[Bioperl-l] Bioperl exceptions

Peter van Heusden pvh at egenetics.com
Thu Jul 22 11:45:12 EDT 2004

Hi Bioperl developers

I'm a bit confused by the current state of play of the Bioperl exception 
class (Bio::Root::Exception). This inherits from Error, but Error.pm is 
not a requirement of Bioperl. It seems to me then that there are two 
exception mechanisms in Bioperl:

1) Exceptions based on exception objects, derived from Error.pm and 
implmented by Bio:Root::Exception and its subclasses.
2) Simple "stack dump" exceptions, which are implemented in Bio::Root's 
throw() method and used if Error.pm is not available.

Is this right? If so, is the necessary result is that Error-based 
exceptions can't be used as part of any core Bioperl class? (Since that 
would force a dependence on Error.pm) I see that in the biodesign.pod 
documentation, the only semantics mentioned are the basic string based 
ones. Does this mean that using exception objects is deprecated (I see 
the Exception.pm class was last updated in Bioperl 1.3.01 days)?


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