thoughts/questions on Seq.pm and Parse.pm

[Steve A. Chervitz]

Chris,

>o Proposed validity markers
>   - A marker that would be set to 'false' whenever Seq.pm makes a call to carp()
>   - A marker to specify valid/invalid biosequence object
> Are these permutations of the same idea or two different things? I'm also
> not sure about how to implement.

I think this (and Steve B's recent comments on this issue) opens up an 
issue that could use some discussion: how to best handle errors and 
exceptions in Perl objects. I've created some modules that I use to help 
manage errors. See the "More advanced object" example at: 

http://genome-www.stanford.edu/~sac/perlOOP/examples/

This is my attempt to manage the wide variety of errors and 
exceptions that can occur in complex objects. The primary motivation 
for this work is to allow objects to handle error conditions without 
killing the script by calling die or croak. The code is at an early 
stage of development (it hasn't received much independent critiquing),
but it may inspire some useful ideas.


Steve Chervitz