Toplevel setting should work now.  Added rank to all coordinate systems. Fixed Danio gene transfer code as well.

modifications so that toplevel is now a pseudo coordinate system representing the highest real coordinate system in a given region

changes to make elegans xrefs work

fixed bug in which undef was being returned from rearrange when zero should have been returned instead

Superseeded by density_feature and density_type

Changed Feature::overlaps so that all it does is a simple integer range comparison, ignoring the possibility that the features could be on different seq_regions.

this could have caused sequence caching problems