/**
* Render the track in the given rectangle.
*
* @param track
* @param locusScores
* @param context
* @param arect
*/
public synchronized void renderScores(
Track track, List<LocusScore> locusScores, RenderContext context, Rectangle arect) {
boolean showMissingData =
PreferenceManager.getInstance().getAsBoolean(PreferenceManager.SHOW_MISSING_DATA_KEY);
Graphics2D noDataGraphics = context.getGraphic2DForColor(UIConstants.NO_DATA_COLOR);
Graphics2D tickGraphics = context.getGraphic2DForColor(Color.BLACK);
Rectangle adjustedRect = calculateDrawingRect(arect);
double origin = context.getOrigin();
double locScale = context.getScale();
Color posColor = track.getColor();
Color negColor = track.getAltColor();
// Get the Y axis definition, consisting of minimum, maximum, and base value. Often
// the base value is == min value which is == 0.
DataRange dataRange = track.getDataRange();
float maxValue = dataRange.getMaximum();
float baseValue = dataRange.getBaseline();
float minValue = dataRange.getMinimum();
boolean isLog = dataRange.isLog();
if (isLog) {
minValue = (float) (minValue == 0 ? 0 : Math.log10(minValue));
maxValue = (float) Math.log10(maxValue);
}
// Calculate the Y scale factor.
double delta = (maxValue - minValue);
double yScaleFactor = adjustedRect.getHeight() / delta;
// Calculate the Y position in pixels of the base value. Clip to bounds of rectangle
double baseDelta = maxValue - baseValue;
int baseY = (int) (adjustedRect.getY() + baseDelta * yScaleFactor);
if (baseY < adjustedRect.y) {
baseY = adjustedRect.y;
} else if (baseY > adjustedRect.y + adjustedRect.height) {
baseY = adjustedRect.y + adjustedRect.height;
}
int lastPx = 0;
for (LocusScore score : locusScores) {
// Note -- don't cast these to an int until the range is checked.
// could get an overflow.
double pX = ((score.getStart() - origin) / locScale);
double dx = Math.ceil((Math.max(1, score.getEnd() - score.getStart())) / locScale) + 1;
if ((pX + dx < 0)) {
continue;
} else if (pX > adjustedRect.getMaxX()) {
break;
}
float dataY = score.getScore();
if (isLog && dataY <= 0) {
continue;
}
if (!Float.isNaN(dataY)) {
// Compute the pixel y location. Clip to bounds of rectangle.
double dy = isLog ? Math.log10(dataY) - baseValue : (dataY - baseValue);
int pY = baseY - (int) (dy * yScaleFactor);
if (pY < adjustedRect.y) {
pY = adjustedRect.y;
} else if (pY > adjustedRect.y + adjustedRect.height) {
pY = adjustedRect.y + adjustedRect.height;
}
Color color = (dataY >= baseValue) ? posColor : negColor;
drawDataPoint(color, (int) dx, (int) pX, baseY, pY, context);
}
if (showMissingData) {
// Draw from lastPx + 1 to pX - 1;
int w = (int) pX - lastPx - 4;
if (w > 0) {
noDataGraphics.fillRect(lastPx + 2, (int) arect.getY(), w, (int) arect.getHeight());
}
}
if (!Float.isNaN(dataY)) {
lastPx = (int) pX + (int) dx;
}
}
if (showMissingData) {
int w = (int) arect.getMaxX() - lastPx - 4;
if (w > 0) {
noDataGraphics.fillRect(lastPx + 2, (int) arect.getY(), w, (int) arect.getHeight());
}
}
}
