Commit a9027267 authored by Magali Ruffier's avatar Magali Ruffier
Browse files

replaced reg variable name with registry

helps for consistency across modules
also makes it easier to grep for registry calls, reg is too generic (regulatory, region, registry...)
parent d82f4d8c
......@@ -83,7 +83,7 @@ use Scalar::Util qw(weaken isweak);
# use Data::Dumper;
my $reg = "Bio::EnsEMBL::Registry";
my $registry = "Bio::EnsEMBL::Registry";
@ISA = qw(Bio::PrimarySeqI);
......@@ -2675,12 +2675,12 @@ sub get_all_Genes{
my $ga;
if($dbtype) {
my $db = $reg->get_db($self->adaptor()->db(), $dbtype);
my $db = $registry->get_db($self->adaptor()->db(), $dbtype);
if(defined($db)){
$ga = $reg->get_adaptor( $db->species(), $db->group(), "Gene" );
$ga = $registry->get_adaptor( $db->species(), $db->group(), "Gene" );
}
else{
$ga = $reg->get_adaptor( $self->adaptor()->db()->species(), $dbtype, "Gene" );
$ga = $registry->get_adaptor( $self->adaptor()->db()->species(), $dbtype, "Gene" );
}
if(!defined $ga) {
warning( "$dbtype genes not available" );
......@@ -2796,11 +2796,11 @@ sub get_all_Transcripts {
my $ta;
if($dbtype) {
my $db = $reg->get_db($self->adaptor()->db(), $dbtype);
my $db = $registry->get_db($self->adaptor()->db(), $dbtype);
if(defined($db)){
$ta = $reg->get_adaptor( $db->species(), $db->group(), "Transcript" );
$ta = $registry->get_adaptor( $db->species(), $db->group(), "Transcript" );
} else{
$ta = $reg->get_adaptor( $self->adaptor()->db()->species(), $dbtype, "Transcript" );
$ta = $registry->get_adaptor( $self->adaptor()->db()->species(), $dbtype, "Transcript" );
}
if(!defined $ta) {
warning( "$dbtype genes not available" );
......@@ -3152,11 +3152,11 @@ sub get_all_MiscFeatures {
my $mfa;
if($dbtype) {
my $db = $reg->get_db($adaptor->db(), $dbtype);
my $db = $registry->get_db($adaptor->db(), $dbtype);
if(defined($db)){
$mfa = $reg->get_adaptor( lc($db->species()), $db->group(), "miscfeature" );
$mfa = $registry->get_adaptor( lc($db->species()), $db->group(), "miscfeature" );
} else{
$mfa = $reg->get_adaptor( $adaptor->db()->species(), $dbtype, "miscfeature" );
$mfa = $registry->get_adaptor( $adaptor->db()->species(), $dbtype, "miscfeature" );
}
if(!defined $mfa) {
warning( "$dbtype misc features not available" );
......
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