/** 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);
}
}
private void processResource(Session session, Element element, HashMap additionalInformation) {
String nodeName = element.getNodeName();
boolean oldSession = nodeName.equals(SessionElement.DATA_FILE.getText());
String label = getAttribute(element, SessionAttribute.LABEL.getText());
String name = getAttribute(element, SessionAttribute.NAME.getText());
String sampleId = getAttribute(element, SessionAttribute.SAMPLE_ID.getText());
String description = getAttribute(element, SessionAttribute.DESCRIPTION.getText());
String type = getAttribute(element, SessionAttribute.TYPE.getText());
String coverage = getAttribute(element, SessionAttribute.COVERAGE.getText());
String trackLine = getAttribute(element, SessionAttribute.TRACK_LINE.getText());
String colorString = getAttribute(element, SessionAttribute.COLOR.getText());
String relPathValue = getAttribute(element, SessionAttribute.RELATIVE_PATH.getText());
boolean isRelativePath = ((relPathValue != null) && relPathValue.equalsIgnoreCase("true"));
String serverURL = getAttribute(element, SessionAttribute.SERVER_URL.getText());
// Older sessions used the "name" attribute for the path.
String path = getAttribute(element, SessionAttribute.PATH.getText());
if (oldSession && name != null) {
path = name;
int idx = name.lastIndexOf("/");
if (idx > 0 && idx + 1 < name.length()) {
name = name.substring(idx + 1);
}
}
ResourceLocator resourceLocator;
if (isRelativePath) {
final String sessionPath = session.getPath();
String absolutePath;
if (sessionPath == null) {
log.error("Null session path -- this is not expected");
MessageUtils.showMessage("Unexpected error loading session: null session path");
return;
}
absolutePath = FileUtils.getAbsolutePath(path, sessionPath);
fullToRelPathMap.put(absolutePath, path);
resourceLocator = new ResourceLocator(serverURL, absolutePath);
// If the resourceLocator is relative, we assume coverage is as well
if (coverage != null) {
String absoluteCoveragePath = FileUtils.getAbsolutePath(coverage, sessionPath);
resourceLocator.setCoverage(absoluteCoveragePath);
}
} else {
resourceLocator = new ResourceLocator(serverURL, path);
resourceLocator.setCoverage(coverage);
}
String url = getAttribute(element, SessionAttribute.URL.getText());
if (url == null) {
url = getAttribute(element, SessionAttribute.FEATURE_URL.getText());
}
resourceLocator.setUrl(url);
String infolink = getAttribute(element, SessionAttribute.HYPERLINK.getText());
if (infolink == null) {
infolink = getAttribute(element, SessionAttribute.INFOLINK.getText());
}
resourceLocator.setInfolink(infolink);
// Label is deprecated in favor of name.
if (name != null) {
resourceLocator.setName(name);
} else {
resourceLocator.setName(label);
}
resourceLocator.setSampleId(sampleId);
resourceLocator.setDescription(description);
// This test added to get around earlier bug in the writer
if (type != null && !type.equals("local")) {
resourceLocator.setType(type);
}
resourceLocator.setCoverage(coverage);
resourceLocator.setTrackLine(trackLine);
if (colorString != null) {
try {
Color c = ColorUtilities.stringToColor(colorString);
resourceLocator.setColor(c);
} catch (Exception e) {
log.error("Error setting color: ", e);
}
}
dataFiles.add(resourceLocator);
NodeList elements = element.getChildNodes();
process(session, elements, additionalInformation);
}