From d7c8125bbb7ee0ff292f5619cf100029fe792d86 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Fri, 12 Sep 2008 13:18:38 +0000
Subject: [PATCH] Added method get_all_DBAdaptors_by_dbname(), which is very
similar to get_all_DBAdaptors_by_connection():
Arg [1] : string, name of database
Returntype : reference to list of DBAdaptors
Exceptions : none
Example : @dba = @{ Bio::EnsEMBL::Registry
->get_all_DBAdaptors_by_dbname($dbname) };
Status : Stable
Some formatting.
---
modules/Bio/EnsEMBL/Registry.pm | 95 ++++++++++++++++++++++-----------
1 file changed, 64 insertions(+), 31 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Registry.pm b/modules/Bio/EnsEMBL/Registry.pm
index 703490d2dd..b9439fc7b3 100644
--- a/modules/Bio/EnsEMBL/Registry.pm
+++ b/modules/Bio/EnsEMBL/Registry.pm
@@ -557,47 +557,81 @@ sub get_DBAdaptor{
=cut
-sub get_all_DBAdaptors{
- my ($class,@args)=@_;
+sub get_all_DBAdaptors {
+ my ( $class, @args ) = @_;
+
my @ret;
+ my ( $species, $group ) = rearrange( [qw(SPECIES GROUP)], @args );
- my ($species, $group) =
- rearrange([qw(SPECIES GROUP)], @args);
- if(defined($species)){
+ if ( defined($species) ) {
$species = $class->get_alias($species);
}
- foreach my $dba (@{$registry_register{'_DBA'}}){
- if(!defined($species) || lc($species) eq lc($dba->species)){
- if(!defined($group) || lc($group) eq lc($dba->group)){
- push @ret, $dba;
+
+ foreach my $dba ( @{ $registry_register{'_DBA'} } ) {
+ if ( !defined($species) || lc($species) eq lc( $dba->species ) ) {
+ if ( !defined($group) || lc($group) eq lc( $dba->group ) ) {
+ push( @ret, $dba );
}
}
}
-
return \@ret;
}
=head2 get_all_DBAdaptors_by_connection
- Arg [1] :dbconnection to use to find DBAdaptors
+ Arg [1] : DBConnection used to find DBAdaptors
Returntype : reference to list of DBAdaptors
- Exceptions : none.
- Example : @dba = @{Bio::EnsEMBL::Registry->get_all_DBAdaptors_by_connection($dbc);
+ Exceptions : none
+ Example : @dba = @{ Bio::EnsEMBL::Registry
+ ->get_all_DBAdaptors_by_connection($dbc) };
Status : Stable
=cut
-sub get_all_DBAdaptors_by_connection{
- my ($self, $dbc_orig) = @_;
+sub get_all_DBAdaptors_by_connection {
+ my ( $self, $dbc_orig ) = @_;
+
my @return;
- foreach my $dba ( @{$registry_register{'_DBA'}}){
- my $dbc = $dba->dbc;
- if($dbc && $dbc->can('equals') && $dbc->equals($dbc_orig)){
- push @return, $dba;
+ foreach my $dba ( @{ $registry_register{'_DBA'} } ) {
+ my $dbc = $dba->dbc();
+
+ if ( defined($dbc)
+ && $dbc->can('equals')
+ && $dbc->equals($dbc_orig) )
+ {
+ push( @return, $dba );
+ }
+ }
+
+ return \@return;
+}
+
+=head2 get_all_DBAdaptors_by_dbname
+
+ Arg [1] : string, name of database
+ Returntype : reference to list of DBAdaptors
+ Exceptions : none
+ Example : @dba = @{ Bio::EnsEMBL::Registry
+ ->get_all_DBAdaptors_by_dbname($dbname) };
+ Status : Stable
+
+=cut
+
+sub get_all_DBAdaptors_by_dbname {
+ my ( $self, $dbname ) = @_;
+
+ my @return;
+
+ foreach my $dba ( @{ $registry_register{'_DBA'} } ) {
+ my $dbc = $dba->dbc();
+
+ if ( defined($dbc) && $dbc->dbname() eq $dbname ) {
+ push( @return, $dba );
}
}
+
return \@return;
}
@@ -1310,18 +1344,17 @@ sub load_registry_from_db {
while ( $sth->fetch() ) {
my $dba =
Bio::EnsEMBL::DBSQL::DBAdaptor->new(
- -group => "core",
- -species => $species,
- -species_id => $species_id,
- -multispecies_db => 1,
- -host => $host,
- -user => $user,
- -pass => $pass,
- -port => $port,
- -dbname => $multidb,
- -wait_timeout => $wait_timeout,
- -no_cache => $no_cache
- );
+ -group => "core",
+ -species => $species,
+ -species_id => $species_id,
+ -multispecies_db => 1,
+ -host => $host,
+ -user => $user,
+ -pass => $pass,
+ -port => $port,
+ -dbname => $multidb,
+ -wait_timeout => $wait_timeout,
+ -no_cache => $no_cache );
( my $sp = $species ) =~ s/_/ /g;
$self->add_alias( $species, $sp );
--
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