From c22a2d5e6ae23a3b5534be98e6cbe5cfa7ec543b Mon Sep 17 00:00:00 2001
From: Web Admin <w3adm@sanger.ac.uk>
Date: Fri, 26 Mar 2004 17:27:06 +0000
Subject: [PATCH] genes can now be got off other databases
---
modules/Bio/EnsEMBL/Slice.pm | 19 +++++++++++++------
1 file changed, 13 insertions(+), 6 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Slice.pm b/modules/Bio/EnsEMBL/Slice.pm
index 94646e2949..32881b3eaa 100644
--- a/modules/Bio/EnsEMBL/Slice.pm
+++ b/modules/Bio/EnsEMBL/Slice.pm
@@ -73,6 +73,7 @@ use Bio::EnsEMBL::Utils::Sequence qw(reverse_comp);
use Bio::EnsEMBL::ProjectionSegment;
+use Data::Dumper;
#inheritance to Bio::EnsEMBL::Root will eventually be removed
@ISA = qw(Bio::EnsEMBL::Root Bio::PrimarySeqI);
@@ -1149,15 +1150,21 @@ sub get_all_SNPs {
=cut
sub get_all_Genes{
- my ($self, $logic_name) = @_;
+ my ($self, $logic_name, $dbtype) = @_;
+ my $db;
+ if($dbtype) {
+ $db = $self->adaptor->db->get_db_adaptor($dbtype);
+ if(!$db) {
+ warning("Don't have db $dbtype returning empty list\n");
+ return [];
+ }
+ } else {
+ $db = $self->adaptor->db;
+ }
- #caching is performed on a per slice basis in the GeneAdaptor
- return $self->adaptor->db->get_GeneAdaptor->fetch_all_by_Slice($self,
- $logic_name);
+ return $db->get_GeneAdaptor()->fetch_all_by_Slice( $self, $logic_name );
}
-
-
=head2 get_all_Genes_by_type
--
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