Some comments added.
Defualt settings changed.

It will become a simple protein DAS client that people can
use to test internal DAS servers with, or use as a basis for
something a bit more exciting.

It will do simple ID name mapping using a lookup file, but the
more elaborate alignment mapping (that never really worked very
well anyway) has been taken out.  This means that a user can
query servers using internal IDs.

There will be more modifications to this project before it's
ready for release.  Not least because the Bio::Das modules have
change quite a bit since the original code was written.  Code is
ugly, that's the other reason.

Added harvester to automatically download SwissProt files, and BaseHarvester to allow all harvesters to be discovered and run automatically. Various tweaks to all files to make them cleaner and more consistent

Added strand argument in the slice subseq method call in alignment_strings. If not present did not return the seq in the right strand when it is < 0

Modified the _mask_features and get_repeatmasked_seq methods to take an additional optional argument to allow not default masking on specific repeat classes or names. Consequently added some changes in RepeatMaskedSlice to take this new argumnent into account. This should not affect any existing script or module

Modified source table to not use timestamp type columns. Made taxonomy ID primary key of species table