DBAdaptor Fixed sql for new schema, write clone, contig, and chromosome methods tested

DBEntryAdaptor Fixed SQL as yet untested
ExonAdaptor Changes to sql to work with the new schema not tested
GeneAdaptor Changes to sql to work with new schemea not tested
RawContigAdaptor changes to work with new schema not tested
RepeatFeatureAdaptor added Fetch by logic name method as now there are two analysis types that can be stored there TRF and RepeatMasker
SimpleFeatureAdaptor added fetch_by_logic_name methods teh fetch_by logic_name and assembly_location doesn't yet work