Examples of bnGUI.OBOES.loadOntology()

bnGUI.OBOES.loadOntology()

eneontology.org/GO.format.shtml#oboflat">http://www.geneontology.org/GO.format.shtml#oboflat for a description of the OBO file format. The OBO for GO can be found online at http://www.geneontology.org. Ontologies loaded by loadOntology can be retrieved through the getOntology function of OBOES.

When loading an ontology, you must specify the path to the OBO file representing the ontology, as well as a user-specified name or handle to the ontology. Ontology names are arbitrary, but it is suggested that they bear some semblance to the actual name of the ontology. You cannot specify the same ontology name to be loaded twice for the same OBOES object. An ontology cannot be unloaded from an existing OBOES object after it is loaded; instead, simply create a new OBOES object. The OBO file path can be a local file, or it can be an online file. If the file is online, the full URL must be used, including the "http://" or "ftp://" prefix. @param OBOFile the path to the OBO file to read in @param ontology_name the user-specified name/handle to give to this ontology @return true if the specified OBO file was read in without problems. falseif a problem was encountered; an error message is also displayed. @see Ontology

        myOB.setCorrectionMethod("benjamini_hochberg");
        myOB.setMaximumPvalue(.05);
        myOB.setMinimumCount(2);


        //This loads the data in
        myOB.loadOntology(ontology.getAbsolutePath(), "gene ontology");
        try {
            myOB.loadAnnotation(annotation_BP.getAbsolutePath(), "gene ontology");
            myOB.loadAnnotation(annotation_CC.getAbsolutePath(), "gene ontology");
            myOB.loadAnnotation(annotation_MF.getAbsolutePath(), "gene ontology");
        } catch (Exception ex) {

        File annotation_MF = new File(FILENAME_ANNOTATION_MF); //molecular function


        myOB.setCorrectionMethod("benjamini_hochberg");
        myOB.setMaximumPvalue(.99);
        myOB.setMinimumCount(1);
        myOB.loadOntology(ontology.getAbsolutePath(), "geneo");
        try {
            myOB.loadAnnotation(annotation_BP.getAbsolutePath(), "geneo");
            myOB.loadAnnotation(annotation_CC.getAbsolutePath(), "geneo");
            myOB.loadAnnotation(annotation_MF.getAbsolutePath(), "geneo");
        } catch (Exception ex) {

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