/**
* Get a graphics object for the baseline. TODO -- make the line style settable by the user
*
* @param context
* @return
*/
private static Graphics2D getBaselineGraphics(RenderContext context) {
Graphics2D baselineGraphics;
baselineGraphics = (Graphics2D) context.getGraphic2DForColor(Color.lightGray).create();
baselineGraphics.setRenderingHint(
RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
return baselineGraphics;
}
/**
* 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();
}
/**
* 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());
}
}
}
protected void drawDataPoint(
Color graphColor, int dx, int pX, int baseY, int pY, RenderContext context) {
context.getGraphic2DForColor(graphColor).fillRect(pX, pY, dx, 2);
}
@Override
public void renderBorder(Track track, RenderContext context, Rectangle arect) {
Rectangle adjustedRect = calculateDrawingRect(arect);
// Draw boundaries if there is room
if (adjustedRect.getHeight() >= 10) {
/// TrackProperties pros = track.getProperties();
// midline
DataRange axisDefinition = track.getDataRange();
float maxValue = axisDefinition.getMaximum();
float baseValue = axisDefinition.getBaseline();
float minValue = axisDefinition.getMinimum();
double maxX = adjustedRect.getMaxX();
double x = adjustedRect.getX();
double y = adjustedRect.getY();
if ((baseValue > minValue) && (baseValue < maxValue)) {
int baseY = computeYPixelValue(adjustedRect, axisDefinition, baseValue);
getBaselineGraphics(context).drawLine((int) x, baseY, (int) maxX, baseY);
}
PreferenceManager prefs = PreferenceManager.getInstance();
Color altColor = track.getAltColor();
Color borderColor =
(prefs.getAsBoolean(PreferenceManager.CHART_COLOR_BORDERS)
&& altColor != null
&& altColor.equals(track.getColor()))
? track.getColor()
: Color.lightGray;
Graphics2D borderGraphics = context.getGraphic2DForColor(borderColor);
// Draw the baseline -- todo, this is a wig track option?
double zeroValue = axisDefinition.getBaseline();
int zeroY = computeYPixelValue(adjustedRect, axisDefinition, zeroValue);
borderGraphics.drawLine(adjustedRect.x, zeroY, adjustedRect.x + adjustedRect.width, zeroY);
// Optionally draw "Y" line (UCSC track line option)
if (track.isDrawYLine()) {
Graphics2D yLineGraphics = context.getGraphic2DForColor(Color.gray);
int yLine = computeYPixelValue(adjustedRect, axisDefinition, track.getYLine());
GraphicUtils.drawDashedLine(
borderGraphics, adjustedRect.x, yLine, adjustedRect.x + adjustedRect.width, yLine);
}
// If the chart has + and - numbers draw both borders or none. This
// needs documented somewhere.
boolean drawBorders = true;
if (minValue * maxValue < 0) {
drawBorders =
prefs.getAsBoolean(PreferenceManager.CHART_DRAW_BOTTOM_BORDER)
&& prefs.getAsBoolean(PreferenceManager.CHART_DRAW_TOP_BORDER);
}
if (drawBorders && prefs.getAsBoolean(PreferenceManager.CHART_DRAW_TOP_BORDER)) {
borderGraphics.drawLine(
adjustedRect.x, adjustedRect.y, adjustedRect.x + adjustedRect.width, adjustedRect.y);
}
if (drawBorders && prefs.getAsBoolean(PreferenceManager.CHART_DRAW_BOTTOM_BORDER)) {
borderGraphics.drawLine(
adjustedRect.x,
adjustedRect.y + adjustedRect.height,
adjustedRect.x + adjustedRect.width,
adjustedRect.y + adjustedRect.height);
}
}
/*
(CHART_DRAW_TOP_BORDER));
prefs.setDrawBottomBorder(getBooleanPreference(CHART_DRAW_BOTTOM_BORDER));
prefs.setColorBorders(getBooleanPreference(CHART_COLOR_BORDERS));
prefs.setDrawAxis(getBooleanPreference(CHART_DRAW_Y_AXIS));
prefs.setDrawTrackName(getBooleanPreference(CHART_DRAW_TRACK_NAME));
prefs.setColorTrackName(getBooleanPreference(CHART_COLOR_TRACK_NAME));
prefs.setAutoscale(getBooleanPreference(CHART_AUTOSCALE));
prefs.setShowDataRange(getBooleanPreference(CHART_SHOW_DATA_RANGE));
*/
}
/**
* Method description
*
* @param track
* @param context
* @param arect
*/
@Override
public void renderAxis(Track track, RenderContext context, Rectangle arect) {
// For now disable axes for all chromosome view
if (context.getChr().equals(Globals.CHR_ALL)) {
return;
}
super.renderAxis(track, context, arect);
Rectangle drawingRect = calculateDrawingRect(arect);
PreferenceManager prefs = PreferenceManager.getInstance();
Color labelColor =
prefs.getAsBoolean(PreferenceManager.CHART_COLOR_TRACK_NAME)
? track.getColor()
: Color.black;
Graphics2D labelGraphics = context.getGraphic2DForColor(labelColor);
labelGraphics.setFont(FontManager.getFont(8));
if (prefs.getAsBoolean(PreferenceManager.CHART_DRAW_TRACK_NAME)) {
// Only attempt if track height is > 25 pixels
if (arect.getHeight() > 25) {
Rectangle labelRect = new Rectangle(arect.x, arect.y + 10, arect.width, 10);
labelGraphics.setFont(FontManager.getFont(10));
GraphicUtils.drawCenteredText(track.getName(), labelRect, labelGraphics);
}
}
if (prefs.getAsBoolean(PreferenceManager.CHART_DRAW_Y_AXIS)) {
Rectangle axisRect = new Rectangle(arect.x, arect.y + 1, AXIS_AREA_WIDTH, arect.height);
DataRange axisDefinition = track.getDataRange();
float maxValue = axisDefinition.getMaximum();
float baseValue = axisDefinition.getBaseline();
float minValue = axisDefinition.getMinimum();
// Bottom (minimum tick mark)
int pY = computeYPixelValue(drawingRect, axisDefinition, minValue);
labelGraphics.drawLine(
axisRect.x + AXIS_AREA_WIDTH - 10, pY, axisRect.x + AXIS_AREA_WIDTH - 5, pY);
GraphicUtils.drawRightJustifiedText(
formatter.format(minValue), axisRect.x + AXIS_AREA_WIDTH - 15, pY, labelGraphics);
// Top (maximum tick mark)
int topPY = computeYPixelValue(drawingRect, axisDefinition, maxValue);
labelGraphics.drawLine(
axisRect.x + AXIS_AREA_WIDTH - 10, topPY, axisRect.x + AXIS_AREA_WIDTH - 5, topPY);
GraphicUtils.drawRightJustifiedText(
formatter.format(maxValue), axisRect.x + AXIS_AREA_WIDTH - 15, topPY + 4, labelGraphics);
// Connect top and bottom
labelGraphics.drawLine(
axisRect.x + AXIS_AREA_WIDTH - 10, topPY, axisRect.x + AXIS_AREA_WIDTH - 10, pY);
// Middle tick mark. Draw only if room
int midPY = computeYPixelValue(drawingRect, axisDefinition, baseValue);
if ((midPY < pY - 15) && (midPY > topPY + 15)) {
labelGraphics.drawLine(
axisRect.x + AXIS_AREA_WIDTH - 10, midPY, axisRect.x + AXIS_AREA_WIDTH - 5, midPY);
GraphicUtils.drawRightJustifiedText(
formatter.format(baseValue),
axisRect.x + AXIS_AREA_WIDTH - 15,
midPY + 4,
labelGraphics);
}
} else if (track.isShowDataRange() && arect.height > 20) {
drawScale(track.getDataRange(), context, arect);
}
}