Hi - Does anyone mind if I change the default behaivor to lazy parsing? Technically this would be a break in backwards compatibility (although only if you have a program that relies on strict parsing).
Last chance to complain. - Mark On Nov 26, 2007 8:02 PM, Allan Kamau <[EMAIL PROTECTED]> wrote: > Hi Mark, > Thank you for your reply. > Calling setModeLazy() method of the object of type BlastLikeSAXParser > did provide the cure. > > Allan. > > > Mark Schreiber wrote: > > Hi Allan - > > > > I think the solution is to call the setParserLazy() or some method > > with a similar name (I don't have the API handy). This will prevent it > > doing the check. > > > > The original idea of this method was you could check against a list of > > version numbers that people had validated. I don't think this is a > > good idea as nothing is truely 100% validated and we haven't kept the > > list up to date. If there are no objections I would propose to make > > this method depricated (and it's opposite method) and change the > > default behaivour to lazy checking. > > > > Best regards. > > > > - Mark > > > > > > On 11/25/07, *Allan Kamau* <[EMAIL PROTECTED] > > > > > <mailto:[EMAIL PROTECTED]>> wrote: > > > > Hi all, > > I've searched for a conclusive answer to the "Program ncbi-blastn > > Version <some value> is not supported" without success. > > I would like to know format of the blast output the Biojava's > > blast-like > > parsing framework likes, including some examples (without the data) of > > how such blast output may be created. > > For example, I am using ncbi-blastn and I am generating the blast > > file > > (which Biojava doesn't like) as follows. > > > > export FORMATDB=/usr/local/share/blast/blast-2.2.17/bin/formatdb; > > export BLASTALL=/usr/local/share/blast/blast-2.2.17/bin/blastall; > > export > > REFERENCES_FASTA_NAME=/study/tmp/somesequence/blast/20071017.fasta; > > export BLAST_REPORT_TABULAR=somesequence.blast.txt > > export BLAST_REPORT_XML=somesequence.blast.xml > > export BLAST_REPORT=somesequence.blast > > export INPUT_FASTA=somesequence.fasta > > export WORK_DIR=/development/study/try1/tmpDataFiles/somesequence > > > > date;time cd $WORK_DIR;cp $REFERENCES_FASTA_NAME .;$FORMATDB -i > > $REFERENCES_FASTA_NAME -p F -o T;echo `pwd`;$BLASTALL -p blastn -d > > $REFERENCES_FASTA_NAME -i $INPUT_FASTA -q -1 -r 1 -m 8 -o > > $BLAST_REPORT_TABULAR;$BLASTALL -p blastn -d > > $REFERENCES_FASTA_NAME -i > > $INPUT_FASTA -q -1 -r 1 -m 7 -o $BLAST_REPORT_XML;date; > > > > Then I supply the $BLAST_REPORT as an argument to "BlastParser" copied > > from " http://biojava.org/wiki/BioJava:CookBook:Blast:Parser"; > > > > Then I get the error below. > > > > > > [EMAIL PROTECTED] try1]$ $ANT_HOME/bin/ant runBlastParser; > > Buildfile: build.xml > > > > runBlastParser: > > [java] org.xml.sax.SAXException: Program ncbi-blastn Version > > 2.2.17 > > is not supported by the biojava blast-like parsing framework > > [java] at > > > > org.biojava.bio.program.sax.BlastLikeSAXParser.interpret(BlastLikeSAXParser.java > > :241) > > [java] at > > > > org.biojava.bio.program.sax.BlastLikeSAXParser.parse(BlastLikeSAXParser.java:160) > > > > Allan. > > _______________________________________________ > > Biojava-l mailing list - [email protected] > > <mailto:[email protected]> > > > > > http://lists.open-bio.org/mailman/listinfo/biojava-l > > > > > > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
