added a multispecies_db example to clear up confusion between is_multispecies method an multispecies_db parameter

warning added if you don't use the -write option

port changed to 3306

Only use the source from the display_xref calculation for the calculation of the gene/transcripts status

rockhyrax added

query_identity is now xref_identity and target_identity is ensembl_identity in the identity_xref table

Moved error msg when attempting to map FROM toplevel - was being masked by a more cryptic error message.

Updated list of allowed linkage types with list from the Ensembl Core
schema.

Updated rest of package code to conform to relatively common Core API
coding practices.