Examples with TopologyFilterFactory org.cytoscape.filter.internal.filters.topology.TopologyFilterFactory used on opensource projects

Example 1 with TopologyFilterFactory

use of org.cytoscape.filter.internal.filters.topology.TopologyFilterFactory in project cytoscape-impl by cytoscape.

the class CreateFilterTaskTest method initMocks.

@Before
public void initMocks() {
    MockitoAnnotations.initMocks(this);
    transformerContainer = new TestTransformerContainer();
    TransformerManagerImpl transformerManager = new TransformerManagerImpl();
    transformerManager.registerFilterFactory(new ColumnFilterFactory(), Collections.emptyMap());
    transformerManager.registerFilterFactory(new DegreeFilterFactory(), Collections.emptyMap());
    transformerManager.registerFilterFactory(new TopologyFilterFactory(), Collections.emptyMap());
    transformerManager.registerFilterFactory(new CompositeFilterFactory<>(CyNetwork.class, CyIdentifiable.class), Collections.emptyMap());
    CyTransformerReaderImpl transformerReader = new CyTransformerReaderImpl();
    transformerReader.registerTransformerManager(transformerManager, Collections.emptyMap());
    when(serviceRegistrar.getService(CyTransformerReader.class)).thenReturn(transformerReader);
    when(serviceRegistrar.getService(TransformerContainer.class, "(container.type=filter)")).thenReturn(transformerContainer);
}

Example 2 with TopologyFilterFactory

use of org.cytoscape.filter.internal.filters.topology.TopologyFilterFactory in project cytoscape-impl by cytoscape.

the class CyActivator method start.

@Override
public void start(BundleContext bc) {
    final CyServiceRegistrar serviceRegistrar = getService(bc, CyServiceRegistrar.class);
    TransformerManagerImpl transformerManager = new TransformerManagerImpl();
    registerService(bc, transformerManager, TransformerManager.class, new Properties());
    registerServiceListener(bc, transformerManager::registerTransformerSource, transformerManager::unregisterTransformerSource, TransformerSource.class);
    registerServiceListener(bc, transformerManager::registerFilterFactory, transformerManager::unregisterFilterFactory, FilterFactory.class);
    registerServiceListener(bc, transformerManager::registerElementTransformerFactory, transformerManager::unregisterElementTransformerFactory, ElementTransformerFactory.class);
    registerServiceListener(bc, transformerManager::registerHolisticTransformerFactory, transformerManager::unregisterHolisticTransformerFactory, HolisticTransformerFactory.class);
    TransformerViewManager transformerViewManager = new TransformerViewManager(transformerManager);
    registerServiceListener(bc, transformerViewManager::registerTransformerViewFactory, transformerViewManager::unregisterTransformerViewFactory, TransformerViewFactory.class);
    registerService(bc, new CyNetworkSource(), TransformerSource.class, new Properties());
    // Filters
    registerService(bc, new DegreeFilterFactory(), FilterFactory.class, new Properties());
    registerService(bc, new ColumnFilterFactory(), FilterFactory.class, new Properties());
    registerService(bc, new TopologyFilterFactory(), FilterFactory.class, new Properties());
    registerService(bc, new CompositeFilterFactory<CyNetwork, CyIdentifiable>(CyNetwork.class, CyIdentifiable.class), FilterFactory.class, new Properties());
    // Transformers
    registerService(bc, new InteractionTransformerFactory(), ElementTransformerFactory.class, new Properties());
    registerService(bc, new AdjacencyTransformerFactory(), ElementTransformerFactory.class, new Properties());
    ModelMonitor modelMonitor = new ModelMonitor();
    registerAllServices(bc, modelMonitor, new Properties());
    ValidationManager validationManager = new ValidationManager();
    registerAllServices(bc, validationManager, new Properties());
    FilterPanelStyle style = new FlatStyle();
    registerService(bc, new DegreeFilterViewFactory(style, modelMonitor), TransformerViewFactory.class, new Properties());
    registerService(bc, new ColumnFilterViewFactory(style, modelMonitor, serviceRegistrar), TransformerViewFactory.class, new Properties());
    registerService(bc, new TopologyFilterViewFactory(style), TransformerViewFactory.class, TopologyFilterViewFactory.getServiceProperties());
    registerService(bc, new InteractionTransformerViewFactory(style), TransformerViewFactory.class, new Properties());
    registerService(bc, new AdjacencyTransformerViewFactory(style, serviceRegistrar), TransformerViewFactory.class, AdjacencyTransformerViewFactory.getServiceProperties());
    LazyWorkQueue queue = new LazyWorkQueue();
    FilterIO filterIo = new FilterIO(serviceRegistrar);
    FilterWorker filterWorker = new FilterWorker(queue, serviceRegistrar);
    FilterPanelController filterPanelController = new FilterPanelController(transformerManager, transformerViewManager, validationManager, filterWorker, modelMonitor, filterIo, style, serviceRegistrar);
    FilterPanel filterPanel = new FilterPanel(filterPanelController, filterWorker, serviceRegistrar);
    TransformerWorker transformerWorker = new TransformerWorker(queue, transformerManager, serviceRegistrar);
    TransformerPanelController transformerPanelController = new TransformerPanelController(transformerManager, transformerViewManager, validationManager, filterPanelController, transformerWorker, filterIo, style, serviceRegistrar);
    TransformerPanel transformerPanel = new TransformerPanel(transformerPanelController, transformerWorker, serviceRegistrar);
    CytoPanelComponent selectPanel = new FilterCytoPanelComponent(transformerViewManager, modelMonitor, filterPanel, transformerPanel);
    registerService(bc, selectPanel, CytoPanelComponent.class, new Properties());
    FilterSettingsManager settingsManager = new FilterSettingsManager(filterPanel, transformerPanel, filterIo);
    registerService(bc, settingsManager, SessionAboutToBeSavedListener.class, new Properties());
    registerService(bc, settingsManager, SessionAboutToBeLoadedListener.class, new Properties());
    registerService(bc, settingsManager, SessionLoadedListener.class, new Properties());
    // new TransformerPanelManager API
    {
        Properties props = new Properties();
        props.setProperty("service.type", "manager");
        props.setProperty("container.type", "filter");
        registerService(bc, filterPanel, TransformerContainer.class, props);
    }
    {
        Properties props = new Properties();
        props.setProperty("service.type", "manager");
        props.setProperty("container.type", "chain");
        registerService(bc, transformerPanel, TransformerContainer.class, props);
    }
    // commands
    {
        Properties props = new Properties();
        props.setProperty(COMMAND, "import");
        props.setProperty(COMMAND_NAMESPACE, "filter");
        props.setProperty(COMMAND_DESCRIPTION, "Import filter JSON from a file.");
        props.setProperty(COMMAND_LONG_DESCRIPTION, "Import filter JSON from a file.");
        registerService(bc, new ImportNamedTransformersTaskFactory(filterIo, filterPanel), TaskFactory.class, props);
    }
    {
        Properties props = new Properties();
        props.setProperty(COMMAND, "export");
        props.setProperty(COMMAND_NAMESPACE, "filter");
        props.setProperty(COMMAND_DESCRIPTION, "Export filter JSON to a file.");
        props.setProperty(COMMAND_LONG_DESCRIPTION, "Export filter JSON to a file.");
        registerService(bc, new ExportNamedTransformersTaskFactory(filterIo, filterPanelController), TaskFactory.class, props);
    }
}

Example 3 with TopologyFilterFactory

use of org.cytoscape.filter.internal.filters.topology.TopologyFilterFactory in project cytoscape-impl by cytoscape.

the class UiScaffold method start.

void start() {
    MockitoAnnotations.initMocks(this);
    Random random = new Random(0);
    NetworkTestSupport networkTestSupport = new NetworkTestSupport();
    CyNetwork network = networkTestSupport.getNetwork();
    CyTable nodeTable = network.getDefaultNodeTable();
    nodeTable.createColumn("Score", Double.class, false);
    nodeTable.createColumn("IsSpecial", Boolean.class, false);
    for (int i = 0; i < TOTAL_NODES; i++) {
        CyNode node = network.addNode();
        network.getRow(node).set("Score", random.nextGaussian());
        network.getRow(node).set("IsSpecial", i % 2 == 0);
    }
    List<CyNode> nodes = network.getNodeList();
    for (int i = 0; i < TOTAL_EDGES; i++) {
        CyNode source = nodes.get(random.nextInt(nodes.size()));
        CyNode target = nodes.get(random.nextInt(nodes.size()));
        network.addEdge(source, target, false);
    }
    when(applicationManager.getCurrentNetworkView()).thenReturn(networkView);
    when(applicationManager.getCurrentNetwork()).thenReturn(network);
    when(networkView.getModel()).thenReturn(network);
    when(serviceRegistrar.getService(CyApplicationManager.class)).thenReturn(applicationManager);
    when(serviceRegistrar.getService(TaskManager.class)).thenReturn(taskManager);
    when(serviceRegistrar.getService(IconManager.class)).thenReturn(iconManager);
    JFrame frame = new JFrame();
    frame.setTitle("Select");
    Map<String, String> properties = Collections.emptyMap();
    TransformerManagerImpl transformerManager = new TransformerManagerImpl();
    transformerManager.registerFilterFactory(new ColumnFilterFactory(), properties);
    transformerManager.registerFilterFactory(new DegreeFilterFactory(), properties);
    transformerManager.registerFilterFactory(new TopologyFilterFactory(), properties);
    transformerManager.registerElementTransformerFactory(new InteractionTransformerFactory(), properties);
    ModelMonitor modelMonitor = new ModelMonitor();
    modelMonitor.handleEvent(new SetCurrentNetworkEvent(applicationManager, network));
    ValidationManager validationManager = new ValidationManager();
    FilterPanelStyle style = new StandardStyle();
    TransformerViewManager transformerViewManager = new TransformerViewManager(transformerManager);
    // transformerViewManager.registerTransformerViewFactory(new ColumnFilterViewFactory(style, modelMonitor), properties);
    transformerViewManager.registerTransformerViewFactory(new DegreeFilterViewFactory(style, modelMonitor), properties);
    transformerViewManager.registerTransformerViewFactory(new TopologyFilterViewFactory(style), properties);
    transformerViewManager.registerTransformerViewFactory(new InteractionTransformerViewFactory(style), properties);
    LazyWorkQueue queue = new LazyWorkQueue();
    FilterWorker filterWorker = new FilterWorker(queue, serviceRegistrar);
    FilterIO filterIo = null;
    FilterPanelController filterPanelController = new FilterPanelController(transformerManager, transformerViewManager, validationManager, filterWorker, modelMonitor, filterIo, style, serviceRegistrar);
    FilterPanel filterPanel = new FilterPanel(filterPanelController, filterWorker, serviceRegistrar);
    TransformerWorker transformerWorker = new TransformerWorker(queue, transformerManager, serviceRegistrar);
    TransformerPanelController transformerPanelController = new TransformerPanelController(transformerManager, transformerViewManager, validationManager, filterPanelController, transformerWorker, filterIo, style, serviceRegistrar);
    TransformerPanel transformerPanel = new TransformerPanel(transformerPanelController, transformerWorker, serviceRegistrar);
    SelectPanel selectPanel = new SelectPanel(filterPanel, transformerPanel);
    JRootPane root = frame.getRootPane();
    root.setLayout(new GridBagLayout());
    root.add(selectPanel, new GridBagConstraints(0, 0, 1, 1, 1, 1, GridBagConstraints.LINE_START, GridBagConstraints.BOTH, new Insets(0, 0, 0, 0), 0, 0));
    frame.setSize(450, 500);
    frame.setLocationRelativeTo(null);
    frame.setVisible(true);
}

Example 4 with TopologyFilterFactory

use of org.cytoscape.filter.internal.filters.topology.TopologyFilterFactory in project cytoscape-impl by cytoscape.

the class FilterIOTest method testLoadOldTopologyFilter.

/**
 * The topology filter was made a composite filter in 3.3. Older versions of cytoscape
 * will export a topology filter without the "transformers" field that is part of
 * composite filters. The filter json parser was enhanced to support this.
 */
@SuppressWarnings("rawtypes")
@Test
public void testLoadOldTopologyFilter() throws IOException {
    TransformerManagerImpl transformerManager = new TransformerManagerImpl();
    Map<String, String> properties = Collections.emptyMap();
    transformerManager.registerFilterFactory(new CompositeFilterFactory<CyNetwork, CyIdentifiable>(CyNetwork.class, CyIdentifiable.class), properties);
    transformerManager.registerFilterFactory(new TopologyFilterFactory(), properties);
    transformerManager.registerFilterFactory(new ColumnFilterFactory(), properties);
    String path = "./src/test/resources/testData/filter/topology-filter-3.2.json";
    byte[] encoded = Files.readAllBytes(Paths.get(path));
    // String contents = new String(encoded);
    // System.out.println(contents);
    CyTransformerReaderImpl reader = new CyTransformerReaderImpl();
    reader.registerTransformerManager(transformerManager, null);
    ByteArrayInputStream inputStream = new ByteArrayInputStream(encoded);
    NamedTransformer<?, ?>[] transformers = reader.read(inputStream);
    Assert.assertNotNull(transformers);
    Assert.assertEquals(1, transformers.length);
    NamedTransformer<?, ?> namedTransformer = transformers[0];
    Assert.assertNotNull(namedTransformer);
    Assert.assertEquals("Default filter", namedTransformer.getName());
    List children = namedTransformer.getTransformers();
    Assert.assertEquals(1, children.size());
    Transformer child = (Transformer) children.get(0);
    Assert.assertNotNull(child);
    Assert.assertTrue(child instanceof CompositeFilter);
    CompositeFilter composite = (CompositeFilter) child;
    Assert.assertEquals(2, composite.getLength());
    Assert.assertTrue(composite.get(0) instanceof TopologyFilter);
    Assert.assertTrue(composite.get(1) instanceof ColumnFilter);
    TopologyFilter topology = (TopologyFilter) composite.get(0);
    Assert.assertEquals(0, topology.getLength());
    Assert.assertEquals(Integer.valueOf(4), topology.getDistance());
    Assert.assertEquals(Integer.valueOf(5), topology.getThreshold());
    ColumnFilter column = (ColumnFilter) composite.get(1);
    Assert.assertEquals("name", column.getColumnName());
}