Jennifer, It sounds like my Alignment object needs to be expanded to support multiple hits. If you can send me an example Blast report which contains multiple hits within the same sequence I can modify the BlastHandler and BlastReport to handle this. Howard --- Jennifer Pan <[EMAIL PROTECTED]> wrote: > Hello Howard and Hello all, > > I was trying to parse a ncbi-blast results file, > using the BlastReport Howard provided. > For a hit sequence that has mutiple MSPs, I could only retrieve one > start and one end position of one MSP within this hit sequence. > -------------------- > for example, I would like to see: > Query NM_00000 > >hit1 [1, 300] > hit1 [400, 600] > hit1 [700, 1000] > >hit2 [1, 700] > >hit 3 [200, 500] > > and I've gotten > Query NM_00000 > >hit1 [400, 600] > >hit2 [1, 700] > >hit 3 [200, 500] > ----------------------------------------- > > Any hint and help here? > > many thanks > > -Jennifer > > -----Original Message----- > From: Howard Ungar [mailto:[EMAIL PROTECTED]] > Sent: Friday, October 19, 2001 11:53 AM > To: richard cai; [EMAIL PROTECTED] > Subject: Re: [Biojava-l] parse blast results > > > --- richard cai <[EMAIL PROTECTED]> wrote: > > Thanks, Howard. This is exactly what I need. > > > > Richard Cai > > > Richard, > There are four files in the attached zip file: > BlastSAXParser.java - contains changes to the parser to explicitly > create a "QueryName" attribute. > BlastHandler.java - uses the parser to read the QueryName attribute > BlastReport.java - prints the results. > Alignment.java - support object to pass data between the handler and > the report. > > Let me know if you need anything else to get this working. > > --- Keith James <[EMAIL PROTECTED]> wrote: > > This stems from the fact that the DTD has undergone recent > > modifications since Simon's group first commited their code. They > > refined the DTD, while incorporating a couple of suggested changes, > > one of which was adding QueryId. > > > > This is why the DTD reads, for example: > > > > <!ELEMENT biojava:Header (biojava:RawOutput, QueryId?, DatabaseId? > )> > > > > so that the new elements (here QueryId and DatabaseId) are not > (yet) > > mandatory. This avoids breaking existing code, but leaves > extraction > > of this information to the user (it's embedded in the > > biojava:RawOutput element). See Javadoc in > > org.biojava.bio.program.ssbind.BlastDBQueryHandler. > > Keith, > I think I tried to get the QueryId from the RawOutput, but the parser > was not starting to include data until later in the Blast Report > file. > I don't think my changes will fit into the current DTD as you > described > it. I could modify what I did to create these attributes in the > rawOutput element if you would like me to. Or would it be better to > consider modifying the DTD (and risk breaking existing code). > Either way, please take a look at what I did and provide some > feedback > about how you would like me to proceed. > > Howard > > > > __________________________________________________ > Do You Yahoo!? > Make a great connection at Yahoo! Personals. > http://personals.yahoo.com
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