// TODO: cache required
protected int getEdgeIndex(EdgeItem e) {
if (isIgnored(e)) {
return -1;
}
NodeItem sourceItem = e.getSourceItem();
NodeItem targetItem = e.getTargetItem();
Iterator<EdgeItem> edges = sourceItem.edges();
// number of equal edges = same target and source
int equalEdges = 0;
// number of nearequal edges = same nodes, but any order target and source
int sameEdges = 0;
int edgeIndex = 0;
int row = e.getRow();
while (edges.hasNext()) {
EdgeItem edge = edges.next();
int edgeRow = edge.getRow();
if (isIgnored(edge)) {
continue;
}
if (edge.getSourceItem() == sourceItem && edge.getTargetItem() == targetItem) {
if (row == edgeRow) {
edgeIndex = equalEdges;
}
equalEdges++;
sameEdges++;
} else if (edge.getSourceItem() == targetItem && edge.getTargetItem() == sourceItem) {
sameEdges++;
}
}
// draw the line straight if we found one edge
if (lineForSingleEdge && edgeIndex == 0 && sameEdges == 1) {
return -1;
} else if (sameEdges > 1) {
edgeIndex++;
}
return edgeIndex;
}
protected boolean isDirected(EdgeItem e) {
return e.isDirected();
}
protected boolean isIgnored(EdgeItem e) {
return e.isAggregating();
}
/** @see prefuse.render.AbstractShapeRenderer#getRawShape(prefuse.visual.VisualItem) */
@Override
protected Shape getRawShape(VisualItem item) {
EdgeItem e = (EdgeItem) item;
VisualItem source = e.getSourceItem();
VisualItem target = e.getTargetItem();
int type = m_edgeType;
int edgeIndex = -1;
getAlignedPoint(m_tmpPoints[0], source.getBounds(), m_xAlign1, m_yAlign1);
getAlignedPoint(m_tmpPoints[1], target.getBounds(), m_xAlign2, m_yAlign2);
m_curWidth = (float) (m_width * getLineWidth(item));
boolean curveCtrlPtsReady = false;
Polygon arrowHead;
// create the arrow head, if needed
if (isDirected(e)
&& m_edgeArrow != Constants.EDGE_ARROW_NONE
&& (arrowHead = getArrowHead(e)) != null) {
// 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 source/target bounding box
VisualItem src = getSourceItem(e, forward);
VisualItem dest = getTargetItem(e, forward);
if (edgeBounded && !e.isAggregating()) {
adjustEndingPoint(start, end, src, dest);
} else if (GraphicsLib.intersectLineRectangle(start, end, dest.getBounds(), m_isctPoints)
> 0) {
end.setLocation(m_isctPoints[0]);
}
// create the arrow head shape
AffineTransform arrowTrans;
if (multipleEdge) {
edgeIndex = adjustEndingPointByMultipleEdge(e, start, end);
if (lineForSingleEdge && edgeIndex < 0) {
type = Constants.EDGE_TYPE_LINE;
arrowTrans = getArrowTrans(start, end, m_curWidth);
} else {
getCurveControlPoints(
edgeIndex, m_ctrlPoints, start.getX(), start.getY(), end.getX(), end.getY());
curveCtrlPtsReady = true;
arrowTrans = getArrowTrans(m_ctrlPoints[0], end, m_curWidth);
}
} else {
arrowTrans = getArrowTrans(start, end, m_curWidth);
}
m_curArrow = m_tmpArrow.set(arrowHead, arrowTrans);
// update the endpoints for the edge shape
// need to bias this by arrow head size
adjustLineEndByArrowHead(e, end);
arrowTrans.transform(end, end);
} else {
m_curArrow = null;
if (edgeBounded && !e.isAggregating()) {
adjustEndingPoint(m_tmpPoints[0], m_tmpPoints[1], source, target);
}
if (multipleEdge) {
edgeIndex = adjustEndingPointByMultipleEdge(e, m_tmpPoints[0], m_tmpPoints[1]);
if (lineForSingleEdge && edgeIndex < 0) {
type = Constants.EDGE_TYPE_LINE;
} else {
getCurveControlPoints(
edgeIndex,
m_ctrlPoints,
m_tmpPoints[0].getX(),
m_tmpPoints[0].getY(),
m_tmpPoints[1].getX(),
m_tmpPoints[1].getY());
curveCtrlPtsReady = true;
}
}
}
// create the edge shape
Shape shape = null;
double sx = m_tmpPoints[0].getX();
double sy = m_tmpPoints[0].getY();
double ex = m_tmpPoints[1].getX();
double ey = m_tmpPoints[1].getY();
switch (type) {
case Constants.EDGE_TYPE_LINE:
m_line.setLine(sx, sy, ex, ey);
shape = m_line;
break;
case Constants.EDGE_TYPE_CURVE:
if (!curveCtrlPtsReady) {
getCurveControlPoints(e, m_ctrlPoints, sx, sy, ex, ey);
}
m_quad.setCurve(sx, sy, m_ctrlPoints[0].getX(), m_ctrlPoints[0].getY(), ex, ey);
shape = m_quad;
break;
default:
throw new IllegalStateException("Unknown edge type");
}
// return the edge shape
return shape;
}
protected VisualItem getTargetItem(EdgeItem e, boolean forward) {
VisualItem target = forward ? e.getTargetItem() : e.getSourceItem();
return target;
}
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;
}