public boolean canCheck(Object thing) { return thing instanceof Model && ((Model)thing).getLevel() == BioPAXLevel.L3; } }
public boolean canCheck(Object thing) { return thing instanceof Model && ((Model)thing).getLevel()==BioPAXLevel.L3; }
public boolean canCheck(Object thing) { return thing instanceof Model && ((Model)thing).getLevel() == BioPAXLevel.L3; }
public boolean canCheck(Object thing) { return thing instanceof Model && ((Model)thing).getLevel() == BioPAXLevel.L3; }
public boolean canCheck(Object thing) { return thing instanceof Model && ((Model)thing).getLevel() == BioPAXLevel.L3; }
public boolean canCheck(Object thing) { return thing instanceof Model && ((Model)thing).getLevel()==BioPAXLevel.L3; }
private String convertToOWL(Model model) { ByteArrayOutputStream out = new ByteArrayOutputStream(); (new SimpleIOHandler(model.getLevel())).convertToOWL(model, out); return out.toString(); }
public void check(final Validation validation, Model model) { if(model.getObjects().isEmpty()) error(validation, model, "empty.biopax.model", false, model.getLevel().toString()); }
public void check(Model model, boolean fix) { if(model.getObjects().isEmpty()) error(model, "empty.biopax.model", false, model.getLevel().toString()); }
/** * This is to refresh 'modelSerialized' property: * generates BioPAX OWL from current model. */ public void updateModelSerialized() { Model model = getModel(); if (model != null) { try { // export to OWL ByteArrayOutputStream outputStream = new ByteArrayOutputStream(); (new SimpleIOHandler(model.getLevel())).convertToOWL(model, outputStream); this.modelSerialized = outputStream.toString("UTF-8"); } catch (IOException e) { throw new BiopaxValidatorException( "Failed to export modified model!", e); } } }
if(model == null || model.getLevel() != BioPAXLevel.L3) { throw new IllegalArgumentException("Failed to create Model! " + extraInfo());
/** * Infers simple interactions from the interactions found in the <em>model</em> for every * interaction rule given; and returns this inferred simple interactions. * @param model model from which simple interactions are going to be inferred * @return a set of inferred simple interactions */ public Set<SimpleInteraction> inferInteractions(Model model) { switch (model.getLevel()) { case L1: case L2: return inferL2(model); case L3: return inferL3(model); default: throw new IllegalBioPAXArgumentException("Unknown BioPAX Level"); } }
public void check(Model model, boolean fix) { AbstractTraverser traverser = new AbstractTraverser( SimpleEditorMap.get(model.getLevel())) { @Override protected void visit(Object value, BioPAXElement parent, Model model, PropertyEditor editor) { if(value instanceof BioPAXElement && !model.contains((BioPAXElement)value)) { error(value, "dangling.value", false, editor.getDomain().getSimpleName(), editor.getProperty()); } } }; // starts from each element in the model and visits its properties for(BioPAXElement e: model.getObjects()) { traverser.traverse(e, model); } } }
private OntModel initializeEmptyOntModel(Model model) { OntModel ontModel = createModel(); String xmlBase = model.getXmlBase(); if (xmlBase == null || xmlBase.equals("")) { xmlBase = "http://biopax.org/paxtools#"; } Ontology base = ontModel.createOntology(xmlBase); String uri = model.getLevel().getNameSpace(); uri = uri.substring(0, uri.length() - 1); if (log.isDebugEnabled()) { log.debug("uri = " + uri); } ontModel.setNsPrefixes(model.getNameSpacePrefixMap()); base.addImport(ontModel.createResource(uri)); ontModel.loadImports(); return ontModel; }
io.mergeDuplicates(true); Model model = io.convertFromOWL(is); if (model.getLevel() != BioPAXLevel.L3) { if (log.isInfoEnabled()) log.info("Converting to BioPAX Level3... " + extraInfo()); model = (new OneTwoThree()).filter(model); if (model != null) { io.setFactory(model.getLevel().getDefaultFactory()); io.convertToOWL(model, os); toReturn = os.toString();
public void check(Model model, boolean fix) { // get all the root elements final Collection<BioPAXElement> rootElements = new HashSet<BioPAXElement>(model.getObjects()); // extends traverser ;) AbstractTraverser checker = new AbstractTraverser( SimpleEditorMap.get(model.getLevel())) { @Override protected void visit(Object value, BioPAXElement parent, Model model, PropertyEditor editor) { if(value instanceof BioPAXElement) rootElements.remove(value); // found, i.e., it is used by another element. } }; // this removes those elements that are referenced from others for(BioPAXElement e : model.getObjects()) { checker.traverse(e, model); } // those left are in fact dangling! for(BioPAXElement thing : rootElements) { if(!(thing instanceof Pathway)) error(thing, "dangling.element", false); } }
public void check(final Validation validation, Model model) { // get all the root elements final Collection<BioPAXElement> rootElements = new HashSet<BioPAXElement>(model.getObjects()); // extends traverser ;) AbstractTraverser checker = new AbstractTraverser( SimpleEditorMap.get(model.getLevel())) { @Override protected void visit(Object value, BioPAXElement parent, Model model, PropertyEditor editor) { if(value instanceof BioPAXElement) rootElements.remove(value); // found, i.e., it is used by another element. } }; // this removes those elements that are referenced from others for(BioPAXElement e : model.getObjects()) { checker.traverse(e, model); } // those left are in fact dangling! for(BioPAXElement thing : rootElements) { if(!(thing instanceof Pathway)) error(validation, thing, "dangling.element", false); } }
/** * Import BioPAX data into a new in-memory model. * * @param in BioPAX data file name. * @return BioPaxUtil new instance (containing the imported BioPAX data) * @throws FileNotFoundException */ public static Model read(final InputStream in) throws FileNotFoundException { Model model = convertFromOwl(in); // immediately convert to BioPAX Level3 model if(model != null && BioPAXLevel.L2.equals(model.getLevel())) { model = new LevelUpgrader().filter(model); } if(model != null) fixDisplayName(model); return model; }
public void run() { taskMonitor.setStatus("Exporting BioPAX..."); CyNetwork currentNetwork = Cytoscape.getCurrentNetwork(); Model bpModel = BioPaxUtil.getNetworkModel(currentNetwork.getIdentifier()); CyAttributes networkAttributes = Cytoscape.getNetworkAttributes(); String bpModelStr = (String) networkAttributes .getAttribute(currentNetwork.getIdentifier(), BioPaxUtil.BIOPAX_MODEL_STRING); try { FileOutputStream fOutput = new FileOutputStream(fileName); if(bpModel == null || bpModelStr == null ) throw new IllegalArgumentException("Invalid/empty BioPAX model."); SimpleExporter simpleExporter = new SimpleExporter(bpModel.getLevel()); simpleExporter.convertToOWL(bpModel, fOutput); fOutput.close(); Object[] ret_val = new Object[3]; ret_val[0] = currentNetwork; ret_val[1] = new File(fileName).toURI(); ret_val[2] = Cytoscape.FILE_BIOPAX; Cytoscape.firePropertyChange(Cytoscape.NETWORK_SAVED, null, ret_val); taskMonitor.setPercentCompleted(100); taskMonitor.setStatus("Network successfully saved to: " + fileName + "."); } catch (IllegalArgumentException e) { taskMonitor.setException(e, "Network is invalid. Cannot be saved."); } catch (IOException e) { taskMonitor.setException(e, "Unable to save network."); } }
log.info("printing " + bpe + " OWL"); try { SimpleExporter simpleExporter = new SimpleExporter(m.getLevel());