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

which is a trifle misleading and will be decomissioned later

more mutilation of James' beautiful adaptor ...

by logic_name and by db name
then methods have been written which use each of the fetch by methods but instead of returning a single feature pair or an
array of feature  pair each one representing one line in the table and containing a cigar string they return an array of feature pairs where
each part of the gapped alignment is repesented by one feature pair in old schema style

Added method restrict_between_positions. Should be make generic and be included in BaseAlignFeature, so it could be used by PepDnaAlignFeature and DnaPepAlignFeature

also added methods to get arrays of features based on assembl location and a single feature based on dbId and
then turn them into and array of feature pairs to represent the gapped alignment

then using teh cigar string splits the single feature into an array of feature pairs  ke it would of been stored in old schema