[Bioperl-l] Bio::Location::Fuzzy, Bio::Location::Split
Thu, 25 Jan 2001 15:44:36 -0600
Hilmar Lapp wrote:
> > full loc -> start..end : minStart..maxEnd
> > <50..100> -> 50..100 : -INF..+INF
> > (78.90)..(100.107) -> 90..100 : 78..107
> I think I am much more in favor of returning the outer-most
> coordinates as the default policy. David, Mark?
In my gut I would also favour outer-most, only because, even with a simple scan
of the data, you are able to say "there's something there" or not. However, the
phrase "$Feature->start/stop returns the outer-most start/stop positions unless
either is undefined in which case that one (or both) return the minimum" gives me
the shivers! Still, this is more of a problem for unsophisticated parsers, which
presumably will be asking unsophisticated questions - what will be most important
for them (I think) is to be given the coordinates which span the maximum "secure"
region. So, yes, I agree that outermost is preferable to innermost.
> whether INF or NaN are good return values in perl
YUCK! Please don't go there... Perhaps returning undef in a call to maxStart
or maxEnd would be better... it functions nicely in testing statements.
[[ Dave just told me he would prefer to return a Location object in a call to
Feature->start that needed to return a fuzzy value, and let the parser choke on
the resulting errors :-) Although this is nice OO Perl, I doubt that most
existing parsers (or their authors) would be very happy with that solution! ]]
Dr. Mark Wilkinson
National Research Council of Canada
Plant Biotechnology Institute
110 Gymnasium Place