[Biojava-l] Genbank SeqIO question

[Keith James]

From: Keith James <kdj@pfes1.sanger.ac.uk>
Date: 31 Jul 2002 10:57:42 +0100
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>>>>> "Neill" == Neill White <nk_white@yahoo.com> writes:

    Neill> Thanks Robin - I was using the latest (1.21) binary.
    Neill> Updating to the current code was a marked improvement.  The
    Neill> input and output genbank files nearly match.  There is a
    Neill> slight issue with an accumulation of '/JoinType="join"'
    Neill> feature table qualifiers on CDS and mRNA records (i.e., if
    Neill> you read in and print out the same genbank record n times,
    Neill> you'll get n '/JoinType="join"' qualifiers for each feature
    Neill> that has a join.  This probably won't break anyone's parser
    Neill> though and is more cosmetic than vital.

There is actually a HashMap under a special key
Feature.PROPERTY_DATA_KEY in the GenBnk/EMBL derived feature
Annotation for storing internal data like this (such that it isn't
printed). I guess it's not being used in this case - I'll take a look.

Keith

-- 

- Keith James <kdj@sanger.ac.uk> bioinformatics programming support -
- Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, UK -