public DefaultTreeModel getTree(ExperimentPanel expPanel) {
DefaultMutableTreeNode root = new DefaultMutableTreeNode(expPanel.getName() + " Overview");
root.add(getPeptideHitsTree(expPanel));
root.add(getPeptideTree(expPanel, true));
root.add(getProteinTree(expPanel, true));
root.add(getClusterTree(expPanel));
root.add(getParsimonyTree(expPanel));
return new DefaultTreeModel(root);
}
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;
}