/** Sets the initial position of the Graph nodes. */
public void initialize() {
if (this.sampleGroups != null) {
Dimension d = this.getSize();
List<List<V>> moleculeGroups = new ArrayList<List<V>>();
for (int i = 0; i < 3; i++) {
moleculeGroups.add(new ArrayList<V>());
}
if (d != null) {
double height = d.getHeight();
double width = d.getWidth();
String groupName;
for (V v : this.getGraph().getVertices()) {
if (this.isUpRegulated(sampleGroups, v)) moleculeGroups.get(1).add(v);
else if (this.isDownRegulated(sampleGroups, v)) moleculeGroups.get(2).add(v);
else moleculeGroups.get(0).add(v);
}
this.radius = (Math.min(height, width)) * 0.3;
int groupRadius = (int) (this.radius / Math.sqrt(moleculeGroups.size()));
int j = 0, x, y;
Point2D.Double graphCenter = new Point2D.Double(width / 2.0, height / 2.0);
PolarPoint2D center = new PolarPoint2D(0, 0, graphCenter);
PolarPoint2D coord = new PolarPoint2D(0, 0, center);
double theta;
for (List<V> group : moleculeGroups) {
theta = (2 * Math.PI * j) / moleculeGroups.size();
j++;
center.setLocation(this.radius, theta, PolarPoint2D.POLAR);
int i = 0;
for (V vertex : group) {
theta = (2 * Math.PI * i) / group.size();
coord.setLocation(groupRadius, theta, PolarPoint2D.POLAR);
this.setLocation(vertex, coord);
i++;
}
}
}
}
}
/**
* Changes the size of the underlying Layout.
*
* @param size The new size for the layout.
*/
private void setSize(Dimension size) {
ObservableCachingLayout<V, E> observableLayout = (ObservableCachingLayout) getGraphLayout();
Layout<V, E> tmpLayout = observableLayout;
while (!AbstractLayout.class.isAssignableFrom(tmpLayout.getClass()))
tmpLayout = ((LayoutDecorator<V, E>) tmpLayout).getDelegate();
AbstractLayout<V, E> layout = (AbstractLayout<V, E>) tmpLayout;
// the first time the graph is resized, re-initialize the layout to make sure it gets
// the right size. Any other time, just scale it. The first resize should be when the
// graph is made visible and laid out.
// this is kind of a hack; there may be a better way to handle this.
// I tried listening for componentShown, but it didn't work properly.
if (layoutInitialized < 1) {
layout.getSize().setSize(size);
layout.initialize();
layoutInitialized++;
return;
}
// change the size of the layout without triggering the automatic resizing.
double wScale = size.getWidth() / layout.getSize().getWidth();
double hScale = size.getHeight() / layout.getSize().getHeight();
double scale = Math.min(wScale, hScale);
layout.getSize().setSize(size);
Collection<V> vertices = new Vector(getVertices());
synchronized (graph) {
for (V v : vertices) {
double x =
layout.getX(v)
* scale; // Math.min( size.getWidth( ) - 10, Math.max( 10, layout.getX( v ) *
// scale ));
double y =
layout.getY(v)
* scale; // Math.min( size.getHeight( ) - 10, Math.max( 10, layout.getY( v ) *
// scale ));
layout.setLocation(v, new Point2D.Double(x, y));
}
}
// alert the ObservableLayout that things have changed.
observableLayout.fireStateChanged();
}
