Added first go at adding triage stuff i.e. why some refseq and uniprot sequences are not found in ensembl. At the moment if there is no match then this is reported else the actual percentages are given for the closet match with the actual cutoff values used.

Added get_all_homologous_Genes to Bio::EnsEMBL::Gene that returns the Bio::EnsEMBL::Gene and Bio::EnsEMBL::Compara::Homology objects for each corresponding homologous gene in the Compara DB. Changed EnsEMBL::Web::Data::Gene to use this call with the benefit that the Compara DB gets hit obce only per GeneView request

Updated to reflect the fact that gene descriptions are now held in the gene table not in a separate gene_description table.

use FULL uniprot files and not species specific .SPC files. Okay this will be alot larger to down load and parse but will contain all the proteins and not just the non-redundant ones. For example. For rat we get 7 more swissprot and 2000 more trembl entrys with the large file.  I may need to add a new option on to the parser now to delete the files after loading for those with small disk space but this should be simple enough.

query

Bug fix: some transcript display_xrefs weren't being assigned correctly if the transcript had more than one associated SwissProt ID and each of the SwissProts was associated with a HUGO ID, e.g. haemoglobin beta/delta chains.

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

Moved delete_existing to separate metod so it can be called at the start of the process, so generated xref_ids are more sensible.

Fixed bug causing some gene display_xrefs to be incorrectly assigned.

Removed hardcoded call to slice fetch_by_region to deal with species where 'chromosomes' in microRNA file are actually scaffolds or chunks. Also cache analysis.