if the supporting feature can't be transformed

field and checks on whether the number of attached exons has increased.

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.

start, end, version constraints can be passed to overridden fetch_by_clone_accession method to speed up external queries

start & end constraints can be passed to overridden fetch_by_Clone method to speed up external queries

Dropped the priority column from external_db table.

deprecated several unused methods in Exon and incorrect implementation of translate method - added replacement peptide method