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

Example 76 with CyEdge

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

the class InteractionTransformer method apply.

@Override
public void apply(CyNetwork network, CyIdentifiable element, TransformerSink<CyIdentifiable> sink) {
    if (action == Action.ADD)
        sink.collect(element);
    if (element instanceof CyEdge) {
        CyEdge edge = (CyEdge) element;
        Filter<CyNetwork, CyIdentifiable> memoizedFilter = super.getMemoizedFilter();
        if (selectSource) {
            CyNode source = edge.getSource();
            if (memoizedFilter.accepts(network, source)) {
                sink.collect(source);
            }
        }
        if (selectTarget) {
            CyNode target = edge.getTarget();
            if (memoizedFilter.accepts(network, target)) {
                sink.collect(target);
            }
        }
    }
}

Example 77 with CyEdge

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

the class RowsSetViewUpdater method updateView.

private final void updateView(final RowsSetEvent e) {
    boolean refreshView = false;
    boolean refreshOtherViews = false;
    // Acquire services once to avoid performance overhead of repeated lookup
    final CyApplicationManager applicationManager = serviceRegistrar.getService(CyApplicationManager.class);
    final CyColumnIdentifierFactory columnIdentifierFactory = serviceRegistrar.getService(CyColumnIdentifierFactory.class);
    final CyNetworkViewManager networkViewManager = serviceRegistrar.getService(CyNetworkViewManager.class);
    final VisualMappingManager visualMappingManager = serviceRegistrar.getService(VisualMappingManager.class);
    final RenderingEngine<CyNetwork> renderer = applicationManager.getCurrentRenderingEngine();
    final CyNetwork network = applicationManager.getCurrentNetwork();
    if (network == null)
        return;
    // 1: Update current network view
    final Collection<CyNetworkView> views = networkViewManager.getNetworkViews(network);
    CyNetworkView networkView = null;
    if (views.isEmpty())
        return;
    else
        networkView = views.iterator().next();
    final VisualStyle vs = visualMappingManager.getVisualStyle(networkView);
    Map<CyRow, View<? extends CyIdentifiable>> rowViewMap = tracker.getRowViewMap(networkView);
    for (final RowSetRecord record : e.getPayloadCollection()) {
        final CyRow row = record.getRow();
        final String columnName = record.getColumn();
        final CyColumn column = row.getTable().getColumn(columnName);
        if (column == null)
            continue;
        final VirtualColumnInfo virtualColInfo = column.getVirtualColumnInfo();
        final boolean virtual = virtualColInfo.isVirtual();
        final View<? extends CyIdentifiable> v = rowViewMap.get(row);
        if (v == null)
            continue;
        if (v.getModel() instanceof CyNode) {
            final CyNode node = (CyNode) v.getModel();
            if (network.containsNode(node) && isStyleAffected(vs, columnName, renderer, columnIdentifierFactory)) {
                vs.apply(row, v);
                refreshView = false;
            }
        } else if (v.getModel() instanceof CyEdge) {
            final CyEdge edge = (CyEdge) v.getModel();
            if (network.containsEdge(edge) && isStyleAffected(vs, columnName, renderer, columnIdentifierFactory)) {
                vs.apply(row, v);
                refreshView = false;
            }
        }
        // If virtual, it may be used in other networks.
        if (refreshView && virtual)
            refreshOtherViews = true;
    // if (refreshView)
    // vs.apply(record.getRow(), (View<? extends CyIdentifiable>) v);
    }
    if (refreshView) {
        vs.apply(networkView);
        networkView.updateView();
        if (refreshOtherViews) {
            // Check other views. If update is required, set the flag.
            for (final CyNetworkView view : networkViewManager.getNetworkViewSet()) {
                if (view == networkView)
                    continue;
                final VisualStyle style = visualMappingManager.getVisualStyle(view);
                if (style == vs) {
                    // Same style is in use. Need to apply.
                    netViewMediator.setUpdateFlag(view);
                }
            }
        }
    }
}

Example 78 with CyEdge

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

the class GraphMLReaderTest method testReadAttrGraph.

@Test
public void testReadAttrGraph() throws Exception {
    File file = new File("src/test/resources/simpleWithAttributes.xml");
    InputStream stream = file.toURI().toURL().openStream();
    GraphMLReader reader = new GraphMLReader(stream, layouts, appManager, netFactory, networkManager, rootFactory);
    assertNotNull(reader);
    reader.run(tm);
    final CyNetwork[] networks = reader.getNetworks();
    assertNotNull(networks);
    assertEquals(1, networks.length);
    final CyNetwork net = networks[0];
    assertEquals(6, net.getNodeCount());
    assertEquals(7, net.getEdgeCount());
    // Check Network Attributes
    final String networkName = net.getDefaultNetworkTable().getRow(net.getSUID()).get(NAME, String.class);
    final Number networkNumber = net.getDefaultNetworkTable().getRow(net.getSUID()).get("number_test", Double.class);
    assertEquals("Small GraphML Network", networkName);
    assertEquals(100.123, networkNumber);
    final CyNode n1 = getNodeByName(net, "n0");
    assertNotNull(n1);
    final CyEdge e1 = getEdgeByName(net, "n0 (-) n1");
    assertNotNull(e1);
    final CyColumn colorCol = net.getDefaultNodeTable().getColumn("color");
    final CyColumn rankCol = net.getDefaultNodeTable().getColumn("rank");
    final CyColumn degreeCol = net.getDefaultNodeTable().getColumn("degree");
    final CyColumn scoreCol = net.getDefaultNodeTable().getColumn("score");
    final CyColumn taggedCol = net.getDefaultNodeTable().getColumn("tagged");
    final CyColumn weightCol = net.getDefaultEdgeTable().getColumn("weight");
    assertNotNull(colorCol);
    assertNotNull(rankCol);
    assertNotNull(degreeCol);
    assertNotNull(scoreCol);
    assertNotNull(taggedCol);
    assertNotNull(weightCol);
    assertEquals(String.class, colorCol.getType());
    assertEquals(Integer.class, rankCol.getType());
    assertEquals(Long.class, degreeCol.getType());
    // GraphML "float" is converted to Double by Cytoscape
    assertEquals(Double.class, scoreCol.getType());
    assertEquals(Boolean.class, taggedCol.getType());
    assertEquals(Double.class, weightCol.getType());
    assertEquals("green", net.getRow(n1).get("color", String.class));
    assertEquals(Integer.valueOf(3), net.getRow(n1).get("rank", Integer.class));
    assertEquals(Long.valueOf(2), net.getRow(n1).get("degree", Long.class));
    assertEquals(Double.valueOf(0.95d), net.getRow(n1).get("score", Double.class));
    assertEquals(Boolean.TRUE, net.getRow(n1).get("tagged", Boolean.class));
    assertEquals(Double.valueOf(1.0d), net.getRow(e1).get("weight", Double.class));
}

Example 79 with CyEdge

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

the class CyGroupImpl method removeMemberEdges.

public void removeMemberEdges() {
    Set<CyEdge> edgesToRemove = new HashSet<>(memberEdges);
    for (CyNetwork network : networkSet) {
        network.removeEdges(edgesToRemove);
    }
    rootNetwork.removeEdges(edgesToRemove);
    memberEdges.clear();
}

Example 80 with CyEdge

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

the class CyGroupImpl method removeNodes.

/**
 * @see org.cytoscape.group.CyGroup#removeNodes()
 */
@Override
public void removeNodes(List<CyNode> nodes) {
    synchronized (lock) {
        List<CyEdge> netEdges = new ArrayList<CyEdge>();
        for (CyNode node : nodes) {
            List<CyEdge> edges = rootNetwork.getAdjacentEdgeList(node, CyEdge.Type.ANY);
            for (CyEdge edge : edges) {
                if (externalEdges.contains(edge))
                    externalEdges.remove(edge);
                else if (memberEdges.contains(edge))
                    memberEdges.remove(edge);
                else {
                    netEdges.add(edge);
                }
            }
        }
        if (netEdges.size() > 0)
            getGroupNetwork().removeEdges(netEdges);
        getGroupNetwork().removeNodes(nodes);
        updateMetaEdges(false);
        for (CyNetwork net : networkSet) {
            updateCountAttributes(net);
        }
    }
    cyEventHelper.fireEvent(new GroupNodesRemovedEvent(CyGroupImpl.this, nodes));
}