removed seq_region_attrib functions now present on AttributeAdaptor instead

modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm

@@ -410,131 +410,6 @@ sub get_seq_region_id {
 }
 
 
-=head2 get_seq_region_attribs
-
-  Arg [1]    : Bio::EnsEMBL::Slice $slice
-               The slice to fetch attributes for
-  Example    : %attribs = %{$slice_adaptor->get_seq_region_attribs($slice)};
-               ($htg_phase) = @{$attribs->{'htg_phase'} || []};
-               @synonyms    = @{$attribs->{'synonym'} || []};
-  Description: Retrieves a reference to a hash containing attrib code values
-               and listref value keys.
-  Returntype : hashref
-  Exceptions : throw if the seq_region of the slice is not in the db
-               throw if incorrect arg provided
-  Caller     : Bio::EnsEMBL::Slice
-
-=cut
-
-sub get_seq_region_attribs {
-  my $self = shift;
-  my $slice = shift;
-
-  if(!ref($slice) || !$slice->isa('Bio::EnsEMBL::Slice')) {
-    throw('Slice argument is required');
-  }
-
-  my $srid = $self->get_seq_region_id($slice);
-
-  if(!$srid) {
-    throw('Slice is not on a seq_region stored in this database.');
-  }
-
-  $self->{'_attribs_cache'} ||= {};
-  if($self->{'_attribs_cache'}->{$srid}) {
-    return $self->{'_attribs_cache'}->{$srid};
-  }
-
-  my $sth = $self->prepare('SELECT at.code, sra.value ' .
-                           'FROM   seq_region_attrib sra, attrib_type at ' .
-                           'WHERE  sra.seq_region_id = ? ' .
-                           'AND    at.attrib_type_id = sra.attrib_type_id');
-
-  $sth->execute($srid);
-
-  my($code, $attrib);
-  $sth->bind_columns(\$code, \$attrib);
-
-  my %attrib_hash;
-  while($sth->fetch()) {
-    $attrib_hash{uc($code)} ||= [];
-    push @{$attrib_hash{uc($code)}}, $attrib;
-  }
-
-  $sth->finish();
-  $self->{'_attribs_cache'}->{$srid} = \%attrib_hash;
-  return \%attrib_hash;
-}
-
-
-
-=head2 set_seq_region_attrib
-
-  Arg [1]    : Bio::EnsEMBL::Slice $slice
-               The seq_region of the slice is the one which gets this attribute set
-  Arg [2]    : string $code
-               code in attrib_type table. This method can not set name or description in
-               that table.
-  Arg [3]    : string $value
-               An attribute value for the given code and seq_region
-  Example    : $slice_adaptor->set_seq_region_attrib
-                                 ( $chromosome_slice, "GeneCount", 23332 )
-  Description: Set an attribute for given slices seq_region.
-  Returntype : none
-  Exceptions : none
-  Caller     : general
-
-=cut
-
-sub set_seq_region_attrib {
-  my $self = shift;
-  my $slice = shift;
-  my $code = shift;
-  my $value = shift;
-
-  my $sth = $self->prepare
-    ("INSERT IGNORE INTO attrib_type set code = ?");
-  $sth->execute($code);
-
-  my $atid = $sth->{'mysql_insertid'};
-
-  $sth->finish();
-
-  if( $self->db->db_handle->{'mysql_info'} == 0 ){
-    # the insert failed because the code is already stored
-    $sth = $self->prepare
-      ("SELECT attrib_type_id FROM attrib_type " .
-       "WHERE code = ?");
-    $sth->execute($code);
-    ($atid) = $sth->fetchrow_array();
-
-    $sth->finish();
-
-    if(!$atid) {
-      throw("Could not store or fetch attrib_type code [$code]\n" .
-	    "Wrong permissions?");
-    }
-  }
-
-  my $srid = $self->get_seq_region_id($slice);
-
-  $sth = $self->prepare
-    ("INSERT INTO seq_region_attrib " .
-     "SET seq_region_id=?, value=?, attrib_type_id=?" );
-  $sth->execute( $srid, $value, $atid );
-
-  $sth->finish();
-
-  #update the cache if it exists already
-  if(exists $self->{'_attribs_cache'} &&
-     exists $self->{'_attribs_cache'}->{$srid}) {
-    $self->{'_attribs_cache'}->{$srid}->{uc($code)} ||= [];
-    push(@{$self->{'_attribs_cache'}->{$srid}->{uc($code)}}, $value);
-  }
-
-  return;
-}
-
 
 =head2 fetch_all