Examples with CyApplicationManager org.cytoscape.application.CyApplicationManager used on opensource projects

Example 21 with CyApplicationManager

use of org.cytoscape.application.CyApplicationManager in project cytoscape-impl by cytoscape.

the class GradientEditor method setValue.

@Override
@SuppressWarnings({ "unchecked", "rawtypes" })
public void setValue(final Object value) {
    if (value instanceof ContinuousMapping == false)
        throw new IllegalArgumentException("Value should be ContinuousMapping: this is " + value);
    final CyApplicationManager appMgr = servicesUtil.get(CyApplicationManager.class);
    final CyNetwork currentNetwork = appMgr.getCurrentNetwork();
    if (currentNetwork == null)
        return;
    ContinuousMapping<?, ?> mTest = (ContinuousMapping<?, ?>) value;
    // TODO: error chekcing
    mapping = (ContinuousMapping<Double, Color>) value;
    Class<? extends CyIdentifiable> type = (Class<? extends CyIdentifiable>) mapping.getVisualProperty().getTargetDataType();
    final CyNetworkTableManager netTblMgr = servicesUtil.get(CyNetworkTableManager.class);
    final CyTable attr = netTblMgr.getTable(appMgr.getCurrentNetwork(), type, CyNetwork.DEFAULT_ATTRS);
    final VisualMappingManager vmMgr = servicesUtil.get(VisualMappingManager.class);
    editorPanel = new GradientEditorPanel(vmMgr.getCurrentVisualStyle(), mapping, attr, editorManager.getValueEditor(Paint.class), servicesUtil);
}

Example 22 with CyApplicationManager

use of org.cytoscape.application.CyApplicationManager in project cytoscape-impl by cytoscape.

the class MappingFunctionFactoryProxy method getMappingFactories.

public Set<VisualMappingFunctionFactory> getMappingFactories() {
    final SortedSet<VisualMappingFunctionFactory> set = new TreeSet<VisualMappingFunctionFactory>(new Comparator<VisualMappingFunctionFactory>() {

        @Override
        public int compare(final VisualMappingFunctionFactory f1, final VisualMappingFunctionFactory f2) {
            // Locale-specific sorting
            final Collator collator = Collator.getInstance(Locale.getDefault());
            collator.setStrength(Collator.PRIMARY);
            return collator.compare(f1.toString(), f2.toString());
        }
    });
    final MappingFunctionFactoryManager mappingFactoryMgr = servicesUtil.get(MappingFunctionFactoryManager.class);
    set.addAll(mappingFactoryMgr.getFactories());
    if (currentColumnName != null && currentTargetDataType != null) {
        // Remove the factories that don't make sense for the current column type
        final CyApplicationManager appMgr = servicesUtil.get(CyApplicationManager.class);
        final CyNetwork net = appMgr.getCurrentNetwork();
        if (net != null) {
            final CyTable table = net.getTable(currentTargetDataType, CyNetwork.DEFAULT_ATTRS);
            final CyColumn column = table.getColumn(currentColumnName);
            if (column != null && !Number.class.isAssignableFrom(column.getType()))
                set.remove(mappingFactoryMgr.getFactory(ContinuousMapping.class));
        }
    }
    return set;
}

Example 23 with CyApplicationManager

use of org.cytoscape.application.CyApplicationManager 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 24 with CyApplicationManager

use of org.cytoscape.application.CyApplicationManager in project cytoscape-impl by cytoscape.

the class LayoutSettingsDialog method getAlgorithmCmb.

private JComboBox<CyLayoutAlgorithm> getAlgorithmCmb() {
    if (algorithmCmb == null) {
        algorithmCmb = new JComboBox<CyLayoutAlgorithm>();
        algorithmCmb.setRenderer(new LayoutAlgorithmListCellRenderer("-- Select algorithm to view settings --"));
        algorithmCmb.addActionListener(new ActionListener() {

            @Override
            public void actionPerformed(ActionEvent e) {
                if (initializing)
                    return;
                final Object o = algorithmCmb.getSelectedItem();
                if (o instanceof CyLayoutAlgorithm) {
                    currentLayout = (CyLayoutAlgorithm) o;
                    final PanelTaskManager taskMgr = serviceRegistrar.getService(PanelTaskManager.class);
                    final CyApplicationManager appMgr = serviceRegistrar.getService(CyApplicationManager.class);
                    // Checking if the context has already been charged, if so there is no need to do it again
                    final Object context = currentLayout.getDefaultLayoutContext();
                    tunablesToSave.add(currentLayout);
                    final DynamicTaskFactoryProvisioner factoryProvisioner = serviceRegistrar.getService(DynamicTaskFactoryProvisioner.class);
                    final TaskFactory provisioner = factoryProvisioner.createFor(wrapWithContext(currentLayout, context));
                    final JPanel tunablePnl = taskMgr.getConfiguration(provisioner, context);
                    layoutAttrPnl = new JPanel();
                    layoutAttrPnl.setLayout(new BoxLayout(layoutAttrPnl, BoxLayout.PAGE_AXIS));
                    // Transparent if Aqua
                    layoutAttrPnl.setOpaque(!LookAndFeelUtil.isAquaLAF());
                    final CyNetworkView view = appMgr.getCurrentNetworkView();
                    setNetworkView(view);
                    getAlgorithmPnl().removeAll();
                    getAlgorithmPnl().add(layoutAttrPnl);
                    if (tunablePnl != null) {
                        tunablePnl.setAlignmentX(Component.CENTER_ALIGNMENT);
                        setPanelsTransparent(tunablePnl);
                        getAlgorithmPnl().add(tunablePnl);
                    }
                    if (currentLayout.getSupportsSelectedOnly() && hasSelectedNodes(view)) {
                        selectedTunable.selectedNodesOnly = true;
                        final JPanel panel = taskMgr.getConfiguration(null, selectedTunable);
                        setPanelsTransparent(panel);
                        getAlgorithmPnl().add(panel);
                    }
                    currentAction = provisioner;
                    LayoutSettingsDialog.this.pack();
                }
            }
        });
    }
    return algorithmCmb;
}

Example 25 with CyApplicationManager

use of org.cytoscape.application.CyApplicationManager in project cytoscape-impl by cytoscape.

the class SelectModeAction method actionPerformed.

@Override
public void actionPerformed(ActionEvent e) {
    final CyApplicationManager applicationManager = serviceRegistrar.getService(CyApplicationManager.class);
    final CyNetworkView view = applicationManager.getCurrentNetworkView();
    if (view != null) {
        if (name.equalsIgnoreCase(NODES)) {
            view.setLockedValue(NETWORK_NODE_SELECTION, Boolean.TRUE);
            view.setLockedValue(NETWORK_EDGE_SELECTION, Boolean.FALSE);
        } else if (name.equalsIgnoreCase(EDGES)) {
            view.setLockedValue(NETWORK_NODE_SELECTION, Boolean.FALSE);
            view.setLockedValue(NETWORK_EDGE_SELECTION, Boolean.TRUE);
        } else if (name.equalsIgnoreCase(ALL)) {
            view.setLockedValue(NETWORK_NODE_SELECTION, Boolean.TRUE);
            view.setLockedValue(NETWORK_EDGE_SELECTION, Boolean.TRUE);
        }
    }
}