} | sub assembly_type
{ my $self = shift;
deprecate('Use CoordSystemAdaptor $csa->fetch_all->[0]->version() instead');
my $csa = $self->get_CoordSystemAdaptor();
my ($cs) = @{$csa->fetch_all()};
return ($cs) ? $cs->version() : undef;} | sub db
{ my ($self, $arg ) = @_;
deprecate("db Should no longer be called from the DBAdaptor. DBConnection should now be used OR preferably the object adaptor itself\n");
return $self->dbc($arg);} | sub db_handle
{ my ($self, @args) = @_;
deprecate("db_handle Should no longer be called from the DBAdaptor. DBConnection should now be used OR preferably the object adaptor itself\n");
$self->dbc->db_handle(@args);
}
1;} | sub dbc
{ my $self = shift;
if(@_){
my $arg = shift;
if(defined($arg)){
if(!$arg->isa('Bio::EnsEMBL::DBSQL::DBConnection')){
throw("$arg is no a DBConnection\n");
}
}
$self->{_dbc} = $arg;
}
return $self->{_dbc};} | sub dbname
{ my ($self, @args) = @_;
deprecate("dbname Should no longer be called from the DBAdaptor. DBConnection should now be used OR preferably the object adaptor itself\n");
$self->dbc->dbname(@args);} | sub disconnect_when_inactive
{ my ($self, @args) = @_;
deprecate("disconnect_when_inactive Should no longer be called from the DBAdaptor. DBConnection should now be used OR preferably the object adaptor itself\n");
$self->dbc->disconnect_when_inactive(@args);} | sub dnadb
{ my $self = shift;
if(@_) {
my $arg = shift;
$reg->add_DNAAdaptor($self->species(),$self->group(),$arg->species(),$arg->group());
}
return $reg->get_DNAAdaptor($self->species(),$self->group()) || $self;
}
use vars '$AUTOLOAD';} | sub driver
{ my ($self, @args) = @_;
deprecate("driver Should no longer be called from the DBAdaptor. DBConnection should now be used OR preferably the object adaptor itself\n");
$self->dbc->driver(@args);} | sub get_ExternalFeatureAdaptors
{ my $self = shift;
return $self->{'_xf_adaptors'};} | sub get_GenericFeatureAdaptors
{
my ($self, @names) = @_;
my %adaptors = ();
if (!@names) {
%adaptors = %{$self->{'generic_feature_adaptors'}};
} else {
foreach my $name (@names) {
if (!exists($self->{'generic_feature_adaptors'}->{$name})) {
throw("No generic feature adaptor has been defined for $name" );
}
$adaptors{$name} = $self->{'generic_feature_adaptors'}->{$name};
}
}
return\% adaptors;} | sub get_SeqRegionCache
{ my $self = shift;
if($self != $self->dnadb()) {
return $self->dnadb()->get_SeqRegionCache();
}
if(!$self->{'seq_region_cache'}) {
$self->{'seq_region_cache'} = Bio::EnsEMBL::Utils::SeqRegionCache->new();
}
return $self->{'seq_region_cache'};
}
} | sub get_adaptor
{ my ($self, $canonical_name, @other_args) = @_;
return $reg->get_adaptor($self->species(),$self->group(),$canonical_name); } | sub get_available_adaptors
{ my %pairs = (
map( { $_ => "Bio::EnsEMBL::DBSQL::${_}Adaptor" } qw(
AffyFeature AffyArray AffyProbe
Analysis ArchiveStableId Attribute
AssemblyExceptionFeature AssemblyMapper CoordSystem
CompressedSequence DBEntry DnaAlignFeature
DensityFeature DensityType Exon
Gene KaryotypeBand MiscSet
MiscFeature OligoArray OligoFeature
OligoProbe PredictionTranscript PredictionExon
ProteinFeature ProteinAlignFeature RepeatConsensus
RepeatFeature Sequence SimpleFeature
Slice SupportingFeature Transcript
TranscriptSupportingFeature Translation UnmappedObject
UnconventionalTranscriptAssociation
AssemblySlice
) ),
map( { $_ => "Bio::EnsEMBL::Map::DBSQL::${_}Adaptor" } qw(
Marker MarkerFeature QtlFeature Qtl Ditag DitagFeature
) ),
'MetaCoordContainer' => 'Bio::EnsEMBL::DBSQL::MetaCoordContainer',
'MetaContainer' => 'Bio::EnsEMBL::DBSQL::MetaContainer',
'SNP' => 'Bio::EnsEMBL::DBSQL::ProxySNPAdaptor',
'GeneCollection' => 'Bio::EnsEMBL::Collection::Gene',
'TranscriptCollection' => 'Bio::EnsEMBL::Collection::Transcript',
'ExonCollection' => 'Bio::EnsEMBL::Collection::Exon',
'RepeatFeatureCollection' =>
'Bio::EnsEMBL::Collection::RepeatFeature' );
return (\% pairs );
}
} | sub group
{ my ($self, $arg ) = @_;
( defined $arg ) &&
( $self->{_group} = $arg );
$self->{_group};} | sub host
{ my ($self, @args) = @_;
deprecate("host Should no longer be called from the DBAdaptor. DBConnection should now be used OR preferably the object adaptor itself\n");
$self->dbc->host(@args);} | sub is_multispecies
{ my ( $self, $arg ) = @_;
if ( defined($arg) ) {
$self->{_is_multispecies} = $arg;
}
return $self->{_is_multispecies};} | sub list_supported_assemblies
{ my($self) = @_;
deprecate('Use CoordSystemAdaptor::fetch_all instead');
my $csa = $self->get_CoordSystemAdaptor();
my %versions;
foreach my $cs (@{$csa->fetch_all()}) {
$versions{$cs->version()} = 1;
}
return keys %versions;} | sub new
{ my ( $class, @args ) = @_;
my $self = bless {}, $class;
my ( $is_multispecies, $species, $species_id, $group, $con, $dnadb,
$no_cache )
= rearrange( [
'MULTISPECIES_DB', 'SPECIES', 'SPECIES_ID', 'GROUP',
'DBCONN', 'DNADB', 'NO_CACHE'
],
@args
);
if ( defined($con) ) { $self->dbc($con) }
else {
$self->dbc( new Bio::EnsEMBL::DBSQL::DBConnection(@args) );
}
if ( defined($species) ) { $self->species($species) }
if ( defined($group) ) { $self->group($group) }
$self = Bio::EnsEMBL::Utils::ConfigRegistry::gen_load($self);
$self->species_id( $species_id || 1 );
$self->is_multispecies( defined($is_multispecies)
&& $is_multispecies == 1 );
if ( defined($dnadb) ) { $self->dnadb($dnadb) }
if ( defined($no_cache) ) { $self->no_cache($no_cache) }
return $self;
}
} | sub no_cache
{ my ($self, $arg ) = @_;
if ( defined $arg ){
if ($arg != 1 && $arg != 0){
throw("$arg is not allowed for this attribute. Only value 1|0 is allowed");
}
$self->{_no_cache} = $arg;
}
$self->{_no_cache};} | sub password
{ my ($self, @args) = @_;
deprecate("password Should no longer be called from the DBAdaptor. DBConnection should now be used OR preferably the object adaptor itself\n");
$self->dbc->password(@args);} | sub port
{ my ($self, @args) = @_;
deprecate("port Should no longer be called from the DBAdaptor. DBConnection should now be used OR preferably the object adaptor itself\n");
$self->dbc->port(@args);} | sub prepare
{ my ($self, @args) = @_;
deprecate("prepare Should no longer be called from the DBAdaptor. DBConnection should now be used OR preferably the object adaptor itself\n");
$self->dbc->prepare(@args);} | sub remove_all_DASFeatureFactories
{ $_[0]->{'_das_ff'} = [];} | sub set_adaptor
{ my ($self, $canonical_name, $module) = @_;
$reg->add_adaptor($self->species(),$self->group(),$canonical_name,$module);
return $module;
}
} | sub species
{ my ( $self, $arg ) = @_;
if ( defined($arg) ) {
$self->{_species} = $arg;
}
$self->{_species};} | sub species_id
{ my ( $self, $arg ) = @_;
if ( defined($arg) ) {
$self->{_species_id} = $arg;
}
return $self->{_species_id};} | sub username
{ my ($self, @args) = @_;
deprecate("username Should no longer be called from the DBAdaptor. DBConnection should now be used OR preferably the object adaptor itself\n");
$self->dbc->username(@args);} | General documentation
Copyright (c) 1999-2009 The European Bioinformatics Institute and
Genome Research Limited. All rights reserved.
This software is distributed under a modified Apache license.
For license details, please see
/info/about/code_licence.html