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

Example 86 with CyNetwork

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

the class LoadNetworkReaderTask method loadNetwork.

private void loadNetwork(final TaskMonitor tm) throws IOException {
    CyNetwork network;
    if (this.rootNetwork == null) {
        network = serviceRegistrar.getService(CyNetworkFactory.class).createNetwork();
        rootNetwork = serviceRegistrar.getService(CyRootNetworkManager.class).getRootNetwork(network);
    } else {
        // CytoscapeServices.cyNetworkFactory.createNetwork();
        network = this.rootNetwork.addSubNetwork();
    }
    tm.setProgress(0.10);
    this.reader.setNetwork(network);
    if (this.cancelled)
        return;
    this.reader.read();
    tm.setProgress(0.80);
    if (this.cancelled)
        return;
    networks = new CyNetwork[] { network };
    tm.setProgress(1.0);
}

Example 87 with CyNetwork

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

the class OBOReaderTest method testOBOReader1.

@Test
public void testOBOReader1() throws Exception {
    File file = new File("./src/test/resources/" + ySlim);
    CyNetwork dag = testFile(file);
    assertEquals(91, dag.getNodeCount());
    assertEquals(dag.getEdgeCount(), 134);
}

Example 88 with CyNetwork

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

the class OBOReaderTest method testOBOReader2.

@Test
public void testOBOReader2() throws Exception {
    File file = new File("./src/test/resources/" + genericSlim);
    CyNetwork dag = testFile(file);
    assertEquals(106, dag.getNodeCount());
    assertEquals(dag.getEdgeCount(), 153);
}

Example 89 with CyNetwork

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

the class CyApplicationManagerImpl method internalSetSelectedNetworks.

private void internalSetSelectedNetworks(List<CyNetwork> networks, List<CyEvent<?>> eventsToFire) {
    Set<CyNetwork> selectedNetworks = networks != null ? new LinkedHashSet<>(networks) : new LinkedHashSet<CyNetwork>();
    selectedNetworks = selectNetworks(selectedNetworks);
    eventsToFire.add(new SetSelectedNetworksEvent(this, new ArrayList<>(selectedNetworks)));
}

Example 90 with CyNetwork

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

the class CyApplicationManagerImpl method handleEvent.

@Override
public void handleEvent(final NetworkAboutToBeDestroyedEvent event) {
    final CyNetwork toBeDestroyed = event.getNetwork();
    final List<CyEvent<?>> eventsToFire = new ArrayList<>();
    synchronized (lock) {
        logger.debug("NetworkAboutToBeDestroyedEvent: " + toBeDestroyed + ". Current: " + currentNetwork);
        if (toBeDestroyed.equals(currentNetwork)) {
            internalSetCurrentNetwork(null, eventsToFire);
        }
    }
    fireEvents(eventsToFire);
}