@Override public void setGraph(ONDEXGraph graph) { this.graph = graph; // hack to get to the selected viewer viewer = OVTK2Desktop.getDesktopResources().getSelectedViewer(); }
public synchronized void processingStarted() { try { OVTK2PropertiesAggregator v = OVTK2Desktop.getDesktopResources().getSelectedViewer(); graphs.put(v, v.getONDEXJUNGGraph()); } catch (Exception e) { e.printStackTrace(); } }
@Override public ONDEXGraph resolveRef(Object arg) throws Exception { try { return OVTK2Desktop.getDesktopResources().getSelectedViewer().getONDEXJUNGGraph(); } catch (NullPointerException e) { throw new FunctionException("Error - unable to find an ONDEX graph! Create the new graph to correct this error.", -1); } } }
@Override public void setGraph(ONDEXGraph graph) { OVTK2Desktop desktop = OVTK2Desktop.getInstance(); // hack to get to the visualisation viewer this.viewer = desktop.getDesktopResources().getSelectedViewer() .getVisualizationViewer(); }
public static OutputPrinter getCommandLine() { // check if there is an active viewer present OVTK2PropertiesAggregator viewer = (OVTK2PropertiesAggregator) OVTK2Desktop.getDesktopResources().getSelectedViewer(); if (viewer == null) { FileMenuAction.getInstance().actionPerformed(new ActionEvent(OVTK2Desktop.getInstance(), ActionEvent.ACTION_PERFORMED, "new")); } return getCommandLine(viewer); }
/** * Creates new form NewJFrame1 */ public SetSelector() throws Exception { if (OVTK2Desktop.getDesktopResources().getSelectedViewer() == null) { return; } OVTK2Desktop.getInstance().getDesktopResources().getParentPane().add(this); graph = OVTK2Desktop.getDesktopResources().getSelectedViewer().getONDEXJUNGGraph(); initComponents(); this.setVisible(true); this.setTitle("Show tagget sets for members"); DefaultListModel listModel = new DefaultListModel(); lSets.setModel(listModel); for (ONDEXConcept c : graph.getConceptsOfConceptClass(MdHelper.createCC(graph, "Superset"))) { JCheckBox check = new JCheckBox(c.getConceptName().getName()); supersets.put(check, c); listModel.addElement(check); } System.err.println("Set selectior initialized."); }
/** * @return gets a stream containing the workflowdescriptor xml file */ private static InputStream getWorkflowComponantDescriptors() { try { Client client = Client.create(); WebResource webResource = client.resource(NexusURLs.NEXUS_DATA_INDEX); MultivaluedMap queryParams = new MultivaluedMapImpl(); queryParams.add("c", "workflow-component-description"); queryParams.add("p", "zip"); queryParams.add("g", "net.sourceforge.ondex"); return webResource.queryParams(queryParams).get(InputStream.class); } catch (Exception e) { OVTK2Desktop.getDesktopResources().getLogger().eventOccurred(new ONDEXEvent(ListPlugins.class, new UnspecifiedErrorEvent(e.toString(), ""))); return null; } }
/** * The constructor just initialises all fields and then minimises the graph * window to prevent flickering. */ public GraphSynchronizer(OVTK2PropertiesAggregator v) { this.v = v; graph = v.getONDEXJUNGGraph(); concepts = new HashSet<ONDEXConcept>(); relations = new HashSet<ONDEXRelation>(); determineMax(); // minimise graph first try { if (v instanceof OVTK2Viewer) ((OVTK2Viewer) v).setIcon(true); // also hide meta graph away OVTK2MetaGraph meta = OVTK2Desktop.getDesktopResources().getSelectedMetagraph(); if (meta != null) meta.setIcon(true); } catch (PropertyVetoException e) { } }
for (ONDEXConcept selected : OVTK2Desktop.getDesktopResources().getSelectedViewer().getPickedNodes()) { tags.addAll(selected.getTags()); OVTK2Desktop.getDesktopResources().getSelectedViewer().getVisualizationViewer().getModel().fireStateChanged();
private void updateSelectedNodes() { selected.clear(); OVTK2PropertiesAggregator viewer = OVTK2Desktop.getDesktopResources() .getSelectedViewer(); if (viewer != null) { PickedState<ONDEXConcept> state = viewer.getVisualizationViewer() .getPickedVertexState(); Set<ONDEXConcept> set = state.getPicked(); for (ONDEXConcept node : set) { ONDEXConcept ac = node; selected.put(ac.getId() + ":" + ac.getPID(), ac.getId()); } } }
OVTK2MetaGraph meta = OVTK2Desktop.getDesktopResources().getSelectedMetagraph(); if (meta != null) meta.setIcon(false);
OVTK2ResourceAssesor resources = OVTK2Desktop.getDesktopResources(); OVTK2Viewer viewer = (OVTK2Viewer) resources.getSelectedViewer();
/** * Method for compatibility with previous versions * * @param title * @param process */ public static void start(String title, final Monitorable process) { // running in Desktop version if (OVTK2Desktop.getDesktopResources().getSelectedViewer() instanceof OVTK2Viewer) start(OVTK2Desktop.getInstance().getMainFrame(), title, process); else start(null, title, process); }
/** * Setup a new OVTK2Viewer. * * @param aog * ONDEXGraph * @param annotations * XML String * @return OVTK2Viewer */ public static OVTK2Viewer initViewer(ONDEXGraph aog, Map<String, String> annotations) { OVTK2Desktop desktop = OVTK2Desktop.getInstance(); ONDEXEventHandler.getEventHandlerForSID(aog.getSID()).addONDEXONDEXListener(OVTK2Desktop.getDesktopResources().getLogger()); OVTK2Viewer viewer = new OVTK2Viewer(aog, annotations); viewer.addInternalFrameListener(desktop); viewer.addVetoableChangeListener(desktop); // for listening to changes in ModalGraphMouse viewer.addItemListener(OVTK2Desktop.getDesktopResources().getToolBar()); desktop.viewers.add(viewer); return viewer; }
OVTK2ResourceAssesor resources = OVTK2Desktop.getDesktopResources(); final OVTK2Viewer viewer = (OVTK2Viewer) resources.getSelectedViewer();
OVTK2ResourceAssesor resources = OVTK2Desktop.getDesktopResources();
OVTK2ResourceAssesor resources = OVTK2Desktop.getDesktopResources(); int option = JOptionPane.NO_OPTION; if ((anVisible = aog.getMetaData().getAttributeName(AppearanceSynchronizer.VISIBLE)) != null && aog.getConceptsOfAttributeName(anVisible).size() > 0) { option = JOptionPane.showConfirmDialog(OVTK2Desktop.getDesktopResources().getParentPane(), Config.language.getProperty("Dialog.Appearance.Found"), Config.language.getProperty("Dialog.Appearance.FoundTitle"), JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
OVTK2ResourceAssesor resources = OVTK2Desktop.getDesktopResources(); final OVTK2Viewer viewer = (OVTK2Viewer) resources.getSelectedViewer();
OVTK2ResourceAssesor resources = OVTK2Desktop.getDesktopResources(); OVTK2Viewer viewer = (OVTK2Viewer) resources.getSelectedViewer();
private void runLayout() { try { OVTK2ResourceAssesor resources = OVTK2Desktop.getDesktopResources(); final OVTK2Viewer viewer = (OVTK2Viewer) resources.getSelectedViewer(); final OVTK2Layouter layouter_new = new GEMLayout(viewer);