-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Sounds good to me.
Mark Schreiber wrote: > 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 > - -- Richard Holland (BioMart) EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK Tel. +44 (0)1223 494416 http://www.biomart.org/ http://www.biojava.org/ -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFHS9fq4C5LeMEKA/QRAm/3AJ9hi2yrSyeK6a3nXtObyJ2MAk0Y1QCeL5HT iYQc6HTdm6fJ+Lcfssnd34g= =VuJJ -----END PGP SIGNATURE----- _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
