private void paintWorld(Graphics2D g) {
for (String country : this.country2shape.keySet()) {
Shape shape = country2shape.get(country);
float color = 0;
if (seen.count(country) != 0) {
color = 1f - (float) (Math.log(seen.count(country)) / Math.log((double) seen.getTotal()));
}
g.setColor(seen.count(country) == 0 ? Color.WHITE : new Color(color, 0f, 0f));
g.fill(shape);
}
for (String country : this.country2shape.keySet()) {
Shape shape = country2shape.get(country);
g.setColor(Color.BLACK);
g.draw(shape);
}
}
private void scan(Graphics2D g, InputStream input) throws IOException {
Set<String> unknownC = new HashSet<String>();
Pattern tab = Pattern.compile("[\t]");
LineIterator in = new LineIteratorImpl(LineReaderUtil.fromBufferedStream(input));
while (in.hasNext()) {
String line = in.next();
String tokens[] = tab.split(line, 5);
if (tokens.length < 4) {
warning("Ignoring " + line);
continue;
}
SAMSequenceRecord rec = this.context.getDictionary().getSequence(tokens[0]);
if (rec == null) {
warning("unknown chromosome " + tokens[0]);
continue;
}
String country = tokens[3].toLowerCase().replaceAll("[ ]", "");
Shape shape = this.country2shape.get(country);
if (shape == null) {
if (!unknownC.contains(country)) {
unknownC.add(country);
warning("unknown country " + country);
}
continue;
}
seen.incr(country);
int midpos = (Integer.parseInt(tokens[1]) + Integer.parseInt(tokens[2])) / 2;
// country center
Point2D.Double pt1 =
new Point2D.Double(shape.getBounds2D().getCenterX(), shape.getBounds2D().getCenterY());
// circle point
Point2D pt3 = this.context.convertPositionToPoint(tokens[0], midpos, getRadiusInt());
double angle = this.context.convertPositionToRadian(rec, midpos);
double angle2 = angle -= Math.PI / 10.0;
double distance13 =
context
.getCenter()
.distance(
new Point2D.Double(
(pt1.getX() + pt3.getX()) / 2.0, (pt1.getY() + pt3.getY()) / 2.0));
// mid point
Point2D pt2 =
new Point2D.Double(
context.getCenterX() + distance13 * Math.cos(angle2),
context.getCenterX() + distance13 * Math.sin(angle2));
Composite old = g.getComposite();
Stroke olds = g.getStroke();
g.setStroke(new BasicStroke(0.8f));
g.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER, 0.02f));
g.setColor(Color.DARK_GRAY);
GeneralPath p = new GeneralPath();
p.moveTo(pt1.getX(), pt1.getY());
p.quadTo(pt2.getX(), pt2.getY(), pt3.getX(), pt3.getY());
p.closePath();
g.draw(p);
g.setComposite(old);
g.setStroke(olds);
}
CloserUtil.close(in);
}
