When called by list_stable_ids() (in e.g. GeneAdaptor) and we're dealing
with a multi-species database, we need to also join with the base
feature table since the stable_id tables do not have seq_region_ids.

Solves a problem raised on the dev list.

Changing from the || test to a ternary statement due to an error raised by EG & the EST pipeline when migrating from v1.136 to v1.37 of this file. If this does not solve it then it must be the throw above which has caused it.

Doh!

Formatting.

Add penalty when source and target are not on the same seq_region
(currently halves the score).

that I remmeber where I'm at tomorrow... or the next day.

just as is done for adding source.

fix for errors in getting a database connection when in disconnect_when_inactive set and is being called to0 fast for the system to keep up with

for the benefit of Region Report tool

Also minor POD corrections.

Functionality suggested by Ensembl Genomes, used when building a variation DB.