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

Example 11 with CyNetworkTableManager

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

the class Cy3SessionReaderImplTest method setUp.

@Before
public void setUp() {
    InputStream is = mock(InputStream.class);
    GroupUtil groupUtil = mock(GroupUtil.class);
    SUIDUpdater suidUpdater = mock(SUIDUpdater.class);
    CyNetworkReaderManager netReaderMgr = mock(CyNetworkReaderManager.class);
    CyPropertyReaderManager propReaderMgr = mock(CyPropertyReaderManager.class);
    VizmapReaderManager vizmapReaderMgr = mock(VizmapReaderManager.class);
    CSVCyReaderFactory csvCyReaderFactory = mock(CSVCyReaderFactory.class);
    CyNetworkTableManager netTblMgr = mock(CyNetworkTableManager.class);
    CyRootNetworkManager rootNetMgr = mock(CyRootNetworkManager.class);
    EquationCompiler compiler = mock(EquationCompiler.class);
    CyServiceRegistrar serviceRegistrar = mock(CyServiceRegistrar.class);
    when(serviceRegistrar.getService(CyNetworkTableManager.class)).thenReturn(netTblMgr);
    when(serviceRegistrar.getService(CyRootNetworkManager.class)).thenReturn(rootNetMgr);
    when(serviceRegistrar.getService(EquationCompiler.class)).thenReturn(compiler);
    ReadCache cache = new ReadCache(serviceRegistrar);
    reader = new Cy3SessionReaderImpl(is, cache, groupUtil, suidUpdater, netReaderMgr, propReaderMgr, vizmapReaderMgr, csvCyReaderFactory, serviceRegistrar);
    tblTestSupport = new TableTestSupport();
}

Example 12 with CyNetworkTableManager

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

the class CySessionManagerImpl method restoreTables.

private void restoreTables(final CySession sess) {
    final Set<CyTable> allTables = new HashSet<>();
    // Register all tables sent through the CySession, if not already registered
    for (final CyTableMetadata metadata : sess.getTables()) {
        allTables.add(metadata.getTable());
    }
    // There may be other network tables in the CyNetworkTableManager that were not serialized in the session file
    // (e.g. Table Facades), so it's necessary to add them to CyTableManager as well
    final CyNetworkTableManager netTblMgr = serviceRegistrar.getService(CyNetworkTableManager.class);
    final CyRootNetworkManager rootNetMgr = serviceRegistrar.getService(CyRootNetworkManager.class);
    for (final CyNetwork net : sess.getNetworks()) {
        allTables.addAll(netTblMgr.getTables(net, CyNetwork.class).values());
        allTables.addAll(netTblMgr.getTables(net, CyNode.class).values());
        allTables.addAll(netTblMgr.getTables(net, CyEdge.class).values());
        if (!(net instanceof CyRootNetwork)) {
            final CyRootNetwork root = rootNetMgr.getRootNetwork(net);
            allTables.addAll(netTblMgr.getTables(root, CyNetwork.class).values());
            allTables.addAll(netTblMgr.getTables(root, CyNode.class).values());
            allTables.addAll(netTblMgr.getTables(root, CyEdge.class).values());
        }
    }
    // Register all tables sent through the CySession, if not already registered
    final CyTableManager tblMgr = serviceRegistrar.getService(CyTableManager.class);
    for (final CyTable tbl : allTables) {
        if (tblMgr.getTable(tbl.getSUID()) == null)
            tblMgr.addTable(tbl);
    }
}

Example 13 with CyNetworkTableManager

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

the class CySessionManagerImpl method createNetworkTablesMetadata.

private Set<CyTableMetadata> createNetworkTablesMetadata(final Set<CyNetwork> networks) {
    final Set<CyTableMetadata> result = new HashSet<>();
    final CyNetworkTableManager netTblMgr = serviceRegistrar.getService(CyNetworkTableManager.class);
    // Create the metadata object for each network table
    for (final CyNetwork network : networks) {
        for (final Class<? extends CyIdentifiable> type : TYPES) {
            final Map<String, CyTable> tableMap = netTblMgr.getTables(network, type);
            for (final Entry<String, CyTable> entry : tableMap.entrySet()) {
                final CyTable tbl = entry.getValue();
                if (tbl.getSavePolicy() == SavePolicy.SESSION_FILE) {
                    final String namespace = entry.getKey();
                    final CyTableMetadata metadata = new CyTableMetadataImpl.CyTableMetadataBuilder().setCyTable(tbl).setNamespace(namespace).setType(type).setNetwork(network).build();
                    result.add(metadata);
                }
            }
        }
    }
    return result;
}

Example 14 with CyNetworkTableManager

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

the class CySessionManagerImpl method getSerializableNetworks.

private Set<CyNetwork> getSerializableNetworks() {
    final Set<CyNetwork> serializableNetworks = new HashSet<>();
    final CyNetworkTableManager netTblMgr = serviceRegistrar.getService(CyNetworkTableManager.class);
    final Set<CyNetwork> allNetworks = netTblMgr.getNetworkSet();
    for (final CyNetwork net : allNetworks) {
        if (net.getSavePolicy() == SavePolicy.SESSION_FILE)
            serializableNetworks.add(net);
    }
    return serializableNetworks;
}

Example 15 with CyNetworkTableManager

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

the class C2DEditor method setValue.

@Override
@SuppressWarnings({ "unchecked", "rawtypes" })
public void setValue(final Object value) {
    if (value instanceof ContinuousMapping == false)
        throw new IllegalArgumentException("Value should be ContinuousMapping: this is " + value);
    final CyApplicationManager appMgr = servicesUtil.get(CyApplicationManager.class);
    final CyNetwork currentNetwork = appMgr.getCurrentNetwork();
    if (currentNetwork == null)
        return;
    ContinuousMapping<?, ?> mTest = (ContinuousMapping<?, ?>) value;
    // TODO: error chekcing
    mapping = (ContinuousMapping<Number, V>) value;
    Class<? extends CyIdentifiable> type = (Class<? extends CyIdentifiable>) mapping.getVisualProperty().getTargetDataType();
    final CyNetworkTableManager netTblMgr = servicesUtil.get(CyNetworkTableManager.class);
    final CyTable attr = netTblMgr.getTable(appMgr.getCurrentNetwork(), type, CyNetwork.DEFAULT_ATTRS);
    final VisualMappingManager vmMgr = servicesUtil.get(VisualMappingManager.class);
    editorPanel = new C2DMappingEditorPanel(vmMgr.getCurrentVisualStyle(), mapping, attr, editorManager, servicesUtil);
}