A non-fussy update method to enable (primarily) the addition of

display_xref_ids calculated in the protein pipeline to genes
that already exist in the db.

As implemented the method can also update the type and analysis
fields.  If any one of the display_xref_id, type or analysis fields
have changed on the gene being updated, all of these fields are
updated.

modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm

@@ -1025,6 +1025,63 @@ sub get_display_xref_id {
 
 
 
+=head2 update
+
+  Arg [1]    : Bio::EnsEMBL::Gene
+  Example    : $gene_adaptor->update($gene);
+  Description: Updates  a gene in the database
+  Returntype : None
+  Exceptions : thrown if the $gene is not a Bio::EnsEMBL::Gene
+               warn if trying to update the number of attached transcripts.  This
+               is a far more complex process and is not yet implemented.
+               warn if the method is called on a gene that does not exist in the
+               database.
+  Caller     : general
+
+=cut
+
+sub update {
+   my ($self,$gene) = @_;
+   my $update = 0;
+
+   if( !defined $gene || !ref $gene || !$gene->isa('Bio::EnsEMBL::Gene') ) {
+       $self->throw("Must update a gene object, not a $gene");
+   }
+
+   my $sth = $self->prepare("SELECT type, analysis_id, transcript_count, display_xref_id 
+                             FROM   gene 
+                             WHERE  gene_id = ?
+                           ");
+
+   $sth->execute($gene->dbID);
+
+   if ( my ($type, $analysis, $transcripts, $dxref_id) = $sth->fetchrow_array() ){
+
+     if ( $dxref_id != $gene->display_xref ) { $update = 1; }
+     elsif ( $type ne $gene->type ) { $update = 1; }
+     elsif ( $analysis != $gene->analysis->dbID ) { $update = 1; }
+     elsif ( $transcripts != scalar(@{$gene->get_all_Transcripts})) {
+       $self->warn("Trying to update the number of transcripts on a stored gene. Not yet implemented.");
+     }
+
+     if ( $update ) {
+
+       $sth = $self->prepare("UPDATE gene
+                              SET    type = '$type',
+                                     analysis_id = $analysis,
+                                     display_xref_id = $dxref_id
+                              WHERE  gene_id = ?
+                            ");
+
+       $sth->execute($gene->dbID);
+     }
+   }
+   else {
+     $self->warn("Trying to update a gene that is not in the database.  Try store\'ing first.");
+   }
+}
+
+
 1;
 __END__