Relaxed reference sequence ID matching when loading annotation files

This is an improvement from JAL-753 that was [implicitly] suggested by a question from Stefan Schmidt via jalview-discuss:

I your manual about annotation files you describe:
http://www.jalview.org/help/oldhelp/html/features/annotationsFormat.html

...
You can associate an annotation with a sequence by preceding its definition with the line:

SEQUENCE_REF seq_name [startIndex]
...

I wonder what the exact format of seq_name is:

Image I get a fasta file like this:
> db|183474|my_pet_protein

Do I have to put in the full id or are other variations ok?

SEQUENCE_REF db|183474|my_pet_protein 1
SEQUENCE_REF 183474 1
SEQUENCE_REF my_pet_protein 1

Background: Since sometimes accession numbers don’t tell you the species name, I would like to add the species info to the sequence name to quickly spot the organism. e.g. my_pet_protein|Escherichia_coli. But then, I would need to change the annotation file seq_name if I can’t use a shorthand…