Store synonyms as well as primary xref accessions in get_valid_codes (needed since some HUGOs map to secondary SwissProt IDs)

add synonyms from the dead names column. NOTE still need to get the Mapper routine to dump non primary xref synonyms

Created; create xrefs & direct_xrefs from stable IDs for WormBase-imported genomes (e.g. elegans). Subclass of DatabaseParser.pm

match only translation for hugo until mart can handle translations and transcripts. Transcript code commented out for now

Fixed bug that was causing a small number of HUGO xrefs to have null labels (hence xref displayed was numeric HGNC instead).

set the label for Uniprot to be the accesion and NOT the ID line names. This is to keep the web looking the same.

UniGene parser first attempt. Not sure it is worth downloading the .data file for the titles as it is a large file but is far easier than trying to guess from the .seq.uniq file.

Updated to reflect the fact that a CCDS may be linked to more than one transcript. Hence need to add xrefs only once, i.e. check for existence before adding.

Added add_direct_xref() - will be needed for future parsers that create direct_xrefs (e.g. CCDSParser).

Made add_xref return xref_id of last-inserted xref so that it can be passed to add_direct_xref.