[Bioperl-l] Bio::Location::Fuzzy CoordinatePolicy questions
hlapp at gmx.net
Thu Sep 7 14:28:16 EDT 2006
I guess there's arguments either way, depending on what you interpret
the contract to to_FTstring() to be.
If you argue that to_FTstring() needs to return a GenBank feature
table-compliant string then you cannot leave it to the
CoordinatePolicy to decide on the end points that satisfy compliance.
Conversely, if you argue that to_FTstring() may return a string which
is GenBank feature table-compliant only in terms of formatting, then
there is freedom of interpretation as to what the end points could be.
I'm leaning to the former, as there isn't a universal standard for
feature location formatting. Or if there is, then this method doesn't
implement it. It really is there to return a GenBank-compliant
string. Or so I think - other opinions welcome, and are likely to exist.
On Sep 7, 2006, at 11:04 AM, Chris Fields wrote:
> Hilmar (or whomever can answer this),
> I was looking at a few bug fixes (bug 992 in particular) and
> noticed that,
> although LocationI-implementing objects are supposed to use a
> CoordinatePolicy for determining start/end coordinates for fuzzy
> Bio::Location::Fuzzy::to_FTstring() does not (it uses max/min_start
> () and
> max/min_end() instead). To me, it seems that this should be
> building the
> location string using the coordinate_policy->start()/end() methods
> (as suggested in the bug report).
> The default CoordinatePolicy for Location::Fuzzy is Bio::Location::
> Would there be any objection to changing this?
> Christopher Fields
> Postdoctoral Researcher - Switzer Lab
> Dept. of Biochemistry
> University of Illinois Urbana-Champaign
: Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net :
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