backwards compatibillity fix

modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm

@@ -681,7 +681,7 @@ sub dnadb {
 
   if(@_) {
     my $arg = shift;
-    $reg->add_DNAAdaptor($self->species(),$self->group(),$arg->group());
+    $reg->add_DNAAdaptor($self->species(),$self->group(),$arg->species(),$arg->group());
   }
 
 #  return $self->{'dnadb'} || $self;

modules/Bio/EnsEMBL/Registry.pm

@@ -159,47 +159,6 @@ sub load_all{
     }
 }
 
-#=head2 check_if_already_there
-#
-#  Arg [DBNAME] : string
-#                 The name of the database to check for.
-#  Arg [HOST] : (optional) string
-#               The domain name of the database host to check for
-#  Arg [PORT] : int
-#               The port to check for when connecting to the database
-#  Arg [DRIVER] : (optional) string
-#                 The type of database driver to check for
-#
-#  Description: Check to see if the database is already stored.
-#  Returntype : 0 if not found else the species and group.
-#  Exceptions : none
-#  
-#
-#=cut
-
-  
-#sub check_if_already_there{
-#  my ($class) = shift;
-#
-#  my ($dbname,$host,$driver,$port,$species, $group ) =
-#    rearrange([qw(DBNAME HOST DRIVER PORT SPECIES GROUP)], @_);
-#
-#  if(defined($registry_register{'_DBA'})){
-#    foreach my $db (@{$registry_register{'_DBA'}}){
-#      my $dbc= $db->db();
-#      if($dbc->host() eq $host and $dbc->dbname() eq $dbname
-#	 and $dbc->driver() eq $driver and $dbc->port() eq $port){
-#	if(defined($species) and defined($group) and 
-#	   $db->species eq $species and $db->group eq $group){
-#	  return ($db->species(),$db->group());
-#	}
-#      }
-#    }
-#  }
-#  return 0;
-#}
-
-
 #
 # add ons.
 #
@@ -382,16 +341,15 @@ sub get_all_DBAdaptors{
 =cut
 
 sub add_DNAAdaptor{
-  my ($class, $species, $group, $dnadb_group) = @_;
+  my ($class, $species, $group, $dnadb_species, $dnadb_group) = @_;
 
   $species = $class->get_alias($species);
   if($dnadb_group->isa('Bio::EnsEMBL::DBSQL::DBAdaptor')){
-#    print STDERR "AHHH ".caller()."\n";
-    $registry_register{$species}{$group}{'_DNA'} = $dnadb_group->group();
+    deprecated("");
   }
   else{
-#    print STDERR "AHHH MEN ".caller()."\n";
     $registry_register{$species}{$group}{'_DNA'} = $dnadb_group;
+    $registry_register{$species}{$group}{'_DNA2'} = $dnadb_species;
   }
 }
 
@@ -410,8 +368,9 @@ sub get_DNAAdaptor{
 
   $species = $class->get_alias($species);
   my $new_group = $registry_register{$species}{$group}{'_DNA'};
+  my $new_species = $registry_register{$species}{$group}{'_DNA2'};
   if( defined $new_group ) {
-    return  $class->get_DBAdaptor($species,$new_group);
+    return  $class->get_DBAdaptor($new_species,$new_group);
   } else {
     return undef;
   }
@@ -525,25 +484,12 @@ sub get_adaptor{
   my $dnadb_group =  $registry_register{$species}{$group}{_DNA};
 
   if( defined($dnadb_group) && defined($dnadb_adaptors{$type}) ) {
-#      print STDERR "new### $group  $dnadb_group \n";
       $group = $dnadb_group;
   }
-#  else{
-#    if (defined($dnadb_adaptors{$type}) ) {
-#      print STDERR "old### $species $group $type no dnadb \n";    
-#    }
-#  }
-#throw in a check to see if we should get the dnadb one and not the normal
-#  if(defined($registry_register{$species}{$type}{'DNADB'}) && $class->get_DNAAdaptor($species,$group)){
-#    my $dna = $class->get_DNAAdaptor($species,$group);
-#    $species = $dna->species();
-#    $group = $dna->group();
-#  }
 
   my $ret = $registry_register{$species}{$group}{$type};
   if(!defined($ret)){
     return undef;
-#    throw("COULD NOT FIND ADAPTOR species=$species\tgroup=$group\ttype=$type\n");
   }
   if(!ref($ret)){ # not instantiated yet
     my $dba = $registry_register{$species}{$group}{'_DB'};

modules/Bio/EnsEMBL/Utils/ConfigRegistry.pm

@@ -52,6 +52,15 @@ use Bio::EnsEMBL::Utils::Exception qw(warning throw  deprecate stack_trace_dump)
 
 =cut
 
+#
+# 1) core. no need to add dnadb
+# 2) not core add dnadb
+# 3) 
+#
+
+
+
+
 sub gen_load{
   my ($dba) = @_;
   my $config_sub;
@@ -102,6 +111,9 @@ sub gen_load{
     $config_sub =  \&Bio::EnsEMBL::Utils::ConfigRegistry::load_haplotype;    
   }
   elsif($dba->isa('Bio::EnsEMBL::Variation::DBSQL::DBAdaptor')){
+    if(!defined($dba->group())){
+      $dba->group('variation');
+    }
     $config_sub =  \&Bio::EnsEMBL::Utils::ConfigRegistry::load_variation;
   }
   elsif($dba->isa('Bio::EnsEMBL::DBSQL::DBAdaptor')){
@@ -203,7 +215,7 @@ sub load_and_attach_dnadb_to_core{
 
   load_adaptors($dba);
   
-  $reg->add_DNAAdaptor($dba->species,$dba->group,"core"); 
+  $reg->add_DNAAdaptor($dba->species,$dba->group,$dba->species,"core"); 
 }
 
 # those that do not need to attach to core:-#
@@ -258,62 +270,6 @@ sub load_vega{
 
 
 
-#special cases;-
-
-
-
-
-sub load_blast{
-    my ($dba) = @_;
-}
-
-
-sub add_blast_link{
-  my ($class, $species, $group) = @_;
-  my $dba =undef;
-  my $blast = undef;
-  print STDERR " add_blast_link called\n";
-
-  if($dba = Bio::EnsEMBL::Registry->get_DBAdaptor($species, $group)){
-  }
-  else{
-    throw("Cannot find $species $group in the registry\n");
-  }
-
-  if($blast = Bio::EnsEMBL::Registry->get_adaptor("NONE", "blast", "Blast")){
-    $dba->add_db_adaptor("Blast",$blast);
-  }
-  else{
-    throw("Sorry no Blast database has been set up to link to.\n");
-  }
-}
-
-
-
-sub load_go{
-
- my ($class, $dba) = @_;
-
- # shouldnt go into the registry ... sorry
-}
-
-
-
-
-
-#sub dnadb_add{
-#  my $class = shift;
-#  my ($dnaspecies, $dnagroup, $species, $group) = @_;
-#
-#  print STDERR "dnadb_add CALLED\n";
-#
-#  my $dnadb =  Bio::EnsEMBL::Registry->get_DBAdaptor($dnaspecies, $dnagroup);
-#  my $featdb = Bio::EnsEMBL::Registry->get_DBAdaptor($species, $group);
-#
-#  $featdb->dnadb($dnadb);
-#}
-#
-#
 sub add_alias{
   my ($class, @args) = @_;
   my ($species, $aliases) = rearrange([qw(SPECIES ALIAS)],@args);
@@ -328,40 +284,6 @@ sub add_alias{
   }
 
 }
-#
-#
-#sub get_alias{
-#  my ($class, $key) = @_;
-#  return Bio::EnsEMBL::Registry->get_alias($key);
-#}
-#
-#
-#
-#sub attach_database{
-#  my ($class, $species, $core, $name1) = @_;
-#
-#
-#  print STDERR " attach_databse called\n";
-#
-#  my $first =  Bio::EnsEMBL::Registry->get_DBAdaptor($species,$name1);
-#  my $coredb = Bio::EnsEMBL::Registry->get_DBAdaptor($species,$core);
-#
-#  Bio::EnsEMBL::Registry->add_db($coredb,$name1, $first);
-#
-#}
-#
-#sub attach_dna{
-#  my ($class, $species, $main, $attach) = @_; 
-#  print STDERR " attach_dna called\n";
-#
-#  my $no_seq =  Bio::EnsEMBL::Registry->get_DBAdaptor($species,$main);
-#  my $seq = Bio::EnsEMBL::Registry->get_DBAdaptor($species,$attach);
-#
-#  Bio::EnsEMBL::Registry->add_DNAAdaptor($species,$no_seq->group,$attach);
-#}
-
-
-
 #
 # overwrite/load new types. Done this way to enable no changes to CVS for
 # external users. External users should add there own "GROUPS" in the file
@@ -369,6 +291,5 @@ sub add_alias{
 #
 
 eval{ require Bio::EnsEMBL::Utils::User_defined_load };
-#if ($@){ print STDERR  "No user defined loads\n"; }
 
 1;