host added for pre-sites

options standardised

Small change to build_transcript_and_gene_display_xrefs subroutine so that gene get their own display_xref instead of being assigned one from a transcript.

Made pattern matching more strict when choosing type (gene, transcript, translation) as 'pseudogene' transcripts had previously been classified as genes.

added optional parameter of code to fetch_all_by_ and remove_from_ so only attibutes with these codes are used

added method delete_cache to remove ALL the assembly caching. Needed for when the assembly is changed

Only the ID, Name and FlyBase_Annotation_IDs are given synonyms (from Alias=).
Removed some unused subroutines.

Also specify host etc to use load_registry_from_db() in project_display_xrefs.pl so don't have to specify everything in conf file.

Now use load_registry_from_db() as well as spcifying settings in config file. Should mean that only Compara has t be defined in conf file.

clarified documentation of fetch_all() regarding combining toplevel and coord system version arguments

added support for retrieving features and slices to be projected from a different database; documentation

data

Added

human -> chimp, macaque, guinea_pig
drosophila -> aedes

reinstated.  The analysis_id in the analysis table and in the
analysis_description table seems to become unsynced otherwise.