there's no ontology database available.

used. Spotted by Magali.

changed, if the version has changed, or if the score is less than 1.

falling below the threshold in the similarity scoring step specifically
due to the source and target exons being on two different seq_regions.

When we get all slices that has genes on them, and we find a slice that
is not a reference slice, make sure that we only fetch the unique region
of it.  This solves the problem of genes getting new stable IDs even
though they haven't changed.

Check the result of the print and die if we have an error. Bits of flatfiles have been missing so hopefully these will now be caught

Moved the warning about the cache not being on back into the constructor & simplified the construction method for the cache. If someone doesn't inherit from this correctly they'll loose the warning but that is all.

Ensembl core is now at v65. Patches to work with flat file handles in core like databases and supporting checksum derived xrefs

Brought in new_fast() as a speed increase.  Should probably consider moving new_fast() up to Storable.pm to give it to as many modules as possible & reduce code duplication

Faster version of rearrange which ditches uc() and order modifying in favor of editing the input parameters directly with a tr///d. This is 35% faster than our original implementation. Test case suite has been run before this commit.

Caches are now created from an accessor rather than building them in the new(). This allows us to remove the new() and lets people inherit from here however they want to. It also stops us from auto-vivifying a plain hash which causes unintentional object retention.

clear_cache() did not de-reference the hash before clearning which could have caused the same situation of creating an auto-vivified hash.

Regression test put in place to stop this from happening again.

Adding a global here to allow for silencing of the no_cache warning. Important for dump applications where caching is not that useful

Use seq_region mappings correctly by getting all external seq_region_ids
for our internal seq_region_id and then using an IN-list in the
subsequent query.