[Biojava-l] Problem parsing biojava xml file

benn benn at mpi-cbg.de
Wed Jun 4 18:16:50 UTC 2008


         Sorry to pepper the board with questions!  I am working on 
BLAST parsing and have the standard output for BLAST working fine with 
JUnit tests.  So I am attempting to recreate this for files in XML 
format comming from blast (blastp), however I have the problem that I 
get a SAXExepttion that content is not allowed before prolog.  I thought 
I could have some invisible characters whihc is causing it to throw a 
wobbly but I cannto see any.  Has anyone else come across the problem.  
for completeness i have attached teh blast file and the code to parse is 

   private List<SeqSimilaritySearchResult> parseBlast(String filename)
           throws IOException, SAXException, BioException {

       InputStream is = new FileInputStream(

       BlastXMLParserFacade parser = new BlastXMLParserFacade();
       SeqSimilarityAdapter adapter = new SeqSimilarityAdapter();
       List<SeqSimilaritySearchResult> results = new 

       SearchContentHandler builder = new BlastLikeSearchBuilder(results,
               new DummySequenceDB("queries"),
               new DummySequenceDBInstallation());


       parser.parse(new InputSource(is));
       return results;


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