Hi, I had same problem earlier and when I tried to debug it, I noticed that parser simply jumps over non matched query sequences in output file. So the non matched data cannot be reached from your ContentHandler-class anyhow. Or that is at least what I think...
In my case the problem was solved easily. That is because I had developed graphical interface for executing BLAST and handling the results in many ways (about wich I don't tell more now), so I also parsed the query file into database before parsing actual output. So when you have all BLAST-queries in one database table and matched queries in another, you can easily get the non matched BLAST-queries by an SQL-query. I also had strange errors with BLAST-parser when parsing very big output files like 200 MB. I don't now remember the case specifically but it was something like the stack was growing during parsing so big that the memory of my computer got short. I didn't save any data into variables in parser, so the growing of stack didn't come from that. I even take all the program code off from my ContentHandler and even then the error occured. The fix for the problem above was that I now split the output file in many parts and parse them separately: the parser is working heavenly great ;) Maybe I have made big work with this parser but it have still been easier than writing my own parser. Regards, Petri ********************************** *Petri Pehkonen *Software Designer / Bioinformatics *Inst. of Applied Biotechnology *University of Kuopio *P.O.B. 1627, Kuopio 70211 FINLAND *Phone (+358)40 7668027 *E-mail [EMAIL PROTECTED] _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
