Fix to method of finding transcript display xrefs; previously xrefs from same source would not be reliably sorted on query/target identity.

allows the removal of only certain types of seq region attributes from
a slice)

Added RefSeq_dna_predicted & RefSeq_peptide_predicted to priority list (below known RefSeqs and SPTREMBL).

Slight change to description filtering logic; use original unfiltered description if anything survived the filtering.

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