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

Example 11 with CyNetworkManager

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

the class CyApplicationManagerImpl method internalSetCurrentNetwork.

private void internalSetCurrentNetwork(CyNetwork network, List<CyEvent<?>> eventsToFire) {
    final CyNetworkManager networkManager = serviceRegistrar.getService(CyNetworkManager.class);
    if (network != null && !networkManager.networkExists(network.getSUID()))
        throw new IllegalArgumentException("Network is not registered in this ApplicationManager: " + network);
    boolean changed = (network == null && currentNetwork != null) || (network != null && !network.equals(currentNetwork));
    if (changed) {
        currentNetwork = network;
        if (network != null) {
            // If the new current network is not selected, reset the selection and select the current one only
            if (!getSelectedNetworks().contains(network))
                internalSetSelectedNetworks(Collections.singletonList(network), eventsToFire);
        }
        eventsToFire.add(new SetCurrentNetworkEvent(this, currentNetwork));
    }
}

Example 12 with CyNetworkManager

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

the class ImportTableDataTask method init.

private final void init() {
    this.name2NetworkMap = new HashMap<>();
    this.name2RootMap = new HashMap<>();
    this.source2targetColumnMap = new HashMap<>();
    this.mappedTables = new ArrayList<>();
    final CyNetworkManager netMgr = serviceRegistrar.getService(CyNetworkManager.class);
    if (netMgr.getNetworkSet().size() > 0) {
        whereImportTable = new ListSingleSelection<>(NETWORK_COLLECTION, NETWORK_SELECTION, UNASSIGNED_TABLE);
        whereImportTable.setSelectedValue(NETWORK_COLLECTION);
        networksPresent = true;
    } else {
        whereImportTable = new ListSingleSelection<>(UNASSIGNED_TABLE);
        whereImportTable.setSelectedValue(UNASSIGNED_TABLE);
    }
    if (byReader) {
        if (reader != null && reader.getTables() != null)
            newTableName = reader.getTables()[0].getTitle();
    } else
        newTableName = globalTable.getTitle();
    if (networksPresent) {
        final List<TableType> options = new ArrayList<>();
        for (TableType type : TableType.values()) options.add(type);
        dataTypeTargetForNetworkCollection = new ListSingleSelection<>(options);
        dataTypeTargetForNetworkCollection.setSelectedValue(TableType.NODE_ATTR);
        dataTypeTargetForNetworkList = new ListSingleSelection<>(options);
        dataTypeTargetForNetworkList.setSelectedValue(TableType.NODE_ATTR);
        for (CyNetwork net : netMgr.getNetworkSet()) {
            final String netName = net.getRow(net).get(CyNetwork.NAME, String.class);
            name2NetworkMap.put(netName, net);
        }
        final CyApplicationManager appMgr = serviceRegistrar.getService(CyApplicationManager.class);
        final List<String> names = new ArrayList<>();
        names.addAll(name2NetworkMap.keySet());
        sort(names);
        if (names.isEmpty()) {
            targetNetworkList = new ListMultipleSelection<>(NO_NETWORKS);
        } else {
            targetNetworkList = new ListMultipleSelection<>(names);
            final CyNetwork currNet = appMgr.getCurrentNetwork();
            if (currNet != null) {
                final String currName = currNet.getRow(currNet).get(CyNetwork.NAME, String.class);
                if (currName != null && targetNetworkList.getPossibleValues().contains(currName))
                    targetNetworkList.setSelectedValues(Collections.singletonList(currName));
            }
            final List<CyNetwork> selectedNetworks = new ArrayList<>();
            for (String netName : targetNetworkList.getSelectedValues()) {
                if (name2NetworkMap.containsKey(netName))
                    selectedNetworks.add(name2NetworkMap.get(netName));
            }
            keyColumnForMappingNetworkList = getColumns(selectedNetworks, dataTypeTargetForNetworkList.getSelectedValue(), CyRootNetwork.DEFAULT_ATTRS);
        }
        final CyRootNetworkManager rootNetMgr = serviceRegistrar.getService(CyRootNetworkManager.class);
        for (CyNetwork net : netMgr.getNetworkSet()) {
            final CyRootNetwork rootNet = rootNetMgr.getRootNetwork(net);
            if (!name2RootMap.containsValue(rootNet))
                name2RootMap.put(rootNet.getRow(rootNet).get(CyRootNetwork.NAME, String.class), rootNet);
        }
        final List<String> rootNames = new ArrayList<>();
        rootNames.addAll(name2RootMap.keySet());
        sort(rootNames);
        targetNetworkCollection = new ListSingleSelection<>(rootNames);
        if (!rootNames.isEmpty()) {
            targetNetworkCollection.setSelectedValue(rootNames.get(0));
            final CyNetwork currNet = appMgr.getCurrentNetwork();
            final CyRootNetwork currRootNet = currNet instanceof CySubNetwork ? rootNetMgr.getRootNetwork(currNet) : null;
            if (currRootNet != null) {
                final String currName = currRootNet.getRow(currRootNet).get(CyNetwork.NAME, String.class);
                if (currName != null && targetNetworkCollection.getPossibleValues().contains(currName))
                    targetNetworkCollection.setSelectedValue(currName);
            }
            keyColumnForMapping = getColumns(Collections.singletonList(name2RootMap.get(targetNetworkCollection.getSelectedValue())), dataTypeTargetForNetworkCollection.getSelectedValue(), CyRootNetwork.SHARED_ATTRS);
        }
    }
}

Example 13 with CyNetworkManager

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

the class OpenSessionTask method run.

/**
 * Clear current session and open the cys file.
 */
@Override
public void run(final TaskMonitor taskMonitor) throws Exception {
    final CyNetworkManager netManager = serviceRegistrar.getService(CyNetworkManager.class);
    final CyTableManager tableManager = serviceRegistrar.getService(CyTableManager.class);
    if (netManager.getNetworkSet().isEmpty() && tableManager.getAllTables(false).isEmpty())
        loadSession(this);
    else
        insertTasksAfterCurrentTask(new OpenSessionWithWarningTask());
}

Example 14 with CyNetworkManager

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

the class DeleteNestedNetworkTaskFactory method isReady.

@Override
public boolean isReady(View<CyNode> nodeView, CyNetworkView networkView) {
    if (!super.isReady(nodeView, networkView))
        return false;
    // Check if there is a network pointer and if it is registered.
    // Nodes with unregistered network pointers should be ignored because they are probably being used as something
    // else other than regular nested networks (e.g. groups).
    final CyNode node = nodeView.getModel();
    final CyNetwork np = node.getNetworkPointer();
    final CyNetwork network = networkView.getModel();
    final CyNetworkManager netMgr = serviceRegistrar.getService(CyNetworkManager.class);
    final CyGroupManager grMgr = serviceRegistrar.getService(CyGroupManager.class);
    return np != null && netMgr.networkExists(np.getSUID()) && !grMgr.isGroup(node, network);
}

Example 15 with CyNetworkManager

use of org.cytoscape.model.CyNetworkManager in project PhenomeScape by soulj.

the class LoadNetworkTask method run.

@Override
public void run(TaskMonitor taskMonitor) throws Exception {
    taskMonitor.setTitle("Loading " + species + " Network");
    taskMonitor.setStatusMessage("Creating network");
    CyNetworkFactory networkFactory = cyServiceRegistrar.getService(CyNetworkFactory.class);
    CyNetwork network = networkFactory.createNetwork();
    network.getRow(network).set(CyNetwork.NAME, NetworkUtils.getUniqueNetworkName(cyServiceRegistrar, species + "Network"));
    network.getDefaultEdgeTable().createColumn("Confidence", Double.class, false);
    Map<String, CyNode> nodeNameMap = new HashMap<String, CyNode>();
    Scanner sc = new Scanner(input);
    nodeNameMap = new HashMap<String, CyNode>();
    while (sc.hasNextLine()) {
        String line = sc.nextLine();
        String[] nodes = line.split("\t");
        CyNode node1 = null;
        CyNode node2 = null;
        if (nodeNameMap.containsKey(nodes[0])) {
            node1 = nodeNameMap.get(nodes[0]);
        } else {
            node1 = network.addNode();
            CyRow attributes = network.getRow(node1);
            attributes.set("name", nodes[0]);
            nodeNameMap.put(nodes[0], node1);
        }
        if (nodeNameMap.containsKey(nodes[1])) {
            node2 = (CyNode) nodeNameMap.get(nodes[1]);
        } else {
            node2 = network.addNode();
            CyRow attributes = network.getRow(node2);
            attributes.set("name", nodes[1]);
            nodeNameMap.put(nodes[1], node2);
        }
        CyEdge myEdge = network.addEdge(node1, node2, false);
        network.getRow(myEdge).set("interaction", "ppi");
        network.getRow(myEdge).set("Confidence", Double.parseDouble(nodes[2]));
        network.getRow(myEdge).set("name", nodes[0] + " (ppi) " + nodes[1]);
    }
    sc.close();
    CyNetworkManager networkManager = cyServiceRegistrar.getService(CyNetworkManager.class);
    networkManager.addNetwork(network);
}