add dbname to SeqRegionSynonym

modules/Bio/EnsEMBL/DBSQL/SeqRegionSynonymAdaptor.pm

@@ -67,26 +67,32 @@ sub store {
 }
 
 sub _tables {
-  return (['seq_region_synonym', 'srs']);
+  return (['seq_region_synonym', 'srs'], ['external_db','exdb']);
 }
 
 sub _columns {
-  return qw(srs.seq_region_synonym_id srs.seq_region_id srs.synonym srs.external_db_id);
+  return qw(srs.seq_region_synonym_id srs.seq_region_id srs.synonym srs.external_db_id exdb.db_name exdb.db_display_name);
+}
+
+sub _left_join{
+    return (['external_db',"exdb.external_db_id = srs.external_db_id"]);
 }
 
 sub _objs_from_sth {
   my ($self, $sth) = @_;
 
   my @results;
-  my ($seq_id, $dbid, $alt_name, $ex_db);
-  $sth->bind_columns(\$dbid, \$seq_id, \$alt_name, \$ex_db);
+  my ($seq_id, $dbid, $alt_name, $ex_db, $dbname, $db_display_name);
+  $sth->bind_columns(\$dbid, \$seq_id, \$alt_name, \$ex_db, \$dbname, \$db_display_name);
 
   push @results, Bio::EnsEMBL::SeqRegionSynonym->new(
-    -adaptor        => $self,
-    -synonym        => $alt_name,
-    -dbID           => $dbid,
-    -external_db_id => $ex_db,
-    -seq_region_id  => $seq_id
+    -adaptor         => $self,
+    -synonym         => $alt_name,
+    -dbID            => $dbid,
+    -external_db_id  => $ex_db,
+    -seq_region_id   => $seq_id,
+    -dbname          => $dbname,
+    -db_display_name => $db_display_name,
   ) while $sth->fetch();
 
   $sth->finish;

modules/Bio/EnsEMBL/SeqRegionSynonym.pm

@@ -78,14 +78,16 @@ sub new {
   
   my $self = bless {},$class;
 
-  my ( $adaptor, $synonym, $ex_db, $seq_region_id, $dbid) =
-    rearrange ( ['ADAPTOR','SYNONYM','EXTERNAL_DB_ID','SEQ_REGION_ID','DBID'], @args );
+  my ( $adaptor, $synonym, $ex_db, $seq_region_id, $dbid, $dbname, $db_display_name) =
+    rearrange ( ['ADAPTOR','SYNONYM','EXTERNAL_DB_ID','SEQ_REGION_ID','DBID', 'DBNAME', 'DB_DISPLAY_NAME'], @args );
 
   $self->adaptor($adaptor);
 
-  if( defined $ex_db ) { $self->external_db_id( $ex_db ) }
-  if( defined $seq_region_id ) { $self->seq_region_id( $seq_region_id ) }
-  if (defined $dbid) { $self->{'dbID'} = $dbid}
+  if( defined $ex_db ) { $self->external_db_id( $ex_db ) } ;
+  if( defined $seq_region_id ) { $self->seq_region_id( $seq_region_id ) } ;
+  if (defined $dbid) { $self->{'dbID'} = $dbid} ;
+  if (defined $dbname) { $self->{'dbname'} = $dbname };
+  if (defined $db_display_name) { $self->{'db_display_name'} = $db_display_name };
 
   if( defined $synonym ) { 
     $self->name( $synonym ) ;
@@ -115,4 +117,25 @@ sub seq_region_id{
   return $self->{'seq_region_id'};
 }
 
+sub dbname {
+  my $self = shift;
+  $self->{'dbname'} = shift if(@_);
+  return $self->{'dbname'};
+}
+
+sub db_display_name {
+  my $self = shift;
+  $self->{'db_display_name'} = shift if(@_);
+  return $self->{'db_display_name'};
+}
+
+sub summary_as_hash {
+  my $self = shift;
+  my %summary;
+  $summary{name} = $self->name;
+  $summary{dbname} = $self->dbname;
+
+  return \%summary;
+}
+
 1;

modules/t/slice.t

@@ -452,6 +452,9 @@ $slice->add_synonym("20ish");
 
 is(@alt_names, 3, "Got 3 alt names");
 
+is($alt_names[1]->name, 'anoth_20', 'Correctly retrieved synonym name');
+is($alt_names[1]->dbname, 'RFAM', 'Correctly retrieved synonym external db');
+
 
 #slcie aleady stored so need to store syns
 my $syn_adap =  $db->get_SeqRegionSynonymAdaptor;