[Bioperl-l] flexible warning/exception in SeqIO

[Ewan Birney]

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


> 
> If people agree, this point becomes light green.
> 
> 	Hilmar
> -- 
> -----------------------------------------------------------------
> Hilmar Lapp                                email: hlapp@gmx.net
> GNF, San Diego, Ca. 92122                  phone: +1 858 812 1757
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