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

Example 81 with CyRootNetwork

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

the class GMLNetworkReaderTest method testReadGmlAttributes.

@Test
public void testReadGmlAttributes() throws Exception {
    final GMLNetworkReader reader = readGML("src/test/resources/testData/gml/example2.gml");
    final CyNetwork[] networks = reader.getNetworks();
    final CyNetworkView[] networkViews = new CyNetworkView[networks.length];
    int i = 0;
    for (CyNetwork net : networks) {
        networkViews[i] = reader.buildCyNetworkView(net);
        i++;
    }
    assertEquals(1, networkViews.length);
    final CyNetworkView view = networkViews[0];
    final CyNetwork net = view.getModel();
    assertEquals(2, net.getNodeCount());
    assertEquals(1, net.getEdgeCount());
    final CyNode n1 = getNodeByName(net, "node1");
    final CyNode n2 = getNodeByName(net, "node2");
    final CyEdge e = getEdgeByName(net, "node1 (pp) node2");
    assertNotNull(n1);
    assertNotNull(n2);
    assertNotNull(e);
    // CyTable Data:
    final CyRootNetwork rootNet = ((CySubNetwork) net).getRootNetwork();
    CyRow row = rootNet.getRow(n1, CyRootNetwork.SHARED_ATTRS);
    assertEquals(new Integer(0), row.get("att1", Integer.class));
    assertEquals(new Double(0.0), row.get("att2", Double.class));
    assertEquals("", row.get("att3", String.class));
    row = rootNet.getRow(n2, CyRootNetwork.SHARED_ATTRS);
    assertEquals(new Integer(10), row.get("att1", Integer.class));
    assertEquals(new Double(10.1), row.get("att2", Double.class));
    assertEquals("MyString", row.get("att3", String.class));
    row = rootNet.getRow(e, CyRootNetwork.SHARED_ATTRS);
    assertEquals(new Integer(2), row.get("att4", Integer.class));
    assertEquals(new Double(2.2), row.get("att5", Double.class));
    assertEquals("Another string...", row.get("att6", String.class));
    // Visual Properties:
    final View<CyNode> nv1 = view.getNodeView(n1);
    final View<CyNode> nv2 = view.getNodeView(n2);
    final View<CyEdge> ev = view.getEdgeView(e);
    assertNotNull(nv1);
    assertNotNull(nv2);
    assertNotNull(ev);
    assertEquals("My GML Network", view.getVisualProperty(NETWORK_TITLE));
    assertEquals(64.0, nv1.getVisualProperty(NODE_WIDTH), 0.0);
    assertEquals(32.0, nv1.getVisualProperty(NODE_HEIGHT), 0.0);
    assertEquals(-66.0, nv1.getVisualProperty(NODE_X_LOCATION), 0.0);
    assertEquals(-71.0, nv1.getVisualProperty(NODE_Y_LOCATION), 0.0);
    assertEquals(Color.decode("#ffcccc"), nv1.getVisualProperty(NODE_FILL_COLOR));
    assertEquals(Color.decode("#ff6666"), nv1.getVisualProperty(NODE_BORDER_PAINT));
    assertEquals(3.0, nv1.getVisualProperty(NODE_BORDER_WIDTH), 0.0);
    assertEquals(NodeShapeVisualProperty.TRIANGLE, nv1.getVisualProperty(NODE_SHAPE));
    assertEquals(40.0, nv2.getVisualProperty(NODE_WIDTH), 0.0);
    assertEquals(39.999, nv2.getVisualProperty(NODE_HEIGHT), 0.001);
    assertEquals(60.5289, nv2.getVisualProperty(NODE_X_LOCATION), 0.0001);
    assertEquals(77.4868, nv2.getVisualProperty(NODE_Y_LOCATION), 0.0001);
    assertEquals(Color.decode("#ffffcc"), nv2.getVisualProperty(NODE_FILL_COLOR));
    assertEquals(Color.decode("#999900"), nv2.getVisualProperty(NODE_BORDER_PAINT));
    assertEquals(4.0, nv2.getVisualProperty(NODE_BORDER_WIDTH), 0.0);
    assertEquals(NodeShapeVisualProperty.OCTAGON, nv2.getVisualProperty(NODE_SHAPE));
    assertEquals(4.0, ev.getVisualProperty(EDGE_WIDTH), 0.0);
    assertEquals(Color.decode("#660066"), ev.getVisualProperty(EDGE_UNSELECTED_PAINT));
    assertEquals(Color.decode("#660066"), ev.getVisualProperty(EDGE_STROKE_UNSELECTED_PAINT));
    assertEquals(LineTypeVisualProperty.SOLID, ev.getVisualProperty(EDGE_LINE_TYPE));
    assertEquals(ArrowShapeVisualProperty.CIRCLE, ev.getVisualProperty(EDGE_SOURCE_ARROW_SHAPE));
    assertEquals(ArrowShapeVisualProperty.DIAMOND, ev.getVisualProperty(EDGE_TARGET_ARROW_SHAPE));
}

Example 82 with CyRootNetwork

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

the class PerfTest method testNetworkCapability.

private void testNetworkCapability(String name) throws Exception {
    CyNetwork[] nets = getNetworks(name);
    CyNetwork net = nets[0];
    List<CyNode> nodeList = net.getNodeList();
    long start = System.currentTimeMillis();
    for (CyNode n : nodeList) {
        List<CyEdge> edges = net.getAdjacentEdgeList(n, CyEdge.Type.ANY);
    }
    long end = System.currentTimeMillis();
    System.out.println("Getting all adjacent edges: " + (end - start));
    /*
		start = System.currentTimeMillis();
		for ( CyNode n : nodeList ) {
			for ( CyNode nn : nodeList ) {
				List<CyEdge> edges = net.getConnectingEdgeList(n,nn,CyEdge.Type.ANY);
			}
		}
		end = System.currentTimeMillis();
		System.out.println("Getting all connecting edges: " + (end - start));
		*/
    start = System.currentTimeMillis();
    for (CyNode n : nodeList) {
        List<CyNode> nodes = net.getNeighborList(n, CyEdge.Type.ANY);
    }
    end = System.currentTimeMillis();
    System.out.println("Getting all neighbor nodes: " + (end - start));
    // create subnetworks
    CyRootNetwork root = rootNetManager.getRootNetwork(net);
    int i = 0;
    for (CyNode n : net.getNodeList()) {
        if (i++ > 1000)
            break;
        List<CyNode> nl = net.getNeighborList(n, CyEdge.Type.ANY);
        Set<CyEdge> es = new HashSet<CyEdge>();
        for (CyNode nn : nl) {
            List<CyEdge> ee = net.getConnectingEdgeList(n, nn, CyEdge.Type.ANY);
            es.addAll(ee);
        }
        root.addSubNetwork(nl, es);
    }
}

Example 83 with CyRootNetwork

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

the class GenericXGMMLReaderTest method testParseCollapsedGroupFrom2x.

@Test
public void testParseCollapsedGroupFrom2x() throws Exception {
    List<CyNetworkView> views = getViews("group_2x_collapsed.xgmml");
    // The group network should not be registered, so the network list must contain only the base network
    assertEquals(1, reader.getNetworks().length);
    CyNetwork net = checkSingleNetwork(views, 2, 1);
    CyRootNetwork rootNet = rootNetManager.getRootNetwork(net);
    CyNode grNode = getNodeByName(rootNet, "metanode 1");
    check2xGroupMetadata(net, grNode, false);
    // Check group network data
    CyNetwork grNet = grNode.getNetworkPointer();
    for (CyNode n : grNet.getNodeList()) {
        assertNotNull(grNet.getRow(n, HIDDEN_ATTRS).get("__metanodeHintX", Double.class));
        assertNotNull(grNet.getRow(n, HIDDEN_ATTRS).get("__metanodeHintY", Double.class));
    }
    assertCustomColumnsAreMutable(rootNet);
    assertCustomColumnsAreMutable(net);
    assertCustomColumnsAreMutable(grNet);
    assertEquals(1, groupManager.getGroupSet(net).size());
    assertTrue(groupManager.isGroup(grNode, net));
}

Example 84 with CyRootNetwork

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

the class GenericXGMMLReaderTest method testParseExpandedGroupFrom2x.

@Test
public void testParseExpandedGroupFrom2x() throws Exception {
    List<CyNetworkView> views = getViews("group_2x_expanded.xgmml");
    // The group network should not be registered, so the network list must contain only the base network
    assertEquals(1, reader.getNetworks().length);
    CyNetwork net = checkSingleNetwork(views, 3, 2);
    CyRootNetwork rootNet = rootNetManager.getRootNetwork(net);
    CyNode grNode = getNodeByName(rootNet, "metanode 1");
    check2xGroupMetadata(net, grNode, true);
    assertCustomColumnsAreMutable(rootNetManager.getRootNetwork(net));
    assertCustomColumnsAreMutable(net);
    assertCustomColumnsAreMutable(grNode.getNetworkPointer());
    assertEquals(1, groupManager.getGroupSet(net).size());
    assertTrue(groupManager.isGroup(grNode, net));
}

Example 85 with CyRootNetwork

use of org.cytoscape.model.subnetwork.CyRootNetwork 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);
    }
}