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

Example 16 with CyApplicationManager

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

the class ControlPanel method updatePanels.

private void updatePanels() {
    final CyApplicationManager appMgr = serviceRegistrar.getService(CyApplicationManager.class);
    final CyNetworkView view = appMgr.getCurrentNetworkView();
    final Collection<View<CyNode>> selectedNodeViews = view != null ? findSelectedNodes(view) : null;
    invokeOnEDT(() -> {
        scalePanel.setEnabled(view != null);
        rotatePanel.setEnabled(view != null);
        final boolean enabled = selectedNodeViews != null && !selectedNodeViews.isEmpty();
        alignPanel.setEnabled(enabled);
        distPanel.setEnabled(enabled);
        stackPanel.setEnabled(enabled);
    });
}

Example 17 with CyApplicationManager

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

the class ControlPanel method handleEvent.

@Override
public void handleEvent(RowsSetEvent e) {
    if (loadingSession)
        return;
    final CyApplicationManager appMgr = serviceRegistrar.getService(CyApplicationManager.class);
    final CyNetworkView currentView = appMgr.getCurrentNetworkView();
    if (currentView == null)
        return;
    final CyTable tbl = e.getSource();
    final CyNetworkTableManager netTblMgr = serviceRegistrar.getService(CyNetworkTableManager.class);
    final CyNetwork net = netTblMgr.getNetworkForTable(tbl);
    if (net == null || !net.equals(currentView.getModel()) || !tbl.equals(net.getDefaultNodeTable()))
        return;
    final Collection<RowSetRecord> selectedRecords = e.getColumnRecords(CyNetwork.SELECTED);
    if (!selectedRecords.isEmpty())
        updatePanels();
}

Example 18 with CyApplicationManager

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

the class VizMapPropertyBuilder method createMappingProperties.

public <K, V> void createMappingProperties(final VisualMappingFunction<K, V> visualMapping, final PropertySheetPanel propertySheetPanel, final VisualMappingFunctionFactory factory) {
    final String attrName = visualMapping.getMappingColumnName();
    if (attrName == null)
        return;
    removeMappingProperties(propertySheetPanel);
    final VisualProperty<V> vp = visualMapping.getVisualProperty();
    final VisualPropertyEditor<V> vpEditor = editorManager.getVisualPropertyEditor(vp);
    if (visualMapping instanceof DiscreteMapping) {
        // Discrete Mapping
        // This set should not contain null!
        final SortedSet<Object> attrSet = new TreeSet<Object>();
        final CyApplicationManager appMgr = servicesUtil.get(CyApplicationManager.class);
        final CyNetwork network = appMgr.getCurrentNetwork();
        if (network != null) {
            final Set<CyIdentifiable> graphObjects = new HashSet<CyIdentifiable>();
            if (network != null) {
                if (vp.getTargetDataType().equals(CyNode.class)) {
                    graphObjects.addAll(network.getNodeList());
                } else if (vp.getTargetDataType().equals(CyEdge.class)) {
                    graphObjects.addAll(network.getEdgeList());
                } else if (vp.getTargetDataType().equals(CyNetwork.class)) {
                    graphObjects.add(network);
                } else {
                    throw new IllegalArgumentException("Data type not supported: " + vp.getTargetDataType());
                }
            }
            if (vp.getTargetDataType() == CyNetwork.class) {
                final CyRow row = network.getRow(network);
                final CyColumn column = row.getTable().getColumn(attrName);
                if (column != null)
                    processDiscretValues(row, attrName, column, column.getType(), attrSet);
            } else {
                // Make sure all data sets have the same data type.
                if (!graphObjects.isEmpty()) {
                    final CyIdentifiable firstEntry = graphObjects.iterator().next();
                    final CyRow firstRow = network.getRow(firstEntry);
                    final CyColumn column = firstRow.getTable().getColumn(attrName);
                    if (column != null) {
                        final Class<?> type = column.getType();
                        for (final CyIdentifiable go : graphObjects) {
                            final CyRow row = network.getRow(go);
                            processDiscretValues(row, attrName, column, type, attrSet);
                        }
                    }
                }
            }
        }
        // Also keep current mapping entries that have non-null values
        for (final Map.Entry<K, V> entry : ((DiscreteMapping<K, V>) visualMapping).getAll().entrySet()) {
            if (entry.getValue() != null)
                attrSet.add(entry.getKey());
        }
        setDiscreteProps(vp, visualMapping, attrSet, vpEditor, propertySheetPanel);
    } else if (visualMapping instanceof ContinuousMapping) {
        // TODO: How do we decide when to reset the range tracer for this mapping?
        final VizMapperProperty<String, VisualMappingFunction, VisualMappingFunction<K, V>> graphicalView = new VizMapperProperty<String, VisualMappingFunction, VisualMappingFunction<K, V>>(CellType.CONTINUOUS, visualMapping.getVisualProperty().getDisplayName() + "_" + GRAPHICAL_MAP_VIEW, visualMapping.getClass());
        graphicalView.setShortDescription("Continuous Mapping from " + visualMapping.getMappingColumnName() + " to " + visualMapping.getVisualProperty().getDisplayName());
        graphicalView.setValue(visualMapping);
        graphicalView.setDisplayName("Current Mapping");
        propertySheetPanel.addProperty(2, graphicalView);
        final PropertySheetTable table = propertySheetPanel.getTable();
        final PropertyRendererRegistry rendReg = (PropertyRendererRegistry) table.getRendererFactory();
        final PropertyEditorRegistry cellEditorFactory = (PropertyEditorRegistry) table.getEditorFactory();
        final PropertyEditor continuousCellEditor = editorManager.getContinuousEditor(vp);
        if (continuousCellEditor == null) {
            throw new NullPointerException("Continuous Mapping cell editor is null.");
        } else {
            // Renderer for Continuous mapping icon cell
            final TableCellRenderer continuousRenderer = vpEditor.getContinuousTableCellRenderer((ContinuousMappingEditor<? extends Number, V>) continuousCellEditor);
            rendReg.registerRenderer(graphicalView, continuousRenderer);
            continuousCellEditor.setValue(visualMapping);
            cellEditorFactory.registerEditor(graphicalView, continuousCellEditor);
        }
    } else if (visualMapping instanceof PassthroughMapping && (attrName != null)) {
    // Doesn't need to display the mapped values!
    } else {
        throw new IllegalArgumentException("Unsupported mapping type: " + visualMapping);
    }
    propertySheetPanel.getTable().repaint();
    propertySheetPanel.repaint();
}

Example 19 with CyApplicationManager

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

the class FitLabelMappingGenerator method generateMap.

@Override
public <T> Map<T, V> generateMap(final Set<T> tableValues) {
    // Generate map for the current network view.
    final CyApplicationManager appMgr = servicesUtil.get(CyApplicationManager.class);
    final CyNetworkView networkView = appMgr.getCurrentNetworkView();
    // If current view is not available, simply return empty map.
    if (networkView == null)
        return Collections.emptyMap();
    // If given set is empty, return empty map.
    if (tableValues == null || tableValues.isEmpty())
        return Collections.emptyMap();
    // This only works with NAME column.
    final T testName = tableValues.iterator().next();
    if (testName instanceof String == false)
        throw new IllegalArgumentException("This generator only works with 'name' column.");
    final CyNetwork network = networkView.getModel();
    final CyTable nodeTable = networkView.getModel().getDefaultNodeTable();
    final VisualMappingManager vmMgr = servicesUtil.get(VisualMappingManager.class);
    final VisualStyle style = vmMgr.getCurrentVisualStyle();
    // Check label size mapping exists or not
    final VisualMappingFunction<?, Integer> fontSizeMapping = style.getVisualMappingFunction(BasicVisualLexicon.NODE_LABEL_FONT_SIZE);
    // Use default label width for checking.  TODO: should we use mapping?
    final Double maxLabelWidth = style.getDefaultValue(BasicVisualLexicon.NODE_LABEL_WIDTH);
    final Map<T, V> valueMap = new HashMap<T, V>();
    for (final T attrVal : tableValues) {
        final Collection<CyRow> rows = nodeTable.getMatchingRows(CyNetwork.NAME, attrVal);
        CyRow row = null;
        if (rows.isEmpty() == false)
            row = rows.iterator().next();
        else
            continue;
        final Long suid = row.get(CyIdentifiable.SUID, Long.class);
        final View<CyNode> nodeView = networkView.getNodeView(network.getNode(suid));
        if (nodeView == null)
            continue;
        final String labelText = nodeView.getVisualProperty(BasicVisualLexicon.NODE_LABEL);
        final int textLen = labelText.length();
        final int fontSize;
        if (fontSizeMapping == null)
            fontSize = style.getDefaultValue(BasicVisualLexicon.NODE_LABEL_FONT_SIZE);
        else
            fontSize = nodeView.getVisualProperty(BasicVisualLexicon.NODE_LABEL_FONT_SIZE);
        final Double width = fontSize * textLen * 0.7;
        if (maxLabelWidth > width)
            valueMap.put(attrVal, (V) width);
        else
            valueMap.put(attrVal, (V) maxLabelWidth);
    }
    return valueMap;
}

Example 20 with CyApplicationManager

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

the class C2CEditor method setValue.

@Override
@SuppressWarnings("unchecked")
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;
    mapping = (ContinuousMapping<K, V>) 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 C2CMappingEditorPanel<K, V>(vmMgr.getCurrentVisualStyle(), mapping, attr, servicesUtil);
}