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

Example 21 with CyEdge

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

the class InDegreeTest method init.

@Before
public void init() {
    final CyNode node = mock(CyNode.class);
    when(node.getSUID()).thenReturn(101L);
    final List<CyEdge> edgeList = mock(List.class);
    when(edgeList.size()).thenReturn(3);
    final CyNetwork network = mock(CyNetwork.class);
    when(network.getAdjacentEdgeList(node, CyEdge.Type.INCOMING)).thenReturn(edgeList);
    when(network.getNode(101L)).thenReturn(node);
    Collection<CyNode> nodes = new ArrayList<CyNode>(1);
    nodes.add(node);
    applicationManager = mock(CyApplicationManager.class);
    when(applicationManager.getCurrentNetwork()).thenReturn(network);
    eventHelper = new DummyCyEventHelper();
    serviceRegistrar = mock(CyServiceRegistrar.class);
    when(serviceRegistrar.getService(CyApplicationManager.class)).thenReturn(applicationManager);
    when(serviceRegistrar.getService(CyEventHelper.class)).thenReturn(eventHelper);
}

Example 22 with CyEdge

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

the class SourceIDTest method init.

@Before
public void init() {
    final CyNode node = mock(CyNode.class);
    when(node.getSUID()).thenReturn(101L);
    final List<CyEdge> edgeList = mock(List.class);
    when(edgeList.size()).thenReturn(3);
    final CyNetwork network = mock(CyNetwork.class);
    final CyEdge edge = mock(CyEdge.class);
    when(edge.getSUID()).thenReturn(11L);
    when(edge.getSource()).thenReturn(node);
    Collection<CyEdge> edges = new ArrayList<CyEdge>(1);
    edges.add(edge);
    when(network.getEdge(11L)).thenReturn(edge);
    applicationManager = mock(CyApplicationManager.class);
    when(applicationManager.getCurrentNetwork()).thenReturn(network);
    eventHelper = new DummyCyEventHelper();
    serviceRegistrar = mock(CyServiceRegistrar.class);
    when(serviceRegistrar.getService(CyApplicationManager.class)).thenReturn(applicationManager);
    when(serviceRegistrar.getService(CyEventHelper.class)).thenReturn(eventHelper);
}

Example 23 with CyEdge

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

the class SIFNetworkReader method createEdge.

private void createEdge(final Interaction itr, final CySubNetwork subNetwork, final Map<Object, CyNode> nMap) {
    CyNode sourceNode = nMap.get(itr.getSource());
    if (sourceNode == null) {
        sourceNode = subNetwork.addNode();
        subNetwork.getRow(sourceNode).set(CyNetwork.NAME, itr.getSource());
        nMap.put(itr.getSource(), subNetwork.getRootNetwork().getNode(sourceNode.getSUID()));
    }
    for (final String target : itr.getTargets()) {
        CyNode targetNode = nMap.get(target);
        if (targetNode == null) {
            targetNode = subNetwork.addNode();
            subNetwork.getRow(targetNode).set(CyNetwork.NAME, target);
            nMap.put(target, subNetwork.getRootNetwork().getNode(targetNode.getSUID()));
        }
        // Add the sourceNode and targetNode to subNetwork
        if (!subNetwork.containsNode(sourceNode)) {
            subNetwork.addNode(sourceNode);
        }
        if (!subNetwork.containsNode(targetNode)) {
            subNetwork.addNode(targetNode);
        }
        final CyEdge edge = subNetwork.addEdge(sourceNode, targetNode, true);
        subNetwork.getRow(edge).set(CyNetwork.NAME, getEdgeName(itr, target));
        subNetwork.getRow(edge).set(CyEdge.INTERACTION, itr.getType());
    }
}

Example 24 with CyEdge

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

the class HandleGraphDone method handle.

@Override
public ParseState handle(String tag, Attributes atts, ParseState current) throws SAXException {
    graphDone();
    // End of document?
    if (manager.graphDoneCount != manager.graphCount)
        return current;
    // Resolve any unresolved node and edge references
    Map<CyNetwork, Set<Long>> nodeMap = manager.getCache().getNodeLinks();
    for (Map.Entry<CyNetwork, Set<Long>> entry : nodeMap.entrySet()) {
        CyNetwork net = entry.getKey();
        Set<Long> ids = entry.getValue();
        if (net != null && ids != null && !ids.isEmpty()) {
            if (net instanceof CySubNetwork) {
                final CySubNetwork sn = (CySubNetwork) net;
                for (Long id : ids) {
                    CyNode n = manager.getCache().getNode(id);
                    if (n != null)
                        sn.addNode(n);
                    else
                        logger.error("Cannot find XLink node with id \"" + id + "\".");
                }
            } else {
                logger.error("Cannot add existing nodes \"" + ids.toArray() + "\" to a network which is not a CySubNetwork");
            }
        }
    }
    // TODO: refactor
    Map<CyNetwork, Set<Long>> edgeMap = manager.getCache().getEdgeLinks();
    for (Map.Entry<CyNetwork, Set<Long>> entry : edgeMap.entrySet()) {
        CyNetwork net = entry.getKey();
        Set<Long> ids = entry.getValue();
        if (net != null && ids != null && !ids.isEmpty()) {
            if (net instanceof CySubNetwork) {
                final CySubNetwork sn = (CySubNetwork) net;
                for (Long id : ids) {
                    final CyEdge e = manager.getCache().getEdge(id);
                    if (e != null)
                        sn.addEdge(e);
                    else
                        logger.error("Cannot find XLink edge with id \"" + id + "\".");
                }
            } else {
                logger.error("Cannot add existing edges \"" + ids.toArray() + "\" to a network which is not a CySubNetwork");
            }
        }
    }
    manager.getCache().deleteUnresolvedNodes();
    resolveEquations();
    resolveNetworkPointers();
    updateSUIDAttributes();
    // TODO: we should not create (and specially register) groups here!
    createGroups();
    return ParseState.NONE;
}

Example 25 with CyEdge

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

the class NewNetworkSelectedNodesOnlyTaskTest method testNewNetworkSelectedNodesOnlyTask.

@Test
public void testNewNetworkSelectedNodesOnlyTask() throws Exception {
    final UndoSupport undoSupport = mock(UndoSupport.class);
    netmgr.addNetwork(net);
    final CyNode node1 = net.addNode();
    final CyNode node2 = net.addNode();
    final CyNode node3 = net.addNode();
    final CyEdge edge1 = net.addEdge(node1, node2, true);
    // final CyEdge edge2 = net.addEdge(node2, node3, true);
    net.getRow(node1).set(CyNetwork.SELECTED, true);
    // net.getRow(node2).set(CyNetwork.SELECTED, true);
    net.getRow(edge1).set(CyNetwork.SELECTED, true);
    int numberOfNetsBeforeTask = netmgr.getNetworkSet().size();
    List<CyNetwork> netListbeforeTask = new ArrayList<CyNetwork>(netmgr.getNetworkSet());
    final NewNetworkSelectedNodesOnlyTask task = new NewNetworkSelectedNodesOnlyTask(undoSupport, net, cyroot, cnvf, netmgr, networkViewManager, cyNetworkNaming, vmm, appManager, eventHelper, groupMgr, renderingEngineManager, serviceRegistrar);
    assertNotNull("task is null!", task);
    task.setTaskIterator(new TaskIterator(task));
    task.run(mock(TaskMonitor.class));
    int numberOfNetsAfterTask = netmgr.getNetworkSet().size();
    assertEquals(1, numberOfNetsAfterTask - numberOfNetsBeforeTask);
    List<CyNetwork> networkList = new ArrayList<CyNetwork>(netmgr.getNetworkSet());
    networkList.removeAll(netListbeforeTask);
    assertEquals(1, networkList.get(0).getNodeList().size());
    assertEquals(0, networkList.get(0).getEdgeList().size());
}