/**
* 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);
}
}
public void renderGenotypeBandSNP(
Variant variant,
RenderContext context,
Rectangle bandRectangle,
int pX0,
int dX,
String sampleName,
VariantTrack.ColorMode coloring,
boolean hideFiltered) {
int pY = (int) bandRectangle.getY();
int dY = (int) bandRectangle.getHeight();
int tOffset = 6;
int bOffset = 8;
Graphics2D g = (Graphics2D) context.getGraphics().create();
if (dX >= 10) {
if (dY > 24) {
Font f = FontManager.getFont(Font.BOLD, Math.min(dX, 12));
g.setFont(f);
} else if (dY > 18) {
Font f = FontManager.getFont(Font.BOLD, Math.min(dX, 8));
tOffset = 4;
bOffset = 5;
g.setFont(f);
}
}
boolean isFiltered = variant.isFiltered() && hideFiltered;
Genotype genotype = variant.getGenotype(sampleName);
if (genotype == null) {
log.error("Now what?");
} else {
Color b1Color = Color.gray;
Color b2Color = Color.gray;
char b1 = ' ';
char b2 = ' ';
// Assign proper coloring
switch (coloring) {
case GENOTYPE:
b1Color = getGenotypeColor(genotype, isFiltered);
b2Color = b1Color;
break;
case ALLELE:
final List<Allele> alleleList = genotype.getAlleles();
if (alleleList.size() > 0) {
b1 = getFirstBase(alleleList.get(0));
b1Color = nucleotideColors.get(b1);
}
if (alleleList.size() > 1) {
b2 = getFirstBase(alleleList.get(1));
b2Color = nucleotideColors.get(b2);
}
break;
case METHYLATION_RATE:
final double goodBaseCount = genotype.getAttributeAsDouble("GB");
b1Color = colorNoCall;
b2Color = b1Color;
final double value = genotype.getAttributeAsDouble("MR");
if (!Double.isNaN(goodBaseCount) && !Double.isNaN(value)) {
if (goodBaseCount < VariantTrack.METHYLATION_MIN_BASE_COUNT || Double.isNaN(value)) {
b1Color = colorNoCall;
b2Color = b1Color;
} else {
float mr = (float) value;
mr /= 100f;
b1Color = convertMethylationRateToColor(mr);
b2Color = b1Color;
}
} else {
log.error(
"GB and MR fields must be defined for all records in a VCF methylation file.");
}
break;
default:
b1Color = colorNoCall;
b2Color = b1Color;
}
int y0 = track.getDisplayMode() == Track.DisplayMode.EXPANDED ? pY + 1 : pY;
int h = Math.max(1, track.getDisplayMode() == Track.DisplayMode.EXPANDED ? dY - 2 : dY);
if (coloring == VariantTrack.ColorMode.GENOTYPE) {
g.setColor(b1Color);
g.fillRect(pX0, y0, dX, h);
} else {
// Color by allele
g.setColor(b1Color);
g.fillRect(pX0, y0, (dX / 2), h);
g.setColor(b2Color);
g.fillRect(pX0 + (dX / 2), y0, (dX / 2), h);
}
if ((dX >= 10) && (dY >= 18)) {
if (b1Color == Color.blue) {
g.setColor(Color.white);
} else {
g.setColor(Color.black);
}
drawCenteredText(g, new char[] {b1}, pX0, pY - tOffset, dX, dY);
drawCenteredText(g, new char[] {b2}, pX0, pY + (dY / 2) - bOffset, dX, dY);
}
}
g.dispose();
}