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

Example 46 with CySubNetwork

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

the class CyNetworkAutoDeleteTest method testAutoDeleteWhenSubnetworkIsDeleted.

@Test
public void testAutoDeleteWhenSubnetworkIsDeleted() {
    CyNetwork network1 = TestCyNetworkFactory.getInstance();
    CyRootNetwork rootNetwork = ((CySubNetwork) network1).getRootNetwork();
    CyNode n1 = network1.addNode();
    CyNode n2 = network1.addNode();
    CyNode n3 = network1.addNode();
    CyEdge e1 = network1.addEdge(n1, n2, false);
    CyEdge e2 = network1.addEdge(n2, n3, false);
    CyNetwork network2 = rootNetwork.addSubNetwork(Arrays.asList(n1, n2), Arrays.asList(e1));
    rootNetwork.removeSubNetwork((CySubNetwork) network1);
    assertFalse(rootNetwork.containsNode(n3));
    assertFalse(network2.containsNode(n3));
    assertFalse(rootNetwork.containsEdge(e2));
    assertFalse(network2.containsEdge(e2));
    assertNull(rootNetwork.getNode(n3.getSUID()));
    assertNull(network2.getNode(n3.getSUID()));
    rowExists(false, rootNetwork, n3);
    rowExists(false, rootNetwork, e2);
}

Example 47 with CySubNetwork

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

the class SessionHandler method setSessionNetworks.

/**
 * @param netOrder Maps CyNetwork SUID to the network position
 */
private void setSessionNetworks(final Map<Long, Integer> netOrder) {
    final CyNetworkManager netMgr = serviceRegistrar.getService(CyNetworkManager.class);
    final List<CySubNetwork> sortedNetworks = new ArrayList<>();
    for (CyNetwork n : netMgr.getNetworkSet()) {
        if (n instanceof CySubNetwork && netMgr.networkExists(n.getSUID()))
            sortedNetworks.add((CySubNetwork) n);
    }
    Collections.sort(sortedNetworks, new Comparator<CySubNetwork>() {

        @Override
        public int compare(final CySubNetwork n1, final CySubNetwork n2) {
            try {
                Integer o1 = netOrder.get(n1.getSUID());
                Integer o2 = netOrder.get(n2.getSUID());
                if (o1 == null)
                    o1 = -1;
                if (o2 == null)
                    o2 = -1;
                return o1.compareTo(o2);
            } catch (final Exception e) {
                logger.error("Cannot sort networks", e);
            }
            return 0;
        }
    });
    final CyApplicationManager applicationMgr = serviceRegistrar.getService(CyApplicationManager.class);
    final CyNetworkViewManager netViewMgr = serviceRegistrar.getService(CyNetworkViewManager.class);
    final List<CyNetwork> selectedNetworks = applicationMgr.getSelectedNetworks();
    final List<CyNetworkView> selectedViews = applicationMgr.getSelectedNetworkViews();
    invokeOnEDT(() -> {
        netPanel.setNetworks(sortedNetworks);
        for (SubNetworkPanel snp : netPanel.getAllSubNetworkItems()) {
            final int count = netViewMgr.getNetworkViews(snp.getModel().getNetwork()).size();
            snp.getModel().setViewCount(count);
        }
        netPanel.setSelectedNetworks(selectedNetworks);
        netViewMediator.getNetworkViewMainPanel().setSelectedNetworkViews(selectedViews);
    });
}

Example 48 with CySubNetwork

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

the class CyRootNetworkImpl method dispose.

@Override
public void dispose() {
    Map<String, CyTable> tableMap;
    serviceRegistrar.unregisterAllServices(columnAdder);
    serviceRegistrar.unregisterAllServices(nameSetListener);
    serviceRegistrar.unregisterAllServices(interactionSetListener);
    serviceRegistrar.unregisterAllServices(networkAddedListenerDelegator);
    serviceRegistrar.unregisterAllServices(networkNameSetListener);
    serviceRegistrar.unregisterService(this, SessionLoadedListener.class);
    for (CySubNetwork network : subNetworks) {
        network.dispose();
    }
    tableMap = networkTableMgr.getTables(this, CyNetwork.class);
    for (CyTable table : tableMap.values()) {
        tableMgr.deleteTableInternal(table.getSUID(), true);
    }
    tableMap = networkTableMgr.getTables(this, CyNode.class);
    for (CyTable table : tableMap.values()) {
        tableMgr.deleteTableInternal(table.getSUID(), true);
    }
    tableMap = networkTableMgr.getTables(this, CyEdge.class);
    for (CyTable table : tableMap.values()) {
        tableMgr.deleteTableInternal(table.getSUID(), true);
    }
    networkTableMgr.removeAllTables(this);
    removedAttributesCache.dispose();
}

Example 49 with CySubNetwork

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

the class CyRootNetworkImpl method removeSubNetwork.

@Override
public void removeSubNetwork(final CySubNetwork sub) {
    synchronized (lock) {
        if (sub == null)
            return;
        if (!subNetworks.contains(sub))
            throw new IllegalArgumentException("Subnetwork not a member of this RootNetwork " + sub);
        if (sub.equals(base)) {
            if (subNetworks.size() == 1)
                throw new IllegalArgumentException("Can't remove base network from RootNetwork because it's the only subnetwork");
            // Chose another base network
            CySubNetwork oldBase = base;
            for (CySubNetwork n : subNetworks) {
                if (!n.equals(oldBase)) {
                    base = n;
                    // Better if the new base network is one that can be saved
                    if (n.getSavePolicy() == SavePolicy.SESSION_FILE)
                        break;
                }
            }
        }
        // clean up pointers for nodes in subnetwork
        sub.removeNodes(sub.getNodeList());
        Map<String, CyTable> tableMap;
        tableMap = networkTableMgr.getTables(sub, CyNetwork.class);
        for (CyTable table : tableMap.values()) {
            tableMgr.deleteTableInternal(table.getSUID(), true);
        }
        tableMap = networkTableMgr.getTables(sub, CyNode.class);
        for (CyTable table : tableMap.values()) {
            tableMgr.deleteTableInternal(table.getSUID(), true);
        }
        tableMap = networkTableMgr.getTables(sub, CyEdge.class);
        for (CyTable table : tableMap.values()) {
            tableMgr.deleteTableInternal(table.getSUID(), true);
        }
        subNetworks.remove(sub);
        sub.dispose();
        garbageCollect();
    }
}

Example 50 with CySubNetwork

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

the class NetworkMainPanel method setNetworks.

/**
 * Replace the current network list with the passed ones.
 */
public void setNetworks(final Collection<CySubNetwork> networks) {
    clear();
    ignoreSelectionEvents = true;
    doNotUpdateCollapseExpandButtons = true;
    try {
        for (final CySubNetwork n : networks) addNetwork((CySubNetwork) n);
    } finally {
        doNotUpdateCollapseExpandButtons = false;
        ignoreSelectionEvents = false;
    }
    getRootNetworkListPanel().update();
    updateNetworkHeader();
    updateNodeEdgeCount();
}