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
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