option -drop_db from xref_parser.pl implemented which prevents the 'yes' command (scripting and logging purposes )

option -dropdb || -drop_db added to create new xref-db without having to enter 'yes' (scripting purposes )

small change to allow both Wills and thepipeline method of storing markers to work

made all registry calls case INsensetive as it was very annoying having to have species, group and type all in the correct case. Also added load_registry_from_db which will load the latest ensembl databases given a database host (and optionally port, user, pass) to search. At prsent only core,variation,estgene,compara and go adaptors are loaded via this method.

ftp://ftp.ebi.ac.uk/pub/databases/SPproteomes/7227.spc

===========>

       ftp://ftp.ebi.ac.uk/pub/databases/integr8/17.D_melanogaster.dat.gz

and invertebrate9.protein.gpff.gz added

get_all_homologous_Genes method catches the exception when calling get_Gene from a compara member object.

add --output-document to wget command linr bit as the file might be changed and not exactly like the url

Modifed get_all_DBLinks to sort xrefs by priority (desc), external db name (asc), display_id (asc) before returning them.

dbprimary_acc_linkable (column 5): default true (1) EXCEPT HUGO
display_label_linkable (column 6): default false(0) EXCEPT HUGO

priority: all set to 1 initially.

allow MArkersymbol sources to be used to get the gene descriptions. If all fails use Marker symbol as gene description regardless of filters.   Still work in progress

Only store descriptions from certain sources (listed in gene_description_sources()) to prevent e.g. IPI being used for description if there's nothing else found.

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