add upstream/downstream flanking 5kb around transcript when consider a variation is involved in the transcript

method documentation, and (b) correct.

merged adaptors removed and more docs added. load_registry_with_web_adaptors deprecated as new web does not allow this to work anymore, but Use load_registry_from_db can now be used instead

pretty much a rewrite of the sub get_all_adaptors. Now takes the optional species, group and type pairs. The adaptors are returned instantiated now.

species and group deprecatied. As these should not be used now that dbc is not part of the dbadaptor anymore.

subroutine clear, now added which will drop all database connections and reset the registry.  NOTE: if you load_all and the registry is loaded the subroutine clear is now automatically called first to clear out the old configuration before loading the new one.

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.