/** User: Jesse Whitworth Date: Jul 16, 2010 */ public class VariantRenderer { // extends FeatureRenderer { private static Logger log = Logger.getLogger(VariantRenderer.class); public static final int BOTTOM_MARGIN = 0; public static final int TOP_MARGIN = 3; private static float alphaValue = 0.2f; public static Color colorHomRef = new Color(235, 235, 235); public static Color colorHomRefAlpha = ColorUtilities.getCompositeColor(colorHomRef, alphaValue); public static Color colorHomVar = new Color(0, 245, 255); public static Color colorHomVarAlpha = ColorUtilities.getCompositeColor(colorHomVar, alphaValue); public static Color colorHet = Color.blue.brighter(); // new Color(107, 30, 115); //Color.blue; public static Color colorHetAlpha = ColorUtilities.getCompositeColor(colorHet, alphaValue); public static Color colorNoCall = Color.white; public static Color colorNoCallAlpha = ColorUtilities.getCompositeColor(colorNoCall, alphaValue); public static final Color colorAlleleBand = Color.red; public static Color colorAlleleBandAlpha = ColorUtilities.getCompositeColor(colorAlleleBand, alphaValue); public static final Color colorAlleleRef = Color.gray; public static Color colorAlleleRefAlpha = ColorUtilities.getCompositeColor(colorAlleleRef, alphaValue); private static final Color blue = new Color(0, 0, 220); public static Color blueAlpha = ColorUtilities.getCompositeColor(blue, alphaValue); static Map<Character, Color> nucleotideColors = new HashMap<Character, Color>(); private VariantTrack track; static { nucleotideColors.put('A', Color.GREEN); nucleotideColors.put('a', Color.GREEN); nucleotideColors.put('C', Color.BLUE); nucleotideColors.put('c', Color.BLUE); nucleotideColors.put('T', Color.RED); nucleotideColors.put('t', Color.RED); nucleotideColors.put('G', new Color(242, 182, 65)); nucleotideColors.put('g', new Color(242, 182, 65)); nucleotideColors.put('N', colorAlleleRef); nucleotideColors.put('n', colorAlleleRef); nucleotideColors.put('.', colorAlleleRef); nucleotideColors.put(null, Color.BLACK); } public VariantRenderer(VariantTrack track) { this.track = track; } /** * 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(); } private Color convertMethylationRateToColor(float mr) { Color color; /* if (mr >= .25) { return Color.getHSBColor((mr - .25f) * (1f / 0.75f), 1, 1); } else { // use a light grey between 0 and 0.25 brightness to indicate moderate methylation at the site. return new Color(1f - mr, 1f - mr, 1f - mr); } */ float v = 1.5f + (mr / 2); // add one to have a floor. getHSBColor removes the floor to yield a fraction // betweeen 0 and 1. return Color.getHSBColor(v, .75f, 1); } public char getFirstBase(Allele allele) { byte[] bases = allele.getBases(); if (bases.length > 0) { return (char) bases[0]; } else { return '.'; } } public Color getGenotypeColor(Genotype genotype, boolean isFiltered) { if (genotype.isNoCall()) { return isFiltered ? colorNoCallAlpha : colorNoCall; } else if (genotype.isHomRef()) { return isFiltered ? colorHomRefAlpha : colorHomRef; } else if (genotype.isHomVar()) { return isFiltered ? colorHomVarAlpha : colorHomVar; } else if (genotype.isHet()) { return isFiltered ? colorHetAlpha : colorHet; } return Color.white; } private void drawCenteredText(Graphics2D g, char[] chars, int x, int y, int w, int h) { // Get measures needed to center the message FontMetrics fm = g.getFontMetrics(); // How many pixels wide is the string int msg_width = fm.charsWidth(chars, 0, 1); // How far above the baseline can the font go? int ascent = fm.getMaxAscent(); // How far below the baseline? int descent = fm.getMaxDescent(); // Use the string width to find the starting point int msgX = x + w / 2 - msg_width / 2; // Use the vertical height of this font to find // the vertical starting coordinate int msgY = y + h / 2 - descent / 2 + ascent / 2; g.drawChars(chars, 0, 1, msgX, msgY); } }