On Monday 01 Nov 2004 14:49, Can Gencer wrote: > Hello everyone, > > We are trying to parse a quite large multiple BLAST results file (around > 4GB), and the computer available has 1GB of RAM. However, when the code > in the cookbook is used ( > "http://www.biojava.org/docs/bj_in_anger/BlastParser.htm";), using the > BlastLikeSAXParser it will give out an OutOfMemory exception after a > short while, and when I monitor the system during the parsing, I don't > see the memory usage going up significantly. It is the > parse(InputSource) method that throws the exception. Is there a way to > solve this problem ? > This is probably not the answer you want but I'm parsing BLAST files at least as large as yours without this problem using the BlastXMLParserFacade class. Perhaps it may be a temporary workaround until someone who understands the other parser responds, I certainly don't.
There is also a alpha/beta-quality parser filter framework that could perhaps be used with the XML parser framework in CVS. Regards, David Huen P.S. A number of fixes have gone into the XML parsing for NCBI Blastn (the only part I use, the other parts may work too)software in CVS which may make it workable for you now. In particular, the irritating DTD related bug appears to be worked around. _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
