[source UniProt::protein_id] and [source Uniprot::EMBL]

Modified medaka to download EMBL and protein_id.

change to subroutine transcript_display+xref_sources so that it now return the list to use and also a hash of those to ignore if they match the regular expression given

Don't project if a GO term with the same accession, but IEA evidence code, exists, as this will lead to duplicates when the projected term has its evidence code changed to IEA after projection

fetch_all_by_external_name() in GeneAdaptor.pm, TranscriptAdaptor.pm,
and in TranslationAdaptor.pm.

This will limit the returned genes, transcripts, or translations, to
those that originates from the named external database.

This also means adding the optional argument to
list_gene_ids_by_extids(), list_transcript_ids_by_extids(),
list_translation_ids_by_extids(), and to _type_by_external_id() in
DBEntryAdaptor.pm.

The matching is done on 'db_name' in the 'external_db' table with LIKE
and an appended '%' to the given $external_db_name.

ficex Go to use ALL tax ids for a particular species (anonpholese fix but useful if more species get strains)

Also keep help text below 80 chars/line.

Added ability to project (apparent)one2many orthologs as well. Multiple targets are labeled "1 of 2", "2 of 2" etc