[Biojava-l] Trouble with GOParser

mark.schreiber at novartis.com mark.schreiber at novartis.com
Thu Jul 14 21:44:08 EDT 2005

Hi -

Can you post the entire stack trace and the version of biojava you are 
using to the list (not direct to me as I'm not an expert on this API)?

- Mark

"Óscar D. Sánchez Jiménez" <osanchez at fis.upv.es>
Sent by: biojava-l-bounces at portal.open-bio.org
07/14/2005 10:37 PM

        To:     biojava-l at biojava.org
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-l] Trouble with GOParser


I am having some troubles wiht GOParser class. I would like to use it in 
order to load an ontology and then display this ontology in a JTree.

This is the code I am testing:

try {
        BufferedReader file = new BufferedReader(new 
        OntologyFactory factory = OntoTools.getDefaultFactory();
        GOParser parser = new GOParser(); 
        Ontology onto = parser.parseGO(file, "trait", "description", 

        } catch (Exception e) {System.out.println(e);};

When I execute it, I get a java.lang.NullPointerException. The line 
causing the exception is the parseGO(...) one. Do you have any idea? I 
am able to read perfectly the ontology with Dag-Edit.

Thanks in advance,

Óscar D. Sánchez

Óscar David Sánchez Jiménez
Telecommunications Engineer - Computer Science Ph.D. student

Grupo de Informática Médica
ITACA - BET (Bioingeniería, Electrónica y Telemedicina)
Universidad Politécnica de Valencia
Camino de Vera s/n E-46022 Valencia (Spain)

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