Add ;mysql_local_infile=1 to DBI initialisation call to work around MySQL change that causes errors such as

	DBD::mysql::db do failed: The used command is not allowed with this MySQL version
	at /nfs/acari/gp1/work/ensembl-test/modules/Bio/EnsEMBL/Test/MultiTestDB.pm line 313.

when using LOAD DATA INFILE.

Retain deprecated fetch_by_AffyArray for backwards compatibility.

failing because it was requesting a sub slice which was longer than
the seq_region in the new caching code

New pairs added to enable the addition of missing pairs. At the moment this is only done for the refseq dna and peptides, but could easily be added to add others

Added a defualt set of aliases for the load_registry_from_db subroutine. Also added no_version_check getter/setter to allow configuration of wether the version checking is done. So you can specifiy in configuration script that you do not want to do the version checking.

supporting features and translation attributes are removed

version_check changed to only check when adaptors are instantiated or not at all if special file exists

Added coding_gene() and coding_transcript() methods to pull data from regulatory_factor_coding table.