Re: DBREF parsing exception...
Andreas Prlic <[email protected]>
| Newsgroups | gmane.comp.java.bio.general |
|---|---|
| Message-ID | <[email protected]> |
Hi Jay, are you using the version from SVN or a particular release? I think this is already fixed in SVN... Andreas On Sun, Mar 6, 2011 at 5:54 PM, Jay Vyas <[email protected]> wrote: > Hi guys : It looks like the PDB parser for biojava is tripping up on the > DBREFs for pdb id 3O62 . Its a little bit of a problem for me because > a bunch of exception stack traces are getting streamed to the screen and > making it difficult for me to debug my code.... > > Is there a way to disable the reading of DBREF lines, or alternatively, is > there > a way to fix the exception ? > > badly formatted line ... DBREF 3O62 A 1 135 UNP P84233 > H32_XENLA 2 136 > java.lang.StringIndexOutOfBoundsException: String index out of range: 68 > at java.lang.String.substring(String.java:1934) > at > org.biojava.bio.structure.io.PDBFileParser.pdb_DBREF_Handler(PDBFileParser.java:1979) > at > org.biojava.bio.structure.io.PDBFileParser.parsePDBFile(PDBFileParser.java:2413) > > -- > Jay Vyas > MMSB/UCHC > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l > -- ----------------------------------------------------------------------- Dr. Andreas Prlic Senior Scientist, RCSB PDB Protein Data Bank University of California, San Diego (+1) 858.246.0526 ----------------------------------------------------------------------- _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l