Examples with CyNetwork org.cytoscape.model.CyNetwork used on opensource projects

Example 41 with CyNetwork

use of org.cytoscape.model.CyNetwork in project cytoscape-api by cytoscape.

the class AbstractParallelPartitionLayoutTask method doLayout.

/**
	 * AbstractGraphPartitionLayout implements the doLayout method
	 * of AbstractBasicLayout in which it calls the layoutParition
	 * method on each LayoutPartition object created for the network.
	 * @param taskMonitor the TaskMonitor provided by the run() method
	 * of the Task.
	 */
@Override
public void doLayout(final TaskMonitor taskMonitor) {
    final CyNetwork network = networkView.getModel();
    if (edgeWeighter != null)
        edgeWeighter.reset();
    this.taskMonitor = taskMonitor;
    boolean useAllNodes = nodesToLayOut.size() == networkView.getNodeViews().size();
    // to lay out selected nodes, partitioning becomes a very bad idea!
    if (singlePartition || !useAllNodes) {
        // We still use the partition abstraction, even if we're
        // not partitioning.  This makes the code further down
        // much cleaner
        LayoutPartition partition = new LayoutPartition(networkView, nodesToLayOut, edgeWeighter);
        partitionList = new ArrayList<LayoutPartition>(1);
        partitionList.add(partition);
    } else {
        partitionList = PartitionUtil.partition(networkView, false, edgeWeighter);
    }
    total_nodes = network.getNodeCount();
    current_start = 0;
    // Set up offsets -- we start with the overall min and max
    double xStart = (partitionList.get(0)).getMinX();
    double yStart = (partitionList.get(0)).getMinY();
    for (LayoutPartition part : partitionList) {
        xStart = Math.min(xStart, part.getMinX());
        yStart = Math.min(yStart, part.getMinY());
    }
    double next_x_start = xStart;
    double next_y_start = yStart;
    double current_max_y = 0;
    double max_dimensions = Math.sqrt((double) network.getNodeCount());
    // give each node room
    max_dimensions *= incr;
    max_dimensions += xStart;
    // Overthread to account for inefficiencies.
    final int numThreads = Runtime.getRuntime().availableProcessors() * 4;
    // the layoutPartition method on each partition.
    class ParallelLayoutTask implements Runnable {

        private final int partitionID;

        public ParallelLayoutTask(int partitionID) {
            this.partitionID = partitionID;
        }

        @Override
        public void run() {
            if (cancelled)
                return;
            LayoutPartition partition = partitionList.get(partitionID);
            // Partitions Requiring Layout
            if (partition.nodeCount() > 1) {
                try {
                    layoutPartition(partition);
                } catch (Throwable _e) {
                    _e.printStackTrace();
                    return;
                }
            } else {
                // Reset our bounds
                partition.resetNodes();
            }
            synchronized (partitionList) {
                current_start += (double) partition.size();
                taskMonitor.setProgress(current_start / total_nodes);
            }
        }
    }
    // Create thread pool, ...
    ExecutorService threadPool = Executors.newFixedThreadPool(numThreads);
    // ... spawn futures, ...
    List<Future<?>> futures = new LinkedList<Future<?>>();
    for (int i = 0; i < partitionList.size(); i++) futures.add(threadPool.submit(new ParallelLayoutTask(i)));
    // ... and wait for them to execute.
    for (Future<?> future : futures) try {
        future.get();
    } catch (Exception e) {
    }
    // Now move the partitions into a reasonably compact grid.
    for (LayoutPartition partition : partitionList) {
        if (cancelled)
            break;
        // get the partition
        current_size = (double) partition.size();
        // Partitions Requiring Layout
        if (partition.nodeCount() > 1) {
            // OFFSET
            if (useAllNodes && !singlePartition)
                partition.offset(next_x_start, next_y_start);
        } else // single nodes
        {
            // Single node -- get it
            LayoutNode node = (LayoutNode) partition.getNodeList().get(0);
            node.setLocation(next_x_start, next_y_start);
            partition.moveNodeToLocation(node);
        }
        double last_max_x = partition.getMaxX();
        double last_max_y = partition.getMaxY();
        if (last_max_y > current_max_y)
            current_max_y = last_max_y;
        if (last_max_x > max_dimensions) {
            next_x_start = xStart;
            next_y_start = current_max_y;
            next_y_start += incr;
        } else {
            next_x_start = last_max_x;
            next_x_start += incr;
        }
    }
}

Example 42 with CyNetwork

use of org.cytoscape.model.CyNetwork in project cytoscape-api by cytoscape.

the class AbstractCyNetworkReader method init.

private void init() {
    name2RootMap = getRootNetworkMap();
    nodeMap = new HashMap<>(10000);
    // initialize the network Collection
    final List<String> rootNames = new ArrayList<>();
    rootNames.addAll(name2RootMap.keySet());
    if (!rootNames.isEmpty()) {
        sort(rootNames);
        rootNames.add(0, CREATE_NEW_COLLECTION_STRING);
    }
    final ListSingleSelection<String> rootNetList = new ListSingleSelection<>(rootNames);
    final CyNetwork net = cyApplicationManager != null ? cyApplicationManager.getCurrentNetwork() : null;
    final CyRootNetwork rootNet = net != null ? cyRootNetworkManager.getRootNetwork(net) : null;
    final String name = rootNet != null ? rootNet.getRow(rootNet).get(CyRootNetwork.NAME, String.class) : CREATE_NEW_COLLECTION_STRING;
    if (rootNames.contains(name))
        rootNetList.setSelectedValue(name);
    else if (rootNames.contains(CREATE_NEW_COLLECTION_STRING))
        rootNetList.setSelectedValue(CREATE_NEW_COLLECTION_STRING);
    setRootNetworkList(rootNetList);
    // initialize renderer list
    final List<NetworkViewRenderer> renderers = new ArrayList<>();
    NetworkViewRenderer defViewRenderer = null;
    if (cyApplicationManager != null) {
        final Set<NetworkViewRenderer> rendererSet = cyApplicationManager.getNetworkViewRendererSet();
        // so the combo-box does not appear to the user, since there is nothing to select anyway.
        if (rendererSet.size() > 1) {
            renderers.addAll(rendererSet);
            Collections.sort(renderers, new Comparator<NetworkViewRenderer>() {

                @Override
                public int compare(NetworkViewRenderer r1, NetworkViewRenderer r2) {
                    return r1.toString().compareToIgnoreCase(r2.toString());
                }
            });
        }
        defViewRenderer = cyApplicationManager.getDefaultNetworkViewRenderer();
    }
    rendererList = new ListSingleSelection<>(renderers);
    if (defViewRenderer != null && renderers.contains(defViewRenderer))
        rendererList.setSelectedValue(defViewRenderer);
}

Example 43 with CyNetwork

use of org.cytoscape.model.CyNetwork in project cytoscape-api by cytoscape.

the class SetCurrentNetworkEventTest method testGoodGetNetwork.

@Test
public void testGoodGetNetwork() {
    CyApplicationManager source = mock(CyApplicationManager.class);
    CyNetwork n = mock(CyNetwork.class);
    SetCurrentNetworkEvent e = new SetCurrentNetworkEvent(source, n);
    assertNotNull(e.getNetwork());
    assertEquals(n, e.getNetwork());
}

Example 44 with CyNetwork

use of org.cytoscape.model.CyNetwork in project cytoscape-api by cytoscape.

the class NetworkAboutToBeDestroyedEventTest method testGetNetwork.

@Test
public final void testGetNetwork() {
    final CyNetworkManager networkManager = mock(CyNetworkManager.class);
    final CyNetwork network = mock(CyNetwork.class);
    final NetworkAboutToBeDestroyedEvent event = new NetworkAboutToBeDestroyedEvent(networkManager, network);
    assertEquals("Network returned by getNetwork() is *not* the one passed into the constructor!", network, event.getNetwork());
}

Example 45 with CyNetwork

use of org.cytoscape.model.CyNetwork in project cytoscape-api by cytoscape.

the class CySessionTest method testSetObjectMap.

@Test
public void testSetObjectMap() {
    Map<Object, CyNetwork> netMap = new HashMap<Object, CyNetwork>();
    CyNetwork net1 = mock(CyNetwork.class);
    netMap.put("A", net1);
    CyNetwork net2 = mock(CyNetwork.class);
    netMap.put("B", net2);
    Map<Object, CyNetworkView> viewMap = new HashMap<Object, CyNetworkView>();
    CyNetworkView view1 = mock(CyNetworkView.class);
    viewMap.put("A", view1);
    Map<Object, CyNode> nodeMap = new HashMap<Object, CyNode>();
    CyNode n1 = mock(CyNode.class);
    nodeMap.put(new Long(1), n1);
    CyNode n2 = mock(CyNode.class);
    nodeMap.put(new Long(2), n2);
    Map<Object, CyEdge> edgeMap = new HashMap<Object, CyEdge>();
    CyEdge e1 = mock(CyEdge.class);
    edgeMap.put(new Long(3), e1);
    Map<Class<? extends CyIdentifiable>, Map<Object, ? extends CyIdentifiable>> objMap = new HashMap<Class<? extends CyIdentifiable>, Map<Object, ? extends CyIdentifiable>>();
    objMap.put(CyNetwork.class, netMap);
    objMap.put(CyNetworkView.class, viewMap);
    objMap.put(CyNode.class, nodeMap);
    objMap.put(CyEdge.class, edgeMap);
    session = new CySession.Builder().objectMap(objMap).build();
    assertNotNull(session);
    assertSame(net1, session.getObject("A", CyNetwork.class));
    assertSame(net2, session.getObject("B", CyNetwork.class));
    assertSame(view1, session.getObject("A", CyNetworkView.class));
    assertSame(n1, session.getObject(new Long(1), CyNode.class));
    assertSame(n2, session.getObject(new Long(2), CyNode.class));
    assertSame(e1, session.getObject(new Long(3), CyEdge.class));
    assertNull(session.getObject("A", View.class));
    assertNull(session.getObject("B", CyNetworkView.class));
}