Go to BioPax Class: " + "
\n"); return sb; } /** * Writes the given content to a file on disk * @param fileName the name of the file to write to * @param content the content to put in the file. */ private static void writeToFile(String fileName, StringBuffer content) { System.out.println("Generating file " + fileName); PrintWriter writer = null; try { writer = new PrintWriter(new File(fileName)); writer.println(content.toString()); } catch (FileNotFoundException e) { e.printStackTrace(); } finally { if (writer != null) { writer.close(); } } } /** Entry point for the example. It loads the BioPax ontology from the web, iterates * over the classes defined in the ontology, and generates HTML from the class names, * parent classes, and comments. * @param args no arguments are expected. */ public static void main(String[] args) { String uri = "http://www.biopax.org/release/biopax-level2.owl"; StringBuffer html = new StringBuffer(HEADER); StringBuffer detail = new StringBuffer(); try { OWLModel owlModel = ProtegeOWL.createJenaOWLModelFromURI(uri); html.append(getClassList(owlModel)); Collection classes = owlModel.getUserDefinedOWLNamedClasses(); int i = 0; for (Iterator it = classes.iterator(); it.hasNext();) { OWLNamedClass cls = (OWLNamedClass) it.next(); detail.append( " " + "Parent: "); Collection superclasses = cls.getNamedSuperclasses(); for (Iterator superclassIt = superclasses.iterator(); superclassIt.hasNext(); ) { String parent = ((OWLNamedClass)superclassIt.next()).getName(); detail.append("" + parent + " "); } detail.append("
\n"); detail.append( " \n"); Collection comments = cls.getComments(); for (Iterator commentIt = comments.iterator(); commentIt.hasNext(); ) { detail.append(commentIt.next()); } detail.append("\n"); i++; } html.append(detail); } catch (Exception e) { e.printStackTrace(); } finally { html.append(FOOTER); } writeToFile("bio_pax_level2.html", html); } }