Removed Exon::contig and BaseAlignFeature::contig methods.

These were causing infinite recursion due to new superclass implementation of entire_seq, attach_seq, and contig methods

modules/Bio/EnsEMBL/BaseAlignFeature.pm

@@ -277,34 +277,6 @@ sub adaptor {
 }
 
 
-=head2 contig
-
-  Arg [1]    : Bio::EnsEMBL::Slice or
-               Bio::EnsEMBL::RawContig $contig
-  Example    : none
-  Description: The sequnence where the coordinates make sense. Channeled to
-               attach_seq/entire_seq from BioPerl
-  Returntype : Slice/RawContig
-  Exceptions : none
-  Caller     : general
-
-=cut
-
-
-sub contig {
-  my $self = shift;
-  if( @_ ) {
-    my $value = shift;
-    #print "setting exons contig to ".$value." \n";
-    $self->attach_seq($value);
-  }
-  else {
-    return $self->entire_seq();
-  }
-}
-
-
-
 =head2 _parse_cigar
 
   Args       : none

modules/Bio/EnsEMBL/Exon.pm

@@ -222,33 +222,6 @@ sub adaptor {
 }
 
 
-
-
-=head2 contig
-
-  Arg [1]    : Bio::EnsEMBL::RawContig/Slice $contig
-  Example    : none
-  Description: get/set for attribute contig. Is channeled to the bioperl
-               comliant entire_seq/attach_seq calls.
-  Returntype : Bio::EnsEMBL::RawContig/Slice
-  Exceptions : none
-  Caller     : general
-
-=cut
-
-
-sub contig {
-  my $self = shift;
-  my $seq = shift;
-  
-  if( $seq ) {
-    $self->attach_seq($seq);
-  }
-
-  return $self->entire_seq();
-}
-
-
 =head2 transform
 
   Arg  1    : Bio::EnsEMBL::Slice $slice

modules/Bio/EnsEMBL/SeqFeature.pm

@@ -293,14 +293,20 @@ sub frame {
 =cut
 
 sub primary_tag{
-    my ($self,$arg) = @_;
+  my ($self,$arg) = @_;
+  
+  if (defined($arg)) {
+    # throw warnings about setting primary tag
+    my ($p,$f,$l) = caller;
+    $self->warn("$f:$l setting primary_tag now deprecated." .
+		"Primary tag is delegated to analysis object");
+  }
 
-    if (defined($arg)) {
-        # throw warnings about setting primary tag
-        my ($p,$f,$l) = caller;
-        $self->warn("$f:$l setting primary_tag now deprecated. Primary tag is delegated to analysis object");
-   }
-   return $self->analysis->gff_feature();
+  unless($self->analysis) {
+    return '';
+  }
+  
+  return $self->analysis->gff_feature();
 }
 
 =head2 source_tag
@@ -322,7 +328,12 @@ sub source_tag{
     if (defined($arg)) {
         # throw warnings about setting primary tag
         my ($p,$f,$l) = caller;
-        $self->warn("$f:$l setting source_tag now deprecated. Source tag is delegated to analysis object");
+        $self->warn("$f:$l setting source_tag now deprecated. " .
+		    "Source tag is delegated to analysis object");
+    }
+
+    unless($self->analysis) {
+      return "";
     }
 
    return $self->analysis->gff_source();

modules/Bio/EnsEMBL/Slice.pm

@@ -345,7 +345,7 @@ sub get_all_RepeatFeatures{
 
 sub get_all_Genes{
    my ($self, $empty_flag) = @_;
-   
+
    #caching is performed on a per slice basis in the GeneAdaptor
    my $gene_adaptor = $self->adaptor->db->get_GeneAdaptor();
    return $gene_adaptor->fetch_by_Slice($self, $empty_flag);