public NodeColorAction(String group) {
super(group, VisualItem.FILLCOLOR, ColorLib.rgba(202, 225, 255, 250));
add("_hover", ColorLib.gray(220, 230));
add("ingroup('_search_')", ColorLib.rgb(255, 190, 190));
add("ingroup('_focus_')", ColorLib.rgb(205, 197, 191));
add(isprocessfilter, ColorLib.rgba(255, 193, 193, 255));
}
public GraphVisualisation(rndalg.Graph graphToShow, Vector<Vertex> cut) {
super();
Graph displayed = new Graph(false);
displayed.addColumn("id", String.class);
displayed.addColumn("isCut", Boolean.class);
this.makeGraph(displayed, graphToShow, cut);
this.addGraph("graph", displayed);
LabelRenderer r = new LabelRenderer("id");
r.setRoundedCorner(10, 10);
r.setHorizontalPadding(5);
r.setVerticalPadding(2);
this.setRendererFactory(new DefaultRendererFactory(r));
ActionList layoutActions = new ActionList(Activity.INFINITY);
ForceDirectedLayout layout = new ForceDirectedLayout("graph");
layoutActions.add(layout);
layoutActions.add(new RepaintAction());
// black text
ColorAction textCA =
new ColorAction("graph.nodes", VisualItem.TEXTCOLOR, ColorLib.rgb(0, 0, 0));
// black edges
// ColorAction edgeCA = new ColorAction("graph.edges", VisualItem.STROKECOLOR,
// ColorLib.rgb(0,0,0));
// edges
ColorAction edgeCA =
new ColorAction(
"graph.edges",
ExpressionParser.predicate("isCut = false"),
VisualItem.STROKECOLOR,
ColorLib.rgb(0, 0, 0));
ColorAction edgeCutCA =
new ColorAction(
"graph.edges",
ExpressionParser.predicate("isCut = true"),
VisualItem.STROKECOLOR,
ColorLib.rgb(255, 0, 0));
// concatenate the color actions
ActionList colorActions = new ActionList();
colorActions.add(textCA);
colorActions.add(edgeCA);
colorActions.add(edgeCutCA);
this.putAction("draw", colorActions);
this.putAction("layout", layoutActions);
this.runAfter("draw", "layout");
this.run("draw");
}
public int getColor(VisualItem item) {
if (ENTROPY_COLOR) return entropyColor(item);
// test
// if (item.getBoolean("cut")){
// return new Color(222,13,107).getRGB();
// }
// color is fixed, what changes as a function of the value is the transparency (alpha)
int color = sca.getColor(item);
// lemmas and senses in the pathToRoot
if (item.isInGroup("pathToRoot")
&& ((item.getInt("type") == 1) || (item.getInt("type") == 4)))
color = ColorScheme.pathToRootColor;
// count off -- just return color
if (NodeColorAction.this.docuBurstActionList.countType.equals(DocuBurstActionList.NOCOUNT))
return color;
float total =
(float)
(item.getFloat(
DocuBurstActionList.CACHECOUNT
+ NodeColorAction.this.docuBurstActionList.countType));
float maxTotal =
NodeColorAction.this.docuBurstActionList.getMaxTotal(
NodeColorAction.this.docuBurstActionList.countType);
if (total < 0) color = ColorScheme.negativeColor;
if (total == 0) {
if (color != ColorScheme.pathToRootColor)
// zero senses get grey, zero lemmas and words get clear
return ColorLib.setAlpha(ColorScheme.zeroOccurrenceSenseColor, ColorScheme.zeroAlpha);
else
// modulate path to root color
return ColorLib.setAlpha(color, ColorScheme.zeroAlpha);
}
// initial alpha for zero and one count
int alpha = ColorScheme.zeroAlpha;
alpha += (int) (((float) total / (float) maxTotal) * (float) (255 - alpha));
if (total < 0)
System.err.println(
"total: " + total + " node: " + item.getString("label") + " alpha: " + alpha);
// this should not occur except for rounding errors
if (alpha > 255) alpha = 255;
return ColorLib.setAlpha(color, alpha);
}
/**
* Create a new, empty FisheyeMenu.
*
* @see #addMenuItem(String, javax.swing.Action)
*/
public FisheyeMenu() {
super(new Visualization());
m_vis.addTable(ITEMS, m_items);
// set up the renderer to use
LabelRenderer renderer = new LabelRenderer(LABEL);
renderer.setHorizontalPadding(0);
renderer.setVerticalPadding(1);
renderer.setHorizontalAlignment(Constants.LEFT);
m_vis.setRendererFactory(new DefaultRendererFactory(renderer));
// set up this display
setSize(100, 470);
setHighQuality(true);
setBorder(BorderFactory.createEmptyBorder(10, 10, 10, 5));
addControlListener(
new ControlAdapter() {
// dispatch an action event to the menu item
public void itemClicked(VisualItem item, MouseEvent e) {
ActionListener al = (ActionListener) item.get(ACTION);
al.actionPerformed(
new ActionEvent(item, e.getID(), "click", e.getWhen(), e.getModifiers()));
}
});
// text color function
// items with the mouse over printed in red, otherwise black
ColorAction colors = new ColorAction(ITEMS, VisualItem.TEXTCOLOR);
colors.setDefaultColor(ColorLib.gray(0));
colors.add("hover()", ColorLib.rgb(255, 0, 0));
// initial layout and coloring
ActionList init = new ActionList();
init.add(new VerticalLineLayout(m_maxHeight));
init.add(colors);
init.add(new RepaintAction());
m_vis.putAction("init", init);
// fisheye distortion based on the current anchor location
ActionList distort = new ActionList();
Distortion feye = new FisheyeDistortion(0, m_scale);
distort.add(feye);
distort.add(colors);
distort.add(new RepaintAction());
m_vis.putAction("distort", distort);
// update the distortion anchor position to be the current
// location of the mouse pointer
addControlListener(new AnchorUpdateControl(feye, "distort"));
}
public int entropyColor(VisualItem item) {
// color is fixed, what changes as a function of the value is the transparency (alpha)
int color = sca.getColor(item);
// lemmas and senses in the pathToRoot
if (item.isInGroup("pathToRoot")
&& ((item.getInt("type") == 1) || (item.getInt("type") == 4)))
color = ColorScheme.pathToRootColor;
// count off -- just return color
if (NodeColorAction.this.docuBurstActionList.countType.equals(DocuBurstActionList.NOCOUNT))
return color;
// float total = item.getFloat(DocuBurstActionList.CONDENTROPY);
float total = item.getFloat(DocuBurstActionList.CONDENTROPY);
float maxTotal =
NodeColorAction.this.docuBurstActionList.getMaxTotal(DocuBurstActionList.CONDENTROPY);
if (total < 0) color = ColorScheme.negativeColor;
if (total == 0) {
if (color != ColorScheme.pathToRootColor)
// zero senses get grey, zero lemmas and words get clear
return ColorLib.setAlpha(color, 255);
else
// modulate path to root color
return ColorLib.setAlpha(color, ColorScheme.zeroAlpha);
}
// initial alpha for zero and one count
int alpha = 10;
float condEntropyMin = NodeColorAction.this.docuBurstActionList.getCondEntropyMinTotal();
// alpha += (int) ( (1 - Math.log(total/maxTotal)/Math.log(condEntropyMin)) * (float) (255 -
// alpha));
alpha +=
(int) ((Math.log(total / maxTotal) / Math.log(condEntropyMin)) * (float) (255 - alpha));
if (total < 0)
System.err.println(
"total: " + total + " node: " + item.getString("label") + " alpha: " + alpha);
// this should not occur except for rounding errors
if (alpha > 255) alpha = 255;
return ColorLib.setAlpha(color, alpha);
}
@Override
public int getColor(VisualItem item) {
// highlight border of glyphs for which search is true
// TODO: thicker borders? more outstanding highlighting?
// do (inefficient) manual comparison (for now)
Iterator itemsInGroup = m_vis.getGroup(Visualization.SEARCH_ITEMS).tuples();
while (itemsInGroup.hasNext()) {
Tuple itemInGroup = (Tuple) itemsInGroup.next();
if (item.getString(DocumentGridTable.NODE_NAME)
.equals(itemInGroup.getString(DocumentGridTable.NODE_NAME))) {
// debug
// System.out.println("debug: "+this.getClass().getName()+": item in
// group! "+item.toString());
return ColorLib.rgb(191, 99, 130);
}
}
if (item.isHover()) {
return Color.LIGHT_GRAY.getRGB();
}
// default border color
// return ColorLib.gray(50);
return Color.DARK_GRAY.getRGB();
}
/** @see prefuse.render.Renderer#render(java.awt.Graphics2D, prefuse.visual.VisualItem) */
@Override
public void render(Graphics2D g, VisualItem item) {
// render the edge line
super.render(g, item);
// render the edge arrow head, if appropriate
if (m_curArrow != null) {
g.setPaint(ColorLib.getColor(item.getFillColor()));
g.fill(m_curArrow);
}
}
public ScatterPlot(Table t, String xfield, String yfield, String sfield) {
super(new Visualization());
// --------------------------------------------------------------------
// STEP 1: setup the visualized data
m_vis.addTable(group, t);
DefaultRendererFactory rf = new DefaultRendererFactory(m_shapeR);
m_vis.setRendererFactory(rf);
// --------------------------------------------------------------------
// STEP 2: create actions to process the visual data
// set up the actions
AxisLayout x_axis = new AxisLayout(group, xfield, Constants.X_AXIS, VisiblePredicate.TRUE);
m_vis.putAction("x", x_axis);
AxisLayout y_axis = new AxisLayout(group, yfield, Constants.Y_AXIS, VisiblePredicate.TRUE);
m_vis.putAction("y", y_axis);
ColorAction color = new ColorAction(group, VisualItem.STROKECOLOR, ColorLib.rgb(100, 100, 255));
m_vis.putAction("color", color);
DataShapeAction shape = new DataShapeAction(group, sfield);
m_vis.putAction("shape", shape);
ActionList draw = new ActionList();
draw.add(x_axis);
draw.add(y_axis);
if (sfield != null) draw.add(shape);
draw.add(color);
draw.add(new RepaintAction());
m_vis.putAction("draw", draw);
// --------------------------------------------------------------------
// STEP 3: set up a display and ui components to show the visualization
setBorder(BorderFactory.createEmptyBorder(10, 10, 10, 10));
setSize(700, 450);
setHighQuality(true);
ToolTipControl ttc = new ToolTipControl(new String[] {xfield, yfield});
addControlListener(ttc);
// --------------------------------------------------------------------
// STEP 4: launching the visualization
m_vis.run("draw");
}
/** @see prefuse.render.Renderer#render(java.awt.Graphics2D, prefuse.visual.VisualItem) */
@Override
public void render(Graphics2D g, VisualItem item) {
Shape s = getShape(item);
GraphicsLib.paint(g, item, m_line, getStroke(item), getRenderType(item));
// check if we have a text label, if so, render it
String str;
if (item.canGetString(VisualItem.LABEL)) {
str = (String) item.getString(VisualItem.LABEL);
if (str != null && !str.equals("")) {
float x = (float) m_box.getMinX();
float y = (float) m_box.getMinY() + m_ascent;
// draw label background
GraphicsLib.paint(g, item, s, null, RENDER_TYPE_FILL);
AffineTransform origTransform = g.getTransform();
AffineTransform transform = this.getTransform(item);
if (transform != null) {
g.setTransform(transform);
}
g.setFont(item.getFont());
g.setColor(ColorLib.getColor(item.getTextColor()));
if (!(str.length() > 5
&& str.substring(str.length() - 5, str.length()).equals("_last"))) {
g.setColor(Color.WHITE);
// TODO properly hunt down source of null str! for now, triage
if (str != null) {
// bump y down by appropriate amount
FontMetrics fm = g.getFontMetrics(item.getFont());
int strHeight = fm.getAscent();
// g.drawString(str, x, y);
g.drawString(str, x, y + strHeight);
}
if (transform != null) {
g.setTransform(origTransform);
}
}
}
}
}
public void renderText(Graphics2D g, VisualItem item, Shape shape) {
String s = getText(item);
int textColor = item.getTextColor();
if (s != null) {
Rectangle2D r = shape.getBounds2D();
g.setPaint(ColorLib.getColor(textColor));
g.setFont(m_font);
FontMetrics fm = g.getFontMetrics();
double size = item.getSize();
double x = r.getX() + size * m_horizBorder;
double y = r.getY() + size * m_vertBorder;
g.drawString(s, (float) x, (float) y + fm.getAscent());
// if ( isHyperlink(item) ) {
// int lx = (int)Math.round(x), ly = (int)Math.round(y);
// g.drawLine(lx,ly,lx+fm.stringWidth(s),ly+fm.getHeight()-1);
// }
}
}
/* (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");
}
public TextColorAction(String group) {
super(group, VisualItem.TEXTCOLOR, ColorLib.gray(0));
add("_hover", ColorLib.rgb(255, 0, 0));
}
public NodeColorAction(
DocuBurstActionList docuBurstActionList, String group, boolean trackSenseIndex) {
super(group, VisualItem.FILLCOLOR, ColorLib.rgba(100, 100, 100, 0));
this.docuBurstActionList = docuBurstActionList;
add("type = 1", new WordCountColorAction(group, VisualItem.FILLCOLOR));
}
public Congress(Table t) {
super(new BorderLayout());
// --------------------------------------------------------------------
// STEP 1: setup the visualized data
final Visualization vis = new Visualization();
m_vis = vis;
final String group = "by_state";
// filter to show only candidates receiving more than $100,000
Predicate p = (Predicate) ExpressionParser.parse("[" + TOTAL_RECEIPTS + "] >= 100000");
VisualTable vt = vis.addTable(group, t, p);
// add a new column containing a label string showing
// candidate name, party, state, year, and total receipts
vt.addColumn(
"label",
"CONCAT(CAP(Candidate), ' (', "
+ "CAP([Party Designation]), '-', [State Code], "
+ "') ', Year, ': $', FORMAT([Total Receipts],2))");
// add calculation for senators
vt.addColumn("Senate", "District <= 0");
vis.setRendererFactory(
new RendererFactory() {
AbstractShapeRenderer sr = new ShapeRenderer();
Renderer arY = new AxisRenderer(Constants.RIGHT, Constants.TOP);
Renderer arX = new AxisRenderer(Constants.CENTER, Constants.FAR_BOTTOM);
public Renderer getRenderer(VisualItem item) {
return item.isInGroup("ylab") ? arY : item.isInGroup("xlab") ? arX : sr;
}
});
// --------------------------------------------------------------------
// STEP 2: create actions to process the visual data
// set up dynamic queries, search set
RangeQueryBinding receiptsQ = new RangeQueryBinding(vt, RECEIPTS);
ListQueryBinding yearsQ = new ListQueryBinding(vt, "Year");
SearchQueryBinding searchQ = new SearchQueryBinding(vt, "Candidate");
// construct the filtering predicate
AndPredicate filter = new AndPredicate(searchQ.getPredicate());
filter.add(yearsQ.getPredicate());
filter.add(receiptsQ.getPredicate());
// set up the actions
AxisLayout xaxis = new AxisLayout(group, "State Code", Constants.X_AXIS, VisiblePredicate.TRUE);
AxisLayout yaxis = new AxisLayout(group, RECEIPTS, Constants.Y_AXIS, VisiblePredicate.TRUE);
// yaxis.setScale(Constants.LOG_SCALE);
yaxis.setRangeModel(receiptsQ.getModel());
receiptsQ.getNumberModel().setValueRange(0, 65000000, 0, 65000000);
xaxis.setLayoutBounds(m_dataB);
yaxis.setLayoutBounds(m_dataB);
AxisLabelLayout ylabels = new AxisLabelLayout("ylab", yaxis, m_ylabB);
NumberFormat nf = NumberFormat.getCurrencyInstance();
nf.setMaximumFractionDigits(0);
ylabels.setNumberFormat(nf);
AxisLabelLayout xlabels = new AxisLabelLayout("xlab", xaxis, m_xlabB, 15);
vis.putAction("xlabels", xlabels);
// dems = blue, reps = red, other = gray
int[] palette =
new int[] {
ColorLib.rgb(150, 150, 255), ColorLib.rgb(255, 150, 150), ColorLib.rgb(180, 180, 180)
};
DataColorAction color =
new DataColorAction(group, "Party", Constants.ORDINAL, VisualItem.STROKECOLOR, palette);
int[] shapes = new int[] {Constants.SHAPE_RECTANGLE, Constants.SHAPE_DIAMOND};
DataShapeAction shape = new DataShapeAction(group, "Senate", shapes);
Counter cntr = new Counter(group);
ActionList draw = new ActionList();
draw.add(cntr);
draw.add(color);
draw.add(shape);
draw.add(xaxis);
draw.add(yaxis);
draw.add(ylabels);
draw.add(new ColorAction(group, VisualItem.FILLCOLOR, 0));
draw.add(new RepaintAction());
vis.putAction("draw", draw);
ActionList update = new ActionList();
update.add(new VisibilityFilter(group, filter));
update.add(cntr);
update.add(xaxis);
update.add(yaxis);
update.add(ylabels);
update.add(new RepaintAction());
vis.putAction("update", update);
UpdateListener lstnr =
new UpdateListener() {
public void update(Object src) {
vis.run("update");
}
};
filter.addExpressionListener(lstnr);
// --------------------------------------------------------------------
// STEP 4: set up a display and ui components to show the visualization
m_display = new Display(vis);
m_display.setItemSorter(
new ItemSorter() {
public int score(VisualItem item) {
int score = super.score(item);
if (item.isInGroup(group)) score += item.getInt(TOTAL_RECEIPTS);
return score;
}
});
m_display.setBorder(BorderFactory.createEmptyBorder(10, 10, 10, 10));
m_display.setSize(700, 450);
m_display.setHighQuality(true);
m_display.addComponentListener(
new ComponentAdapter() {
public void componentResized(ComponentEvent e) {
displayLayout();
}
});
displayLayout();
m_details = new JFastLabel(m_title);
m_details.setPreferredSize(new Dimension(75, 20));
m_details.setVerticalAlignment(SwingConstants.BOTTOM);
m_total.setPreferredSize(new Dimension(500, 20));
m_total.setHorizontalAlignment(SwingConstants.RIGHT);
m_total.setVerticalAlignment(SwingConstants.BOTTOM);
ToolTipControl ttc = new ToolTipControl("label");
Control hoverc =
new ControlAdapter() {
public void itemEntered(VisualItem item, MouseEvent evt) {
if (item.isInGroup(group)) {
m_total.setText(item.getString("label"));
item.setFillColor(item.getStrokeColor());
item.setStrokeColor(ColorLib.rgb(0, 0, 0));
item.getVisualization().repaint();
}
}
public void itemExited(VisualItem item, MouseEvent evt) {
if (item.isInGroup(group)) {
m_total.setText(m_totalStr);
item.setFillColor(item.getEndFillColor());
item.setStrokeColor(item.getEndStrokeColor());
item.getVisualization().repaint();
}
}
};
m_display.addControlListener(ttc);
m_display.addControlListener(hoverc);
// --------------------------------------------------------------------
// STEP 5: launching the visualization
this.addComponentListener(lstnr);
// details
Box infoBox = new Box(BoxLayout.X_AXIS);
infoBox.add(Box.createHorizontalStrut(5));
infoBox.add(m_details);
infoBox.add(Box.createHorizontalGlue());
infoBox.add(Box.createHorizontalStrut(5));
infoBox.add(m_total);
infoBox.add(Box.createHorizontalStrut(5));
// set up search box
JSearchPanel searcher = searchQ.createSearchPanel();
searcher.setLabelText("Candidate: ");
searcher.setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 0));
// create dynamic queries
Box radioBox = new Box(BoxLayout.X_AXIS);
radioBox.add(Box.createHorizontalStrut(5));
radioBox.add(searcher);
radioBox.add(Box.createHorizontalGlue());
radioBox.add(Box.createHorizontalStrut(5));
radioBox.add(yearsQ.createRadioGroup());
radioBox.add(Box.createHorizontalStrut(16));
JRangeSlider slider = receiptsQ.createVerticalRangeSlider();
slider.setThumbColor(null);
slider.setMinExtent(150000);
slider.addMouseListener(
new MouseAdapter() {
public void mousePressed(MouseEvent e) {
m_display.setHighQuality(false);
}
public void mouseReleased(MouseEvent e) {
m_display.setHighQuality(true);
m_display.repaint();
}
});
vis.run("draw");
vis.run("xlabels");
add(infoBox, BorderLayout.NORTH);
add(m_display, BorderLayout.CENTER);
add(slider, BorderLayout.EAST);
add(radioBox, BorderLayout.SOUTH);
UILib.setColor(this, ColorLib.getColor(255, 255, 255), Color.GRAY);
slider.setForeground(Color.LIGHT_GRAY);
UILib.setFont(radioBox, FontLib.getFont("Tahoma", 15));
m_details.setFont(FontLib.getFont("Tahoma", 18));
m_total.setFont(FontLib.getFont("Tahoma", 16));
}
public trial(int st, String n) {
// setup a visualisation
super(new Visualization());
System.out.println(st + " " + n);
// generate a graph
initGraph(n, st);
// standard labelRenderer for the given label
LabelRenderer nodeRenderer = new LabelRenderer(LABEL);
// rendererFactory for the visualization items
DefaultRendererFactory rendererFactory = new DefaultRendererFactory();
// set the labelRenderer
rendererFactory.setDefaultRenderer(nodeRenderer);
m_vis.setRendererFactory(rendererFactory);
// Color Actions
ColorAction nodeText = new ColorAction(NODES, VisualItem.TEXTCOLOR);
nodeText.setDefaultColor(ColorLib.gray(0));
ColorAction nodeStroke = new ColorAction(NODES, VisualItem.STROKECOLOR);
nodeStroke.setDefaultColor(ColorLib.gray(100));
ColorAction nodeFill = new ColorAction(NODES, VisualItem.FILLCOLOR);
nodeFill.setDefaultColor(ColorLib.gray(255));
ColorAction edgeStrokes = new ColorAction(EDGES, VisualItem.STROKECOLOR);
edgeStrokes.setDefaultColor(ColorLib.gray(100));
// ColorAction fill = new ColorAction(NODES, VisualItem.FILLCOLOR,
ColorLib.rgb(200, 200, 255);
// fill.add(VisualItem.FIXED, ColorLib.rgb(255,100,100));
// fill.add(VisualItem.HIGHLIGHT, ColorLib.rgb(255,200,125));
// bundle the color actions
ActionList draw = new ActionList();
// draw.add(fill);
draw.add(new ColorAction(NODES, VisualItem.STROKECOLOR, 0));
draw.add(new ColorAction(NODES, VisualItem.TEXTCOLOR, ColorLib.rgb(0, 0, 0)));
draw.add(new ColorAction(EDGES, VisualItem.FILLCOLOR, ColorLib.gray(200)));
draw.add(new ColorAction(EDGES, VisualItem.STROKECOLOR, ColorLib.gray(200)));
draw.add(nodeText);
draw.add(nodeStroke);
draw.add(nodeFill);
draw.add(edgeStrokes);
ActionList animate = new ActionList(Activity.INFINITY);
// animate.add(fill);
animate.add(new RepaintAction());
m_nodeRenderer = new LabelRenderer(m_label);
m_nodeRenderer.setRenderType(AbstractShapeRenderer.RENDER_TYPE_FILL);
m_nodeRenderer.setHorizontalAlignment(Constants.LEFT);
m_nodeRenderer.setRoundedCorner(8, 8);
m_edgeRenderer = new EdgeRenderer(Constants.EDGE_TYPE_CURVE);
DefaultRendererFactory rf = new DefaultRendererFactory(m_nodeRenderer);
m_vis.setRendererFactory(rf);
// DataSizeAction
DataSizeAction nodeDataSizeAction = new DataSizeAction(NODES, SIZE);
draw.add(nodeDataSizeAction);
m_vis.putAction("draw", draw);
m_vis.putAction("layout", animate);
m_vis.runAfter("draw", "layout");
// create the layout action for the graph
NodeLinkTreeLayout treeLayout = new NodeLinkTreeLayout(GRAPH, m_orientation, 80, 5, 10);
treeLayout.setLayoutAnchor(new Point2D.Double(250, -150));
m_vis.putAction("treeLayout", treeLayout);
m_vis.addFocusGroup("selected");
CollapsedSubtreeLayout subLayout = new CollapsedSubtreeLayout(GRAPH, m_orientation);
m_vis.putAction("subLayout", subLayout);
m_vis.run("treeLayout");
m_vis.run("draw");
pan(250, 250);
setHighQuality(true);
addControlListener(new ZoomControl());
addControlListener(new PanControl());
addControlListener(new DragControl(true));
addControlListener(new NodeClicked());
addControlListener(new FocusControl());
registerKeyboardAction(
new OrientAction(Constants.ORIENT_LEFT_RIGHT),
"left-to-right",
KeyStroke.getKeyStroke("ctrl 1"),
WHEN_FOCUSED);
registerKeyboardAction(
new OrientAction(Constants.ORIENT_TOP_BOTTOM),
"top-to-bottom",
KeyStroke.getKeyStroke("ctrl 2"),
WHEN_FOCUSED);
registerKeyboardAction(
new OrientAction(Constants.ORIENT_RIGHT_LEFT),
"right-to-left",
KeyStroke.getKeyStroke("ctrl 3"),
WHEN_FOCUSED);
registerKeyboardAction(
new OrientAction(Constants.ORIENT_BOTTOM_TOP),
"bottom-to-top",
KeyStroke.getKeyStroke("ctrl 4"),
WHEN_FOCUSED);
TupleSet search = new PrefixSearchTupleSet();
m_vis.addFocusGroup(Visualization.SEARCH_ITEMS, search);
search.addTupleSetListener(
new TupleSetListener() {
public void tupleSetChanged(TupleSet t, Tuple[] add, Tuple[] rem) {
m_vis.cancel("animatePaint");
m_vis.run("fullPaint");
m_vis.run("animatePaint");
}
});
}
public PhysioMapRadialGraphView(
SemGenSettings sets, Graph g, String label, SemSimModel semsimmodel) {
super(new Visualization());
this.semsimmodel = semsimmodel;
// -- set up visualization --
m_vis.add(tree, g);
m_vis.setInteractive(treeEdges, null, false);
// -- set up renderers --
LabelRenderer m_nodeRenderer = new LabelRenderer(label);
m_nodeRenderer.setRenderType(AbstractShapeRenderer.RENDER_TYPE_DRAW_AND_FILL);
m_nodeRenderer.setHorizontalAlignment(Constants.CENTER);
m_nodeRenderer.setRoundedCorner(8, 8);
EdgeRenderer m_edgeRenderer =
new EdgeRenderer(Constants.EDGE_TYPE_LINE, prefuse.Constants.EDGE_ARROW_REVERSE);
m_edgeRenderer.setArrowType(prefuse.Constants.EDGE_ARROW_REVERSE);
m_edgeRenderer.setArrowHeadSize(8, 8);
// MAYBE HERE?
DefaultRendererFactory rf = new DefaultRendererFactory(m_nodeRenderer);
rf.add(new InGroupPredicate(treeEdges), m_edgeRenderer);
m_vis.setRendererFactory(rf);
// m_vis.
// -- set up processing actions --
// colors
ItemAction nodeColor = new NodeColorAction(treeNodes);
ItemAction borderColor = new BorderColorAction(treeNodes);
m_vis.putAction("borderColor", borderColor);
ItemAction textColor = new TextColorAction(treeNodes);
m_vis.putAction("textColor", textColor);
ItemAction edgeColor =
new ColorAction(treeEdges, VisualItem.STROKECOLOR, ColorLib.rgb(0, 0, 0));
ItemAction arrowColor = new ArrowColorAction(treeEdges);
m_vis.putAction("arrowColor", arrowColor);
FontAction fonts = new FontAction(treeNodes, FontLib.getFont("Verdana", 12));
fonts.add("ingroup('_focus_')", FontLib.getFont("Verdana", 12));
// recolor
// When recolor, do these actions
ActionList recolor = new ActionList();
recolor.add(nodeColor);
recolor.add(borderColor);
recolor.add(textColor);
recolor.add(arrowColor);
m_vis.putAction("recolor", recolor);
// repaint
ActionList repaint = new ActionList();
repaint.add(recolor);
repaint.add(new RepaintAction());
m_vis.putAction("repaint", repaint);
// animate paint change
ActionList animatePaint = new ActionList(400);
animatePaint.add(new ColorAnimator(treeNodes));
animatePaint.add(new RepaintAction());
m_vis.putAction("animatePaint", animatePaint);
// create the tree layout action
RadialTreeLayout treeLayout = new RadialTreeLayout(tree);
treeLayout.setAutoScale(true);
m_vis.putAction("treeLayout", treeLayout);
CollapsedSubtreeLayout subLayout = new CollapsedSubtreeLayout(tree);
m_vis.putAction("subLayout", subLayout);
// create the filtering and layout
ActionList filter = new ActionList();
filter.add(new TreeRootAction(tree));
filter.add(fonts);
filter.add(treeLayout);
filter.add(borderColor);
filter.add(subLayout);
filter.add(textColor);
filter.add(nodeColor);
filter.add(edgeColor);
filter.add(arrowColor);
m_vis.putAction("filter", filter);
// animated transition
ActionList animate = new ActionList(700);
animate.setPacingFunction(new SlowInSlowOutPacer());
animate.add(new QualityControlAnimator());
animate.add(new VisibilityAnimator(tree));
animate.add(new PolarLocationAnimator(treeNodes, linear));
animate.add(new ColorAnimator(treeNodes));
animate.add(new RepaintAction());
m_vis.putAction("animate", animate);
m_vis.alwaysRunAfter("filter", "animate");
// ------------------------------------------------
// initialize the display
setSize(sets.getAppWidth() - ExtractorTab.leftpanewidth - 50, sets.getAppHeight() - 235);
setItemSorter(new TreeDepthItemSorter());
addControlListener(new DragControl());
addControlListener(new ZoomToFitControl());
addControlListener(new ZoomControl());
addControlListener(new PanControl());
addControlListener(new FocusControl(1, "filter"));
addControlListener(new HoverActionControl("repaint"));
// ------------------------------------------------
// filter graph and perform layout
m_vis.run("filter");
// maintain a set of items that should be interpolated linearly
// this isn't absolutely necessary, but makes the animations nicer
// the PolarLocationAnimator should read this set and act accordingly
m_vis.addFocusGroup(linear, new DefaultTupleSet());
m_vis
.getGroup(Visualization.FOCUS_ITEMS)
.addTupleSetListener(
new TupleSetListener() {
public void tupleSetChanged(TupleSet t, Tuple[] add, Tuple[] rem) {
TupleSet linearInterp = m_vis.getGroup(linear);
if (add.length < 1) return;
linearInterp.clear();
for (Node n = (Node) add[0]; n != null; n = n.getParent()) linearInterp.addTuple(n);
}
});
SearchTupleSet search = new PrefixSearchTupleSet();
m_vis.addFocusGroup(Visualization.SEARCH_ITEMS, search);
search.addTupleSetListener(
new TupleSetListener() {
public void tupleSetChanged(TupleSet t, Tuple[] add, Tuple[] rem) {
m_vis.cancel("animatePaint");
m_vis.run("recolor");
m_vis.run("animatePaint");
}
});
}
static {
// EDGE_COLORS.put("refers_to", ColorLib.rgb(0, 0, 0));
QUERYSET_COLORS.put("start", ColorLib.rgb(0, 175, 0));
QUERYSET_COLORS.put("source", ColorLib.rgb(0, 175, 0));
QUERYSET_COLORS.put("end", ColorLib.rgb(220, 0, 0));
QUERYSET_COLORS.put("target", ColorLib.rgb(220, 0, 0));
QUERYSET_COLORS.put("start,end", ColorLib.rgb(220, 0, 220));
QUERYSET_COLORS.put("source,target", ColorLib.rgb(220, 0, 220));
QUERYSET_COLORS.put("rank", ColorLib.rgb(0, 175, 220));
NODE_COLORS.put("Node", ColorLib.rgb(240, 240, 240));
// Saturated greens
NODE_COLORS.put("Sequence", ColorLib.rgb(211, 247, 163));
NODE_COLORS.put("Gene", ColorLib.rgb(211, 247, 163));
NODE_COLORS.put("Protein", ColorLib.rgb(199, 240, 178));
NODE_COLORS.put("Enzyme", ColorLib.rgb(193, 234, 174));
// NODE_COLORS.put("ProteinGroup", ColorLib.rgb(199, 240, 178));
NODE_COLORS.put("AllelicVariant", ColorLib.rgb(199, 240, 178));
// Beige
NODE_COLORS.put("Article", ColorLib.rgb(250, 230, 160));
// Cyans (to do, make greener)
NODE_COLORS.put("HomologGroup", ColorLib.rgb(187, 237, 215));
NODE_COLORS.put("OrthologGroup", ColorLib.rgb(194, 237, 218));
// Desaturated blues
NODE_COLORS.put("GO", ColorLib.rgb(185, 218, 234));
NODE_COLORS.put("BiologicalProcess", ColorLib.rgb(185, 218, 234));
NODE_COLORS.put("MolecularFunction", ColorLib.rgb(189, 223, 239));
NODE_COLORS.put("CellularComponent", ColorLib.rgb(174, 214, 234));
// Light purples
NODE_COLORS.put("Ligand", ColorLib.rgb(210, 203, 240));
NODE_COLORS.put("Substance", ColorLib.rgb(210, 203, 240));
NODE_COLORS.put("Compound", ColorLib.rgb(210, 203, 240));
NODE_COLORS.put("Drug", ColorLib.rgb(203, 196, 233));
NODE_COLORS.put("Glycan", ColorLib.rgb(198, 200, 242));
// Pink
NODE_COLORS.put("GenomicContext", ColorLib.rgb(255, 215, 253));
// Blues
NODE_COLORS.put("Locus", ColorLib.rgb(180, 196, 239)); // unused
NODE_COLORS.put("Phenotype", ColorLib.rgb(193, 209, 255));
// NODE_COLORS.put("Locus/Phenotype, ColorLib.rgb(195, 199, 242));
// TMP MAPPING for illustration purposes BY LERONEN! Should never get to SVN!
NODE_COLORS.put("Gene/Phenotype", ColorLib.rgb(211, 247, 163));
// NODE_COLORS.put("Gene/Phenotype", ColorLib.rgb(193, 223, 242));
// Greens
NODE_COLORS.put("Family", ColorLib.rgb(179, 226, 192));
NODE_COLORS.put("Region", ColorLib.rgb(195, 229, 204));
NODE_COLORS.put("Domain", ColorLib.rgb(195, 229, 204));
NODE_COLORS.put("Repeat", ColorLib.rgb(195, 229, 204));
NODE_COLORS.put("Site", ColorLib.rgb(190, 229, 201));
NODE_COLORS.put("ActiveSite", ColorLib.rgb(190, 229, 201));
NODE_COLORS.put("BindingSite", ColorLib.rgb(190, 229, 201));
NODE_COLORS.put("PostTranslationalModification", ColorLib.rgb(190, 229, 201));
// Purple
NODE_COLORS.put("Pathway", ColorLib.rgb(208, 185, 231));
// Browns
NODE_COLORS.put("Tissue", ColorLib.rgb(229, 218, 189));
// NODE_COLORS.put("Organism", ColorLib.rgb(229, 215, 177));
NODE_COLORS.put("MeSHHeading", ColorLib.rgb(239, 231, 176));
NODE_COLORS.put("OMIM", ColorLib.rgb(239, 231, 176));
}
public ArrowColorAction(String group) {
super(group, VisualItem.FILLCOLOR, ColorLib.rgb(0, 0, 0));
}
public static JComponent demo(Graph g, String label) {
// create a new, empty visualization for our data
final Visualization vis = new Visualization();
VisualGraph vg = vis.addGraph(graph, g);
vis.setValue(edges, null, VisualItem.INTERACTIVE, Boolean.FALSE);
int[] palette =
new int[] {
ColorLib.rgb(77, 175, 74),
ColorLib.rgb(55, 126, 184),
ColorLib.rgb(228, 26, 28),
ColorLib.rgb(152, 78, 163),
ColorLib.rgb(255, 127, 0)
};
int[] shape_palette =
new int[] {Constants.SHAPE_ELLIPSE, Constants.SHAPE_RECTANGLE, Constants.SHAPE_TRIANGLE_UP};
TupleSet focusGroup = vis.getGroup(Visualization.FOCUS_ITEMS);
focusGroup.addTupleSetListener(
new TupleSetListener() {
public void tupleSetChanged(TupleSet ts, Tuple[] add, Tuple[] rem) {
for (int i = 0; i < rem.length; ++i) ((VisualItem) rem[i]).setFixed(false);
for (int i = 0; i < add.length; ++i) {
((VisualItem) add[i]).setFixed(false);
((VisualItem) add[i]).setFixed(true);
}
vis.run("draw");
}
});
// set up the renderers
/* ShapeRenderer s = new ShapeRenderer();
s.rectangle(0, 0, 30, 30);
vis.setRendererFactory(new DefaultRendererFactory(s));*/
MyRenderer tr = new MyRenderer(label);
// MyRenderer tr = new MyRenderer(label);
DefaultRendererFactory d = new DefaultRendererFactory(tr);
EdgeRenderer MyEdgeRenderer = new EdgeRenderer();
d.add(new InGroupPredicate(edges), MyEdgeRenderer);
vis.setRendererFactory(d);
// -- set up the actions ----------------------------------------------
int maxhops = 1024, hops = 1024;
final GraphDistanceFilter filter = new GraphDistanceFilter(graph, hops);
ActionList draw = new ActionList();
draw.add(filter);
// draw.add(new ColorAction(nodes, VisualItem.FILLCOLOR, ColorLib.rgb(180,180,255)));
draw.add(new ColorAction(nodes, VisualItem.STROKECOLOR, 0));
draw.add(new ColorAction(nodes, VisualItem.TEXTCOLOR, ColorLib.rgb(0, 0, 0)));
draw.add(new ColorAction(edges, VisualItem.FILLCOLOR, ColorLib.gray(100)));
draw.add(new ColorAction(edges, VisualItem.STROKECOLOR, ColorLib.gray(170)));
draw.add(new DataShapeAction(nodes, "type", shape_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));
// create an action list containing all color assignments
ActionList color = new ActionList();
color.add(fill);
color.add(text);
color.add(edges);
// ColorAction fill = new ColorAction(nodes,
// VisualItem.FILLCOLOR, ColorLib.rgb(200,200,255));
fill.add("_fixed", ColorLib.rgb(255, 100, 100));
fill.add("_highlight", ColorLib.rgb(255, 200, 125));
// Instead have to use GridLayout here - how do i create
ForceDirectedLayout fdl = new ForceDirectedLayout(graph);
// GridLayout fdl = new GridLayout(graph);
ForceSimulator fsim = fdl.getForceSimulator();
fsim.getForces()[0].setParameter(0, -5f);
ActionList animate = new ActionList(Activity.INFINITY);
// ActionList animate = new ActionList(vis);
animate.add(fdl);
animate.add(fill);
animate.add(new RepaintAction());
// finally, we register our ActionList with the Visualization.
// we can later execute our Actions by invoking a method on our
// Visualization, using the name we've chosen below.
vis.putAction("draw", draw);
vis.putAction("layout", animate);
vis.runAfter("draw", "layout");
vis.putAction("color", color);
// vis.putAction("layout", layout);
// --------------------------------------------------------------------
// STEP 4: set up a display to show the visualization
Display display = new Display(vis);
display.setSize(2000, 2000);
display.setForeground(Color.GRAY);
display.setBackground(Color.WHITE);
// main display controls
display.addControlListener(new FocusControl(1));
display.addControlListener(new DragControl());
display.addControlListener(new PanControl());
display.addControlListener(new ZoomControl());
display.addControlListener(new WheelZoomControl());
display.addControlListener(new ZoomToFitControl());
display.addControlListener(new NeighborHighlightControl());
display.setForeground(Color.GRAY);
display.setBackground(Color.WHITE);
// --------------------------------------------------------------------
// STEP 5: launching the visualization
// create a panel for editing force values
final JForcePanel fpanel = new JForcePanel(fsim);
final JValueSlider slider = new JValueSlider("Distance", 0, maxhops, hops);
slider.addChangeListener(
new ChangeListener() {
public void stateChanged(ChangeEvent e) {
filter.setDistance(slider.getValue().intValue());
vis.run("draw");
}
});
slider.setBackground(Color.WHITE);
slider.setPreferredSize(new Dimension(300, 30));
slider.setMaximumSize(new Dimension(300, 30));
Box cf = new Box(BoxLayout.Y_AXIS);
cf.add(slider);
cf.setBorder(BorderFactory.createTitledBorder("Connectivity Filter"));
fpanel.add(cf);
fpanel.add(Box.createVerticalGlue());
// create a new JSplitPane to present the interface
JSplitPane split = new JSplitPane();
split.setLeftComponent(display);
split.setRightComponent(fpanel);
split.setOneTouchExpandable(true);
split.setContinuousLayout(false);
split.setDividerLocation(530);
split.setDividerLocation(800);
// position and fix the default focus node
NodeItem focus = (NodeItem) vg.getNode(0);
PrefuseLib.setX(focus, null, 400);
PrefuseLib.setY(focus, null, 250);
focusGroup.setTuple(focus);
// now we run our action list and return
return split;
}
public int getColor(VisualItem item) {
if (m_vis.isInGroup(item, Visualization.SEARCH_ITEMS)) return ColorLib.rgb(255, 190, 190);
else if (m_vis.isInGroup(item, Visualization.FOCUS_ITEMS)) return ColorLib.rgb(198, 229, 229);
else if (item.getDOI() > -1) return ColorLib.rgb(164, 193, 193);
else return ColorLib.rgba(255, 255, 255, 0);
}
public ConcordanceTree() {
super(new Visualization());
m_display_self = this;
m_label = NAME;
tree = new Tree();
Table ntable = tree.getNodeTable();
ntable.addColumn(NAME, String.class);
ntable.addColumn(NODECOUNT, int.class);
ntable.addColumn(ROWCOUNT, int.class);
resetTree();
m_vis.add(TREE, tree);
// m_vis.add(TREE, t, new WordCountPredicate());
m_nodeRenderer = new LabelRenderer(m_label);
m_nodeRenderer.setRenderType(AbstractShapeRenderer.RENDER_TYPE_FILL);
m_nodeRenderer.setHorizontalAlignment(Constants.LEFT);
m_nodeRenderer.setRoundedCorner(8, 8);
m_edgeRenderer = new EdgeRenderer(Constants.EDGE_TYPE_CURVE);
DefaultRendererFactory rf = new DefaultRendererFactory(m_nodeRenderer);
rf.add(new InGroupPredicate(TREEEDGES), m_edgeRenderer);
m_vis.setRendererFactory(rf);
// colors
ItemAction nodeColor = new NodeColorAction(TREENODES);
ItemAction textColor = new ColorAction(TREENODES, VisualItem.TEXTCOLOR, ColorLib.rgb(0, 0, 0));
m_vis.putAction("textColor", textColor);
ItemAction edgeColor =
new ColorAction(TREEEDGES, VisualItem.STROKECOLOR, ColorLib.rgb(255, 155, 155));
// quick repaint
ActionList repaint = new ActionList();
repaint.add(nodeColor);
// WordSizeAction wsaction = new WordSizeAction(TREEEDGES);
repaint.add(new RepaintAction());
m_vis.putAction("repaint", repaint);
// full paint
ActionList fullPaint = new ActionList();
fullPaint.add(nodeColor);
m_vis.putAction("fullPaint", fullPaint);
// animate paint change
ActionList animatePaint = new ActionList(400);
animatePaint.add(new ColorAnimator(TREENODES));
animatePaint.add(new RepaintAction());
m_vis.putAction("animatePaint", animatePaint);
// create the tree layout action
NodeLinkTreeLayout treeLayout = new NodeLinkTreeLayout(TREE, m_orientation, 10, 0, 0);
Point2D anchor = new Point2D.Double(25, HEIGHT / 2);
treeLayout.setLayoutAnchor(anchor);
m_vis.putAction("treeLayout", treeLayout);
CollapsedSubtreeLayout subLayout = new CollapsedSubtreeLayout(TREE, m_orientation);
m_vis.putAction("subLayout", subLayout);
AutoPanAction autoPan = new AutoPanAction();
AutoCenterAction autocenter = new AutoCenterAction();
AutoFitAction autofit = new AutoFitAction();
ActionList positioning = new ActionList();
positioning.add(autofit);
m_vis.putAction("positioning", positioning);
ActionList fna = new ActionList();
fna.add(new WordFontAction(TREENODES, defaultTreeFont));
// fna.add(new EdgeWidthAction(TREEEDGES));
// fna.add(new WordSizeAction(TREEEDGES));
m_vis.putAction("fontnodeaction", fna);
// create the filtering and layout
ActionList filter = new ActionList();
filter.add(fna);
filter.add(fisheyetreefilter);
// VisibilityFilter visibfilter = new VisibilityFilter(new WordCountPredicate());
// filter.add(visibfilter);
filter.add(treeLayout);
filter.add(subLayout);
filter.add(textColor);
filter.add(nodeColor);
filter.add(edgeColor);
m_vis.putAction("filter", filter);
// This doesn't quite work as expected; the layout is calculated
// for the entire tree and low freq nodes are simply not shown,
// leaving gaps in the layout
//
// setPredicate(new WordCountPredicate());
// animated transition
ActionList animate = new ActionList(1000);
animate.setPacingFunction(new SlowInSlowOutPacer());
// animate.add(autoPan);
animate.add(new QualityControlAnimator());
animate.add(new VisibilityAnimator(TREE));
animate.add(new LocationAnimator(TREENODES));
animate.add(new ColorAnimator(TREENODES));
animate.add(new RepaintAction());
m_vis.putAction("animate", animate);
m_vis.alwaysRunAfter("filter", "animate");
// create animator for orientation changes
ActionList orient = new ActionList(2000);
orient.setPacingFunction(new SlowInSlowOutPacer());
// orient.add(autoPan);
// orient.add(autocenter);
orient.add(new QualityControlAnimator());
orient.add(new LocationAnimator(TREENODES));
orient.add(new RepaintAction());
// orient.add(autofit);
m_vis.putAction("orient", orient);
// ------------------------------------------------
// initialize the display
setSize(WIDTH, HEIGHT);
setItemSorter(new TreeDepthItemSorter());
addControlListener(new ZoomToFitControl());
addControlListener(new ZoomControl());
addControlListener(new WheelZoomControl());
addControlListener(new PanControl());
addControlListener(new FocusControl(1, "filter"));
addControlListener(new ToolTipControl(NODECOUNT));
registerKeyboardAction(
new OrientAction(Constants.ORIENT_LEFT_RIGHT),
"left-to-right",
KeyStroke.getKeyStroke("ctrl 1"),
WHEN_IN_FOCUSED_WINDOW);
registerKeyboardAction(
new OrientAction(Constants.ORIENT_TOP_BOTTOM),
"top-to-bottom",
KeyStroke.getKeyStroke("ctrl 2"),
WHEN_IN_FOCUSED_WINDOW);
registerKeyboardAction(
new OrientAction(Constants.ORIENT_RIGHT_LEFT),
"right-to-left",
KeyStroke.getKeyStroke("ctrl 3"),
WHEN_IN_FOCUSED_WINDOW);
registerKeyboardAction(
new OrientAction(Constants.ORIENT_BOTTOM_TOP),
"bottom-to-top",
KeyStroke.getKeyStroke("ctrl 4"),
WHEN_IN_FOCUSED_WINDOW);
registerKeyboardAction(
new FisheyeExpandAction(-1),
"collapse-one",
KeyStroke.getKeyStroke("ctrl 5"),
WHEN_IN_FOCUSED_WINDOW);
registerKeyboardAction(
new FisheyeExpandAction(+1),
"expand-one",
KeyStroke.getKeyStroke("ctrl 6"),
WHEN_IN_FOCUSED_WINDOW);
// ------------------------------------------------
// filter graph and perform layout
setOrientation(m_orientation);
m_vis.run("filter");
/*
TupleSet search = new PrefixSearchTupleSet();
m_vis.addFocusGroup(Visualization.SEARCH_ITEMS, search);
search.addTupleSetListener(new TupleSetListener() {
public void tupleSetChanged(TupleSet t, Tuple[] add, Tuple[] rem) {
m_vis.cancel("animatePaint");
m_vis.run("fullPaint");
m_vis.run("animatePaint");
}
});
*/
}
public MPtrack(Table t) {
super(new BorderLayout());
// --------------------------------------------------------------------
// STEP 1: setup the visualized data
final Visualization vis = new Visualization();
m_vis = vis;
final String group = "by_state";
VisualTable vt = vis.addTable(group, t);
vis.setRendererFactory(
new RendererFactory() {
AbstractShapeRenderer sr = new ShapeRenderer(30);
Renderer arY = new AxisRenderer(Constants.RIGHT, Constants.TOP);
Renderer arX = new AxisRenderer(Constants.CENTER, Constants.FAR_BOTTOM);
public Renderer getRenderer(VisualItem item) {
return item.isInGroup("ylab") ? arY : item.isInGroup("xlab") ? arX : sr;
}
});
// --------------------------------------------------------------------
// set up the actions
AxisLayout xaxis = new AxisLayout(group, "States", Constants.X_AXIS, VisiblePredicate.TRUE);
AxisLayout yaxis = new AxisLayout(group, PARTY, Constants.Y_AXIS, VisiblePredicate.TRUE);
// yaxis.setScale(Constants.LOG_SCALE);
xaxis.setLayoutBounds(m_dataB);
yaxis.setLayoutBounds(m_dataB);
AxisLabelLayout ylabels = new AxisLabelLayout("ylab", yaxis, m_ylabB, 5);
AxisLabelLayout xlabels = new AxisLabelLayout("xlab", xaxis, m_xlabB, 5);
vis.putAction("xlabels", xlabels);
int[] palette = new int[] {ColorLib.rgb(150, 150, 255)};
int[] palette2 = new int[200];
for (int i = 0; i < 200; i++) {
palette2[i] = ColorLib.rgba(255, 0, 0, 2 * i);
}
/*
DataColorAction color = new DataColorAction(group, "Party",
Constants.ORDINAL, VisualItem.STROKECOLOR, palette);
*/
DataColorAction color2 =
new DataColorAction(group, "Attendance", Constants.ORDINAL, VisualItem.FILLCOLOR, palette2);
ActionList draw = new ActionList();
draw.add(color2);
draw.add(xaxis);
draw.add(yaxis);
draw.add(ylabels);
draw.add(new RepaintAction());
vis.putAction("draw", draw);
ActionList update = new ActionList();
update.add(xaxis);
update.add(yaxis);
update.add(ylabels);
update.add(new RepaintAction());
vis.putAction("update", update);
UpdateListener lstnr =
new UpdateListener() {
public void update(Object src) {
vis.run("update");
}
};
// --------------------------------------------------------------------
// STEP 4: set up a display and ui components to show the visualization
m_display = new Display(vis);
m_display.setBorder(BorderFactory.createEmptyBorder(10, 10, 10, 10));
m_display.setSize(700, 450);
m_display.setHighQuality(true);
m_display.addComponentListener(
new ComponentAdapter() {
public void componentResized(ComponentEvent e) {
displayLayout();
}
});
displayLayout();
m_details = new JFastLabel(m_title);
m_details.setPreferredSize(new Dimension(75, 20));
m_details.setVerticalAlignment(SwingConstants.BOTTOM);
ToolTipControl ttc = new ToolTipControl("label");
Control hoverc =
new ControlAdapter() {
public void itemEntered(VisualItem item, MouseEvent evt) {
if (item.isInGroup(group)) {
item.setFillColor(item.getStrokeColor());
item.setStrokeColor(ColorLib.rgb(0, 0, 0));
item.getVisualization().repaint();
}
}
public void itemExited(VisualItem item, MouseEvent evt) {
if (item.isInGroup(group)) {
item.setFillColor(item.getEndFillColor());
item.setStrokeColor(item.getEndStrokeColor());
item.getVisualization().repaint();
}
}
};
m_display.addControlListener(ttc);
m_display.addControlListener(hoverc);
// --------------------------------------------------------------------
// STEP 5: launching the visualization
this.addComponentListener(lstnr);
// details
Box infoBox = new Box(BoxLayout.X_AXIS);
infoBox.add(Box.createHorizontalStrut(5));
infoBox.add(m_details);
infoBox.add(Box.createHorizontalGlue());
infoBox.add(Box.createHorizontalStrut(5));
infoBox.add(Box.createHorizontalStrut(5));
// create dynamic queries
Box radioBox = new Box(BoxLayout.X_AXIS);
radioBox.add(Box.createHorizontalStrut(5));
radioBox.add(Box.createHorizontalGlue());
radioBox.add(Box.createHorizontalStrut(5));
radioBox.add(Box.createHorizontalStrut(16));
vis.run("draw");
vis.run("xlabels");
add(infoBox, BorderLayout.NORTH);
add(m_display, BorderLayout.CENTER);
add(radioBox, BorderLayout.SOUTH);
UILib.setColor(this, ColorLib.getColor(255, 255, 255), Color.GRAY);
UILib.setFont(radioBox, FontLib.getFont("Tahoma", 15));
m_details.setFont(FontLib.getFont("Tahoma", 18));
}
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");
}
/*
* Constructor for the class
* This is where all the important stuff happens
*/
public TabularDataVis(Table t) {
super(new BorderLayout());
/*
* Step 1: Setup the Visualization
*/
// create a new visualization object, and assign it to the global variable
final Visualization vis = new Visualization();
g_vis = vis;
// create a visual abstraction of the table data (loaded in the buildFrame method)
// call our data "canUrban"
VisualTable vt = vis.addTable("canUrban", t);
// add a new column containing a label string showing
// the Geographic name and population
// note: uses the prefuse expression language
vt.addColumn(
"label", "CONCAT([Geographic name], ' (Population: ', FORMAT([2006 Population],0), ')')");
// add a new column that divides the provinces by their geographic location (derived values)
// note: uses the prefuse expression language
vt.addColumn(
"geographic location",
"IF ([Province]='BC') THEN 1 ELSE "
+ "(IF ([Province] = 'AB' OR [Province] = 'SK' OR [Province] = 'MB') THEN 2 ELSE "
+ "(IF ([Province] = 'ON' OR [Province] = 'QC') THEN 3 ELSE"
+ "(IF ([Province] = 'NS' OR [Province] = 'NB' OR [Province] = 'PE' OR [Province] = 'NL') THEN 4 ELSE 5)))");
// add a new column that converts the population data to ordinal data (derived values)
// note: uses the prefuse expression language
vt.addColumn(
"population ordinal",
"IF ([2006 Population] > 5000000) THEN 7 ELSE "
+ "(IF ([2006 Population] > 1000000) THEN 6 ELSE "
+ "(IF ([2006 Population] > 250000) THEN 5 ELSE "
+ "(IF ([2006 Population] > 100000) THEN 4 ELSE "
+ "(IF ([2006 Population] > 50000) THEN 3 ELSE "
+ "(IF ([2006 Population] > 20000) THEN 2 ELSE 1)))))");
// create a new renderer factory for drawing the visual items
vis.setRendererFactory(
new RendererFactory() {
// specify the default shape renderer (the actions will decide how to actually render the
// visual elements)
AbstractShapeRenderer sr = new ShapeRenderer();
// renderers for the axes
Renderer arY = new AxisRenderer(Constants.RIGHT, Constants.TOP);
Renderer arX = new AxisRenderer(Constants.CENTER, Constants.FAR_BOTTOM);
// return the appropriate renderer for a given visual item
public Renderer getRenderer(VisualItem item) {
return item.isInGroup("ylab") ? arY : item.isInGroup("xlab") ? arX : sr;
}
});
/*
* Step 2: Add X-Axis
*/
// add the x-axis
AxisLayout xaxis =
new AxisLayout("canUrban", "Province", Constants.X_AXIS, VisiblePredicate.TRUE);
// ensure the axis spans the width of the data container
xaxis.setLayoutBounds(g_dataB);
// add the labels to the x-axis
AxisLabelLayout xlabels = new AxisLabelLayout("xlab", xaxis, g_xlabB, 15);
/*
* Step 3: Add the Y-Axis and its dynamic query feature
*/
// dynamic query based on population data
RangeQueryBinding populationQ = new RangeQueryBinding(vt, "2006 Population");
AndPredicate filter = new AndPredicate(populationQ.getPredicate());
// add the y-axis
AxisLayout yaxis =
new AxisLayout("canUrban", "2006 Population", Constants.Y_AXIS, VisiblePredicate.TRUE);
// set the range controls on the y-axis
yaxis.setRangeModel(populationQ.getModel());
populationQ.getNumberModel().setValueRange(0, 6000000, 0, 6000000);
// ensure the y-axis spans the height of the data container
yaxis.setLayoutBounds(g_dataB);
// add the labels to the y-axis
AxisLabelLayout ylabels = new AxisLabelLayout("ylab", yaxis, g_ylabB);
NumberFormat nf = NumberFormat.getIntegerInstance();
nf.setMaximumFractionDigits(0);
ylabels.setNumberFormat(nf);
/*
* Step 4: Add the search box
*/
// dynamic query based on Geographic name data
SearchQueryBinding searchQ = new SearchQueryBinding(vt, "Geographic name");
filter.add(searchQ.getPredicate()); // reuse the same filter as the population query
/*
* Step 5: Colours and Shapes
*/
// assign a set of five perceptually distinct colours to assign to the provinces
// chosen from ColorBrewer (5-class qualitative Set1)
int[] palette =
new int[] {
ColorLib.rgb(77, 175, 74),
ColorLib.rgb(55, 126, 184),
ColorLib.rgb(228, 26, 28),
ColorLib.rgb(152, 78, 163),
ColorLib.rgb(255, 127, 0)
};
// specify the stroke (exterior line) based on the ordinal data
DataColorAction color =
new DataColorAction(
"canUrban", "geographic location", Constants.ORDINAL, VisualItem.STROKECOLOR, palette);
// specify the fill (interior) as a static colour (white)
ColorAction fill = new ColorAction("canUrban", VisualItem.FILLCOLOR, 0);
// represent all the data points with rectangles
ShapeAction shape = new ShapeAction("canUrban", Constants.SHAPE_RECTANGLE);
// assign the size of the visual element based on the population data (we
// converted the 2006 Population data to ordinal values)
DataSizeAction size = new DataSizeAction("canUrban", "population ordinal");
// setup a counter to keep track of which data points are currently being viewed
Counter cntr = new Counter("canUrban");
/*
* Step 6: Create the action list for drawing the visual elements
*/
ActionList draw = new ActionList();
draw.add(cntr);
draw.add(color);
draw.add(fill);
draw.add(shape);
draw.add(size);
draw.add(xaxis);
draw.add(yaxis);
draw.add(ylabels);
draw.add(new RepaintAction());
vis.putAction("draw", draw);
vis.putAction("xlabels", xlabels);
/*
* create the action list for updating the visual elements
* (during interactive operations and re-sizing of the window)
*/
ActionList update = new ActionList();
update.add(new VisibilityFilter("canUrban", filter)); // filter performs the size/name filtering
update.add(cntr);
update.add(xaxis);
update.add(yaxis);
update.add(ylabels);
update.add(new RepaintAction());
vis.putAction("update", update);
// create an update listener that will update the visualization when fired
UpdateListener lstnr =
new UpdateListener() {
public void update(Object src) {
vis.run("update");
}
};
// add this update listener to the filter, so that when the filter changes (i.e.,
// the user adjusts the axis parameters, or enters a name for filtering), the
// visualization is updated
filter.addExpressionListener(lstnr);
/*
* Step 7: Setup the Display and the other Interface components
* (scroll bar, query box, tool tips)
*/
// create the display
g_display = new Display(vis);
// set the display properties
g_display.setBorder(BorderFactory.createEmptyBorder(10, 20, 10, 20));
g_display.setSize(700, 450);
g_display.setHighQuality(true);
// call the function that sets the sizes of the containers that contain
// the data and the axes
displayLayout();
// whenever the window is re-sized, update the layout of the axes
g_display.addComponentListener(
new ComponentAdapter() {
public void componentResized(ComponentEvent e) {
displayLayout();
}
});
// title label (top left)
JFastLabel g_details = new JFastLabel("Canadian Urban Population");
g_details.setPreferredSize(new Dimension(350, 20));
g_details.setVerticalAlignment(SwingConstants.BOTTOM);
// total label (top right)
g_total.setPreferredSize(new Dimension(350, 20));
g_total.setHorizontalAlignment(SwingConstants.RIGHT);
g_total.setVerticalAlignment(SwingConstants.BOTTOM);
// tool tips
ToolTipControl ttc = new ToolTipControl("label");
Control hoverc =
new ControlAdapter() {
public void itemEntered(VisualItem item, MouseEvent evt) {
if (item.isInGroup("canUrban")) {
g_total.setText(item.getString("label"));
item.setFillColor(item.getStrokeColor());
item.setStrokeColor(ColorLib.rgb(0, 0, 0));
item.getVisualization().repaint();
}
}
public void itemExited(VisualItem item, MouseEvent evt) {
if (item.isInGroup("canUrban")) {
g_total.setText(g_totalStr);
item.setFillColor(item.getEndFillColor());
item.setStrokeColor(item.getEndStrokeColor());
item.getVisualization().repaint();
}
}
};
g_display.addControlListener(ttc);
g_display.addControlListener(hoverc);
// vertical slider for adjusting the population filter
JRangeSlider slider = populationQ.createVerticalRangeSlider();
slider.setThumbColor(null);
slider.setToolTipText("drag the arrows to filter the data");
// smallest window: 200,000
slider.setMinExtent(200000);
slider.addMouseListener(
new MouseAdapter() {
public void mousePressed(MouseEvent e) {
g_display.setHighQuality(false);
}
public void mouseReleased(MouseEvent e) {
g_display.setHighQuality(true);
g_display.repaint();
}
});
// search box
JSearchPanel searcher = searchQ.createSearchPanel();
searcher.setLabelText("Urban Centre: ");
searcher.setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 0));
/*
* Step 8: Create Containers for the Interface Elements
*/
// add the listener to this component
this.addComponentListener(lstnr);
// container for elements at the top of the screen
Box topContainer = new Box(BoxLayout.X_AXIS);
topContainer.add(Box.createHorizontalStrut(5));
topContainer.add(g_details);
topContainer.add(Box.createHorizontalGlue());
topContainer.add(Box.createHorizontalStrut(5));
topContainer.add(g_total);
topContainer.add(Box.createHorizontalStrut(5));
// container for elements at the bottom of the screen
Box bottomContainer = new Box(BoxLayout.X_AXIS);
bottomContainer.add(Box.createHorizontalStrut(5));
bottomContainer.add(searcher);
bottomContainer.add(Box.createHorizontalGlue());
bottomContainer.add(Box.createHorizontalStrut(5));
bottomContainer.add(Box.createHorizontalStrut(16));
// fonts, colours, etc.
UILib.setColor(this, ColorLib.getColor(255, 255, 255), Color.GRAY);
slider.setForeground(Color.LIGHT_GRAY);
UILib.setFont(bottomContainer, FontLib.getFont("Tahoma", 15));
g_details.setFont(FontLib.getFont("Tahoma", 18));
g_total.setFont(FontLib.getFont("Tahoma", 16));
// add the containers to the JPanel
add(topContainer, BorderLayout.NORTH);
add(g_display, BorderLayout.CENTER);
add(slider, BorderLayout.EAST);
add(bottomContainer, BorderLayout.SOUTH);
/*
* Step 9: Start the Visualization
*/
vis.run("draw");
vis.run("xlabels");
}
/**
* Color palette for the BMVis visualization.
*
* @author Kimmo Kulovesi
*/
public class ColorPalette {
/** Predefined edge type stroke colors. */
public static final HashMap<String, Integer> EDGE_COLORS = new HashMap<String, Integer>();
/** Predefined node type colors. */
public static final HashMap<String, Integer> NODE_COLORS = new HashMap<String, Integer>();
/** Predefined queryset colors. */
public static final HashMap<String, Integer> QUERYSET_COLORS = new HashMap<String, Integer>();
static {
// EDGE_COLORS.put("refers_to", ColorLib.rgb(0, 0, 0));
QUERYSET_COLORS.put("start", ColorLib.rgb(0, 175, 0));
QUERYSET_COLORS.put("source", ColorLib.rgb(0, 175, 0));
QUERYSET_COLORS.put("end", ColorLib.rgb(220, 0, 0));
QUERYSET_COLORS.put("target", ColorLib.rgb(220, 0, 0));
QUERYSET_COLORS.put("start,end", ColorLib.rgb(220, 0, 220));
QUERYSET_COLORS.put("source,target", ColorLib.rgb(220, 0, 220));
QUERYSET_COLORS.put("rank", ColorLib.rgb(0, 175, 220));
NODE_COLORS.put("Node", ColorLib.rgb(240, 240, 240));
// Saturated greens
NODE_COLORS.put("Sequence", ColorLib.rgb(211, 247, 163));
NODE_COLORS.put("Gene", ColorLib.rgb(211, 247, 163));
NODE_COLORS.put("Protein", ColorLib.rgb(199, 240, 178));
NODE_COLORS.put("Enzyme", ColorLib.rgb(193, 234, 174));
// NODE_COLORS.put("ProteinGroup", ColorLib.rgb(199, 240, 178));
NODE_COLORS.put("AllelicVariant", ColorLib.rgb(199, 240, 178));
// Beige
NODE_COLORS.put("Article", ColorLib.rgb(250, 230, 160));
// Cyans (to do, make greener)
NODE_COLORS.put("HomologGroup", ColorLib.rgb(187, 237, 215));
NODE_COLORS.put("OrthologGroup", ColorLib.rgb(194, 237, 218));
// Desaturated blues
NODE_COLORS.put("GO", ColorLib.rgb(185, 218, 234));
NODE_COLORS.put("BiologicalProcess", ColorLib.rgb(185, 218, 234));
NODE_COLORS.put("MolecularFunction", ColorLib.rgb(189, 223, 239));
NODE_COLORS.put("CellularComponent", ColorLib.rgb(174, 214, 234));
// Light purples
NODE_COLORS.put("Ligand", ColorLib.rgb(210, 203, 240));
NODE_COLORS.put("Substance", ColorLib.rgb(210, 203, 240));
NODE_COLORS.put("Compound", ColorLib.rgb(210, 203, 240));
NODE_COLORS.put("Drug", ColorLib.rgb(203, 196, 233));
NODE_COLORS.put("Glycan", ColorLib.rgb(198, 200, 242));
// Pink
NODE_COLORS.put("GenomicContext", ColorLib.rgb(255, 215, 253));
// Blues
NODE_COLORS.put("Locus", ColorLib.rgb(180, 196, 239)); // unused
NODE_COLORS.put("Phenotype", ColorLib.rgb(193, 209, 255));
// NODE_COLORS.put("Locus/Phenotype, ColorLib.rgb(195, 199, 242));
// TMP MAPPING for illustration purposes BY LERONEN! Should never get to SVN!
NODE_COLORS.put("Gene/Phenotype", ColorLib.rgb(211, 247, 163));
// NODE_COLORS.put("Gene/Phenotype", ColorLib.rgb(193, 223, 242));
// Greens
NODE_COLORS.put("Family", ColorLib.rgb(179, 226, 192));
NODE_COLORS.put("Region", ColorLib.rgb(195, 229, 204));
NODE_COLORS.put("Domain", ColorLib.rgb(195, 229, 204));
NODE_COLORS.put("Repeat", ColorLib.rgb(195, 229, 204));
NODE_COLORS.put("Site", ColorLib.rgb(190, 229, 201));
NODE_COLORS.put("ActiveSite", ColorLib.rgb(190, 229, 201));
NODE_COLORS.put("BindingSite", ColorLib.rgb(190, 229, 201));
NODE_COLORS.put("PostTranslationalModification", ColorLib.rgb(190, 229, 201));
// Purple
NODE_COLORS.put("Pathway", ColorLib.rgb(208, 185, 231));
// Browns
NODE_COLORS.put("Tissue", ColorLib.rgb(229, 218, 189));
// NODE_COLORS.put("Organism", ColorLib.rgb(229, 215, 177));
NODE_COLORS.put("MeSHHeading", ColorLib.rgb(239, 231, 176));
NODE_COLORS.put("OMIM", ColorLib.rgb(239, 231, 176));
}
/** Node text color. */
public static final int NODE_TEXT = ColorLib.gray(0);
/** Groupnode border stroke color. */
public static final int GROUPNODE_STROKE = ColorLib.gray(0);
/** Edgenode fill color. */
public static final int EDGENODE_FILL = 0;
/**
* Default node fill color. This is generally unused, due to the use of type-specific colors set
* in NODE_COLORS.
*/
public static final int DEFAULT_FILL = ColorLib.rgb(200, 215, 255);
/** Selected node color. */
public static final int NODE_SELECT = ColorLib.rgb(255, 100, 100);
/** Node hover highlight color. */
public static final int NODE_HOVER = ColorLib.rgb(255, 155, 140);
/** Node hover neighbor highlight color. */
public static final int NEIGHBOR_HOVER = ColorLib.rgb(255, 175, 0);
/** Selected node hover highlight color. */
public static final int SELECT_HOVER = ColorLib.rgb(255, 120, 120);
/** Node hover neighbor highlight color for selected nodes. */
public static final int SELECT_NEIGHBOR = ColorLib.rgb(255, 100, 35);
/** Default edge stroke color. */
public static final int DEFAULT_EDGE_STROKE = ColorLib.rgb(15, 15, 15);
}
public void itemReleased(VisualItem item, MouseEvent evt) {
item.setFillColor(ColorLib.rgb(255, 255, 255));
item.setStrokeColor(item.getEndStrokeColor());
item.getVisualization().repaint();
}
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 BorderColorAction(String group) {
super(group, VisualItem.STROKECOLOR, ColorLib.rgba(0, 0, 255, 255));
add(isprocessfilter, ColorLib.rgba(176, 23, 31, 255));
}
@Override
public void render(Graphics2D g, VisualItem item) {
if (item.isVisible()) {
item.setShape(Constants.SHAPE_RECTANGLE);
RectangularShape shape = (RectangularShape) getShape(item);
if (shape != null) {
shape
.getBounds2D()
.setRect(
(double) item.get(VisualItem.X),
(double) item.get(VisualItem.Y),
item.getSize(),
item.getSize());
// draw basic glyph
Color strokeColor = ColorLib.getColor(item.getStrokeColor());
Color fillColor = ColorLib.getColor(item.getFillColor());
// int size = (int)item.getSize();
int x = (int) item.getX() + bufferPx;
int y = (int) item.getY() + bufferPx;
int w = (int) item.getDouble(WIDTH) - 2 * bufferPx;
int h = (int) item.getDouble(HEIGHT) - 2 * bufferPx;
g.setPaint(fillColor);
g.fillRect(x, y, w, h);
// draw string on-top of glyph, filling the glyph's area
// String s = "doc=" + item.getString(NODE_NAME) + "\n";
String s = "";
// set text: full document if no search term, else excerpts containing the search term
String queryStr = searchQ.getSearchSet().getQuery();
String focusText = item.getString(DocumentGridTable.NODE_FOCUS_TEXT);
if (queryStr != null
&& !queryStr.isEmpty()
&& focusText != null
&& !focusText.equals("null")
&& !focusText.equals("")) {
// if search query and terms present in document, use term-containing spans
s += focusText;
} else if (queryStr != null
&& !queryStr.isEmpty()
&& focusText.equals(FOCUS_SENT_SPLITTER)) {
// if search query but no terms present in document, use blank
s += "";
} else if ((queryStr == null || queryStr.isEmpty()) && item.canGetInt(NODE_ID)) {
// if no search query, build feature-oriented summary based on color attribute
s = controller.getDocumentSummary(item.getInt(NODE_ID), colorAttrName);
}
// TODO : idea: set font size dynamically based on number of active nodes? based on size
// of rect?
int fontSize = 10;
item.setFont(FontLib.getFont("Tahoma", Font.PLAIN, fontSize));
Font f = item.getFont();
// compute width, height for the given text
// NOTE: this logic has been moved into drawStringMultiline
// int[] textDims = getTextDims(g, f, s);
// debug
// System.out.println("debug: "+this.getClass().getName()+":
// drawStringMultiline at x="+x1+", y="+y1+", w="+w+", h="+h);
drawStringMultiline(g, f, s, x, y, w, h);
}
}
}
public AggregateDemo() {
// initialize display and data
super(new Visualization());
initDataGroups();
// set up the renderers
// draw the nodes as basic shapes
Renderer nodeR = new ShapeRenderer(20);
// draw aggregates as polygons with curved edges
Renderer polyR = new PolygonRenderer(Constants.POLY_TYPE_CURVE);
((PolygonRenderer) polyR).setCurveSlack(0.15f);
// modification to try drawing edges to aggregates
Renderer edgeR =
new EdgeRenderer() {
@Override
protected Shape getRawShape(VisualItem item) {
EdgeItem edge = (EdgeItem) item;
VisualItem item1 = edge.getSourceItem();
VisualItem item2 = edge.getTargetItem();
item2 = (AggregateItem) at.getAggregates(item2).next();
int type = m_edgeType;
getAlignedPoint(m_tmpPoints[0], item1.getBounds(), m_xAlign1, m_yAlign1);
getAlignedPoint(m_tmpPoints[1], item2.getBounds(), m_xAlign2, m_yAlign2);
m_curWidth = (float) (m_width * getLineWidth(item));
// create the arrow head, if needed
EdgeItem e = (EdgeItem) item;
if (e.isDirected() && m_edgeArrow != Constants.EDGE_ARROW_NONE) {
// get starting and ending edge endpoints
boolean forward = (m_edgeArrow == Constants.EDGE_ARROW_FORWARD);
Point2D start = null, end = null;
start = m_tmpPoints[forward ? 0 : 1];
end = m_tmpPoints[forward ? 1 : 0];
// compute the intersection with the target bounding box
VisualItem dest = forward ? e.getTargetItem() : e.getSourceItem();
int i =
GraphicsLib.intersectLineRectangle(start, end, dest.getBounds(), m_isctPoints);
if (i > 0) end = m_isctPoints[0];
// create the arrow head shape
AffineTransform at = getArrowTrans(start, end, m_curWidth);
m_curArrow = at.createTransformedShape(m_arrowHead);
// update the endpoints for the edge shape
// need to bias this by arrow head size
Point2D lineEnd = m_tmpPoints[forward ? 1 : 0];
lineEnd.setLocation(0, -m_arrowHeight);
at.transform(lineEnd, lineEnd);
} else {
m_curArrow = null;
}
// create the edge shape
Shape shape = null;
double n1x = m_tmpPoints[0].getX();
double n1y = m_tmpPoints[0].getY();
double n2x = m_tmpPoints[1].getX();
double n2y = m_tmpPoints[1].getY();
switch (type) {
case Constants.EDGE_TYPE_LINE:
m_line.setLine(n1x, n1y, n2x, n2y);
shape = m_line;
break;
case Constants.EDGE_TYPE_CURVE:
getCurveControlPoints(edge, m_ctrlPoints, n1x, n1y, n2x, n2y);
m_cubic.setCurve(
n1x,
n1y,
m_ctrlPoints[0].getX(),
m_ctrlPoints[0].getY(),
m_ctrlPoints[1].getX(),
m_ctrlPoints[1].getY(),
n2x,
n2y);
shape = m_cubic;
break;
default:
throw new IllegalStateException("Unknown edge type");
}
// return the edge shape
return shape;
}
};
DefaultRendererFactory drf = new DefaultRendererFactory(nodeR, edgeR);
drf.add("ingroup('aggregates')", polyR);
m_vis.setRendererFactory(drf);
// set up the visual operators
// first set up all the color actions
ColorAction nStroke = new ColorAction(NODES, VisualItem.STROKECOLOR);
nStroke.setDefaultColor(ColorLib.gray(100));
nStroke.add("_hover", ColorLib.gray(50));
ColorAction nFill = new ColorAction(NODES, VisualItem.FILLCOLOR);
nFill.setDefaultColor(ColorLib.gray(255));
nFill.add("_hover", ColorLib.gray(200));
ColorAction nEdges = new ColorAction(EDGES, VisualItem.STROKECOLOR);
nEdges.setDefaultColor(ColorLib.gray(100));
ColorAction aStroke = new ColorAction(AGGR, VisualItem.STROKECOLOR);
aStroke.setDefaultColor(ColorLib.gray(200));
aStroke.add("_hover", ColorLib.rgb(255, 100, 100));
int[] palette =
new int[] {
ColorLib.rgba(255, 200, 200, 255),
ColorLib.rgba(200, 255, 200, 255),
ColorLib.rgba(200, 200, 255, 255)
};
ColorAction aFill =
new DataColorAction(AGGR, "id", Constants.NOMINAL, VisualItem.FILLCOLOR, palette);
// bundle the color actions
ActionList colors = new ActionList();
colors.add(nStroke);
colors.add(nFill);
colors.add(nEdges);
colors.add(aStroke);
colors.add(aFill);
// now create the main layout routine
ActionList layout = new ActionList(Activity.INFINITY);
layout.add(colors);
layout.add(new ForceDirectedLayout(GRAPH, true));
layout.add(new AggregateLayout(AGGR));
layout.add(new RepaintAction());
m_vis.putAction("layout", layout);
// set up the display
setSize(500, 500);
pan(250, 250);
setHighQuality(true);
addControlListener(new AggregateDragControl());
addControlListener(new ZoomControl());
addControlListener(new PanControl());
// set things running
m_vis.run("layout");
}
