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

Example 56 with CyNetwork

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

the class DetermineDistinctValuesTask method run.

/**
 *  DOCUMENT ME!
 */
public void run(TaskMonitor taskMonitor) {
    taskMonitor.setProgress(-1);
    // Obtain distinct attribute values
    CyNetwork network = applicationManager.getCurrentNetwork();
    Iterator<? extends CyIdentifiable> iterator;
    if (parentDialog.getIndexType() == QuickFind.INDEX_NODES) {
        iterator = network.getNodeList().iterator();
    } else {
        iterator = network.getEdgeList().iterator();
    }
    String[] values = CyAttributesUtil.getDistinctAttributeValues(network, iterator, attributeKey, 5);
    if ((values != null) && (values.length > 0)) {
        for (int i = 0; i < values.length; i++) {
            tableModel.setValueAt(values[i], i, 0);
        }
        parentDialog.enableApplyButton(true);
    } else {
        VisualLexicon lexicon = applicationManager.getCurrentRenderingEngine().getVisualLexicon();
        CyNetworkView view = applicationManager.getCurrentNetworkView();
        String title = VisualPropertyUtil.get(lexicon, view, "NETWORK_TITLE", BasicVisualLexicon.NETWORK, String.class);
        tableModel.setValueAt("No values found in network:  " + title + ".  Cannot create index.", 0, 0);
    }
}

Example 57 with CyNetwork

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

the class FilterUtil method isDynamicFilter.

// If a network size (node count and edge count) is less than DYNAMIC_FILTER_THRESHOLD, return true
// Otherwise, return false
public static boolean isDynamicFilter(CompositeFilter pFilter) {
    CyNetwork theNetwork = pFilter.getNetwork();
    if (theNetwork == null) {
        return false;
    }
    int nodeCount = theNetwork.getNodeCount();
    int edgeCount = theNetwork.getEdgeCount();
    int dynamicFilterThresholdValue = -1;
    // // TODO: What do we do about CyInit*?
    // String dynamicFilterThreshold = CytoscapeInit.getProperties().getProperty(DYNAMIC_FILTER_THRESHOLD);
    // if (dynamicFilterThreshold == null) { // threshold not defined, use the default value
    dynamicFilterThresholdValue = DEFAULT_DYNAMIC_FILTER_THRESHOLD;
    if (pFilter.getAdvancedSetting().isNodeChecked() && pFilter.getAdvancedSetting().isEdgeChecked()) {
        // Select both nodes and edges
        if (nodeCount > dynamicFilterThresholdValue || edgeCount > dynamicFilterThresholdValue) {
            return false;
        }
        return true;
    } else if (pFilter.getAdvancedSetting().isNodeChecked()) {
        // Select node only
        if (nodeCount < dynamicFilterThresholdValue) {
            return true;
        }
    } else if (pFilter.getAdvancedSetting().isEdgeChecked()) {
        // select edge only
        if (edgeCount < dynamicFilterThresholdValue) {
            return true;
        }
    }
    return false;
}

Example 58 with CyNetwork

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

the class CySessionManagerImpl method getCurrentSession.

@Override
public CySession getCurrentSession() {
    // Apps who want to save anything to a session will have to listen for this event
    // and will then be responsible for adding files through SessionAboutToBeSavedEvent.addAppFiles(..)
    final SessionAboutToBeSavedEvent savingEvent = new SessionAboutToBeSavedEvent(this);
    final CyEventHelper eventHelper = serviceRegistrar.getService(CyEventHelper.class);
    eventHelper.fireEvent(savingEvent);
    final Set<CyNetwork> networks = getSerializableNetworks();
    final CyNetworkViewManager nvMgr = serviceRegistrar.getService(CyNetworkViewManager.class);
    final Set<CyNetworkView> netViews = nvMgr.getNetworkViewSet();
    // Visual Styles Map
    final Map<CyNetworkView, String> stylesMap = new HashMap<>();
    final VisualMappingManager vmMgr = serviceRegistrar.getService(VisualMappingManager.class);
    if (netViews != null) {
        for (final CyNetworkView nv : netViews) {
            final VisualStyle style = vmMgr.getVisualStyle(nv);
            if (style != null)
                stylesMap.put(nv, style.getTitle());
        }
    }
    final Map<String, List<File>> appMap = savingEvent.getAppFileListMap();
    final Set<CyTableMetadata> metadata = createTablesMetadata(networks);
    final Set<VisualStyle> styles = vmMgr.getAllVisualStyles();
    final Set<CyProperty<?>> props = getAllProperties();
    // Build the session
    final CySession sess = new CySession.Builder().properties(props).appFileListMap(appMap).tables(metadata).networks(networks).networkViews(netViews).visualStyles(styles).viewVisualStyleMap(stylesMap).build();
    return sess;
}

Example 59 with CyNetwork

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

the class CySessionManagerImpl method restoreNetworkSelection.

private void restoreNetworkSelection(final CySession sess, final List<CyNetwork> selectedNets) {
    // If the current view/network was not set, set the first selected network as current
    if (!selectedNets.isEmpty()) {
        final CyNetwork cn = selectedNets.get(0);
        final CyApplicationManager appMgr = serviceRegistrar.getService(CyApplicationManager.class);
        appMgr.setCurrentNetwork(cn);
        // Also set the current view, if there is one
        final CyNetworkViewManager nvMgr = serviceRegistrar.getService(CyNetworkViewManager.class);
        final Collection<CyNetworkView> cnViews = nvMgr.getNetworkViews(cn);
        final CyNetworkView cv = cnViews.isEmpty() ? null : cnViews.iterator().next();
        appMgr.setCurrentNetworkView(cv);
        // The selected networks must be set after setting the current one!
        appMgr.setSelectedNetworks(selectedNets);
    }
}

Example 60 with CyNetwork

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

the class CySessionManagerImpl method restoreNetworks.

private void restoreNetworks(final CySession sess) {
    logger.debug("Restoring networks...");
    Set<CyNetwork> networks = sess.getNetworks();
    final CyNetworkManager netMgr = serviceRegistrar.getService(CyNetworkManager.class);
    for (CyNetwork n : networks) {
        netMgr.addNetwork(n, false);
    }
}