Examples with CyApplicationManager org.cytoscape.application.CyApplicationManager used on opensource projects

Example 26 with CyApplicationManager

use of org.cytoscape.application.CyApplicationManager in project cytoscape-impl by cytoscape.

the class SelectModeAction method menuSelected.

@Override
public void menuSelected(MenuEvent e) {
    final JCheckBoxMenuItem item = getThisItem();
    if (item != null) {
        final CyApplicationManager applicationManager = serviceRegistrar.getService(CyApplicationManager.class);
        final CyNetworkView view = applicationManager.getCurrentNetworkView();
        if (view == null)
            item.setSelected(false);
        else if (view.getVisualProperty(NETWORK_NODE_SELECTION) && view.getVisualProperty(NETWORK_EDGE_SELECTION))
            item.setSelected(name.equalsIgnoreCase(ALL));
        else if (view.getVisualProperty(NETWORK_NODE_SELECTION))
            item.setSelected(name.equalsIgnoreCase(NODES));
        else if (view.getVisualProperty(NETWORK_EDGE_SELECTION))
            item.setSelected(name.equalsIgnoreCase(EDGES));
        else
            item.setSelected(false);
    }
    updateEnableState();
}

Example 27 with CyApplicationManager

use of org.cytoscape.application.CyApplicationManager in project cytoscape-impl by cytoscape.

the class TransformerWorker method doWork.

@Override
public void doWork(ProgressMonitor monitor) {
    if (controller == null) {
        return;
    }
    final CyApplicationManager applicationManager = serviceRegistrar.getService(CyApplicationManager.class);
    CyNetworkView networkView = applicationManager.getCurrentNetworkView();
    CyNetwork network;
    if (networkView != null) {
        network = networkView.getModel();
    } else {
        network = applicationManager.getCurrentNetwork();
    }
    if (network == null) {
        return;
    }
    ProgressMonitor filterMonitor = new SubProgressMonitor(monitor, 0.0, 0.4);
    ProgressMonitor chainMonitor = new SubProgressMonitor(monitor, 0.4, 0.98);
    monitor.setProgress(0.0);
    monitor.setStatusMessage(null);
    Sink sink = new Sink(network);
    long startTime = System.currentTimeMillis();
    try {
        List<Transformer<CyNetwork, CyIdentifiable>> transformers = controller.getTransformers(view);
        FilterElement selected = (FilterElement) controller.getStartWithComboBoxModel().getSelectedItem();
        TransformerSource<CyNetwork, CyIdentifiable> source = createSource(network, selected, filterMonitor);
        for (Transformer<?, ?> transformer : transformers) {
            if (transformer instanceof MemoizableTransformer) {
                ((MemoizableTransformer) transformer).startCaching();
            }
        }
        try {
            transformerManager.execute(network, source, transformers, sink, chainMonitor);
        } finally {
            for (Transformer<?, ?> transformer : transformers) {
                if (transformer instanceof MemoizableTransformer) {
                    ((MemoizableTransformer) transformer).clearCache();
                }
            }
        }
        if (networkView != null) {
            networkView.updateView();
        }
    } finally {
        long duration = System.currentTimeMillis() - startTime;
        monitor.setProgress(1.0);
        monitor.setStatusMessage(String.format("Selected %d %s and %d %s in %dms", sink.nodeCount, sink.nodeCount == 1 ? "node" : "nodes", sink.edgeCount, sink.edgeCount == 1 ? "edge" : "edges", duration));
    }
}

Example 28 with CyApplicationManager

use of org.cytoscape.application.CyApplicationManager in project cytoscape-impl by cytoscape.

the class FilterWorker method doWork.

@Override
public void doWork(ProgressMonitor monitor) {
    if (controller == null) {
        return;
    }
    final CyApplicationManager applicationManager = serviceRegistrar.getService(CyApplicationManager.class);
    CyNetworkView networkView = applicationManager.getCurrentNetworkView();
    CyNetwork network;
    if (networkView != null) {
        network = networkView.getModel();
    } else {
        network = applicationManager.getCurrentNetwork();
    }
    if (network == null) {
        return;
    }
    monitor.setProgress(0);
    monitor.setStatusMessage(null);
    int nodeCount = 0;
    int edgeCount = 0;
    int counter = 0;
    long startTime = System.currentTimeMillis();
    try {
        Filter<CyNetwork, CyIdentifiable> filter = controller.getFilter();
        if (filter instanceof CompositeFilter) {
            // If we have an empty CompositeFilter, bail out.
            CompositeFilter<CyNetwork, CyIdentifiable> composite = (CompositeFilter<CyNetwork, CyIdentifiable>) filter;
            if (composite.getLength() == 0) {
                return;
            }
        }
        if (filter instanceof MemoizableTransformer) {
            ((MemoizableTransformer) filter).startCaching();
        }
        try {
            List<CyNode> nodeList = network.getNodeList();
            List<CyEdge> edgeList = network.getEdgeList();
            double total = nodeList.size() + edgeList.size();
            List<CyIdentifiable> selected = new ArrayList<>();
            List<CyIdentifiable> unselected = new ArrayList<>();
            for (CyNode node : nodeList) {
                if (monitor.isCancelled()) {
                    return;
                }
                boolean accepted = filter.accepts(network, node);
                if (accepted) {
                    selected.add(node);
                    nodeCount++;
                } else {
                    unselected.add(node);
                }
                monitor.setProgress(++counter / total);
            }
            for (CyEdge edge : edgeList) {
                if (monitor.isCancelled()) {
                    return;
                }
                boolean accepted = filter.accepts(network, edge);
                if (accepted) {
                    selected.add(edge);
                    edgeCount++;
                } else {
                    unselected.add(edge);
                }
                monitor.setProgress(++counter / total);
            }
            // now do the selection
            for (CyIdentifiable element : unselected) {
                CyRow row = network.getRow(element);
                if (row.get(CyNetwork.SELECTED, Boolean.class)) {
                    row.set(CyNetwork.SELECTED, Boolean.FALSE);
                }
            }
            for (CyIdentifiable element : selected) {
                CyRow row = network.getRow(element);
                if (!row.get(CyNetwork.SELECTED, Boolean.class)) {
                    row.set(CyNetwork.SELECTED, Boolean.TRUE);
                }
            }
        } finally {
            if (filter instanceof MemoizableTransformer) {
                ((MemoizableTransformer) filter).clearCache();
            }
        }
        if (networkView != null) {
            networkView.updateView();
        }
    } finally {
        long duration = System.currentTimeMillis() - startTime;
        monitor.setProgress(1.0);
        monitor.setStatusMessage(String.format("Selected %d %s and %d %s in %dms", nodeCount, nodeCount == 1 ? "node" : "nodes", edgeCount, edgeCount == 1 ? "edge" : "edges", duration));
    }
}

Example 29 with CyApplicationManager

use of org.cytoscape.application.CyApplicationManager in project cytoscape-impl by cytoscape.

the class VisualStyleTest method setUp.

@Before
@SuppressWarnings("unchecked")
public void setUp() throws Exception {
    NetworkViewTestSupport nvts = new NetworkViewTestSupport();
    network = nvts.getNetworkFactory().createNetwork();
    node1 = network.addNode();
    node2 = network.addNode();
    node3 = network.addNode();
    edge = network.addEdge(node1, node2, true);
    CyTable nodeTable = network.getDefaultNodeTable();
    nodeTable.createColumn(attrName, String.class, true);
    nodeTable.getRow(node1.getSUID()).set(attrName, "red");
    nodeTable.getRow(node2.getSUID()).set(attrName, "green");
    nodeTable.getRow(node3.getSUID()).set(attrName, "foo");
    networkView = nvts.getNetworkViewFactory().createNetworkView(network);
    // Create root node.
    final NullVisualProperty minimalRoot = new NullVisualProperty("MINIMAL_ROOT", "Minimal Root Visual Property");
    final BasicVisualLexicon minimalLex = new BasicVisualLexicon(minimalRoot);
    final Set<VisualLexicon> lexSet = new HashSet<VisualLexicon>();
    lexSet.add(minimalLex);
    final VisualMappingFunctionFactory ptFactory = mock(VisualMappingFunctionFactory.class);
    eventHelper = mock(CyEventHelper.class);
    final RenderingEngineFactory<CyNetwork> reFatory = mock(RenderingEngineFactory.class);
    when(reFatory.getVisualLexicon()).thenReturn(minimalLex);
    final NetworkViewRenderer nvRenderer = mock(NetworkViewRenderer.class);
    when(nvRenderer.getRenderingEngineFactory(NetworkViewRenderer.DEFAULT_CONTEXT)).thenReturn(reFatory);
    final CyApplicationManager appManager = mock(CyApplicationManager.class);
    when(appManager.getCurrentNetworkViewRenderer()).thenReturn(nvRenderer);
    final CyServiceRegistrar serviceRegistrar = mock(CyServiceRegistrar.class);
    when(serviceRegistrar.getService(CyEventHelper.class)).thenReturn(eventHelper);
    when(serviceRegistrar.getService(CyApplicationManager.class)).thenReturn(appManager);
    VisualProperty<NullDataType> rootVisualProperty = mock(VisualProperty.class);
    BasicVisualLexicon lexicon = new BasicVisualLexicon(rootVisualProperty);
    vpSet = new HashSet<VisualProperty<Paint>>();
    vpSet.add(BasicVisualLexicon.NODE_BORDER_PAINT);
    vpSet.add(BasicVisualLexicon.NODE_FILL_COLOR);
    dependency = new VisualPropertyDependency<Paint>("dep1", "Dep 1", vpSet, lexicon);
    final VisualStyleFactoryImpl visualStyleFactory = new VisualStyleFactoryImpl(serviceRegistrar, ptFactory);
    originalTitle = "Style 1";
    newTitle = "Style 2";
    style = visualStyleFactory.createVisualStyle(originalTitle);
    style.setDefaultValue(NODE_SIZE, DEF_NODE_SIZE);
    style.setDefaultValue(NODE_FILL_COLOR, DEF_NODE_COLOR);
    reset(eventHelper);
}

Example 30 with CyApplicationManager

use of org.cytoscape.application.CyApplicationManager in project cytoscape-impl by cytoscape.

the class AbstractApplyHandler method apply.

@Override
public void apply(final CyRow row, final View<T> view) {
    if (updateDependencyMaps)
        updateDependencyMaps();
    // Clear visual properties first
    view.clearVisualProperties();
    // Get current Visual Lexicon
    final CyApplicationManager appMgr = serviceRegistrar.getService(CyApplicationManager.class);
    final VisualLexicon lexicon = appMgr.getCurrentNetworkViewRenderer().getRenderingEngineFactory(NetworkViewRenderer.DEFAULT_CONTEXT).getVisualLexicon();
    final LinkedList<VisualLexiconNode> descendants = new LinkedList<VisualLexiconNode>();
    descendants.addAll(lexicon.getVisualLexiconNode(rootVisualProperty).getChildren());
    while (!descendants.isEmpty()) {
        final VisualLexiconNode node = descendants.pop();
        final VisualProperty<?> vp = node.getVisualProperty();
        if (vp.getTargetDataType() != targetDataType)
            // Because NETWORK has node/edge properties as descendants as well
            continue;
        final VisualMappingFunction<?, ?> mapping = style.getVisualMappingFunction(vp);
        final Object value = mapping != null ? mapping.getMappedValue(row) : null;
        if (value == null) {
            // Apply the default value...
            applyDefaultValue(view, vp, lexicon);
        } else {
            // Apply the mapped value...
            applyMappedValue(view, vp, value);
        }
        descendants.addAll(node.getChildren());
    }
}