[Bioperl-l] flexible warning/exception in SeqIO

Hilmar Lapp hlapp@gmx.net
Sun, 28 Jan 2001 12:34:36 -0800

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

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).

If people agree, this point becomes light green.

Hilmar Lapp                                email: hlapp@gmx.net
GNF, San Diego, Ca. 92122                  phone: +1 858 812 1757