[Biojava-dev] [Bug 2467] BioJava : IOTools.writeFasta() : Infinite Exception loop

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2467





------- Comment #3 from mark.schreiber at novartis.com  2008-03-12 01:23 EST -------
sigh... Don't even get me started on Fasta's so-called "format".

I think the best solution to the missing
name/accession/gi/description/whatever-else-you-feel-like-putting-behind-the >
is to set all of the above to an empty string ("").  This would be the closest
to what the user put in (ie nothing).

Calling it "unknown" or something else actually conveys some information where
there was none to begin with. Also someone may intentionally use the word
"unknown" which might have meaning to them, us using a default would conflict
with this. Additionally roundtripping would be a problem as it would go in with
no name and come out with a "unknown".

OK, so two bugs to fix. Infinite loop in the exception handling and tolerating
description lines with no information.


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