Refactored versions of external name and external db which now uses the

relevant_xref_id columns.

modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm

@@ -901,6 +901,85 @@ sub deleteObj {
   #flush the cache
   %{$self->{'_slice_gene_cache'}} = ();
 }
+
+
+=head2 get_external_name
+
+  Arg [1]    : int $dbID
+               the database identifier of the gene whose external name is 
+               sought
+  Example    : $external_name = $gene_adaptor->get_external_name(42);
+  Description: Retrieves the external name for a gene.  This is implemented
+               by joining across the xref and gene tables, using the 
+               relevant_xref_id column.
+  Returntype : string
+  Exceptions : thrown if $dbId arg is not defined
+  Caller     : general
+
+=cut
+
+sub get_external_name {
+  my ($self, $dbID) = @_;
+
+  if( !defined $dbID ) {
+      $self->throw("Must call with a dbID");
+  }
+
+  my $sth = $self->prepare("SELECT x.display_label 
+                            FROM   gene g, 
+                                   xref x 
+                            WHERE  g.gene_id = ?
+                              AND  g.relevant_xref_id = x.xref_id
+                           ");
+  $sth->execute($dbID);
+
+  my ($xref) = $sth->fetchrow_array();
+  if( !defined $xref ) {
+    return undef;
+  }
+
+  return $xref;
+}
+
+=head2 get_external_dbname
+
+  Arg [1]    : int $dbID
+               the database identifier of the gene for which the name of
+               external db from which its external name is derived.
+  Example    : $external_dbname = $gene_adaptor->get_external_dbname(42);
+  Description: Retrieves the external db name for a gene from which its external
+               name is derived..  This is implemented by joining across the xref, 
+               gene and external_db tables, using the relevant_xref_id column.
+  Returntype : string
+  Exceptions : thrown if $dbId arg is not defined
+  Caller     : general
+
+=cut
+
+sub get_external_dbname {
+  my ($self, $dbID) = @_;
+
+  if( !defined $dbID ) {
+      $self->throw("Must call with a dbID");
+  }
+
+  my $sth = $self->prepare("SELECT e.db_name 
+                            FROM   gene g, 
+                                   xref x, 
+                                   external_db e
+                            WHERE  g.gene_id = ?
+                              AND  g.relevant_xref_id = x.xref_id
+                              AND  x.external_db_id = e.external_db_id
+                           ");
+  $sth->execute($dbID);
+
+  my ($db_name) = $sth->fetchrow_array();
+  if( !defined $db_name ) {
+    return undef;
+  }
+
+  return $db_name;
+}
 							
 
 

modules/Bio/EnsEMBL/Gene.pm

@@ -380,11 +380,7 @@ sub dbID {
 
   Arg [1]    : string $external_name
   Example    : none
-  Description: get/set for attribute external_name. It initially calculates
-               the longest transcript for the gene in question and then 
-               delegates the call to the external_name method on Transcript.
-               Species dependant searching is handled by this method on
-               Transcript.
+  Description: get/set for attribute external_name.
   Returntype : string
   Exceptions : none
   Caller     : general
@@ -392,6 +388,18 @@ sub dbID {
 =cut
 
 sub external_name {
+  my ($self, $ext_name) = @_;
+
+  if(defined $ext_name) { 
+    $self->{'_ext_name'} = $ext_name;
+  } 
+
+  if( exists $self->{'_ext_name'} ) {
+    return $self->{'_ext_name'};
+  }
+
+  $self->{'_ext_name'} = $self->adaptor->get_external_name($self->dbID);
+  return $self->{'_ext_name'};
 
 }
 
@@ -401,11 +409,7 @@ sub external_name {
   Arg [1]    : string $external_db
   Example    : none
   Description: get/set for attribute external_db. The db is the one that 
-               belongs to the external_name.  It initially calculates
-               the longest transcript for the gene in question and then 
-               delegates the call to the external_db method on Transcript.
-               Species dependant searching is handled by this method on
-               Transcript.
+               belongs to the external_name.  
   Returntype : string
   Exceptions : none
   Caller     : general
@@ -413,7 +417,18 @@ sub external_name {
 =cut
 
 sub external_db {
-  my ($self, $arg ) = @_;
+  my ($self, $ext_dbname) = @_;
+
+  if(defined $ext_dbname) { 
+    $self->{'_ext_dbname'} = $ext_dbname;
+  } 
+
+  if( exists $self->{'_ext_dbname'} ) {
+    return $self->{'_ext_dbname'};
+  }
+
+  $self->{'_ext_dbname'} = $self->adaptor->get_external_dbname($self->dbID);
+  return $self->{'_ext_dbname'};
 
 }