Hi Charles! I've "found" a solution now. After dealing a couple of days with the terrible xml output of blast and BioJava's BlastXMLParser (which also wasn't working properly), I decided to have a look at the source code and try to figure out myself what was wrong with the BlastLikeSAXParser. So I checked out the present status of the source code via the anonymous svn checkout (howto here: http://biojava.org/wiki/CVS_to_SVN_Migration). After a couple of hours and me not finding an error that could cause this behavior, I thought I'll just give it a try and compiled the checked out source via ant. Then used the new created biojava.jar and suddenly everything went perfectly! So, whatever the error was (unfortunately I don't have the old source code to make a diff on certain files), it is already corrected in the up-to-the-minute version in the subversion system. Try it out!
Cheers, Marcel Charles Imbusch wrote: > Hello Marcel, > > I also do experience the problem that the parser is skipping > the even result numbers. I have not found a sufficient solution > for that, so I gave up on parsing on a blast result file containing > multiple results. Instead I splitted up the big fasta file into > serveral ones, so that I just get one result for one fasta file. > That works, even it's not the best solution for it. > > Let me know if you find another solution for that problem. > > Cheers, > Charles > > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
