Examples with CySubNetwork org.cytoscape.model.subnetwork.CySubNetwork used on opensource projects

Example 41 with CySubNetwork

use of org.cytoscape.model.subnetwork.CySubNetwork in project cytoscape-impl by cytoscape.

the class GenericXGMMLReaderTest method check2xGroupMetadata.

private void check2xGroupMetadata(final CyNetwork net, final CyNode gn, final boolean expanded) {
    assertNotNull("The group node is null", gn);
    // Test 2.x group parsed as network pointer
    if (!expanded) {
        for (CyNode n : net.getNodeList()) {
            if (net.getRow(n, CyNetwork.HIDDEN_ATTRS).isSet(GroupUtil.GROUP_STATE_ATTRIBUTE))
                assertNotNull(n.getNetworkPointer());
            else
                // The other nodes have no network pointer!
                assertNull(n.getNetworkPointer());
        }
    } else {
        CyRootNetwork rootNet = ((CySubNetwork) net).getRootNetwork();
        for (CyNode n : rootNet.getNodeList()) {
            if (rootNet.getRow(n, CyNetwork.HIDDEN_ATTRS).isSet(GroupUtil.GROUP_STATE_ATTRIBUTE))
                assertNotNull(n.getNetworkPointer());
            else
                // The other nodes have no network pointer!
                assertNull(n.getNetworkPointer());
        }
    }
    CyNetwork np = gn.getNetworkPointer();
    assertNotNull(np);
    assertEquals(2, np.getNodeCount());
    assertEquals(1, np.getEdgeCount());
    // Check if the nested graph's attribute was imported to the network pointer
    CyRow npRow = np.getRow(np);
    assertEquals("Lorem Ipsum", npRow.get("gr_att_1", String.class));
    // Check external edges metadata (must be added by the reader!)
    CyRow nphRow = np.getRow(np, HIDDEN_ATTRS);
    List<Long> extEdgeIds = nphRow.getList(GroupUtil.EXTERNAL_EDGE_ATTRIBUTE, Long.class);
    assertEquals(1, extEdgeIds.size());
    CyRootNetwork rootNet = rootNetManager.getRootNetwork(np);
    assertNotNull(rootNet.getEdge(extEdgeIds.get(0)));
}

Example 42 with CySubNetwork

use of org.cytoscape.model.subnetwork.CySubNetwork in project cytoscape-impl by cytoscape.

the class CyNetworkManagerImpl method destroyNetwork.

@Override
public void destroyNetwork(final CyNetwork network) {
    if (network == null)
        throw new NullPointerException("Network is null");
    final Long networkId = network.getSUID();
    synchronized (lock) {
        if (!networkMap.containsKey(networkId))
            throw new IllegalArgumentException("network is not recognized by this NetworkManager");
    }
    final CyEventHelper cyEventHelper = serviceRegistrar.getService(CyEventHelper.class);
    // let everyone know!
    cyEventHelper.fireEvent(new NetworkAboutToBeDestroyedEvent(CyNetworkManagerImpl.this, network));
    synchronized (lock) {
        // check again within the lock in case something has changed
        if (!networkMap.containsKey(networkId))
            throw new IllegalArgumentException("network is not recognized by this NetworkManager");
        for (CyNode n : network.getNodeList()) network.getRow(n).set(CyNetwork.SELECTED, false);
        for (CyEdge e : network.getEdgeList()) network.getRow(e).set(CyNetwork.SELECTED, false);
        networkMap.remove(networkId);
    }
    if (network instanceof CySubNetwork) {
        final CySubNetwork subNetwork = (CySubNetwork) network;
        final CyRootNetwork rootNetwork = subNetwork.getRootNetwork();
        final CySubNetwork baseNetwork = rootNetwork.getBaseNetwork();
        if (!subNetwork.equals(baseNetwork) || rootNetwork.getSubNetworkList().size() > 1) {
            rootNetwork.removeSubNetwork(subNetwork);
            network.dispose();
        }
        if (!hasRegisteredNetworks(rootNetwork))
            rootNetwork.dispose();
    } else {
        network.dispose();
    }
    // let everyone know that some network is gone
    cyEventHelper.fireEvent(new NetworkDestroyedEvent(CyNetworkManagerImpl.this));
}

Example 43 with CySubNetwork

use of org.cytoscape.model.subnetwork.CySubNetwork in project cytoscape-impl by cytoscape.

the class CyNetworkAutoDeleteTest method testRestoreBug3838_2.

@Test
public void testRestoreBug3838_2() {
    CyNetwork network1 = TestCyNetworkFactory.getInstance();
    CyRootNetwork rootNetwork = ((CySubNetwork) network1).getRootNetwork();
    CyNode n1 = network1.addNode();
    CyNode n2 = network1.addNode();
    CyEdge e1 = network1.addEdge(n1, n2, false);
    network1.removeNodes(Arrays.asList(n1, n2));
    assertFalse(rootNetwork.containsNode(n1));
    assertFalse(rootNetwork.containsNode(n2));
    assertFalse(rootNetwork.containsEdge(e1));
    assertFalse(network1.containsNode(n1));
    assertFalse(network1.containsNode(n2));
    assertFalse(network1.containsEdge(e1));
    rootNetwork.restoreEdge(e1);
    assertTrue(rootNetwork.containsNode(n1));
    assertTrue(rootNetwork.containsNode(n2));
    assertTrue(rootNetwork.containsEdge(e1));
    assertFalse(network1.containsNode(n1));
    assertFalse(network1.containsNode(n2));
    assertFalse(network1.containsEdge(e1));
    network1.removeNodes(Arrays.asList(n1, n2));
    assertTrue(rootNetwork.containsNode(n1));
    assertTrue(rootNetwork.containsNode(n2));
    assertTrue(rootNetwork.containsEdge(e1));
    assertFalse(network1.containsNode(n1));
    assertFalse(network1.containsNode(n2));
    assertFalse(network1.containsEdge(e1));
    rootNetwork.restoreEdge(e1);
    assertTrue(rootNetwork.containsNode(n1));
    assertTrue(rootNetwork.containsNode(n2));
    assertTrue(rootNetwork.containsEdge(e1));
    assertFalse(network1.containsNode(n1));
    assertFalse(network1.containsNode(n2));
    assertFalse(network1.containsEdge(e1));
}

Example 44 with CySubNetwork

use of org.cytoscape.model.subnetwork.CySubNetwork in project cytoscape-impl by cytoscape.

the class CyNetworkAutoDeleteTest method testAutoDeleteFromRootNetwork.

@Test
public void testAutoDeleteFromRootNetwork() {
    CyNetwork network1 = TestCyNetworkFactory.getInstance();
    CyRootNetwork rootNetwork = ((CySubNetwork) network1).getRootNetwork();
    CyNode n1 = network1.addNode();
    CyNode n2 = network1.addNode();
    CyNode n3 = network1.addNode();
    CyEdge e1 = network1.addEdge(n1, n2, false);
    CyEdge e2 = network1.addEdge(n2, n3, false);
    CyNetwork network2 = rootNetwork.addSubNetwork(Arrays.asList(n1, n2, n3), Arrays.asList(e1, e2));
    // Things should work as expected when removing a node from a single subnetwork
    network1.removeNodes(Collections.singleton(n1));
    assertTrue(rootNetwork.containsNode(n1));
    assertFalse(network1.containsNode(n1));
    assertTrue(network2.containsNode(n1));
    // should also automatically remove the edge that's connected to n1, but only from network1
    assertTrue(rootNetwork.containsEdge(e1));
    assertFalse(network1.containsEdge(e1));
    assertTrue(network2.containsEdge(e1));
    assertNotNull(rootNetwork.getNode(n1.getSUID()));
    assertNull(network1.getNode(n1.getSUID()));
    rowExists(true, rootNetwork, n1);
    rowExists(false, network1, n1);
    rowExists(true, network2, n1);
    rowExists(true, rootNetwork, e1);
    rowExists(false, network1, e1);
    rowExists(true, network2, e1);
    // Now remove n1 and e1 from the other subnetwork, that should auto-delete from the root network
    network2.removeNodes(Collections.singleton(n1));
    assertFalse(rootNetwork.containsNode(n1));
    assertFalse(network1.containsNode(n1));
    assertFalse(network2.containsNode(n1));
    assertFalse(rootNetwork.containsEdge(e1));
    assertFalse(network1.containsEdge(e1));
    assertFalse(network2.containsEdge(e1));
    assertNull(rootNetwork.getNode(n1.getSUID()));
    assertNull(network1.getNode(n1.getSUID()));
    rowExists(false, rootNetwork, n1);
    rowExists(false, network1, n1);
    rowExists(false, network2, n1);
    rowExists(false, rootNetwork, e1);
    rowExists(false, network1, e1);
    rowExists(false, network2, e1);
}

Example 45 with CySubNetwork

use of org.cytoscape.model.subnetwork.CySubNetwork in project cytoscape-impl by cytoscape.

the class CyNetworkAutoDeleteTest method testRestoreEdgeRestoresSourceAndTarget.

@Test
public void testRestoreEdgeRestoresSourceAndTarget() {
    // Better version of above test
    CyNetwork network1 = TestCyNetworkFactory.getInstance();
    CyRootNetwork rootNetwork = ((CySubNetwork) network1).getRootNetwork();
    CyNode n1 = network1.addNode();
    CyNode n2 = network1.addNode();
    CyNode n3 = network1.addNode();
    CyEdge e1 = network1.addEdge(n1, n2, false);
    CyEdge e2 = network1.addEdge(n2, n3, false);
    CyNetwork network2 = rootNetwork.addSubNetwork(Arrays.asList(n1, n2, n3), Arrays.asList(e1, e2));
    network1.removeNodes(Arrays.asList(n1, n2));
    network2.removeNodes(Arrays.asList(n1, n2));
    assertFalse(rootNetwork.containsNode(n1));
    assertFalse(rootNetwork.containsNode(n2));
    assertFalse(rootNetwork.containsEdge(e1));
    assertFalse(network1.containsNode(n1));
    assertFalse(network2.containsNode(n1));
    assertFalse(network1.containsNode(n2));
    assertFalse(network2.containsNode(n2));
    assertFalse(network1.containsEdge(e1));
    assertFalse(network2.containsEdge(e1));
    rootNetwork.restoreEdge(e1);
    assertTrue(rootNetwork.containsNode(n1));
    assertTrue(rootNetwork.containsNode(n2));
    assertTrue(rootNetwork.containsEdge(e1));
    assertFalse(network1.containsNode(n1));
    assertFalse(network2.containsNode(n1));
    assertFalse(network1.containsNode(n2));
    assertFalse(network2.containsNode(n2));
    assertFalse(network1.containsEdge(e1));
    assertFalse(network2.containsEdge(e1));
}