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ENSCORESW-3110- Code to handle stop codon readthrough in 12 transcripts. The code edits the amino acid sequence to display the stop codon readthrough with an X

ENSCORESW-3110- Code to handle stop codon readthrough in 12 transcripts. The code edits the amino acid sequence to display the stop codon readthrough with an X

Set an object's default version to 1 when it is created, rather than when it is stored, to allow undef versions (which can then be stored as NULLs in the database).

This reverts commit 3e24194c.

stable_id_version setter/getter for core object types, sets stable_id with a . delimited version or fetches stable_id with .version concatonated (if version is set)

'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

This means that CoordSystem, DensityType, Map::Marker, Map::Ditag, Map::Qtl,
MiscSet, OntologyTerm and SeqRegionSynonym have now a fast constructor available.

Accordingly, new_fast is removed from Analysis, Feature, DataFile, DBEntry, RepeatConsensus,
Translation and UnmappedObject together with the import of weaken and isweak from
Scalar::Util.

Minor POD corrections

for the benefit of Region Report tool

Add the following proxy methods:

* get_all_object_xrefs()    alias for get_all_DBEntries()
* get_all_xrefs()           alias for get_all_DBLinks()

These have no documentation as of yet.

translation's transcript.