Commit b3e3219d authored by Ian Longden's avatar Ian Longden
Browse files

merged adaptors removed and more docs added. load_registry_with_web_adaptors...

merged adaptors removed and more docs added. load_registry_with_web_adaptors deprecated as new web does not allow this to work anymore, but Use load_registry_from_db can now be used instead
parent 5a9967a9
......@@ -102,7 +102,6 @@ package Bio::EnsEMBL::Registry;
use strict;
use Bio::EnsEMBL::DBSQL::MergedAdaptor;
use Bio::EnsEMBL::DBSQL::DBAdaptor;
use Bio::EnsEMBL::Utils::Exception qw( deprecate throw warning );
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
......@@ -190,7 +189,6 @@ sub clear{
my ($self);
foreach my $dba (@{$registry_register{'_DBA'}}){
print $dba."\n";
......@@ -347,12 +345,8 @@ sub get_DBAdaptor{
$species = $class->get_alias($species);
if(defined($group)){ # group defined so return standard DB Adaptor
return $registry_register{$species}{lc($group)}{'_DB'};
else{ #return a merged db adaptor
return new_merged Bio::EnsEMBL::DBSQL::DBAdaptor($species);
return $registry_register{$species}{lc($group)}{'_DB'};
=head2 get_all_DBAdaptors
......@@ -495,7 +489,7 @@ sub add_adaptor{
# print STDERR "REGADD $species \t $group \t $type\t to the registry\n";
if(!defined ($registry_register{lc($type)}{$species})){
my @list =();
......@@ -684,6 +678,16 @@ sub alias_exists{
return 0;
=head2 set_disconnect_when_inactive
Example : Bio::EnsEMBL::Registry->set_disconnect_when_inactive();
Description: Set the flag to make sure that the database connection is dropped if
not being used on each database.
Returntype : none
Exceptions : none
sub set_disconnect_when_inactive{
foreach my $dba ( @{get_all_DBAdaptors()}){
my $dbc = $dba->dbc;
......@@ -693,6 +697,16 @@ sub set_disconnect_when_inactive{
=head2 disconnect_all
Example : Bio::EnsEMBL::Registry->disconnect_all();
Description: disconnect from all the databases.
Returntype : none
Exceptions : none
sub disconnect_all {
foreach my $dba ( get_all_DBAdaptors() ){
my $dbc = $dba->dbc;
......@@ -934,21 +948,16 @@ sub load_registry_from_db{
=head2 load_registry_with_web_adaptors
Will load the registry with all the Adaptors used in the Web server.
Providing Sitedefs and SpeciesDefs can be found on PERL5LIB path.
=head2 DEPRECATED load_registry_with_web_adaptors
Example : Bio::EnsEMBL::Registry->load_registry_with_web_adaptors();
Returntype : none
Exceptions : Will die if Sitedefs or SpeciesDefs is not found on the
PERL5LIB path.
DEPRECATED: Use load_registry_from_db instead.
sub load_registry_with_web_adaptors{
my $class = shift;
deprecate('Use the load_registry_from_db instead');
eval{ require SiteDefs };
if ($@){ die "Can't use - $@\n"; }
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