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 it 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 in question? In that case, I'm not sure which properties 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
