[Bioperl-l] flexible warning/exception in SeqIO

[Jason Stajich]

On Sun, 28 Jan 2001, Ewan Birney wrote:

> On Sun, 28 Jan 2001, Hilmar Lapp wrote:
> 
> > This is on our tasklist. To reiterate briefly the background, we
> > had a discussion a while ago that there are many applications
> > which would rather lose an entry of a databank file or a feature
> > of an entry than choking due to an exception being thrown. The
> > reason for such exceptions are entries which are either
> > misformatted or contain syntax not yet understood by BioPerl
> > (there will be significantly less though due to the new location
> > model).
> > 
> > The conclusion was that we want to have some flexibility on the
> > client side, who can turn such incidents into exceptions if he/she
> > wants to, but the default would be to only warn.
> > 
> > I'm not sure but as I understood the changes to RootI every object
> > has the ability to turn warn() into throw() by saying
> > $obj->verbose(2). Is that right, and if so, do people agree that
> > this fulfills the requirements in SeqIO warn/throw flexibility
> > (which implies that the SeqIO code only warn()s).
> 
> I agree. So the SeqIO code should ->warn in recoverable positions and
> ->throw on utterly non-recoverable positions

This is exactly what I think as well.  It gives the most flexibility.  I
think with RichSeq we can handle things like parsing optional qualifiers 
(bug #160 -- PID) from GenBank format and any other lost features.

> 
> 
> > 
> > If people agree, this point becomes light green.
Grun ist gut.
> > 
> > 	Hilmar
> > -- 
> > -----------------------------------------------------------------
> > Hilmar Lapp                                email: hlapp@gmx.net
> > GNF, San Diego, Ca. 92122                  phone: +1 858 812 1757
> > -----------------------------------------------------------------
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> > 
> 
> -----------------------------------------------------------------
> Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
> <birney@ebi.ac.uk>. 
> -----------------------------------------------------------------
> 
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Jason Stajich
jason@chg.mc.duke.edu
Center for Human Genetics
Duke University Medical Center 
http://www.chg.duke.edu/