small queue for exonerate to finish.  Also added spaces after -R and -J
switches.

Making consistent through plants species the use of ncRNA_EG source for maintaining ncRNA genes xrefs asscoiated with logic_name ncrna_eg

ChEMBL xrefs are now being imported

- get_assembly_name
- get_assembly_date
- get_genebuild_start_date
- get_genebuild_method
- get_genebuild_initial_release_date
- get_genebuild_last_geneset_update

bug fixes for methods:
- get_toplevel
- get_karyotype
- get_coord_systems

returns a listref of all unique assembly versions available

will return a single string with the value of the default version of the assembly

replaced by GenomeContainer, hopefully more generic and in line with what already exists
presenting most of the generic features the assemblyadaptor add, but less REST only focused
will be further expanded with a genome table

This work allows for the hosting of more than one variation database (similar to
core-like databases such as rnaseq or otherfeatures). The Slice methods for core objects
allowed the specification of the database type. Variation methods now have the same
option. We have pushed much common logic into 4 methods to provide this automatic
defaulting behaviour.

We needed more methods to be able to handle alt allele group interactions. We also
needed to make sure a single gene could not be added more than once. Think we got
this one fixed

Removed dependencies on non-core APIs.

Introduced two methods to translate to SO accessions and names.

This was missed off the first implementation of the table. It has resulted
in silly long query times because MySQL was forced into performing full
table scans to find evidence related to the transcript. Adding an index
in should fix this.

exception message.