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

patch was mentioned in meta table but not actually applied

when inserting 3 entries in parallel, should only store once
but depending on how fast mysql catches up, the return dbID corresponds to the first or the last attempt
now allowing for this change of mind

After talking to Compara we found the need to support additional
lookups with the full id cache. Since all values are stored in memory
the lookup is very easy to compute.

The production and web teams have reported odd going ons when people copy from
staging onto another server. This is because this script optimises databases
before copying. These DBs should already be optimised so there is no need
to do this stage. In fact it can alter the checksums of the MYI files which
causes the webteam to wonder if data has been switched out without them knowing.

Leo submitted patch. We support pgsql as a way of defining the driver. This
is inline with us accepting sqlite as a valid synonym for DBD::SQLite.

To provide improved querying of caches we now support SQL statements. These
queries return a list of keys (normally primary key db identifiers) defining
a list of objects to return. It is up to sub-BaseCache implementations to
deal with the nitty gritty of cache mis-hits (something they need to do
anyway).

- seq: pass defined slice intervals to trigger the correct program flow in SequenceAdaptor
- project: removed since believed to have bugs
- project_org: removed since it's not used anywhere

The code previously allowed bogus numbers through into the final slice which
caused errors in later methods. The website crashed because of this. We will
reject anything that was not an integer if the start or end was defined.