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

Example 61 with CyEdge

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

the class CySubNetworkImpl method addEdge.

@Override
public CyEdge addEdge(final CyNode source, final CyNode target, final boolean isDirected) {
    // important that it's edgeAdd and not addEdge
    final CyEdge ret;
    synchronized (this) {
        // first add an edge to the root network
        ret = parent.addEdge(source, target, isDirected);
        // then add the resulting CyEdge to this network
        addEdgeInternal(source, target, isDirected, ret);
        getRow(ret).set(CyNetwork.SELECTED, false);
    }
    if (fireAddedNodesAndEdgesEvents)
        eventHelper.addEventPayload((CyNetwork) this, ret, AddedEdgesEvent.class);
    return ret;
}

Example 62 with CyEdge

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

the class CySubNetworkImpl method removeEdges.

@Override
public boolean removeEdges(final Collection<CyEdge> edges) {
    if (edges == null || edges.isEmpty())
        return false;
    // Possible error if one of the edges isn't contained in subnetwork, but
    // since this is only a notification, maybe that's OK.
    eventHelper.fireEvent(new AboutToRemoveEdgesEvent(this, edges));
    CyTable hiddenTable = getTable(CyEdge.class, CyNetwork.HIDDEN_ATTRS);
    CyTable localTable = getTable(CyEdge.class, CyNetwork.LOCAL_ATTRS);
    CyTable defaultTable = getTable(CyEdge.class, CyNetwork.DEFAULT_ATTRS);
    List<Long> suids = new ArrayList<>();
    for (CyEdge edge : edges) {
        if (containsEdge(edge)) {
            // getRow(edge).set(CyNetwork.SELECTED, false);
            suids.add(edge.getSUID());
        }
    }
    boolean ret = removeEdgesInternal(edges);
    hiddenTable.deleteRows(suids);
    defaultTable.deleteRows(suids);
    if (ret) {
        parent.subnetworkEdgesRemoved(edges);
    }
    if (ret) {
        eventHelper.fireEvent(new RemovedEdgesEvent(this));
    }
    return ret;
}

Example 63 with CyEdge

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

the class CySubNetworkImpl method removeNodes.

@Override
public boolean removeNodes(final Collection<CyNode> nodes) {
    if (nodes == null || nodes.isEmpty())
        return false;
    eventHelper.fireEvent(new AboutToRemoveNodesEvent(this, nodes));
    CyTable nodeHiddenTable = getTable(CyNode.class, CyNetwork.HIDDEN_ATTRS);
    CyTable nodeDefaultTable = getTable(CyNode.class, CyNetwork.DEFAULT_ATTRS);
    CyTable edgeHiddenTable = getTable(CyEdge.class, CyNetwork.HIDDEN_ATTRS);
    CyTable edgeDefaultTable = getTable(CyEdge.class, CyNetwork.DEFAULT_ATTRS);
    List<Long> nodeSuids = new ArrayList<>();
    Set<Long> edgeSuids = new HashSet<>();
    for (CyNode node : nodes) {
        if (this.containsNode(node)) {
            Long nodeSuid = node.getSUID();
            if (nodeDefaultTable.rowExists(nodeSuid))
                nodeSuids.add(nodeSuid);
            for (CyEdge edge : getAdjacentEdgeIterable(node, Type.ANY)) {
                Long edgeSuid = edge.getSUID();
                if (edgeDefaultTable.rowExists(edgeSuid)) {
                    edgeSuids.add(edgeSuid);
                }
            }
        }
    }
    boolean ret = removeNodesInternal(nodes);
    nodeHiddenTable.deleteRows(nodeSuids);
    nodeDefaultTable.deleteRows(nodeSuids);
    edgeHiddenTable.deleteRows(edgeSuids);
    edgeDefaultTable.deleteRows(edgeSuids);
    if (ret) {
        parent.subnetworkNodesRemoved(nodes);
    }
    if (ret) {
        eventHelper.fireEvent(new RemovedNodesEvent(this));
    }
    return ret;
}

Example 64 with CyEdge

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

the class DefaultTablesNetwork method getRow.

public CyRow getRow(final CyIdentifiable entry, final String tableName) {
    if (entry == null)
        throw new NullPointerException("null entry");
    if (tableName == null)
        throw new NullPointerException("null table name");
    CyTable table;
    // The table returned should be immutable.
    if (entry instanceof CyNode && containsNode((CyNode) entry))
        table = networkTableManager.getTable(networkRef.get(), CyNode.class, tableName);
    else if (entry instanceof CyEdge && containsEdge((CyEdge) entry))
        table = networkTableManager.getTable(networkRef.get(), CyEdge.class, tableName);
    else if (entry instanceof CyNetwork && entry.equals(this)) {
        if (networkRef == null)
            throw new IllegalArgumentException("Network reference is null.  This should not be null.");
        final CyNetwork n = networkRef.get();
        table = networkTableManager.getTable(n, CyNetwork.class, tableName);
    } else
        throw new IllegalArgumentException("unrecognized (table entry): " + entry.toString() + "  (table name): " + tableName);
    if (table == null)
        throw new NullPointerException("Table does not exist: " + tableName);
    return table.getRow(entry.getSUID());
}

Example 65 with CyEdge

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

the class CySubNetworkTest method testAddExistingEdgeEventBeforeNetworkAdd.

@Test
public void testAddExistingEdgeEventBeforeNetworkAdd() {
    CyNode nx1 = root.addNode();
    CyNode nx2 = root.addNode();
    CyEdge ex1 = root.addEdge(nx1, nx2, false);
    CySubNetwork sub = root.addSubNetwork();
    sub.addNode(nx1);
    sub.addNode(nx2);
    sub.addEdge(ex1);
    Object payload = deh.getLastPayload();
    assertNull(payload);
}