private Set<View<CyNode>> getLayoutNodes(CyLayoutAlgorithm layout, CyNetworkView networkView) {
if (layout.getSupportsSelectedOnly() && selectedTunable.selectedNodesOnly) {
Set<View<CyNode>> nodeViews = new HashSet<View<CyNode>>();
CyNetwork network = networkView.getModel();
for (View<CyNode> view : networkView.getNodeViews()) {
if (network.getRow(view.getModel()).get(CyNetwork.SELECTED, Boolean.class)
&& view.getVisualProperty(BasicVisualLexicon.NODE_VISIBLE)) {
nodeViews.add(view);
}
}
return nodeViews;
}
return CyLayoutAlgorithm.ALL_NODE_VIEWS;
}
public void undo() {
final Collection<CyNetworkView> views = networkViewManager.getNetworkViews(network);
CyNetworkView view = null;
if (views.size() != 0) view = views.iterator().next();
networkCenterX = view.getVisualProperty(NETWORK_CENTER_X_LOCATION);
networkCenterY = view.getVisualProperty(NETWORK_CENTER_Y_LOCATION);
networkCenterZ = view.getVisualProperty(NETWORK_CENTER_Z_LOCATION);
networkScaleFactor = view.getVisualProperty(NETWORK_SCALE_FACTOR);
final Collection<View<CyNode>> nodeViews = view.getNodeViews();
nodesAndLocations = new WeakHashMap<CyNode, NodeLocations>(nodeViews.size());
for (final View<CyNode> nodeView : nodeViews)
nodesAndLocations.put(nodeView.getModel(), new NodeLocations(nodeView));
networkViewManager.destroyNetworkView(view);
}
public void redo() {
;
final CyNetworkView view = viewFactory.createNetworkView(network);
networkViewManager.addNetworkView(view);
for (final View<CyNode> nodeView : view.getNodeViews())
nodesAndLocations.get(nodeView.getModel()).restoreLocations(nodeView);
view.setVisualProperty(NETWORK_CENTER_X_LOCATION, networkCenterX);
view.setVisualProperty(NETWORK_CENTER_Y_LOCATION, networkCenterY);
view.setVisualProperty(NETWORK_CENTER_Z_LOCATION, networkCenterZ);
view.setVisualProperty(NETWORK_SCALE_FACTOR, networkScaleFactor);
eventHelper.flushPayloadEvents();
view.updateView();
}
private final void clearAll(
final CyNetworkView netView, final View<? extends CyIdentifiable> nodeView) {
boolean needToUpdateView = false;
final VisualStyle style = vmm.getCurrentVisualStyle();
for (VisualProperty<?> vp : vpSet) {
final boolean lock = nodeView.isDirectlyLocked(vp);
if (lock) {
nodeView.clearValueLock(vp);
needToUpdateView = true;
}
}
if (needToUpdateView) {
style.apply(netView);
netView.updateView();
}
}
public TaskIterator createTaskIterator(View<CyNode> nView, CyNetworkView netView) {
List<CyNode> selectedNodes =
CyTableUtil.getNodesInState(netView.getModel(), CyNetwork.SELECTED, true);
if (selectedNodes == null || selectedNodes.size() == 0)
selectedNodes = Collections.singletonList(nView.getModel());
return new TaskIterator(
new SMARTSSearchTask(netView.getModel(), selectedNodes, scope, showResult, settings));
}
/**
* Apply bypass
*
* @param netView
* @param graphObjectView
* @param vp
*/
private final void applBypassValue(
final CyNetworkView netView,
final View<? extends CyIdentifiable> graphObjectView,
VisualProperty<?> vp) {
final ValueEditor<Object> editor =
(ValueEditor<Object>) editorManager.getValueEditor(vp.getRange().getType());
final Object bypassValue = editor.showEditor(null, graphObjectView.getVisualProperty(vp));
// Set lock for the vp
graphObjectView.setLockedValue(vp, bypassValue);
// Apply the new value only for the given view
// TODO don't do this, because it overwrites some bypassed values with default ones!!! Calling
// setLockedValue should be enough
// final CyRow row = netView.getModel().getRow(graphObjectView.getModel());
// vmm.getCurrentVisualStyle().apply(row, graphObjectView);
// Redraw the view
netView.updateView();
}
@SuppressWarnings({"unchecked", "rawtypes"})
@Override
public void apply(final CyRow row, final View<? extends CyIdentifiable> view) {
if (view == null) {
logger.warn("Tried to apply Visual Style to null view");
return;
}
ApplyHandler handler = null;
for (final Class<?> viewType : applyHandlersMap.keySet()) {
if (viewType.isAssignableFrom(view.getModel().getClass())) {
handler = applyHandlersMap.get(viewType);
break;
}
}
if (handler == null)
throw new IllegalArgumentException("This view type is not supported: " + view.getClass());
handler.apply(row, view);
}
/**
* Directly update view object.
*
* @param view
* @param rootNode
* @param lexicon
*/
public Response updateView(
final View<? extends CyIdentifiable> view,
final JsonNode rootNode,
final VisualLexicon lexicon) {
for (final JsonNode vpNode : rootNode) {
String vpName = vpNode.get(MAPPING_VP).textValue();
final VisualProperty<?> vp = getVisualProperty(vpName, lexicon);
final JsonNode value = vpNode.get(MAPPING_DISCRETE_VALUE);
if (vp == null || value == null) {
continue;
}
Object parsedValue = null;
if (value.isTextual()) {
parsedValue = vp.parseSerializableString(value.asText());
} else {
parsedValue = vp.parseSerializableString(value.toString());
}
view.setVisualProperty(vp, parsedValue);
}
return Response.ok().build();
}
@Override
public List<BarLayer> getLayers(
CyNetworkView networkView, View<? extends CyIdentifiable> nodeView) {
CyNetwork network = networkView.getModel();
if (!(nodeView.getModel() instanceof CyNode)) return null;
layers = new ArrayList<>();
CyNode node = (CyNode) nodeView.getModel();
// Create all of our pie slices. Each slice becomes a layer
if (attributes != null && attributes.size() > 0) {
// System.out.println("Getting data from attributes for node "+node);
values = getDataFromAttributes(network, node, attributes, labels);
// System.out.println("Data from attributes returns "+values.size()+" values");
colorList = convertInputToColor(colorString, values);
}
// Protect against missing values in the input stream
// if (values == null || colorList == null) return layers;
if (labels != null
&& labels.size() > 0
&& (labels.size() != values.size() || labels.size() != colorList.size())) {
logger.error(
"barchart: number of labels ("
+ labels.size()
+ "), values ("
+ values.size()
+ "), and colors ("
+ colorList.size()
+ ") don't match");
return null;
}
List<BarLayer> labelList = new ArrayList<BarLayer>();
double minValue = 0.000001;
double maxValue = -minValue;
for (Double val : values) {
if (val == null) continue;
minValue = Math.min(minValue, val);
maxValue = Math.max(maxValue, val);
}
double labelMin = minValue;
if (normalized) {
minValue = rangeMin;
maxValue = rangeMax;
}
int nBars = values.size();
Font font = getFont();
for (int bar = 0; bar < nBars; bar++) {
String label = null;
if (labels != null && labels.size() > 0) label = labels.get(bar);
if (values.get(bar) == null || values.get(bar) == 0.0) continue;
// System.out.println("Creating bar #"+bar);
// Create the slice
BarLayer bl =
new BarLayer(
bar,
nBars,
separation,
values.get(bar),
minValue,
maxValue,
normalized,
ybase,
colorList.get(bar),
showAxes,
borderWidth,
scale);
if (bl == null) continue;
layers.add(bl);
// System.out.println("BarLayer: "+bar+" bounds: "+bl.getShape().getBounds2D());
if (label != null) {
// System.out.println("Creating label for bar #"+bar);
// Now, create the label
BarLayer labelLayer =
new BarLayer(
bar,
nBars,
separation,
minValue,
maxValue,
normalized,
labelMin,
ybase,
label,
font,
labelColor,
showAxes,
scale);
if (labelLayer != null) labelList.add(labelLayer);
}
}
// System.out.println("Created "+layers.size()+" bar layers");
// Now add all of our labels so they will be on top of our slices
if (labelList != null && labelList.size() > 0) layers.addAll(labelList);
// System.out.println("Created "+layers.size()+" total layers");
shapeLayers = layers;
return layers;
}
public TaskIterator createTaskIterator(View<CyEdge> arg0, CyNetworkView arg1) {
return new TaskIterator(new RemoveEdgeTask(mgr, arg0.getModel()));
}
public boolean isReady(View<CyEdge> edgeView, CyNetworkView networkView) {
if (super.isReady(edgeView, networkView) && mgr.setsCount() == 0) return false;
if (mgr.isInSet(edgeView.getModel().getSUID())) return true;
return false;
}
void restoreLocations(final View<CyNode> nodeView) {
nodeView.setVisualProperty(NODE_X_LOCATION, xLocation);
nodeView.setVisualProperty(NODE_Y_LOCATION, yLocation);
nodeView.setVisualProperty(NODE_Z_LOCATION, zLocation);
}
NodeLocations(final View<CyNode> nodeView) {
xLocation = nodeView.getVisualProperty(NODE_X_LOCATION);
yLocation = nodeView.getVisualProperty(NODE_Y_LOCATION);
zLocation = nodeView.getVisualProperty(NODE_Z_LOCATION);
}
/**
* @param netView
* @param view a View<CyNode>, View<CyEdge> or View<CyNetwork> object
* @return
*/
public CyMenuItem build(final CyNetworkView netView, final View<? extends CyIdentifiable> view) {
final Class<? extends CyIdentifiable> targetClass = view.getModel().getClass();
final Queue<VisualLexiconNode> queue =
new PriorityQueue<VisualLexiconNode>(50, new VisualLexiconNodeComparator());
final Map<VisualLexiconNode, JMenuItem> menuMap = new HashMap<VisualLexiconNode, JMenuItem>();
final JMenu rootJMenu = new JMenu(ROOT_MENU_LABEL);
final CyMenuItem rootMenu = new CyMenuItem(rootJMenu, ROOT_GRAVITY);
queue.addAll(root.getChildren());
menuMap.put(root, rootMenu.getMenuItem());
// Node size, width and height
JMenuItem menuItemNodeSize = null;
JMenuItem menuItemNodeWidth = null;
JMenuItem menuItemNodeHeight = null;
final Set<VisualLexiconNode> nextNodes = new HashSet<VisualLexiconNode>();
while (!queue.isEmpty()) {
final VisualLexiconNode curretNode = queue.poll();
final VisualProperty<?> vp = curretNode.getVisualProperty();
if (vp.getTargetDataType().isAssignableFrom(targetClass)) {
final Collection<VisualLexiconNode> children = curretNode.getChildren();
nextNodes.addAll(children);
final JMenuItem menu;
if (children.isEmpty() && PropertySheetUtil.isCompatible(vp)) {
final boolean lock = view.isDirectlyLocked(vp);
if (lock) {
menu = new JMenu(vp.getDisplayName());
final JMenuItem clear = new JMenuItem("Clear");
clear.addActionListener(
new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
view.clearValueLock(vp);
netView.updateView();
}
});
final JMenuItem edit = new JMenuItem("Edit Bypass");
edit.addActionListener(
new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
applBypassValue(netView, view, vp);
}
});
menu.add(clear);
menu.add(edit);
// Update color
menu.setForeground(ENABLED_COLOR);
menu.setIcon(ENABLED_ICON);
menu.setFont(ENABLED_FONT);
VisualLexiconNode parent = curretNode.getParent();
while (parent != root) {
JMenuItem enabledPath = menuMap.get(parent);
enabledPath.setForeground(ENABLED_COLOR);
enabledPath.setIcon(ENABLED_ICON);
enabledPath.setFont(ENABLED_FONT);
parent = parent.getParent();
}
rootJMenu.setIcon(ENABLED_ICON);
rootJMenu.setForeground(ENABLED_COLOR);
rootJMenu.setFont(ENABLED_FONT);
vpSet.add(vp);
} else {
menu = new JMenuItem(vp.getDisplayName());
menu.addActionListener(
new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
applBypassValue(netView, view, vp);
}
});
if (vp.getDisplayName()
.equalsIgnoreCase(BasicVisualLexicon.NODE_WIDTH.getDisplayName())) {
menuItemNodeWidth = menu;
}
if (vp.getDisplayName()
.equalsIgnoreCase(BasicVisualLexicon.NODE_HEIGHT.getDisplayName())) {
menuItemNodeHeight = menu;
}
}
} else {
menu = new JMenu(vp.getDisplayName());
if (vp.getDisplayName().equalsIgnoreCase(BasicVisualLexicon.NODE_SIZE.getDisplayName())) {
menuItemNodeSize = menu;
vp_nodeSize = vp;
}
}
if (PropertySheetUtil.isCompatible(vp)) {
menuMap.get(curretNode.getParent()).add(menu);
menuMap.put(curretNode, menu);
}
}
if (queue.isEmpty()) {
queue.addAll(nextNodes);
nextNodes.clear();
}
}
// handle node size
if (menuItemNodeSize != null) {
//
JMenuItem menuItemNodeSize1 = new JMenuItem(vp_nodeSize.getDisplayName());
menuItemNodeSize1.addActionListener(
new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
applBypassValue(netView, view, vp_nodeSize);
}
});
menuItemNodeSize.add(menuItemNodeSize1);
// Check if nose size is locked
boolean nodeSizeIsLocked = false;
java.util.Iterator it =
vmm.getCurrentVisualStyle().getAllVisualPropertyDependencies().iterator();
while (it.hasNext()) {
org.cytoscape.view.vizmap.VisualPropertyDependency dep =
(org.cytoscape.view.vizmap.VisualPropertyDependency) it.next();
if (dep.getDisplayName().equalsIgnoreCase("Lock node width and height")
&& dep.isDependencyEnabled()) {
nodeSizeIsLocked = true;
}
}
if (nodeSizeIsLocked) {
// In case the Node size is locked, disable menuItem Node_width and Nod_height
if (menuItemNodeWidth != null) menuItemNodeWidth.setEnabled(false);
if (menuItemNodeHeight != null) menuItemNodeHeight.setEnabled(false);
} else {
// In case the Node size is not locked, disable menuItem Node_size
if (menuItemNodeSize1 != null) menuItemNodeSize1.setEnabled(false);
}
}
final JSeparator separator = new JSeparator();
final JMenuItem resetMenu = new JMenuItem("Reset All");
resetMenu.addActionListener(
new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
clearAll(netView, view);
}
});
rootJMenu.add(separator);
rootJMenu.add(resetMenu);
return rootMenu;
}
private void checkView(final CyNetworkView view) {
assertEquals(Color.BLACK, view.getVisualProperty(NETWORK_BACKGROUND_PAINT));
assertEquals(new Double(639.0d), view.getVisualProperty(NETWORK_WIDTH));
assertEquals(new Double(624.0d), view.getVisualProperty(NETWORK_HEIGHT));
assertEquals(
new Double(3091.2991395970175d), view.getVisualProperty(NETWORK_CENTER_X_LOCATION));
assertEquals(new Double(3610.396738076269d), view.getVisualProperty(NETWORK_CENTER_Y_LOCATION));
assertEquals(new Double(0.05044042295795177d), view.getVisualProperty(NETWORK_SCALE_FACTOR));
// All nodes have the same size, border and shape
final View<CyNode> nv = view.getNodeView(view.getModel().getNodeList().iterator().next());
assertEquals(80, nv.getVisualProperty(NODE_WIDTH).intValue());
assertEquals(30, nv.getVisualProperty(NODE_HEIGHT).intValue());
assertEquals(NodeShapeVisualProperty.ROUND_RECTANGLE, nv.getVisualProperty(NODE_SHAPE));
assertEquals(180, nv.getVisualProperty(NODE_TRANSPARENCY).intValue());
assertEquals(2, nv.getVisualProperty(NODE_BORDER_WIDTH).intValue());
assertEquals(LineTypeVisualProperty.SOLID, nv.getVisualProperty(NODE_BORDER_LINE_TYPE));
assertEquals(new Color(153, 153, 255), nv.getVisualProperty(NODE_BORDER_PAINT));
assertEquals(255, nv.getVisualProperty(NODE_BORDER_TRANSPARENCY).intValue());
assertEquals(new Color(255, 255, 255), nv.getVisualProperty(NODE_LABEL_COLOR));
assertEquals(255, nv.getVisualProperty(NODE_LABEL_TRANSPARENCY).intValue());
// All edges have the same width and other properties
final View<CyEdge> ev = view.getEdgeView(view.getModel().getEdgeList().iterator().next());
assertEquals(new Double(1.0), ev.getVisualProperty(EDGE_WIDTH));
assertEquals(255, ev.getVisualProperty(EDGE_TRANSPARENCY).intValue());
assertEquals(ArrowShapeVisualProperty.NONE, ev.getVisualProperty(EDGE_SOURCE_ARROW_SHAPE));
assertEquals(ArrowShapeVisualProperty.NONE, ev.getVisualProperty(EDGE_TARGET_ARROW_SHAPE));
}
public boolean isReady(View<CyNode> nView, CyNetworkView netView) {
if (nView != null && settings.hasNodeCompounds(Collections.singletonList(nView.getModel())))
return true;
return selectedNodesReady(netView.getModel());
}