Hi, I think BlastLikeSAXParser is a parser for ordinary (non XML) blast output files. It can not recognize xml's.
BlastXMLParserFacade is for XML parsing. Another question: does biojava has any support for psi-blast result parsing? Thanks, Valdemaras Repšys On 6/19/06, Jose Duarte <[EMAIL PROTECTED]> wrote: > > Jose Duarte wrote: > > >[EMAIL PROTECTED] wrote: > > > > > > > >>Hi -= > >> > >>I'm not sure where the percent identity gets sent but you can find out > by > >>using the example code > >>(http://biojava.org/wiki/BioJava:CookBook:Blast:Echo). > >> > >>It is also a nice code base for making a custom blast parser that is not > >>so object heavy. > >> > >> > >Thanks, that sounds good. However I have tried to run the BlastEcho.java > >code and got following error: > > > >Exception in thread "main" org.xml.sax.SAXException: Could not recognise > >the format of this file as one supported by the framework. > > at > >org.biojava.bio.program.sax.BlastLikeSAXParser.parse( > BlastLikeSAXParser.java:182) > > at BlastEcho.echo(BlastEcho.java:29) > > at BlastEcho.main(BlastEcho.java:75) > > > >I am pretty sure that my xml file is well formated blast output. > >Actually I've been parsing it already with code using biojava's > >BlastXMLParser without problems. My blast version is blastp 2.2.10. > > > >Also this is happening despite BlastEcho calling the setModeLazy() > >method of the parser object. As I understand it shouldn't be checking > >for versions using this mode. > > > > > > I think I can answer my question now. I just found out that for some > reason replacing line 17 in BlastEcho.java: > > BlastLikeSAXParser parser = new BlastLikeSAXParser(); > > for: > > BlastXMLParserFacade parser = new BlastXMLParserFacade(); > > it all works fine. > > I have no idea what's the difference between the BlastLikeSAXParser and > the BlastXMLParserFacade classes but it looks as it works as good. I can > change the code in the wiki if somebody can confirm this is correct. > > Cheers > > Jose > > _______________________________________________ > Biojava-l mailing list - [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
