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

Example 76 with CySubNetwork

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

the class SessionXGMMLNetworkWriterTest method testNetworkPointerFromSameRootNetwork.

@Test
public void testNetworkPointerFromSameRootNetwork() {
    // Create a subnetwork from the same root
    CySubNetwork subNet = rootNet.addSubNetwork();
    // To force all nested node graphs to be written as XLinks!
    setRegistered(subNet, true);
    // Set it as network pointer to 2 nodes
    CyNode n1 = net.getNodeList().get(0);
    CyNode n2 = net.getNodeList().get(1);
    n1.setNetworkPointer(subNet);
    n2.setNetworkPointer(subNet);
    write(rootNet);
    // Test
    assertEquals(2, evalNumber("count(/x:graph//x:node/x:att/x:graph)"));
    assertEquals("" + subNet.getSUID(), getElementId("//x:node[@id=" + n1.getSUID() + "]/x:att/x:graph"));
    assertEquals("" + subNet.getSUID(), getElementId("//x:node[@id=" + n2.getSUID() + "]/x:att/x:graph"));
}

Example 77 with CySubNetwork

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

the class SessionXGMMLNetworkWriterTest method testUnregisteredSubNetworkSavedIfSessionSavePolicy.

@Test
public void testUnregisteredSubNetworkSavedIfSessionSavePolicy() throws UnsupportedEncodingException {
    CySubNetwork sn = rootNet.addSubNetwork();
    // It doesn't matter
    setRegistered(sn, false);
    write(rootNet);
    assertEquals("0", evalString("/x:graph/x:att/x:graph[@id=" + sn.getSUID() + "]/@cy:registered"));
}

Example 78 with CySubNetwork

use of org.cytoscape.model.subnetwork.CySubNetwork 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 79 with CySubNetwork

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

the class ReadDataManager method createEdge.

protected CyEdge createEdge(final Object sourceId, final Object targetId, Object id, final String label, final boolean directed, final CyNetwork net) {
    if (id == null)
        id = label;
    CyNode source = cache.getNode(sourceId);
    CyNode target = cache.getNode(targetId);
    final boolean haveTarget = target != null;
    final boolean haveSource = source != null;
    // (it can happen if the edge is written before its nodes in the XGMML document)
    if (!haveSource)
        source = createNode(sourceId, null, net);
    if (!haveTarget)
        target = createNode(targetId, null, net);
    // Create the edge
    final CyNetwork curNet = getCurrentNetwork();
    final CyEdge edge = createEdge(source, target, id, label, directed, net);
    if (curNet instanceof CySubNetwork) {
        // If the actual node elements are not parsed later, they should be deleted from this subnetwork.
        if (!haveSource)
            cache.addUnresolvedNode(source, (CySubNetwork) curNet);
        if (!haveTarget)
            cache.addUnresolvedNode(target, (CySubNetwork) curNet);
    }
    return edge;
}

Example 80 with CySubNetwork

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

the class ReadDataManager method createEdge.

protected CyEdge createEdge(final CyNode source, final CyNode target, Object id, final String label, final boolean directed, CyNetwork net) {
    CyEdge edge = null;
    if (id == null)
        id = label;
    if (net instanceof CySubNetwork && this.getParentNetwork() != null) {
        // Do not create the element again if the network is a sub-network and the edge already exists!
        edge = cache.getEdge(id);
        if (edge != null)
            ((CySubNetwork) net).addEdge(edge);
    }
    if (edge == null) {
        // OK, create it
        // But first get the actual source/target instances from the current network,
        // because both node instances have to belong to the same root or sub-network.
        CyNode actualSrc = net.getNode(source.getSUID());
        CyNode actualTgt = net.getNode(target.getSUID());
        // For 2.x groups
        List<Long> extEdgeIds = null;
        if ((getDocumentVersion() < 3.0 || !isSessionFormat()) && (actualSrc == null || actualTgt == null)) {
            // The nodes might have been added to other sub-networks, but not to the current one.
            // If that is the case, the root network should have both nodes,
            // so let's just add the edge to the root.
            final CyRootNetwork rootNet = getRootNetwork();
            if (actualSrc == null)
                actualSrc = rootNet.getNode(source.getSUID());
            if (actualTgt == null)
                actualTgt = rootNet.getNode(target.getSUID());
            // Does the current subnetwork belong to a 2.x group?
            if (getDocumentVersion() < 3.0 && !compoundNodeStack.isEmpty() && networkStack.size() > 1) {
                // Get the current compound node
                final CyNode grNode = compoundNodeStack.peek();
                // Get the network of that node (the current one is its network pointer)
                final CyNetwork parentNet = cache.getNetwork(networkStack.elementAt(networkStack.size() - 2));
                // Check for the group's metadata attribute
                final CyRow gnhRow = parentNet.getRow(grNode, CyNetwork.HIDDEN_ATTRS);
                if (gnhRow.isSet(GROUP_STATE_ATTRIBUTE)) {
                    // It's a group!
                    // Get the network pointer's hidden row
                    final CyRow nphRow = net.getRow(net, CyNetwork.HIDDEN_ATTRS);
                    // Add extra metadata for external edges, so that the information is not lost
                    if (nphRow.getTable().getColumn(EXTERNAL_EDGE_ATTRIBUTE) == null) {
                        nphRow.getTable().createListColumn(EXTERNAL_EDGE_ATTRIBUTE, Long.class, false);
                        // These are already the new SUIDs. Let's tell the SUIDUpdater to ignore this column,
                        // in order to prevent it from replacing the correct list by an empty one.
                        suidUpdater.ignoreColumn(nphRow.getTable(), EXTERNAL_EDGE_ATTRIBUTE);
                    }
                    extEdgeIds = nphRow.getList(EXTERNAL_EDGE_ATTRIBUTE, Long.class);
                    if (extEdgeIds == null) {
                        nphRow.set(EXTERNAL_EDGE_ATTRIBUTE, new ArrayList<Long>());
                        extEdgeIds = nphRow.getList(EXTERNAL_EDGE_ATTRIBUTE, Long.class);
                    }
                }
            }
            net = rootNet;
        }
        edge = net.addEdge(actualSrc, actualTgt, directed);
        if (extEdgeIds != null)
            extEdgeIds.add(edge.getSUID());
        mapSUIDs(id, edge.getSUID());
    }
    // Add to internal cache:
    cache.cache(id, edge);
    return edge;
}