public void eventRegistered(EventObject e) {
if (e.getSource() == model && model.isReady()) {
setCanPaint(true);
setWantsPaint(true);
notifyListeners();
}
}
public void paintItem(Graphics2D g, int x1, int y1, int x2, int y2) {
if (!model.isReady()) {
return;
}
Set<Genome> genomes = model.getGenomes();
if (genomes == null) {
g.drawString("No Genomes Yet", x1 + 40, y1 + 40);
return;
}
Genome currentGenome = model.getCurrentGenome();
if (currentGenome == null) {
g.drawString("Haven't moved", x1 + 40, y1 + 40);
return;
}
genomes.remove(currentGenome);
if (genomes.size() == 0) {
g.drawString("Single genome isn't very interesting", x1 + 40, y1 + 40);
return;
}
cs.reset();
int h = y2 - y1;
int midY = y1 + h / 2;
int rstart = getRegion().getStart();
int rend = getRegion().getEnd();
Stroke old = g.getStroke();
Stroke thin = new BasicStroke(1);
Stroke medium = new BasicStroke(3);
Stroke thick = new BasicStroke(6);
for (Genome genome : genomes) {
Region best = model.getBestRegion(genome);
if (best == null) {
continue;
}
String bestc = best.getChrom();
int ostart = best.getStart();
int oend = best.getEnd();
java.util.List<MultiZAlignRegion> alignedRegions = model.getAlignedRegions(genome);
for (MultiZAlignRegion align : alignedRegions) {
if (align.getOtherChrom().equals(bestc)) {
g.setColor(
cs.colorAt(
hashPosPair(
align.getStart(),
align.getEnd(),
align.getOtherStart(),
align.getOtherEnd(),
cs.colorCount())));
int rsx = getXPos(align.getStart(), rstart, rend, x1, x2);
int osx = getXPos(align.getOtherStart(), ostart, oend, x1, x2);
int rex = getXPos(align.getEnd(), rstart, rend, x1, x2);
int oex = getXPos(align.getOtherEnd(), ostart, oend, x1, x2);
g.setStroke(medium);
if (myGenome == currentGenome) {
g.drawLine(rsx, midY, rex, midY);
g.drawLine(rsx, y1, rsx, y2);
g.drawLine(rex, y1, rex, y2);
addLabel(rsx, y1, rex - rsx, y2, align.toString());
} else {
g.drawLine(osx, midY, oex, midY);
g.drawLine(osx, y1, osx, y2);
g.drawLine(oex, y1, oex, y2);
addLabel(osx, y1, oex - osx, y2, align.toString());
}
}
}
}
g.setStroke(old);
g.setColor(Color.BLACK);
g.drawString(model.getAlignment(), x1 + 5, y2);
}
public void cleanup() {
super.cleanup();
model.removeEventListener(this);
}