The ID for simple features seem to be poorly defined and repetitive. Better
to supress for the sake of GFF3.

readable format for pipelines, etc.

The idea is good. Consult multiple adaptors as if they are one logical
adaptor with the same query. Thing is that the old version was abused. Let's
stop that now and bring in this nicer new version which does work well

Seems that our earlier design was incorrect and we do want to only
have 1 gene in 1 alt allele group. So adding the constraint in.

Currently this is functionality wanted for compara when people just build
a connection and then they lack any kind of link back to the compara
schema.

There was code in the GeneAdaptor which could be handled by the DBEntryAdaptor
and would be more reusable by others if it was there. Also added a test
case for the new method get_distinct_external_dbs() in DBEntryAdaptor.

We now check the roundtripping of to_hash(). Should not have built this
method without a test case. Would have fixed the issue long ago!

Before we missed of the preceeding - in these params. That is now fixed.

of Bio::EnsEMBL::XS::Utils::Argument, if installed.

The method has been renamed to rearrange_pp (from Pure Perl).

Method in GeneAdaptor fetch_all_alt_alleles() was not working as it did prior to
our changes. It normally returned everything bar itself. That has been fixed.

Also stopped a warning which was driving the webteam mad.

[ENSCORESW-720] and [ENSCORESW-721]. Allowing default HashRef in execute() and sleep for less than a second.

First issue raised by Lee from EG. He wanted to be able to work with hash refs
in the same way you can do with ArrayRefs. Done and dusted.

Second issue raised by me. Want to sleep for periods less than 1 second for the test
suite sanity.

Rose ORM framework.

Add 'HAP' to the list of types of patches to project so that the haplotypes sequence mappings and karyotype bands won't be missed again.

that should not happen, but non-species database will not have a version
this includes ancestral sequences databases

we now have a display_name meta_key, added method get_display_name

Patch submitted by Yuri Delia as aliases were added into the registry
even if a database was not found e.g. ontology. Additions moved
into the if blocks when we find and DB and constructed its adaptor.

Reverted Production DB dependency in order to allow Xref pipeline to run. Changes can be reinstated once slightly more mature.