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diff variant_effect_predictor/Bio/EnsEMBL/DBSQL/DBAdaptor.pm @ 0:1f6dce3d34e0
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| author | mahtabm |
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| date | Thu, 11 Apr 2013 02:01:53 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/variant_effect_predictor/Bio/EnsEMBL/DBSQL/DBAdaptor.pm Thu Apr 11 02:01:53 2013 -0400 @@ -0,0 +1,1065 @@ +=head1 LICENSE + + Copyright (c) 1999-2012 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 + + http://www.ensembl.org/info/about/code_licence.html + +=head1 CONTACT + + Please email comments or questions to the public Ensembl + developers list at <dev@ensembl.org>. + + Questions may also be sent to the Ensembl help desk at + <helpdesk@ensembl.org>. + +=cut + +=head1 NAME + +Bio::EnsEMBL::DBSQL::DBAdaptor + +=head1 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 ); + +=head1 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. + +=head1 METHODS + +=cut + +package Bio::EnsEMBL::DBSQL::DBAdaptor; + +use strict; + +use Bio::EnsEMBL::DBSQL::DBConnection; +use Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor; +use Bio::EnsEMBL::Utils::SeqRegionCache; +use Bio::EnsEMBL::Utils::Exception qw(throw warning deprecate); +use Bio::EnsEMBL::Utils::Argument qw(rearrange); +use Bio::EnsEMBL::Registry; +use Bio::EnsEMBL::Utils::ConfigRegistry; + +my $reg = "Bio::EnsEMBL::Registry"; + +=head2 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 [..] : 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 : Stable + +=cut + +sub new { + my ( $class, @args ) = @_; + + my $self = bless {}, $class; + + my ( $is_multispecies, $species, $species_id, $group, $con, $dnadb, + $no_cache, $dbname ) + = rearrange( [ + 'MULTISPECIES_DB', 'SPECIES', 'SPECIES_ID', 'GROUP', + 'DBCONN', 'DNADB', 'NO_CACHE', 'DBNAME' + ], + @args + ); + + if ( defined($con) ) { $self->dbc($con) } + else { + if(! defined $dbname) { + throw "-DBNAME is a required parameter when creating a DBAdaptor"; + } + $self->dbc( new Bio::EnsEMBL::DBSQL::DBConnection(@args) ); + } + + if ( defined($species) ) { $self->species($species) } + if ( defined($group) ) { $self->group($group) } + + + $self = Bio::EnsEMBL::Utils::ConfigRegistry::gen_load($self); + +# if(!defined($species) ){ +# $reg->find_and_add_aliases($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; +} ## end sub new + +=head2 clear_caches + + Example : $dba->clear_caches(); + Description : Loops through all linked adaptors and clears their + caches if C<clear_cache()> is implemented. Not all caches + are cleared & the DBAdaptor instance should be removed from + the registry to clear these remaining essential caches. + Returntype : None + Exceptions : None + +=cut + +sub clear_caches { + my ($self) = @_; + my $adaptors = Bio::EnsEMBL::Registry->get_all_adaptors( + $self->species(), $self->group()); + while (my $adaptor = shift @{$adaptors}) { + if($adaptor->can('clear_cache')) { + $adaptor->clear_cache(); + } + } + return; +} + +=head2 dbc + + 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 : Stable + +=cut + +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}; +} + + + +=head2 add_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', $lite_db_adaptor); + Description: Attaches another database instance to this database so + that it can be used in instances where it is required. + Returntype : none + Exceptions : none + Caller : EnsWeb + Status : At Risk + : may get deprecated, please use add_db from the registry instead + +=cut + +sub add_db_adaptor { + my ($self, $name, $adaptor) = @_; + + unless($name && $adaptor && ref $adaptor) { + throw('adaptor and name arguments are required'); + } + + Bio::EnsEMBL::Registry->add_db($self, $name, $adaptor); + +} + + +=head2 remove_db_adaptor + + Arg [1] : string $name + the name of the database to detach from this database. + Example : $lite_db = $db->remove_db_adaptor('lite'); + Description: Detaches a database instance from this database and returns + it. + Returntype : none + Exceptions : none + Caller : ? + Status : At Risk + : mey get deprecated, use remove_db instead from the Registry + +=cut + +sub remove_db_adaptor { + my ($self, $name) = @_; + + return Bio::EnsEMBL::Registry->remove_db($self, $name); +} + + +=head2 get_all_db_adaptors + + Arg [1] : none + Example : @attached_dbs = values %{$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 + : may get deprecated soon + : please use Bio::EnsEMBL::Registry->get_all_db_adaptors + +=cut + +sub get_all_db_adaptors { + my ($self) = @_; + return Bio::EnsEMBL::Registry->get_all_db_adaptors($self); +} + + + +=head2 get_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 $name or undef if + no such attached database exists + Returntype : Bio::EnsEMBL::DBSQL::DBConnection + Exceptions : none + Caller : ? + Status : At Risk + : may get deprecated soon + : please use Bio::EnsEMBL::Registry->get_db_adaptors + +=cut + +sub get_db_adaptor { + my ($self, $name) = @_; + + return Bio::EnsEMBL::Registry->get_db($self, $name); +} + +=head2 get_available_adaptors + + Example : my %pairs = %{$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 : Stable + +=cut + +sub get_available_adaptors { + my %pairs = ( + # Firstly those that just have an adaptor named after there object + # in the main DBSQL directory. + map( { $_ => "Bio::EnsEMBL::DBSQL::${_}Adaptor" } qw( + Analysis ArchiveStableId Attribute + AssemblyExceptionFeature AssemblyMapper CoordSystem + CompressedSequence DBEntry DnaAlignFeature + DensityFeature DensityType Exon + Gene KaryotypeBand MiscSet + MiscFeature PredictionTranscript PredictionExon + ProteinFeature ProteinAlignFeature RepeatConsensus + RepeatFeature Sequence SeqRegionSynonym SimpleFeature + Slice SupportingFeature Transcript + TranscriptSupportingFeature Translation UnmappedObject + UnconventionalTranscriptAssociation AssemblySlice + SplicingEvent SplicingEventFeature SplicingTranscriptPair + Operon OperonTranscript + DataFile Assembly + IntronSupportingEvidence + ) ), + # Those whose adaptors are in Map::DBSQL + map( { $_ => "Bio::EnsEMBL::Map::DBSQL::${_}Adaptor" } qw( + Marker MarkerFeature QtlFeature Qtl Ditag DitagFeature + ) ), + # Finally the exceptions... those that have non-standard mapping + # between object / adaptor .... + # 'Blast' => 'Bio::EnsEMBL::External::BlastAdaptor', + 'MetaCoordContainer' => 'Bio::EnsEMBL::DBSQL::MetaCoordContainer', + 'MetaContainer' => 'Bio::EnsEMBL::DBSQL::MetaContainer', + 'SNP' => 'Bio::EnsEMBL::DBSQL::ProxySNPAdaptor', + ); + + return ( \%pairs ); +} ## end sub get_available_adaptors + +########################################################### +# +# Support for DAS +# +########################################################### + +=head2 add_DASFeatureFactory + + Arg [1] : Bio::EnsEMBL::ExternalFeatureFactory $value + Example : none + Description: Attaches a DAS Feature Factory to this method. + ExternalFeatureFactory objects are not really used right now. + They may be reintroduced or taken out completely. The fate + of this function is unknown (although it is presently needed). + Returntype : none + Exceptions : none + Caller : EnsWeb + Status : At Risk + : with the new web code this may not be needed/supported + +=cut + +sub add_DASFeatureFactory{ + + my ($self,$value) = @_; + + push(@{$self->{'_das_ff'}},$value); +} + + +sub remove_all_DASFeatureFactories { + $_[0]->{'_das_ff'} = []; +} +=head2 _each_DASFeatureFactory + + Args : none + Example : none + Description: Not sure if this is used, or if it should be removed. It + does not seem to be used at the moment + Returntype : Bio::EnsEMBL::ExternalFeatureFactory + Exceptions : none + Caller : ?? + Status : At Risk + : with the new web code this may not be needed/supported + +=cut + +sub _each_DASFeatureFactory{ + my ($self) = @_; + + return @{$self->{'_das_ff'}||[]} +} + + +################################################################## +# +# SUPPORT FOR EXTERNAL FEATURE FACTORIES +# +################################################################## + + + +=head2 add_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 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 + +=cut + +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(); + } + + #use a generic track name if one hasn't been defined + unless(defined $track_name) { + $track_name = "External features"; + } + + #if the track name exists add numbers to the end until a free name is found + 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); +} + + + +=head2 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 : general + +=cut + +sub get_ExternalFeatureAdaptors { + my $self = shift; + + return $self->{'_xf_adaptors'}; +} + + +=head2 add_ExternalFeatureFactory + + Arg [1] : Bio::EnsEMBL::DB::ExternalFeatureFactoryI $value + Example : $db_adaptor->add_ExternalFeatureFactory + Description: It is recommended that add_ExternalFeatureAdaptor be used + instead. See documentation for + Bio::EnsEMBL::External::ExternalFeatureAdaptor + + Adds an external feature factory to the core database + so that features from external sources can be displayed in + ensembl. This method is still available mainly for legacy + support for external EnsEMBL installations. + Returntype : none + Exceptions : none + Caller : external + +=cut + +sub add_ExternalFeatureFactory{ + my ($self,$value) = @_; + + $self->add_ExternalFeatureAdaptor($value); +} + +# +# OVERWRITABLE STANDARD ADAPTORS +# + +=head2 get_adaptor + + Arg [1] : Canonical data type for which an adaptor is required. + Example : $db_adaptor->get_adaptor("Protein") + Description: Gets an adaptor object for a standard data type. + Returntype : Adaptor Object of arbitrary type or undef + Exceptions : none + Caller : external + Status : Medium Risk + : please use the Registry method, as at some time this + : may no longer be supprted. + +=cut + +sub get_adaptor { + my ($self, $canonical_name, @other_args) = @_; + + return $reg->get_adaptor($self->species(),$self->group(),$canonical_name); +} + + + +=head2 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", $ga) + Description: Stores the object which represents the adaptor for the + arg1 data type. + Returntype : none + Exceptions : none + Caller : external + Status : Medium Risk + : please use the Registry method, as at some time this + : may no longer be supprted. + +=cut + +sub set_adaptor { + my ($self, $canonical_name, $module) = @_; + + $reg->add_adaptor($self->species(),$self->group(),$canonical_name,$module); + + return $module; +} + + +# +# GENERIC FEATURE ADAPTORS +# + +=head2 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 : $db->get_GenericFeature("SomeFeature", "SomeOtherFeature") + Description: Returns a hash containing the named feature adaptors (or + all feature adaptors). + Returntype : reference to a Hash containing the named + feature adaptors (or all feature adaptors). + Exceptions : If any of the the named generic feature adaptors do not exist. + Caller : external + +=cut + +sub get_GenericFeatureAdaptors { + + my ($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; +} + + +=head2 add_GenericFeatureAdaptor + + Arg [1] : The name of the feature. + Arg [2] : Adaptor object for a generic feature. + Example : $db->add_GenericFeatureAdaptor("SomeFeature", + "Bio::EnsEMBL::DBSQL::SomeFeatureAdaptor") + Description: Stores the object which represents the adaptor for the + named feature type. + Returntype : none + Exceptions : + Caller : external + +=cut + +sub add_GenericFeatureAdaptor { + my ($self, $name, $adaptor_obj) = @_; + + # check that $adaptor is an object that subclasses BaseFeatureAdaptor + if (!$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; +} + +=head2 species + + 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 + +=cut + +sub species { + my ( $self, $arg ) = @_; + + if ( defined($arg) ) { + $self->{_species} = $arg; + } + + $self->{_species}; +} + +=head2 all_species + + Args : NONE + Example : @all_species = @{$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 : Stable + +=cut + +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'}; +} ## end sub all_species + + +=head2 is_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 : Stable + +=cut + +sub is_multispecies { + my ( $self, $arg ) = @_; + + if ( defined($arg) ) { + $self->{_is_multispecies} = $arg; + } + + return $self->{_is_multispecies}; +} + + +=head2 species_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 : Stable + +=cut + +sub species_id { + my ( $self, $arg ) = @_; + + if ( defined($arg) ) { + $self->{_species_id} = $arg; + } + + return $self->{_species_id}; +} + + +=head2 no_cache + + Arg [1] : (optional) int $arg + The new value of the no cache attribute used by this DBAdaptor. + Example : $no_cache = $dba->no_cache(); + Description: Getter/Setter for the no_cache to use for + this connection. There is currently no point in setting + this value after the connection has already been established + by the constructor. + Returntype : int + Exceptions : none + Caller : new + Status : Stable + +=cut + +sub no_cache { + my ($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}; +} + + +=head2 group + + Arg [1] : (optional) string $arg + The new value of the group used by this DBAdaptor. + Example : $group = $dba->group() + Description: Getter/Setter for the group of to use for + this connection. There is currently no point in setting + this value after the connection has already been established + by the constructor. + Returntype : string + Exceptions : none + Caller : new + Status : Stable + +=cut + +sub group { + my ($self, $arg ) = @_; + ( defined $arg ) && + ( $self->{_group} = $arg ); + $self->{_group}; +} + +=head2 get_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 : Stable + +=cut + +sub get_SeqRegionCache { + my $self = shift; + + # use the cache from the database where seq_regions are stored + if($self != $self->dnadb()) { + return $self->dnadb()->get_SeqRegionCache(); + } + + if(!$self->{'seq_region_cache'}) { + $self->{'seq_region_cache'} = Bio::EnsEMBL::Utils::SeqRegionCache->new(); + } + + return $self->{'seq_region_cache'}; +} + + + +#convenient method to retrieve the schema_build version for the database being used + +sub _get_schema_build{ + my ($self) = @_; + + #avoided using dnadb by default to avoid obfuscation of behaviour + + my @dbname = split/_/, $self->dbc->dbname(); + + #warn "dbname is $schema_build"; + + my $schema_build = pop @dbname; + $schema_build = pop(@dbname).'_'.$schema_build; + + + return $schema_build; +} + + +=head2 dnadb + + 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 + +=cut + +sub dnadb { + my $self = shift; + + if(@_) { + my $arg = shift; + $reg->add_DNAAdaptor($self->species(),$self->group(),$arg->species(),$arg->group()); + } + +# return $self->{'dnadb'} || $self; + return $reg->get_DNAAdaptor($self->species(),$self->group()) || $self; +} + + +use vars '$AUTOLOAD'; + +sub AUTOLOAD { + my ( $self, @args ) = @_; + + my $type; + if ( $AUTOLOAD =~ /^.*::get_(\w+)Adaptor$/ ) { + $type = $1; + } elsif ( $AUTOLOAD =~ /^.*::get_(\w+)$/ ) { + $type = $1; + } else { + throw( sprintf( "Could not work out type for %s\n", $AUTOLOAD ) ); + } + + my $ret = $reg->get_adaptor( $self->species(), $self->group(), $type ); + + return $ret if $ret; + + warning( sprintf( + "Could not find %s adaptor in the registry for %s %s\n", + $type, $self->species(), $self->group() ) ); + + throw( sprintf( + "Could not get adaptor %s for %s %s\n", + $type, $self->species(), $self->group() ) ); + +} ## end sub AUTOLOAD + +sub DESTROY { } # required due to AUTOLOAD + + +######################### +# sub DEPRECATED METHODS +######################### +=head2 db + + Description: DEPRECATED + +=cut + +sub db{ + my ($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 source { deprecate('Do not use - this method does nothing'); } + + +=head2 assembly_type + + Description: DEPRECATED - Use CoordSystemAdaptor to obtain default coordinate + system instead. + +=cut + +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) ? $cs->version() : undef; +} + + + +=head2 list_supported_assemblies + + Description: DEPRECATED - Use CoordSystemAdaptor to obtain list of top-level + coordinate systems instead + +=cut + +sub list_supported_assemblies { + my($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 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"); + $self->dbc->prepare(@args); +} + +sub dbname{ + my ($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"); + $self->dbc->disconnect_when_inactive(@args); +} + +sub reconnect_when_lost{ + my ($self, @args) = @_; + + deprecate("reconnect_when_lost Should no longer be called from the DBAdaptor. DBConnection should now be used OR preferably the object adaptor itself\n"); + $self->dbc->reconnect_when_lost(@args); +} + + +sub host{ + my ($self, @args) = @_; + + deprecate("host Should no longer be called from the DBAdaptor. DBConnection should now be used OR preferably the object adaptor itself\n"); + $self->dbc->host(@args); +} +sub username{ + my ($self, @args) = @_; + + deprecate("username Should no longer be called from the DBAdaptor. DBConnection should now be used OR preferably the object adaptor itself\n"); + $self->dbc->username(@args); +} +sub password{ + my ($self, @args) = @_; + + deprecate("password Should no longer be called from the DBAdaptor. DBConnection should now be used OR preferably the object adaptor itself\n"); + $self->dbc->password(@args); +} +sub driver{ + my ($self, @args) = @_; + + deprecate("driver Should no longer be called from the DBAdaptor. DBConnection should now be used OR preferably the object adaptor itself\n"); + $self->dbc->driver(@args); +} +sub port{ + my ($self, @args) = @_; + + deprecate("port Should no longer be called from the DBAdaptor. DBConnection should now be used OR preferably the object adaptor itself\n"); + $self->dbc->port(@args); +} + +sub db_handle{ + my ($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;