[Biojava-l] Problem while using BlastXMLParserFacade

[benn]

Hello,

        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 
coming from blast (blastp), however I have the problem that I get a 
SAXException that content is not allowed before prolog.  I thought I 
could have some invisible characters which is causing it to throw a 
wobbly but I cannot see any.  Has anyone else come across the problem?  
For completeness, the file can be downloaded at : 
http://idisk-srv1.mpi-cbg.de/~benn/xmloutput.xml (the mailing list 
server would not me attach the file to the email) and the code which 
parses is below:

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

      InputStream is = new FileInputStream(
              "src/test/resources/blast/standardoutput.blastp");

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

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

      adapter.setSearchContentHandler(builder);

      parser.parse(new InputSource(is));
      return results;
  }
</code>

Cheers,

Neil