public void setRegion(Region r) {
super.setRegion(r);
watsonProbes.clear();
crickProbes.clear();
points = null;
scale.setScale(0.0, 1.0);
Iterator<ExpressionProbe> probes = prober.execute(r);
while (probes.hasNext()) {
ExpressionProbe probe = probes.next();
int bp = probe.getLocation();
double value = probe.mean();
if (!Double.isNaN(value)) {
if (probe.getStrand() == '+') {
watsonProbes.add(new Pair<Integer, Double>(bp, value));
} else {
crickProbes.add(new Pair<Integer, Double>(bp, value));
}
scale.updateScale(value);
}
}
}
public void paintItem(Graphics g, int x1, int y1, int x2, int y2) {
Graphics2D g2 = (Graphics2D) g;
g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
PaintableScale xScale = getPropertyValue(xScaleKey);
PaintableScale yScale = getPropertyValue(yScaleKey);
Color color = getPropertyValue(colorKey);
Double min = xScale.getMin(), max = xScale.getMax();
Double range = max - min;
int w = x2 - x1 + 1;
int h = y2 - y1 + 1;
int px = -1, py = -1;
g.setColor(Color.black);
if (xScale.getMin() < 0.0 && xScale.getMax() > 0.0) {
double zf = xScale.fractionalOffset(0.0);
int x = x1 + (int) Math.round(zf * (double) w);
g.drawLine(x, y1, x, y2);
}
if (yScale.getMin() < 0.0 && yScale.getMax() > 0.0) {
double zf = yScale.fractionalOffset(0.0);
int y = y2 - (int) Math.round(zf * (double) h);
g.drawLine(x1, y, x2, y);
}
g.setColor(color);
for (int x = x1; x <= x2; x++) {
Double xInput = min + ((double) (x - x1) / (double) w) * range;
Double yOutput = function.eval(xInput);
if (yOutput != null) {
double yf = yScale.fractionalOffset(yOutput);
int y = y2 - (int) Math.round(yf * (double) h);
if (px != -1 && py != -1) {
g.drawLine(px, py, x, y);
}
px = x;
py = y;
} else {
px = py = -1;
}
}
}
public int getYOffset(double value) {
double frac = scale.fractionalOffset(value);
int pix = (int) Math.round(frac * (double) height);
return pix;
}
public void paintRegion(Graphics2D g, int x1, int y1, int w, int h) {
int h2 = h / 2;
int rad = 3;
int diam = rad * 2;
Color lg = Color.cyan;
Color dg = Color.orange;
lg = new Color(lg.getRed(), lg.getGreen(), lg.getBlue(), 75);
dg = new Color(dg.getRed(), dg.getGreen(), dg.getBlue(), 75);
/*
* Draw the Baseline
*/
g.setColor(Color.black);
g.drawLine(x1, y1 + h, x1 + w, y1 + h);
Stroke oldStroke = g.getStroke();
g.setStroke(new BasicStroke((float) 2.0));
/*
* Draw the datapoints
*/
for (ExprPoint ep : points) {
if (ep.strand == '+') {
g.setColor(lg);
} else {
g.setColor(dg);
}
g.drawOval(x1 + ep.x - rad, y1 + ep.y - rad, diam, diam);
}
g.setStroke(oldStroke);
/*
* Paint the hash marks...
*/
if (!displayOppositeChannel) {
g.setColor(Color.black);
boolean flipper = true;
for (int value = 100;
value <= scale.getMax();
value *= (flipper ? 5 : 2), flipper = !flipper) {
int yoff = getYOffset((double) value);
String line = String.format("%d", value);
int uy = y1 + h2 - yoff, ly = y1 + h2 + yoff;
g.drawLine(x1, uy, x1 + 10, uy);
g.drawString(line, x1 + 12, uy + 5);
g.drawLine(x1, ly, x1 + 10, ly);
g.drawString(line, x1 + 12, ly + 5);
}
}
/*
* Draw any selections.
*/
g.setColor(Color.black);
for (Point p : selections.keySet()) {
ExprPoint ep = selections.get(p);
g.drawLine(p.x, p.y, ep.x, ep.y);
g.drawString(ep.getLabel(), p.x, p.y);
}
/*
* Draw the label in the upper-right hand corner.
*/
g.setColor(Color.black);
Font oldFont = g.getFont();
Font newFont = new Font("Arial", Font.BOLD, 24);
g.setFont(newFont);
FontMetrics fm = g.getFontMetrics();
int lblHeight = fm.getAscent() + fm.getDescent();
int lblWidth = fm.charsWidth(label.toCharArray(), 0, label.length());
int padding = 5;
int lblx = x1 + w - lblWidth - padding;
int lbly = y1 + lblHeight + padding;
g.drawString(label, lblx, lbly);
g.setFont(oldFont);
}
