From c5d9fb814987f4dc85944387c9a6877572329121 Mon Sep 17 00:00:00 2001
From: Graham McVicker <mcvicker@sanger.ac.uk>
Date: Mon, 15 Mar 2004 17:02:21 +0000
Subject: [PATCH] Changed deprecated method get_default_assembly() so that it
actually works still, and changed deprecated warning
---
modules/Bio/EnsEMBL/DBSQL/MetaContainer.pm | 15 +++++++++++----
1 file changed, 11 insertions(+), 4 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/MetaContainer.pm b/modules/Bio/EnsEMBL/DBSQL/MetaContainer.pm
index c21577f79c..581b1efa88 100644
--- a/modules/Bio/EnsEMBL/DBSQL/MetaContainer.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/MetaContainer.pm
@@ -224,17 +224,24 @@ sub get_taxonomy_id {
=head2 get_default_assembly
-Description: DEPRECATED. Use CoordSystemAdaptor::fetch_top_level instead to
- obtain the assembly version.
+ Description: DEPRECATED. Use the version of the coordinate system you are
+ interested in instead.
+
+ Example: #use this instead
+ my ($highest_cs) = @{$db->get_CoordSystemAdaptor->fetch_all()};
+ my $assembly = $highest_cs->version();
=cut
sub get_default_assembly {
my $self = shift;
- deprecate('Use CoordSystemAdaptor::fetch_top_level instead');
+ deprecate("Use version of coordinate system you are interested in instead.\n".
+ "Example:\n".
+ ' ($cs) = @{$coord_system_adaptor->fetch_all()};'."\n" .
+ ' $assembly = $cs->version();');
- my $cs = $self->db->get_CoordSystemAdaptor->fetch_top_level();
+ my ($cs) = @{$self->db->get_CoordSystemAdaptor->fetch_all()};
return $cs->version();
}
--
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