required for RefSeqCoordinateParser

some sanity checks to make sure the file contains the data we expect

recovered from cvs commits in 2012, not tested

Change to xref_config.ini for flycatcher

Removed method 'set_source_id_to_external_name' to revert back to the default behaviour which is to report the display db name in the source field of the gene description.

Removed method 'set_source_id_to_external_name' to revert back to the default behaviour which is to report the display db name in the source field of the gene description.

Added ncRNA_EG::EG source to species, Triticum aestivum

changed attributes to use correct casing as per GFF spec

changed attributes to use correct casing as per http://gmod.org/wiki/GFF3. Extended testcase to include transcript to test Parent attribute

fix for _get_by_slice on feature-less slices

ensure that even for slices with no features, the adaptor bind params are left clean and empty once the method completes

update argument description for sub_Slice method

corrected url for codon table

test 5.12 and 5.14 for future compatibility checks

Update example to functional code, changed indents

I'm guessing the marker code is less used, as there's quite some inconsistency in the code / examples. Making this example functional.

default port is now 3306

makes comparison easier when duplicates made their way into the database

Changes for C. elegans / Ensembl Genomes xrefs

Make executable to make vega pipeline simpler.