replaced print STDERR with warn ( otherwise website crashes). added stable_id,...

replaced print STDERR with warn ( otherwise website crashes). added stable_id, display_xref and feature_Slice functions

modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm

@@ -123,11 +123,11 @@ sub new {
   my $meta_container = $self->db->get_MetaContainer();
   my @values = $meta_container->list_value_by_key("LRG");
   if(defined(@values) and scalar(@values) and $values[0]->[0]){
-    print "LRG is true and set to ".$values[0]->[0]."\n";
+#     "LRG is true and set to ".$values[0]->[0]."\n";
     $self->{'lrg_region_test'} = $values[0]->[0];
   }
   else{
-    print "LRG NOT set\n";
+#    print "LRG NOT set\n";
   }
 
   return $self;
@@ -1079,7 +1079,7 @@ sub fetch_by_Feature{
 
   my $slice = $feature->slice();
   if(!$slice || (!$slice->isa('Bio::EnsEMBL::Slice') && !$slice->isa('Bio::EnsEMBL::LRGSlice') )) {
-    print "slcie is ---".ref($slice)."\n";
+    warn "slcie is ---".ref($slice)."\n";
     throw('Feature must be attached to a valid slice.');
   }
 

modules/Bio/EnsEMBL/LRGSlice.pm

@@ -143,6 +143,7 @@ sub new{
  return $self;
 }
 
+
 use vars '$AUTOLOAD';
 
 
@@ -154,7 +155,7 @@ sub AUTOLOAD {
 
 
   if($method =~ /^get_all_Attribute/){
-    print STDERR "get_all_Attribbutes called\n";
+#    print STDERR "get_all_Attribbutes called\n";
     return  $self->{'_orig_slice'}->$method(@_);    
   }
   elsif($method =~ /^get_all_/ ){
@@ -167,10 +168,10 @@ sub AUTOLOAD {
         $ft->end($temp);
       }	
       if(($ft->start+$ft->slice->start) > $self->{'_chrom_slice'}->end or ($ft->end+$ft->slice->start) < $self->{'_chrom_slice'}->start){
-	print STDERR "start before orig start???\n";
+#	print STDERR "start before orig start???\n";
 	next;
       }
-      print STDERR "FT: ".$ft->dbID."\t(".$ft->start.") ".($ft->start+$ft->slice->start)."\t(".$ft->end.") ".($ft->end+$ft->slice->start)."   ".$ft->slice->seq_region_name."\n";
+#      warn "FT: ".$ft->dbID."\t(".$ft->start.") ".($ft->start+$ft->slice->start)."\t(".$ft->end.") ".($ft->end+$ft->slice->start)."   ".$ft->slice->seq_region_name."\n";
       my $new_ft = $ft->transfer($self->{'_orig_slice'});  
       if(defined($new_ft)){
 #	print "NEW FT: ".$new_ft."\t".($new_ft->start+$new_ft->slice->start)."\t".($new_ft->end+$new_ft->slice->start)."\n";
@@ -178,16 +179,34 @@ sub AUTOLOAD {
       }
       else{
       # DO i want to give a message here or just ignore them???
-	print STDERR "problem transfering $ft start =".($ft->start+$ft->slice->start)." end= ".($ft->end+$ft->slice->end)."\n";
+#	warn  "problem transfering $ft start =".($ft->start+$ft->slice->start)." end= ".($ft->end+$ft->slice->end)."\n";
       }
    }
     
     return \@new_features;
   }
 #  print "CAlling $method on lrg slice\n";
+#  warn "Calling ($method) from ", join ' * ', caller(0);
+
   return  $self->{'_orig_slice'}->$method(@_);
 }
 
+sub stable_id {
+    my $self = shift;
+    return $self->seq_region_name;
+}
+
+
+sub display_xref {
+    my $self = shift;
+    return $self->seq_region_name;
+}
+
+sub feature_Slice {
+    my $self = shift;
+    return $self->{_chrom_slice};
+}
+
 sub DESTROY{
 }