AnalysisAdaptor - logic_name must be unique so fetch_by_logic_name now only returns one analysis object
DnaAlignFeatureAdaptor - formatting print statements etc
ProteinAlignFeatureAdaptor - Now follows the same format as DnaAlignFeatureAdaptor, has methods to fetch by contig, slice and assembly location and when constrainted by score
or percent id all methods can take an optional type which is logic name
RepeatFeatureAdaptor
PredictionTranscriptAdaptor all have methods which fetch by slice, contig_id and assembly location and each method has optional type which should be logic_name
SimpleFeatureAdaptor