/** 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++;
}
}
}
}
}
