private void renderArcMode(Graphics2D g2, GraphPaneAdapter gp, Resolution r) {
ColourScheme cs = (ColourScheme) instructions.get(DrawingInstruction.COLOUR_SCHEME);
Color bgcolor = cs.getColor(ColourKey.OPAQUE_GRAPH);
AxisRange axisRange = (AxisRange) instructions.get(DrawingInstruction.AXIS_RANGE);
if (r == Resolution.HIGH) {
g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
gp.setXRange(axisRange.getXRange());
gp.setYRange(axisRange.getYRange());
for (Record record : data) {
Interval inter = ((IntervalRecord) record).getInterval();
int arcLength = inter.getLength();
double arcHeight = Math.log((double) arcLength);
double rectWidth = arcLength * gp.getUnitWidth();
double rectHeight = arcHeight * 2 * gp.getUnitHeight();
double xOrigin = gp.transformXPos(inter.getStart());
double yOrigin = gp.transformYPos(arcHeight);
g2.setColor(bgcolor);
g2.draw(new Arc2D.Double(xOrigin, yOrigin, rectWidth, rectHeight, -180, -180, Arc2D.OPEN));
}
}
}
private void renderSquishMode(Graphics2D g2, GraphPaneAdapter gp, Resolution r)
throws RenderingException {
ColourScheme cs = (ColourScheme) instructions.get(DrawingInstruction.COLOUR_SCHEME);
Color bgcolor = cs.getColor(ColourKey.TRANSLUCENT_GRAPH);
Color linecolor = cs.getColor(ColourKey.INTERVAL_LINE);
AxisRange axisRange = (AxisRange) instructions.get(DrawingInstruction.AXIS_RANGE);
if (r == Resolution.HIGH) {
gp.setXRange(axisRange.getXRange());
gp.setYRange(axisRange.getYRange());
double unitWidth = gp.getUnitWidth();
double unitHeight = gp.getUnitHeight();
double y = gp.transformYPos(0.0);
for (Record record : data) {
Interval inter = ((IntervalRecord) record).getInterval();
double x = gp.transformXPos(inter.getStart());
double w = unitWidth * inter.getLength();
double h = unitHeight;
Rectangle2D.Double rect = new Rectangle2D.Double(x, y - unitHeight, w, unitHeight);
g2.setColor(bgcolor);
g2.fill(rect);
if (w > 5) {
g2.setColor(linecolor);
g2.draw(rect);
}
}
} else {
throw new RenderingException("Zoom in to see intervals", RenderingException.LOWEST_PRIORITY);
}
}
private void renderPackMode(Graphics2D g2, GraphPaneAdapter gp, Resolution r)
throws RenderingException {
ColourScheme cs = (ColourScheme) instructions.get(DrawingInstruction.COLOUR_SCHEME);
AxisRange axisRange = (AxisRange) instructions.get(DrawingInstruction.AXIS_RANGE);
if (r == Resolution.HIGH) {
IntervalPacker packer = new IntervalPacker(data);
List<List<IntervalRecord>> intervals = packer.pack(2);
gp.setXRange(axisRange.getXRange());
int maxYRange;
int numIntervals = intervals.size();
// Set the Y range to the closest value of 10, 20, 50, 100, n*100
if (numIntervals <= 10) maxYRange = 10;
else if (numIntervals <= 20) maxYRange = 20;
else if (numIntervals <= 50) maxYRange = 50;
else if (numIntervals <= 100) maxYRange = 100;
else maxYRange = numIntervals;
gp.setYRange(new Range(0, maxYRange));
// resize frame if necessary
if (gp.needsToResize()) return;
double unitHeight = gp.getUnitHeight();
double unitWidth = gp.getUnitWidth();
int offset = gp.getOffset();
Color textColor = cs.getColor(ColourKey.INTERVAL_TEXT);
Color bgColor = cs.getColor(ColourKey.OPAQUE_GRAPH);
Color lineColor = cs.getColor(ColourKey.INTERVAL_LINE);
// scan the map of intervals and draw the intervals for each level
for (int k = 0; k < intervals.size(); k++) {
List<IntervalRecord> intervalsThisLevel = intervals.get(k);
for (IntervalRecord intervalRecord : intervalsThisLevel) {
Interval interval = intervalRecord.getInterval();
double x = gp.transformXPos(interval.getStart());
// double y = gp.transformYPos(k)-unitHeight;
double y = gp.getHeight() - unitHeight * (k + 1) - offset;
double w = interval.getLength() * unitWidth;
// if (w < 1) continue; // don't draw intervals less than one pixel wide
double h = unitHeight;
Rectangle2D.Double intervalRect = new Rectangle2D.Double(x, y, w, h);
g2.setColor(bgColor);
g2.fill(intervalRect);
recordToShapeMap.put(intervalRecord, intervalRect);
if (w > 5) {
g2.setColor(lineColor);
g2.draw(intervalRect);
}
String geneName = intervalRecord.getName();
if (geneName != null) {
g2.setColor(textColor);
FontMetrics fm = g2.getFontMetrics();
drawFeatureLabel(
g2, geneName, x, y + unitHeight * 0.5 + (fm.getHeight() - fm.getDescent()) * 0.5);
}
}
}
}
}
