[Biojava-dev] Errors versus Exceptions

[PATERSON Trevor]

 resending cos of bad headers

________________________________

From: PATERSON Trevor 
Sent: 17 May 2010 13:02
To: biojava-dev at lists.open-bio.org
Subject: Errors versus Exceptions


Could I ask a quick question about why BJ3 seems to use Errors rather than Exceptions 
- maybe this is already documented somewhere on the wiki for BJ3 or 1 - and you can point me there.
 
Obviously for us dataloading from remote databases we need to have a method to catch connection,sql, datamapping errors etc.
We ususally throw DataAccessExceptions when this happens, which wrap any java.net, Ibatis and SQL exceptions.
 
It is difficult for us to plug in our lazyload over your signatures in the BJ3 sequence readers, as these don't throw exceptions, 
because you seem to use Errors throughout - which dont need to be declared. Infact I cant actually see examples of you catching 
and responding to thrown errors.
 
for example the setContents routine of the Sequence Readers throws a  CompoundNotFoundError if there is no mapping for a base - 
but I can't see what is done with this.
 
According to the Java Lang Spec, errors are used for "serious problems that a reasonable application 
should not try to catch" - but I would have thought finding an unrecognized base in a sequence was 
just the sort of thing that should be thrown and caught and acted on. As error throwables are not reported 
in the signature - developers don't have any clue ( or requirement) that they should be catching and dealing with errors - which
seems a bit dangerous to me... If Exceptions were thrownrather than Errors that would force the developer to handle runtime errors
 
Cheers Trevor

-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.