Hi - I have seen this problem twice. Once it was due to 'invisible' white space before the XML. If you call trim() on the String that you get from the file you can get rid of this. You may not even be able to see it as some meta-characters are non-printing. The other problem is if your file was produced and saved on linux/unix and parsed on Windows. Problems can occur due to the different line feeds and carriage returns. While Java automatically knows which combination works for which operating it will assume the file you are working on came from your operating system. If this is the problem you can solve it using the unix utility dos2unix or unix2dos depending on which way you are going.
- Mark On Thu, Jun 5, 2008 at 7:49 PM, benn <[EMAIL PROTECTED]> wrote: > > 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 > _______________________________________________ > 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
