[Biojava-l] Help with Stax and AGAVE xml

[Schreiber, Mark]

Hi -

I have been using the following snippet of code to read files from xembl
that are in AGAVE format. Features seem to be added to the constructed
sequence object ok but annotations seem to go missing.

Do I need to add some sort of listener somewhere? I'm a bit concerned
about using the SeqIOAdapter as a SeqIOListener as it doesn't do
anything, however there doesn't seem to be an appropriate implementation
to use.

Any advice?


    final AGAVEHandler handler = new AGAVEHandler();
    
    SeqIOListener siol = new SeqIOAdapter();
    handler.setFeatureListener(siol);


    SAX2StAXAdaptor adaptor = new SAX2StAXAdaptor(handler);
    XMLReader xmlReader = new SAXParser();
    FileReader fr = new FileReader(args[0]);
    InputSource is = new InputSource(fr);

    xmlReader.setContentHandler(adaptor);
    xmlReader.parse(is);


Mark Schreiber
Bioinformatics
AgResearch Invermay
PO Box 50034
Mosgiel
New Zealand
 
PH:   +64 3 489 9175
FAX:  +64 3 489 3739


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