Commit 0c96aa04 authored by Ian Longden's avatar Ian Longden
Browse files

get_all_DBAdaptors has optional species and group pairs. POD stuff updated also

parent a3ad0eb5
......@@ -13,7 +13,9 @@ Bio::EnsEMBL::Registry
=head1 SYNOPSIS
$gene_adaptor = Bio::EnsEMBL::Registry->get_adaptor("Homo Sapiens","core","Gene"))
Bio::EnsEMBL::Registry->load_all("configuration_file");
$gene_adaptor = Bio::EnsEMBL::Registry->get_adaptor("homo_sapiens","core","gene"))
=head1 DESCRIPTION
......@@ -109,11 +111,9 @@ use DBI;
use vars qw(%registry_register);
$registry_register{'_WARN'} = 0;
=head2 load_all
Will load the registry with the configuration file which is obtained from
the first in the following and in that order.
......@@ -133,7 +133,6 @@ sub load_all{
my $class = shift;
my $web_reg = shift;
#$registry_register{'_WARN'} = 0; # default report overwriting
if(defined($registry_register{'seen'})){
print STDERR "Clearing previuosly loaded configuration from Registry\n";
$class->clear();
......@@ -176,6 +175,7 @@ sub load_all{
=head2 clear
Will clear the registry and disconnect from all databases.
Example : Bio::EnsEMBL::Registry->clear();
......@@ -351,16 +351,36 @@ sub get_DBAdaptor{
=head2 get_all_DBAdaptors
Example : @dba = @{Bio::EnsEMBL::Registry->get_all_DBAdaptors();
Returntype : list of DBAdaptors
Exceptions : none
Arg [SPECIES]: (optional) string
species name to get adaptors for
Arg [GROUP] : (optional) string
group name to get adaptors for
Example : @dba = @{Bio::EnsEMBL::Registry->get_all_DBAdaptors()};
: @human_dbas = @{Bio::EnsEMBL::Registry->get_all_DBAdaptors(-species => 'human')};
Returntype : list of DBAdaptors
Exceptions : none
=cut
sub get_all_DBAdaptors{
my ($class)=@_;
my ($class,@args)=@_;
my @ret;
return @{$registry_register{'_DBA'}};
my ($species, $group) =
rearrange([qw(SPECIES GROUP)], @args);
if(defined($species)){
$species = $class->get_alias($species);
}
foreach my $dba (@{$registry_register{'_DBA'}}){
if(!defined($species) || $species eq $dba->species){
if(!defined($group) || lc($group) eq lc($dba->group)){
push @ret, $dba;
}
}
}
return \@ret;
}
=head2 get_all_DBAdaptors_by_connection
......@@ -975,6 +995,7 @@ sub load_registry_with_web_adaptors{
}
=head2 set_default_track
Sets a flag to say that that this species/group are a default track and do not
need to be added as another web track.
......@@ -994,6 +1015,7 @@ sub set_default_track{
}
=head2 default_track
Check flag to see if this is a default track
Arg [1] : name of the species to get the adaptors for in the registry.
......@@ -1017,6 +1039,7 @@ sub default_track{
=head2 add_new_tracks
Will add new gene tracks to the configuration of the WEB server if they are
not of the type default and the configuration already has genes in the display.
......
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