DBAdaptor examples replaced with registry ones. This was confusing people on the API course

modules/Bio/EnsEMBL/DBSQL/AnalysisAdaptor.pm

@@ -15,11 +15,14 @@ Bio::EnsEMBL::DBSQL::AnalysisAdaptor
 
 =head1 SYNOPSIS
 
-  use Bio::EnsEMBL::DBSQL::DBAdaptor;
+  use Bio::EnsEMBL::Registry;
 
-  $db = Bio::EnsEMBL::DBSQL::DBAdaptor->new(...);
+  Bio::EnsEMBL::Registry->load_registry_from_db(
+              -host => 'ensembldb.ensembl.org',
+              -user => 'anonymous'
+  );
 
-  $analysis_adaptor = $db_adaptor->get_AnalysisAdaptor;
+  $analysis_adaptor = Bio::EnsEMBL::Registry->get_adaptor("human", "core", "analysis");
 
   my $analysis = $analysis_adaptor->fetch_by_logic_name('genscan');
 

modules/Bio/EnsEMBL/DBSQL/AssemblyMapperAdaptor.pm

@@ -13,10 +13,15 @@
 
 =head1 SYNOPSIS
 
-  my $db = Bio::EnsEMBL::DBSQL::DBAdaptor->new(...);
+  use Bio::EnsEMBL::Registry;
 
-  my $asma = $dba->get_AssemblyMapperAdaptor();
-  my $csa  = $dba->get_CoordSystemAdaptor();
+  Bio::EnsEMBL::Registry->load_registry_from_db(
+              -host => 'ensembldb.ensembl.org',
+              -user => 'anonymous'
+  );
+
+  $asma = Bio::EnsEMBL::Registry->get_adaptor("human", "core", "assemblymapper");
+  $csa = Bio::EnsEMBL::Registry->get_adaptor("human", "core", "coordsystem");
 
   my $chr33_cs   = $csa->fetch_by_name('chromosome', 'NCBI33');
   my $chr34_cs   = $csa->fetch_by_name('chromosome', 'NCBI34');

modules/Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm

@@ -9,9 +9,15 @@ Bio::EnsEMBL::DBSQL::CoordSystemAdaptor
 
 =head1 SYNOPSIS
 
-  my $db = Bio::EnsEMBL::DBSQL::DBAdaptor->new(...);
 
-  my $csa = $db->get_CoordSystemAdaptor();
+  use Bio::EnsEMBL::Registry;
+
+  Bio::EnsEMBL::Registry->load_registry_from_db(
+              -host => 'ensembldb.ensembl.org',
+              -user => 'anonymous'
+  );
+
+  $csa = Bio::EnsEMBL::Registry->get_adaptor("human", "core", "coordsystem");
 
   #
   # Get all coord systems in the database:

modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm

@@ -7,11 +7,14 @@ storage of Gene objects
 
 =head1 SYNOPSIS
 
-  use Bio::EnsEMBL::DBSQL::DBAdaptor;
+  use Bio::EnsEMBL::Registry;
 
-  $dba = Bio::EnsEMBL::DBSQL::DBAdaptor->new(...);
+  Bio::EnsEMBL::Registry->load_registry_from_db(
+              -host => 'ensembldb.ensembl.org',
+              -user => 'anonymous',
+  );
 
-  $gene_adaptor = $dba->get_GeneAdaptor();
+  $gene_adaptor = Bio::EnsEMBL::Registry->get_adaptor("human", "core", "gene");
 
   $gene = $gene_adaptor->fetch_by_dbID(1234);
 
@@ -19,7 +22,7 @@ storage of Gene objects
 
   @genes = @{$gene_adaptor->fetch_all_by_external_name('BRCA2')};
 
-  $slice_adaptor = $db->get_SliceAdaptor;
+  $slice_adaptor = Bio::EnsEMBL::Registry->get_adaptor("human", "core", "slice");;
   $slice = $slice_adaptor->fetch_by_region('chromosome', '1', 1, 1000000);
   @genes = @{$gene_adaptor->fetch_all_by_Slice($slice)};
 

modules/Bio/EnsEMBL/DBSQL/ProteinFeatureAdaptor.pm

@@ -15,14 +15,14 @@ Bio::EnsEMBL::DBSQL::ProteinFeatureAdaptor
 
 =head1 SYNOPSIS
 
-  use Bio::EnsEMBL::DBSQL::DBAdaptor;
-  use Bio::EnsEMBL::DBSQL::ProteinFeatureAdaptor;
-
-  $db = new Bio::EnsEMBL::DBSQL::DBAdaptor( -user => 'root', 
-                                            -db => 'pog' ,
-                                            -host => 'caldy' ,
-                                            -driver => 'mysql' );
-  my $pfa = $db->get_ProteinFeatureAdaptor();
+  use Bio::EnsEMBL::Registry;
+
+  Bio::EnsEMBL::Registry->load_registry_from_db(
+              -host => 'ensembldb.ensembl.org',
+              -user => 'anonymous'
+  );
+
+  $pfa = Bio::EnsEMBL::Registry->get_adaptor("human", "core", "proteinfeature");
 
   my @prot_feats = @{$pfa->fetch_all_by_translation_id(1231)};
 

modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm

@@ -16,12 +16,17 @@ the creation of Slice objects.
 
 =head1 SYNOPSIS
 
-  use Bio::EnsEMBL::DBSQL::DBAdaptor;
   use Bio::EnsEMBL::Utils::Slice qw(split_Slices);
+  use Bio::EnsEMBL::Registry;
+
+  Bio::EnsEMBL::Registry->load_registry_from_db(
+              -host => 'ensembldb.ensembl.org',
+              -user => 'anonymous'
+  );
+
+  $slice_adaptor = Bio::EnsEMBL::Registry->get_adaptor("human", "core", "slice");
 
-  $db = Bio::EnsEMBL::DBSQL::DBAdaptor->new(...);
 
-  $slice_adaptor = $db->get_SliceAdaptor();
 
   # get a slice on the entire chromosome X
   $chr_slice = $slice_adaptor->fetch_by_region('chromosome','X');

modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm

@@ -7,10 +7,14 @@ interaction relating to the storage and retrieval of Transcripts
 
 =head1 SYNOPSIS
 
-  $db = Bio::EnsEMBL::DBSQL::DBAdaptor->new(...);
-  $slice_adaptor = $db->get_SliceAdaptor();
+  use Bio::EnsEMBL::Registry;
 
-  $transcript_adaptor = $db->get_TranscriptAdaptor();
+  Bio::EnsEMBL::Registry->load_registry_from_db(
+              -host => 'ensembldb.ensembl.org',
+              -user => 'anonymous'
+  );
+
+  $transcript_adaptor = Bio::EnsEMBL::Registry->get_adaptor("human", "core", "transcript");
 
   $transcript = $transcript_adaptor->fetch_by_dbID(1234);
 

modules/Bio/EnsEMBL/DBSQL/TranslationAdaptor.pm

@@ -23,10 +23,17 @@ Transcript object first, and then fetching the Translation.
 
 =head1 SYNOPSIS
 
-  my $db = Bio::EnsEMBL::DBSQL::DBAdaptor->new(...);
+  use Bio::EnsEMBL::Registry;
+
+  Bio::EnsEMBL::Registry->load_registry_from_db(
+              -host => 'ensembldb.ensembl.org',
+              -user => 'anonymous'
+  );
+
+  $transcript_adaptor = Bio::EnsEMBL::Registry->get_adaptor("human", "core", "transcript");
+  $translation_adaptor = Bio::EnsEMBL::Registry->get_adaptor("human", "core", "translation");
+
 
-  my $transcript_adaptor = $db->get_TranscriptAdaptor();
-  my $translation_adaptor = $db->get_TranslationAdaptor();
   my $transcript = $transcript_adaptor->fetch_by_dbID(131243);
   my $translation = $translation_adaptor->fetch_by_Transcript($transcript);