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

Added depreciated waning to write_contig, write_clone, and _insertSequence methods in DBAdaptor
Added a use Bio::LocationI statement to RepeatFeatureAdaptor as lack of it was causing complier errors

another analysis type and a dna sequnece which is used to produce a gene which will translate;

 added extra insert statements to include dna seqs (not real) and extra analysis types for new tests

addition of method used in Fgensh to make a transcript when you just have a sequence and not a contig

minor bug fixes and addition of method to get things by logic name in case Fgenesh is being run at teh same time as genscan

added a international name variable and accessor as this is the column which replaces chromosome in the new schema

All contain a variety of bug fixes, ProteinAlignFeatureAdaptor  has been altered to return DnaPepAlignFeatures

AssemblyMapper - altered the way certain methods were called so arguments are passed in the correct order
BaseAlignFeature - added feature validation to _generic_parse_features method
SeqFeature removed checking for Source tag and Primary tag from feature validation method as these are now deprecited

Added a test for ProteinAlignFeatureAdaptor and altered the dnaalignfeature test to work with the alterd base align
feature

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

removed unneeded 'use's
whitespace tidied

GeneAdaptor etc altered SQL to work with new schema now have genes stored in database