targetted at Genebuild method calls.  Not tested.

Actually is rewrite based on the lite version

They return strings and not PrimerySeq objects
Slice is/should be the PrimarySeq object.

PrimarySeq, giving the transcript and its evidence
properly aligned. Note: code not yet OO. I will make it so.

Slice + RawContigAdaptor added fetch_all repeat, simple, prediction and similarity feature methods, all can accept and optional type whic should be logic_name

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

added new methods to get things by contig_id, slice or assembly location and also using score and percent_id as constraints
all methods can take an optional type which is logic_name and then feature realting to that logic_name only will be returned

altered fetch_by_assembly_location so returns assembly coordinates rather than raw contig coordinates and so features not on golden path are skipped

The only modelue with any significant changes other than that is Transcript where moltype
has been changed to alphabet due to another change in Bioperl 1.0

A base class for all ensembl classes to inherit from rather than directly inheriting from Bio::Root::Root or
Bio::Root::RootI, for the moment this inherits from Bio::Root::Root so will only work with Bioperl 1.0 not 0.72 but this
can easily be changed if necessary

added assembly location gets and tested all the way to Slice. refactored DnaAlignFeature assembly getting to be flexible wrt to constraints