Made the circular slice code compartmentalised to just SliceAdaptor (making...

Made the circular slice code compartmentalised to just SliceAdaptor (making cache initalisation code easier) and we now only build circular slices when the seqregion it is based off is flagged as circular

modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm

@@ -398,18 +398,24 @@ sub fetch_by_region {
 
   if ( !defined($end) ) { $end = $length }
 
+  #If this was given then check if we've got a circular seq region otherwise
+  #let it fall through to the normal Slice method
   if ( $end + 1 < $start ) {
-    my $new_sl =
-      Bio::EnsEMBL::CircularSlice->new(
-                                   -COORD_SYSTEM    => $cs,
-                                   -SEQ_REGION_NAME => $seq_region_name,
-                                   -SEQ_REGION_LENGTH => $length,
-                                   -START             => $start,
-                                   -END               => $end,
-                                   -STRAND            => 1,
-                                   -ADAPTOR           => $self );
-
-    return $new_sl;
+    my $cs_id = $cs->dbID();
+    my $seq_region_id = $self->{'sr_name_cache'}->{"$seq_region_name:$cs_id"} = $arr->[0];
+    if($self->is_circular($seq_region_id)) {
+      my $new_sl =
+        Bio::EnsEMBL::CircularSlice->new(
+                                     -COORD_SYSTEM    => $cs,
+                                     -SEQ_REGION_NAME => $seq_region_name,
+                                     -SEQ_REGION_LENGTH => $length,
+                                     -START             => $start,
+                                     -END               => $end,
+                                     -STRAND            => 1,
+                                     -ADAPTOR           => $self );
+  
+      return $new_sl;
+    }
   }
 
   if ( defined( $self->{'lrg_region_test'} )
@@ -1048,6 +1054,26 @@ sub is_reference {
   return 1;
 }
 
+=head2 is_circular
+
+  Arg[1]      : int seq_region_id
+  Example     : my $circular = $slice_adptor->is_circular($seq_region_id);
+  Description : Indicates if the sequence region was circular or not
+  Returntype  : Boolean
+  
+=cut
+
+sub is_circular {
+  my ($self, $id) = @_;
+  
+  if (! defined $self->{is_circular}) {
+    $self->_build_circular_slice_cache();
+  }
+  
+  return 0 if $self->{is_circular} == 0;
+  return (exists $self->{circular_sr_id_cache}->{$id}) ? 1 : 0;
+}
+
 =head2 fetch_by_band
 
  Title   : fetch_by_band

modules/Bio/EnsEMBL/Slice.pm

@@ -532,29 +532,19 @@ sub is_toplevel {
   Description: Returns 1 if slice is a circular slice else 0
   Returntype : int
   Caller     : general
-  Status     : At Risk
+  Status     : Stable
 
 =cut
 
 sub is_circular {
   my ($self) = @_;
-
-  if ( !defined( $self->adaptor() ) ) { return 0 }
-
-  if ( !defined( $self->{'circular'} ) ) {
-    $self->{'circular'} = 0;  
-
-    if ( !defined($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;
-	}
-    }
+  my $adaptor = $self->adaptor();
+  return 0 if ! defined $adaptor;
+  if (! exists $self->{'circular'}) {
+    my $id = $adaptor->get_seq_region_id($self);
+    $self->{circular} = $adaptor->is_circular($id);
   }
-  return $self->{'circular'};
+  return $self->{circular};
 }
 
 =head2 invert