Bioperl: RFI response, appendix (fwd)

Steven E. Brenner
Wed, 11 Mar 1998 18:10:07 -0800 (PST)


> Steve wrote,
> >>>>>>>>
> 8. Highly fault-tolerant. 
> ...       It is preferrable to throw fatal exceptions when data
>           inconsistencies or other serious problems are encountered,
>           rather than generating warnings that cannot be
>           programmatically handled, or relying on a polling mechanism,
>           or relying on the software's inherent ability to accomodate
>           the discrepency.
> <<<<<<<<
> As before, I'd suggest to prefer warnings to fatal exceptions.
> Some of my runs take days (90 sequences, each 3000 nucleotides each,
> are subjected to thousands of alignment calculations), and I don't wanna 
> lose the end result b/c of some stupid exception. Fatal exceptions are OK
> for small scripts, but not for larger applications, as long as there
> is a reasonable way to handle them: garbage in, garbage out is OK for
> me as long as warnings are issued.

You can always trap the exceptions and thus avoid having things die.
It's relatively easy to convert an excpetion into a warning, but nearly
impossible to do the reverse.


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