/**
* Render the site track (the top, summary view of the site).
*
* @param variant
* @param bandRectangle
* @param pX0
* @param dX
* @param context
*/
public void renderSiteBand(
Variant variant, Rectangle bandRectangle, int pX0, int dX, RenderContext context) {
final boolean filtered = variant.isFiltered();
final Color alleleColor;
final Color refColor;
double percent;
if (track.getColorMode() == VariantTrack.ColorMode.METHYLATION_RATE) {
alleleColor = this.convertMethylationRateToColor((float) variant.getMethlationRate() / 100);
percent = variant.getCoveredSampleFraction();
refColor = filtered ? colorAlleleRefAlpha : colorAlleleRef; // Gray
} else {
alleleColor = filtered ? colorAlleleBandAlpha : colorAlleleBand; // Red
double af = variant.getAlleleFraction();
if (af < 0) {
double[] afreqs = variant.getAlleleFreqs();
if (afreqs != null && afreqs.length > 0) {
af = afreqs[0];
}
}
percent = Math.min(1, af);
if (percent <= 0) {
percent = 0;
refColor = filtered ? colorAlleleRefAlpha : colorAlleleRef; // Gray
} else {
refColor = filtered ? blueAlpha : blue; // Blue
}
}
final int bottomY = bandRectangle.y + bandRectangle.height - BOTTOM_MARGIN;
final int barHeight = bandRectangle.height - TOP_MARGIN - BOTTOM_MARGIN;
final int alleleBarHeight = (int) (percent * barHeight);
final int remainderHeight = barHeight - alleleBarHeight;
if (remainderHeight > 0) {
Graphics2D g = context.getGraphic2DForColor(refColor);
g.fillRect(pX0, bottomY - alleleBarHeight - remainderHeight, dX, remainderHeight);
}
if (alleleBarHeight > 0) {
Graphics2D g = context.getGraphic2DForColor(alleleColor);
g.fillRect(pX0, bottomY - alleleBarHeight, dX, alleleBarHeight);
}
}
