[Biojava-l] Genbank parsing problem

[Brian King]

> I've recently run across a problem with parsing of
Genbank files 
> containing unbounded locations.

Our solution in the AGAVE Java library was to create a
location object in an "invalid" state when the
location was out of range or the location string was
otherwise unparseable.  The location object stored the
string image of the original GenBank location so it
could write it out later, and it had an invalid flag
that could be tested.  If the location object was in
an invalid state any methods getting position data
would throw an exception.  The programmer would always
have to check if the location was valid before trying
to get the positions.  This was often a painful style
of programming, but it assured that we not losing
data, that we were not using invalid data, and that we
could parse the complete database without being
stopped by invalid location strings.

Regards,
Brian


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