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Our lookups of primary accessions and display labels with the Xref table was
flawed. Seems MySQL can only use 1 index per query and it is not possible to
create a single index that can handle querying on two columns when either
could be our matching value. Solution is to break the query into two parts
each targetting a single column. MySQL is a lot happier about this and
query times have dropped from 30 seconds on USEast to 18ms (9ms per query).

does not work with 73 databases as they have not been patched yet
will come back in 74

Trying to stop the website from warning so much about querying the
ontology schema for stable ids.

allows for use with schema_patcher script and proper release version control

now supports meta for schema_patcher and release version control

Code has been altered to support new REST requirements.

does not inherit feature one
'ID' field from generic method has been replaced by 'Description' field as display_id is not unique for repeats

added fetch_stable_id_event and get_event methods for archivestableid, in adaptor and object modules respectively
allows to get the specific event of an archive stable id related to a given stable id
finally gives access to score

also updated existing tests to use is rather than ok whenever possible

Using while shift will eventually cause an undef to be processed. This
is how the while loop detects a false condition. We cannot lc() an
undef. Do not do this in the while. Only do it in the loop

if biotypes between transcripts differ, add penalty
if biotype groups between transcripts differ, add even more penalty

allows to return protein feature specific attributes for translation rest endpoint

with rest stack trace, \n is ignored and the query looks like columnFROM
it is not going to affect the running of the query, but can be confusing, so adding a space before the FROM

The method was called on the wrong object. Swithced around and tested

'logic_name' can be the analysis' logic_name, or the db name if nothing found
allows to fetch 'low_complexity' regions without knowing that the analysis is seg
only works if no protein_features were added to that translation
mimicks the webcode behaviour like in http://www.ensembl.org/Homo_sapiens/Transcript/Domains?db=core;g=ENSG00000139618;r=13:32889611-32973805;t=ENST00000544455

Nick in Ensembl Genomes has seen an issue with bacteria databases where
we exceed the number of connections on MySQL. As we loop through DBAdaptors
we do not disconnect. That means an ID which appears later on will have
opened all prior databases. The connection is still active. We now
disconnect this.

we have too many reg starting variables to use shortened names

replaced reg with registry for more explicit code

if we use first_registry and last_registry throughout the module, we can probably afford to use registry rather than reg for the simpler cases

helps for consistency across modules
also makes it easier to grep for registry calls, reg is too generic (regulatory, region, registry...)

seq_regon_name would never have worked, so the warn would have ended up as a fail

Simple formatting changes suggested by Bron. Will make the example cut-paste
usable.

Patch submitted by Leo for PGSQL default port number.

We have decided to revert this change. GeneBuilder code has a link to the
existing functionality manifesting itself as subtle silent breakages. The
old functionality has been brought back. Warning added about how possibly
bad using the array from this function is.

Test schemas should not need this. It also gets in the way of SQL
diffs so just ignore it for the moment.

The test schema was out of sync for ages due to it never being patched
using the patch sets. This is no longer the case. We needed a one
shot resynchronisation between the live schema and this test schema. All
test cases have been run and still pass. Assuming the processes
has not destroyed data. Any data changes seem to be related to different
levels of precision being emitted in the files.

Meta coord was updated.

if your meta_coord table is wrong, you should run update_meta_coord.pl, not meta_levels.pl

added sources for chimp, cod and anolis

transcript_direct_xref is added if exon overlap between ensembl transcript and refseq transcript scores high
but translation_direct_xref is only added if ensembl translation and refseq translations match
if they don't match, do not add direct xref, this gap will hopefully be filled up by the exonerate alignments