Hi Amr, 2010/10/26 Amr Al-Hossary <[email protected]>: > We can add some thing like an exception tracing queue, that can be checked > for later by the caller.
thanks for your suggestion. In terms of API I would prefer if we can separare a user from inconsistencies in the files and I hope we won't need such a queue... If something is off, the code is written to ignore or work around issues... Abdreas > would that be OK? > > Amr > >> Date: Tue, 26 Oct 2010 21:11:28 -0700 >> From: [email protected] >> To: [email protected] >> CC: [email protected] >> Subject: Re: [Biojava-l] Bad PDB files and batch processing with >> PDBFileReader >> >> Hi Daniel, >> >> can you explain a bit more what you are doing, in particular what >> errors you would like to deal with on your end? You should not need >> to worry too much about exception handling. Are there any special >> cases you are interested in? In this case we should support you with >> a clean interface rather than exception handling from your end... >> >> Andreas >> >> >> >> On Tue, Oct 26, 2010 at 8:54 PM, Daniel Asarnow <[email protected]> >> wrote: >> > Hi all, >> > Let me first say thanks to all the BioJava community members for >> > delivering such a useful set of libraries, and that I'm still a newbie >> > when i! t comes to BioJava (and Java) so forgive me if my question is >> > too trivial. >> > >> > I am doing work on lots (at least thousands) of PDB files from RCSB. >> > As is commonly known, these are often rife with errors which can lead >> > to exceptions during parsing with PDBFileParser. Because >> > PDBFileParser's methods contain their own try-catch blocks, exception >> > propagation stops there and my code proceeds blindly along regardless >> > of any error checking I do. I would like to catch the exceptions up >> > in my code where the parser is called, so that I can branch to a >> > continue statement and have my batch processing loops move on to the >> > next file. >> > Should I edit out the try-catch blocks and compile my own version of >> > the library? Or should I test the returned StructureImpl objects for >> > possession of the fields i! n question? In that case, I'm not sure >> > which proper ties will give the most general success information...and >> > I'd rather not have to check for /every/ property being correct. >> > >> > If there is some great way to check if an exception was caught down a >> > series of nested method calls, please hit me over the head with it. >> > >> > Thanks! >> > >> > -da >> > _______________________________________________ >> > Biojava-l mailing list - [email protected] >> > http://lists.open-bio.org/mailman/listinfo/biojava-l >> > >> >> >> _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
