[Biojava-dev] Errors versus Exceptions

[Andy Yates]

Is the problem in the code the fact that errors are used or that they are not declared on the method signatures?

On a more design note I do not like checked exceptions for two reasons. The first is they seem to make more junior developers catch Exception and swallow it. The second is whenever I've been Java coding in the past whenever a checked exception gets thrown (say IOException because of incorrect file permissions) I cannot deal with it which in the past has meant I either forward on the problem or re-throw in an unchecked exception. 

That said as Scooter mentioned the exception system was rushed out in the hackathon and did not have much work put into it. 

Andy

On 17 May 2010, at 13:15, PATERSON Trevor wrote:

> 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.
> 
> 
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev

-- 
Andrew Yates                   Ensembl Genomes Engineer
EMBL-EBI                       Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/