@Test
public void testRepeatGroup() {
Table t = new Table();
Graph g = new Graph();
try {
m_vis.add("t", t);
Assert.fail("Should not allow duplicate groups");
} catch (Exception e) {
}
try {
m_vis.addFocusGroup(Visualization.FOCUS_ITEMS, t);
Assert.fail("Should not allow duplicate groups");
} catch (Exception e) {
}
try {
m_vis.add("g", g);
Assert.fail("Should not allow duplicate groups");
} catch (Exception e) {
}
m_vis.removeGroup("t");
try {
m_vis.add("t", t);
} catch (Exception e) {
Assert.fail("Should be able to re-use group name after removal");
}
m_vis.removeGroup("g");
try {
m_vis.add("g", t);
} catch (Exception e) {
Assert.fail("Should be able to re-use group name after removal");
}
}
@Before
public void setUp() {
m_vis = new Visualization();
m_t = TableTest.getTestCaseTable();
m_g = GraphTest.getTestCaseGraph();
m_t0 = m_t.getTuple(0);
m_n0 = m_g.getNode(0);
VisualTable vt = (VisualTable) m_vis.add("t", m_t);
VisualGraph vg = (VisualGraph) m_vis.add("g", m_g);
m_vt0 = vt.getItem(0);
m_vn0 = (NodeItem) vg.getNode(0);
TupleSet ts = m_vis.getFocusGroup(Visualization.FOCUS_ITEMS);
ts.addTuple(m_vt0);
ts.addTuple(m_vn0);
}
public Display getGraphDisplay(
GraphLayoutType glType, final ExperimentPanel expPanel, String highlightName) {
Display display = new Display();
int X = expPanel.getDetailWidth();
int Y = expPanel.getDetailHeight();
display.setSize(X, Y); // set display size
// display.setHighQuality(true);
// display.setPreferredSize(new Dimension(600,600));
display.addControlListener(new DragControl()); // drag items around
display.addControlListener(new PanControl()); // pan with background left-drag
display.addControlListener(new WheelZoomControl()); // zoom with vertical right-drag
display.addControlListener(
new ZoomToFitControl(Visualization.ALL_ITEMS, 50, 500, Control.MIDDLE_MOUSE_BUTTON));
display.addControlListener(new NeighborHighlightControl());
Visualization vis = new Visualization();
if (clusterGraph == null) {
clusterGraph = this.toGraph();
}
vis.add("graph", clusterGraph);
LabelRenderer r = new LabelRenderer("name");
r.setHorizontalAlignment(Constants.CENTER);
// r.setRoundedCorner(8, 8); // round the corners
DefaultRendererFactory rf = new DefaultRendererFactory(r);
rf.setDefaultEdgeRenderer(new EdgeRenderer(Constants.EDGE_TYPE_CURVE));
vis.setRendererFactory(rf);
int[] palette = new int[] {ColorLib.rgb(255, 180, 180), ColorLib.rgb(190, 190, 255)};
DataColorAction fill =
new DataColorAction(
"graph.nodes", "type", Constants.NOMINAL, VisualItem.FILLCOLOR, palette);
fill.add(VisualItem.FIXED, ColorLib.rgb(255, 100, 100));
fill.add(VisualItem.HIGHLIGHT, ColorLib.rgb(255, 200, 125));
int[] text_palette = new int[] {ColorLib.gray(0), ColorLib.gray(255)};
DataColorAction text =
new DataColorAction(
"graph.nodes",
"indeterminate",
Constants.NUMERICAL,
VisualItem.TEXTCOLOR,
text_palette);
// ColorAction text = new ColorAction("graph.nodes", VisualItem.TEXTCOLOR, ColorLib.gray(0));
ColorAction edges = new ColorAction("graph.edges", VisualItem.STROKECOLOR, ColorLib.gray(200));
ActionList color = new ActionList(Activity.INFINITY);
color.add(text);
color.add(fill);
color.add(edges);
color.add(new RepaintAction());
if (highlightName != null) {
String pred = "name='" + highlightName + "'";
Iterator iter = vis.items("graph.nodes", ExpressionParser.predicate(pred));
while (iter.hasNext()) {
NodeItem ni = (NodeItem) iter.next();
highlightedItem = ni;
ni.setFixed(true);
Iterator iterEdge = ni.edges();
while (iterEdge.hasNext()) {
EdgeItem eItem = (EdgeItem) iterEdge.next();
NodeItem nItem = eItem.getAdjacentItem(ni);
if (eItem.isVisible()) {
eItem.setHighlighted(true);
nItem.setHighlighted(true);
}
}
}
}
ActionList layout = new ActionList();
switch (glType) {
case BALLOON_TREE:
layout.add(new BalloonTreeLayout("graph"));
break;
case FORCE_DIRECTED:
layout = new ActionList(Activity.INFINITY);
layout.add(new ForceDirectedLayout("graph"));
break;
case NODE_LINK_TREE:
layout.add(new NodeLinkTreeLayout("graph"));
break;
case RADIAL_TREE:
layout.add(new RadialTreeLayout("graph"));
break;
}
// layout.add(fill);
layout.add(new RepaintAction());
vis.putAction("color", color);
vis.putAction("layout", layout);
display.setVisualization(vis);
vis.run("color");
vis.run("layout");
// Rectangle2D bounds = vis.getBounds(Visualization.ALL_ITEMS);
// GraphicsLib.expand(bounds, 50 + (int)(1/display.getScale()));
// DisplayLib.fitViewToBounds(display,bounds,1);
// vis.runAfter("layout",1000);
Control shutoffHighlight =
new HoverActionControl("color") {
// public void itemEntered(VisualItem item, MouseEvent evt) {
// }
public void itemExited(VisualItem item, MouseEvent evt) {
if (highlightedItem != null) {
highlightedItem.setFixed(false);
Iterator iterEdge = highlightedItem.edges();
while (iterEdge.hasNext()) {
EdgeItem eItem = (EdgeItem) iterEdge.next();
NodeItem nItem = eItem.getAdjacentItem(highlightedItem);
if (eItem.isVisible()) {
eItem.setHighlighted(false);
nItem.setHighlighted(false);
}
}
highlightedItem = null;
}
}
};
display.addControlListener(shutoffHighlight);
Control selectItem =
new FocusControl() {
public void itemClicked(VisualItem item, MouseEvent evt) {
if (item.isInGroup("graph.nodes")) {
if (item.getString("type").equals("peptide")) {
Peptide pep = minPeptides.get(item.getString("name"));
expPanel.showPeptide(pep, true);
}
if (item.getString("type").equals("protein")) {
Protein pro = minProteins.get(item.getString("name"));
expPanel.showProtein(pro, true);
}
String pred = "name='" + item.getString("name") + "'";
Iterator iter =
item.getVisualization().items("graph.nodes", ExpressionParser.predicate(pred));
while (iter.hasNext()) {
NodeItem ni = (NodeItem) iter.next();
highlightedItem = ni;
ni.setFixed(true);
Iterator iterEdge = ni.edges();
while (iterEdge.hasNext()) {
EdgeItem eItem = (EdgeItem) iterEdge.next();
NodeItem nItem = eItem.getAdjacentItem(ni);
if (eItem.isVisible()) {
eItem.setHighlighted(true);
nItem.setHighlighted(true);
}
}
}
}
}
};
display.addControlListener(selectItem);
final JPopupMenu menu = new JPopupMenu();
// Create and add a menu item
// JMenuItem printItem = new JMenuItem("Print This");
// printItem.addActionListener(new java.awt.event.ActionListener() {
// public void actionPerformed(java.awt.event.ActionEvent evt) {
// PrintUtilities.printComponent(display);
// }
// });
// menu.add(printItem);
// Set the component to show the popup menu
display.addMouseListener(
new MouseAdapter() {
public void mousePressed(MouseEvent evt) {
if (evt.isPopupTrigger()) {
menu.show(evt.getComponent(), evt.getX(), evt.getY());
}
}
public void mouseReleased(MouseEvent evt) {
if (evt.isPopupTrigger()) {
menu.show(evt.getComponent(), evt.getX(), evt.getY());
}
}
});
display.pan(X / 2.0, Y / 2.0);
return display;
}
public static void main(String[] argv) {
// -- 1. load the data ------------------------------------------------
// load the socialnet.xml file. it is assumed that the file can be
// found at the root of the java classpath
Graph graph = null;
try {
graph = new GraphMLReader().readGraph(System.in);
} catch (DataIOException e) {
e.printStackTrace();
System.err.println("Error loading graph. Exiting...");
System.exit(1);
}
// -- 2. the visualization --------------------------------------------
// add the graph to the visualization as the data group "graph"
// nodes and edges are accessible as "graph.nodes" and "graph.edges"
Visualization vis = new Visualization();
vis.add("graph", graph);
vis.setInteractive("graph.edges", null, false);
// -- 3. the renderers and renderer factory ---------------------------
// draw the "name" label for NodeItems
LabelRenderer r = new LabelRenderer("label");
r.setRoundedCorner(8, 8); // round the corners
EdgeRenderer eRender =
new EdgeRenderer(Constants.EDGE_TYPE_CURVE, Constants.EDGE_ARROW_FORWARD);
// create a new default renderer factory
// return our name label renderer as the default for all non-EdgeItems
// includes straight line edges for EdgeItems by default
vis.setRendererFactory(new DefaultRendererFactory(r, eRender));
// -- 4. the processing actions ---------------------------------------
// create our nominal color palette
// pink for females, baby blue for males
int[] palette =
new int[] {
ColorLib.rgb(190, 190, 255), ColorLib.rgb(255, 180, 180), ColorLib.rgb(128, 128, 128),
};
// map nominal data values to colors using our provided palette
DataColorAction fill =
new DataColorAction(
"graph.nodes", "type", Constants.NOMINAL, VisualItem.FILLCOLOR, palette);
// use black for node text
ColorAction text = new ColorAction("graph.nodes", VisualItem.TEXTCOLOR, ColorLib.gray(0));
// use light grey for edges
ColorAction edges = new ColorAction("graph.edges", VisualItem.STROKECOLOR, ColorLib.gray(200));
ColorAction arrows = new ColorAction("graph.edges", VisualItem.FILLCOLOR, ColorLib.gray(200));
// create an action list containing all color assignments
ActionList color = new ActionList();
color.add(fill);
color.add(text);
color.add(edges);
color.add(arrows);
// Add a size action
DataSizeAction size = new DataSizeAction("graph.nodes", "type", 2, Constants.LINEAR_SCALE);
vis.putAction("size", size);
// create an action list with an animated layout
ActionList layout = new ActionList(Activity.INFINITY);
layout.add(new ForceDirectedLayout("graph"));
layout.add(new RepaintAction());
// add the actions to the visualization
vis.putAction("color", color);
vis.putAction("layout", layout);
// -- 5. the display and interactive controls -------------------------
Display d = new Display(vis);
d.setSize(720, 500); // set display size
// drag individual items around
d.addControlListener(new DragControl());
// pan with left-click drag on background
d.addControlListener(new PanControl());
// zoom with right-click drag
d.addControlListener(new ZoomControl());
// -- 6. launch the visualization -------------------------------------
// create a new window to hold the visualization
JFrame frame = new JFrame("IFDS Visualization");
// ensure application exits when window is closed
frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
frame.add(d);
frame.pack(); // layout components in window
frame.setVisible(true); // show the window
// assign the colors
vis.run("color");
// start up the animated layout
vis.run("layout");
}
/* (non-Javadoc)
* @see org.lukep.javavis.visualisation.views.AbstractVisualisationView#visit(org.lukep.javavis.visualisation.visualisers.PrefuseVisualiser, org.lukep.javavis.ui.swing.WorkspaceContext, prefuse.Display)
*/
@Override
public void visit(PrefuseVisualiser visualiser, WorkspaceContext wspContext, Display display) {
display.reset();
// -- 1. load the data ------------------------------------------------
Graph graph = new Graph();
graph.addColumn("type", String.class);
graph.addColumn("name", String.class);
graph.addColumn("model", IGenericModelNode.class);
graph.addColumn("metricMeasurement", double.class);
// create package vertices
ProjectModel modelStore = wspContext.getModelStore();
HashMap<IGenericModelNode, Node> parentNodeMap =
new HashMap<IGenericModelNode, Node>(modelStore.getPackageMap().size() + 10);
Node curNode;
for (PackageModel pkg : modelStore.getPackageMap().values()) {
// add the package node
curNode = graph.addNode();
curNode.setString("type", pkg.getModelTypeName());
curNode.setString("name", pkg.getSimpleName());
curNode.set("model", pkg);
// link to the parent with an edge
IGenericModelNode parentPackage = pkg.getParent();
if (parentPackage != null
&& parentPackage instanceof PackageModel
&& parentNodeMap.containsKey(parentPackage)) {
// link to the parent package with an edge
graph.addEdge(parentNodeMap.get(parentPackage), curNode);
}
parentNodeMap.put(pkg, curNode);
}
// create class and method nodes
Queue<IGenericModelNode> modelQueue =
new LinkedList<IGenericModelNode>(modelStore.getClassMap().values());
IGenericModelNode model;
while (modelQueue.peek() != null) {
model = modelQueue.remove();
curNode = graph.addNode();
curNode.setString("type", model.getModelTypeName());
curNode.setString("name", model.getSimpleName());
curNode.set("model", model);
// add children to iterModels
if (model.getChildCount() > 0) {
for (Relationship r : model.getChildren())
if (r.getRelationshipType() == RelationshipType.ENCLOSED_IN)
modelQueue.add(r.getTarget());
parentNodeMap.put(model, curNode);
}
// link to the parent package
if (parentNodeMap.containsKey(model.getParent())) {
graph.addEdge(parentNodeMap.get(model.getParent()), curNode);
}
// grab metric measurement if applicable
if (model instanceof IMeasurableNode
&& wspContext.getMetric().testAppliesTo(model.getModelTypeName())) {
curNode.setDouble(
"metricMeasurement",
((IMeasurableNode) (model)).getMetricMeasurement(wspContext.getMetric()).getResult());
}
}
// -- 2. the visualisation --------------------------------------------
// TODO implement a Visualization cache
Visualization vis = new Visualization();
vis.add("graph", graph);
vis.setInteractive("graph.edges", null, false);
// -- 3. the renderers and renderer factory ---------------------------
LabelRenderer r = new LabelRenderer("name");
r.setRoundedCorner(8, 8);
vis.setRendererFactory(new DefaultRendererFactory(r));
// -- 4. the processing actions ---------------------------------------
// create our nominal color palette
// pink for classes, baby blue for packages
int[] palette = ColorLib.getCoolPalette();
// create a metric palette
int[] mPalette = ColorLib.getInterpolatedPalette(0xFF00AA6D, 0xFFFFAA6D);
// TODO replace
int[] mPalette2 = new int[mPalette.length + 1];
mPalette2[0] = Color.lightGray.getRGB();
for (int i = 1; i < mPalette.length; i++) mPalette2[i] = mPalette[i];
// map nominal data values to colors using our provided palette
DataColorAction fill =
new DataColorAction(
"graph.nodes", "type", Constants.NOMINAL, VisualItem.FILLCOLOR, palette);
DataColorAction fillMetrics =
new DataColorAction(
"graph.nodes",
"metricMeasurement",
Constants.NUMERICAL,
VisualItem.FILLCOLOR,
mPalette2);
// use black for node text
ColorAction text = new ColorAction("graph.nodes", VisualItem.TEXTCOLOR, ColorLib.gray(0));
// use light grey for edges
ColorAction edges = new ColorAction("graph.edges", VisualItem.STROKECOLOR, ColorLib.gray(200));
// create an action list containing all color assignments
ActionList colour = new ActionList();
colour.add(fillMetrics);
colour.add(text);
colour.add(edges);
// create an action list with an animated layout
ActionList layout = new ActionList(Activity.INFINITY);
// layout.add(new ForceDirectedLayout("graph"));
layout.add(new NodeLinkTreeLayout("graph"));
layout.add(new RepaintAction());
// add the actions to the visualisation
vis.putAction("colour", colour);
vis.putAction("layout", layout);
// -- 5. the display and interactive controls -------------------------
display.setVisualization(vis);
// -- 6. launch the visualization -------------------------------------
vis.run("colour");
vis.run("layout");
}
