[Biojava-l] Bad PDB files and batch processing with PDBFileReader

Andreas Prlic andreas at sdsc.edu
Wed Oct 27 06:01:38 UTC 2010

Hi Amr,

2010/10/26 Amr Al-Hossary <amr_alhossary at hotmail.com>:
> 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...


> would that be OK?
> Amr
>> Date: Tue, 26 Oct 2010 21:11:28 -0700
>> From: andreas at sdsc.edu
>> To: dasarnow at gmail.com
>> CC: biojava-l at lists.open-bio.org
>> 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 <dasarnow at gmail.com>
>> 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  -  Biojava-l at lists.open-bio.org
>> > http://lists.open-bio.org/mailman/listinfo/biojava-l
>> >

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