From d03598f11c62607e6fa7e5afdf7085eaaaf35d6e Mon Sep 17 00:00:00 2001
From: Monika Komorowska <mk8@sanger.ac.uk>
Date: Mon, 18 Apr 2011 15:25:00 +0000
Subject: [PATCH] Changes to is_circular method.
---
modules/Bio/EnsEMBL/Slice.pm | 14 ++++++++++----
1 file changed, 10 insertions(+), 4 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Slice.pm b/modules/Bio/EnsEMBL/Slice.pm
index 285acc8896..9703cd79ec 100644
--- a/modules/Bio/EnsEMBL/Slice.pm
+++ b/modules/Bio/EnsEMBL/Slice.pm
@@ -533,12 +533,18 @@ sub is_circular {
if ( !defined( $self->adaptor() ) ) { return 0 }
if ( !defined( $self->{'circular'} ) ) {
- my $attrs = $self->get_all_Attributes('circular_seq');
- if ( defined($attrs) ) {
- $self->{'circular'} = ( scalar( @{$attrs} ) > 0 );
+ $self->{'circular'} = 0;
+
+ if ( !defined($self->adaptor()->{'is_circular'}) ){
+ $self->adaptor()->_build_circular_slice_cache();
+ }
+
+ if ($self->adaptor()->{'is_circular'}) {
+ if ( exists($self->adaptor()->{'circular_sr_id_cache'}->{ $self->adaptor()->get_seq_region_id($self) } ) ) {
+ $self->{'circular'} = 1;
+ }
}
}
-
return $self->{'circular'};
}
--
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