コード例 #1
0
  @Before
  public void setUp() throws Exception {
    NetworkTestSupport netSupport = new NetworkTestSupport();
    TableTestSupport tableSupport = new TableTestSupport();

    CyNetworkFactory cyNetworkFactory = netSupport.getNetworkFactory();

    tableFactory = tableSupport.getTableFactory();
    tableManager = mock(CyTableManager.class);
    dag = cyNetworkFactory.createNetwork();
    tm = mock(TaskMonitor.class);

    serviceRegistrar = mock(CyServiceRegistrar.class);
    when(serviceRegistrar.getService(CyTableFactory.class)).thenReturn(tableFactory);
    when(serviceRegistrar.getService(CyTableManager.class)).thenReturn(tableManager);
  }
コード例 #2
0
  @Override
  public void run(TaskMonitor taskMonitor) throws Exception {
    parentTaskMonitor = taskMonitor;
    long start = System.currentTimeMillis();

    taskMonitor.setProgress(0.01d);
    taskMonitor.setTitle("Loading PSI-MI 2.5.x XML File ");
    taskMonitor.setStatusMessage("Loading data file in PSI-MI 2.5 XML format.");

    // support to add network into existing collection
    this.initNodeMap();

    PsimiXmlReader reader = new PsimiXmlReader();
    EntrySet result = reader.read(inputStream);
    taskMonitor.setProgress(0.4d);
    taskMonitor.setStatusMessage("Data Loaded.  Mapping Data to Network...");

    if (cancelFlag) {
      inputStream.close();
      reader = null;
      result = null;
      return;
    }

    // network = cyNetworkFactory.createNetwork();
    String networkCollectionName = this.rootNetworkList.getSelectedValue().toString();
    if (networkCollectionName.equalsIgnoreCase(CRERATE_NEW_COLLECTION_STRING)) {
      // This is a new network collection, create a root network and a subnetwork, which is a base
      // subnetwork
      network = cyNetworkFactory.createNetwork();
    } else {
      // Add a new subNetwork to the given collection
      network = this.name2RootMap.get(networkCollectionName).addSubNetwork();
    }

    mapper = new PSIMI25EntryMapper(network, result);
    mapper.map();

    taskMonitor.setProgress(1.0d);
    logger.info(
        "PSI-MI XML Data Import finihsed in " + (System.currentTimeMillis() - start) + " msec.");
  }